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: GN9V1

Calculation Name: 3WVZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3WVZ

Chain ID: A

ChEMBL ID:

UniProt ID: Q53FT3

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 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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1859734.613929
FMO2-HF: Nuclear repulsion 1782635.072405
FMO2-HF: Total energy -77099.541524
FMO2-MP2: Total energy -77320.856757


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.
-9.947-4.50.653-2.993-3.1090.003
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 : 0.013 / q_NPA : 0.001
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].
3A-1GLY0-0.0120.0022.755-5.220-2.0620.249-1.775-1.6330.010
4A0SER00.0090.0014.3770.1980.287-0.001-0.019-0.0700.000
5A1MET00.0100.0217.440-0.362-0.3620.0000.0000.0000.000
6A2PHE0-0.003-0.0118.593-0.287-0.2870.0000.0000.0000.000
7A3GLY00.0270.01112.3760.0520.0520.0000.0000.0000.000
8A4CYS0-0.059-0.02015.705-0.041-0.0410.0000.0000.0000.000
9A5LEU00.0130.00518.469-0.009-0.0090.0000.0000.0000.000
10A6VAL00.0660.04222.128-0.010-0.0100.0000.0000.0000.000
11A7ALA00.003-0.00625.320-0.004-0.0040.0000.0000.0000.000
12A8GLY00.0190.00728.482-0.004-0.0040.0000.0000.0000.000
13A9ARG10.8110.89925.567-0.175-0.1750.0000.0000.0000.000
14A10LEU00.0150.00522.982-0.003-0.0030.0000.0000.0000.000
15A11VAL0-0.026-0.01418.2980.0110.0110.0000.0000.0000.000
16A12GLN0-0.015-0.00617.1300.0380.0380.0000.0000.0000.000
17A13THR00.016-0.01613.5090.0070.0070.0000.0000.0000.000
18A14ALA0-0.025-0.00611.8190.1350.1350.0000.0000.0000.000
19A15ALA0-0.0100.01310.823-0.086-0.0860.0000.0000.0000.000
20A16GLN00.0250.00410.6980.1570.1570.0000.0000.0000.000
21A17GLN0-0.017-0.0163.906-1.356-1.0820.002-0.137-0.1390.001
22A18VAL0-0.038-0.0158.854-0.134-0.1340.0000.0000.0000.000
23A19ALA00.0190.0078.121-0.236-0.2360.0000.0000.0000.000
24A20GLU-1-0.962-0.9732.711-2.477-1.2250.376-0.663-0.965-0.005
25A21ASP-1-0.842-0.9123.4210.3671.0410.027-0.399-0.302-0.003
26A22LYS10.8170.9046.074-0.565-0.5650.0000.0000.0000.000
27A23PHE0-0.010-0.0095.1710.0570.0570.0000.0000.0000.000
28A24VAL00.0110.00210.364-0.184-0.1840.0000.0000.0000.000
29A25PHE0-0.020-0.01113.6960.0610.0610.0000.0000.0000.000
30A26ASP-1-0.779-0.88116.6130.2810.2810.0000.0000.0000.000
31A27LEU0-0.080-0.04719.849-0.003-0.0030.0000.0000.0000.000
32A28PRO00.0370.01222.802-0.018-0.0180.0000.0000.0000.000
33A29ASP-1-0.861-0.91025.9280.1450.1450.0000.0000.0000.000
34A30TYR00.0590.01326.853-0.003-0.0030.0000.0000.0000.000
35A31GLU-1-0.874-0.94828.5270.1240.1240.0000.0000.0000.000
36A32SER0-0.116-0.05131.273-0.008-0.0080.0000.0000.0000.000
37A33ILE0-0.020-0.00426.0390.0050.0050.0000.0000.0000.000
38A34ASN00.0140.02429.913-0.006-0.0060.0000.0000.0000.000
39A35HIS0-0.004-0.01227.7680.0000.0000.0000.0000.0000.000
40A36VAL00.0080.00821.4540.0050.0050.0000.0000.0000.000
41A37VAL0-0.035-0.01121.702-0.011-0.0110.0000.0000.0000.000
42A38VAL00.0280.01616.2370.0260.0260.0000.0000.0000.000
43A39PHE0-0.007-0.02416.986-0.036-0.0360.0000.0000.0000.000
