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: 9M3J2

Calculation Name: 1IIB-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1IIB

Chain ID: A

ChEMBL ID:

UniProt ID: P69795

Base Structure: X-ray

Registration Date: 2025-07-10

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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 193
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -736070.16336
FMO2-HF: Nuclear repulsion 697780.727919
FMO2-HF: Total energy -38289.435442
FMO2-MP2: Total energy -38401.458364


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:3:LYS)


Summations of interaction energy for fragment #1(A:3:LYS)
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.
-3.461-3.1439.227-5.238-4.307-0.022
Interaction energy analysis for fragmet #1(A:3:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.120 / q_NPA : 0.021
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].
4A4LYS10.7831.0133.769-3.170-2.5610.011-0.255-0.3650.001
5A5HIS00.090-0.1153.781-2.297-1.082-0.012-0.690-0.5140.004
6A5HIS0-0.0560.1325.2830.2630.312-0.001-0.011-0.0360.000
7A6ILE00.110-0.0726.6330.6210.6210.0000.0000.0000.000
8A6ILE0-0.0990.0797.5380.0740.0740.0000.0000.0000.000
9A7TYR00.041-0.1079.567-0.178-0.1780.0000.0000.0000.000
10A7TYR0-0.0800.0829.0650.1650.1650.0000.0000.0000.000
11A8LEU00.077-0.09212.6010.1200.1200.0000.0000.0000.000
12A8LEU0-0.0720.08013.5240.0170.0170.0000.0000.0000.000
13A9PHE00.094-0.08915.919-0.052-0.0520.0000.0000.0000.000
14A9PHE0-0.1050.12515.410-0.005-0.0050.0000.0000.0000.000
15A10SER00.122-0.08819.1480.0420.0420.0000.0000.0000.000
16A10SER0-0.0820.05521.5910.0040.0040.0000.0000.0000.000
17A11SER00.063-0.04222.412-0.027-0.0270.0000.0000.0000.000
18A11SER00.0060.09126.9490.0030.0030.0000.0000.0000.000
19A12ALA00.068-0.11224.8880.0010.0010.0000.0000.0000.000
20A12ALA0-0.1150.12025.1510.0040.0040.0000.0000.0000.000
21A13GLY00.055-0.08122.763-0.017-0.0170.0000.0000.0000.000
22A14MET00.1130.00122.240-0.040-0.0400.0000.0000.0000.000
23A14MET0-0.0650.12325.753-0.004-0.0040.0000.0000.0000.000
24A15SER00.080-0.06822.891-0.024-0.0240.0000.0000.0000.000
25A15SER0-0.0160.07424.3750.0080.0080.0000.0000.0000.000
26A16THR00.030-0.08820.3740.0010.0010.0000.0000.0000.000
27A16THR0-0.0240.09318.3500.0080.0080.0000.0000.0000.000
28A17SER00.053-0.08718.237-0.042-0.0420.0000.0000.0000.000
29A17SER0-0.0310.07919.565-0.012-0.0120.0000.0000.0000.000
30A18LEU00.100-0.08618.417-0.054-0.0540.0000.0000.0000.000
31A18LEU0-0.1020.10621.6840.0070.0070.0000.0000.0000.000
32A19LEU00.088-0.10118.873-0.006-0.0060.0000.0000.0000.000
33A19LEU0-0.0790.11017.4520.0040.0040.0000.0000.0000.000
34A20VAL00.110-0.09914.8260.0250.0250.0000.0000.0000.000
35A20VAL0-0.0640.12213.008-0.004-0.0040.0000.0000.0000.000
36A21SER0-0.016-0.11314.267-0.090-0.0900.0000.0000.0000.000
37A21SER0-0.0660.05517.6010.0240.0240.0000.0000.0000.000
38A22LYS00.070-0.08715.810-0.026-0.0260.0000.0000.0000.000
39A22LYS10.8961.06018.2990.2480.2480.0000.0000.0000.000
