FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 8NK9Y

Calculation Name: 3GW2-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3GW2

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2025-07-08

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

DOI:

Apendix: None


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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 178
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -588699.536158
FMO2-HF: Nuclear repulsion 554377.305004
FMO2-HF: Total energy -34322.231154
FMO2-MP2: Total energy -34423.597988


3D Structure Molmil
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:7:ARG)


Summations of interaction energy for fragment #1(A:7:ARG)
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.
-0.7542.059-0.009-1.56-1.2430.006
Interaction energy analysis for fragmet #1(A:7:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.143 / q_NPA : 0.061
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].
4A8LYS10.8961.0663.8080.6681.0770.003-0.176-0.2360.001
5A9ALA00.073-0.0943.611-1.0971.281-0.009-1.354-1.0150.005
6A9ALA0-0.0180.1254.5410.0280.074-0.001-0.008-0.0360.000
7A10ALA00.062-0.1064.548-1.634-1.654-0.002-0.0220.0440.000
8A10ALA0-0.0710.1118.3890.0980.0980.0000.0000.0000.000
9A11LEU00.117-0.1227.4670.4600.4600.0000.0000.0000.000
10A11LEU0-0.0550.1357.990-0.046-0.0460.0000.0000.0000.000
11A12LEU00.031-0.1178.2270.3550.3550.0000.0000.0000.000
12A12LEU0-0.0530.0957.138-0.001-0.0010.0000.0000.0000.000
13A13ASP00.099-0.0799.8280.2550.2550.0000.0000.0000.000
14A13ASP-1-0.926-0.8479.100-1.583-1.5830.0000.0000.0000.000
15A14GLN00.054-0.10611.8310.1740.1740.0000.0000.0000.000
16A14GLN0-0.0450.12413.249-0.043-0.0430.0000.0000.0000.000
17A15VAL00.073-0.10912.9010.1320.1320.0000.0000.0000.000
18A15VAL0-0.0660.11512.597-0.005-0.0050.0000.0000.0000.000
19A16ALA00.161-0.07313.9860.1110.1110.0000.0000.0000.000
20A16ALA0-0.0770.10314.328-0.005-0.0050.0000.0000.0000.000
21A17ARG00.001-0.13115.8400.0850.0850.0000.0000.0000.000
22A17ARG10.8061.05113.0390.7800.7800.0000.0000.0000.000
23A18VAL00.049-0.10617.5150.0660.0660.0000.0000.0000.000
24A18VAL0-0.0640.12517.605-0.002-0.0020.0000.0000.0000.000
25A19GLY00.070-0.08118.4340.0490.0490.0000.0000.0000.000
26A20LYS00.1310.02719.9000.0470.0470.0000.0000.0000.000
27A20LYS10.8411.05120.4320.3170.3170.0000.0000.0000.000
28A21ALA00.044-0.12021.7350.0400.0400.0000.0000.0000.000
29A21ALA0-0.0840.10722.504-0.003-0.0030.0000.0000.0000.000
30A22LEU00.059-0.11123.1110.0300.0300.0000.0000.0000.000
31A22LEU0-0.0230.13621.976-0.001-0.0010.0000.0000.0000.000
32A23ALA00.120-0.06724.3650.0260.0260.0000.0000.0000.000
33A23ALA0-0.1020.10023.933-0.003-0.0030.0000.0000.0000.000
34A24ASN00.030-0.11925.8460.0090.0090.0000.0000.0000.000
35A24ASN0-0.1190.04129.3170.0060.0060.0000.0000.0000.000
