Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 3J6JL

Calculation Name: 2BM7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BM7

Chain ID: A

ChEMBL ID:

UniProt ID: I6YBX3

Base Structure: X-ray

Registration Date: 2023-09-24

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1819147.237776
FMO2-HF: Nuclear repulsion 1748893.882826
FMO2-HF: Total energy -70253.35495
FMO2-MP2: Total energy -70453.488172


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(A:3:GLN)


Summations of interaction energy for fragment #1(A:3: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.
-7.250.4724.739-4.785-7.678-0.014
Interaction energy analysis for fragmet #1(A:3:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.005
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].
3A5VAL00.020-0.0122.9860.1902.6510.067-1.088-1.4400.003
4A6ASP-1-0.810-0.8555.6620.4690.4690.0000.0000.0000.000
5A7CYS0-0.046-0.0247.850-0.448-0.4480.0000.0000.0000.000
6A8GLU-1-0.904-0.94710.687-0.010-0.0100.0000.0000.0000.000
7A9PHE0-0.035-0.0237.529-0.170-0.1700.0000.0000.0000.000
8A10THR00.021-0.00613.2620.0910.0910.0000.0000.0000.000
9A11GLY0-0.0040.00416.992-0.036-0.0360.0000.0000.0000.000
10A12ARG10.7640.87110.5040.6500.6500.0000.0000.0000.000
11A13ASP-1-0.777-0.88416.358-0.165-0.1650.0000.0000.0000.000
12A14PHE0-0.026-0.0169.473-0.104-0.1040.0000.0000.0000.000
13A15ARG10.7870.87014.4740.1520.1520.0000.0000.0000.000
14A16ASP-1-0.844-0.91017.251-0.090-0.0900.0000.0000.0000.000
15A17GLU-1-0.820-0.88510.855-0.603-0.6030.0000.0000.0000.000
16A18ASP-1-0.845-0.89211.7410.1090.1090.0000.0000.0000.000
17A19LEU0-0.009-0.0107.074-0.116-0.1160.0000.0000.0000.000
18A20SER0-0.032-0.0478.2580.2580.2580.0000.0000.0000.000
19A21ARG10.8850.9417.315-0.190-0.1900.0000.0000.0000.000
20A22LEU0-0.0170.0232.542-0.0210.6240.555-0.411-0.789-0.001
21A23HIS0-0.029-0.0172.258-3.033-1.1632.295-1.164-3.0010.006
22A24THR00.0140.0062.528-4.556-1.9381.823-2.118-2.324-0.022
23A25GLU-1-0.854-0.9214.7163.7223.850-0.001-0.004-0.1240.000
24A26ARG10.7450.8366.846-2.246-2.2460.0000.0000.0000.000
25A27ALA0-0.0040.0227.303-0.271-0.2710.0000.0000.0000.000
26A28MET0-0.016-0.0229.4070.1830.1830.0000.0000.0000.000
27A29PHE00.0120.0137.215-0.144-0.1440.0000.0000.0000.000
28A30SER0-0.013-0.01213.3260.1130.1130.0000.0000.0000.000
29A31GLU-1-0.827-0.91017.154-0.056-0.0560.0000.0000.0000.000
30A32CYS0-0.052-0.01114.906-0.056-0.0560.0000.0000.0000.000
31A33ASP-1-0.769-0.85916.894-0.016-0.0160.0000.0000.0000.000
32A34PHE00.0430.00610.789-0.033-0.0330.0000.0000.0000.000
33A35SER00.017-0.00515.7260.0490.0490.0000.0000.0000.000
34A36GLY0-0.043-0.02518.485-0.034-0.0340.0000.0000.0000.000
35A37VAL0-0.0600.00112.1730.0050.0050.0000.0000.0000.000
36A38ASN0-0.060-0.04714.2240.1100.1100.0000.0000.0000.000
