Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: ZVGZN

Calculation Name: 1VHC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1VHC

Chain ID: A

ChEMBL ID:

UniProt ID: P44480

Base Structure: X-ray

Registration Date: 2023-09-23

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2385100.549719
FMO2-HF: Nuclear repulsion 2305566.447673
FMO2-HF: Total energy -79534.102045
FMO2-MP2: Total energy -79767.850002


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:2:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
-1.190.298-0.019-0.608-0.860.003
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / q_NPA : -0.020
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].
3A4THR00.0470.0043.777-0.4820.895-0.018-0.597-0.7610.003
4A5THR00.0760.0086.5300.0470.0470.0000.0000.0000.000
5A6GLN00.0040.0079.2970.0750.0750.0000.0000.0000.000
6A7GLN00.0600.0426.857-0.411-0.4110.0000.0000.0000.000
7A8ILE0-0.0040.0115.5010.1220.1220.0000.0000.0000.000
8A9ILE0-0.010-0.0029.2300.1860.1860.0000.0000.0000.000
9A10GLU-1-0.768-0.87212.490-0.384-0.3840.0000.0000.0000.000
10A11LYS10.9420.9887.1421.2631.2630.0000.0000.0000.000
11A12LEU0-0.043-0.02612.0530.1110.1110.0000.0000.0000.000
12A13ARG10.8450.91214.4700.4520.4520.0000.0000.0000.000
13A14GLU-1-0.963-0.97513.608-0.445-0.4450.0000.0000.0000.000
14A15LEU0-0.017-0.00213.2730.0430.0430.0000.0000.0000.000
15A16LYS10.8890.92817.5110.3050.3050.0000.0000.0000.000
16A17ILE0-0.038-0.01319.6210.0230.0230.0000.0000.0000.000
17A18VAL0-0.006-0.00415.951-0.021-0.0210.0000.0000.0000.000
18A19PRO00.0080.01017.5880.0250.0250.0000.0000.0000.000
19A20VAL0-0.044-0.02518.468-0.006-0.0060.0000.0000.0000.000
20A21ILE00.0370.00718.4580.0110.0110.0000.0000.0000.000
21A22ALA0-0.033-0.02520.6660.0120.0120.0000.0000.0000.000
22A23LEU0-0.0010.00320.630-0.007-0.0070.0000.0000.0000.000
23A24ASP-1-0.837-0.91124.1190.0210.0210.0000.0000.0000.000
24A25ASN00.004-0.00926.0260.0170.0170.0000.0000.0000.000
25A26ALA00.0320.01020.998-0.009-0.0090.0000.0000.0000.000
26A27ASP-1-0.875-0.93921.5270.0560.0560.0000.0000.0000.000
27A28ASP-1-0.835-0.90423.479-0.006-0.0060.0000.0000.0000.000
28A29ILE0-0.067-0.04417.281-0.017-0.0170.0000.0000.0000.000
29A30LEU0-0.0010.01618.232-0.019-0.0190.0000.0000.0000.000
30A31PRO00.0500.03320.628-0.018-0.0180.0000.0000.0000.000
31A32LEU0-0.0030.01621.086-0.014-0.0140.0000.0000.0000.000
32A33ALA00.021-0.00216.874-0.018-0.0180.0000.0000.0000.000
33A34ASP-1-0.815-0.89518.762-0.103-0.1030.0000.0000.0000.000
34A35THR0-0.083-0.05720.698-0.010-0.0100.0000.0000.0000.000
35A36LEU0-0.028-0.00618.796-0.004-0.0040.0000.0000.0000.000
36A37ALA00.0380.03517.114-0.015-0.0150.0000.0000.0000.000
37A38LYS10.8830.94518.6950.0830.0830.0000.0000.0000.000
38A39ASN0-0.083-0.04222.1350.0100.0100.0000.0000.0000.000
39A40GLY00.0420.03019.7520.0020.0020.0000.0000.0000.000
40A41LEU0-0.015-0.00717.807-0.021-0.0210.0000.0000.0000.000
41A42SER0-0.020-0.01813.5760.0400.0400.0000.0000.0000.000
42A43VAL0-0.014-0.00812.602-0.081-0.0810.0000.0000.0000.000
