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: Z72KN

Calculation Name: 2OF5-H-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2OF5

Chain ID: H

ChEMBL ID:

UniProt ID: P78560

Base Structure: X-ray

Registration Date: 2025-07-11

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 189
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -736580.76978
FMO2-HF: Nuclear repulsion 697637.381593
FMO2-HF: Total energy -38943.388187
FMO2-MP2: Total energy -39057.612529


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(H:777:MET)


Summations of interaction energy for fragment #1(H:777:MET)
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.
-3.419-0.3441.73-1.464-3.340.007
Interaction energy analysis for fragmet #1(H:777:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.187 / q_NPA : 0.062
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].
4H778ASN0-0.1470.0464.291-0.726-0.3460.000-0.129-0.2510.000
5H779LEU00.062-0.1283.882-0.9680.493-0.013-0.795-0.653-0.001
6H779LEU0-0.0750.1213.115-0.6640.2250.629-0.628-0.8900.007
7H780GLY00.056-0.0786.127-0.165-0.1650.0000.0000.0000.000
8H781ASP00.0270.0339.823-0.161-0.1610.0000.0000.0000.000
9H781ASP-1-0.883-0.82413.1920.4230.4230.0000.0000.0000.000
10H782ALA00.156-0.06712.3360.0940.0940.0000.0000.0000.000
11H782ALA0-0.1140.06814.838-0.024-0.0240.0000.0000.0000.000
12H783GLU00.079-0.10514.6110.0060.0060.0000.0000.0000.000
13H783GLU-1-1.028-0.85617.7740.2440.2440.0000.0000.0000.000
14H784THR00.007-0.10214.649-0.029-0.0290.0000.0000.0000.000
15H784THR0-0.118-0.00213.7100.0190.0190.0000.0000.0000.000
16H785GLY00.061-0.02412.9300.0380.0380.0000.0000.0000.000
17H786PHE00.045-0.0288.5410.1300.1300.0000.0000.0000.000
18H786PHE0-0.1060.0777.455-0.120-0.1200.0000.0000.0000.000
19H787LEU00.060-0.1036.775-0.518-0.5180.0000.0000.0000.000
20H787LEU0-0.0680.0966.5860.2190.2190.0000.0000.0000.000
21H788THR00.060-0.0853.8041.9151.9930.003-0.041-0.0400.000
22H788THR0-0.0660.0415.192-0.204-0.2040.0000.0000.0000.000
23H789GLN00.134-0.0733.1911.3822.0850.106-0.326-0.482-0.002
24H789GLN0-0.0360.1062.5500.435-0.6540.9880.722-0.6200.003
25H790SER00.043-0.0623.932-0.294-0.2680.008-0.0400.0050.000
26H790SER0-0.0190.0698.209-0.092-0.0920.0000.0000.0000.000
27H791ASN00.086-0.0466.844-0.414-0.4140.0000.0000.0000.000
28H791ASN0-0.0220.1197.1390.1360.1360.0000.0000.0000.000
29H792LEU00.151-0.0695.404-0.903-0.9030.0000.0000.0000.000
30H792LEU0-0.0920.1173.8760.1220.3190.003-0.060-0.1400.000
31H793LEU00.101-0.1106.842-0.355-0.3550.0000.0000.0000.000
32H793LEU0-0.0990.0957.720-0.034-0.0340.0000.0000.0000.000
33H794SER0-0.014-0.1038.669-0.222-0.2220.0000.0000.0000.000
34H794SER0-0.0420.06210.885-0.091-0.0910.0000.0000.0000.000
35H795VAL00.126-0.06710.417-0.261-0.2610.0000.0000.0000.000
36H795VAL0-0.1050.0849.8450.0300.0300.0000.0000.0000.000
37H796ALA00.072-0.10910.329-0.139-0.1390.0000.0000.0000.000
38H796ALA0-0.0940.0939.959-0.005-0.0050.0000.0000.0000.000
39H797GLY0-0.003-0.10911.772-0.137-0.1370.0000.0000.0000.000
