FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 89Q5Y

Calculation Name: 2GK9-B-Xray372

Preferred Name: Phosphatidylinositol-5-phosphate 4-kinase type-2 gamma

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2GK9

Chain ID: B

ChEMBL ID: CHEMBL1770034

UniProt ID: Q8TBX8

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 254
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3527581.346133
FMO2-HF: Nuclear repulsion 3422298.18049
FMO2-HF: Total energy -105283.165644
FMO2-MP2: Total energy -105588.882329


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(B:45:ASP)


Summations of interaction energy for fragment #1(B:45:ASP)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-74.28-67.01120.979-12.808-15.4390.17
Interaction energy analysis for fragmet #1(B:45:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.785 / q_NPA : -0.902
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3B47LEU00.0020.0162.282-19.979-16.0212.719-2.934-3.7430.033
4B48VAL00.026-0.0021.887-30.224-30.15511.229-4.896-6.4010.060
5B49GLY00.0200.0183.866-13.273-12.5980.023-0.374-0.3250.003
6B50VAL0-0.006-0.0106.168-6.112-6.1120.0000.0000.0000.000
7B51PHE0-0.013-0.0066.629-4.819-4.8190.0000.0000.0000.000
8B52LEU0-0.014-0.0036.802-3.955-3.9550.0000.0000.0000.000
9B53TRP00.0270.0129.548-3.115-3.1150.0000.0000.0000.000
10B54GLY00.018-0.00311.261-2.156-2.1560.0000.0000.0000.000
11B55VAL0-0.008-0.00212.019-1.908-1.9080.0000.0000.0000.000
12B56ALA00.0180.00513.640-1.604-1.6040.0000.0000.0000.000
13B57HIS0-0.085-0.04315.510-0.673-0.6730.0000.0000.0000.000
14B58SER0-0.028-0.03416.815-0.798-0.7980.0000.0000.0000.000
15B59ILE0-0.0020.00017.888-1.082-1.0820.0000.0000.0000.000
16B60ASN0-0.033-0.02519.074-1.504-1.5040.0000.0000.0000.000
17B61GLU-1-0.872-0.90521.42912.74612.7460.0000.0000.0000.000
18B62LEU0-0.027-0.02522.054-0.757-0.7570.0000.0000.0000.000
19B63SER0-0.085-0.05724.272-0.723-0.7230.0000.0000.0000.000
20B64GLN0-0.024-0.01326.174-0.813-0.8130.0000.0000.0000.000
21B65VAL0-0.0340.00326.869-0.451-0.4510.0000.0000.0000.000
22B66PRO00.0150.02129.1760.1640.1640.0000.0000.0000.000
23B67PRO00.005-0.00129.5980.0950.0950.0000.0000.0000.000
24B68PRO0-0.016-0.00129.707-0.370-0.3700.0000.0000.0000.000
25B69VAL00.001-0.01432.7670.0720.0720.0000.0000.0000.000
26B70MET0-0.061-0.02635.095-0.153-0.1530.0000.0000.0000.000
27B71LEU00.0020.01729.2200.1290.1290.0000.0000.0000.000
28B72LEU00.0310.00532.698-0.305-0.3050.0000.0000.0000.000
29B73PRO00.025-0.01232.0410.3520.3520.0000.0000.0000.000
30B74ASP-1-0.824-0.91431.19210.08110.0810.0000.0000.0000.000
31B75ASP-1-0.764-0.86528.17111.19911.1990.0000.0000.0000.000
32B76PHE0-0.015-0.02926.5530.6020.6020.0000.0000.0000.000
33B77LYS10.7920.89526.509-9.797-9.7970.0000.0000.0000.000
34B78ALA0-0.0040.02825.9280.0840.0840.0000.0000.0000.000
35B79SER0-0.077-0.04920.6680.7610.7610.0000.0000.0000.000
36B80SER00.0280.02820.247-0.669-0.6690.0000.0000.0000.000
37B81LYS10.9420.95518.363-13.615-13.6150.0000.0000.0000.000
38B82ILE00.0370.03816.618-0.825-0.8250.0000.0000.0000.000
