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: GNG21

Calculation Name: 2WVN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2WVN

Chain ID: A

ChEMBL ID:

UniProt ID: Q03689

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2531509.598038
FMO2-HF: Nuclear repulsion 2447673.822758
FMO2-HF: Total energy -83835.77528
FMO2-MP2: Total energy -84081.337378


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:11:ALA)


Summations of interaction energy for fragment #1(A:11: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.
-10.705-9.2068.283-5.161-4.62-0.044
Interaction energy analysis for fragmet #1(A:11:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : 0.003
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].
3A13ASN0-0.026-0.0033.869-1.3150.431-0.009-0.984-0.7540.003
4A14VAL00.0470.0196.2750.0810.0810.0000.0000.0000.000
5A15ALA00.0460.0348.4740.1650.1650.0000.0000.0000.000
6A16GLY00.0290.0188.5860.1480.1480.0000.0000.0000.000
7A17LEU0-0.037-0.0133.8740.1050.3000.000-0.039-0.1560.000
8A18PHE00.0760.0288.0060.2600.2600.0000.0000.0000.000
9A19ASN00.005-0.00411.5780.1870.1870.0000.0000.0000.000
10A20ASN00.014-0.0049.0650.2420.2420.0000.0000.0000.000
11A21CYS0-0.0230.01910.6860.1270.1270.0000.0000.0000.000
12A22VAL0-0.002-0.00512.9650.0680.0680.0000.0000.0000.000
13A23ASP-1-0.753-0.88013.911-0.214-0.2140.0000.0000.0000.000
14A24CYS0-0.081-0.03912.4250.0540.0540.0000.0000.0000.000
15A25PHE0-0.020-0.02315.3300.0390.0390.0000.0000.0000.000
16A26GLU-1-0.834-0.89218.354-0.137-0.1370.0000.0000.0000.000
17A27TYR0-0.097-0.04316.2600.0280.0280.0000.0000.0000.000
18A28VAL0-0.048-0.00719.7270.0220.0220.0000.0000.0000.000
19A29GLN00.0230.00221.9420.0000.0000.0000.0000.0000.000
20A30LEU0-0.010-0.01125.6450.0070.0070.0000.0000.0000.000
21A31GLY00.0700.03328.564-0.002-0.0020.0000.0000.0000.000
22A32ARG10.9250.95530.830-0.009-0.0090.0000.0000.0000.000
23A33PRO0-0.016-0.01532.686-0.002-0.0020.0000.0000.0000.000
24A34PHE0-0.015-0.00928.583-0.001-0.0010.0000.0000.0000.000
25A35GLY0-0.012-0.00634.047-0.002-0.0020.0000.0000.0000.000
26A36ARG10.8240.87236.7650.0080.0080.0000.0000.0000.000
27A37ASP-1-0.829-0.88035.133-0.015-0.0150.0000.0000.0000.000
28A38TYR00.0590.03430.048-0.003-0.0030.0000.0000.0000.000
29A39GLU-1-0.771-0.87932.057-0.040-0.0400.0000.0000.0000.000
30A40ARG10.9340.96332.7560.0250.0250.0000.0000.0000.000
31A41CYS0-0.049-0.02529.618-0.002-0.0020.0000.0000.0000.000
32A42GLN0-0.022-0.01925.5130.0040.0040.0000.0000.0000.000
33A43LEU00.0240.01727.840-0.007-0.0070.0000.0000.0000.000
34A44ARG10.7600.83828.5350.0300.0300.0000.0000.0000.000
35A45LEU0-0.0140.00022.091-0.006-0.0060.0000.0000.0000.000