40H798ARG00.091-0.00414.254-0.119-0.1190.0000.0000.0000.000
41H798ARG10.6630.95814.871-0.604-0.6040.0000.0000.0000.000
42H799LEU0-0.009-0.10615.620-0.063-0.0630.0000.0000.0000.000
43H799LEU0-0.0690.08913.6600.0000.0000.0000.0000.0000.000
44H800GLY00.078-0.08617.043-0.041-0.0410.0000.0000.0000.000
45H801LEU00.028-0.02319.2200.0310.0310.0000.0000.0000.000
46H801LEU0-0.0640.09722.281-0.006-0.0060.0000.0000.0000.000
47H802ASP00.036-0.12520.930-0.031-0.0310.0000.0000.0000.000
48H802ASP-1-0.794-0.74219.8540.4720.4720.0000.0000.0000.000
49H803TRP00.043-0.09116.7060.0200.0200.0000.0000.0000.000
50H803TRP0-0.0510.11415.010-0.015-0.0150.0000.0000.0000.000
51H804PRO0-0.014-0.14017.1230.0380.0380.0000.0000.0000.000
52H805ALA00.0860.00219.4300.0020.0020.0000.0000.0000.000
53H805ALA0-0.0370.12521.014-0.006-0.0060.0000.0000.0000.000
54H806VAL00.092-0.09116.253-0.036-0.0360.0000.0000.0000.000
55H806VAL0-0.0660.11114.5740.0090.0090.0000.0000.0000.000
56H807ALA00.194-0.07115.0240.0700.0700.0000.0000.0000.000
57H807ALA0-0.1240.06715.691-0.015-0.0150.0000.0000.0000.000
58H808LEU00.059-0.09516.0510.0220.0220.0000.0000.0000.000
59H808LEU0-0.1320.06620.402-0.019-0.0190.0000.0000.0000.000
60H809HIS0-0.032-0.11518.917-0.032-0.0320.0000.0000.0000.000
61H809HIS10.8161.04418.675-0.454-0.4540.0000.0000.0000.000
62H810LEU00.093-0.09414.100-0.033-0.0330.0000.0000.0000.000
63H810LEU0-0.0670.12011.8000.0070.0070.0000.0000.0000.000
64H811GLY00.000-0.09314.5850.0350.0350.0000.0000.0000.000
65H812VAL00.003-0.04416.005-0.063-0.0630.0000.0000.0000.000
66H812VAL0-0.0830.11714.039-0.003-0.0030.0000.0000.0000.000
67H813SER00.103-0.04216.687-0.006-0.0060.0000.0000.0000.000
68H813SER0-0.0410.05720.543-0.007-0.0070.0000.0000.0000.000
69H814TYR00.161-0.07919.9410.0120.0120.0000.0000.0000.000
70H814TYR0-0.0490.11023.102-0.001-0.0010.0000.0000.0000.000
71H815ARG00.090-0.06622.452-0.002-0.0020.0000.0000.0000.000
72H815ARG10.7971.01021.156-0.075-0.0750.0000.0000.0000.000
73H816GLU00.059-0.11717.973-0.035-0.0350.0000.0000.0000.000
74H816GLU-1-0.856-0.77617.0360.1190.1190.0000.0000.0000.000
75H817VAL00.134-0.08318.216-0.001-0.0010.0000.0000.0000.000
76H817VAL0-0.0890.09717.9080.0020.0020.0000.0000.0000.000
77H818GLN00.066-0.09619.2020.0000.0000.0000.0000.0000.000
78H818GLN0-0.1460.06623.376-0.014-0.0140.0000.0000.0000.000
79H819ARG00.069-0.09520.254-0.011-0.0110.0000.0000.0000.000
80H819ARG10.6780.93215.312-0.066-0.0660.0000.0000.0000.000
81H820ILE00.107-0.08016.668-0.050-0.0500.0000.0000.0000.000
82H820ILE0-0.1000.10114.1920.0060.0060.0000.0000.0000.000
83H821ARG00.135-0.07217.894-0.013-0.0130.0000.0000.0000.000
84H821ARG10.8331.04820.763-0.225-0.2250.0000.0000.0000.000
85H822HIS00.090-0.07620.557-0.006-0.0060.0000.0000.0000.000
86H822HIS0-0.1250.06922.8440.0060.0060.0000.0000.0000.000
87H823GLU00.088-0.09219.364-0.013-0.0130.0000.0000.0000.000
88H823GLU-1-0.925-0.79816.840-0.020-0.0200.0000.0000.0000.000
89H824PHE00.020-0.09218.081-0.037-0.0370.0000.0000.0000.000
