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: VRL21

Calculation Name: 1WSC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WSC

Chain ID: A

ChEMBL ID:

UniProt ID: Q976G0

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 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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2659881.371698
FMO2-HF: Nuclear repulsion 2572043.501519
FMO2-HF: Total energy -87837.870178
FMO2-MP2: Total energy -88096.693776


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.
-7.553-19.05639.328-14.626-13.1950.058
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 : 0.091 / q_NPA : 0.064
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].
3A5GLN0-0.067-0.0633.357-0.6223.0140.013-1.869-1.7790.007
4A6LEU0-0.047-0.0151.6451.033-0.95111.817-4.283-5.5500.000
5A7VAL00.0070.0012.489-5.720-4.9021.522-0.514-1.825-0.019
6A8ALA00.0180.0174.1010.7090.937-0.001-0.032-0.1960.000
7A9VAL00.0680.0195.2320.1370.183-0.0010.000-0.0440.000
8A10ASN0-0.052-0.0157.946-0.400-0.4000.0000.0000.0000.000
9A11GLU-1-0.819-0.9335.308-5.581-5.5810.0000.0000.0000.000
10A12LEU0-0.084-0.03510.0150.0480.0480.0000.0000.0000.000
11A13ASN00.0550.04612.5000.2560.2560.0000.0000.0000.000
12A14GLU-1-0.844-0.95315.894-0.314-0.3140.0000.0000.0000.000
13A15ASN00.029-0.00518.3790.0620.0620.0000.0000.0000.000
14A16LEU00.0190.00312.9600.0170.0170.0000.0000.0000.000
15A17GLY00.0190.01916.2400.0180.0180.0000.0000.0000.000
16A18LYS10.8800.95218.0290.3850.3850.0000.0000.0000.000
17A19VAL0-0.015-0.00617.4280.0390.0390.0000.0000.0000.000
18A20LEU0-0.014-0.00914.0080.0370.0370.0000.0000.0000.000
19A21ILE00.0410.02318.1660.0540.0540.0000.0000.0000.000
20A22LYS10.9080.96121.7130.4200.4200.0000.0000.0000.000
21A23ILE0-0.0040.01317.4300.0260.0260.0000.0000.0000.000
22A24ALA00.0160.01521.4630.0350.0350.0000.0000.0000.000
23A25ARG10.7950.90422.7830.2020.2020.0000.0000.0000.000
24A26ASP-1-0.809-0.93524.870-0.325-0.3250.0000.0000.0000.000
25A27SER0-0.022-0.01722.9500.0080.0080.0000.0000.0000.000
26A28ILE00.0020.00925.5090.0220.0220.0000.0000.0000.000
27A29ALA00.0170.01528.2140.0170.0170.0000.0000.0000.000
28A30ASN0-0.059-0.02828.0640.0100.0100.0000.0000.0000.000
29A31LYS10.9170.95627.1070.2210.2210.0000.0000.0000.000
30A32LEU0-0.0300.00631.0380.0160.0160.0000.0000.0000.000
31A33GLY0-0.046-0.01833.3100.0130.0130.0000.0000.0000.000
32A34ILE0-0.095-0.04333.4130.0030.0030.0000.0000.0000.000
33A35LEU0-0.0040.00128.3210.0000.0000.0000.0000.0000.000
34A36LYS10.9310.95132.1590.1720.1720.0000.0000.0000.000
35A37ILE00.0190.00926.434-0.010-0.0100.0000.0000.0000.000
