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

tag_button

FMODB ID: YN1M2

Calculation Name: 1BM8-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1BM8

Chain ID: A

ChEMBL ID:

UniProt ID: P39678

Base Structure: X-ray

Registration Date: 2025-07-07

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 190
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -799984.960675
FMO2-HF: Nuclear repulsion 760692.637193
FMO2-HF: Total energy -39292.323481
FMO2-MP2: Total energy -39409.646331


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:4:GLN)


Summations of interaction energy for fragment #1(A:4:GLN)
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.
-0.0719999999999993.8140.335-1.519-2.7030.007
Interaction energy analysis for fragmet #1(A:4:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.132 / q_NPA : 0.046
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].
4A5ILE0-0.0690.1203.602-0.4360.1380.018-0.239-0.3530.001
5A6TYR00.032-0.1173.870-1.2810.437-0.011-0.967-0.7400.004
6A6TYR0-0.0670.1033.5540.080-0.0120.0650.370-0.3430.000
7A7SER00.110-0.0726.4060.3840.3840.0000.0000.0000.000
8A7SER0-0.0560.08710.6090.1220.1220.0000.0000.0000.000
9A8ALA00.065-0.09210.148-0.008-0.0080.0000.0000.0000.000
10A8ALA0-0.0550.10410.562-0.022-0.0220.0000.0000.0000.000
11A9ARG00.085-0.10712.1670.0660.0660.0000.0000.0000.000
12A9ARG10.7651.02416.4780.4970.4970.0000.0000.0000.000
13A10TYR0-0.007-0.12515.894-0.005-0.0050.0000.0000.0000.000
14A10TYR0-0.0850.05011.6740.0790.0790.0000.0000.0000.000
15A11SER00.064-0.04917.9850.0170.0170.0000.0000.0000.000
16A11SER0-0.0830.06821.319-0.002-0.0020.0000.0000.0000.000
17A12GLY00.038-0.10221.3430.0330.0330.0000.0000.0000.000
18A13VAL00.033-0.02319.9310.0270.0270.0000.0000.0000.000
19A13VAL0-0.0680.10918.4680.0050.0050.0000.0000.0000.000
20A14ASP00.130-0.08416.427-0.057-0.0570.0000.0000.0000.000
21A14ASP-1-0.857-0.77716.337-0.604-0.6040.0000.0000.0000.000
22A15VAL0-0.023-0.12313.4430.1130.1130.0000.0000.0000.000
23A15VAL0-0.0620.08511.9400.0000.0000.0000.0000.0000.000
24A16TYR00.140-0.0799.835-0.103-0.1030.0000.0000.0000.000
25A16TYR0-0.0360.1169.1250.0060.0060.0000.0000.0000.000
26A17GLU00.084-0.1088.2660.3430.3430.0000.0000.0000.000
27A17GLU-1-0.830-0.7067.888-1.406-1.4060.0000.0000.0000.000
28A18PHE00.149-0.0704.866-1.307-1.3070.0000.0000.0000.000
29A18PHE0-0.0830.0913.115-0.3460.1340.026-0.153-0.3530.000
30A19ILE00.045-0.1273.5760.9181.1250.004-0.020-0.1910.000
31A19ILE0-0.0930.1202.570-0.6770.0230.232-0.425-0.5080.002
32A20HIS00.164-0.0494.0090.3460.6450.001-0.085-0.2150.000
33A20HIS0-0.0670.0907.222-0.054-0.0540.0000.0000.0000.000
34A21SER00.058-0.0626.845-0.127-0.1270.0000.0000.0000.000
35A21SER0-0.0220.0719.8240.0020.0020.0000.0000.0000.000
36A22THR0-0.017-0.1189.485-0.042-0.0420.0000.0000.0000.000
37A22THR0-0.0990.06711.279-0.039-0.0390.0000.0000.0000.000
38A23GLY0-0.024-0.1089.782-0.004-0.0040.0000.0000.0000.000
39A24SER00.0090.0367.847-0.010-0.0100.0000.0000.0000.000