90H824PHE0-0.0580.08615.5000.0020.0020.0000.0000.0000.000
91H825ARG00.144-0.04619.5610.0270.0270.0000.0000.0000.000
92H825ARG10.7080.96222.974-0.030-0.0300.0000.0000.0000.000
93H826ASP0-0.017-0.13022.5600.0200.0200.0000.0000.0000.000
94H826ASP-1-0.911-0.83222.9900.0260.0260.0000.0000.0000.000
95H827ASP00.087-0.12419.378-0.002-0.0020.0000.0000.0000.000
96H827ASP-1-0.939-0.81317.9620.1230.1230.0000.0000.0000.000
97H828LEU00.146-0.08818.3320.0060.0060.0000.0000.0000.000
98H828LEU0-0.1200.08818.807-0.004-0.0040.0000.0000.0000.000
99H829ASP00.087-0.08215.9070.0640.0640.0000.0000.0000.000
100H829ASP-1-0.909-0.79914.7380.3160.3160.0000.0000.0000.000
101H830GLU00.113-0.11513.6300.0990.0990.0000.0000.0000.000
102H830GLU-1-0.918-0.78612.2540.0070.0070.0000.0000.0000.000
103H831GLN00.058-0.11013.5830.0170.0170.0000.0000.0000.000
104H831GLN0-0.1220.05017.1510.0240.0240.0000.0000.0000.000
105H832ILE00.028-0.11113.7520.0190.0190.0000.0000.0000.000
106H832ILE0-0.0860.11712.5220.0140.0140.0000.0000.0000.000
107H833ARG00.094-0.0929.8200.2190.2190.0000.0000.0000.000
108H833ARG10.7070.9539.683-0.219-0.2190.0000.0000.0000.000
109H834HIS00.149-0.0748.9910.1740.1740.0000.0000.0000.000
110H834HIS0-0.0450.12012.3860.0070.0070.0000.0000.0000.000
111H835MET00.083-0.08510.246-0.012-0.0120.0000.0000.0000.000
112H835MET0-0.1570.09712.217-0.003-0.0030.0000.0000.0000.000
113H836LEU00.101-0.1039.081-0.035-0.0350.0000.0000.0000.000
114H836LEU0-0.0810.1137.883-0.021-0.0210.0000.0000.0000.000
115H837PHE00.049-0.1065.2830.8670.8670.0000.0000.0000.000
116H837PHE0-0.0980.0924.0570.0760.2620.000-0.061-0.1260.000
117H838SER00.096-0.0846.054-0.029-0.0290.0000.0000.0000.000
118H838SER0-0.0360.07210.211-0.104-0.1040.0000.0000.0000.000
119H839TRP0-0.010-0.1118.760-0.268-0.2680.0000.0000.0000.000
120H839TRP0-0.0930.0888.0020.0330.0330.0000.0000.0000.000
121H840ALA00.103-0.0954.495-0.915-0.884-0.001-0.009-0.0210.000
122H840ALA0-0.0580.1063.6290.3450.5580.007-0.097-0.1220.000
123H841GLU00.089-0.0935.2410.1290.1290.0000.0000.0000.000
124H841GLU-1-1.025-0.8705.311-2.384-2.3840.0000.0000.0000.000
125H842ARG00.003-0.0965.941-0.215-0.2150.0000.0000.0000.000
126H842ARG10.7810.99110.020-0.494-0.4940.0000.0000.0000.000
127H843GLN00.003-0.1257.288-0.327-0.3270.0000.0000.0000.000
128H843GLN0-0.1540.0647.700-0.142-0.1420.0000.0000.0000.000
129H844ALA00.180-0.0695.6060.5960.5960.0000.0000.0000.000
130H844ALA0-0.0680.1136.152-0.146-0.1460.0000.0000.0000.000
131H845GLY0-0.038-0.1256.593-0.458-0.4580.0000.0000.0000.000
132H846GLN00.0340.0439.7980.2190.2190.0000.0000.0000.000
133H846GLN0-0.0830.06610.742-0.077-0.0770.0000.0000.0000.000
134H847PRO00.036-0.08912.696-0.008-0.0080.0000.0000.0000.000
135H848GLY00.0530.02613.1380.1040.1040.0000.0000.0000.000
136H849ALA00.093-0.01610.119-0.088-0.0880.0000.0000.0000.000
137H849ALA0-0.0470.1289.3760.0520.0520.0000.0000.0000.000
138H850VAL00.067-0.13210.3920.1510.1510.0000.0000.0000.000
139H850VAL0-0.0370.1478.8890.0250.0250.0000.0000.0000.000
