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: VQQ31

Calculation Name: 1XTZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XTZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q12189

Base Structure: X-ray

Registration Date: 2023-09-21

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 OptH
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 246
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3137249.49838
FMO2-HF: Nuclear repulsion 3043077.508993
FMO2-HF: Total energy -94171.989387
FMO2-MP2: Total energy -94453.427865


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(A:19:GLU)


Summations of interaction energy for fragment #1(A:19:GLU)
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.
-144.36-144.24827.924-15.099-12.9330.137
Interaction energy analysis for fragmet #1(A:19:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.858 / q_NPA : -0.924
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].
3A21ALA00.0070.0263.608-4.319-2.4840.007-0.718-1.1230.002
4A22LYS10.8180.8962.151-117.465-109.3993.965-5.877-6.1530.078
5A23ARG11.0090.9994.080-33.809-33.536-0.001-0.088-0.1840.000
6A24ALA0-0.0110.0116.021-3.832-3.8320.0000.0000.0000.000
7A25ALA0-0.002-0.0088.118-2.772-2.7720.0000.0000.0000.000
8A26ALA0-0.013-0.0128.529-2.443-2.4430.0000.0000.0000.000
9A27TYR0-0.057-0.0669.476-2.837-2.8370.0000.0000.0000.000
10A28ARG10.8480.89912.333-18.414-18.4140.0000.0000.0000.000
11A29ALA0-0.0200.00513.369-1.325-1.3250.0000.0000.0000.000
12A30VAL00.0210.00814.074-1.204-1.2040.0000.0000.0000.000
13A31ASP-1-0.791-0.86816.21316.77916.7790.0000.0000.0000.000
14A32GLU-1-0.841-0.90417.92614.94414.9440.0000.0000.0000.000
15A33ASN0-0.096-0.06118.096-1.459-1.4590.0000.0000.0000.000
16A34LEU0-0.012-0.00219.396-0.439-0.4390.0000.0000.0000.000
17A35LYS10.9380.97221.343-11.702-11.7020.0000.0000.0000.000
18A36PHE0-0.005-0.01320.964-0.270-0.2700.0000.0000.0000.000
19A37ASP-1-0.903-0.94026.16510.16910.1690.0000.0000.0000.000
20A38ASP-1-0.962-0.98128.20310.16610.1660.0000.0000.0000.000
21A39HIS0-0.077-0.03424.1090.2370.2370.0000.0000.0000.000
22A40LYS10.9640.97726.382-10.237-10.2370.0000.0000.0000.000
23A41ILE0-0.051-0.02725.2050.2760.2760.0000.0000.0000.000
24A42ILE00.0470.01819.1810.0980.0980.0000.0000.0000.000
25A43GLY0-0.016-0.01620.1420.0970.0970.0000.0000.0000.000
26A44ILE00.0230.00014.2780.8330.8330.0000.0000.0000.000
27A45GLY00.0480.01314.647-0.579-0.5790.0000.0000.0000.000
28A46SER0-0.019-0.03813.0300.8690.8690.0000.0000.0000.000
29A47GLY0-0.067-0.0369.7841.4131.4130.0000.0000.0000.000
30A48SER00.0380.0224.8510.1640.280-0.001-0.006-0.1080.000
31A49THR0-0.013-0.0054.35615.54115.805-0.001-0.012-0.2500.000