36A38ASN00.0430.04627.0970.0060.0060.0000.0000.0000.000
37A39LEU00.015-0.00723.078-0.023-0.0230.0000.0000.0000.000
38A40GLU-1-0.884-0.93822.598-0.431-0.4310.0000.0000.0000.000
39A41ASP-1-0.848-0.93422.293-0.473-0.4730.0000.0000.0000.000
40A42TYR0-0.110-0.04622.612-0.052-0.0520.0000.0000.0000.000
41A43LEU00.0210.01018.877-0.053-0.0530.0000.0000.0000.000
42A44SER0-0.022-0.01318.520-0.103-0.1030.0000.0000.0000.000
43A45SER0-0.077-0.04019.414-0.052-0.0520.0000.0000.0000.000
44A46LEU0-0.033-0.00517.491-0.028-0.0280.0000.0000.0000.000
45A47ASN0-0.012-0.02316.256-0.109-0.1090.0000.0000.0000.000
46A48ASP-1-0.846-0.91612.963-1.639-1.6390.0000.0000.0000.000
47A49PRO00.015-0.01910.088-0.085-0.0850.0000.0000.0000.000
48A50ILE0-0.0050.0118.327-0.475-0.4750.0000.0000.0000.000
49A51LEU0-0.0030.0039.251-0.121-0.1210.0000.0000.0000.000
50A52ASN0-0.011-0.01010.3500.4500.4500.0000.0000.0000.000
51A53LYS10.9040.9814.1607.1987.294-0.001-0.006-0.0880.000
52A54LYS10.9120.9466.0972.2752.2750.0000.0000.0000.000
53A55GLY00.0250.0126.536-0.413-0.4130.0000.0000.0000.000
54A56LEU0-0.012-0.0019.0440.0470.0470.0000.0000.0000.000
55A57ALA00.0270.00712.143-0.092-0.0920.0000.0000.0000.000
56A58PHE00.0200.02415.0900.0560.0560.0000.0000.0000.000
57A59VAL0-0.034-0.01418.591-0.056-0.0560.0000.0000.0000.000
58A60THR00.0010.00221.4760.0240.0240.0000.0000.0000.000
59A61LEU0-0.011-0.00524.590-0.032-0.0320.0000.0000.0000.000
60A62GLU-1-0.792-0.87027.2370.0580.0580.0000.0000.0000.000
61A63THR0-0.038-0.02430.129-0.023-0.0230.0000.0000.0000.000
62A64TYR00.030-0.01032.9850.0060.0060.0000.0000.0000.000
63A65TYR0-0.001-0.00734.4630.0000.0000.0000.0000.0000.000
64A66GLY0-0.038-0.01836.370-0.003-0.0030.0000.0000.0000.000
65A67ASN00.000-0.00136.586-0.009-0.0090.0000.0000.0000.000
66A68SER0-0.011-0.00734.7350.0080.0080.0000.0000.0000.000
67A69THR0-0.036-0.04830.411-0.009-0.0090.0000.0000.0000.000
68A70SER00.0160.00933.5950.0170.0170.0000.0000.0000.000
69A71LEU0-0.0060.02028.950-0.014-0.0140.0000.0000.0000.000
70A72ARG10.7750.84630.3030.0130.0130.0000.0000.0000.000
71A73GLY00.0120.02629.253-0.007-0.0070.0000.0000.0000.000
72A74CYS0-0.078-0.04224.114-0.006-0.0060.0000.0000.0000.000
73A75ILE00.0310.03422.3010.0160.0160.0000.0000.0000.000
74A76GLY00.031-0.01019.459-0.039-0.0390.0000.0000.0000.000
75A77TYR0-0.076-0.02116.9900.0220.0220.0000.0000.0000.000
76A78VAL00.038-0.00614.832-0.017-0.0170.0000.0000.0000.000
77A79GLU-1-0.965-0.96215.1230.5380.5380.0000.0000.0000.000
78A80ALA00.013-0.00213.1670.1390.1390.0000.0000.0000.000
79A81VAL0-0.044-0.0167.636-0.099-0.0990.0000.0000.0000.000
80A82ALA0-0.016-0.01510.765-0.091-0.0910.0000.0000.0000.000
