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: NN4NQ

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 OptH
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 -1818729.350106
FMO2-HF: Nuclear repulsion 1748477.808684
FMO2-HF: Total energy -70251.541422
FMO2-MP2: Total energy -70451.781971


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.
-3.3992.6875.353-4.206-7.233-0.014
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 : -0.045 / q_NPA : -0.037
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].
3A5VAL00.034-0.0172.9950.5882.6120.033-0.649-1.4080.002
4A6ASP-1-0.862-0.9105.6640.7460.7460.0000.0000.0000.000
5A7CYS0-0.0460.0067.406-0.267-0.2670.0000.0000.0000.000
6A8GLU-1-0.889-0.95210.2840.7710.7710.0000.0000.0000.000
7A9PHE0-0.035-0.0277.875-0.061-0.0610.0000.0000.0000.000
8A10THR0-0.014-0.02313.4600.0250.0250.0000.0000.0000.000
9A11GLY00.0210.02017.079-0.032-0.0320.0000.0000.0000.000
10A12ARG10.8970.95411.755-0.709-0.7090.0000.0000.0000.000
11A13ASP-1-0.867-0.94816.4560.4330.4330.0000.0000.0000.000
12A14PHE0-0.054-0.02410.4970.0440.0440.0000.0000.0000.000
13A15ARG10.9260.95815.154-0.308-0.3080.0000.0000.0000.000
14A16ASP-1-0.981-1.00017.7740.2920.2920.0000.0000.0000.000
15A17GLU-1-0.923-0.94012.3690.7790.7790.0000.0000.0000.000
16A18ASP-1-0.862-0.95612.0760.3850.3850.0000.0000.0000.000
17A19LEU0-0.031-0.0168.0040.1640.1640.0000.0000.0000.000
18A20SER00.0230.0018.7470.1400.1400.0000.0000.0000.000
19A21ARG10.8960.9447.6530.8160.8160.0000.0000.0000.000
20A22LEU00.0140.0373.307-0.835-0.4330.023-0.093-0.3320.000
21A23HIS0-0.068-0.0372.066-3.900-2.3933.054-1.400-3.1610.005
22A24THR0-0.0040.0122.387-2.253-0.2612.244-2.058-2.178-0.021
23A25GLU-1-0.933-0.9814.8793.2303.391-0.001-0.006-0.1540.000
24A26ARG10.8460.9166.558-2.109-2.1090.0000.0000.0000.000
25A27ALA0-0.0160.0177.111-0.210-0.2100.0000.0000.0000.000
26A28MET0-0.009-0.0189.239-0.042-0.0420.0000.0000.0000.000
27A29PHE0-0.005-0.0137.575-0.028-0.0280.0000.0000.0000.000
28A30SER00.010-0.01713.526-0.014-0.0140.0000.0000.0000.000
29A31GLU-1-0.916-0.95917.2850.3700.3700.0000.0000.0000.000
30A32CYS0-0.071-0.02714.9040.0040.0040.0000.0000.0000.000
31A33ASP-1-0.749-0.87916.8480.4000.4000.0000.0000.0000.000
32A34PHE00.003-0.01511.0700.0430.0430.0000.0000.0000.000
33A35SER00.015-0.00816.128-0.013-0.0130.0000.0000.0000.000
34A36GLY0-0.0190.00819.0010.0010.0010.0000.0000.0000.000
35A37VAL0-0.0290.01912.719-0.011-0.0110.0000.0000.0000.000
36A38ASN0-0.075-0.03614.683-0.019-0.0190.0000.0000.0000.000
37A39LEU00.013-0.0109.5370.1040.1040.0000.0000.0000.000
38A40ALA00.0250.01912.1190.0360.0360.0000.0000.0000.000
39A41GLU-1-0.941-0.97810.6470.0280.0280.0000.0000.0000.000
40A42SER0-0.092-0.0308.2460.0340.0340.0000.0000.0000.000
