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: N9Q8Q

Calculation Name: 5DBK-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5DBK

Chain ID: B

ChEMBL ID:

UniProt ID: M1Q3P9

Base Structure: X-ray

Registration Date: 2023-09-19

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 OptHSide
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 352
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5759246.320115
FMO2-HF: Nuclear repulsion 5612688.492983
FMO2-HF: Total energy -146557.827132
FMO2-MP2: Total energy -146985.399327


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:67:ASP)


Summations of interaction energy for fragment #1(B:67: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.
89.33493.5080.054-1.591-2.6390.005
Interaction energy analysis for fragmet #1(B:67:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.965 / q_NPA : -0.996
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].
3B69GLU-1-0.910-0.9622.77724.13727.5710.053-1.452-2.0360.005
4B70GLU-1-0.971-0.9863.78740.04340.6600.002-0.134-0.4850.000
5B71ASP-1-0.874-0.9405.36731.26731.390-0.001-0.005-0.1180.000
6B72VAL00.0710.0367.959-4.433-4.4330.0000.0000.0000.000
7B73LYS10.7970.8977.911-26.045-26.0450.0000.0000.0000.000
8B74GLY00.0440.0159.666-2.284-2.2840.0000.0000.0000.000
9B75LYS10.8410.91311.455-23.249-23.2490.0000.0000.0000.000
10B76LEU0-0.088-0.05311.314-2.156-2.1560.0000.0000.0000.000
11B77ASP-1-0.786-0.86013.39919.23919.2390.0000.0000.0000.000
12B78GLU-1-0.929-0.95715.62818.08818.0880.0000.0000.0000.000
13B79TRP0-0.051-0.03717.155-1.166-1.1660.0000.0000.0000.000
14B80LEU0-0.0060.00318.471-1.019-1.0190.0000.0000.0000.000
15B81ASN0-0.033-0.03319.359-1.397-1.3970.0000.0000.0000.000
16B82ALA00.0000.00721.910-0.733-0.7330.0000.0000.0000.000
17B83LEU0-0.006-0.00421.277-0.737-0.7370.0000.0000.0000.000
18B84VAL0-0.040-0.00924.199-0.630-0.6300.0000.0000.0000.000
19B85HIS0-0.009-0.00925.639-0.917-0.9170.0000.0000.0000.000
20B86LEU0-0.056-0.01827.661-0.397-0.3970.0000.0000.0000.000
21B87ASP-1-0.823-0.90826.49310.97110.9710.0000.0000.0000.000
22B88LYS10.9850.95226.702-9.218-9.2180.0000.0000.0000.000
23B89GLN0-0.038-0.00527.3120.0240.0240.0000.0000.0000.000
24B90GLN00.0170.00123.5160.7320.7320.0000.0000.0000.000
25B91VAL0-0.027-0.00922.6230.5480.5480.0000.0000.0000.000
26B92GLU-1-0.791-0.89422.46711.69311.6930.0000.0000.0000.000
27B93ARG10.8690.93420.060-14.810-14.8100.0000.0000.0000.000
28B94ILE00.0420.02317.0060.4360.4360.0000.0000.0000.000
29B95TYR0-0.033-0.01617.9770.6590.6590.0000.0000.0000.000
30B96GLU-1-0.952-0.97519.31413.04513.0450.0000.0000.0000.000
31B97GLU-1-0.830-0.91116.38017.55717.5570.0000.0000.0000.000