44A40MET0-0.0110.01812.0830.0510.0510.0000.0000.0000.000
45A41LEU0-0.047-0.02511.598-0.064-0.0640.0000.0000.0000.000
46A42GLY0-0.018-0.00213.964-0.046-0.0460.0000.0000.0000.000
47A43THR0-0.038-0.0169.864-0.070-0.0700.0000.0000.0000.000
48A44ILE00.0130.0056.680-0.122-0.1220.0000.0000.0000.000
49A45PRO0-0.026-0.01110.5770.1000.1000.0000.0000.0000.000
50A46PHE00.014-0.0089.767-0.027-0.0270.0000.0000.0000.000
51A47PRO00.0290.0037.089-0.039-0.0390.0000.0000.0000.000
52A48GLU-1-0.925-0.9709.935-0.082-0.0820.0000.0000.0000.000
53A49GLY00.0310.01912.900-0.010-0.0100.0000.0000.0000.000
54A50MET0-0.052-0.0158.9990.0240.0240.0000.0000.0000.000
55A51GLY00.007-0.01312.905-0.007-0.0070.0000.0000.0000.000
56A52GLY00.0210.01412.2720.0410.0410.0000.0000.0000.000
57A53SER0-0.015-0.02013.522-0.040-0.0400.0000.0000.0000.000
58A54VAL0-0.030-0.01415.0580.0540.0540.0000.0000.0000.000
59A55TYR0-0.031-0.03815.614-0.054-0.0540.0000.0000.0000.000
60A56PHE00.0240.00619.0130.0280.0280.0000.0000.0000.000
61A57SER00.0390.03620.967-0.020-0.0200.0000.0000.0000.000
62A58TYR0-0.026-0.05123.0120.0080.0080.0000.0000.0000.000
63A59PRO0-0.030-0.00726.531-0.002-0.0020.0000.0000.0000.000
64A60ASP-1-0.840-0.93729.4470.0890.0890.0000.0000.0000.000
65A61SER0-0.013-0.02531.910-0.004-0.0040.0000.0000.0000.000
66A62ASN0-0.112-0.03530.2200.0010.0010.0000.0000.0000.000
67A63GLY00.0360.01427.3130.0050.0050.0000.0000.0000.000
68A64MET0-0.032-0.06123.662-0.003-0.0030.0000.0000.0000.000
69A65PRO00.0060.01420.1330.0200.0200.0000.0000.0000.000
70A66VAL0-0.0120.03622.023-0.009-0.0090.0000.0000.0000.000
71A67TRP00.0650.00517.7300.0210.0210.0000.0000.0000.000
72A68GLN00.0320.02822.030-0.019-0.0190.0000.0000.0000.000
73A69LEU0-0.013-0.00319.4560.0200.0200.0000.0000.0000.000
74A70LEU0-0.022-0.01521.181-0.019-0.0190.0000.0000.0000.000
75A71GLY00.004-0.00920.919-0.020-0.0200.0000.0000.0000.000
76A72PHE00.0120.01418.1360.0170.0170.0000.0000.0000.000
77A73VAL0-0.041-0.00314.611-0.012-0.0120.0000.0000.0000.000
78A74THR00.0420.01115.6800.0050.0050.0000.0000.0000.000
79A75ASN00.0870.03013.4920.0410.0410.0000.0000.0000.000
80A76GLY0-0.0100.01316.795-0.007-0.0070.0000.0000.0000.000
81A77LYS10.8420.91719.449-0.145-0.1450.0000.0000.0000.000
82A78PRO00.0560.03517.2130.0180.0180.0000.0000.0000.000
83A79SER0-0.001-0.00117.4910.0360.0360.0000.0000.0000.000
84A80ALA0-0.024-0.01419.952-0.026-0.0260.0000.0000.0000.000
85A81ILE00.0050.00722.1070.0170.0170.0000.0000.0000.000
86A82PHE00.0050.00220.036-0.013-0.0130.0000.0000.0000.000
87A83LYS10.9000.95125.416-0.099-0.0990.0000.0000.0000.000
88A84ILE00.0240.00224.4740.0010.0010.0000.0000.0000.000
89A85SER0-0.036-0.02427.739-0.001-0.0010.0000.0000.0000.000
90A86GLY0-0.012-0.01131.409-0.004-0.0040.0000.0000.0000.000
91A87LEU0-0.062-0.02127.098-0.005-0.0050.0000.0000.0000.000
92A88LYS10.8410.90131.338-0.077-0.0770.0000.0000.0000.000
93A89SER00.0750.04430.6210.0040.0040.0000.0000.0000.000
94A90GLY0-0.0160.00529.943-0.007-0.0070.0000.0000.0000.000
95A91GLU-1-0.860-0.90730.1350.0740.0740.0000.0000.0000.000
96A92GLY00.0080.00126.5670.0080.0080.0000.0000.0000.000
