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: 9MKM2

Calculation Name: 3KF8-B-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 3KF8

Chain ID: B

ChEMBL ID:

UniProt ID: C5M4J8

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 228
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -964707.132542
FMO2-HF: Nuclear repulsion 917779.971246
FMO2-HF: Total energy -46927.161296
FMO2-MP2: Total energy -47063.119554


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:2:SER)


Summations of interaction energy for fragment #1(B:2:SER)
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.
1.3565.7660.005-2.272-2.1410.003
Interaction energy analysis for fragmet #1(B:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.090 / q_NPA : 0.053
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].
4B3LYS10.8411.0543.559-2.722-2.0370.015-0.311-0.3880.001
5B4ILE00.079-0.0693.810-1.3281.017-0.026-1.394-0.9240.004
6B4ILE0-0.1210.0716.388-0.036-0.0360.0000.0000.0000.000
7B5ILE00.015-0.1186.940-0.097-0.0970.0000.0000.0000.000
8B5ILE0-0.0790.1236.6620.0200.0200.0000.0000.0000.000
9B6LEU00.119-0.1139.476-0.109-0.1090.0000.0000.0000.000
10B6LEU0-0.0520.11611.851-0.021-0.0210.0000.0000.0000.000
11B7ILE00.078-0.12812.813-0.080-0.0800.0000.0000.0000.000
12B7ILE0-0.0990.14114.639-0.012-0.0120.0000.0000.0000.000
13B8PRO00.054-0.10413.3030.1300.1300.0000.0000.0000.000
14B9SER00.0960.01114.2120.1280.1280.0000.0000.0000.000
15B9SER0-0.0350.08817.899-0.036-0.0360.0000.0000.0000.000
16B10ASN00.031-0.05414.115-0.031-0.0310.0000.0000.0000.000
17B10ASN0-0.1090.05213.576-0.040-0.0400.0000.0000.0000.000
18B11ILE00.077-0.08010.7240.1050.1050.0000.0000.0000.000
19B11ILE0-0.0850.08310.0940.0140.0140.0000.0000.0000.000
20B12PRO00.016-0.10910.9230.2110.2110.0000.0000.0000.000
21B13GLN00.0300.00213.0260.0370.0370.0000.0000.0000.000
22B13GLN0-0.0420.07914.2250.0190.0190.0000.0000.0000.000
23B14GLU00.070-0.0679.322-0.215-0.2150.0000.0000.0000.000
24B14GLU-1-0.971-0.8468.2411.6161.6160.0000.0000.0000.000
25B15PHE0-0.012-0.1048.3870.2620.2620.0000.0000.0000.000
26B15PHE0-0.0820.0864.096-0.383-0.0830.004-0.104-0.2000.001
27B16PRO00.052-0.1099.331-0.133-0.1330.0000.0000.0000.000
28B17GLU00.0640.01711.091-0.132-0.1320.0000.0000.0000.000
29B17GLU-1-1.037-0.88710.9160.7340.7340.0000.0000.0000.000
30B18ALA00.128-0.07810.085-0.116-0.1160.0000.0000.0000.000
31B18ALA0-0.0680.0979.2980.0550.0550.0000.0000.0000.000
32B19SER00.043-0.10210.758-0.127-0.1270.0000.0000.0000.000
33B19SER0-0.0520.05012.824-0.064-0.0640.0000.0000.0000.000
34B20ILE00.100-0.07612.4900.0770.0770.0000.0000.0000.000
35B20ILE0-0.0750.10016.401-0.011-0.0110.0000.0000.0000.000
