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: JQ1Q9

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 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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1818802.627626
FMO2-HF: Nuclear repulsion 1748549.999156
FMO2-HF: Total energy -70252.62847
FMO2-MP2: Total energy -70452.778601


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.
-6.0491.1844.417-4.427-7.222-0.01
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 : -0.015 / q_NPA : -0.007
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].
3A5VAL00.043-0.0153.0210.2652.8410.029-1.058-1.5460.005
4A6ASP-1-0.808-0.8445.7440.5080.5080.0000.0000.0000.000
5A7CYS0-0.057-0.0177.590-0.499-0.4990.0000.0000.0000.000
6A8GLU-1-0.900-0.95110.2840.1820.1820.0000.0000.0000.000
7A9PHE0-0.032-0.0247.323-0.157-0.1570.0000.0000.0000.000
8A10THR00.000-0.01813.3980.0860.0860.0000.0000.0000.000
9A11GLY00.0130.01916.992-0.034-0.0340.0000.0000.0000.000
10A12ARG10.8630.94510.5490.4950.4950.0000.0000.0000.000
11A13ASP-1-0.795-0.90415.923-0.065-0.0650.0000.0000.0000.000
12A14PHE0-0.063-0.0389.186-0.059-0.0590.0000.0000.0000.000
13A15ARG10.8340.89914.2040.0800.0800.0000.0000.0000.000
14A16ASP-1-0.927-0.97716.797-0.038-0.0380.0000.0000.0000.000
15A17GLU-1-0.873-0.91410.824-0.396-0.3960.0000.0000.0000.000
16A18ASP-1-0.826-0.91212.1270.1980.1980.0000.0000.0000.000
17A19LEU0-0.051-0.0227.138-0.037-0.0370.0000.0000.0000.000
18A20SER00.006-0.0278.5160.2690.2690.0000.0000.0000.000
19A21ARG10.8970.9467.599-0.089-0.0890.0000.0000.0000.000
20A22LEU00.0050.0383.2230.0180.5510.049-0.131-0.4510.000
21A23HIS0-0.045-0.0202.251-3.661-1.6842.252-1.214-3.0150.006
22A24THR0-0.0060.0022.403-3.587-1.5892.088-2.019-2.067-0.021
23A25GLU-1-0.853-0.9274.9003.8734.022-0.001-0.005-0.1430.000
24A26ARG10.7480.8306.995-2.377-2.3770.0000.0000.0000.000
25A27ALA0-0.0290.0147.124-0.293-0.2930.0000.0000.0000.000
26A28MET0-0.006-0.0109.2580.1530.1530.0000.0000.0000.000
27A29PHE0-0.010-0.0207.434-0.146-0.1460.0000.0000.0000.000
28A30SER0-0.009-0.01813.5260.0780.0780.0000.0000.0000.000
29A31GLU-1-0.845-0.92417.2840.0210.0210.0000.0000.0000.000
30A32CYS0-0.066-0.02614.690-0.058-0.0580.0000.0000.0000.000
31A33ASP-1-0.779-0.87616.7510.0590.0590.0000.0000.0000.000
32A34PHE00.013-0.00810.865-0.021-0.0210.0000.0000.0000.000
33A35SER00.023-0.01315.8810.0450.0450.0000.0000.0000.000
34A36GLY0-0.0050.00718.354-0.030-0.0300.0000.0000.0000.000
35A37VAL0-0.0560.00612.2970.0020.0020.0000.0000.0000.000
36A38ASN0-0.076-0.05814.0320.0780.0780.0000.0000.0000.000
37A39LEU00.015-0.0109.3600.0230.0230.0000.0000.0000.000
38A40ALA00.0110.01412.1000.1260.1260.0000.0000.0000.000
39A41GLU-1-0.932-0.97810.5820.4320.4320.0000.0000.0000.000