32B98LEU00.0200.01813.2080.8930.8930.0000.0000.0000.000
33B99GLN0-0.025-0.01314.4180.3280.3280.0000.0000.0000.000
34B100GLY0-0.052-0.01615.741-0.206-0.2060.0000.0000.0000.000
35B101GLU-1-0.829-0.90810.73222.95722.9570.0000.0000.0000.000
36B102MET0-0.041-0.02610.3871.6961.6960.0000.0000.0000.000
37B103LYS10.8670.94712.158-16.975-16.9750.0000.0000.0000.000
38B104HIS0-0.010-0.0079.096-1.247-1.2470.0000.0000.0000.000
39B105VAL00.0290.0446.0320.5250.5250.0000.0000.0000.000
40B106LEU0-0.020-0.0247.234-2.518-2.5180.0000.0000.0000.000
41B107ASP-1-0.793-0.8946.66225.05525.0550.0000.0000.0000.000
42B108PHE00.007-0.0138.681-0.979-0.9790.0000.0000.0000.000
43B109GLU-1-0.980-0.97410.32620.85920.8590.0000.0000.0000.000
44B110ILE00.0730.0237.222-0.817-0.8170.0000.0000.0000.000
45B111ILE0-0.028-0.01010.628-1.139-1.1390.0000.0000.0000.000
46B112ASN0-0.080-0.06712.760-1.566-1.5660.0000.0000.0000.000
47B113TYR0-0.063-0.04312.889-1.581-1.5810.0000.0000.0000.000
48B114TYR00.0880.04414.135-0.979-0.9790.0000.0000.0000.000
49B115LYS10.8450.89415.892-14.092-14.0920.0000.0000.0000.000
50B116LEU0-0.028-0.00818.539-0.835-0.8350.0000.0000.0000.000
51B117LEU00.0210.03416.628-0.795-0.7950.0000.0000.0000.000
52B118TYR00.0370.02420.055-0.602-0.6020.0000.0000.0000.000
53B119THR0-0.083-0.05421.688-0.674-0.6740.0000.0000.0000.000
54B120ARG10.8230.90923.375-11.584-11.5840.0000.0000.0000.000
55B121TYR00.004-0.01823.192-0.481-0.4810.0000.0000.0000.000
56B122LEU00.005-0.00325.108-0.387-0.3870.0000.0000.0000.000
57B123ILE0-0.035-0.00927.663-0.389-0.3890.0000.0000.0000.000
58B124MET0-0.0400.00827.113-0.337-0.3370.0000.0000.0000.000
59B125LYS10.7440.86827.434-11.001-11.0010.0000.0000.0000.000
60B126ARG10.9290.96230.881-8.481-8.4810.0000.0000.0000.000
61B127ASP-1-0.839-0.90630.6558.8468.8460.0000.0000.0000.000
62B128ILE00.005-0.00531.6160.2040.2040.0000.0000.0000.000
63B129SER00.0340.01633.0730.0630.0630.0000.0000.0000.000
64B130ALA00.0450.01928.8080.1020.1020.0000.0000.0000.000
65B131LEU0-0.036-0.01027.9030.3430.3430.0000.0000.0000.000
66B132GLU-1-0.877-0.95229.0508.4248.4240.0000.0000.0000.000
67B133GLU-1-0.870-0.90528.5729.9899.9890.0000.0000.0000.000
68B134GLU-1-0.782-0.87722.89112.14312.1430.0000.0000.0000.000
69B135LEU0-0.0040.00825.6140.2970.2970.0000.0000.0000.000
70B136ASP-1-0.762-0.87927.4929.0489.0480.0000.0000.0000.000
71B137LYS10.7300.85824.341-10.717-10.7170.0000.0000.0000.000
72B138LEU00.0110.00220.8060.1490.1490.0000.0000.0000.000
73B139LYS10.8620.94023.934-8.772-8.7720.0000.0000.0000.000
74B140LYS10.8720.92623.998-11.174-11.1740.0000.0000.0000.000
75B141VAL0-0.055-0.02819.700-0.015-0.0150.0000.0000.0000.000