32A50VAL00.0390.0246.506-2.544-2.5440.0000.0000.0000.000
33A51VAL00.0290.0355.688-2.986-2.9860.0000.0000.0000.000
34A52TYR00.002-0.0391.573-29.125-39.56723.955-8.398-5.1150.057
35A53VAL0-0.013-0.0048.522-2.750-2.7500.0000.0000.0000.000
36A54ALA0-0.0010.00311.481-2.038-2.0380.0000.0000.0000.000
37A55GLU-1-0.838-0.8688.63529.33429.3340.0000.0000.0000.000
38A56ARG10.7910.89212.111-20.735-20.7350.0000.0000.0000.000
39A57ILE00.003-0.01613.719-1.544-1.5440.0000.0000.0000.000
40A58GLY00.0680.02515.726-1.165-1.1650.0000.0000.0000.000
41A59GLN0-0.020-0.01812.091-2.128-2.1280.0000.0000.0000.000
42A60TYR0-0.066-0.05016.949-1.143-1.1430.0000.0000.0000.000
43A61LEU0-0.030-0.00419.805-0.883-0.8830.0000.0000.0000.000
44A62HIS0-0.071-0.03818.543-0.842-0.8420.0000.0000.0000.000
45A63ASP-1-0.886-0.92921.36412.43112.4310.0000.0000.0000.000
46A64PRO00.000-0.00423.155-0.247-0.2470.0000.0000.0000.000
47A65LYS10.8820.94824.973-12.168-12.1680.0000.0000.0000.000
48A66PHE00.005-0.00923.260-0.263-0.2630.0000.0000.0000.000
49A67TYR00.0070.03024.950-0.105-0.1050.0000.0000.0000.000
50A68GLU-1-0.893-0.95025.90010.09310.0930.0000.0000.0000.000
51A69VAL0-0.024-0.01626.841-0.111-0.1110.0000.0000.0000.000
52A70ALA00.0360.00322.5350.0700.0700.0000.0000.0000.000
53A71SER0-0.008-0.00924.0590.3950.3950.0000.0000.0000.000
54A72LYS10.8400.92626.251-10.120-10.1200.0000.0000.0000.000
55A73PHE0-0.0060.02721.669-0.153-0.1530.0000.0000.0000.000
56A74ILE0-0.027-0.01024.535-0.024-0.0240.0000.0000.0000.000
57A75CYS0-0.031-0.00519.2100.0790.0790.0000.0000.0000.000
58A76ILE0-0.0030.00021.164-0.331-0.3310.0000.0000.0000.000
59A77PRO00.0050.00618.4050.7560.7560.0000.0000.0000.000
60A78THR0-0.034-0.00616.345-0.263-0.2630.0000.0000.0000.000
61A79GLY00.1170.06618.3310.0400.0400.0000.0000.0000.000
62A80PHE00.014-0.00417.4290.4010.4010.0000.0000.0000.000
63A81GLN00.0050.0029.969-0.303-0.3030.0000.0000.0000.000
64A82SER0-0.0100.01513.1960.3460.3460.0000.0000.0000.000
65A83ARG11.0010.98114.629-14.681-14.6810.0000.0000.0000.000
66A84ASN0-0.032-0.02713.340-1.922-1.9220.0000.0000.0000.000
67A85LEU00.0300.0269.3300.0700.0700.0000.0000.0000.000
68A86ILE0-0.0080.02013.378-0.178-0.1780.0000.0000.0000.000
69A87LEU0-0.016-0.00716.734-0.607-0.6070.0000.0000.0000.000
70A88ASP-1-0.968-0.97913.45121.84521.8450.0000.0000.0000.000
71A89ASN0-0.020-0.03712.253-0.172-0.1720.0000.0000.0000.000
72A90LYS10.8340.92316.245-17.213-17.2130.0000.0000.0000.000
73A91LEU00.0290.02717.032-0.726-0.7260.0000.0000.0000.000
74A92GLN0-0.044-0.04020.674-0.296-0.2960.0000.0000.0000.000
75A93LEU00.0000.00420.3200.4300.4300.0000.0000.0000.000
76A94GLY0-0.015-0.01123.052-0.687-0.6870.0000.0000.0000.000
