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: 6G8GZ

Calculation Name: 3KF6-B-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3KF6

Chain ID: B

ChEMBL ID:

UniProt ID: Q0E7J7

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 199
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -799672.589368
FMO2-HF: Nuclear repulsion 758065.408772
FMO2-HF: Total energy -41607.180596
FMO2-MP2: Total energy -41726.389494


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(B:498:PRO)


Summations of interaction energy for fragment #1(B:498:PRO)
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.
-0.1493.2860.098-1.426-2.1060.004
Interaction energy analysis for fragmet #1(B:498:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.078 / q_NPA : 0.012
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].
3B499LEU0-0.0400.1162.960-0.7960.2780.103-0.332-0.8450.001
4B500GLY00.038-0.0753.076-0.6921.490-0.003-1.071-1.1080.003
5B501SER00.015-0.0025.107-0.120-0.063-0.002-0.005-0.0500.000
6B501SER0-0.0040.0737.7780.0250.0250.0000.0000.0000.000
7B502ASP00.059-0.0607.8990.1200.1200.0000.0000.0000.000
8B502ASP-1-0.812-0.7588.511-0.853-0.8530.0000.0000.0000.000
9B503SER00.070-0.09310.122-0.138-0.1380.0000.0000.0000.000
10B503SER0-0.0210.09314.1990.0200.0200.0000.0000.0000.000
11B504ALA00.060-0.09512.508-0.004-0.0040.0000.0000.0000.000
12B504ALA0-0.0760.10011.630-0.006-0.0060.0000.0000.0000.000
13B505LYS00.075-0.10913.3330.0450.0450.0000.0000.0000.000
14B505LYS10.7410.98917.0100.2110.2110.0000.0000.0000.000
15B506LEU00.088-0.10316.824-0.027-0.0270.0000.0000.0000.000
16B506LEU0-0.1250.08917.9140.0000.0000.0000.0000.0000.000
17B507ILE0-0.011-0.11918.4850.0270.0270.0000.0000.0000.000
18B507ILE0-0.0580.09118.120-0.001-0.0010.0000.0000.0000.000
19B508PHE00.134-0.10220.197-0.014-0.0140.0000.0000.0000.000
20B508PHE0-0.0990.10723.8130.0020.0020.0000.0000.0000.000
21B509ILE00.139-0.06720.670-0.011-0.0110.0000.0000.0000.000
22B509ILE0-0.0950.11219.7610.0000.0000.0000.0000.0000.000
23B510ASN00.040-0.08321.661-0.006-0.0060.0000.0000.0000.000
24B510ASN0-0.1130.05426.0770.0030.0030.0000.0000.0000.000
25B511GLN00.091-0.09323.1170.0110.0110.0000.0000.0000.000
26B511GLN0-0.0300.10722.506-0.011-0.0110.0000.0000.0000.000
27B512ILE00.105-0.07919.788-0.001-0.0010.0000.0000.0000.000
28B512ILE0-0.0900.10617.797-0.004-0.0040.0000.0000.0000.000
29B513ASN00.086-0.08720.338-0.016-0.0160.0000.0000.0000.000
30B513ASN0-0.0920.07422.507-0.012-0.0120.0000.0000.0000.000
31B514ASP00.064-0.10322.9780.0080.0080.0000.0000.0000.000
32B514ASP-1-0.953-0.83823.673-0.132-0.1320.0000.0000.0000.000
33B515CYS00.039-0.13019.4950.0120.0120.0000.0000.0000.000
34B515CYS0-0.0850.14418.672-0.009-0.0090.0000.0000.0000.000
35B516LYS00.078-0.07119.7290.0060.0060.0000.0000.0000.000
36B516LYS10.8961.06119.0740.1250.1250.0000.0000.0000.000
37B517ASP00.058-0.09816.958-0.036-0.0360.0000.0000.0000.000
38B517ASP-1-0.861-0.77617.118-0.190-0.1900.0000.0000.0000.000
39B518GLY0-0.020-0.12312.6770.0200.0200.0000.0000.0000.000
40B519GLN00.0990.00712.043-0.107-0.1070.0000.0000.0000.000
41B519GLN0-0.0520.10715.6550.0230.0230.0000.0000.0000.000