36A25GLY00.083-0.06129.591-0.002-0.0020.0000.0000.0000.000
37A26ARG00.1190.03432.1690.0040.0040.0000.0000.0000.000
38A26ARG10.7450.99234.7840.1180.1180.0000.0000.0000.000
39A27ARG00.090-0.08330.4400.0090.0090.0000.0000.0000.000
40A27ARG10.6880.97026.1040.2320.2320.0000.0000.0000.000
41A28LEU00.028-0.12830.254-0.005-0.0050.0000.0000.0000.000
42A28LEU0-0.0480.13927.4820.0000.0000.0000.0000.0000.000
43A29GLN00.142-0.06931.085-0.002-0.0020.0000.0000.0000.000
44A29GLN0-0.0250.08635.4800.0010.0010.0000.0000.0000.000
45A30ILE00.052-0.07133.0500.0100.0100.0000.0000.0000.000
46A30ILE0-0.0960.06032.0680.0000.0000.0000.0000.0000.000
47A31LEU00.029-0.11330.0980.0040.0040.0000.0000.0000.000
48A31LEU0-0.0920.08727.034-0.004-0.0040.0000.0000.0000.000
49A32ASP00.132-0.08831.384-0.001-0.0010.0000.0000.0000.000
50A32ASP-1-0.919-0.83233.997-0.145-0.1450.0000.0000.0000.000
51A33LEU00.084-0.08534.3370.0060.0060.0000.0000.0000.000
52A33LEU0-0.1600.07236.0890.0010.0010.0000.0000.0000.000
53A34LEU00.012-0.09033.4310.0100.0100.0000.0000.0000.000
54A34LEU0-0.1330.05232.138-0.002-0.0020.0000.0000.0000.000
55A35ALA00.114-0.09033.282-0.006-0.0060.0000.0000.0000.000
56A35ALA0-0.0950.11332.332-0.002-0.0020.0000.0000.0000.000
57A36GLN00.095-0.09434.0140.0050.0050.0000.0000.0000.000
58A36GLN0-0.0970.07831.3470.0000.0000.0000.0000.0000.000
59A37GLY00.000-0.11035.0380.0100.0100.0000.0000.0000.000
60A38GLU00.1560.00935.170-0.006-0.0060.0000.0000.0000.000
61A38GLU-1-0.935-0.78734.252-0.139-0.1390.0000.0000.0000.000
62A39ARG00.009-0.11636.0550.0090.0090.0000.0000.0000.000
63A39ARG10.8841.07737.6980.1080.1080.0000.0000.0000.000
64A40ALA00.172-0.07636.934-0.010-0.0100.0000.0000.0000.000
65A40ALA0-0.0970.10640.7080.0020.0020.0000.0000.0000.000
66A41VAL00.060-0.11437.4650.0020.0020.0000.0000.0000.000
67A41VAL0-0.0860.09235.7340.0000.0000.0000.0000.0000.000
68A42GLU00.103-0.09038.265-0.002-0.0020.0000.0000.0000.000
69A42GLU-1-0.886-0.75142.742-0.091-0.0910.0000.0000.0000.000
70A43ALA00.131-0.07541.6250.0030.0030.0000.0000.0000.000
71A43ALA0-0.0850.09841.3420.0000.0000.0000.0000.0000.000
72A44ILE00.079-0.07537.4460.0050.0050.0000.0000.0000.000
73A44ILE0-0.0830.09234.981-0.001-0.0010.0000.0000.0000.000
74A45ALA00.125-0.06638.830-0.002-0.0020.0000.0000.0000.000
75A45ALA0-0.0910.08039.6140.0000.0000.0000.0000.0000.000
76A46THR0-0.017-0.10140.1070.0000.0000.0000.0000.0000.000
77A46THR0-0.0620.05144.0950.0020.0020.0000.0000.0000.000
78A47ALA00.102-0.07842.0240.0040.0040.0000.0000.0000.000
79A47ALA0-0.0640.10641.0520.0000.0000.0000.0000.0000.000
80A48THR0-0.040-0.10838.6800.0030.0030.0000.0000.0000.000
81A48THR0-0.0560.06436.757-0.002-0.0020.0000.0000.0000.000
82A49GLY00.073-0.04740.1360.0000.0000.0000.0000.0000.000
83A50MET0-0.008-0.03839.1520.0030.0030.0000.0000.0000.000