40A23MET00.074-0.10113.6990.0660.0660.0000.0000.0000.000
41A23MET0-0.1210.09012.283-0.012-0.0120.0000.0000.0000.000
42A24ARG00.075-0.08011.0530.0290.0290.0000.0000.0000.000
43A24ARG10.7431.00510.4491.1321.1320.0000.0000.0000.000
44A25ALA00.161-0.04912.007-0.043-0.0430.0000.0000.0000.000
45A25ALA0-0.1210.08416.2690.0140.0140.0000.0000.0000.000
46A26GLN00.046-0.09114.2550.0260.0260.0000.0000.0000.000
47A26GLN0-0.1120.05814.1150.0480.0480.0000.0000.0000.000
48A27ALA00.130-0.0809.5400.1900.1900.0000.0000.0000.000
49A27ALA0-0.0870.0798.502-0.053-0.0530.0000.0000.0000.000
50A28GLU00.085-0.0939.9600.1030.1030.0000.0000.0000.000
51A28GLU-1-1.036-0.8589.930-0.838-0.8380.0000.0000.0000.000
52A29LYS00.145-0.05111.7410.0790.0790.0000.0000.0000.000
53A29LYS10.7821.01815.1940.0390.0390.0000.0000.0000.000
54A30TYR0-0.067-0.09412.8070.0250.0250.0000.0000.0000.000
55A30TYR0-0.1620.01012.369-0.001-0.0010.0000.0000.0000.000
56A31GLU00.148-0.0779.6980.0980.0980.0000.0000.0000.000
57A31GLU-1-0.997-0.8469.9290.2300.2300.0000.0000.0000.000
58A32VAL00.099-0.1037.4030.3960.3960.0000.0000.0000.000
59A32VAL0-0.1170.0806.421-0.005-0.0050.0000.0000.0000.000
60A33PRO00.029-0.0992.511-1.386-0.8550.432-0.467-0.4960.000
61A34VAL00.014-0.0202.1142.2870.2588.760-4.067-2.663-0.028
62A34VAL0-0.0520.0984.8330.1830.1830.0000.0000.0000.000
63A35ILE00.109-0.1064.285-0.092-0.011-0.001-0.032-0.0490.000
64A35ILE0-0.0610.1303.324-0.004-0.1510.0400.284-0.1770.001
65A36ILE00.070-0.0825.6640.2680.277-0.0020.000-0.0070.000
66A36ILE0-0.1090.0768.5190.0630.0630.0000.0000.0000.000
67A37GLU00.086-0.1109.4120.0110.0110.0000.0000.0000.000
68A37GLU-1-0.890-0.8119.890-1.434-1.4340.0000.0000.0000.000
69A38ALA00.142-0.08012.2190.0520.0520.0000.0000.0000.000
70A38ALA0-0.0840.08516.5550.0150.0150.0000.0000.0000.000
71A39PHE0-0.083-0.12615.931-0.029-0.0290.0000.0000.0000.000
72A39PHE0-0.0300.09613.1010.0050.0050.0000.0000.0000.000
73A40PRO00.065-0.06818.2290.0260.0260.0000.0000.0000.000
74A41GLU00.089-0.01121.140-0.034-0.0340.0000.0000.0000.000
75A41GLU-1-0.869-0.81323.932-0.220-0.2200.0000.0000.0000.000
76A42THR00.000-0.09922.9590.0110.0110.0000.0000.0000.000
77A42THR0-0.0170.06724.492-0.010-0.0100.0000.0000.0000.000
78A43LEU00.026-0.08920.1360.0310.0310.0000.0000.0000.000
79A43LEU0-0.0740.10319.406-0.014-0.0140.0000.0000.0000.000
80A44ALA00.102-0.10019.029-0.051-0.0510.0000.0000.0000.000
81A44ALA0-0.0320.12120.4570.0080.0080.0000.0000.0000.000
82A45GLY00.020-0.10918.870-0.004-0.0040.0000.0000.0000.000
83A46GLU00.1020.02219.7560.0140.0140.0000.0000.0000.000
84A46GLU-1-0.883-0.77419.132-0.456-0.4560.0000.0000.0000.000
85A47LYS00.009-0.15615.842-0.009-0.0090.0000.0000.0000.000
86A47LYS10.7461.01214.8360.5500.5500.0000.0000.0000.000
87A48GLY00.067-0.08914.391-0.096-0.0960.0000.0000.0000.000
88A49GLN00.084-0.02114.4000.0070.0070.0000.0000.0000.000
89A49GLN0-0.0640.10816.0440.0090.0090.0000.0000.0000.000
90A50ASN0-0.008-0.08411.6580.1350.1350.0000.0000.0000.000
91A50ASN0-0.1050.06711.0830.0070.0070.0000.0000.0000.000