81A83PRO00.0160.01010.282-0.124-0.1240.0000.0000.0000.000
82A84LEU00.0520.0209.0340.3270.3270.0000.0000.0000.000
83A85LYS10.8610.92612.2231.3141.3140.0000.0000.0000.000
84A86GLU-1-0.915-0.96414.698-0.705-0.7050.0000.0000.0000.000
85A87ILE0-0.062-0.02413.4550.1350.1350.0000.0000.0000.000
86A88VAL00.0350.01215.3540.1140.1140.0000.0000.0000.000
87A89SER0-0.022-0.00817.7450.0770.0770.0000.0000.0000.000
88A90LYS10.9510.96618.7240.2610.2610.0000.0000.0000.000
89A91ALA00.0100.00419.4420.0450.0450.0000.0000.0000.000
90A92ALA00.0370.03221.3140.0360.0360.0000.0000.0000.000
91A93ILE0-0.023-0.01523.6370.0270.0270.0000.0000.0000.000
92A94ALA00.0120.00524.1380.0200.0200.0000.0000.0000.000
93A95ALA00.0060.00624.5310.0250.0250.0000.0000.0000.000
94A96ALA0-0.010-0.01126.4180.0130.0130.0000.0000.0000.000
95A97PHE0-0.064-0.05429.1220.0030.0030.0000.0000.0000.000
96A98SER0-0.023-0.01527.707-0.001-0.0010.0000.0000.0000.000
97A99ASP-1-0.705-0.79029.0190.1070.1070.0000.0000.0000.000
98A100PRO0-0.011-0.01429.770-0.008-0.0080.0000.0000.0000.000
99A101ARG10.7800.84428.325-0.119-0.1190.0000.0000.0000.000
100A102PHE0-0.0110.00531.363-0.002-0.0020.0000.0000.0000.000
101A103PRO0-0.0100.00635.213-0.001-0.0010.0000.0000.0000.000
102A104PRO00.0360.01633.972-0.001-0.0010.0000.0000.0000.000
103A105LEU0-0.032-0.01231.113-0.001-0.0010.0000.0000.0000.000
104A106SER0-0.010-0.00834.433-0.010-0.0100.0000.0000.0000.000
105A107LYS10.9320.93136.3470.1050.1050.0000.0000.0000.000
106A108GLY00.0010.00137.449-0.005-0.0050.0000.0000.0000.000
107A109GLU-1-0.761-0.84635.944-0.032-0.0320.0000.0000.0000.000
108A110PHE00.0190.01429.542-0.002-0.0020.0000.0000.0000.000
109A111ASP-1-0.873-0.95133.118-0.136-0.1360.0000.0000.0000.000
110A112ASN0-0.055-0.02535.264-0.006-0.0060.0000.0000.0000.000
111A113ILE0-0.030-0.00429.7150.0130.0130.0000.0000.0000.000
112A114ILE0-0.0210.00027.399-0.022-0.0220.0000.0000.0000.000
113A115ILE0-0.026-0.03423.2020.0170.0170.0000.0000.0000.000
114A116GLU-1-0.846-0.91521.2650.0490.0490.0000.0000.0000.000
115A117VAL0-0.017-0.01316.6760.0070.0070.0000.0000.0000.000
116A118THR00.0130.01315.3190.0070.0070.0000.0000.0000.000
117A119VAL0-0.040-0.01910.212-0.031-0.0310.0000.0000.0000.000
118A120LEU00.008-0.00510.8370.0870.0870.0000.0000.0000.000
119A121THR0-0.0020.0075.164-0.169-0.1690.0000.0000.0000.000
120A122LYS10.9690.9805.710-4.195-4.1950.0000.0000.0000.000
121A123PRO00.0260.0166.1631.9471.9470.0000.0000.0000.000
122A124GLN0-0.139-0.1011.603-5.772-20.11525.979-7.922-3.7130.070
123A125GLU-1-0.909-0.9626.7281.7051.7050.0000.0000.0000.000
124A126ILE0-0.046-0.0198.2840.8150.8150.0000.0000.0000.000