41A43GLN0-0.010-0.0166.679-0.155-0.1550.0000.0000.0000.000
42A44HIS10.8440.8956.855-1.097-1.0970.0000.0000.0000.000
43A45ARG10.9770.9977.821-1.634-1.6340.0000.0000.0000.000
44A46GLY00.0700.0149.2080.2730.2730.0000.0000.0000.000
45A47SER0-0.020-0.0239.3670.1320.1320.0000.0000.0000.000
46A48ALA0-0.022-0.02411.767-0.183-0.1830.0000.0000.0000.000
47A49PHE00.0210.02010.0140.0640.0640.0000.0000.0000.000
48A50ARG10.9360.97315.221-0.665-0.6650.0000.0000.0000.000
49A51ASN00.0190.00218.473-0.022-0.0220.0000.0000.0000.000
50A52CYS0-0.0530.02416.2310.0160.0160.0000.0000.0000.000
51A53THR00.0310.02018.662-0.028-0.0280.0000.0000.0000.000
52A54PHE0-0.027-0.01614.4070.0540.0540.0000.0000.0000.000
53A55GLU-1-0.887-0.96019.5420.2460.2460.0000.0000.0000.000
54A56ARG10.9210.94421.311-0.254-0.2540.0000.0000.0000.000
55A57THR00.028-0.00315.663-0.014-0.0140.0000.0000.0000.000
56A58THR0-0.081-0.03916.885-0.065-0.0650.0000.0000.0000.000
57A59LEU00.0870.04713.6220.0510.0510.0000.0000.0000.000
58A60TRP0-0.0390.04315.8440.0090.0090.0000.0000.0000.000
59A61HIS00.017-0.01615.418-0.007-0.0070.0000.0000.0000.000
60A62SER0-0.030-0.04812.500-0.010-0.0100.0000.0000.0000.000
61A63THR0-0.043-0.03611.230-0.143-0.1430.0000.0000.0000.000
62A64PHE0-0.022-0.00211.2210.2770.2770.0000.0000.0000.000
63A65ALA00.0320.01311.784-0.156-0.1560.0000.0000.0000.000
64A66GLN00.0210.01712.7380.2880.2880.0000.0000.0000.000
65A67CYS0-0.0860.01412.4130.2040.2040.0000.0000.0000.000
66A68SER0-0.007-0.00314.962-0.137-0.1370.0000.0000.0000.000
67A69MET00.0130.00814.8660.0750.0750.0000.0000.0000.000
68A70LEU0-0.026-0.01018.671-0.047-0.0470.0000.0000.0000.000
69A71GLY00.0480.01621.0330.0200.0200.0000.0000.0000.000
70A72SER0-0.034-0.00518.424-0.012-0.0120.0000.0000.0000.000
71A73VAL0-0.016-0.01020.978-0.031-0.0310.0000.0000.0000.000
72A74PHE0-0.009-0.00817.7660.0130.0130.0000.0000.0000.000
73A75VAL00.0470.03322.739-0.033-0.0330.0000.0000.0000.000
74A76ALA0-0.0090.00724.1460.0060.0060.0000.0000.0000.000
75A77CYS00.0100.04720.5860.0200.0200.0000.0000.0000.000
76A78ARG10.8630.92420.049-0.251-0.2510.0000.0000.0000.000
77A79LEU00.0100.00018.8440.0330.0330.0000.0000.0000.000
78A80ARG10.8370.91220.684-0.172-0.1720.0000.0000.0000.000
79A81PRO00.007-0.01619.492-0.019-0.0190.0000.0000.0000.000
80A82LEU00.0020.00816.0960.0240.0240.0000.0000.0000.000
81A83THR0-0.002-0.00115.860-0.055-0.0550.0000.0000.0000.000
82A84LEU0-0.019-0.00416.0620.0910.0910.0000.0000.0000.000
83A85ASP-1-0.890-0.94915.9150.4270.4270.0000.0000.0000.000
84A86ASP-1-0.870-0.94016.8620.5810.5810.0000.0000.0000.000
85A87VAL0-0.012-0.00816.5060.0800.0800.0000.0000.0000.000
86A88ASP-1-0.852-0.93718.8370.3590.3590.0000.0000.0000.000
87A89PHE00.006-0.02219.5060.0370.0370.0000.0000.0000.000