77A95SER0-0.008-0.01524.1540.4640.4640.0000.0000.0000.000
78A96ILE00.0690.02125.088-0.289-0.2890.0000.0000.0000.000
79A97GLU-1-0.910-0.96126.87311.25711.2570.0000.0000.0000.000
80A98GLN0-0.076-0.03229.712-0.567-0.5670.0000.0000.0000.000
81A99TYR0-0.034-0.02127.466-0.341-0.3410.0000.0000.0000.000
82A100PRO00.0350.02828.0710.3440.3440.0000.0000.0000.000
83A101ARG10.8780.93029.428-9.469-9.4690.0000.0000.0000.000
84A102ILE00.0450.02823.181-0.020-0.0200.0000.0000.0000.000
85A103ASP-1-0.845-0.90525.68711.26911.2690.0000.0000.0000.000
86A104ILE0-0.026-0.00920.200-0.063-0.0630.0000.0000.0000.000
87A105ALA00.0140.02619.6920.2100.2100.0000.0000.0000.000
88A106PHE00.0190.01514.3880.1190.1190.0000.0000.0000.000
89A107ASP-1-0.762-0.91213.80923.33023.3300.0000.0000.0000.000
90A108GLY00.0000.01111.3790.5990.5990.0000.0000.0000.000
91A109ALA0-0.007-0.01011.855-2.403-2.4030.0000.0000.0000.000
92A110ASP-1-0.858-0.93211.96927.47327.4730.0000.0000.0000.000
93A111GLU-1-0.790-0.90013.52418.13518.1350.0000.0000.0000.000
94A112VAL0-0.022-0.00115.155-0.472-0.4720.0000.0000.0000.000
95A113ASP-1-0.792-0.90417.90913.92013.9200.0000.0000.0000.000
96A114GLU-1-0.872-0.94521.15712.14412.1440.0000.0000.0000.000
97A115ASN0-0.099-0.05723.240-0.561-0.5610.0000.0000.0000.000
98A116LEU0-0.075-0.03019.409-0.109-0.1090.0000.0000.0000.000
99A117GLN00.0540.04821.7730.3240.3240.0000.0000.0000.000
100A118LEU0-0.050-0.03617.5650.8280.8280.0000.0000.0000.000
101A119ILE00.0080.01817.570-0.949-0.9490.0000.0000.0000.000
102A120LYS10.8080.91214.904-19.948-19.9480.0000.0000.0000.000
103A121GLY00.0950.03715.785-1.172-1.1720.0000.0000.0000.000
104A122GLY0-0.0020.00213.744-0.607-0.6070.0000.0000.0000.000
105A123GLY0-0.025-0.02113.6510.1900.1900.0000.0000.0000.000
106A124ALA0-0.052-0.03014.252-0.640-0.6400.0000.0000.0000.000
107A125CYS0-0.0030.00716.444-0.935-0.9350.0000.0000.0000.000
108A126LEU00.0430.01518.377-0.121-0.1210.0000.0000.0000.000
109A127PHE00.0020.00119.857-0.368-0.3680.0000.0000.0000.000
110A128GLN00.005-0.01020.909-0.012-0.0120.0000.0000.0000.000
111A129GLU-1-0.834-0.93815.41221.07821.0780.0000.0000.0000.000
112A130LYS10.8400.93319.632-13.588-13.5880.0000.0000.0000.000
113A131LEU0-0.0330.01622.774-0.499-0.4990.0000.0000.0000.000
114A132VAL00.0090.00820.261-0.497-0.4970.0000.0000.0000.000
115A133SER00.000-0.02320.446-0.346-0.3460.0000.0000.0000.000
116A134THR0-0.085-0.05122.365-0.489-0.4890.0000.0000.0000.000
117A135SER0-0.019-0.01725.458-0.756-0.7560.0000.0000.0000.000
118A136ALA0-0.059-0.01723.708-0.278-0.2780.0000.0000.0000.000
119A137LYS10.8990.95225.648-11.105-11.1050.0000.0000.0000.000
120A138THR0-0.049-0.01322.052-0.269-0.2690.0000.0000.0000.000