36A46ASP-1-0.727-0.84723.850-0.096-0.0960.0000.0000.0000.000
37A47ILE00.0150.00025.264-0.013-0.0130.0000.0000.0000.000
38A48ALA0-0.025-0.00722.581-0.010-0.0100.0000.0000.0000.000
39A49LYS10.7700.88120.0490.1370.1370.0000.0000.0000.000
40A50ALA00.0170.00721.392-0.025-0.0250.0000.0000.0000.000
41A51ARG10.7960.88123.3410.0870.0870.0000.0000.0000.000
42A52LEU00.0010.00715.734-0.014-0.0140.0000.0000.0000.000
43A53SER0-0.055-0.05319.062-0.031-0.0310.0000.0000.0000.000
44A54ARG10.7680.83720.3890.1100.1100.0000.0000.0000.000
45A55TRP00.0110.01114.503-0.026-0.0260.0000.0000.0000.000
46A56GLY00.015-0.00117.694-0.018-0.0180.0000.0000.0000.000
47A57GLU-1-0.851-0.90818.506-0.223-0.2230.0000.0000.0000.000
48A58ALA0-0.008-0.01221.8260.0000.0000.0000.0000.0000.000
49A59VAL0-0.060-0.02517.3520.0080.0080.0000.0000.0000.000
50A60LYS10.9310.96919.3930.2040.2040.0000.0000.0000.000
51A61ILE00.0040.02012.641-0.034-0.0340.0000.0000.0000.000
52A62ASN00.0150.01414.764-0.145-0.1450.0000.0000.0000.000
53A63ASP-1-0.878-0.94216.747-0.377-0.3770.0000.0000.0000.000
54A64ASP-1-0.769-0.85717.365-0.383-0.3830.0000.0000.0000.000
55A65PRO0-0.001-0.01415.249-0.079-0.0790.0000.0000.0000.000
56A66ARG10.7710.86013.6370.2430.2430.0000.0000.0000.000
57A67PHE00.0170.01211.474-0.062-0.0620.0000.0000.0000.000
58A68HIS0-0.041-0.03610.064-0.259-0.2590.0000.0000.0000.000
59A69SER0-0.045-0.0158.658-0.142-0.1420.0000.0000.0000.000
60A70ASP-1-0.830-0.9311.943-13.161-14.3208.186-3.848-3.179-0.049
61A71ALA00.0340.0224.9400.1860.252-0.001-0.002-0.0630.000
62A72PRO00.0190.0337.2670.1540.1540.0000.0000.0000.000
63A73THR00.018-0.01010.4120.1120.1120.0000.0000.0000.000
64A74ASP-1-0.793-0.87713.739-0.234-0.2340.0000.0000.0000.000
65A75LYS10.9760.97514.0900.0220.0220.0000.0000.0000.000
66A76SER00.0220.01415.5960.0160.0160.0000.0000.0000.000
67A77VAL0-0.023-0.00910.842-0.014-0.0140.0000.0000.0000.000
68A78GLN0-0.073-0.04710.910-0.013-0.0130.0000.0000.0000.000
69A79LEU0-0.007-0.00211.5080.0280.0280.0000.0000.0000.000
70A80ALA00.0160.01012.6520.0160.0160.0000.0000.0000.000
71A81LYS10.7930.9012.6113.4594.0510.108-0.285-0.4140.002
72A82SER00.0400.0218.8700.0610.0610.0000.0000.0000.000
73A83ILE0-0.0060.00010.5350.0500.0500.0000.0000.0000.000
74A84VAL0-0.016-0.0118.9650.0230.0230.0000.0000.0000.000
75A85GLU-1-0.891-0.9734.681-0.250-0.191-0.001-0.003-0.0540.000
76A86GLU-1-0.925-0.9658.9210.2100.2100.0000.0000.0000.000
77A87ILE00.0080.00812.5030.0240.0240.0000.0000.0000.000
78A88LEU0-0.007-0.0097.9240.0180.0180.0000.0000.0000.000
79A89LEU00.0260.0139.8530.0480.0480.0000.0000.0000.000
80A90LEU0-0.0460.01012.8280.0150.0150.0000.0000.0000.000
81A91PHE00.0430.00914.1090.0140.0140.0000.0000.0000.000