125A127ASP-1-0.952-0.96910.1491.4781.4780.0000.0000.0000.000
126A128VAL00.0100.00312.163-0.141-0.1410.0000.0000.0000.000
127A129GLU-1-0.886-0.94815.0321.1861.1860.0000.0000.0000.000
128A130ASN0-0.051-0.02518.210-0.176-0.1760.0000.0000.0000.000
129A131ARG10.8780.92916.804-1.345-1.3450.0000.0000.0000.000
130A132TRP00.0890.03719.8750.0400.0400.0000.0000.0000.000
131A133GLU-1-1.010-1.00817.4520.9340.9340.0000.0000.0000.000
132A134LEU0-0.031-0.01614.9690.0990.0990.0000.0000.0000.000
133A135PRO00.0280.00716.2390.1450.1450.0000.0000.0000.000
134A136LYS10.9470.97817.562-0.734-0.7340.0000.0000.0000.000
135A137LYS10.8420.93712.352-1.458-1.4580.0000.0000.0000.000
136A138ILE0-0.056-0.01812.0240.5050.5050.0000.0000.0000.000
137A139LYS10.9170.96713.978-0.895-0.8950.0000.0000.0000.000
138A140VAL00.0160.01015.4820.0570.0570.0000.0000.0000.000
139A141GLY00.001-0.00317.497-0.095-0.0950.0000.0000.0000.000
140A142GLU-1-0.992-1.01512.5050.6670.6670.0000.0000.0000.000
141A143ASP-1-0.839-0.93310.7092.3402.3400.0000.0000.0000.000
142A144GLY0-0.0060.00512.135-0.243-0.2430.0000.0000.0000.000
143A145LEU0-0.011-0.02812.7490.4070.4070.0000.0000.0000.000
144A146ILE0-0.018-0.00712.435-0.161-0.1610.0000.0000.0000.000
145A147VAL00.0130.00915.0240.1760.1760.0000.0000.0000.000
146A148GLU-1-0.903-0.96715.4191.4751.4750.0000.0000.0000.000
147A149TYR0-0.025-0.01018.7960.0360.0360.0000.0000.0000.000
148A150GLY00.0180.01420.851-0.087-0.0870.0000.0000.0000.000
149A151ILE0-0.005-0.03122.3050.0170.0170.0000.0000.0000.000
150A152LEU0-0.026-0.01623.2630.0050.0050.0000.0000.0000.000
151A153TYR0-0.0180.02723.667-0.041-0.0410.0000.0000.0000.000
152A154SER00.0370.00518.8240.0950.0950.0000.0000.0000.000
153A155GLY00.0350.02919.590-0.103-0.1030.0000.0000.0000.000
154A156LEU0-0.036-0.01615.1350.1540.1540.0000.0000.0000.000
155A157LEU0-0.013-0.01617.290-0.168-0.1680.0000.0000.0000.000
156A158LEU0-0.022-0.00616.0680.1590.1590.0000.0000.0000.000
157A159PRO00.007-0.00813.633-0.032-0.0320.0000.0000.0000.000
158A160GLN00.0840.03416.2000.0440.0440.0000.0000.0000.000
159A161VAL0-0.0120.00719.657-0.032-0.0320.0000.0000.0000.000
160A162PRO00.0330.01618.641-0.062-0.0620.0000.0000.0000.000
161A163MET0-0.0140.01820.311-0.047-0.0470.0000.0000.0000.000
162A164GLU-1-0.899-0.94922.7490.3570.3570.0000.0000.0000.000
163A165TYR0-0.060-0.02825.124-0.067-0.0670.0000.0000.0000.000
164A166CYS0-0.086-0.00726.084-0.009-0.0090.0000.0000.0000.000
165A167TRP00.0160.01022.9670.0080.0080.0000.0000.0000.000
166A168ASP-1-0.802-0.86623.6410.6070.6070.0000.0000.0000.000
167A169GLU-1-0.764-0.93318.7860.8890.8890.0000.0000.0000.000