92A51ALA00.117-0.0899.819-0.322-0.3220.0000.0000.0000.000
93A51ALA0-0.0640.09711.3350.0210.0210.0000.0000.0000.000
94A52ASP00.045-0.1148.0690.1690.1690.0000.0000.0000.000
95A52ASP-1-0.871-0.7956.351-0.026-0.0260.0000.0000.0000.000
96A53VAL00.047-0.0889.4030.2350.2350.0000.0000.0000.000
97A53VAL0-0.0940.0919.8660.0090.0090.0000.0000.0000.000
98A54VAL00.100-0.11211.956-0.185-0.1850.0000.0000.0000.000
99A54VAL0-0.0790.11414.531-0.005-0.0050.0000.0000.0000.000
100A55LEU00.105-0.08514.8840.0880.0880.0000.0000.0000.000
101A55LEU0-0.1080.08613.526-0.004-0.0040.0000.0000.0000.000
102A56LEU00.034-0.13516.747-0.064-0.0640.0000.0000.0000.000
103A56LEU0-0.0330.14119.5170.0020.0020.0000.0000.0000.000
104A57GLY00.021-0.09920.3530.0180.0180.0000.0000.0000.000
105A58PRO00.019-0.01322.3110.0150.0150.0000.0000.0000.000
106A59GLN00.062-0.01525.4380.0180.0180.0000.0000.0000.000
107A59GLN0-0.0160.11025.040-0.009-0.0090.0000.0000.0000.000
108A60ILE00.008-0.08525.6750.0120.0120.0000.0000.0000.000
109A60ILE0-0.0840.10322.265-0.003-0.0030.0000.0000.0000.000
110A61ALA00.194-0.06925.494-0.003-0.0030.0000.0000.0000.000
111A61ALA0-0.0730.09426.4440.0030.0030.0000.0000.0000.000
112A62TYR00.042-0.10926.5210.0100.0100.0000.0000.0000.000
113A62TYR0-0.0650.10330.4140.0000.0000.0000.0000.0000.000
114A63MET00.059-0.12126.5520.0150.0150.0000.0000.0000.000
115A63MET0-0.0510.11525.673-0.010-0.0100.0000.0000.0000.000
116A64LEU00.071-0.07824.165-0.010-0.0100.0000.0000.0000.000
117A64LEU0-0.0950.10622.2900.0000.0000.0000.0000.0000.000
118A65PRO0-0.010-0.13524.6400.0030.0030.0000.0000.0000.000
119A66GLU00.045-0.04726.6350.0130.0130.0000.0000.0000.000
120A66GLU-1-0.970-0.83327.036-0.096-0.0960.0000.0000.0000.000
121A67ILE00.143-0.04822.4660.0020.0020.0000.0000.0000.000
122A67ILE0-0.0940.08720.466-0.007-0.0070.0000.0000.0000.000
123A68GLN00.072-0.11021.888-0.014-0.0140.0000.0000.0000.000
124A68GLN0-0.1210.08121.8540.0050.0050.0000.0000.0000.000
125A69ARG00.055-0.09322.9400.0140.0140.0000.0000.0000.000
126A69ARG10.8631.04226.8030.0420.0420.0000.0000.0000.000
127A70LEU00.093-0.05923.4170.0150.0150.0000.0000.0000.000
128A70LEU0-0.1270.09222.218-0.006-0.0060.0000.0000.0000.000
129A71LEU0-0.049-0.13019.007-0.005-0.0050.0000.0000.0000.000
130A71LEU0-0.0920.08617.049-0.008-0.0080.0000.0000.0000.000
131A72PRO00.079-0.08519.6750.0180.0180.0000.0000.0000.000
132A73ASN00.0440.03917.9480.0320.0320.0000.0000.0000.000
133A73ASN0-0.0950.04716.767-0.034-0.0340.0000.0000.0000.000
134A74LYS00.038-0.15015.1450.0620.0620.0000.0000.0000.000
135A74LYS10.8071.03911.8970.1930.1930.0000.0000.0000.000
136A75PRO0-0.016-0.05913.603-0.008-0.0080.0000.0000.0000.000
137A76VAL00.116-0.02115.560-0.053-0.0530.0000.0000.0000.000
138A76VAL0-0.0980.09317.717-0.008-0.0080.0000.0000.0000.000
139A77GLU00.013-0.09317.9370.0270.0270.0000.0000.0000.000
140A77GLU-1-0.981-0.85817.2020.0820.0820.0000.0000.0000.000
141A78VAL00.057-0.11619.161-0.046-0.0460.0000.0000.0000.000
142A78VAL0-0.0440.11323.0440.0010.0010.0000.0000.0000.000