121A139PHE00.0200.01017.6820.4060.4060.0000.0000.0000.000
122A140ILE0-0.019-0.00815.570-0.259-0.2590.0000.0000.0000.000
123A141VAL00.0280.01113.7980.9210.9210.0000.0000.0000.000
124A142VAL0-0.0010.0068.999-0.328-0.3280.0000.0000.0000.000
125A143ALA0-0.059-0.0398.8342.1802.1800.0000.0000.0000.000
126A144ASP-1-0.749-0.8455.90642.87242.8720.0000.0000.0000.000
127A145SER00.0460.0218.000-1.602-1.6020.0000.0000.0000.000
128A146ARG10.8290.8806.953-40.368-40.3680.0000.0000.0000.000
129A147LYS10.8190.9118.815-34.894-34.8940.0000.0000.0000.000
130A148LYS10.9441.00312.861-18.483-18.4830.0000.0000.0000.000
131A149SER0-0.013-0.03315.576-0.377-0.3770.0000.0000.0000.000
132A150PRO0-0.058-0.03918.522-0.456-0.4560.0000.0000.0000.000
133A151LYS10.8780.95121.091-11.972-11.9720.0000.0000.0000.000
134A152HIS00.0400.03423.481-0.276-0.2760.0000.0000.0000.000
135A153LEU00.0000.01919.9240.6700.6700.0000.0000.0000.000
136A154GLY00.0590.03620.351-0.793-0.7930.0000.0000.0000.000
137A155LYS10.9150.98820.059-14.237-14.2370.0000.0000.0000.000
138A156ASN0-0.042-0.05315.641-0.741-0.7410.0000.0000.0000.000
139A157TRP0-0.050-0.00212.3171.7821.7820.0000.0000.0000.000
140A158ARG10.8280.87816.891-15.415-15.4150.0000.0000.0000.000
141A159GLN0-0.022-0.01914.880-0.894-0.8940.0000.0000.0000.000
142A160GLY00.0670.05219.175-0.534-0.5340.0000.0000.0000.000
143A161VAL0-0.038-0.01919.8491.0661.0660.0000.0000.0000.000
144A162PRO00.0080.02518.103-0.640-0.6400.0000.0000.0000.000
145A163ILE00.000-0.00421.358-0.247-0.2470.0000.0000.0000.000
146A164GLU-1-0.756-0.84723.72113.82513.8250.0000.0000.0000.000
147A165ILE00.004-0.00425.510-0.485-0.4850.0000.0000.0000.000
148A166VAL00.0410.01328.9560.1430.1430.0000.0000.0000.000
149A167PRO00.0430.03129.729-0.160-0.1600.0000.0000.0000.000
150A168SER0-0.027-0.01431.7050.0280.0280.0000.0000.0000.000
151A169SER0-0.055-0.02732.701-0.215-0.2150.0000.0000.0000.000
152A170TYR00.0370.01330.666-0.019-0.0190.0000.0000.0000.000
153A171VAL00.0090.00632.3290.0980.0980.0000.0000.0000.000
154A172ARG10.8850.92835.191-8.460-8.4600.0000.0000.0000.000
155A173VAL00.0430.02530.467-0.045-0.0450.0000.0000.0000.000
156A174LYS10.9160.95230.311-10.396-10.3960.0000.0000.0000.000
157A175ASN00.006-0.00332.5490.1280.1280.0000.0000.0000.000
158A176ASP-1-0.790-0.88035.2688.6248.6240.0000.0000.0000.000
159A177LEU0-0.038-0.02228.9230.0100.0100.0000.0000.0000.000
160A178LEU0-0.027-0.01331.8240.0790.0790.0000.0000.0000.000
161A179GLU-1-0.971-0.98134.3228.1308.1300.0000.0000.0000.000
162A180GLN0-0.055-0.03536.963-0.308-0.3080.0000.0000.0000.000
163A181LEU0-0.094-0.04232.040-0.007-0.0070.0000.0000.0000.000
164A182HIS0-0.0230.00533.4910.2500.2500.0000.0000.0000.000