40A24SER0-0.0930.0058.2180.0770.0770.0000.0000.0000.000
41A25ILE00.022-0.1488.4100.2500.2500.0000.0000.0000.000
42A25ILE0-0.0640.1188.7550.0330.0330.0000.0000.0000.000
43A26MET00.077-0.0929.228-0.296-0.2960.0000.0000.0000.000
44A26MET0-0.1220.08511.6330.0690.0690.0000.0000.0000.000
45A27LYS00.118-0.09711.7920.1560.1560.0000.0000.0000.000
46A27LYS10.6890.99111.6200.3940.3940.0000.0000.0000.000
47A28ARG00.085-0.09813.265-0.138-0.1380.0000.0000.0000.000
48A28ARG10.6400.92016.8570.3580.3580.0000.0000.0000.000
49A29LYS00.041-0.09715.8730.0520.0520.0000.0000.0000.000
50A29LYS10.7901.01212.9610.8480.8480.0000.0000.0000.000
51A30LYS00.067-0.05216.4610.0310.0310.0000.0000.0000.000
52A30LYS10.7690.98120.0860.3080.3080.0000.0000.0000.000
53A31ASP00.074-0.08419.1960.0310.0310.0000.0000.0000.000
54A31ASP-1-0.811-0.77719.892-0.328-0.3280.0000.0000.0000.000
55A32ASP00.083-0.06216.4070.0260.0260.0000.0000.0000.000
56A32ASP-1-0.853-0.79115.197-0.352-0.3520.0000.0000.0000.000
57A33TRP00.105-0.11817.1040.0180.0180.0000.0000.0000.000
58A33TRP0-0.1170.08119.5290.0030.0030.0000.0000.0000.000
59A34VAL00.072-0.09815.249-0.083-0.0830.0000.0000.0000.000
60A34VAL0-0.0410.11713.2770.0040.0040.0000.0000.0000.000
61A35ASN00.143-0.06015.1310.0760.0760.0000.0000.0000.000
62A35ASN0-0.1090.07415.1000.0320.0320.0000.0000.0000.000
63A36ALA00.163-0.09015.780-0.021-0.0210.0000.0000.0000.000
64A36ALA0-0.0740.10619.7440.0070.0070.0000.0000.0000.000
65A37THR00.016-0.09418.0250.0350.0350.0000.0000.0000.000
66A37THR0-0.0540.06018.8510.0000.0000.0000.0000.0000.000
67A38HIS00.043-0.10313.8840.0530.0530.0000.0000.0000.000
68A38HIS0-0.0690.09412.886-0.054-0.0540.0000.0000.0000.000
69A39ILE00.103-0.05813.837-0.002-0.0020.0000.0000.0000.000
70A39ILE0-0.0950.09513.8970.0010.0010.0000.0000.0000.000
71A40LEU00.080-0.08114.8460.0500.0500.0000.0000.0000.000
72A40LEU0-0.1020.07318.9840.0040.0040.0000.0000.0000.000
73A41LYS0-0.023-0.14414.9800.0500.0500.0000.0000.0000.000
74A41LYS10.8881.04714.0250.4630.4630.0000.0000.0000.000
75A42ALA00.142-0.04712.4010.0400.0400.0000.0000.0000.000
76A42ALA0-0.0570.11911.767-0.006-0.0060.0000.0000.0000.000
77A43ALA00.115-0.08813.2630.0760.0760.0000.0000.0000.000
78A43ALA0-0.0940.09117.326-0.004-0.0040.0000.0000.0000.000
79A44ASN0-0.019-0.11316.0160.0150.0150.0000.0000.0000.000
80A44ASN0-0.0720.09715.1210.0050.0050.0000.0000.0000.000
81A45PHE00.076-0.11617.4770.0100.0100.0000.0000.0000.000
82A45PHE0-0.0060.13420.293-0.003-0.0030.0000.0000.0000.000
83A46ALA00.208-0.07520.281-0.031-0.0310.0000.0000.0000.000
84A46ALA0-0.0460.13823.6720.0020.0020.0000.0000.0000.000
85A47LYS00.075-0.08022.7230.0020.0020.0000.0000.0000.000
86A47LYS10.9011.07323.1510.1350.1350.0000.0000.0000.000
87A48ALA00.111-0.10623.804-0.009-0.0090.0000.0000.0000.000
88A48ALA0-0.0230.13627.9950.0020.0020.0000.0000.0000.000
89A49LYS00.011-0.08725.1780.0040.0040.0000.0000.0000.000
90A49LYS10.7891.04023.012-0.007-0.0070.0000.0000.0000.000