143A79ILE00.070-0.07819.8490.0310.0310.0000.0000.0000.000
144A79ILE0-0.1090.06817.870-0.006-0.0060.0000.0000.0000.000
145A80ASP00.111-0.09320.579-0.003-0.0030.0000.0000.0000.000
146A80ASP-1-0.892-0.81422.367-0.035-0.0350.0000.0000.0000.000
147A81SER00.063-0.06223.175-0.020-0.0200.0000.0000.0000.000
148A81SER0-0.0290.07027.0960.0040.0040.0000.0000.0000.000
149A82LEU00.114-0.09125.882-0.019-0.0190.0000.0000.0000.000
150A82LEU0-0.0830.11826.5080.0020.0020.0000.0000.0000.000
151A83LEU00.062-0.13421.910-0.007-0.0070.0000.0000.0000.000
152A83LEU0-0.0950.10220.0600.0000.0000.0000.0000.0000.000
153A84TYR00.094-0.08022.005-0.019-0.0190.0000.0000.0000.000
154A84TYR0-0.1130.06921.0780.0060.0060.0000.0000.0000.000
155A85GLY0-0.051-0.12022.968-0.016-0.0160.0000.0000.0000.000
156A86LYS00.1070.01725.608-0.009-0.0090.0000.0000.0000.000
157A86LYS10.7871.01724.1170.0590.0590.0000.0000.0000.000
158A87VAL00.020-0.09622.0200.0050.0050.0000.0000.0000.000
159A87VAL0-0.1320.08621.074-0.006-0.0060.0000.0000.0000.000
160A88ASP00.125-0.10920.839-0.022-0.0220.0000.0000.0000.000
161A88ASP-1-0.934-0.80020.334-0.063-0.0630.0000.0000.0000.000
162A89GLY00.049-0.09617.0320.0000.0000.0000.0000.0000.000
163A90LEU00.1390.01615.550-0.026-0.0260.0000.0000.0000.000
164A90LEU0-0.1110.09915.1950.0080.0080.0000.0000.0000.000
165A91GLY0-0.013-0.12215.8950.0360.0360.0000.0000.0000.000
166A92VAL00.1030.01316.5430.0580.0580.0000.0000.0000.000
167A92VAL0-0.0270.11615.309-0.005-0.0050.0000.0000.0000.000
168A93LEU00.120-0.09912.447-0.001-0.0010.0000.0000.0000.000
169A93LEU0-0.1130.1059.321-0.005-0.0050.0000.0000.0000.000
170A94LYS00.015-0.10712.2720.0680.0680.0000.0000.0000.000
171A94LYS10.8731.04815.341-0.102-0.1020.0000.0000.0000.000
172A95ALA00.100-0.09714.3660.0960.0960.0000.0000.0000.000
173A95ALA0-0.0570.12516.512-0.009-0.0090.0000.0000.0000.000
174A96ALA00.126-0.07611.9850.0740.0740.0000.0000.0000.000
175A96ALA0-0.0600.10511.386-0.033-0.0330.0000.0000.0000.000
176A97VAL00.090-0.1029.8890.0370.0370.0000.0000.0000.000
177A97VAL0-0.1090.0948.5930.0220.0220.0000.0000.0000.000
178A98ALA00.053-0.10310.8070.1780.1780.0000.0000.0000.000
179A98ALA0-0.0740.09715.557-0.012-0.0120.0000.0000.0000.000
180A99ALA00.080-0.10914.2630.0860.0860.0000.0000.0000.000
181A99ALA0-0.0240.13213.862-0.019-0.0190.0000.0000.0000.000
182A100ILE00.069-0.08810.074-0.056-0.0560.0000.0000.0000.000
183A100ILE0-0.1130.0747.5510.0550.0550.0000.0000.0000.000
184A101LYS00.086-0.06011.5950.1210.1210.0000.0000.0000.000
185A101LYS10.8311.01211.445-0.800-0.8000.0000.0000.0000.000
186A102LYS00.109-0.08613.1680.0310.0310.0000.0000.0000.000
187A102LYS10.8401.06216.683-0.209-0.2090.0000.0000.0000.000
188A103ALA00.056-0.09814.718-0.047-0.0470.0000.0000.0000.000
189A103ALA0-0.0570.10513.766-0.012-0.0120.0000.0000.0000.000
190A104ALA00.053-0.09913.133-0.089-0.0890.0000.0000.0000.000
191A104ALA0-0.1070.08612.3180.0570.0570.0000.0000.0000.000
192A105ALA0-0.085-0.12614.479-0.006-0.0060.0000.0000.0000.000
193A105ALA00.0140.01516.8680.0060.0060.0000.0000.0000.000