165A183ALA0-0.036-0.01329.3150.2080.2080.0000.0000.0000.000
166A184GLU-1-0.907-0.95828.34410.97910.9790.0000.0000.0000.000
167A185LYS10.8550.92824.388-12.896-12.8960.0000.0000.0000.000
168A186VAL00.0090.01527.0790.3010.3010.0000.0000.0000.000
169A187ASP-1-0.880-0.93424.42512.03412.0340.0000.0000.0000.000
170A188ILE0-0.0130.00225.1970.2790.2790.0000.0000.0000.000
171A189ARG10.7800.86116.695-18.114-18.1140.0000.0000.0000.000
172A190GLN0-0.041-0.03822.360-0.576-0.5760.0000.0000.0000.000
173A191GLY00.0210.00220.4920.7900.7900.0000.0000.0000.000
174A192GLY0-0.028-0.00219.3440.7230.7230.0000.0000.0000.000
175A193SER0-0.001-0.02118.816-0.426-0.4260.0000.0000.0000.000
176A194ALA0-0.0020.01318.476-0.556-0.5560.0000.0000.0000.000
177A195LYS10.8510.91620.598-13.237-13.2370.0000.0000.0000.000
178A196ALA00.0420.03223.4780.1230.1230.0000.0000.0000.000
179A197GLY00.0160.00526.295-0.278-0.2780.0000.0000.0000.000
180A198PRO0-0.0110.01124.9070.5960.5960.0000.0000.0000.000
181A199VAL00.0390.01219.721-0.001-0.0010.0000.0000.0000.000
182A200VAL0-0.041-0.02222.863-0.569-0.5690.0000.0000.0000.000
183A201THR0-0.040-0.03621.7990.4040.4040.0000.0000.0000.000
184A202ASP-1-0.834-0.93019.63416.16516.1650.0000.0000.0000.000
185A203ASN0-0.101-0.05522.978-0.604-0.6040.0000.0000.0000.000
186A204ASN0-0.056-0.02425.937-0.358-0.3580.0000.0000.0000.000
187A205ASN0-0.014-0.00826.358-0.900-0.9000.0000.0000.0000.000
188A206PHE00.001-0.00125.7190.3440.3440.0000.0000.0000.000
189A207ILE00.0340.00920.5480.0510.0510.0000.0000.0000.000
190A208ILE0-0.028-0.01123.881-0.203-0.2030.0000.0000.0000.000
191A209ASP-1-0.767-0.84920.08716.83116.8310.0000.0000.0000.000
192A210ALA00.008-0.01522.852-0.455-0.4550.0000.0000.0000.000
193A211ASP-1-0.824-0.90524.13513.63113.6310.0000.0000.0000.000
194A212PHE00.015-0.01125.083-0.536-0.5360.0000.0000.0000.000
195A213GLY00.0890.06425.834-0.313-0.3130.0000.0000.0000.000
196A214GLU-1-0.994-1.01324.02613.26213.2620.0000.0000.0000.000
197A215ILE0-0.014-0.00923.760-0.535-0.5350.0000.0000.0000.000
198A216SER0-0.004-0.00926.8360.2060.2060.0000.0000.0000.000
199A217ASP-1-0.889-0.95429.5069.9969.9960.0000.0000.0000.000
200A218PRO00.0260.00625.748-0.166-0.1660.0000.0000.0000.000
201A219ARG10.9000.94527.817-10.639-10.6390.0000.0000.0000.000
202A220LYS10.8720.94230.104-9.372-9.3720.0000.0000.0000.000
203A221LEU00.0660.04227.021-0.127-0.1270.0000.0000.0000.000
204A222HIS00.0250.03127.3940.1820.1820.0000.0000.0000.000
205A223ARG10.9040.94329.141-9.284-9.2840.0000.0000.0000.000
206A224GLU-1-0.884-0.94032.7259.2599.2590.0000.0000.0000.000
207A225ILE00.0380.01727.557-0.139-0.1390.0000.0000.0000.000
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