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: GNGQ1

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 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 223
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2657660.114278
FMO2-HF: Nuclear repulsion 2569819.736589
FMO2-HF: Total energy -87840.377688
FMO2-MP2: Total energy -88098.999126


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.
-12.738-11.28814.744-7.093-9.1020.024
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 : 0.065 / q_NPA : 0.029
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].
3A5GLN0-0.007-0.0293.9020.6952.496-0.005-0.870-0.9260.003
4A6LEU0-0.0290.0011.754-0.3810.6215.614-2.639-3.9770.005
5A7VAL00.0060.0022.581-5.328-3.7520.840-1.034-1.382-0.015
6A8ALA0-0.003-0.0023.599-0.490-0.1720.002-0.064-0.2570.000
7A9VAL00.0640.0225.3410.3340.365-0.0010.000-0.0300.000
8A10ASN0-0.012-0.0067.2890.0340.0340.0000.0000.0000.000
9A11GLU-1-0.781-0.8785.554-3.947-3.9470.0000.0000.0000.000
10A12LEU0-0.069-0.0209.8550.1170.1170.0000.0000.0000.000
11A13ASN00.0480.01212.4830.2350.2350.0000.0000.0000.000
12A14GLU-1-0.835-0.93715.646-0.332-0.3320.0000.0000.0000.000
13A15ASN00.0130.00918.3440.0560.0560.0000.0000.0000.000
14A16LEU00.0140.00712.7590.0100.0100.0000.0000.0000.000
15A17GLY00.0370.02315.9860.0160.0160.0000.0000.0000.000
16A18LYS10.7860.89118.0250.3490.3490.0000.0000.0000.000
17A19VAL00.0070.00717.6880.0380.0380.0000.0000.0000.000
18A20LEU0-0.0070.00013.8640.0240.0240.0000.0000.0000.000
19A21ILE00.0260.01018.2130.0470.0470.0000.0000.0000.000
20A22LYS10.8540.90721.8080.3720.3720.0000.0000.0000.000
21A23ILE0-0.016-0.00517.4000.0270.0270.0000.0000.0000.000
22A24ALA00.0210.00421.3600.0340.0340.0000.0000.0000.000
23A25ARG10.7850.86922.7750.2190.2190.0000.0000.0000.000
24A26ASP-1-0.799-0.86824.523-0.303-0.3030.0000.0000.0000.000
25A27SER00.004-0.02522.6820.0150.0150.0000.0000.0000.000
26A28ILE00.0090.01525.6710.0240.0240.0000.0000.0000.000
27A29ALA00.0180.01328.3460.0180.0180.0000.0000.0000.000
28A30ASN0-0.064-0.02828.1640.0120.0120.0000.0000.0000.000
29A31LYS10.8470.90927.4670.2030.2030.0000.0000.0000.000
30A32LEU00.0080.02131.2630.0140.0140.0000.0000.0000.000
31A33GLY0-0.013-0.00233.3500.0100.0100.0000.0000.0000.000
32A34ILE0-0.037-0.00633.7250.0050.0050.0000.0000.0000.000
33A35LEU00.0050.00128.1770.0040.0040.0000.0000.0000.000
34A36LYS10.8410.90831.9830.1530.1530.0000.0000.0000.000
35A37ILE00.0290.01826.171-0.006-0.0060.0000.0000.0000.000
36A38ASN00.0270.01027.3200.0220.0220.0000.0000.0000.000
37A39LEU0-0.001-0.01022.998-0.020-0.0200.0000.0000.0000.000
38A40GLU-1-0.911-0.94522.707-0.340-0.3400.0000.0000.0000.000
