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: 43ZVN

Calculation Name: 2W1T-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2W1T

Chain ID: A

ChEMBL ID:

UniProt ID: P37554

Base Structure: X-ray

Registration Date: 2023-06-20

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1708651.961319
FMO2-HF: Nuclear repulsion 1640386.371616
FMO2-HF: Total energy -68265.589703
FMO2-MP2: Total energy -68463.58018


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:ALA)


Summations of interaction energy for fragment #1(A:3:ALA)
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.
-0.3681.6810.009-0.992-1.0640.003
Interaction energy analysis for fragmet #1(A:3:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.002
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].
3A5GLY00.0290.0213.185-1.5460.3860.010-0.984-0.9570.003
4A6ILE0-0.055-0.0255.2140.1560.273-0.001-0.008-0.1070.000
5A7VAL00.0280.0207.6870.2090.2090.0000.0000.0000.000
6A8ARG10.8600.9399.432-0.290-0.2900.0000.0000.0000.000
7A9ARG10.9370.96312.416-0.072-0.0720.0000.0000.0000.000
8A10ILE00.0350.03815.4020.0190.0190.0000.0000.0000.000
9A11ASP-1-0.829-0.89917.4130.1470.1470.0000.0000.0000.000
10A12ASP-1-0.810-0.89021.0630.1130.1130.0000.0000.0000.000
11A13LEU0-0.044-0.04224.1620.0070.0070.0000.0000.0000.000
12A14GLY0-0.0090.01020.9790.0050.0050.0000.0000.0000.000
13A15ARG10.7760.86519.811-0.121-0.1210.0000.0000.0000.000
14A16VAL00.0530.00713.345-0.007-0.0070.0000.0000.0000.000
15A17VAL0-0.035-0.01215.0450.0210.0210.0000.0000.0000.000
16A18ILE00.0710.03512.2020.0370.0370.0000.0000.0000.000
17A19PRO0-0.028-0.0069.799-0.084-0.0840.0000.0000.0000.000
18A20LYS10.9560.97813.040-0.145-0.1450.0000.0000.0000.000
19A21GLU-1-0.804-0.93211.1850.3130.3130.0000.0000.0000.000
20A22ILE00.0370.0177.6860.0280.0280.0000.0000.0000.000
21A23ARG10.9440.96511.623-0.358-0.3580.0000.0000.0000.000
22A24ARG10.8400.93514.748-0.345-0.3450.0000.0000.0000.000
23A25THR00.0180.0069.985-0.037-0.0370.0000.0000.0000.000
24A26LEU0-0.0100.00210.4710.0210.0210.0000.0000.0000.000
25A27ARG10.7730.86714.232-0.269-0.2690.0000.0000.0000.000
26A28ILE0-0.0030.02014.305-0.014-0.0140.0000.0000.0000.000
27A29ARG10.7390.83218.363-0.226-0.2260.0000.0000.0000.000
28A30GLU-1-0.975-0.99521.5780.1840.1840.0000.0000.0000.000
29A31GLY00.0280.01223.568-0.012-0.0120.0000.0000.0000.000
30A32ASP-1-0.761-0.87121.0740.2610.2610.0000.0000.0000.000
31A33PRO0-0.0060.01621.6180.0210.0210.0000.0000.0000.000
32A34LEU0-0.032-0.02716.1540.0340.0340.0000.0000.0000.000
33A35GLU-1-0.835-0.91118.4570.2380.2380.0000.0000.0000.000
34A36ILE0-0.028-0.02816.8040.0610.0610.0000.0000.0000.000
35A37PHE0-0.018-0.00415.847-0.046-0.0460.0000.0000.0000.000
36A38VAL0-0.025-0.01315.8080.0350.0350.0000.0000.0000.000