36B21SER0-0.008-0.10114.572-0.024-0.0240.0000.0000.0000.000
37B21SER0-0.0550.05015.256-0.009-0.0090.0000.0000.0000.000
38B22ASN0-0.077-0.08610.952-0.115-0.1150.0000.0000.0000.000
39B22ASN0-0.1000.04910.142-0.074-0.0740.0000.0000.0000.000
40B23PRO00.061-0.0729.5920.1530.1530.0000.0000.0000.000
41B24GLU00.094-0.0175.575-0.370-0.3700.0000.0000.0000.000
42B24GLU-1-0.982-0.8203.5393.2153.8340.011-0.325-0.306-0.002
43B25ARG00.086-0.1164.734-0.175-0.157-0.002-0.008-0.0080.000
44B25ARG10.6540.9574.400-1.073-1.000-0.001-0.009-0.0630.000
45B26LEU00.053-0.1223.8362.0142.3840.004-0.121-0.252-0.001
46B26LEU0-0.0270.1344.879-0.179-0.1790.0000.0000.0000.000
47B27ARG00.167-0.0395.593-0.594-0.5940.0000.0000.0000.000
48B27ARG10.7721.0226.433-0.047-0.0470.0000.0000.0000.000
49B28ILE00.009-0.0997.5000.1010.1010.0000.0000.0000.000
50B28ILE0-0.0610.0839.918-0.004-0.0040.0000.0000.0000.000
51B29LEU00.089-0.05910.640-0.090-0.0900.0000.0000.0000.000
52B29LEU0-0.0940.08611.349-0.030-0.0300.0000.0000.0000.000
53B30ALA00.107-0.09213.4030.0180.0180.0000.0000.0000.000
54B30ALA0-0.0790.09015.3480.0130.0130.0000.0000.0000.000
55B31GLN00.088-0.10516.502-0.039-0.0390.0000.0000.0000.000
56B31GLN0-0.0720.08721.0230.0030.0030.0000.0000.0000.000
57B32VAL00.095-0.11620.2240.0360.0360.0000.0000.0000.000
58B32VAL0-0.0880.13520.5120.0000.0000.0000.0000.0000.000
59B33LYS00.011-0.12822.009-0.028-0.0280.0000.0000.0000.000
60B33LYS10.8001.05222.661-0.197-0.1970.0000.0000.0000.000
61B34ASP00.059-0.12324.366-0.020-0.0200.0000.0000.0000.000
62B34ASP-1-0.949-0.83626.4880.1640.1640.0000.0000.0000.000
63B35PHE00.066-0.07924.5970.0260.0260.0000.0000.0000.000
64B35PHE0-0.0650.09024.920-0.006-0.0060.0000.0000.0000.000
65B36ILE00.092-0.11126.339-0.019-0.0190.0000.0000.0000.000
66B36ILE0-0.1040.11826.5160.0000.0000.0000.0000.0000.000
67B37PRO00.023-0.10427.8170.0070.0070.0000.0000.0000.000
68B38HIS00.0520.02129.8780.0020.0020.0000.0000.0000.000
69B38HIS0-0.1150.06531.862-0.008-0.0080.0000.0000.0000.000
70B39GLU00.061-0.13128.151-0.008-0.0080.0000.0000.0000.000
71B39GLU-1-0.948-0.83627.2270.1970.1970.0000.0000.0000.000
72B40SER00.016-0.06225.8570.0190.0190.0000.0000.0000.000
73B40SER0-0.0040.08525.108-0.005-0.0050.0000.0000.0000.000
74B41THR00.023-0.08822.9080.0170.0170.0000.0000.0000.000
75B41THR0-0.0600.07022.3920.0090.0090.0000.0000.0000.000
76B42ILE00.079-0.09421.567-0.027-0.0270.0000.0000.0000.000
77B42ILE0-0.0730.10118.324-0.001-0.0010.0000.0000.0000.000
78B43VAL00.113-0.11121.0450.0440.0440.0000.0000.0000.000
79B43VAL0-0.1290.11223.173-0.003-0.0030.0000.0000.0000.000
80B44ILE00.023-0.09518.477-0.043-0.0430.0000.0000.0000.000