39A41ASP-1-0.815-0.89222.350-0.359-0.3590.0000.0000.0000.000
40A42TYR0-0.095-0.05623.131-0.045-0.0450.0000.0000.0000.000
41A43LEU00.0140.01018.454-0.042-0.0420.0000.0000.0000.000
42A44SER0-0.017-0.02018.148-0.084-0.0840.0000.0000.0000.000
43A45SER0-0.080-0.04518.889-0.047-0.0470.0000.0000.0000.000
44A46LEU0-0.004-0.00317.208-0.023-0.0230.0000.0000.0000.000
45A47ASN0-0.012-0.01215.996-0.099-0.0990.0000.0000.0000.000
46A48ASP-1-0.828-0.90512.459-1.365-1.3650.0000.0000.0000.000
47A49PRO00.019-0.0129.346-0.074-0.0740.0000.0000.0000.000
48A50ILE0-0.027-0.0118.034-0.405-0.4050.0000.0000.0000.000
49A51LEU00.0090.0059.457-0.015-0.0150.0000.0000.0000.000
50A52ASN0-0.034-0.01810.5090.2800.2800.0000.0000.0000.000
51A53LYS10.8180.9113.3265.5785.8490.006-0.054-0.2230.000
52A54LYS10.8570.9296.3012.1502.1500.0000.0000.0000.000
53A55GLY00.0340.0076.577-0.400-0.4000.0000.0000.0000.000
54A56LEU0-0.0090.0089.1610.1380.1380.0000.0000.0000.000
55A57ALA0-0.006-0.00312.159-0.107-0.1070.0000.0000.0000.000
56A58PHE00.0190.00115.0850.0710.0710.0000.0000.0000.000
57A59VAL0-0.0230.00218.662-0.049-0.0490.0000.0000.0000.000
58A60THR0-0.035-0.03621.5620.0340.0340.0000.0000.0000.000
59A61LEU00.0210.01924.681-0.027-0.0270.0000.0000.0000.000
60A62GLU-1-0.766-0.86727.471-0.055-0.0550.0000.0000.0000.000
61A63THR0-0.015-0.00430.511-0.013-0.0130.0000.0000.0000.000
62A64TYR00.0510.01533.3510.0060.0060.0000.0000.0000.000
63A65TYR0-0.004-0.00834.8250.0010.0010.0000.0000.0000.000
64A66GLY0-0.033-0.01936.642-0.003-0.0030.0000.0000.0000.000
65A67ASN0-0.028-0.01636.701-0.006-0.0060.0000.0000.0000.000
66A68SER00.0010.00634.7010.0050.0050.0000.0000.0000.000
67A69THR0-0.002-0.02230.714-0.006-0.0060.0000.0000.0000.000
68A70SER0-0.017-0.00333.8380.0140.0140.0000.0000.0000.000
69A71LEU0-0.038-0.00928.408-0.010-0.0100.0000.0000.0000.000
70A72ARG10.7310.82330.6960.0620.0620.0000.0000.0000.000
71A73GLY00.0350.02729.5550.0000.0000.0000.0000.0000.000
72A74CYS0-0.106-0.07123.518-0.005-0.0050.0000.0000.0000.000
73A75ILE00.0140.01622.5420.0210.0210.0000.0000.0000.000
74A76GLY00.0340.00319.286-0.040-0.0400.0000.0000.0000.000
75A77TYR0-0.084-0.03217.0580.0340.0340.0000.0000.0000.000
76A78VAL00.036-0.01114.715-0.035-0.0350.0000.0000.0000.000
77A79GLU-1-0.957-0.95514.9210.3480.3480.0000.0000.0000.000
78A80ALA00.017-0.00113.5300.1150.1150.0000.0000.0000.000
79A81VAL0-0.044-0.0157.949-0.077-0.0770.0000.0000.0000.000
80A82ALA0-0.016-0.01110.994-0.040-0.0400.0000.0000.0000.000
81A83PRO00.0050.00710.462-0.128-0.1280.0000.0000.0000.000
82A84LEU00.0370.0189.3780.2630.2630.0000.0000.0000.000
83A85LYS10.8530.92512.3281.0791.0790.0000.0000.0000.000