91A50ARG00.095-0.08221.9900.0100.0100.0000.0000.0000.000
92A50ARG10.8251.02919.0050.1500.1500.0000.0000.0000.000
93A51THR0-0.002-0.06423.111-0.006-0.0060.0000.0000.0000.000
94A51THR0-0.0470.05826.026-0.003-0.0030.0000.0000.0000.000
95A52ARG00.176-0.04425.992-0.006-0.0060.0000.0000.0000.000
96A52ARG10.8491.02828.2010.0390.0390.0000.0000.0000.000
97A53ILE00.150-0.05024.6650.0020.0020.0000.0000.0000.000
98A53ILE0-0.1110.08823.0480.0010.0010.0000.0000.0000.000
99A54LEU00.108-0.08524.6820.0060.0060.0000.0000.0000.000
100A54LEU0-0.1120.06721.484-0.005-0.0050.0000.0000.0000.000
101A55GLU00.052-0.13625.283-0.003-0.0030.0000.0000.0000.000
102A55GLU-1-0.955-0.84028.989-0.078-0.0780.0000.0000.0000.000
103A56LYS0-0.026-0.08428.3920.0000.0000.0000.0000.0000.000
104A56LYS10.8141.01929.4610.0620.0620.0000.0000.0000.000
105A57GLU00.089-0.10025.7450.0050.0050.0000.0000.0000.000
106A57GLU-1-0.928-0.82725.041-0.033-0.0330.0000.0000.0000.000
107A58VAL00.060-0.06324.5040.0070.0070.0000.0000.0000.000
108A58VAL0-0.0740.07222.641-0.004-0.0040.0000.0000.0000.000
109A59LEU00.050-0.09725.832-0.007-0.0070.0000.0000.0000.000
110A59LEU0-0.0840.07826.589-0.001-0.0010.0000.0000.0000.000
111A60LYS00.072-0.08228.522-0.004-0.0040.0000.0000.0000.000
112A60LYS10.7900.99328.2200.0600.0600.0000.0000.0000.000
113A61GLU00.044-0.09427.0780.0080.0080.0000.0000.0000.000
114A61GLU-1-0.938-0.81925.853-0.068-0.0680.0000.0000.0000.000
115A62THR00.056-0.08927.450-0.005-0.0050.0000.0000.0000.000
116A62THR0-0.0130.09426.1950.0000.0000.0000.0000.0000.000
117A63HIS00.050-0.08424.587-0.008-0.0080.0000.0000.0000.000
118A63HIS0-0.0750.07224.766-0.005-0.0050.0000.0000.0000.000
119A64GLU00.145-0.10224.1680.0160.0160.0000.0000.0000.000
120A64GLU-1-0.919-0.76723.641-0.284-0.2840.0000.0000.0000.000
121A65LYS00.048-0.08723.801-0.025-0.0250.0000.0000.0000.000
122A65LYS10.8041.01526.6160.1410.1410.0000.0000.0000.000
123A66VAL00.146-0.09222.9530.0250.0250.0000.0000.0000.000
124A66VAL0-0.1060.12821.944-0.003-0.0030.0000.0000.0000.000
125A67GLN00.063-0.12123.219-0.026-0.0260.0000.0000.0000.000
126A67GLN0-0.0800.10724.155-0.004-0.0040.0000.0000.0000.000
127A68GLY00.053-0.08525.6970.0000.0000.0000.0000.0000.000
128A69GLY00.0120.00623.780-0.001-0.0010.0000.0000.0000.000
129A70PHE00.072-0.03122.110-0.035-0.0350.0000.0000.0000.000
130A70PHE0-0.0530.12823.0010.0010.0010.0000.0000.0000.000
131A71GLY00.048-0.07419.552-0.029-0.0290.0000.0000.0000.000
132A72LYS00.061-0.01114.9460.0590.0590.0000.0000.0000.000
133A72LYS10.8131.01211.0561.1081.1080.0000.0000.0000.000
134A73TYR00.127-0.06315.857-0.035-0.0350.0000.0000.0000.000
135A73TYR0-0.0420.10517.007-0.003-0.0030.0000.0000.0000.000
136A74GLN00.072-0.10417.6010.0150.0150.0000.0000.0000.000
137A74GLN0-0.0900.09220.314-0.005-0.0050.0000.0000.0000.000
138A75GLY0-0.057-0.11518.750-0.029-0.0290.0000.0000.0000.000
139A76THR00.0840.02620.878-0.003-0.0030.0000.0000.0000.000
140A76THR0-0.0470.06822.2740.0130.0130.0000.0000.0000.000