82A92GLU-1-0.852-0.90111.4920.4060.4060.0000.0000.0000.000
83A93SER0-0.058-0.05114.7250.0170.0170.0000.0000.0000.000
84A94ALA0-0.0110.01317.760-0.005-0.0050.0000.0000.0000.000
85A95GLN00.0140.01115.6930.0260.0260.0000.0000.0000.000
86A96LYS10.8090.87814.398-0.297-0.2970.0000.0000.0000.000
87A97THR0-0.063-0.04320.0340.0050.0050.0000.0000.0000.000
88A98SER00.005-0.00522.189-0.002-0.0020.0000.0000.0000.000
89A99LYS10.9740.98018.221-0.123-0.1230.0000.0000.0000.000
90A100ARG10.8170.91322.741-0.106-0.1060.0000.0000.0000.000
91A101TYR0-0.0220.01026.423-0.002-0.0020.0000.0000.0000.000
92A102GLU-1-0.807-0.90525.0760.0420.0420.0000.0000.0000.000
93A103LEU0-0.076-0.02626.963-0.001-0.0010.0000.0000.0000.000
94A104VAL0-0.063-0.03329.6260.0010.0010.0000.0000.0000.000
95A105ALA0-0.0150.00632.159-0.004-0.0040.0000.0000.0000.000
96A106ASP-1-0.793-0.88333.9420.0220.0220.0000.0000.0000.000
97A107GLN00.020-0.00934.744-0.004-0.0040.0000.0000.0000.000
98A108GLN0-0.116-0.06935.391-0.005-0.0050.0000.0000.0000.000
99A109ASP-1-0.855-0.94133.7860.0120.0120.0000.0000.0000.000
100A110LEU0-0.029-0.01029.980-0.001-0.0010.0000.0000.0000.000
101A111VAL0-0.047-0.00731.152-0.003-0.0030.0000.0000.0000.000
102A112VAL00.003-0.00127.9150.0010.0010.0000.0000.0000.000
103A113PHE0-0.099-0.03131.2620.0000.0000.0000.0000.0000.000
104A114GLU-1-0.866-0.94329.023-0.045-0.0450.0000.0000.0000.000
105A115ASP-1-0.704-0.82631.154-0.058-0.0580.0000.0000.0000.000
106A116LYS10.8360.91932.9600.0260.0260.0000.0000.0000.000
107A117ASP-1-0.824-0.90335.301-0.023-0.0230.0000.0000.0000.000
108A118MET0-0.0640.00331.2890.0020.0020.0000.0000.0000.000
109A119LYS10.8680.91337.2510.0320.0320.0000.0000.0000.000
110A120PRO0-0.025-0.02838.654-0.003-0.0030.0000.0000.0000.000
111A121ILE00.0310.02638.763-0.003-0.0030.0000.0000.0000.000
112A122GLY00.0620.03636.219-0.003-0.0030.0000.0000.0000.000
113A123ARG10.8200.88834.3760.0410.0410.0000.0000.0000.000
114A124ALA0-0.014-0.00633.977-0.005-0.0050.0000.0000.0000.000
115A125LEU00.0060.00733.599-0.006-0.0060.0000.0000.0000.000
116A126HIS0-0.051-0.04527.364-0.006-0.0060.0000.0000.0000.000
117A127ARG10.8180.88329.2940.0610.0610.0000.0000.0000.000
118A128ARG10.8850.94829.6220.0770.0770.0000.0000.0000.000
119A129LEU00.025-0.00127.734-0.009-0.0090.0000.0000.0000.000
120A130ASN00.006-0.00624.649-0.025-0.0250.0000.0000.0000.000
121A131ASP-1-0.907-0.94225.337-0.128-0.1280.0000.0000.0000.000
122A132LEU0-0.053-0.01526.228-0.014-0.0140.0000.0000.0000.000
123A133VAL0-0.008-0.00921.595-0.017-0.0170.0000.0000.0000.000
124A134SER0-0.023-0.02921.931-0.028-0.0280.0000.0000.0000.000
125A135ARG10.8970.95222.8440.1430.1430.0000.0000.0000.000