39B83LYS10.8830.93216.562-14.661-14.6610.0000.0000.0000.000
40B84VAL0-0.0020.01515.619-1.165-1.1650.0000.0000.0000.000
41B85ASN00.009-0.01616.8480.8840.8840.0000.0000.0000.000
42B86ASN00.0190.01117.199-1.284-1.2840.0000.0000.0000.000
43B87HIS00.0180.00119.3100.6310.6310.0000.0000.0000.000
44B88LEU0-0.039-0.02521.470-0.354-0.3540.0000.0000.0000.000
45B89PHE0-0.0160.02020.612-0.309-0.3090.0000.0000.0000.000
46B90HIS00.0760.02914.804-0.311-0.3110.0000.0000.0000.000
47B91ARG10.8810.92313.956-17.486-17.4860.0000.0000.0000.000
48B92GLU-1-0.931-0.95111.32020.50220.5020.0000.0000.0000.000
49B93ASN0-0.013-0.0137.9262.2082.2080.0000.0000.0000.000
50B94LEU00.0240.0258.4092.6072.6070.0000.0000.0000.000
51B95PRO00.0080.0069.088-1.752-1.7520.0000.0000.0000.000
52B96SER00.016-0.00411.860-0.856-0.8560.0000.0000.0000.000
53B97HIS0-0.0140.00314.166-0.590-0.5900.0000.0000.0000.000
54B98PHE00.0210.01911.0791.6661.6660.0000.0000.0000.000
55B99LYS10.7740.86612.183-23.746-23.7460.0000.0000.0000.000
56B100PHE00.0410.04710.9372.1982.1980.0000.0000.0000.000
57B101LYS10.8760.94313.660-18.753-18.7530.0000.0000.0000.000
58B102GLU-1-0.785-0.87215.00818.06518.0650.0000.0000.0000.000
59B103TYR00.012-0.02116.114-1.742-1.7420.0000.0000.0000.000
60B104CYS0-0.0060.01019.8370.1840.1840.0000.0000.0000.000
61B105PRO00.0160.00721.270-0.218-0.2180.0000.0000.0000.000
62B106GLN0-0.014-0.02222.5810.0480.0480.0000.0000.0000.000
63B107VAL00.0120.00924.833-0.249-0.2490.0000.0000.0000.000
64B108PHE00.001-0.00620.428-0.080-0.0800.0000.0000.0000.000
65B109ARG10.8590.92722.912-12.103-12.1030.0000.0000.0000.000
66B110ASN00.0330.02624.520-0.366-0.3660.0000.0000.0000.000
67B111LEU0-0.028-0.01223.225-0.369-0.3690.0000.0000.0000.000
68B112ARG10.8150.89919.635-15.678-15.6780.0000.0000.0000.000
69B113ASP-1-0.824-0.89323.94810.36510.3650.0000.0000.0000.000
70B114ARG10.8450.90627.514-10.486-10.4860.0000.0000.0000.000
71B115PHE0-0.046-0.01123.460-0.276-0.2760.0000.0000.0000.000
72B116GLY0-0.0040.00726.2670.0980.0980.0000.0000.0000.000
73B117ILE0-0.075-0.05020.8060.2930.2930.0000.0000.0000.000
74B118ASP-1-0.772-0.88424.24612.28712.2870.0000.0000.0000.000
75B119ASP-1-0.772-0.87921.63814.32914.3290.0000.0000.0000.000
76B120GLN00.010-0.00720.3751.0301.0300.0000.0000.0000.000
77B121ASP-1-0.881-0.93620.28013.40013.4000.0000.0000.0000.000
78B122TYR0-0.032-0.02914.8810.8470.8470.0000.0000.0000.000
79B123LEU00.0130.01515.7551.1681.1680.0000.0000.0000.000
80B124VAL0-0.0040.00915.3391.3531.3530.0000.0000.0000.000
81B125SER00.001-0.02915.4110.9820.9820.0000.0000.0000.000
82B126LEU0-0.081-0.04611.4000.9620.9620.0000.0000.0000.000
83B127THR0-0.044-0.03510.6121.9091.9090.0000.0000.0000.000
84B128ARG10.8890.94612.199-16.650-16.6500.0000.0000.0000.000
85B129ASN0-0.010-0.00311.485-1.884-1.8840.0000.0000.0000.000
86B130PRO00.0110.0146.1150.1820.1820.0000.0000.0000.000
87B131PRO0-0.0080.0035.775-2.498-2.4980.0000.0000.0000.000
88B132SER0-0.075-0.0366.8761.3221.3220.0000.0000.0000.000
89B133GLU-1-0.891-0.9576.55336.70336.7030.0000.0000.0000.000
90B134SER0-0.075-0.0557.879-4.952-4.9520.0000.0000.0000.000
