FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: 6G4JZ

Calculation Name: 3C8I-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 3C8I

Chain ID: A

ChEMBL ID:

UniProt ID: Q6NIK4

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 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 238
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1044973.711728
FMO2-HF: Nuclear repulsion 996156.819378
FMO2-HF: Total energy -48816.89235
FMO2-MP2: Total energy -48958.554433


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:15:ASP)


Summations of interaction energy for fragment #1(A:15: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.
-2.5650.2240.022-1.325-1.4860.006
Interaction energy analysis for fragmet #1(A:15:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.121 / q_NPA : -0.002
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].
4A16LEU0-0.1910.0814.2550.0730.5390.003-0.277-0.1920.001
5A17VAL00.007-0.1403.781-2.167-0.788-0.008-0.739-0.6320.004
6A17VAL0-0.0590.1354.469-0.0100.058-0.001-0.016-0.0520.000
7A18PRO0-0.017-0.0996.4730.7500.7500.0000.0000.0000.000
8A19ALA00.2090.03810.198-0.299-0.2990.0000.0000.0000.000
9A19ALA0-0.1010.08710.9220.0070.0070.0000.0000.0000.000
10A20MET00.066-0.12712.3480.1340.1340.0000.0000.0000.000
11A20MET0-0.1280.10515.904-0.014-0.0140.0000.0000.0000.000
12A21ILE00.089-0.11516.108-0.065-0.0650.0000.0000.0000.000
13A21ILE0-0.1090.11018.9170.0070.0070.0000.0000.0000.000
14A22ALA00.078-0.09719.1220.0200.0200.0000.0000.0000.000
15A22ALA0-0.0320.11819.109-0.013-0.0130.0000.0000.0000.000
16A23GLU00.090-0.14120.8360.0070.0070.0000.0000.0000.000
17A23GLU-1-0.871-0.74623.008-0.202-0.2020.0000.0000.0000.000
18A24VAL00.029-0.10522.7930.0000.0000.0000.0000.0000.000
19A24VAL0-0.0990.09523.5970.0030.0030.0000.0000.0000.000
20A25ASN00.040-0.08825.3350.0000.0000.0000.0000.0000.000
21A25ASN0-0.1280.05925.5030.0030.0030.0000.0000.0000.000
22A26PRO00.025-0.12127.5390.0140.0140.0000.0000.0000.000
23A27ARG0-0.025-0.01227.8850.0150.0150.0000.0000.0000.000
24A27ARG10.8881.05728.329-0.007-0.0070.0000.0000.0000.000
25A28ASP00.079-0.09223.8400.0210.0210.0000.0000.0000.000
26A28ASP-1-0.830-0.78023.369-0.111-0.1110.0000.0000.0000.000
27A29MET00.109-0.05821.9420.0030.0030.0000.0000.0000.000
28A29MET0-0.1210.07119.0020.0080.0080.0000.0000.0000.000
29A30VAL00.070-0.10519.2440.0090.0090.0000.0000.0000.000
30A30VAL0-0.0490.12418.854-0.006-0.0060.0000.0000.0000.000
31A31VAL00.049-0.10415.4910.0250.0250.0000.0000.0000.000
32A31VAL0-0.0810.09613.9370.0070.0070.0000.0000.0000.000
33A32MET00.200-0.09415.155-0.044-0.0440.0000.0000.0000.000
34A32MET0-0.1390.11115.114-0.002-0.0020.0000.0000.0000.000