42B520LYS00.151-0.08911.1780.0010.0010.0000.0000.0000.000
43B520LYS10.6661.0007.1821.1171.1170.0000.0000.0000.000
44B521LEU00.009-0.13512.1030.0690.0690.0000.0000.0000.000
45B521LEU0-0.0610.11814.3560.0110.0110.0000.0000.0000.000
46B522ARG00.138-0.06012.601-0.082-0.0820.0000.0000.0000.000
47B522ARG10.8011.00613.6800.2650.2650.0000.0000.0000.000
48B523PHE00.039-0.08014.7360.0320.0320.0000.0000.0000.000
49B523PHE0-0.0480.09514.7810.0030.0030.0000.0000.0000.000
50B524LEU00.107-0.10916.806-0.023-0.0230.0000.0000.0000.000
51B524LEU0-0.1400.09419.7370.0040.0040.0000.0000.0000.000
52B525GLY00.017-0.11619.4870.0090.0090.0000.0000.0000.000
53B526CYS00.1460.00421.128-0.010-0.0100.0000.0000.0000.000
54B526CYS0-0.1750.11325.0440.0050.0050.0000.0000.0000.000
55B527VAL00.109-0.11522.023-0.004-0.0040.0000.0000.0000.000
56B527VAL0-0.0770.13620.294-0.001-0.0010.0000.0000.0000.000
57B528GLN00.122-0.06422.8070.0120.0120.0000.0000.0000.000
58B528GLN0-0.0720.10124.8580.0020.0020.0000.0000.0000.000
59B529SER00.028-0.10623.4230.0120.0120.0000.0000.0000.000
60B529SER0-0.0510.04423.6650.0040.0040.0000.0000.0000.000
61B530TYR00.031-0.08720.902-0.011-0.0110.0000.0000.0000.000
62B530TYR0-0.0210.12017.023-0.005-0.0050.0000.0000.0000.000
63B531LYS00.083-0.07120.9840.0110.0110.0000.0000.0000.000
64B531LYS10.8901.05123.2720.1080.1080.0000.0000.0000.000
65B532ASN00.032-0.05420.660-0.012-0.0120.0000.0000.0000.000
66B532ASN0-0.0880.05021.4060.0030.0030.0000.0000.0000.000
67B533GLY00.148-0.04716.4840.0020.0020.0000.0000.0000.000
68B534ILE00.065-0.00315.711-0.039-0.0390.0000.0000.0000.000
69B534ILE0-0.0890.10716.6060.0030.0030.0000.0000.0000.000
70B535LEU00.145-0.10417.4100.0280.0280.0000.0000.0000.000
71B535LEU0-0.1000.11316.429-0.003-0.0030.0000.0000.0000.000
72B536ARG00.124-0.08518.455-0.021-0.0210.0000.0000.0000.000
73B536ARG10.7771.02422.5100.1310.1310.0000.0000.0000.000
74B537LEU00.056-0.10920.1340.0150.0150.0000.0000.0000.000
75B537LEU0-0.0270.11417.317-0.003-0.0030.0000.0000.0000.000
76B538ILE00.044-0.10121.257-0.002-0.0020.0000.0000.0000.000
77B538ILE0-0.1020.09525.0930.0020.0020.0000.0000.0000.000
78B539ASP00.090-0.12024.209-0.003-0.0030.0000.0000.0000.000
79B539ASP-1-0.916-0.81323.878-0.140-0.1400.0000.0000.0000.000
80B540GLY00.022-0.07825.8260.0030.0030.0000.0000.0000.000
81B541SER0-0.0030.00829.632-0.001-0.0010.0000.0000.0000.000
82B541SER0-0.0150.09731.3690.0020.0020.0000.0000.0000.000
83B542SER0-0.009-0.08726.6980.0050.0050.0000.0000.0000.000
84B542SER00.0040.06725.900-0.005-0.0050.0000.0000.0000.000
85B543SER0-0.024-0.10023.7850.0010.0010.0000.0000.0000.000
86B543SER0-0.0010.06324.1970.0050.0050.0000.0000.0000.000
87B544VAL00.027-0.09719.7390.0120.0120.0000.0000.0000.000
88B544VAL0-0.0380.11918.007-0.001-0.0010.0000.0000.0000.000
89B545THR0-0.044-0.11119.2820.0010.0010.0000.0000.0000.000
90B545THR0-0.0360.06918.6400.0080.0080.0000.0000.0000.000
91B546CYS00.168-0.07015.251-0.015-0.0150.0000.0000.0000.000
92B546CYS0-0.1400.08614.549-0.009-0.0090.0000.0000.0000.000
93B547ASP00.133-0.08514.0810.0330.0330.0000.0000.0000.000
94B547ASP-1-0.849-0.76013.238-0.291-0.2910.0000.0000.0000.000