37A39ASP-1-0.847-0.90813.1750.2180.2180.0000.0000.0000.000
38A40ARG10.8690.90715.201-0.141-0.1410.0000.0000.0000.000
39A41ASP-1-0.936-0.96612.4960.0160.0160.0000.0000.0000.000
40A42GLY0-0.065-0.02714.498-0.009-0.0090.0000.0000.0000.000
41A43ASP-1-0.919-0.9568.8660.6550.6550.0000.0000.0000.000
42A44VAL0-0.030-0.01511.390-0.043-0.0430.0000.0000.0000.000
43A45ILE0-0.0050.00910.2790.1460.1460.0000.0000.0000.000
44A46LEU0-0.018-0.01611.885-0.096-0.0960.0000.0000.0000.000
45A47LYS10.8660.93312.663-0.200-0.2000.0000.0000.0000.000
46A48LYS10.7620.85315.222-0.365-0.3650.0000.0000.0000.000
47A49TYR0-0.091-0.06018.092-0.006-0.0060.0000.0000.0000.000
48A50SER0-0.022-0.04821.311-0.012-0.0120.0000.0000.0000.000
49A51PRO00.0670.03623.672-0.009-0.0090.0000.0000.0000.000
50A52ILE00.0340.00527.039-0.010-0.0100.0000.0000.0000.000
51A53SER0-0.056-0.03824.129-0.005-0.0050.0000.0000.0000.000
52A54GLU-1-0.890-0.92224.3030.1810.1810.0000.0000.0000.000
53A55LEU0-0.026-0.00426.851-0.011-0.0110.0000.0000.0000.000
54A56GLY00.0320.00429.205-0.010-0.0100.0000.0000.0000.000
55A57ASP-1-0.901-0.95530.3210.0860.0860.0000.0000.0000.000
56A58PHE0-0.033-0.00733.780-0.007-0.0070.0000.0000.0000.000
57A59ALA0-0.0070.00332.416-0.005-0.0050.0000.0000.0000.000
58A60LYS10.8240.90933.869-0.069-0.0690.0000.0000.0000.000
59A61GLU-1-0.871-0.95435.3250.0630.0630.0000.0000.0000.000
60A62TYR0-0.028-0.01338.077-0.004-0.0040.0000.0000.0000.000
61A63ALA00.002-0.00636.605-0.003-0.0030.0000.0000.0000.000
62A64ASP-1-0.803-0.88438.7090.0580.0580.0000.0000.0000.000
63A65ALA00.0180.01541.107-0.003-0.0030.0000.0000.0000.000
64A66LEU0-0.039-0.02440.210-0.003-0.0030.0000.0000.0000.000
65A67TYR0-0.0260.00642.295-0.003-0.0030.0000.0000.0000.000
66A68ASP-1-0.901-0.95744.1340.0430.0430.0000.0000.0000.000
67A69SER0-0.102-0.04646.708-0.002-0.0020.0000.0000.0000.000
68A70LEU0-0.055-0.03245.423-0.001-0.0010.0000.0000.0000.000
69A71GLY0-0.0240.00747.414-0.001-0.0010.0000.0000.0000.000
70A72HIS0-0.029-0.03044.3880.0000.0000.0000.0000.0000.000
71A73SER0-0.043-0.00539.6570.0010.0010.0000.0000.0000.000
72A74VAL00.0150.00538.2700.0010.0010.0000.0000.0000.000
73A75LEU0-0.052-0.02033.4170.0010.0010.0000.0000.0000.000
74A76ILE00.0060.00732.194-0.002-0.0020.0000.0000.0000.000
75A77CYS0-0.066-0.01928.546-0.001-0.0010.0000.0000.0000.000
76A78ASP-1-0.686-0.79424.1360.1970.1970.0000.0000.0000.000
77A79ARG10.8020.85524.072-0.171-0.1710.0000.0000.0000.000
78A80ASP-1-0.800-0.87621.4890.2660.2660.0000.0000.0000.000
79A81VAL0-0.001-0.00822.480-0.007-0.0070.0000.0000.0000.000
80A82TYR0-0.013-0.03325.348-0.004-0.0040.0000.0000.0000.000
81A83ILE0-0.0040.00026.3980.0010.0010.0000.0000.0000.000
82A84ALA00.0010.00828.872-0.005-0.0050.0000.0000.0000.000
83A85VAL0-0.029-0.01032.0620.0010.0010.0000.0000.0000.000