76B142TYR00.0540.03621.9350.4000.4000.0000.0000.0000.000
77B143LYS10.9580.96523.572-9.814-9.8140.0000.0000.0000.000
78B144LYS10.9320.96918.804-13.247-13.2470.0000.0000.0000.000
79B145TYR00.0320.03718.6760.7230.7230.0000.0000.0000.000
80B146SER00.1220.07016.794-0.701-0.7010.0000.0000.0000.000
81B147PRO00.0440.00918.924-0.451-0.4510.0000.0000.0000.000
82B148PHE00.0970.06018.309-0.497-0.4970.0000.0000.0000.000
83B149GLN00.008-0.01414.356-0.795-0.7950.0000.0000.0000.000
84B150LYS10.7560.86920.115-12.898-12.8980.0000.0000.0000.000
85B151LEU00.0140.01523.412-0.504-0.5040.0000.0000.0000.000
86B152LEU00.0520.02319.928-0.478-0.4780.0000.0000.0000.000
87B153TYR0-0.0120.00824.017-0.437-0.4370.0000.0000.0000.000
88B154MET0-0.065-0.03125.519-0.401-0.4010.0000.0000.0000.000
89B155TYR0-0.019-0.02826.449-0.548-0.5480.0000.0000.0000.000
90B156GLY00.0410.01827.286-0.281-0.2810.0000.0000.0000.000
91B157ARG10.8580.90528.340-9.704-9.7040.0000.0000.0000.000
92B158GLY00.0370.02131.143-0.334-0.3340.0000.0000.0000.000
93B159LEU00.0300.01629.654-0.290-0.2900.0000.0000.0000.000
94B160LEU00.0210.02231.835-0.189-0.1890.0000.0000.0000.000
95B161CYS0-0.077-0.03733.590-0.269-0.2690.0000.0000.0000.000
96B162CYS0-0.035-0.01336.050-0.262-0.2620.0000.0000.0000.000
97B163LEU0-0.026-0.01434.094-0.177-0.1770.0000.0000.0000.000
98B164GLN0-0.075-0.02636.905-0.233-0.2330.0000.0000.0000.000
99B165TYR0-0.017-0.00639.353-0.239-0.2390.0000.0000.0000.000
100B166ARG10.8660.94338.982-7.667-7.6670.0000.0000.0000.000
101B167TRP00.0910.02039.3490.2280.2280.0000.0000.0000.000
102B168LYS10.8650.93041.011-7.192-7.1920.0000.0000.0000.000
103B169ASP-1-0.869-0.94838.5287.4547.4540.0000.0000.0000.000
104B170GLY0-0.011-0.01536.2470.2290.2290.0000.0000.0000.000
105B171LEU00.0400.02336.1330.2600.2600.0000.0000.0000.000
106B172ASP-1-0.832-0.91237.4637.7267.7260.0000.0000.0000.000
107B173TYR0-0.086-0.05431.9750.2730.2730.0000.0000.0000.000
108B174LEU00.0350.02632.6220.3130.3130.0000.0000.0000.000
109B175LEU00.0300.02033.6600.1470.1470.0000.0000.0000.000
110B176LYS10.9020.95531.997-8.383-8.3830.0000.0000.0000.000
111B177THR0-0.029-0.03828.3560.3450.3450.0000.0000.0000.000
112B178GLU-1-0.850-0.93229.5718.9068.9060.0000.0000.0000.000
113B179VAL0-0.043-0.02531.2960.1510.1510.0000.0000.0000.000
114B180MET0-0.0180.00025.5650.1270.1270.0000.0000.0000.000
115B181ALA00.0020.01126.6560.3800.3800.0000.0000.0000.000
116B182LYS10.9911.01127.573-8.951-8.9510.0000.0000.0000.000
117B183GLU-1-1.002-0.99327.92610.18110.1810.0000.0000.0000.000
118B184GLN0-0.091-0.05622.2650.6580.6580.0000.0000.0000.000
119B185GLY0-0.0100.00724.0010.4390.4390.0000.0000.0000.000
120B186TYR0-0.031-0.03322.6730.4480.4480.0000.0000.0000.000