95B548VAL00.036-0.10711.520-0.082-0.0820.0000.0000.0000.000
96B548VAL0-0.0980.08312.4070.0020.0020.0000.0000.0000.000
97B549THR00.071-0.07912.081-0.012-0.0120.0000.0000.0000.000
98B549THR0-0.0400.04712.5520.0180.0180.0000.0000.0000.000
99B550VAL0-0.008-0.1108.0310.0770.0770.0000.0000.0000.000
100B550VAL0-0.0360.1097.061-0.008-0.0080.0000.0000.0000.000
101B551VAL00.078-0.0848.139-0.033-0.0330.0000.0000.0000.000
102B551VAL0-0.1270.0767.667-0.013-0.0130.0000.0000.0000.000
103B552LEU00.090-0.1339.561-0.001-0.0010.0000.0000.0000.000
104B552LEU0-0.1050.11413.5690.0070.0070.0000.0000.0000.000
105B553PRO0-0.066-0.13612.8370.0010.0010.0000.0000.0000.000
106B554ASP00.0510.00714.3970.0120.0120.0000.0000.0000.000
107B554ASP-1-0.933-0.84014.649-0.166-0.1660.0000.0000.0000.000
108B555VAL0-0.010-0.12816.0800.0200.0200.0000.0000.0000.000
109B555VAL0-0.0540.11217.4440.0010.0010.0000.0000.0000.000
110B556SER00.010-0.10018.990-0.017-0.0170.0000.0000.0000.000
111B556SER0-0.0330.06823.2720.0010.0010.0000.0000.0000.000
112B557ILE00.135-0.06720.0050.0070.0070.0000.0000.0000.000
113B557ILE0-0.1100.08616.866-0.003-0.0030.0000.0000.0000.000
114B558GLN00.124-0.09420.9540.0070.0070.0000.0000.0000.000
115B558GLN0-0.1200.10624.8890.0060.0060.0000.0000.0000.000
116B559LYS00.122-0.10224.065-0.010-0.0100.0000.0000.0000.000
117B559LYS10.7571.02526.6640.1000.1000.0000.0000.0000.000
118B560HIS0-0.052-0.10925.7180.0050.0050.0000.0000.0000.000
119B560HIS0-0.0910.06927.7160.0060.0060.0000.0000.0000.000
120B561GLU00.182-0.07423.5230.0070.0070.0000.0000.0000.000
121B561GLU-1-0.859-0.79120.990-0.153-0.1530.0000.0000.0000.000
122B562TRP00.067-0.11222.181-0.004-0.0040.0000.0000.0000.000
123B562TRP0-0.0840.09422.410-0.001-0.0010.0000.0000.0000.000
124B563LEU00.054-0.13517.7120.0110.0110.0000.0000.0000.000
125B563LEU0-0.0070.14916.505-0.004-0.0040.0000.0000.0000.000
126B564ASN00.139-0.05716.2340.0060.0060.0000.0000.0000.000
127B564ASN0-0.1110.06815.338-0.004-0.0040.0000.0000.0000.000
128B565ILE00.039-0.10912.840-0.008-0.0080.0000.0000.0000.000
129B565ILE0-0.0340.13212.2160.0000.0000.0000.0000.0000.000
130B566VAL00.085-0.11710.2080.0650.0650.0000.0000.0000.000
131B566VAL0-0.1090.0999.2820.0000.0000.0000.0000.0000.000
132B567GLY00.050-0.0758.908-0.085-0.0850.0000.0000.0000.000
133B568ARG00.043-0.0069.9610.0130.0130.0000.0000.0000.000
134B568ARG10.7610.9726.8321.1251.1250.0000.0000.0000.000
135B569LYS00.140-0.08711.5160.0020.0020.0000.0000.0000.000
136B569LYS10.6891.01516.2890.1910.1910.0000.0000.0000.000
137B570ARG00.087-0.09114.971-0.012-0.0120.0000.0000.0000.000
138B570ARG10.6770.92212.3120.3180.3180.0000.0000.0000.000
139B571GLN00.116-0.05115.6240.0200.0200.0000.0000.0000.000
140B571GLN0-0.1070.05918.897-0.001-0.0010.0000.0000.0000.000
141B572ASP00.059-0.13319.289-0.023-0.0230.0000.0000.0000.000
142B572ASP-1-0.917-0.79623.133-0.148-0.1480.0000.0000.0000.000
143B573GLY0-0.003-0.11421.6240.0080.0080.0000.0000.0000.000
144B574ILE00.0580.00818.1570.0050.0050.0000.0000.0000.000
145B574ILE0-0.1080.09315.7230.0030.0030.0000.0000.0000.000
146B575VAL00.072-0.11314.3700.0060.0060.0000.0000.0000.000
147B575VAL0-0.0680.09512.5180.0030.0030.0000.0000.0000.000