84A86GLU-1-0.877-0.95615.036-0.642-0.6420.0000.0000.0000.000
85A87ILE0-0.072-0.02413.1240.1120.1120.0000.0000.0000.000
86A88VAL00.0490.02115.5110.0900.0900.0000.0000.0000.000
87A89SER00.0270.03117.9160.0800.0800.0000.0000.0000.000
88A90LYS10.9460.96818.4120.2510.2510.0000.0000.0000.000
89A91ALA00.0170.00919.4970.0420.0420.0000.0000.0000.000
90A92ALA00.0270.02021.4040.0310.0310.0000.0000.0000.000
91A93ILE0-0.036-0.01823.8040.0240.0240.0000.0000.0000.000
92A94ALA00.0260.01024.3560.0190.0190.0000.0000.0000.000
93A95ALA0-0.008-0.00324.7100.0200.0200.0000.0000.0000.000
94A96ALA00.0010.00526.6810.0110.0110.0000.0000.0000.000
95A97PHE0-0.071-0.05229.3150.0070.0070.0000.0000.0000.000
96A98SER0-0.029-0.01528.2330.0020.0020.0000.0000.0000.000
97A99ASP-1-0.700-0.80929.2440.0140.0140.0000.0000.0000.000
98A100PRO0-0.015-0.01930.060-0.003-0.0030.0000.0000.0000.000
99A101ARG10.8000.87727.731-0.022-0.0220.0000.0000.0000.000
100A102PHE0-0.0060.00731.313-0.001-0.0010.0000.0000.0000.000
101A103PRO00.0130.01535.6330.0000.0000.0000.0000.0000.000
102A104PRO00.0440.02934.167-0.003-0.0030.0000.0000.0000.000
103A105LEU0-0.0130.00731.3440.0020.0020.0000.0000.0000.000
104A106SER0-0.026-0.04234.699-0.005-0.0050.0000.0000.0000.000
105A107LYS10.9280.93836.6820.1040.1040.0000.0000.0000.000
106A108GLY00.0210.02337.861-0.005-0.0050.0000.0000.0000.000
107A109GLU-1-0.742-0.82335.885-0.067-0.0670.0000.0000.0000.000
108A110PHE00.0150.01529.951-0.004-0.0040.0000.0000.0000.000
109A111ASP-1-0.856-0.91733.110-0.151-0.1510.0000.0000.0000.000
110A112ASN0-0.066-0.03735.417-0.001-0.0010.0000.0000.0000.000
111A113ILE0-0.0170.00829.7690.0080.0080.0000.0000.0000.000
112A114ILE00.0150.01227.537-0.016-0.0160.0000.0000.0000.000
113A115ILE0-0.027-0.01423.6380.0100.0100.0000.0000.0000.000
114A116GLU-1-0.791-0.86921.449-0.085-0.0850.0000.0000.0000.000
115A117VAL0-0.012-0.01917.0880.0050.0050.0000.0000.0000.000
116A118THR00.0030.01315.671-0.008-0.0080.0000.0000.0000.000
117A119VAL0-0.029-0.02010.661-0.015-0.0150.0000.0000.0000.000
118A120LEU00.0080.00310.5360.0430.0430.0000.0000.0000.000
119A121THR0-0.003-0.0054.854-0.038-0.0380.0000.0000.0000.000
120A122LYS10.8960.9365.320-4.910-4.9100.0000.0000.0000.000
121A123PRO00.0090.0116.1951.0241.0240.0000.0000.0000.000
122A124GLN0-0.027-0.0181.855-8.945-12.4948.288-2.432-2.3070.031
123A125GLU-1-0.792-0.8857.1921.2851.2850.0000.0000.0000.000
124A126ILE0-0.028-0.0148.9120.5360.5360.0000.0000.0000.000
125A127ASP-1-0.899-0.95310.4951.2531.2530.0000.0000.0000.000
126A128VAL0-0.025-0.01512.463-0.047-0.0470.0000.0000.0000.000
127A129GLU-1-0.854-0.91315.1800.8040.8040.0000.0000.0000.000