88A90THR00.000-0.01322.887-0.041-0.0410.0000.0000.0000.000
89A91LEU0-0.027-0.02724.2450.0290.0290.0000.0000.0000.000
90A92ALA0-0.0060.03922.719-0.002-0.0020.0000.0000.0000.000
91A93VAL00.003-0.01924.320-0.035-0.0350.0000.0000.0000.000
92A94LEU00.0340.01622.4950.0150.0150.0000.0000.0000.000
93A95GLY0-0.0060.01126.122-0.014-0.0140.0000.0000.0000.000
94A96GLY00.005-0.00328.4800.0090.0090.0000.0000.0000.000
95A97ASN0-0.094-0.05424.3600.0100.0100.0000.0000.0000.000
96A98ASP-1-0.782-0.90326.3370.1600.1600.0000.0000.0000.000
97A99LEU00.027-0.00223.9270.0150.0150.0000.0000.0000.000
98A100ARG10.8560.92526.127-0.145-0.1450.0000.0000.0000.000
99A101GLY0-0.0180.00826.882-0.001-0.0010.0000.0000.0000.000
100A102LEU0-0.0380.00021.939-0.004-0.0040.0000.0000.0000.000
101A103ASN00.0120.00823.018-0.001-0.0010.0000.0000.0000.000
102A104LEU00.025-0.00722.7380.0290.0290.0000.0000.0000.000
103A105THR00.003-0.02924.379-0.008-0.0080.0000.0000.0000.000
104A106GLY0-0.0320.00223.7150.0250.0250.0000.0000.0000.000
105A107CYS0-0.0410.01022.0830.0410.0410.0000.0000.0000.000
106A108ARG10.8960.95121.197-0.457-0.4570.0000.0000.0000.000
107A109LEU0-0.030-0.00924.9240.0250.0250.0000.0000.0000.000
108A110ARG10.9410.94727.450-0.263-0.2630.0000.0000.0000.000
109A111GLU-1-0.900-0.95828.6510.2360.2360.0000.0000.0000.000
110A112THR0-0.041-0.00526.2470.0040.0040.0000.0000.0000.000
111A113SER0-0.055-0.02128.392-0.026-0.0260.0000.0000.0000.000
112A114LEU00.011-0.02028.0010.0120.0120.0000.0000.0000.000
113A115VAL00.011-0.00230.857-0.012-0.0120.0000.0000.0000.000
114A116ASP-1-0.876-0.94232.3330.1570.1570.0000.0000.0000.000
115A117THR0-0.070-0.02428.4160.0000.0000.0000.0000.0000.000
116A118ASP-1-0.824-0.91730.1620.1350.1350.0000.0000.0000.000
117A119LEU00.034-0.00328.5180.0130.0130.0000.0000.0000.000
118A120ARG10.8800.93830.821-0.124-0.1240.0000.0000.0000.000
119A121LYS10.9050.94531.339-0.088-0.0880.0000.0000.0000.000
120A122CYS0-0.0610.01927.403-0.001-0.0010.0000.0000.0000.000
121A123VAL0-0.0210.00127.301-0.015-0.0150.0000.0000.0000.000
122A124LEU00.0350.01327.4710.0200.0200.0000.0000.0000.000
123A125ARG10.9130.95629.462-0.140-0.1400.0000.0000.0000.000
124A126GLY00.0230.00528.6720.0160.0160.0000.0000.0000.000
125A127ALA0-0.0300.01127.6280.0120.0120.0000.0000.0000.000
126A128ASP-1-0.791-0.85628.3760.2100.2100.0000.0000.0000.000
127A129LEU0-0.001-0.00529.5310.0160.0160.0000.0000.0000.000
128A130SER0-0.069-0.05831.939-0.013-0.0130.0000.0000.0000.000
129A131GLY00.039-0.00132.9480.0130.0130.0000.0000.0000.000
130A132ALA0-0.0240.01831.6870.0070.0070.0000.0000.0000.000
131A133ARG10.9160.95232.603-0.203-0.2030.0000.0000.0000.000
132A134THR00.042-0.00233.4040.0090.0090.0000.0000.0000.000
133A135THR00.0120.00735.610-0.007-0.0070.0000.0000.0000.000