35A33ALA00.094-0.09410.6590.1690.1690.0000.0000.0000.000
36A33ALA0-0.0920.0919.722-0.035-0.0350.0000.0000.0000.000
37A34LEU00.067-0.09410.9070.0180.0180.0000.0000.0000.000
38A34LEU0-0.1350.08411.1410.0580.0580.0000.0000.0000.000
39A35VAL00.027-0.0997.498-0.288-0.2880.0000.0000.0000.000
40A35VAL0-0.0460.0987.365-0.093-0.0930.0000.0000.0000.000
41A36ASN00.163-0.0696.8400.6420.6420.0000.0000.0000.000
42A36ASN0-0.0670.0926.6740.4810.4810.0000.0000.0000.000
43A37THR00.013-0.1027.535-0.742-0.7420.0000.0000.0000.000
44A37THR0-0.0450.05211.0510.0110.0110.0000.0000.0000.000
45A38ASN00.128-0.04510.0660.1920.1920.0000.0000.0000.000
46A38ASN0-0.0880.06910.4010.1450.1450.0000.0000.0000.000
47A39VAL00.091-0.0888.729-0.549-0.5490.0000.0000.0000.000
48A39VAL0-0.0980.10910.5110.0470.0470.0000.0000.0000.000
49A40ASP00.076-0.1329.384-0.195-0.1950.0000.0000.0000.000
50A40ASP-1-0.928-0.78012.570-0.858-0.8580.0000.0000.0000.000
51A41PRO0-0.049-0.1276.851-0.014-0.0140.0000.0000.0000.000
52A42THR0-0.013-0.0028.8830.0420.0420.0000.0000.0000.000
53A42THR0-0.0660.03012.1860.0760.0760.0000.0000.0000.000
54A43LEU00.042-0.10512.1900.1780.1780.0000.0000.0000.000
55A43LEU0-0.0710.11412.9500.0020.0020.0000.0000.0000.000
56A44PRO0-0.028-0.11312.348-0.103-0.1030.0000.0000.0000.000
57A45PRO0-0.020-0.01810.181-0.049-0.0490.0000.0000.0000.000
58A46ARG00.1500.01811.3550.2130.2130.0000.0000.0000.000
59A46ARG10.7141.03712.3240.9530.9530.0000.0000.0000.000
60A47TRP00.068-0.09711.741-0.240-0.2400.0000.0000.0000.000
61A47TRP0-0.1200.0618.7800.0140.0140.0000.0000.0000.000
62A48ALA00.106-0.10111.8040.2190.2190.0000.0000.0000.000
63A48ALA0-0.0280.12111.890-0.013-0.0130.0000.0000.0000.000
64A49LEU00.003-0.13112.173-0.211-0.2110.0000.0000.0000.000
65A49LEU0-0.0400.09914.5510.0330.0330.0000.0000.0000.000
66A50ALA00.148-0.05312.0170.0990.0990.0000.0000.0000.000
67A50ALA0-0.0780.10911.342-0.062-0.0620.0000.0000.0000.000
68A51THR0-0.010-0.09413.398-0.011-0.0110.0000.0000.0000.000
69A51THR0-0.0370.08316.7980.0100.0100.0000.0000.0000.000
70A52ARG00.115-0.09314.724-0.031-0.0310.0000.0000.0000.000
71A52ARG10.7721.02211.1370.2490.2490.0000.0000.0000.000
72A53ASN00.150-0.05716.0650.0230.0230.0000.0000.0000.000
73A53ASN0-0.1310.06420.4190.0210.0210.0000.0000.0000.000
74A54ILE00.009-0.11917.6450.0000.0000.0000.0000.0000.000
75A54ILE0-0.0850.08815.4850.0110.0110.0000.0000.0000.000
76A55THR00.084-0.07318.910-0.011-0.0110.0000.0000.0000.000
77A55THR0-0.0360.08221.8550.0030.0030.0000.0000.0000.000
78A56ALA00.096-0.10619.872-0.015-0.0150.0000.0000.0000.000
79A56ALA0-0.0470.11921.2510.0040.0040.0000.0000.0000.000
80A57ILE00.010-0.13217.4320.0100.0100.0000.0000.0000.000