168A170GLU-1-0.910-0.96520.5530.7320.7320.0000.0000.0000.000
169A171THR0-0.040-0.03122.7590.0060.0060.0000.0000.0000.000
170A172PHE0-0.011-0.00116.267-0.004-0.0040.0000.0000.0000.000
171A173LEU0-0.008-0.00216.6880.0640.0640.0000.0000.0000.000
172A174ALA00.0050.01220.4410.0050.0050.0000.0000.0000.000
173A175GLU-1-0.896-0.97123.6700.5230.5230.0000.0000.0000.000
174A176THR0-0.058-0.04218.135-0.004-0.0040.0000.0000.0000.000
175A177CYS0-0.059-0.01521.5330.0810.0810.0000.0000.0000.000
176A178ILE00.0280.03023.014-0.032-0.0320.0000.0000.0000.000
177A179LYS10.8360.92722.076-0.682-0.6820.0000.0000.0000.000
178A180ALA0-0.024-0.00821.652-0.018-0.0180.0000.0000.0000.000
179A181GLY0-0.032-0.00823.609-0.022-0.0220.0000.0000.0000.000
180A182LEU0-0.075-0.03922.545-0.022-0.0220.0000.0000.0000.000
181A183GLU-1-0.868-0.94426.5510.4670.4670.0000.0000.0000.000
182A184PRO00.007-0.00826.0330.0600.0600.0000.0000.0000.000
183A185ASP-1-0.921-0.95625.2330.6170.6170.0000.0000.0000.000
184A187TRP00.0790.01419.4720.0870.0870.0000.0000.0000.000
185A188LEU0-0.033-0.00420.0760.0930.0930.0000.0000.0000.000
186A189ASN00.0010.00722.501-0.008-0.0080.0000.0000.0000.000
187A190ASN00.0510.00419.8800.1380.1380.0000.0000.0000.000
188A191LYS10.8820.94719.609-0.536-0.5360.0000.0000.0000.000
189A192VAL0-0.0180.00718.7600.0050.0050.0000.0000.0000.000
190A193LYS10.9210.98114.659-1.411-1.4110.0000.0000.0000.000
191A194ILE00.0550.02613.493-0.116-0.1160.0000.0000.0000.000
192A195LYS10.9060.9689.732-2.335-2.3350.0000.0000.0000.000
193A196LYS10.9600.9947.639-4.418-4.4180.0000.0000.0000.000
194A197PHE0-0.047-0.0187.9681.1391.1390.0000.0000.0000.000
195A198GLN00.0530.0436.496-0.455-0.4550.0000.0000.0000.000
196A199GLY00.043-0.0039.824-0.056-0.0560.0000.0000.0000.000
197A200ILE0-0.059-0.01812.046-0.023-0.0230.0000.0000.0000.000
198A201ILE00.0300.02314.322-0.020-0.0200.0000.0000.0000.000
199A202PHE00.0170.01914.282-0.045-0.0450.0000.0000.0000.000
200A203ARG10.8890.92719.621-0.007-0.0070.0000.0000.0000.000
201A204GLU-1-0.767-0.85823.290-0.183-0.1830.0000.0000.0000.000
202A205GLU-1-0.857-0.92626.486-0.088-0.0880.0000.0000.0000.000
203A206LYS10.9270.93629.1370.1100.1100.0000.0000.0000.000
204A207PRO0-0.019-0.00230.229-0.018-0.0180.0000.0000.0000.000
205A208LYS10.8780.95129.3000.1520.1520.0000.0000.0000.000
206A209SER0-0.098-0.03528.403-0.009-0.0090.0000.0000.0000.000
207A210GLU-1-0.888-0.96127.464-0.316-0.3160.0000.0000.0000.000
208A211LYS10.9060.95826.7100.1060.1060.0000.0000.0000.000
209A212ILE0-0.0080.00820.2940.0150.0150.0000.0000.0000.000
210A213LEU00.0220.00823.652-0.004-0.0040.0000.0000.0000.000
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