148B576ASP00.129-0.07010.5740.0600.0600.0000.0000.0000.000
149B576ASP-1-0.880-0.7759.513-0.457-0.4570.0000.0000.0000.000
150B577VAL00.044-0.1119.678-0.105-0.1050.0000.0000.0000.000
151B577VAL0-0.1000.1079.3480.0160.0160.0000.0000.0000.000
152B578LEU00.068-0.1035.6700.0250.0250.0000.0000.0000.000
153B578LEU0-0.1000.0884.096-0.193-0.0710.000-0.018-0.1030.000
154B579LEU00.038-0.1255.644-0.096-0.0960.0000.0000.0000.000
155B579LEU0-0.0730.0826.4150.0320.0320.0000.0000.0000.000
156B580ILE00.101-0.0938.3890.0190.0190.0000.0000.0000.000
157B580ILE00.0030.14610.7900.0060.0060.0000.0000.0000.000
158B581ARG0-0.013-0.12811.9700.0040.0040.0000.0000.0000.000
159B581ARG10.8791.06210.1510.3080.3080.0000.0000.0000.000
160B582SER00.101-0.05114.869-0.009-0.0090.0000.0000.0000.000
161B582SER00.0000.06919.1480.0070.0070.0000.0000.0000.000
162B583ALA00.028-0.08718.582-0.003-0.0030.0000.0000.0000.000
163B583ALA0-0.0920.06719.787-0.001-0.0010.0000.0000.0000.000
164B584VAL00.056-0.13921.0280.0070.0070.0000.0000.0000.000
165B584VAL0-0.0440.14622.6490.0010.0010.0000.0000.0000.000
166B585GLY00.005-0.10524.2170.0020.0020.0000.0000.0000.000
167B586ILE00.0660.00224.3160.0090.0090.0000.0000.0000.000
168B586ILE0-0.0820.10821.922-0.002-0.0020.0000.0000.0000.000
169B587ASN00.158-0.04125.6800.0010.0010.0000.0000.0000.000
170B587ASN0-0.0830.07228.967-0.001-0.0010.0000.0000.0000.000
171B588LEU00.066-0.11526.542-0.002-0.0020.0000.0000.0000.000
172B588LEU0-0.0590.11924.7130.0010.0010.0000.0000.0000.000
173B589PRO0-0.013-0.12327.575-0.003-0.0030.0000.0000.0000.000
174B590ARG00.1280.02929.6320.0000.0000.0000.0000.0000.000
175B590ARG10.8461.03829.3480.0710.0710.0000.0000.0000.000
176B591TYR00.112-0.07824.9880.0020.0020.0000.0000.0000.000
177B591TYR0-0.0830.09619.903-0.003-0.0030.0000.0000.0000.000
178B592ARG00.107-0.07625.576-0.007-0.0070.0000.0000.0000.000
179B592ARG10.8921.06826.9660.0930.0930.0000.0000.0000.000
180B593GLN00.152-0.04627.016-0.002-0.0020.0000.0000.0000.000
181B593GLN0-0.0730.11230.1840.0010.0010.0000.0000.0000.000
182B594MET00.093-0.08026.4210.0040.0040.0000.0000.0000.000
183B594MET0-0.1020.07225.7540.0000.0000.0000.0000.0000.000
184B595VAL00.061-0.11323.9790.0020.0020.0000.0000.0000.000
185B595VAL0-0.0850.09422.141-0.002-0.0020.0000.0000.0000.000
186B596SER00.049-0.07424.700-0.005-0.0050.0000.0000.0000.000
187B596SER0-0.0700.02728.5760.0020.0020.0000.0000.0000.000
188B597GLU00.097-0.07027.9860.0000.0000.0000.0000.0000.000
189B597GLU-1-0.968-0.85729.419-0.079-0.0790.0000.0000.0000.000
190B598ARG00.056-0.07924.7530.0080.0080.0000.0000.0000.000
191B598ARG10.8531.03520.0620.1400.1400.0000.0000.0000.000
192B599GLN00.042-0.08725.169-0.005-0.0050.0000.0000.0000.000
193B599GLN0-0.1180.07122.6420.0080.0080.0000.0000.0000.000
194B600LYS0-0.003-0.12326.5350.0010.0010.0000.0000.0000.000
195B600LYS10.8511.04230.2100.0870.0870.0000.0000.0000.000
196B601CYS00.096-0.07928.8910.0060.0060.0000.0000.0000.000
197B601CYS0-0.1560.06629.0050.0020.0020.0000.0000.0000.000
198B602ASP0-0.129-0.15026.624-0.009-0.0090.0000.0000.0000.000
199B602ASP-1-0.823-0.90129.472-0.065-0.0650.0000.0000.0000.000