81B44ILE0-0.0620.08615.4330.0070.0070.0000.0000.0000.000
82B45ASP00.112-0.11818.9350.0340.0340.0000.0000.0000.000
83B45ASP-1-0.862-0.80720.4920.2810.2810.0000.0000.0000.000
84B46LYS00.117-0.04417.0090.0020.0020.0000.0000.0000.000
85B46LYS10.7900.99617.595-0.225-0.2250.0000.0000.0000.000
86B47VAL00.082-0.12617.582-0.018-0.0180.0000.0000.0000.000
87B47VAL0-0.0870.12917.161-0.004-0.0040.0000.0000.0000.000
88B48PRO0-0.039-0.14519.518-0.007-0.0070.0000.0000.0000.000
89B49THR0-0.040-0.03222.2770.0170.0170.0000.0000.0000.000
90B49THR0-0.0440.07223.4720.0020.0020.0000.0000.0000.000
91B50ILE00.103-0.02318.993-0.026-0.0260.0000.0000.0000.000
92B50ILE0-0.0900.08916.5290.0000.0000.0000.0000.0000.000
93B51THR00.077-0.05119.622-0.023-0.0230.0000.0000.0000.000
94B51THR0-0.0090.07618.080-0.004-0.0040.0000.0000.0000.000
95B52SER00.023-0.06220.9420.0080.0080.0000.0000.0000.000
96B52SER0-0.0190.06424.1660.0000.0000.0000.0000.0000.000
97B53GLU00.040-0.14219.922-0.013-0.0130.0000.0000.0000.000
98B53GLU-1-0.936-0.79817.4840.3830.3830.0000.0000.0000.000
99B54GLN00.114-0.08121.377-0.003-0.0030.0000.0000.0000.000
100B54GLN0-0.1010.08322.2800.0120.0120.0000.0000.0000.000
101B55SER00.033-0.09719.8870.0330.0330.0000.0000.0000.000
102B55SER0-0.0470.05319.3330.0180.0180.0000.0000.0000.000
103B56THR0-0.018-0.09619.897-0.046-0.0460.0000.0000.0000.000
104B56THR0-0.0300.07321.073-0.009-0.0090.0000.0000.0000.000
105B57TYR00.073-0.07119.8760.0450.0450.0000.0000.0000.000
106B57TYR0-0.0750.07822.533-0.013-0.0130.0000.0000.0000.000
107B58ILE00.072-0.07518.234-0.016-0.0160.0000.0000.0000.000
108B58ILE0-0.0600.11015.0910.0100.0100.0000.0000.0000.000
109B59ASN00.041-0.09119.680-0.015-0.0150.0000.0000.0000.000
110B59ASN0-0.0840.06122.175-0.008-0.0080.0000.0000.0000.000
111B60ILE00.138-0.06817.6150.0200.0200.0000.0000.0000.000
112B60ILE0-0.0410.10114.7220.0090.0090.0000.0000.0000.000
113B61CYS00.128-0.11418.897-0.036-0.0360.0000.0000.0000.000
114B61CYS0-0.1470.13221.166-0.008-0.0080.0000.0000.0000.000
115B62ILE00.102-0.11019.6980.0330.0330.0000.0000.0000.000
116B62ILE0-0.1210.09018.1500.0000.0000.0000.0000.0000.000
117B63PHE00.209-0.05320.590-0.025-0.0250.0000.0000.0000.000
118B63PHE0-0.0870.07623.663-0.001-0.0010.0000.0000.0000.000
119B64ASN0-0.046-0.09221.546-0.023-0.0230.0000.0000.0000.000
120B64ASN0-0.1070.05120.533-0.018-0.0180.0000.0000.0000.000
121B65LEU00.124-0.09719.911-0.012-0.0120.0000.0000.0000.000
122B65LEU0-0.0680.08216.5140.0010.0010.0000.0000.0000.000
123B66LEU00.057-0.09121.204-0.016-0.0160.0000.0000.0000.000
124B66LEU0-0.0680.09624.472-0.002-0.0020.0000.0000.0000.000