84A86SER0-0.019-0.03334.884-0.002-0.0020.0000.0000.0000.000
85A87GLY00.0820.06038.6260.0010.0010.0000.0000.0000.000
86A88SER0-0.030-0.03137.414-0.003-0.0030.0000.0000.0000.000
87A89SER0-0.085-0.06635.9890.0020.0020.0000.0000.0000.000
88A90LYS10.9640.95333.049-0.063-0.0630.0000.0000.0000.000
89A91LYS10.8550.91331.201-0.043-0.0430.0000.0000.0000.000
90A92ASP-1-0.792-0.86230.8220.0560.0560.0000.0000.0000.000
91A93TYR00.007-0.02530.7320.0010.0010.0000.0000.0000.000
92A94LEU0-0.020-0.00328.3580.0070.0070.0000.0000.0000.000
93A95ASN0-0.029-0.02023.8080.0050.0050.0000.0000.0000.000
94A96LYS10.7860.91423.793-0.069-0.0690.0000.0000.0000.000
95A97SER00.012-0.00422.1500.0010.0010.0000.0000.0000.000
96A98ILE00.0120.01224.692-0.016-0.0160.0000.0000.0000.000
97A99SER0-0.018-0.03326.7970.0090.0090.0000.0000.0000.000
98A100GLU-1-0.893-0.95828.2050.1010.1010.0000.0000.0000.000
99A101MET0-0.0590.00329.8360.0010.0010.0000.0000.0000.000
100A102LEU00.0710.03330.471-0.002-0.0020.0000.0000.0000.000
101A103GLU-1-0.769-0.85525.0370.1810.1810.0000.0000.0000.000
102A104ARG10.9320.96729.563-0.083-0.0830.0000.0000.0000.000
103A105THR0-0.025-0.02232.373-0.005-0.0050.0000.0000.0000.000
104A106MET0-0.040-0.01128.731-0.002-0.0020.0000.0000.0000.000
105A107ASP-1-0.780-0.86428.9780.1390.1390.0000.0000.0000.000
106A108GLN0-0.052-0.03832.360-0.002-0.0020.0000.0000.0000.000
107A109ARG10.7920.90930.953-0.123-0.1230.0000.0000.0000.000
108A110SER0-0.074-0.03736.628-0.002-0.0020.0000.0000.0000.000
109A111SER0-0.044-0.03638.9340.0030.0030.0000.0000.0000.000
110A112VAL0-0.0160.00239.475-0.002-0.0020.0000.0000.0000.000
111A113LEU0-0.026-0.01242.2360.0010.0010.0000.0000.0000.000
112A114GLU-1-0.859-0.91241.9370.0510.0510.0000.0000.0000.000
113A115SER0-0.029-0.03244.715-0.001-0.0010.0000.0000.0000.000
114A116ASP-1-0.865-0.92847.0350.0340.0340.0000.0000.0000.000
115A117ALA0-0.068-0.03444.4020.0020.0020.0000.0000.0000.000
116A118LYS10.8110.89843.285-0.033-0.0330.0000.0000.0000.000
117A119SER0-0.043-0.00939.516-0.002-0.0020.0000.0000.0000.000
118A120VAL00.0090.00336.6890.0010.0010.0000.0000.0000.000
119A121GLN00.0060.00531.0890.0070.0070.0000.0000.0000.000
120A122LEU00.0120.04433.3650.0040.0040.0000.0000.0000.000
121A123VAL00.0110.01527.8780.0100.0100.0000.0000.0000.000
122A124ASN0-0.014-0.02424.555-0.011-0.0110.0000.0000.0000.000
123A125GLY0-0.025-0.00527.5920.0000.0000.0000.0000.0000.000
124A126ILE0-0.067-0.03029.296-0.008-0.0080.0000.0000.0000.000
125A127ASP-1-0.854-0.91732.0290.0600.0600.0000.0000.0000.000
126A128GLU-1-0.798-0.87935.0180.0620.0620.0000.0000.0000.000
127A129ASP-1-0.838-0.91138.0250.0360.0360.0000.0000.0000.000
128A130MET00.0070.00438.4450.0020.0020.0000.0000.0000.000
129A131ASN0-0.059-0.01143.104-0.001-0.0010.0000.0000.0000.000