40A42SER0-0.0650.0008.2680.2190.2190.0000.0000.0000.000
41A43GLN0-0.016-0.0286.749-0.419-0.4190.0000.0000.0000.000
42A44HIS10.8230.8826.836-0.666-0.6660.0000.0000.0000.000
43A45ARG10.9160.9538.117-1.885-1.8850.0000.0000.0000.000
44A46GLY00.0680.0179.5410.1460.1460.0000.0000.0000.000
45A47SER0-0.033-0.0289.3970.0000.0000.0000.0000.0000.000
46A48ALA0-0.029-0.02611.789-0.079-0.0790.0000.0000.0000.000
47A49PHE00.0170.0189.795-0.033-0.0330.0000.0000.0000.000
48A50ARG10.9360.97415.224-0.281-0.2810.0000.0000.0000.000
49A51ASN0-0.018-0.02318.477-0.024-0.0240.0000.0000.0000.000
50A52CYS0-0.0530.02716.257-0.034-0.0340.0000.0000.0000.000
51A53THR00.0270.01318.6530.0230.0230.0000.0000.0000.000
52A54PHE0-0.014-0.01214.2840.0000.0000.0000.0000.0000.000
53A55GLU-1-0.884-0.95219.5250.0750.0750.0000.0000.0000.000
54A56ARG10.8660.91721.108-0.060-0.0600.0000.0000.0000.000
55A57THR00.006-0.02115.704-0.010-0.0100.0000.0000.0000.000
56A58THR0-0.066-0.03916.8350.0030.0030.0000.0000.0000.000
57A59LEU00.0530.02613.5360.0320.0320.0000.0000.0000.000
58A60TRP0-0.036-0.00815.8410.0430.0430.0000.0000.0000.000
59A61HIS00.016-0.00915.3550.0180.0180.0000.0000.0000.000
60A62SER00.0000.01612.5790.0800.0800.0000.0000.0000.000
61A63THR0-0.028-0.03211.264-0.121-0.1210.0000.0000.0000.000
62A64PHE0-0.024-0.00211.1720.3320.3320.0000.0000.0000.000
63A65ALA00.0500.01511.867-0.151-0.1510.0000.0000.0000.000
64A66GLN00.0170.02512.9220.2930.2930.0000.0000.0000.000
65A67CYS0-0.0930.00712.6250.1570.1570.0000.0000.0000.000
66A68SER00.0110.00215.210-0.118-0.1180.0000.0000.0000.000
67A69MET00.0130.00815.0030.0130.0130.0000.0000.0000.000
68A70LEU0-0.023-0.00718.678-0.044-0.0440.0000.0000.0000.000
69A71GLY00.0580.02321.037-0.012-0.0120.0000.0000.0000.000
70A72SER0-0.040-0.01018.471-0.033-0.0330.0000.0000.0000.000
71A73VAL0-0.030-0.01720.9750.0060.0060.0000.0000.0000.000
72A74PHE0-0.007-0.01217.694-0.005-0.0050.0000.0000.0000.000
73A75VAL00.0410.03422.727-0.008-0.0080.0000.0000.0000.000
74A76ALA0-0.0030.00824.126-0.004-0.0040.0000.0000.0000.000
75A77CYS00.0290.06620.583-0.001-0.0010.0000.0000.0000.000
76A78ARG10.8720.94120.077-0.158-0.1580.0000.0000.0000.000
77A79LEU00.000-0.00318.8540.0330.0330.0000.0000.0000.000
78A80ARG10.8280.91420.674-0.179-0.1790.0000.0000.0000.000
79A81PRO00.021-0.01219.741-0.032-0.0320.0000.0000.0000.000
80A82LEU0-0.0020.00015.8960.0230.0230.0000.0000.0000.000
81A83THR0-0.0170.00215.621-0.084-0.0840.0000.0000.0000.000
82A84LEU0-0.0110.00215.9810.1020.1020.0000.0000.0000.000
83A85ASP-1-0.832-0.92015.8430.7350.7350.0000.0000.0000.000
84A86ASP-1-0.821-0.89816.9500.6130.6130.0000.0000.0000.000
85A87VAL0-0.020-0.01016.5010.0670.0670.0000.0000.0000.000
86A88ASP-1-0.822-0.89418.9930.2840.2840.0000.0000.0000.000