125B67GLU00.135-0.09424.526-0.007-0.0070.0000.0000.0000.000
126B67GLU-1-1.051-0.86925.6810.0780.0780.0000.0000.0000.000
127B68ALA00.086-0.10322.419-0.014-0.0140.0000.0000.0000.000
128B68ALA0-0.0830.09721.6970.0010.0010.0000.0000.0000.000
129B69CYS00.062-0.14921.736-0.016-0.0160.0000.0000.0000.000
130B69CYS0-0.1470.10420.9390.0120.0120.0000.0000.0000.000
131B70SER00.052-0.01322.566-0.009-0.0090.0000.0000.0000.000
132B70SER0-0.0560.04323.3420.0000.0000.0000.0000.0000.000
133B71SER00.074-0.08124.1770.0170.0170.0000.0000.0000.000
134B71SER0-0.0070.08228.441-0.006-0.0060.0000.0000.0000.000
135B72ARG00.072-0.08125.8730.0120.0120.0000.0000.0000.000
136B72ARG10.7241.00024.665-0.069-0.0690.0000.0000.0000.000
137B73VAL00.056-0.12521.562-0.003-0.0030.0000.0000.0000.000
138B73VAL0-0.0680.12719.5470.0000.0000.0000.0000.0000.000
139B74LEU00.083-0.12222.1750.0260.0260.0000.0000.0000.000
140B74LEU0-0.0750.11522.914-0.001-0.0010.0000.0000.0000.000
141B75VAL00.066-0.11024.8000.0060.0060.0000.0000.0000.000
142B75VAL0-0.1520.07926.898-0.003-0.0030.0000.0000.0000.000
143B76PRO00.020-0.07525.5180.0030.0030.0000.0000.0000.000
144B77GLY0-0.034-0.02825.051-0.016-0.0160.0000.0000.0000.000
145B78THR0-0.063-0.00723.577-0.011-0.0110.0000.0000.0000.000
146B78THR0-0.0340.05821.678-0.005-0.0050.0000.0000.0000.000
147B79LEU00.099-0.07320.1550.0300.0300.0000.0000.0000.000
148B79LEU0-0.0880.10219.507-0.003-0.0030.0000.0000.0000.000
149B80VAL00.015-0.13517.544-0.040-0.0400.0000.0000.0000.000
150B80VAL0-0.0190.11116.4880.0030.0030.0000.0000.0000.000
151B81ASN00.175-0.05913.5120.0390.0390.0000.0000.0000.000
152B81ASN0-0.1760.04211.598-0.026-0.0260.0000.0000.0000.000
153B82ILE00.041-0.11212.329-0.070-0.0700.0000.0000.0000.000
154B82ILE0-0.0810.08512.5660.0000.0000.0000.0000.0000.000
155B83ASP00.162-0.0359.2730.1840.1840.0000.0000.0000.000
156B83ASP-1-0.888-0.7988.9410.1820.1820.0000.0000.0000.000
157B84ALA00.102-0.1178.779-0.176-0.1760.0000.0000.0000.000
158B84ALA0-0.0440.10010.490-0.010-0.0100.0000.0000.0000.000
159B85PHE00.016-0.0768.2500.3610.3610.0000.0000.0000.000
160B85PHE0-0.0540.0818.997-0.055-0.0550.0000.0000.0000.000
161B86TYR00.120-0.0758.955-0.340-0.3400.0000.0000.0000.000
162B86TYR0-0.1020.1059.0780.0770.0770.0000.0000.0000.000
163B87ASP00.039-0.12210.0240.2400.2400.0000.0000.0000.000
164B87ASP-1-0.807-0.76413.6540.6590.6590.0000.0000.0000.000
165B88GLY00.061-0.07412.438-0.081-0.0810.0000.0000.0000.000
166B89GLU00.008-0.03413.688-0.031-0.0310.0000.0000.0000.000
167B89GLU-1-1.039-0.86117.7750.4170.4170.0000.0000.0000.000
168B90SER0-0.060-0.12816.005-0.017-0.0170.0000.0000.0000.000
169B90SER0-0.0620.06416.635-0.033-0.0330.0000.0000.0000.000