84A50MET0-0.0770.10134.890-0.003-0.0030.0000.0000.0000.000
85A51ASN00.128-0.03340.6380.0030.0030.0000.0000.0000.000
86A51ASN0-0.0450.08039.970-0.003-0.0030.0000.0000.0000.000
87A52LEU00.125-0.10639.436-0.007-0.0070.0000.0000.0000.000
88A52LEU0-0.0330.12740.3640.0000.0000.0000.0000.0000.000
89A53THR00.010-0.07637.611-0.008-0.0080.0000.0000.0000.000
90A53THR0-0.0100.07136.9170.0010.0010.0000.0000.0000.000
91A54THR00.091-0.07035.752-0.011-0.0110.0000.0000.0000.000
92A54THR0-0.0450.07435.8080.0040.0040.0000.0000.0000.000
93A55ALA00.149-0.05634.653-0.012-0.0120.0000.0000.0000.000
94A55ALA0-0.0670.11836.8700.0020.0020.0000.0000.0000.000
95A56SER00.062-0.07533.835-0.011-0.0110.0000.0000.0000.000
96A56SER0-0.0510.06434.342-0.003-0.0030.0000.0000.0000.000
97A57ALA00.071-0.10531.477-0.013-0.0130.0000.0000.0000.000
98A57ALA0-0.0760.10931.8890.0010.0010.0000.0000.0000.000
99A58ASN00.011-0.08229.858-0.018-0.0180.0000.0000.0000.000
100A58ASN0-0.0660.06931.335-0.008-0.0080.0000.0000.0000.000
101A59LEU00.161-0.08729.259-0.017-0.0170.0000.0000.0000.000
102A59LEU0-0.0790.10431.4240.0010.0010.0000.0000.0000.000
103A60GLN00.072-0.09927.998-0.016-0.0160.0000.0000.0000.000
104A60GLN0-0.0830.12028.098-0.007-0.0070.0000.0000.0000.000
105A61ALA00.152-0.07325.466-0.028-0.0280.0000.0000.0000.000
106A61ALA0-0.1090.09526.2040.0030.0030.0000.0000.0000.000
107A62LEU00.083-0.11324.383-0.034-0.0340.0000.0000.0000.000
108A62LEU0-0.0850.10126.4280.0010.0010.0000.0000.0000.000
109A63LYS00.108-0.07524.322-0.025-0.0250.0000.0000.0000.000
110A63LYS10.8531.06425.1520.2650.2650.0000.0000.0000.000
111A64SER0-0.067-0.13522.084-0.020-0.0200.0000.0000.0000.000
112A64SER0-0.0690.05121.7530.0010.0010.0000.0000.0000.000
113A65GLY0-0.003-0.09019.891-0.050-0.0500.0000.0000.0000.000
114A66GLY0-0.029-0.01519.810-0.040-0.0400.0000.0000.0000.000
115A67LEU00.089-0.00121.5130.0020.0020.0000.0000.0000.000
116A67LEU0-0.0740.10921.5220.0020.0020.0000.0000.0000.000
117A68VAL00.028-0.10324.1000.0170.0170.0000.0000.0000.000
118A68VAL0-0.0510.10827.2490.0030.0030.0000.0000.0000.000
119A69GLU00.066-0.13125.965-0.022-0.0220.0000.0000.0000.000
120A69GLU-1-0.872-0.77625.521-0.225-0.2250.0000.0000.0000.000
121A70ALA00.107-0.09927.7530.0100.0100.0000.0000.0000.000
122A70ALA0-0.0980.07730.2970.0000.0000.0000.0000.0000.000
123A71ARG0-0.026-0.10330.693-0.008-0.0080.0000.0000.0000.000
124A71ARG10.7510.97432.8930.1240.1240.0000.0000.0000.000
125A72ARG00.116-0.11833.5250.0010.0010.0000.0000.0000.000
126A72ARG10.8201.06734.9850.1320.1320.0000.0000.0000.000
127A73GLU00.084-0.12036.7060.0000.0000.0000.0000.0000.000
128A73GLU-1-0.881-0.73739.278-0.103-0.1030.0000.0000.0000.000
129A74GLY00.040-0.08640.1700.0030.0030.0000.0000.0000.000
130A75THR00.0370.00541.487-0.005-0.0050.0000.0000.0000.000
131A75THR0-0.0320.08544.0600.0020.0020.0000.0000.0000.000