91B135GLU-1-0.757-0.8599.75123.59123.5910.0000.0000.0000.000
92B136GLY0-0.101-0.06012.273-1.030-1.0300.0000.0000.0000.000
93B137SER0-0.080-0.06615.450-1.767-1.7670.0000.0000.0000.000
94B138ASP-1-0.900-0.91414.54818.03918.0390.0000.0000.0000.000
95B139GLY00.0100.01412.0490.2360.2360.0000.0000.0000.000
96B140ARG10.7600.8462.050-97.953-95.8547.009-4.522-4.5860.074
97B141PHE0-0.045-0.0238.788-1.567-1.5670.0000.0000.0000.000
98B142LEU00.0250.0134.0942.5352.8450.001-0.082-0.2290.000
99B143ILE00.0030.0278.307-2.328-2.3280.0000.0000.0000.000
100B144SER00.0410.02410.5941.2561.2560.0000.0000.0000.000
101B145TYR0-0.011-0.01911.640-0.714-0.7140.0000.0000.0000.000
102B146ASP-1-0.797-0.85512.86015.54415.5440.0000.0000.0000.000
103B147ARG10.7830.87214.818-18.322-18.3220.0000.0000.0000.000
104B148THR00.0070.00416.051-0.114-0.1140.0000.0000.0000.000
105B149LEU0-0.029-0.00614.451-0.792-0.7920.0000.0000.0000.000
106B150VAL0-0.009-0.00611.8350.7830.7830.0000.0000.0000.000
107B151ILE0-0.0020.0108.269-1.399-1.3990.0000.0000.0000.000
108B152LYS10.9330.9599.432-19.316-19.3160.0000.0000.0000.000
109B153GLU-1-0.762-0.8715.49754.26954.358-0.0010.000-0.0880.000
110B154VAL0-0.073-0.0359.042-2.469-2.4690.0000.0000.0000.000
111B155SER00.003-0.03212.3440.8600.8600.0000.0000.0000.000
112B156SER0-0.032-0.06514.8510.2200.2200.0000.0000.0000.000
113B157GLU-1-0.858-0.91217.38215.97415.9740.0000.0000.0000.000
114B158ASP-1-0.780-0.85616.14518.74218.7420.0000.0000.0000.000
115B159ILE0-0.053-0.03015.134-0.524-0.5240.0000.0000.0000.000
116B160ALA0-0.0100.00718.878-0.757-0.7570.0000.0000.0000.000
117B161ASP-1-0.854-0.92621.92812.70312.7030.0000.0000.0000.000
118B162MET0-0.0520.00319.322-0.833-0.8330.0000.0000.0000.000
119B163HIS0-0.006-0.02921.106-0.666-0.6660.0000.0000.0000.000
120B164SER0-0.095-0.04724.241-0.689-0.6890.0000.0000.0000.000
121B165ASN0-0.002-0.00823.514-0.745-0.7450.0000.0000.0000.000
122B166LEU00.0000.01322.707-0.376-0.3760.0000.0000.0000.000
123B167SER00.004-0.00925.614-0.304-0.3040.0000.0000.0000.000
124B168ASN00.0130.00129.137-0.280-0.2800.0000.0000.0000.000
125B169TYR00.005-0.01823.296-0.245-0.2450.0000.0000.0000.000
126B170HIS00.007-0.00627.458-0.221-0.2210.0000.0000.0000.000
127B171GLN00.003-0.00828.806-0.508-0.5080.0000.0000.0000.000
128B172TYR0-0.092-0.07229.987-0.543-0.5430.0000.0000.0000.000
129B173ILE00.0410.01926.300-0.307-0.3070.0000.0000.0000.000
130B174VAL00.0160.01630.578-0.207-0.2070.0000.0000.0000.000
131B175LYS10.9010.95233.388-9.024-9.0240.0000.0000.0000.000
132B176CYS0-0.087-0.01431.333-0.240-0.2400.0000.0000.0000.000
133B177HIS10.8410.91533.540-8.978-8.9780.0000.0000.0000.000
134B178GLY00.0840.05429.130-0.015-0.0150.0000.0000.0000.000
135B179ASN0-0.009-0.01228.7070.1120.1120.0000.0000.0000.000
136B180THR00.015-0.00426.864-0.373-0.3730.0000.0000.0000.000
137B181LEU0-0.0020.00027.3210.2080.2080.0000.0000.0000.000
138B182LEU0-0.0140.00625.0800.2680.2680.0000.0000.0000.000
139B183PRO00.0560.03219.657-0.010-0.0100.0000.0000.0000.000
140B184GLN00.0310.05021.055-0.220-0.2200.0000.0000.0000.000
141B185PHE00.043-0.00517.9850.6930.6930.0000.0000.0000.000