37A39LEU00.022-0.0018.757-0.019-0.0190.0000.0000.0000.000
38A40ALA0-0.0020.01611.6610.1310.1310.0000.0000.0000.000
39A41GLU-1-0.884-0.96410.2240.4480.4480.0000.0000.0000.000
40A42SER0-0.0310.0207.8910.2530.2530.0000.0000.0000.000
41A43GLN0-0.034-0.0306.862-0.458-0.4580.0000.0000.0000.000
42A44HIS10.8390.8996.980-0.625-0.6250.0000.0000.0000.000
43A45ARG10.8810.9298.339-1.869-1.8690.0000.0000.0000.000
44A46GLY00.0470.0289.7390.0720.0720.0000.0000.0000.000
45A47SER0-0.019-0.0319.228-0.067-0.0670.0000.0000.0000.000
46A48ALA0-0.052-0.03711.659-0.046-0.0460.0000.0000.0000.000
47A49PHE00.0190.0109.629-0.053-0.0530.0000.0000.0000.000
48A50ARG10.9430.98015.107-0.162-0.1620.0000.0000.0000.000
49A51ASN0-0.037-0.03418.526-0.027-0.0270.0000.0000.0000.000
50A52CYS0-0.0650.00116.387-0.037-0.0370.0000.0000.0000.000
51A53THR00.0120.00418.6430.0340.0340.0000.0000.0000.000
52A54PHE0-0.002-0.00514.142-0.010-0.0100.0000.0000.0000.000
53A55GLU-1-0.864-0.94419.3650.0370.0370.0000.0000.0000.000
54A56ARG10.7990.86521.1440.0040.0040.0000.0000.0000.000
55A57THR00.006-0.00215.3040.0000.0000.0000.0000.0000.000
56A58THR0-0.050-0.02416.3390.0190.0190.0000.0000.0000.000
57A59LEU00.0600.01513.3450.0140.0140.0000.0000.0000.000
58A60TRP0-0.0060.01315.2710.0590.0590.0000.0000.0000.000
59A61HIS0-0.017-0.02914.8770.0370.0370.0000.0000.0000.000
60A62SER0-0.0100.01512.0740.0930.0930.0000.0000.0000.000
61A63THR0-0.054-0.04011.004-0.198-0.1980.0000.0000.0000.000
62A64PHE0-0.005-0.01111.3520.2880.2880.0000.0000.0000.000
63A65ALA00.019-0.00112.386-0.145-0.1450.0000.0000.0000.000
64A66GLN00.0120.03013.2060.2890.2890.0000.0000.0000.000
65A67CYS0-0.088-0.01012.6710.0870.0870.0000.0000.0000.000
66A68SER0-0.019-0.01315.237-0.111-0.1110.0000.0000.0000.000
67A69MET00.0210.00914.985-0.002-0.0020.0000.0000.0000.000
68A70LEU00.0030.00818.583-0.043-0.0430.0000.0000.0000.000
69A71GLY00.0450.01821.229-0.021-0.0210.0000.0000.0000.000
70A72SER0-0.050-0.02018.443-0.040-0.0400.0000.0000.0000.000
71A73VAL0-0.023-0.01521.0670.0140.0140.0000.0000.0000.000
72A74PHE0-0.004-0.00617.184-0.010-0.0100.0000.0000.0000.000
73A75VAL00.0230.02122.288-0.001-0.0010.0000.0000.0000.000
74A76ALA00.0070.00523.551-0.005-0.0050.0000.0000.0000.000
75A77CYS0-0.0070.02820.076-0.006-0.0060.0000.0000.0000.000
76A78ARG10.8540.92319.470-0.114-0.1140.0000.0000.0000.000
77A79LEU00.0110.00418.8690.0340.0340.0000.0000.0000.000
78A80ARG10.8210.92020.326-0.170-0.1700.0000.0000.0000.000
79A81PRO0-0.004-0.01319.586-0.033-0.0330.0000.0000.0000.000
80A82LEU00.005-0.00315.5590.0140.0140.0000.0000.0000.000
81A83THR0-0.0060.00615.138-0.089-0.0890.0000.0000.0000.000
82A84LEU0-0.0080.00015.8470.0960.0960.0000.0000.0000.000
83A85ASP-1-0.812-0.91615.6370.8530.8530.0000.0000.0000.000
84A86ASP-1-0.797-0.88017.0090.6180.6180.0000.0000.0000.000