132A76ARG00.022-0.08841.193-0.001-0.0010.0000.0000.0000.000
133A76ARG10.7920.96941.2570.0920.0920.0000.0000.0000.000
134A77GLN00.096-0.09136.8310.0000.0000.0000.0000.0000.000
135A77GLN0-0.0770.09033.0210.0060.0060.0000.0000.0000.000
136A78TYR00.002-0.13935.8740.0030.0030.0000.0000.0000.000
137A78TYR0-0.0710.08936.3050.0010.0010.0000.0000.0000.000
138A79TYR00.066-0.09732.340-0.006-0.0060.0000.0000.0000.000
139A79TYR0-0.0550.07029.9050.0040.0040.0000.0000.0000.000
140A80ARG00.083-0.07531.1200.0110.0110.0000.0000.0000.000
141A80ARG10.7811.00328.9110.1840.1840.0000.0000.0000.000
142A81ILE00.156-0.09028.329-0.014-0.0140.0000.0000.0000.000
143A81ILE0-0.0970.11827.137-0.001-0.0010.0000.0000.0000.000
144A82ALA00.046-0.14924.6700.0200.0200.0000.0000.0000.000
145A82ALA0-0.0660.13824.041-0.006-0.0060.0000.0000.0000.000
146A83GLY0-0.012-0.10624.824-0.004-0.0040.0000.0000.0000.000
147A84GLU00.1440.03525.745-0.006-0.0060.0000.0000.0000.000
148A84GLU-1-0.945-0.81125.747-0.176-0.1760.0000.0000.0000.000
149A85ASP00.106-0.10121.6400.0180.0180.0000.0000.0000.000
150A85ASP-1-0.911-0.82120.882-0.291-0.2910.0000.0000.0000.000
151A86VAL00.034-0.10722.877-0.014-0.0140.0000.0000.0000.000
152A86VAL0-0.1000.09022.096-0.002-0.0020.0000.0000.0000.000
153A87ALA00.122-0.08223.977-0.002-0.0020.0000.0000.0000.000
154A87ALA0-0.0760.10828.1170.0040.0040.0000.0000.0000.000
155A88ARG00.077-0.10125.2850.0120.0120.0000.0000.0000.000
156A88ARG10.7280.97422.1050.2290.2290.0000.0000.0000.000
157A89LEU00.120-0.08322.4020.0160.0160.0000.0000.0000.000
158A89LEU0-0.1360.07820.014-0.011-0.0110.0000.0000.0000.000
159A90PHE00.050-0.08923.473-0.003-0.0030.0000.0000.0000.000
160A90PHE0-0.0940.08326.741-0.003-0.0030.0000.0000.0000.000
161A91ALA00.134-0.08626.5640.0050.0050.0000.0000.0000.000
162A91ALA0-0.0810.10328.3830.0020.0020.0000.0000.0000.000
163A92LEU00.109-0.08924.8030.0170.0170.0000.0000.0000.000
164A92LEU0-0.1190.09022.150-0.004-0.0040.0000.0000.0000.000
165A93VAL00.083-0.08624.8770.0110.0110.0000.0000.0000.000
166A93VAL0-0.1270.06523.951-0.006-0.0060.0000.0000.0000.000
167A94GLN00.068-0.09725.6190.0020.0020.0000.0000.0000.000
168A94GLN0-0.1050.06529.7970.0080.0080.0000.0000.0000.000
169A95VAL00.111-0.06428.9370.0090.0090.0000.0000.0000.000
170A95VAL0-0.1110.07228.3110.0000.0000.0000.0000.0000.000
171A96VAL00.103-0.07225.4860.0140.0140.0000.0000.0000.000
172A96VAL0-0.1480.04323.654-0.005-0.0050.0000.0000.0000.000
173A97ALA00.089-0.08626.9730.0060.0060.0000.0000.0000.000
174A97ALA0-0.1300.06328.560-0.001-0.0010.0000.0000.0000.000
175A98ASP00.040-0.11129.2340.0050.0050.0000.0000.0000.000
176A98ASP-1-1.016-0.85332.054-0.104-0.1040.0000.0000.0000.000
177A99GLU0-0.219-0.20529.4420.0150.0150.0000.0000.0000.000
178A99GLU-1-0.896-0.93729.312-0.111-0.1110.0000.0000.0000.000