170B91ILE00.118-0.09613.4980.1190.1190.0000.0000.0000.000
171B91ILE0-0.0760.10412.1770.0050.0050.0000.0000.0000.000
172B92ASN00.049-0.10013.225-0.105-0.1050.0000.0000.0000.000
173B92ASN0-0.1630.04713.589-0.091-0.0910.0000.0000.0000.000
174B93PRO00.009-0.10212.8820.0740.0740.0000.0000.0000.000
175B94VAL00.028-0.01712.998-0.045-0.0450.0000.0000.0000.000
176B94VAL0-0.0920.09111.393-0.009-0.0090.0000.0000.0000.000
177B95ASP00.102-0.12613.892-0.057-0.0570.0000.0000.0000.000
178B95ASP-1-0.923-0.83513.4770.0770.0770.0000.0000.0000.000
179B96ILE00.024-0.09914.1400.0690.0690.0000.0000.0000.000
180B96ILE0-0.0940.08616.0190.0020.0020.0000.0000.0000.000
181B97TYR00.044-0.11616.290-0.021-0.0210.0000.0000.0000.000
182B97TYR0-0.0790.11913.474-0.022-0.0220.0000.0000.0000.000
183B98GLU00.172-0.07117.5710.0210.0210.0000.0000.0000.000
184B98GLU-1-0.896-0.79721.6570.0520.0520.0000.0000.0000.000
185B99VAL0-0.023-0.13717.757-0.027-0.0270.0000.0000.0000.000
186B99VAL0-0.0590.13715.724-0.008-0.0080.0000.0000.0000.000
187B100ASN00.120-0.07819.1620.0190.0190.0000.0000.0000.000
188B100ASN0-0.1130.07421.8910.0000.0000.0000.0000.0000.000
189B101GLY00.075-0.09120.618-0.004-0.0040.0000.0000.0000.000
190B102ALA00.1030.00222.4710.0080.0080.0000.0000.0000.000
191B102ALA0-0.0790.10623.997-0.002-0.0020.0000.0000.0000.000
192B103ASN00.038-0.10618.835-0.013-0.0130.0000.0000.0000.000
193B103ASN0-0.1180.05717.881-0.026-0.0260.0000.0000.0000.000
194B104PHE00.049-0.04018.757-0.036-0.0360.0000.0000.0000.000
195B104PHE0-0.0980.07415.5210.0060.0060.0000.0000.0000.000
196B105THR00.019-0.10119.7990.0270.0270.0000.0000.0000.000
197B105THR0-0.0230.04721.489-0.006-0.0060.0000.0000.0000.000
198B106MET00.196-0.06019.885-0.002-0.0020.0000.0000.0000.000
199B106MET0-0.0960.09922.0040.0040.0040.0000.0000.0000.000
200B107GLU00.033-0.12919.7420.0020.0020.0000.0000.0000.000
201B107GLU-1-0.890-0.80421.086-0.095-0.0950.0000.0000.0000.000
202B108ASN00.149-0.06217.089-0.038-0.0380.0000.0000.0000.000
203B108ASN0-0.1660.04516.667-0.030-0.0300.0000.0000.0000.000
204B109ILE00.075-0.09515.271-0.057-0.0570.0000.0000.0000.000
205B109ILE0-0.0940.10115.9850.0110.0110.0000.0000.0000.000
206B110GLN00.102-0.08414.9330.0100.0100.0000.0000.0000.000
207B110GLN0-0.0950.07918.145-0.010-0.0100.0000.0000.0000.000
208B111LEU00.139-0.05414.881-0.014-0.0140.0000.0000.0000.000
209B111LEU0-0.1080.07413.264-0.007-0.0070.0000.0000.0000.000
210B112ILE00.059-0.10311.141-0.173-0.1730.0000.0000.0000.000
211B112ILE0-0.1060.0759.8570.0160.0160.0000.0000.0000.000
212B113ASP00.074-0.09110.271-0.103-0.1030.0000.0000.0000.000
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