126A136ARG10.7190.82321.1460.1800.1800.0000.0000.0000.000
127A137GLN0-0.050-0.02916.207-0.068-0.0680.0000.0000.0000.000
128A138LYS10.8110.90117.9220.4240.4240.0000.0000.0000.000
129A139GLN0-0.033-0.01211.022-0.034-0.0340.0000.0000.0000.000
130A140THR00.0760.03116.3890.0130.0130.0000.0000.0000.000
131A141SER0-0.058-0.01312.0780.0290.0290.0000.0000.0000.000
132A142LEU00.0100.01511.487-0.145-0.1450.0000.0000.0000.000
133A143ALA0-0.018-0.0088.6840.0500.0500.0000.0000.0000.000
134A144LYS10.9550.97310.8440.0840.0840.0000.0000.0000.000
135A145LYS10.7870.88111.2160.3230.3230.0000.0000.0000.000
136A146THR0-0.050-0.03914.9700.0060.0060.0000.0000.0000.000
137A147ALA00.0150.01518.4260.0020.0020.0000.0000.0000.000
138A148TRP0-0.032-0.00918.2260.0290.0290.0000.0000.0000.000
139A149ALA00.0640.04422.242-0.011-0.0110.0000.0000.0000.000
140A150LEU00.0060.01822.9830.0140.0140.0000.0000.0000.000
141A151TYR0-0.034-0.06526.019-0.006-0.0060.0000.0000.0000.000
142A152ASP-1-0.775-0.87428.7720.0280.0280.0000.0000.0000.000
143A153GLY00.0520.03228.789-0.002-0.0020.0000.0000.0000.000
144A154LYS10.8820.93329.569-0.022-0.0220.0000.0000.0000.000
145A155SER0-0.036-0.03824.9200.0030.0030.0000.0000.0000.000
146A156LEU0-0.0170.01024.528-0.001-0.0010.0000.0000.0000.000
147A157GLU-1-0.789-0.87925.388-0.030-0.0300.0000.0000.0000.000
148A158LYS10.9090.97522.034-0.075-0.0750.0000.0000.0000.000
149A159ILE0-0.005-0.00419.9420.0000.0000.0000.0000.0000.000
150A160VAL00.0250.00921.816-0.012-0.0120.0000.0000.0000.000
151A161ASP-1-0.828-0.88624.018-0.028-0.0280.0000.0000.0000.000
152A162GLN0-0.003-0.01119.6880.0040.0040.0000.0000.0000.000
153A163VAL00.0030.01118.351-0.009-0.0090.0000.0000.0000.000
154A164ALA00.0010.01320.294-0.017-0.0170.0000.0000.0000.000
155A165ARG10.7350.82222.1120.0300.0300.0000.0000.0000.000
156A166PHE00.0160.00117.002-0.009-0.0090.0000.0000.0000.000
157A167VAL00.004-0.00618.729-0.024-0.0240.0000.0000.0000.000
158A168ASP-1-0.792-0.87220.195-0.077-0.0770.0000.0000.0000.000
159A169GLU-1-1.005-1.02618.548-0.042-0.0420.0000.0000.0000.000
160A170LEU00.0050.00714.564-0.011-0.0110.0000.0000.0000.000
161A171GLU-1-0.803-0.89518.548-0.154-0.1540.0000.0000.0000.000
162A172LYS10.9090.96721.9360.0660.0660.0000.0000.0000.000
163A173ALA0-0.0410.00618.2900.0080.0080.0000.0000.0000.000
164A174PHE0-0.032-0.02715.869-0.030-0.0300.0000.0000.0000.000
165A175PRO00.0100.02021.9370.0100.0100.0000.0000.0000.000
166A176ILE0-0.008-0.01321.376-0.008-0.0080.0000.0000.0000.000
167A177GLU-1-0.813-0.90825.635-0.116-0.1160.0000.0000.0000.000
168A178ALA0-0.012-0.00827.6130.0040.0040.0000.0000.0000.000
169A179VAL0-0.038-0.01226.5290.0030.0030.0000.0000.0000.000