141A77TRP0-0.006-0.12719.567-0.009-0.0090.0000.0000.0000.000
142A77TRP0-0.1080.10415.426-0.023-0.0230.0000.0000.0000.000
143A78VAL00.046-0.11019.6470.0230.0230.0000.0000.0000.000
144A78VAL0-0.0340.11019.4740.0040.0040.0000.0000.0000.000
145A79PRO00.045-0.06919.656-0.029-0.0290.0000.0000.0000.000
146A80LEU00.1700.01717.9090.0060.0060.0000.0000.0000.000
147A80LEU0-0.1180.11415.5220.0080.0080.0000.0000.0000.000
148A81ASN00.043-0.08418.4410.0120.0120.0000.0000.0000.000
149A81ASN0-0.0450.07722.524-0.014-0.0140.0000.0000.0000.000
150A82ILE00.116-0.08020.8540.0230.0230.0000.0000.0000.000
151A82ILE0-0.0630.10322.012-0.002-0.0020.0000.0000.0000.000
152A83ALA00.068-0.10617.2200.0220.0220.0000.0000.0000.000
153A83ALA0-0.0930.08616.226-0.012-0.0120.0000.0000.0000.000
154A84LYS00.052-0.08316.7700.0010.0010.0000.0000.0000.000
155A84LYS10.8071.03515.9060.0630.0630.0000.0000.0000.000
156A85GLN00.214-0.05117.7650.0260.0260.0000.0000.0000.000
157A85GLN0-0.0850.09322.168-0.007-0.0070.0000.0000.0000.000
158A86LEU00.084-0.09219.8630.0270.0270.0000.0000.0000.000
159A86LEU0-0.1360.08118.581-0.005-0.0050.0000.0000.0000.000
160A87ALA00.087-0.09915.7370.0090.0090.0000.0000.0000.000
161A87ALA0-0.0630.09314.992-0.005-0.0050.0000.0000.0000.000
162A88GLU00.029-0.12517.0150.0380.0380.0000.0000.0000.000
163A88GLU-1-0.969-0.85318.5450.0480.0480.0000.0000.0000.000
164A89LYS00.069-0.06119.3550.0230.0230.0000.0000.0000.000
165A89LYS10.7861.01622.1850.0050.0050.0000.0000.0000.000
166A90PHE0-0.011-0.08919.8140.0120.0120.0000.0000.0000.000
167A90PHE0-0.1120.04919.028-0.006-0.0060.0000.0000.0000.000
168A91SER00.067-0.09018.317-0.004-0.0040.0000.0000.0000.000
169A91SER0-0.0360.08418.8590.0070.0070.0000.0000.0000.000
170A92VAL00.049-0.11814.2100.0590.0590.0000.0000.0000.000
171A92VAL0-0.0960.10213.129-0.009-0.0090.0000.0000.0000.000
172A93TYR00.110-0.08812.7910.0040.0040.0000.0000.0000.000
173A93TYR0-0.0430.10216.018-0.021-0.0210.0000.0000.0000.000
174A94ASP00.090-0.12312.633-0.047-0.0470.0000.0000.0000.000
175A94ASP-1-0.932-0.82713.2350.3440.3440.0000.0000.0000.000
176A95GLN00.062-0.1059.5090.1660.1660.0000.0000.0000.000
177A95GLN0-0.0580.0959.708-0.012-0.0120.0000.0000.0000.000
178A96LEU00.035-0.0997.9890.0540.0540.0000.0000.0000.000
179A96LEU0-0.0760.0889.292-0.034-0.0340.0000.0000.0000.000
180A97LYS00.050-0.1019.744-0.183-0.1830.0000.0000.0000.000
181A97LYS10.8691.10211.071-0.365-0.3650.0000.0000.0000.000
182A98PRO00.042-0.0936.238-0.074-0.0740.0000.0000.0000.000
183A99LEU00.1140.0088.041-0.135-0.1350.0000.0000.0000.000
184A99LEU0-0.1100.0977.722-0.024-0.0240.0000.0000.0000.000
185A100PHE00.012-0.1308.999-0.069-0.0690.0000.0000.0000.000
186A100PHE0-0.0760.08112.856-0.017-0.0170.0000.0000.0000.000
187A101ASP00.064-0.07711.522-0.044-0.0440.0000.0000.0000.000
188A101ASP-1-0.930-0.84011.1340.2770.2770.0000.0000.0000.000
189A102PHE0-0.015-0.1009.4870.0590.0590.0000.0000.0000.000
190A102PHE00.0100.0146.444-0.146-0.1460.0000.0000.0000.000