85A87VAL00.002-0.00416.8140.0740.0740.0000.0000.0000.000
86A88ASP-1-0.815-0.88219.2680.2560.2560.0000.0000.0000.000
87A89PHE00.0440.00419.4770.0000.0000.0000.0000.0000.000
88A90THR00.001-0.01122.746-0.039-0.0390.0000.0000.0000.000
89A91LEU0-0.015-0.03024.477-0.002-0.0020.0000.0000.0000.000
90A92ALA0-0.0300.02422.722-0.016-0.0160.0000.0000.0000.000
91A93VAL0-0.022-0.02624.161-0.009-0.0090.0000.0000.0000.000
92A94LEU00.0480.01822.2610.0080.0080.0000.0000.0000.000
93A95GLY00.0120.02425.7780.0000.0000.0000.0000.0000.000
94A96GLY00.0080.00428.404-0.003-0.0030.0000.0000.0000.000
95A97ASN0-0.083-0.04324.289-0.001-0.0010.0000.0000.0000.000
96A98ASP-1-0.780-0.86026.2250.1650.1650.0000.0000.0000.000
97A99LEU00.0610.00623.7330.0160.0160.0000.0000.0000.000
98A100ARG10.8090.87825.951-0.129-0.1290.0000.0000.0000.000
99A101GLY0-0.009-0.00527.1270.0070.0070.0000.0000.0000.000
100A102LEU0-0.0290.00321.6310.0140.0140.0000.0000.0000.000
101A103ASN00.0120.00622.799-0.044-0.0440.0000.0000.0000.000
102A104LEU00.0340.00522.7510.0300.0300.0000.0000.0000.000
103A105THR0-0.009-0.02824.697-0.021-0.0210.0000.0000.0000.000
104A106GLY0-0.0170.00524.0180.0360.0360.0000.0000.0000.000
105A107CYS0-0.067-0.00822.3070.0280.0280.0000.0000.0000.000
106A108ARG10.7800.86821.398-0.432-0.4320.0000.0000.0000.000
107A109LEU0-0.012-0.01824.7270.0130.0130.0000.0000.0000.000
108A110ARG10.9170.95027.385-0.200-0.2000.0000.0000.0000.000
109A111GLU-1-0.887-0.94828.5230.1220.1220.0000.0000.0000.000
110A112THR0-0.0270.00125.973-0.009-0.0090.0000.0000.0000.000
111A113SER0-0.027-0.02028.371-0.009-0.0090.0000.0000.0000.000
112A114LEU00.010-0.00627.7820.0100.0100.0000.0000.0000.000
113A115VAL00.0080.01030.589-0.002-0.0020.0000.0000.0000.000
114A116ASP-1-0.882-0.94432.1840.0860.0860.0000.0000.0000.000
115A117THR0-0.064-0.03127.871-0.001-0.0010.0000.0000.0000.000
116A118ASP-1-0.816-0.89630.1100.1290.1290.0000.0000.0000.000
117A119LEU00.0590.01627.6070.0150.0150.0000.0000.0000.000
118A120ARG10.8640.92430.427-0.118-0.1180.0000.0000.0000.000
119A121LYS10.8030.86131.290-0.132-0.1320.0000.0000.0000.000
120A122CYS0-0.0530.02727.2390.0070.0070.0000.0000.0000.000
121A123VAL0-0.034-0.01927.318-0.018-0.0180.0000.0000.0000.000
122A124LEU00.0470.01727.4330.0220.0220.0000.0000.0000.000
123A125ARG10.9210.96929.188-0.232-0.2320.0000.0000.0000.000
124A126GLY00.0270.01028.7610.0220.0220.0000.0000.0000.000
125A127ALA0-0.0190.01928.0450.0110.0110.0000.0000.0000.000
126A128ASP-1-0.772-0.86228.6190.1790.1790.0000.0000.0000.000
127A129LEU0-0.010-0.00729.5080.0070.0070.0000.0000.0000.000
128A130SER0-0.021-0.03431.889-0.017-0.0170.0000.0000.0000.000
129A131GLY00.0240.00832.8190.0050.0050.0000.0000.0000.000
130A132ALA0-0.045-0.00531.712-0.005-0.0050.0000.0000.0000.000
131A133ARG10.8400.90932.158-0.118-0.1180.0000.0000.0000.000