97A93SER0-0.036-0.01522.729-0.005-0.0050.0000.0000.0000.000
98A94GLN00.0160.00922.9300.0070.0070.0000.0000.0000.000
99A95HIS0-0.0030.00218.8570.0230.0230.0000.0000.0000.000
100A96PRO00.0110.01514.449-0.018-0.0180.0000.0000.0000.000
101A97PHE0-0.005-0.00412.5260.0140.0140.0000.0000.0000.000
102A98GLY00.0140.00615.181-0.026-0.0260.0000.0000.0000.000
103A99ALA0-0.013-0.00414.491-0.014-0.0140.0000.0000.0000.000
104A100MET00.007-0.00615.943-0.018-0.0180.0000.0000.0000.000
105A101ASN0-0.035-0.01715.8920.0080.0080.0000.0000.0000.000
106A102ILE00.0320.03015.3780.0350.0350.0000.0000.0000.000
107A103VAL0-0.020-0.01418.818-0.032-0.0320.0000.0000.0000.000
108A104ARG10.8570.94421.559-0.187-0.1870.0000.0000.0000.000
109A105THR0-0.009-0.01224.077-0.018-0.0180.0000.0000.0000.000
110A106PRO00.029-0.00827.2880.0080.0080.0000.0000.0000.000
111A107SER00.0570.03529.736-0.001-0.0010.0000.0000.0000.000
112A108VAL0-0.0370.00023.2290.0030.0030.0000.0000.0000.000
113A109ALA0-0.0100.01824.0560.0000.0000.0000.0000.0000.000
114A110GLN0-0.013-0.02218.515-0.003-0.0030.0000.0000.0000.000
115A111ILE0-0.031-0.00416.572-0.030-0.0300.0000.0000.0000.000
116A112GLY00.0170.01314.8650.0600.0600.0000.0000.0000.000
117A113ILE0-0.049-0.02911.487-0.076-0.0760.0000.0000.0000.000
118A114SER0-0.031-0.04210.7360.1560.1560.0000.0000.0000.000
119A115VAL0-0.019-0.0167.042-0.061-0.0610.0000.0000.0000.000
120A116GLU-1-0.743-0.8449.9380.1820.1820.0000.0000.0000.000
121A117LEU00.0280.01412.819-0.016-0.0160.0000.0000.0000.000
122A118LEU00.014-0.01314.9720.0210.0210.0000.0000.0000.000
123A119ASP-1-0.907-0.95017.532-0.006-0.0060.0000.0000.0000.000
124A120SER0-0.015-0.02217.283-0.003-0.0030.0000.0000.0000.000
125A121MET0-0.062-0.00816.0290.0070.0070.0000.0000.0000.000
126A122ALA0-0.043-0.00919.3390.0040.0040.0000.0000.0000.000
127A123GLN0-0.033-0.01422.291-0.006-0.0060.0000.0000.0000.000
128A124GLN0-0.0310.00118.5520.0100.0100.0000.0000.0000.000
129A125THR0-0.019-0.02323.282-0.006-0.0060.0000.0000.0000.000
130A126PRO0-0.035-0.01623.3710.0050.0050.0000.0000.0000.000
131A127VAL00.0150.02325.335-0.011-0.0110.0000.0000.0000.000
132A128GLY00.0220.01128.0430.0010.0010.0000.0000.0000.000
133A129ASN0-0.065-0.05130.6860.0010.0010.0000.0000.0000.000
134A130ALA00.0770.05725.8080.0030.0030.0000.0000.0000.000
135A131ALA00.0250.01526.8490.0070.0070.0000.0000.0000.000
136A132VAL0-0.055-0.02827.756-0.009-0.0090.0000.0000.0000.000
137A133SER00.028-0.00129.523-0.001-0.0010.0000.0000.0000.000
138A134SER0-0.0150.00232.263-0.001-0.0010.0000.0000.0000.000
139A135VAL00.0520.00334.973-0.001-0.0010.0000.0000.0000.000
140A136ASP-1-0.862-0.92436.3450.0550.0550.0000.0000.0000.000
141A137SER00.0120.00836.4610.0010.0010.0000.0000.0000.000
142A138PHE0-0.027-0.01938.363-0.002-0.0020.0000.0000.0000.000
143A139THR00.0210.00540.843-0.003-0.0030.0000.0000.0000.000
144A140GLN00.0150.01138.518-0.003-0.0030.0000.0000.0000.000
145A141PHE0-0.005-0.00442.552-0.002-0.0020.0000.0000.0000.000
146A142THR00.0120.00344.502-0.002-0.0020.0000.0000.0000.000
147A143GLN00.0080.00344.2830.0000.0000.0000.0000.0000.000
148A144LYS10.9620.98642.738-0.055-0.0550.0000.0000.0000.000