128A130ASN0-0.071-0.03518.406-0.128-0.1280.0000.0000.0000.000
129A131ARG10.8560.92917.907-0.954-0.9540.0000.0000.0000.000
130A132TRP00.0740.02020.1840.0130.0130.0000.0000.0000.000
131A133GLU-1-0.856-0.90817.3790.7230.7230.0000.0000.0000.000
132A134LEU0-0.0080.01214.8640.0580.0580.0000.0000.0000.000
133A135PRO00.0140.00416.1810.0810.0810.0000.0000.0000.000
134A136LYS10.7920.88617.719-0.575-0.5750.0000.0000.0000.000
135A137LYS10.8390.90412.368-0.981-0.9810.0000.0000.0000.000
136A138ILE0-0.071-0.01112.0960.3120.3120.0000.0000.0000.000
137A139LYS10.8530.89813.687-0.385-0.3850.0000.0000.0000.000
138A140VAL00.0270.01014.897-0.002-0.0020.0000.0000.0000.000
139A141GLY00.0000.00617.032-0.052-0.0520.0000.0000.0000.000
140A142GLU-1-0.858-0.92511.4980.1570.1570.0000.0000.0000.000
141A143ASP-1-0.777-0.87510.0531.3101.3100.0000.0000.0000.000
142A144GLY0-0.0060.00211.826-0.133-0.1330.0000.0000.0000.000
143A145LEU0-0.014-0.02212.2950.2690.2690.0000.0000.0000.000
144A146ILE0-0.010-0.01113.179-0.145-0.1450.0000.0000.0000.000
145A147VAL00.0330.01815.3510.1420.1420.0000.0000.0000.000
146A148GLU-1-0.818-0.91515.4211.2011.2010.0000.0000.0000.000
147A149TYR0-0.036-0.02219.3590.0360.0360.0000.0000.0000.000
148A150GLY00.0410.02221.261-0.061-0.0610.0000.0000.0000.000
149A151ILE0-0.006-0.02822.6130.0020.0020.0000.0000.0000.000
150A152LEU0-0.041-0.00923.894-0.019-0.0190.0000.0000.0000.000
151A153TYR0-0.0110.01924.325-0.032-0.0320.0000.0000.0000.000
152A154SER00.002-0.00119.1040.0690.0690.0000.0000.0000.000
153A155GLY00.0530.03820.135-0.073-0.0730.0000.0000.0000.000
154A156LEU0-0.044-0.01615.8380.0920.0920.0000.0000.0000.000
155A157LEU0-0.014-0.02317.303-0.101-0.1010.0000.0000.0000.000
156A158LEU00.0020.00515.9570.0800.0800.0000.0000.0000.000
157A159PRO00.0390.01013.028-0.021-0.0210.0000.0000.0000.000
158A160GLN00.0470.02815.8870.0160.0160.0000.0000.0000.000
159A161VAL0-0.022-0.00219.308-0.014-0.0140.0000.0000.0000.000
160A162PRO00.0560.01518.518-0.026-0.0260.0000.0000.0000.000
161A163MET0-0.0060.02719.696-0.023-0.0230.0000.0000.0000.000
162A164GLU-1-0.836-0.90322.3210.1480.1480.0000.0000.0000.000
163A165TYR0-0.040-0.03124.641-0.026-0.0260.0000.0000.0000.000
164A166CYS0-0.122-0.01325.4980.0040.0040.0000.0000.0000.000
165A167TRP00.0260.00922.4760.0090.0090.0000.0000.0000.000
166A168ASP-1-0.810-0.87823.0460.3390.3390.0000.0000.0000.000
167A169GLU-1-0.775-0.90517.9060.5390.5390.0000.0000.0000.000
168A170GLU-1-0.805-0.90820.5600.5280.5280.0000.0000.0000.000
169A171THR0-0.039-0.03223.0200.0100.0100.0000.0000.0000.000
170A172PHE0-0.015-0.00715.8120.0040.0040.0000.0000.0000.000