87A89PHE00.016-0.01719.4680.0060.0060.0000.0000.0000.000
88A90THR0-0.010-0.02022.897-0.040-0.0400.0000.0000.0000.000
89A91LEU0-0.011-0.01824.2530.0070.0070.0000.0000.0000.000
90A92ALA0-0.0040.04322.738-0.013-0.0130.0000.0000.0000.000
91A93VAL0-0.004-0.02524.316-0.014-0.0140.0000.0000.0000.000
92A94LEU00.0270.01622.5120.0060.0060.0000.0000.0000.000
93A95GLY00.0050.02226.117-0.002-0.0020.0000.0000.0000.000
94A96GLY00.0150.00328.4690.0000.0000.0000.0000.0000.000
95A97ASN0-0.095-0.05224.3890.0050.0050.0000.0000.0000.000
96A98ASP-1-0.757-0.85026.3250.1700.1700.0000.0000.0000.000
97A99LEU00.0460.00623.9290.0170.0170.0000.0000.0000.000
98A100ARG10.8160.87426.123-0.141-0.1410.0000.0000.0000.000
99A101GLY0-0.0130.00226.9490.0060.0060.0000.0000.0000.000
100A102LEU0-0.044-0.00321.8680.0110.0110.0000.0000.0000.000
101A103ASN00.0200.01922.987-0.033-0.0330.0000.0000.0000.000
102A104LEU00.016-0.00522.6830.0350.0350.0000.0000.0000.000
103A105THR0-0.016-0.04824.380-0.019-0.0190.0000.0000.0000.000
104A106GLY0-0.0180.01123.7610.0330.0330.0000.0000.0000.000
105A107CYS0-0.0560.00022.2620.0400.0400.0000.0000.0000.000
106A108ARG10.8240.87921.266-0.438-0.4380.0000.0000.0000.000
107A109LEU0-0.041-0.02224.9390.0150.0150.0000.0000.0000.000
108A110ARG10.9210.94827.461-0.213-0.2130.0000.0000.0000.000
109A111GLU-1-0.911-0.96928.6610.1460.1460.0000.0000.0000.000
110A112THR0-0.050-0.01026.241-0.003-0.0030.0000.0000.0000.000
111A113SER0-0.039-0.02028.398-0.015-0.0150.0000.0000.0000.000
112A114LEU00.001-0.02128.0100.0100.0100.0000.0000.0000.000
113A115VAL00.013-0.00430.856-0.004-0.0040.0000.0000.0000.000
114A116ASP-1-0.874-0.93932.3250.1010.1010.0000.0000.0000.000
115A117THR0-0.065-0.02528.258-0.001-0.0010.0000.0000.0000.000
116A118ASP-1-0.784-0.88930.2640.1320.1320.0000.0000.0000.000
117A119LEU00.0500.00728.2820.0150.0150.0000.0000.0000.000
118A120ARG10.8510.92330.820-0.121-0.1210.0000.0000.0000.000
119A121LYS10.8260.89331.424-0.127-0.1270.0000.0000.0000.000
120A122CYS0-0.0520.02627.2910.0050.0050.0000.0000.0000.000
121A123VAL0-0.036-0.01427.337-0.018-0.0180.0000.0000.0000.000
122A124LEU00.0430.01827.4360.0210.0210.0000.0000.0000.000
123A125ARG10.9210.96529.376-0.215-0.2150.0000.0000.0000.000
124A126GLY00.0290.00528.7060.0210.0210.0000.0000.0000.000
125A127ALA0-0.0360.01027.8590.0100.0100.0000.0000.0000.000
126A128ASP-1-0.771-0.85528.5200.1870.1870.0000.0000.0000.000
127A129LEU00.002-0.00229.7020.0090.0090.0000.0000.0000.000
128A130SER0-0.060-0.05532.006-0.016-0.0160.0000.0000.0000.000
129A131GLY00.0540.01632.9610.0070.0070.0000.0000.0000.000
130A132ALA0-0.0350.01231.682-0.001-0.0010.0000.0000.0000.000
131A133ARG10.9150.95332.607-0.129-0.1290.0000.0000.0000.000
132A134THR00.044-0.00433.4050.0070.0070.0000.0000.0000.000