134A136GLY00.0600.04236.3710.0060.0060.0000.0000.0000.000
135A137ALA0-0.0360.00434.0490.0010.0010.0000.0000.0000.000
136A138ARG10.9150.95534.114-0.134-0.1340.0000.0000.0000.000
137A139LEU00.0530.01532.7520.0080.0080.0000.0000.0000.000
138A140ASP-1-0.864-0.91235.4740.1110.1110.0000.0000.0000.000
139A141ASP-1-0.904-0.95835.9420.0980.0980.0000.0000.0000.000
140A142ALA0-0.049-0.01432.9130.0020.0020.0000.0000.0000.000
141A143ASP-1-0.810-0.90531.8870.1220.1220.0000.0000.0000.000
142A144LEU00.0500.00932.4350.0130.0130.0000.0000.0000.000
143A145ARG10.7950.89434.234-0.111-0.1110.0000.0000.0000.000
144A146GLY00.0380.01633.2810.0100.0100.0000.0000.0000.000
145A147ALA0-0.0350.01932.3280.0080.0080.0000.0000.0000.000
146A148THR00.0020.00332.918-0.014-0.0140.0000.0000.0000.000
147A149VAL0-0.010-0.01834.1340.0100.0100.0000.0000.0000.000
148A150ASP-1-0.792-0.88036.6520.1580.1580.0000.0000.0000.000
149A151PRO0-0.012-0.03239.286-0.003-0.0030.0000.0000.0000.000
150A152VAL00.007-0.00839.196-0.006-0.0060.0000.0000.0000.000
151A153LEU00.0590.06435.539-0.003-0.0030.0000.0000.0000.000
152A154TRP00.0200.00339.183-0.004-0.0040.0000.0000.0000.000
153A155ARG10.8310.91542.280-0.112-0.1120.0000.0000.0000.000
154A156THR0-0.046-0.03139.7920.0010.0010.0000.0000.0000.000
155A157ALA00.0230.03437.4680.0010.0010.0000.0000.0000.000
156A158SER0-0.061-0.04638.836-0.005-0.0050.0000.0000.0000.000
157A159LEU00.029-0.01338.4040.0050.0050.0000.0000.0000.000
158A160VAL00.0040.01240.660-0.004-0.0040.0000.0000.0000.000
159A161GLY00.0540.02640.5860.0010.0010.0000.0000.0000.000
160A162ALA0-0.040-0.01237.7650.0020.0020.0000.0000.0000.000
161A163ARG10.8630.92634.829-0.106-0.1060.0000.0000.0000.000
162A164VAL00.0360.01837.2790.0080.0080.0000.0000.0000.000
163A165ASP-1-0.819-0.90838.0610.1180.1180.0000.0000.0000.000
164A166VAL00.016-0.00940.581-0.001-0.0010.0000.0000.0000.000
165A167ASP-1-0.878-0.93441.1700.1060.1060.0000.0000.0000.000
166A168GLN0-0.024-0.03236.169-0.007-0.0070.0000.0000.0000.000
167A169ALA0-0.041-0.02141.864-0.002-0.0020.0000.0000.0000.000
168A170VAL00.0040.00144.909-0.003-0.0030.0000.0000.0000.000
169A171ALA00.0400.00943.236-0.002-0.0020.0000.0000.0000.000
170A172PHE00.0160.02443.9110.0000.0000.0000.0000.0000.000
171A173ALA00.0110.01045.781-0.002-0.0020.0000.0000.0000.000
172A174ALA00.0660.04847.580-0.002-0.0020.0000.0000.0000.000
173A175ALA0-0.089-0.03445.676-0.001-0.0010.0000.0000.0000.000
174A176HIS10.8070.85746.683-0.090-0.0900.0000.0000.0000.000
175A177GLY00.0140.00850.862-0.004-0.0040.0000.0000.0000.000
176A178LEU0-0.0140.01652.317-0.003-0.0030.0000.0000.0000.000
177A179CYS0-0.024-0.02052.9240.0030.0030.0000.0000.0000.000
178A180LEU0-0.0060.01350.751-0.002-0.0020.0000.0000.0000.000