81A57ILE0-0.0490.12715.491-0.001-0.0010.0000.0000.0000.000
82A58PRO0-0.002-0.09316.950-0.024-0.0240.0000.0000.0000.000
83A59GLY00.0640.02518.4950.0470.0470.0000.0000.0000.000
84A60ILE00.0400.00520.484-0.011-0.0110.0000.0000.0000.000
85A60ILE0-0.1520.07017.761-0.006-0.0060.0000.0000.0000.000
86A61GLU00.079-0.12021.575-0.020-0.0200.0000.0000.0000.000
87A61GLU-1-0.926-0.82523.1570.1710.1710.0000.0000.0000.000
88A62GLY0-0.005-0.12625.286-0.002-0.0020.0000.0000.0000.000
89A63ASP00.1090.02027.615-0.018-0.0180.0000.0000.0000.000
90A63ASP-1-0.959-0.84728.0930.0610.0610.0000.0000.0000.000
91A64THR0-0.029-0.10823.620-0.027-0.0270.0000.0000.0000.000
92A64THR00.0180.08822.592-0.003-0.0030.0000.0000.0000.000
93A65ARG00.133-0.02222.852-0.011-0.0110.0000.0000.0000.000
94A65ARG10.7821.03723.2150.0120.0120.0000.0000.0000.000
95A66LYS00.064-0.10223.414-0.006-0.0060.0000.0000.0000.000
96A66LYS10.8181.03524.674-0.003-0.0030.0000.0000.0000.000
97A67VAL00.117-0.11622.6830.0040.0040.0000.0000.0000.000
98A67VAL0-0.0780.13122.9590.0020.0020.0000.0000.0000.000
99A68GLY0-0.023-0.12220.9850.0160.0160.0000.0000.0000.000
100A69THR0-0.0030.01020.095-0.009-0.0090.0000.0000.0000.000
101A69THR0-0.1050.01718.9220.0010.0010.0000.0000.0000.000
102A70ARG00.111-0.08916.206-0.055-0.0550.0000.0000.0000.000
103A70ARG10.7630.99915.449-0.032-0.0320.0000.0000.0000.000
104A71ILE00.041-0.12214.1040.0880.0880.0000.0000.0000.000
105A71ILE0-0.0870.10712.5840.0090.0090.0000.0000.0000.000
106A72PRO0-0.008-0.0859.893-0.147-0.1470.0000.0000.0000.000
107A73ALA00.1190.0148.1360.3780.3780.0000.0000.0000.000
108A73ALA0-0.0680.0938.474-0.082-0.0820.0000.0000.0000.000
109A74VAL00.074-0.1054.086-0.476-0.433-0.001-0.041-0.0010.000
110A74VAL0-0.0670.1133.1290.0870.4940.029-0.146-0.2900.001
111A75ALA00.114-0.0973.5051.2831.6020.001-0.110-0.2100.000
112A75ALA0-0.0630.1163.596-0.143-0.1390.0000.035-0.0390.000
113A76VAL00.071-0.1214.257-1.319-1.216-0.001-0.031-0.0700.000
114A76VAL0-0.1260.0926.2770.1400.1400.0000.0000.0000.000
115A77THR00.059-0.1136.5370.1370.1370.0000.0000.0000.000
116A77THR0-0.0050.1165.953-0.084-0.0840.0000.0000.0000.000
117A78GLY0-0.050-0.1038.4670.3820.3820.0000.0000.0000.000
118A79GLN00.1420.01012.146-0.046-0.0460.0000.0000.0000.000
119A79GLN0-0.1820.04115.9360.0610.0610.0000.0000.0000.000
120A80ARG00.077-0.09013.734-0.146-0.1460.0000.0000.0000.000
121A80ARG10.7210.96412.6720.8270.8270.0000.0000.0000.000
122A81SER0-0.025-0.10914.6580.1040.1040.0000.0000.0000.000
123A81SER0-0.0410.06017.8860.0250.0250.0000.0000.0000.000
124A82VAL00.050-0.11116.972-0.088-0.0880.0000.0000.0000.000
125A82VAL0-0.0760.11417.5340.0070.0070.0000.0000.0000.000