170A180CYS0-0.031-0.02824.531-0.006-0.0060.0000.0000.0000.000
171A181HIS00.0240.01127.2070.0010.0010.0000.0000.0000.000
172A182LYS10.8400.92130.9130.1030.1030.0000.0000.0000.000
173A183LEU0-0.008-0.02025.5930.0020.0020.0000.0000.0000.000
174A184ALA00.0070.00729.4550.0010.0010.0000.0000.0000.000
175A185GLU-1-0.829-0.90730.529-0.081-0.0810.0000.0000.0000.000
176A186ILE0-0.0190.00031.3940.0030.0030.0000.0000.0000.000
177A187GLU-1-0.809-0.87727.058-0.144-0.1440.0000.0000.0000.000
178A188ILE0-0.023-0.01931.5540.0050.0050.0000.0000.0000.000
179A189GLU-1-0.935-0.96535.120-0.094-0.0940.0000.0000.0000.000
180A190GLU-1-0.887-0.91535.575-0.093-0.0930.0000.0000.0000.000
181A191VAL0-0.059-0.03436.5210.0030.0030.0000.0000.0000.000
182A192GLU-1-0.812-0.90139.137-0.065-0.0650.0000.0000.0000.000
183A193ASP-1-0.852-0.90341.947-0.049-0.0490.0000.0000.0000.000
184A194GLU-1-0.835-0.93842.403-0.039-0.0390.0000.0000.0000.000
185A195ALA0-0.0420.00142.9550.0000.0000.0000.0000.0000.000
186A196SER0-0.017-0.03838.5740.0000.0000.0000.0000.0000.000
187A197LEU00.0230.02438.110-0.002-0.0020.0000.0000.0000.000
188A198THR0-0.002-0.01338.4850.0000.0000.0000.0000.0000.000
189A199ILE0-0.064-0.03435.8490.0010.0010.0000.0000.0000.000
190A200LEU00.0150.00032.6660.0000.0000.0000.0000.0000.000
191A201LYS10.8910.94234.1760.0380.0380.0000.0000.0000.000
192A202ASP-1-0.829-0.90135.499-0.037-0.0370.0000.0000.0000.000
193A203ALA0-0.059-0.02132.2400.0040.0040.0000.0000.0000.000
194A204ALA00.0560.02330.7090.0010.0010.0000.0000.0000.000
195A205GLY00.0410.02231.273-0.001-0.0010.0000.0000.0000.000
196A206GLY0-0.031-0.01031.5220.0030.0030.0000.0000.0000.000
197A207ILE0-0.050-0.01926.8110.0020.0020.0000.0000.0000.000
198A208ASP-1-0.745-0.86226.591-0.116-0.1160.0000.0000.0000.000
199A209ALA00.0150.01328.6480.0030.0030.0000.0000.0000.000
200A210ALA00.0690.04629.3200.0030.0030.0000.0000.0000.000
201A211MET00.0120.00928.6930.0040.0040.0000.0000.0000.000
202A212SER0-0.053-0.03831.9010.0050.0050.0000.0000.0000.000
203A213ASP-1-0.890-0.94934.303-0.060-0.0600.0000.0000.0000.000
204A214ALA0-0.018-0.00534.3050.0030.0030.0000.0000.0000.000
205A215ALA0-0.017-0.01135.9910.0020.0020.0000.0000.0000.000
206A216ALA0-0.028-0.01437.7920.0030.0030.0000.0000.0000.000
207A217GLN0-0.017-0.01837.6030.0050.0050.0000.0000.0000.000
208A218LYS10.7790.88339.7710.0710.0710.0000.0000.0000.000
209A219ILE0-0.007-0.00941.8120.0020.0020.0000.0000.0000.000
210A220ASP-1-0.897-0.94644.057-0.040-0.0400.0000.0000.0000.000
211A221ALA0-0.085-0.03644.5790.0020.0020.0000.0000.0000.000
212A222ILE0-0.068-0.02345.7220.0000.0000.0000.0000.0000.000
213A223VAL0-0.111-0.04948.1170.0040.0040.0000.0000.0000.000