133A135THR00.0140.00835.611-0.001-0.0010.0000.0000.0000.000
134A136GLY00.0700.04836.3660.0020.0020.0000.0000.0000.000
135A137ALA0-0.046-0.00133.9890.0030.0030.0000.0000.0000.000
136A138ARG10.8510.91334.109-0.121-0.1210.0000.0000.0000.000
137A139LEU00.0480.01332.4850.0110.0110.0000.0000.0000.000
138A140ASP-1-0.811-0.88735.4760.1170.1170.0000.0000.0000.000
139A141ASP-1-0.857-0.92435.9790.1290.1290.0000.0000.0000.000
140A142ALA0-0.0230.00432.8040.0080.0080.0000.0000.0000.000
141A143ASP-1-0.783-0.86331.8900.1720.1720.0000.0000.0000.000
142A144LEU00.0470.01032.4070.0140.0140.0000.0000.0000.000
143A145ARG10.7920.86534.110-0.167-0.1670.0000.0000.0000.000
144A146GLY00.0290.00633.3060.0150.0150.0000.0000.0000.000
145A147ALA0-0.0370.02132.5230.0080.0080.0000.0000.0000.000
146A148THR00.0000.00033.043-0.015-0.0150.0000.0000.0000.000
147A149VAL0-0.008-0.02234.2720.0060.0060.0000.0000.0000.000
148A150ASP-1-0.802-0.88736.7850.1280.1280.0000.0000.0000.000
149A151PRO0-0.007-0.02639.311-0.001-0.0010.0000.0000.0000.000
150A152VAL0-0.006-0.01339.300-0.003-0.0030.0000.0000.0000.000
151A153LEU00.0640.06435.375-0.003-0.0030.0000.0000.0000.000
152A154TRP00.0250.00539.033-0.003-0.0030.0000.0000.0000.000
153A155ARG10.8260.90442.287-0.090-0.0900.0000.0000.0000.000
154A156THR0-0.057-0.03739.779-0.002-0.0020.0000.0000.0000.000
155A157ALA00.0270.03637.459-0.001-0.0010.0000.0000.0000.000
156A158SER0-0.071-0.04638.844-0.004-0.0040.0000.0000.0000.000
157A159LEU00.024-0.01838.3480.0070.0070.0000.0000.0000.000
158A160VAL0-0.0020.00740.6630.0000.0000.0000.0000.0000.000
159A161GLY00.0560.02540.5090.0030.0030.0000.0000.0000.000
160A162ALA0-0.051-0.01837.7060.0060.0060.0000.0000.0000.000
161A163ARG10.8200.89234.510-0.160-0.1600.0000.0000.0000.000
162A164VAL00.0390.01937.2480.0090.0090.0000.0000.0000.000
163A165ASP-1-0.806-0.89838.0340.1440.1440.0000.0000.0000.000
164A166VAL00.010-0.01240.593-0.004-0.0040.0000.0000.0000.000
165A167ASP-1-0.878-0.93041.2710.1150.1150.0000.0000.0000.000
166A168GLN0-0.026-0.03636.146-0.008-0.0080.0000.0000.0000.000
167A169ALA0-0.030-0.01641.925-0.005-0.0050.0000.0000.0000.000
168A170VAL00.0100.00144.940-0.006-0.0060.0000.0000.0000.000
169A171ALA00.0330.01143.349-0.005-0.0050.0000.0000.0000.000
170A172PHE00.0100.01843.738-0.004-0.0040.0000.0000.0000.000
171A173ALA00.0190.01045.846-0.004-0.0040.0000.0000.0000.000
172A174ALA00.0610.05147.751-0.004-0.0040.0000.0000.0000.000
173A175ALA0-0.082-0.02745.737-0.004-0.0040.0000.0000.0000.000
174A176HIS10.8130.86846.655-0.086-0.0860.0000.0000.0000.000
175A177GLY00.0100.00850.870-0.003-0.0030.0000.0000.0000.000
176A178LEU0-0.0060.01952.591-0.003-0.0030.0000.0000.0000.000
177A179CYS0-0.034-0.02453.0310.0030.0030.0000.0000.0000.000
178A180LEU00.0050.01550.698-0.001-0.0010.0000.0000.0000.000