126A83GLY00.002-0.09819.2740.0640.0640.0000.0000.0000.000
127A84ASN00.1190.03121.7850.0080.0080.0000.0000.0000.000
128A84ASN0-0.1390.04122.0690.0200.0200.0000.0000.0000.000
129A85GLN00.033-0.07417.5600.0330.0330.0000.0000.0000.000
130A85GLN0-0.0490.08416.3340.0460.0460.0000.0000.0000.000
131A86ASP00.138-0.07915.9530.0500.0500.0000.0000.0000.000
132A86ASP-1-0.882-0.76514.969-0.831-0.8310.0000.0000.0000.000
133A87SER00.003-0.09812.560-0.145-0.1450.0000.0000.0000.000
134A87SER0-0.0040.08013.4340.0510.0510.0000.0000.0000.000
135A88TRP00.045-0.11510.5700.2310.2310.0000.0000.0000.000
136A88TRP0-0.0570.1027.5220.1780.1780.0000.0000.0000.000
137A89ASP00.093-0.08311.995-0.065-0.0650.0000.0000.0000.000
138A89ASP-1-0.911-0.80015.927-0.705-0.7050.0000.0000.0000.000
139A90GLN00.046-0.13713.1460.0800.0800.0000.0000.0000.000
140A90GLN0-0.0340.11213.5110.0040.0040.0000.0000.0000.000
141A91ILE00.050-0.0849.182-0.010-0.0100.0000.0000.0000.000
142A91ILE0-0.0360.1227.222-0.066-0.0660.0000.0000.0000.000
143A92SER00.054-0.0729.4320.0820.0820.0000.0000.0000.000
144A92SER0-0.0490.07510.6200.1080.1080.0000.0000.0000.000
145A93PRO00.012-0.0738.183-0.119-0.1190.0000.0000.0000.000
146A94MET00.102-0.0227.7460.1000.1000.0000.0000.0000.000
147A94MET0-0.1220.1077.803-0.059-0.0590.0000.0000.0000.000
148A95PRO0-0.009-0.1068.4630.2150.2150.0000.0000.0000.000
149A96ILE00.1330.0199.5110.0480.0480.0000.0000.0000.000
150A96ILE0-0.0690.1197.1130.0360.0360.0000.0000.0000.000
151A97ALA00.112-0.09710.1740.1260.1260.0000.0000.0000.000
152A97ALA0-0.0660.09814.760-0.029-0.0290.0000.0000.0000.000
153A98TRP0-0.024-0.12912.917-0.044-0.0440.0000.0000.0000.000
154A98TRP0-0.1100.05412.372-0.038-0.0380.0000.0000.0000.000
155A99ALA00.109-0.07211.700-0.141-0.1410.0000.0000.0000.000
156A99ALA0-0.1190.08410.9900.0790.0790.0000.0000.0000.000
157A100THR00.016-0.10513.041-0.068-0.0680.0000.0000.0000.000
158A100THR0-0.0480.05813.317-0.034-0.0340.0000.0000.0000.000
159A101PRO00.002-0.07614.5650.0700.0700.0000.0000.0000.000
160A102ASP00.0850.02417.128-0.086-0.0860.0000.0000.0000.000
161A102ASP-1-0.885-0.83316.7810.6870.6870.0000.0000.0000.000
162A103SER00.093-0.04516.8810.0800.0800.0000.0000.0000.000
163A103SER0-0.0260.05920.6550.0000.0000.0000.0000.0000.000
164A104SER0-0.039-0.10017.864-0.022-0.0220.0000.0000.0000.000
165A104SER0-0.0150.07217.870-0.023-0.0230.0000.0000.0000.000
166A105VAL00.061-0.07514.051-0.002-0.0020.0000.0000.0000.000
167A105VAL0-0.0810.08912.0350.0290.0290.0000.0000.0000.000
168A106ILE00.091-0.11012.9660.1760.1760.0000.0000.0000.000
169A106ILE0-0.0920.11612.955-0.007-0.0070.0000.0000.0000.000
170A107ALA00.153-0.08213.908-0.035-0.0350.0000.0000.0000.000