121B187HIS00.015-0.00925.590-0.700-0.7000.0000.0000.0000.000
122B188GLU-1-0.749-0.85626.45811.50111.5010.0000.0000.0000.000
123B189THR00.014-0.02528.743-0.241-0.2410.0000.0000.0000.000
124B190GLY0-0.004-0.00430.999-0.307-0.3070.0000.0000.0000.000
125B191LEU0-0.0100.00429.790-0.235-0.2350.0000.0000.0000.000
126B192TYR00.0290.01032.370-0.198-0.1980.0000.0000.0000.000
127B193TYR00.0150.01235.448-0.240-0.2400.0000.0000.0000.000
128B194ASN00.0260.00832.631-0.394-0.3940.0000.0000.0000.000
129B195ILE00.0040.01234.398-0.204-0.2040.0000.0000.0000.000
130B196ALA00.0230.01137.874-0.225-0.2250.0000.0000.0000.000
131B197LEU0-0.0340.00238.787-0.227-0.2270.0000.0000.0000.000
132B198ALA0-0.011-0.01238.984-0.160-0.1600.0000.0000.0000.000
133B199TYR00.003-0.01840.738-0.216-0.2160.0000.0000.0000.000
134B200THR0-0.002-0.02143.819-0.190-0.1900.0000.0000.0000.000
135B201HIS0-0.037-0.01042.822-0.228-0.2280.0000.0000.0000.000
136B202LEU0-0.134-0.05943.703-0.077-0.0770.0000.0000.0000.000
137B203ASP-1-0.922-0.95347.1065.8885.8880.0000.0000.0000.000
138B204ILE0-0.046-0.01346.169-0.093-0.0930.0000.0000.0000.000
139B205HIS00.0460.01747.4270.1380.1380.0000.0000.0000.000
140B206HIS00.011-0.01448.2860.1520.1520.0000.0000.0000.000
141B207LEU0-0.008-0.00244.0250.0710.0710.0000.0000.0000.000
142B208ALA00.0330.02243.6670.1860.1860.0000.0000.0000.000
143B209ILE00.0120.00143.7280.1700.1700.0000.0000.0000.000
144B210HIS0-0.019-0.00240.397-0.053-0.0530.0000.0000.0000.000
145B211PHE00.0170.00137.5650.0890.0890.0000.0000.0000.000
146B212VAL0-0.010-0.00739.6170.2190.2190.0000.0000.0000.000
147B213ASN0-0.0090.00141.6320.0230.0230.0000.0000.0000.000
148B214MET00.0280.02936.7550.0520.0520.0000.0000.0000.000
149B215ALA0-0.023-0.00836.6310.2230.2230.0000.0000.0000.000
150B216LEU0-0.031-0.01837.4390.1330.1330.0000.0000.0000.000
151B217GLU-1-0.942-0.98339.0857.7407.7400.0000.0000.0000.000
152B218GLY00.0180.00835.0830.1020.1020.0000.0000.0000.000
153B219PHE00.000-0.03233.4090.1870.1870.0000.0000.0000.000
154B220ARG10.8840.93636.522-7.307-7.3070.0000.0000.0000.000
155B221SER0-0.0200.00334.428-0.025-0.0250.0000.0000.0000.000
156B222GLU-1-0.845-0.88831.25310.16810.1680.0000.0000.0000.000
157B223ALA0-0.0230.00133.8800.0870.0870.0000.0000.0000.000
158B224LYS10.8450.92930.375-10.088-10.0880.0000.0000.0000.000
159B225ALA00.0430.00236.621-0.109-0.1090.0000.0000.0000.000
160B226ARG10.9000.96435.969-8.594-8.5940.0000.0000.0000.000
161B227ASN00.003-0.00734.544-0.143-0.1430.0000.0000.0000.000
162B228ILE00.0100.02238.603-0.134-0.1340.0000.0000.0000.000
163B229ILE00.0340.00841.278-0.162-0.1620.0000.0000.0000.000
164B230ASN00.0280.01839.007-0.275-0.2750.0000.0000.0000.000