142B186LEU00.002-0.00617.759-0.831-0.8310.0000.0000.0000.000
143B187GLY00.007-0.00517.195-0.356-0.3560.0000.0000.0000.000
144B188MET0-0.0070.02515.4880.8430.8430.0000.0000.0000.000
145B189TYR0-0.024-0.01712.314-1.357-1.3570.0000.0000.0000.000
146B190ARG10.8720.94511.908-20.836-20.8360.0000.0000.0000.000
147B191VAL0-0.0190.0016.877-2.199-2.1990.0000.0000.0000.000
148B192SER0-0.028-0.0519.4681.1181.1180.0000.0000.0000.000
149B193VAL00.019-0.0077.632-1.302-1.3020.0000.0000.0000.000
150B194ASP-1-0.908-0.94210.49823.29923.2990.0000.0000.0000.000
151B195ASN0-0.083-0.04712.748-1.034-1.0340.0000.0000.0000.000
152B196GLU-1-0.835-0.8779.13633.91933.9190.0000.0000.0000.000
153B197ASP-1-0.854-0.91811.76621.41721.4170.0000.0000.0000.000
154B198SER00.0550.0287.975-1.132-1.1320.0000.0000.0000.000
155B199TYR0-0.041-0.03710.001-1.572-1.5720.0000.0000.0000.000
156B200MET0-0.0040.0195.182-0.239-0.170-0.0010.000-0.0670.000
157B201LEU0-0.0060.00210.734-2.473-2.4730.0000.0000.0000.000
158B202VAL00.0140.00712.2251.4411.4410.0000.0000.0000.000
159B203MET0-0.0050.00214.281-2.062-2.0620.0000.0000.0000.000
160B204ARG10.8460.91616.301-12.591-12.5910.0000.0000.0000.000
161B205ASN0-0.033-0.01917.195-0.009-0.0090.0000.0000.0000.000
162B206MET0-0.0030.01118.510-0.814-0.8140.0000.0000.0000.000
163B207PHE0-0.017-0.01619.790-0.791-0.7910.0000.0000.0000.000
164B208SER0-0.0090.00920.8990.2140.2140.0000.0000.0000.000
165B209HIS00.1050.05519.4060.3400.3400.0000.0000.0000.000
166B210ARG10.9370.97520.367-11.347-11.3470.0000.0000.0000.000
167B211LEU0-0.041-0.02823.243-0.315-0.3150.0000.0000.0000.000
168B212PRO00.0330.03220.8970.2720.2720.0000.0000.0000.000
169B213VAL0-0.033-0.01321.747-0.658-0.6580.0000.0000.0000.000
170B214HIS0-0.063-0.04722.5580.6930.6930.0000.0000.0000.000
171B215ARG10.8300.90525.199-10.166-10.1660.0000.0000.0000.000
172B216LYS10.9380.95418.488-15.978-15.9780.0000.0000.0000.000
173B217TYR0-0.058-0.04724.712-0.093-0.0930.0000.0000.0000.000
174B218ASP-1-0.810-0.87023.15413.79113.7910.0000.0000.0000.000
175B219LEU0-0.044-0.02225.092-0.463-0.4630.0000.0000.0000.000
176B220LYS10.8760.94723.026-13.222-13.2220.0000.0000.0000.000
177B221GLY0-0.055-0.05529.006-0.554-0.5540.0000.0000.0000.000
178B239THR0-0.037-0.04219.475-0.184-0.1840.0000.0000.0000.000
179B240LEU00.0190.02422.683-0.141-0.1410.0000.0000.0000.000
180B241ARG11.0231.00226.386-11.335-11.3350.0000.0000.0000.000
181B242ASP-1-0.749-0.85728.01710.07310.0730.0000.0000.0000.000
182B243MET0-0.023-0.01430.930-0.259-0.2590.0000.0000.0000.000
183B244ASP-1-0.879-0.93229.88410.01310.0130.0000.0000.0000.000
184B245PHE00.009-0.00630.401-0.195-0.1950.0000.0000.0000.000
185B246LEU00.0170.02332.222-0.223-0.2230.0000.0000.0000.000
186B247ASN00.0020.01034.475-0.211-0.2110.0000.0000.0000.000
187B248LYS10.7840.87732.106-9.748-9.7480.0000.0000.0000.000
188B249ASN0-0.053-0.02335.897-0.195-0.1950.0000.0000.0000.000
189B250GLN00.0270.03332.6770.0720.0720.0000.0000.0000.000
190B251LYS10.9360.96435.681-8.258-8.2580.0000.0000.0000.000
191B252VAL00.0880.04236.2440.2090.2090.0000.0000.0000.000