171A107ALA0-0.0710.10317.463-0.014-0.0140.0000.0000.0000.000
172A108ARG00.058-0.09413.830-0.106-0.1060.0000.0000.0000.000
173A108ARG10.8821.07212.334-0.863-0.8630.0000.0000.0000.000
174A109ALA00.109-0.0639.844-0.036-0.0360.0000.0000.0000.000
175A109ALA0-0.0630.1009.4710.0390.0390.0000.0000.0000.000
176A110GLU00.090-0.13310.255-0.097-0.0970.0000.0000.0000.000
177A110GLU-1-0.891-0.78813.7390.1710.1710.0000.0000.0000.000
178A111SER0-0.014-0.08512.738-0.141-0.1410.0000.0000.0000.000
179A111SER0-0.0690.04713.7070.0020.0020.0000.0000.0000.000
180A112THR00.006-0.0769.795-0.156-0.1560.0000.0000.0000.000
181A112THR0-0.1100.0228.2060.1170.1170.0000.0000.0000.000
182A113ILE00.090-0.0869.137-0.037-0.0370.0000.0000.0000.000
183A113ILE0-0.1240.0987.978-0.027-0.0270.0000.0000.0000.000
184A114PRO00.008-0.0939.6340.0120.0120.0000.0000.0000.000
185A115SER00.0790.02112.680-0.083-0.0830.0000.0000.0000.000
186A115SER0-0.0290.07217.0360.0190.0190.0000.0000.0000.000
187A116GLU00.010-0.14815.7690.0030.0030.0000.0000.0000.000
188A116GLU-1-0.842-0.76515.223-0.323-0.3230.0000.0000.0000.000
189A117GLN00.118-0.09212.0860.0100.0100.0000.0000.0000.000
190A117GLN0-0.0570.1269.009-0.182-0.1820.0000.0000.0000.000
191A118TRP00.108-0.07913.608-0.079-0.0790.0000.0000.0000.000
192A118TRP0-0.1350.08112.208-0.066-0.0660.0000.0000.0000.000
193A119THR00.047-0.08715.1940.0030.0030.0000.0000.0000.000
194A119THR0-0.0680.05418.4610.0220.0220.0000.0000.0000.000
195A120THR0-0.015-0.10716.3440.0580.0580.0000.0000.0000.000
196A120THR0-0.0430.06815.347-0.007-0.0070.0000.0000.0000.000
197A121LEU00.134-0.07615.1060.0080.0080.0000.0000.0000.000
198A121LEU0-0.1110.12513.0380.0030.0030.0000.0000.0000.000
199A122SER00.061-0.08416.1800.0130.0130.0000.0000.0000.000
200A122SER0-0.0760.05719.1480.0290.0290.0000.0000.0000.000
201A123LYS00.040-0.09819.4450.0330.0330.0000.0000.0000.000
202A123LYS10.8281.04920.6960.2770.2770.0000.0000.0000.000
203A124ASN00.017-0.07918.9080.0440.0440.0000.0000.0000.000
204A124ASN0-0.0850.05018.010-0.002-0.0020.0000.0000.0000.000
205A125LEU00.195-0.05719.618-0.037-0.0370.0000.0000.0000.000
206A125LEU0-0.0910.10618.6000.0050.0050.0000.0000.0000.000
207A126ASN00.052-0.09020.5320.0060.0060.0000.0000.0000.000
208A126ASN0-0.1160.04723.837-0.022-0.0220.0000.0000.0000.000
209A127LYS00.056-0.08621.5320.0370.0370.0000.0000.0000.000
210A127LYS10.8401.04520.5190.4550.4550.0000.0000.0000.000
211A128LEU00.158-0.08020.775-0.042-0.0420.0000.0000.0000.000
212A128LEU0-0.1160.09820.4310.0000.0000.0000.0000.0000.000
213A129ASP00.064-0.11921.844-0.028-0.0280.0000.0000.0000.000
214A129ASP-1-0.922-0.80126.186-0.242-0.2420.0000.0000.0000.000
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