165B231CYS0-0.0250.00040.057-0.025-0.0250.0000.0000.0000.000
166B232GLN00.0260.00742.815-0.082-0.0820.0000.0000.0000.000
167B233ILE00.000-0.00245.645-0.157-0.1570.0000.0000.0000.000
168B234LEU00.0190.01142.467-0.115-0.1150.0000.0000.0000.000
169B235ILE00.0000.01145.111-0.122-0.1220.0000.0000.0000.000
170B236ALA0-0.0050.00148.231-0.138-0.1380.0000.0000.0000.000
171B237VAL00.0070.02049.361-0.152-0.1520.0000.0000.0000.000
172B238SER00.0290.01649.196-0.118-0.1180.0000.0000.0000.000
173B239TYR0-0.020-0.03050.877-0.120-0.1200.0000.0000.0000.000
174B240THR0-0.090-0.05554.034-0.175-0.1750.0000.0000.0000.000
175B241GLU-1-0.930-0.96551.6205.9935.9930.0000.0000.0000.000
176B242LYS10.8970.94455.796-5.510-5.5100.0000.0000.0000.000
177B243GLY00.0130.00756.8240.0520.0520.0000.0000.0000.000
178B244GLN0-0.026-0.00358.616-0.048-0.0480.0000.0000.0000.000
179B245TYR00.1350.05858.2900.0130.0130.0000.0000.0000.000
180B246GLU-1-0.847-0.91258.7435.1615.1610.0000.0000.0000.000
181B247GLU-1-0.954-0.97653.2425.9785.9780.0000.0000.0000.000
182B248ALA00.1050.05954.2860.0960.0960.0000.0000.0000.000
183B249LEU0-0.039-0.03154.5930.0700.0700.0000.0000.0000.000
184B250LYS10.8830.94555.642-5.494-5.4940.0000.0000.0000.000
185B251MET00.0410.03948.7040.1020.1020.0000.0000.0000.000
186B252TYR00.036-0.01750.9510.0830.0830.0000.0000.0000.000
187B253GLU-1-0.854-0.91352.9735.6225.6220.0000.0000.0000.000
188B254SER0-0.073-0.04250.0210.0310.0310.0000.0000.0000.000
189B255ILE0-0.043-0.01947.7310.1180.1180.0000.0000.0000.000
190B256LEU0-0.016-0.00149.7230.0740.0740.0000.0000.0000.000
191B257ARG10.8030.88452.339-5.711-5.7110.0000.0000.0000.000
192B258GLU-1-0.794-0.85045.4737.1667.1660.0000.0000.0000.000
193B259ALA0-0.0010.01248.016-0.037-0.0370.0000.0000.0000.000
194B260THR0-0.015-0.02741.4630.0780.0780.0000.0000.0000.000
195B261SER0-0.064-0.03244.1490.0150.0150.0000.0000.0000.000
196B262PHE00.0200.00239.5430.2190.2190.0000.0000.0000.000
197B263ALA00.004-0.00938.521-0.146-0.1460.0000.0000.0000.000
198B264ASP-1-0.784-0.90840.5727.6397.6390.0000.0000.0000.000
199B265LYS10.8190.90642.919-6.956-6.9560.0000.0000.0000.000
200B266ASP-1-0.787-0.90044.8326.7676.7670.0000.0000.0000.000
201B267VAL00.0310.01544.276-0.143-0.1430.0000.0000.0000.000
202B268LEU00.0120.00542.454-0.093-0.0930.0000.0000.0000.000
203B269LEU0-0.008-0.00146.691-0.128-0.1280.0000.0000.0000.000
204B270ALA00.0430.03249.825-0.155-0.1550.0000.0000.0000.000
205B271ILE00.0320.03047.646-0.142-0.1420.0000.0000.0000.000
206B272THR0-0.023-0.02049.481-0.091-0.0910.0000.0000.0000.000
207B273LEU0-0.046-0.03051.892-0.117-0.1170.0000.0000.0000.000
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