130A132SER00.0450.02944.8580.0000.0000.0000.0000.0000.000
131A133TYR00.012-0.02338.5230.0030.0030.0000.0000.0000.000
132A134THR0-0.051-0.03541.527-0.001-0.0010.0000.0000.0000.000
133A135VAL00.023-0.00235.8070.0030.0030.0000.0000.0000.000
134A136GLY00.0470.01438.055-0.004-0.0040.0000.0000.0000.000
135A137PRO0-0.014-0.00634.3380.0040.0040.0000.0000.0000.000
136A138ILE0-0.0250.00232.604-0.005-0.0050.0000.0000.0000.000
137A139VAL0-0.055-0.03232.9410.0080.0080.0000.0000.0000.000
138A140ALA00.0360.02432.562-0.007-0.0070.0000.0000.0000.000
139A141ASN0-0.096-0.06432.2400.0040.0040.0000.0000.0000.000
140A142GLY0-0.0050.00834.1530.0000.0000.0000.0000.0000.000
141A143ASP-1-0.839-0.94128.3760.1550.1550.0000.0000.0000.000
142A144PRO0-0.0300.00230.470-0.002-0.0020.0000.0000.0000.000
143A145ILE00.0120.00927.6940.0110.0110.0000.0000.0000.000
144A146GLY00.028-0.00428.1900.0090.0090.0000.0000.0000.000
145A147ALA0-0.033-0.01230.287-0.006-0.0060.0000.0000.0000.000
146A148VAL00.0190.01833.4000.0020.0020.0000.0000.0000.000
147A149VAL0-0.016-0.01334.929-0.002-0.0020.0000.0000.0000.000
148A150ILE00.0070.00737.747-0.001-0.0010.0000.0000.0000.000
149A151PHE00.045-0.00737.1730.0000.0000.0000.0000.0000.000
150A152SER00.0600.04141.998-0.002-0.0020.0000.0000.0000.000
151A153LYS10.8110.87438.651-0.051-0.0510.0000.0000.0000.000
152A154ASP-1-0.892-0.93644.9450.0360.0360.0000.0000.0000.000
153A155GLN0-0.060-0.03948.187-0.002-0.0020.0000.0000.0000.000
154A156THR0-0.024-0.01348.0700.0010.0010.0000.0000.0000.000
155A157MET0-0.0460.00144.6820.0000.0000.0000.0000.0000.000
156A158GLY00.0480.00948.173-0.002-0.0020.0000.0000.0000.000
157A159GLU-1-0.785-0.89348.8080.0490.0490.0000.0000.0000.000
158A160VAL0-0.0090.01249.5150.0020.0020.0000.0000.0000.000
159A161GLU-1-0.740-0.87245.3670.0460.0460.0000.0000.0000.000
160A162HIS10.8030.89244.012-0.052-0.0520.0000.0000.0000.000
161A163LYS10.8230.87744.806-0.048-0.0480.0000.0000.0000.000
162A164ALA00.0010.03245.1180.0020.0020.0000.0000.0000.000
163A165VAL00.0130.00340.1730.0030.0030.0000.0000.0000.000
164A166GLU-1-0.781-0.85940.6940.0620.0620.0000.0000.0000.000
165A167THR0-0.066-0.04442.2800.0020.0020.0000.0000.0000.000
166A168ALA0-0.0160.00139.5260.0020.0020.0000.0000.0000.000
167A169ALA00.0000.00537.5200.0040.0040.0000.0000.0000.000
168A170GLY00.0060.00038.1200.0040.0040.0000.0000.0000.000
169A171PHE0-0.023-0.01039.0860.0010.0010.0000.0000.0000.000
170A172LEU00.031-0.00135.0390.0020.0020.0000.0000.0000.000
171A173ALA00.0180.00934.8670.0060.0060.0000.0000.0000.000
172A174ARG10.9090.94535.309-0.069-0.0690.0000.0000.0000.000
173A175GLN0-0.092-0.04134.886-0.002-0.0020.0000.0000.0000.000
174A176MET0-0.0410.00129.4720.0020.0020.0000.0000.0000.000
175A177GLU-1-0.886-0.92932.7770.0970.0970.0000.0000.0000.000