149A145MET0-0.020-0.00447.442-0.002-0.0020.0000.0000.0000.000
150A146LEU0-0.0190.00850.281-0.002-0.0020.0000.0000.0000.000
151A147ASP-1-0.796-0.88650.2330.0360.0360.0000.0000.0000.000
152A148ASN0-0.078-0.02451.002-0.002-0.0020.0000.0000.0000.000
153A149PHE00.0320.01552.993-0.001-0.0010.0000.0000.0000.000
154A150TYR00.0370.02255.825-0.002-0.0020.0000.0000.0000.000
155A151ASN0-0.047-0.03454.391-0.002-0.0020.0000.0000.0000.000
156A152PHE00.0170.01956.952-0.001-0.0010.0000.0000.0000.000
157A153ALA00.0030.00658.655-0.001-0.0010.0000.0000.0000.000
158A154SER0-0.032-0.03760.601-0.001-0.0010.0000.0000.0000.000
159A155SER0-0.104-0.05060.706-0.001-0.0010.0000.0000.0000.000
160A156PHE0-0.009-0.00561.6380.0000.0000.0000.0000.0000.000
161A157ALA0-0.061-0.01365.714-0.001-0.0010.0000.0000.0000.000
162A158VAL00.0090.00467.6120.0000.0000.0000.0000.0000.000
163A159SER0-0.036-0.04271.223-0.001-0.0010.0000.0000.0000.000
164A160GLN00.051-0.01674.3350.0000.0000.0000.0000.0000.000
165A161ALA0-0.021-0.00877.6570.0000.0000.0000.0000.0000.000
166A162GLN00.0030.02472.0640.0000.0000.0000.0000.0000.000
167A163MET0-0.0280.01573.9290.0000.0000.0000.0000.0000.000
168A164THR00.0240.02475.7380.0000.0000.0000.0000.0000.000
169A165PRO0-0.049-0.04377.4740.0000.0000.0000.0000.0000.000
170A166SER0-0.016-0.04075.1650.0000.0000.0000.0000.0000.000
171A167PRO0-0.006-0.00877.7800.0000.0000.0000.0000.0000.000
172A168SER0-0.0050.00276.4460.0000.0000.0000.0000.0000.000
173A169GLU-1-0.900-0.90171.7120.0220.0220.0000.0000.0000.000
174A170MET0-0.035-0.01672.300-0.001-0.0010.0000.0000.0000.000
175A171PHE00.0380.01271.2810.0010.0010.0000.0000.0000.000
176A172ILE0-0.017-0.00866.581-0.001-0.0010.0000.0000.0000.000
177A173PRO00.0130.00969.6810.0000.0000.0000.0000.0000.000
178A174ALA00.1090.03967.0430.0000.0000.0000.0000.0000.000
179A175ASN00.009-0.00466.1730.0010.0010.0000.0000.0000.000
180A176VAL0-0.006-0.00166.4830.0000.0000.0000.0000.0000.000
181A177VAL00.0270.01362.1030.0000.0000.0000.0000.0000.000
182A178LEU00.0270.02460.9360.0010.0010.0000.0000.0000.000
183A179LYS10.8560.91361.441-0.021-0.0210.0000.0000.0000.000
184A180TRP0-0.028-0.01456.7770.0000.0000.0000.0000.0000.000
185A181TYR0-0.028-0.04053.6990.0000.0000.0000.0000.0000.000
186A182GLU-1-0.790-0.87656.8880.0240.0240.0000.0000.0000.000
187A183ASN0-0.049-0.03657.1780.0000.0000.0000.0000.0000.000
188A184PHE0-0.0020.00152.6640.0000.0000.0000.0000.0000.000
189A185GLN00.0150.00652.6980.0000.0000.0000.0000.0000.000
190A186ARG10.8990.95452.259-0.022-0.0220.0000.0000.0000.000
191A187ARG10.9120.95253.166-0.025-0.0250.0000.0000.0000.000
192A188LEU0-0.008-0.00448.6950.0000.0000.0000.0000.0000.000
193A189ALA0-0.0070.00148.2480.0010.0010.0000.0000.0000.000
194A190GLN0-0.038-0.01948.486-0.001-0.0010.0000.0000.0000.000
195A191ASN0-0.002-0.00448.7360.0010.0010.0000.0000.0000.000
196A192PRO00.0560.03344.876-0.001-0.0010.0000.0000.0000.000
197A193LEU00.0010.00544.2830.0010.0010.0000.0000.0000.000
198A194PHE0-0.064-0.02848.535-0.001-0.0010.0000.0000.0000.000
199A195TRP0-0.033-0.00547.186-0.001-0.0010.0000.0000.0000.000