171A173LEU00.0050.00217.2390.0440.0440.0000.0000.0000.000
172A174ALA0-0.0110.01120.6670.0090.0090.0000.0000.0000.000
173A175GLU-1-0.900-0.96423.5250.3230.3230.0000.0000.0000.000
174A176THR0-0.064-0.05218.1390.0020.0020.0000.0000.0000.000
175A177CYS0-0.099-0.02921.4940.0840.0840.0000.0000.0000.000
176A178ILE00.0360.03623.379-0.017-0.0170.0000.0000.0000.000
177A179LYS10.8730.93022.197-0.415-0.4150.0000.0000.0000.000
178A180ALA0-0.028-0.00121.792-0.005-0.0050.0000.0000.0000.000
179A181GLY0-0.037-0.01423.795-0.004-0.0040.0000.0000.0000.000
180A182LEU0-0.064-0.04223.250-0.006-0.0060.0000.0000.0000.000
181A183GLU-1-0.859-0.93227.1650.3500.3500.0000.0000.0000.000
182A184PRO0-0.003-0.01326.5220.0380.0380.0000.0000.0000.000
183A185ASP-1-0.868-0.93425.6140.4190.4190.0000.0000.0000.000
184A187TRP00.0520.00419.8030.0620.0620.0000.0000.0000.000
185A188LEU0-0.011-0.00620.4430.0730.0730.0000.0000.0000.000
186A189ASN0-0.037-0.01323.1130.0120.0120.0000.0000.0000.000
187A190ASN00.017-0.02719.3080.1020.1020.0000.0000.0000.000
188A191LYS10.9180.96020.032-0.410-0.4100.0000.0000.0000.000
189A192VAL0-0.0150.01419.4820.0160.0160.0000.0000.0000.000
190A193LYS10.8310.92214.176-1.442-1.4420.0000.0000.0000.000
191A194ILE00.0450.01814.169-0.121-0.1210.0000.0000.0000.000
192A195LYS10.7610.87210.231-1.310-1.3100.0000.0000.0000.000
193A196LYS10.8070.8918.305-2.146-2.1460.0000.0000.0000.000
194A197PHE0-0.022-0.0067.6010.7110.7110.0000.0000.0000.000
195A198GLN00.0380.0206.145-0.472-0.4720.0000.0000.0000.000
196A199GLY00.008-0.0179.478-0.088-0.0880.0000.0000.0000.000
197A200ILE0-0.047-0.01811.937-0.007-0.0070.0000.0000.0000.000
198A201ILE00.0030.00914.234-0.009-0.0090.0000.0000.0000.000
199A202PHE00.0240.02414.641-0.018-0.0180.0000.0000.0000.000
200A203ARG10.8370.89219.7730.1080.1080.0000.0000.0000.000
201A204GLU-1-0.756-0.86823.529-0.208-0.2080.0000.0000.0000.000
202A205GLU-1-0.805-0.88526.668-0.142-0.1420.0000.0000.0000.000
203A206LYS10.9310.95629.3510.1310.1310.0000.0000.0000.000
204A207PRO0-0.031-0.00230.788-0.015-0.0150.0000.0000.0000.000
205A208LYS10.8220.89829.3000.1580.1580.0000.0000.0000.000
206A209SER0-0.057-0.01728.050-0.003-0.0030.0000.0000.0000.000
207A210GLU-1-0.849-0.94227.381-0.299-0.2990.0000.0000.0000.000
208A211LYS10.8480.92126.8530.1460.1460.0000.0000.0000.000
209A212ILE0-0.040-0.00820.6710.0080.0080.0000.0000.0000.000
210A213LEU00.0200.00723.775-0.001-0.0010.0000.0000.0000.000
211A214ILE0-0.014-0.00917.536-0.008-0.0080.0000.0000.0000.000
212A215ILE0-0.017-0.00619.3250.0250.0250.0000.0000.0000.000
213A216LYS10.8390.89515.5510.1730.1730.0000.0000.0000.000
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