140H851GLY00.033-0.09411.104-0.074-0.0740.0000.0000.0000.000
141H852LEU00.058-0.01414.137-0.096-0.0960.0000.0000.0000.000
142H852LEU0-0.0730.10313.405-0.010-0.0100.0000.0000.0000.000
143H853LEU00.121-0.07211.428-0.195-0.1950.0000.0000.0000.000
144H853LEU0-0.0950.0948.7870.0890.0890.0000.0000.0000.000
145H854VAL00.048-0.12212.867-0.056-0.0560.0000.0000.0000.000
146H854VAL0-0.0910.10513.983-0.005-0.0050.0000.0000.0000.000
147H855GLN00.163-0.05215.549-0.071-0.0710.0000.0000.0000.000
148H855GLN0-0.0810.08818.045-0.012-0.0120.0000.0000.0000.000
149H856ALA00.093-0.11016.326-0.115-0.1150.0000.0000.0000.000
150H856ALA0-0.0600.11715.3920.0120.0120.0000.0000.0000.000
151H857LEU00.081-0.08916.654-0.085-0.0850.0000.0000.0000.000
152H857LEU0-0.1090.10013.7540.0050.0050.0000.0000.0000.000
153H858GLU00.097-0.08317.748-0.054-0.0540.0000.0000.0000.000
154H858GLU-1-0.862-0.76419.8000.5320.5320.0000.0000.0000.000
155H859GLN00.023-0.09320.658-0.055-0.0550.0000.0000.0000.000
156H859GLN0-0.1540.04920.730-0.032-0.0320.0000.0000.0000.000
157H860SER0-0.077-0.12720.256-0.054-0.0540.0000.0000.0000.000
158H860SER0-0.0510.02919.251-0.001-0.0010.0000.0000.0000.000
159H861ASP00.124-0.07021.6060.0130.0130.0000.0000.0000.000
160H861ASP-1-1.028-0.86024.9180.3170.3170.0000.0000.0000.000
161H862ARG00.051-0.11219.805-0.042-0.0420.0000.0000.0000.000
162H862ARG10.6430.94319.093-0.496-0.4960.0000.0000.0000.000
163H863GLN00.159-0.09019.6870.0870.0870.0000.0000.0000.000
164H863GLN0-0.1250.06123.299-0.004-0.0040.0000.0000.0000.000
165H864ASP00.118-0.06920.8790.0320.0320.0000.0000.0000.000
166H864ASP-1-0.915-0.81320.7100.4950.4950.0000.0000.0000.000
167H865VAL00.034-0.10216.870-0.020-0.0200.0000.0000.0000.000
168H865VAL0-0.0630.09114.8390.0130.0130.0000.0000.0000.000
169H866ALA00.122-0.09216.3150.1350.1350.0000.0000.0000.000
170H866ALA0-0.0500.10318.621-0.015-0.0150.0000.0000.0000.000
171H867GLU00.042-0.14217.3710.0790.0790.0000.0000.0000.000
172H867GLU-1-0.950-0.79921.0460.4170.4170.0000.0000.0000.000
173H868GLU00.123-0.09316.914-0.037-0.0370.0000.0000.0000.000
174H868GLU-1-0.949-0.80815.0580.7830.7830.0000.0000.0000.000
175H869VAL00.039-0.11613.3290.0040.0040.0000.0000.0000.000
176H869VAL0-0.1120.07911.7840.0510.0510.0000.0000.0000.000
177H870ARG00.095-0.07313.8540.1150.1150.0000.0000.0000.000
178H870ARG10.7120.94217.651-0.596-0.5960.0000.0000.0000.000
179H871ALA00.163-0.03916.493-0.003-0.0030.0000.0000.0000.000
180H871ALA0-0.0970.08617.693-0.013-0.0130.0000.0000.0000.000
181H872VAL0-0.016-0.10213.346-0.104-0.1040.0000.0000.0000.000
182H872VAL0-0.1310.05611.5070.0270.0270.0000.0000.0000.000
183H873LEU00.125-0.09512.6770.0530.0530.0000.0000.0000.000
184H873LEU0-0.1530.08211.4060.0490.0490.0000.0000.0000.000
185H874GLU00.075-0.09913.608-0.014-0.0140.0000.0000.0000.000
186H874GLU-1-1.057-0.87217.6380.4250.4250.0000.0000.0000.000
187H875LEU00.064-0.13915.272-0.070-0.0700.0000.0000.0000.000
188H875LEU0-0.1640.06914.235-0.014-0.0140.0000.0000.0000.000
189H876GLY0-0.049-0.11114.9380.0150.0150.0000.0000.0000.000