192B253TYR0-0.062-0.02838.452-0.035-0.0350.0000.0000.0000.000
193B254ILE0-0.018-0.01333.5100.1450.1450.0000.0000.0000.000
194B255GLY00.0500.02537.4180.0420.0420.0000.0000.0000.000
195B256GLU-1-0.915-0.95339.5727.0787.0780.0000.0000.0000.000
196B257GLU-1-0.822-0.91741.7047.3347.3340.0000.0000.0000.000
197B258GLU-1-0.860-0.94536.5128.2618.2610.0000.0000.0000.000
198B259LYS10.8540.93637.059-8.122-8.1220.0000.0000.0000.000
199B260LYS10.8260.91038.450-7.140-7.1400.0000.0000.0000.000
200B261ILE00.0520.02535.8060.1570.1570.0000.0000.0000.000
201B262PHE0-0.016-0.01030.2990.2260.2260.0000.0000.0000.000
202B263LEU00.0360.00834.5720.2010.2010.0000.0000.0000.000
203B264GLU-1-0.990-0.99737.0248.1658.1650.0000.0000.0000.000
204B265LYS10.8600.93431.885-9.471-9.4710.0000.0000.0000.000
205B266LEU00.0660.03530.9550.1150.1150.0000.0000.0000.000
206B267LYS10.8950.95433.468-8.146-8.1460.0000.0000.0000.000
207B268ARG10.7990.89732.126-9.622-9.6220.0000.0000.0000.000
208B269ASP-1-0.726-0.84529.94010.48110.4810.0000.0000.0000.000
209B270VAL00.0180.00731.0810.2760.2760.0000.0000.0000.000
210B271GLU-1-0.902-0.95632.6598.5998.5990.0000.0000.0000.000
211B272PHE0-0.052-0.02027.7970.0140.0140.0000.0000.0000.000
212B273LEU0-0.011-0.00627.0230.1000.1000.0000.0000.0000.000
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216B277LYS10.8860.94629.949-10.279-10.2790.0000.0000.0000.000
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220B281TYR00.0320.00424.6260.3920.3920.0000.0000.0000.000
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222B283LEU0-0.049-0.01624.8320.2700.2700.0000.0000.0000.000
223B284LEU00.0010.00920.1070.0070.0070.0000.0000.0000.000
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225B286GLY00.0390.00524.5050.4750.4750.0000.0000.0000.000
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227B288HIS10.9000.95226.077-10.948-10.9480.0000.0000.0000.000
228B289ASP-1-0.879-0.92228.2129.9009.9000.0000.0000.0000.000
229B290ILE00.002-0.00330.3880.1290.1290.0000.0000.0000.000
230B366GLU-1-0.775-0.86532.4739.4119.4110.0000.0000.0000.000
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232B368TYR0-0.021-0.04829.0830.1820.1820.0000.0000.0000.000
233B369PHE0-0.016-0.01724.6010.0360.0360.0000.0000.0000.000
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238B374ASP-1-0.896-0.92719.96115.85415.8540.0000.0000.0000.000
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241B404HIS00.002-0.01136.1200.2340.2340.0000.0000.0000.000
242B405PRO00.0270.01632.303-0.091-0.0910.0000.0000.0000.000
243B406GLU-1-0.913-0.93934.3338.1648.1640.0000.0000.0000.000
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248B411ARG10.9550.97735.764-8.723-8.7230.0000.0000.0000.000
249B412PHE00.0240.02128.826-0.026-0.0260.0000.0000.0000.000
250B413LEU00.009-0.00533.9030.0220.0220.0000.0000.0000.000
251B414ASP-1-0.963-0.95835.9047.7787.7780.0000.0000.0000.000
252B415PHE00.003-0.00831.924-0.018-0.0180.0000.0000.0000.000
253B416ILE0-0.060-0.02831.1100.0190.0190.0000.0000.0000.000
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