132A134THR00.038-0.01533.4170.0040.0040.0000.0000.0000.000
133A135THR0-0.022-0.01235.5000.0000.0000.0000.0000.0000.000
134A136GLY00.0710.04636.5240.0000.0000.0000.0000.0000.000
135A137ALA0-0.0330.00433.5430.0020.0020.0000.0000.0000.000
136A138ARG10.8240.90333.734-0.113-0.1130.0000.0000.0000.000
137A139LEU00.0480.00732.2610.0110.0110.0000.0000.0000.000
138A140ASP-1-0.766-0.85835.1780.1160.1160.0000.0000.0000.000
139A141ASP-1-0.859-0.92335.6590.1380.1380.0000.0000.0000.000
140A142ALA0-0.0260.00432.7880.0070.0070.0000.0000.0000.000
141A143ASP-1-0.814-0.87931.8320.1860.1860.0000.0000.0000.000
142A144LEU00.0530.02432.2930.0150.0150.0000.0000.0000.000
143A145ARG10.8230.89034.510-0.175-0.1750.0000.0000.0000.000
144A146GLY00.0230.00033.6890.0150.0150.0000.0000.0000.000
145A147ALA0-0.058-0.00332.5090.0060.0060.0000.0000.0000.000
146A148THR00.0130.00933.045-0.016-0.0160.0000.0000.0000.000
147A149VAL0-0.006-0.01633.9820.0060.0060.0000.0000.0000.000
148A150ASP-1-0.779-0.87336.5540.1220.1220.0000.0000.0000.000
149A151PRO0-0.022-0.03739.173-0.002-0.0020.0000.0000.0000.000
150A152VAL00.0120.00838.936-0.005-0.0050.0000.0000.0000.000
151A153LEU00.0490.05935.214-0.004-0.0040.0000.0000.0000.000
152A154TRP00.016-0.01039.019-0.002-0.0020.0000.0000.0000.000
153A155ARG10.8230.89442.284-0.085-0.0850.0000.0000.0000.000
154A156THR0-0.034-0.02339.497-0.002-0.0020.0000.0000.0000.000
155A157ALA00.0440.04437.168-0.001-0.0010.0000.0000.0000.000
156A158SER0-0.077-0.05938.280-0.004-0.0040.0000.0000.0000.000
157A159LEU00.042-0.00338.2400.0080.0080.0000.0000.0000.000
158A160VAL00.0050.00140.338-0.001-0.0010.0000.0000.0000.000
159A161GLY00.0430.01440.2690.0050.0050.0000.0000.0000.000
160A162ALA0-0.038-0.01037.9750.0070.0070.0000.0000.0000.000
161A163ARG10.8290.91234.435-0.172-0.1720.0000.0000.0000.000
162A164VAL00.0490.02937.1190.0110.0110.0000.0000.0000.000
163A165ASP-1-0.836-0.92538.2180.1510.1510.0000.0000.0000.000
164A166VAL00.0210.00040.723-0.005-0.0050.0000.0000.0000.000
165A167ASP-1-0.864-0.92241.4600.1180.1180.0000.0000.0000.000
166A168GLN0-0.042-0.04435.997-0.009-0.0090.0000.0000.0000.000
167A169ALA0-0.0040.00241.780-0.005-0.0050.0000.0000.0000.000
168A170VAL00.001-0.00244.930-0.006-0.0060.0000.0000.0000.000
169A171ALA00.0220.00843.207-0.005-0.0050.0000.0000.0000.000
170A172PHE00.0150.00943.625-0.005-0.0050.0000.0000.0000.000
171A173ALA00.0070.00745.752-0.005-0.0050.0000.0000.0000.000
172A174ALA00.0510.03247.937-0.004-0.0040.0000.0000.0000.000
173A175ALA0-0.059-0.01845.539-0.004-0.0040.0000.0000.0000.000
174A176HIS10.7920.88046.212-0.086-0.0860.0000.0000.0000.000
175A177GLY00.0160.01950.610-0.003-0.0030.0000.0000.0000.000
176A178LEU0-0.025-0.00352.823-0.002-0.0020.0000.0000.0000.000
177A179CYS0-0.017-0.00852.8580.0030.0030.0000.0000.0000.000
178A180LEU0-0.0040.00250.934-0.001-0.0010.0000.0000.0000.000