43A44ALA0-0.0020.00313.4110.0510.0510.0000.0000.0000.000
44A45GLU-1-0.878-0.93413.644-0.153-0.1530.0000.0000.0000.000
45A46ILE0-0.004-0.01014.9080.0130.0130.0000.0000.0000.000
46A47THR0-0.046-0.02116.8300.0250.0250.0000.0000.0000.000
47A48PHE00.065-0.00115.2220.0130.0130.0000.0000.0000.000
48A49ARG10.8810.94820.1560.0200.0200.0000.0000.0000.000
49A50SER0-0.029-0.01322.614-0.006-0.0060.0000.0000.0000.000
50A51GLU-1-0.893-0.95022.2950.1070.1070.0000.0000.0000.000
51A52ALA00.0080.01322.4750.0150.0150.0000.0000.0000.000
52A53ALA0-0.031-0.00618.0150.0070.0070.0000.0000.0000.000
53A54ALA00.0520.01016.2240.0090.0090.0000.0000.0000.000
54A55ASP-1-0.802-0.88816.3360.2060.2060.0000.0000.0000.000
55A56ALA00.0060.00517.878-0.002-0.0020.0000.0000.0000.000
56A57ILE0-0.021-0.01411.499-0.016-0.0160.0000.0000.0000.000
57A58ARG10.8620.91513.008-0.239-0.2390.0000.0000.0000.000
58A59LEU0-0.027-0.00614.092-0.003-0.0030.0000.0000.0000.000
59A60LEU0-0.0020.00313.288-0.023-0.0230.0000.0000.0000.000
60A61ARG10.7900.8816.8640.0740.0740.0000.0000.0000.000
61A62ALA0-0.024-0.01311.066-0.043-0.0430.0000.0000.0000.000
62A63ASN0-0.043-0.02313.229-0.045-0.0450.0000.0000.0000.000
63A64ARG10.8460.91213.1060.1190.1190.0000.0000.0000.000
64A65PRO00.0180.0088.930-0.057-0.0570.0000.0000.0000.000
65A66ASP-1-0.954-0.9777.662-0.559-0.5590.0000.0000.0000.000
66A67PHE0-0.008-0.0068.730-0.122-0.1220.0000.0000.0000.000
67A68LEU0-0.028-0.0017.830-0.097-0.0970.0000.0000.0000.000
68A69ILE00.002-0.0138.5050.1270.1270.0000.0000.0000.000
69A70ALA00.0070.0239.0390.0200.0200.0000.0000.0000.000
70A71ALA00.0340.03411.5710.0370.0370.0000.0000.0000.000
71A72GLY00.0560.01613.689-0.028-0.0280.0000.0000.0000.000
72A73THR0-0.102-0.05716.8290.0260.0260.0000.0000.0000.000
73A74VAL00.0410.03715.1080.0170.0170.0000.0000.0000.000
74A75LEU0-0.019-0.01818.466-0.019-0.0190.0000.0000.0000.000
75A76THR0-0.051-0.04020.5670.0040.0040.0000.0000.0000.000
76A77ALA00.034-0.00718.3430.0090.0090.0000.0000.0000.000
77A78GLU-1-0.851-0.92117.6310.2470.2470.0000.0000.0000.000
78A79GLN00.0370.02717.8880.0270.0270.0000.0000.0000.000
79A80VAL00.0130.01812.9260.0320.0320.0000.0000.0000.000
80A81VAL00.0150.00213.0660.0940.0940.0000.0000.0000.000
81A82LEU00.0210.02413.4360.1050.1050.0000.0000.0000.000
82A83ALA00.0120.00712.2060.0400.0400.0000.0000.0000.000
83A84LYS10.8590.9365.550-1.571-1.5710.0000.0000.0000.000
84A85SER00.0010.0008.9480.2830.2830.0000.0000.0000.000
85A86SER0-0.088-0.05611.233-0.025-0.0250.0000.0000.0000.000
86A87GLY00.0270.0218.157-0.093-0.0930.0000.0000.0000.000
87A88ALA0-0.019-0.0097.542-0.096-0.0960.0000.0000.0000.000
88A89ASP-1-0.813-0.8994.563-0.794-0.683-0.001-0.011-0.0990.000
89A90PHE0-0.056-0.0385.837-0.204-0.2040.0000.0000.0000.000
90A91VAL00.0140.0108.5680.0970.0970.0000.0000.0000.000
91A92VAL00.0040.01212.208-0.071-0.0710.0000.0000.0000.000
92A93THR0-0.029-0.03815.4520.0350.0350.0000.0000.0000.000
93A94PRO0-0.011-0.00418.875-0.017-0.0170.0000.0000.0000.000
94A95GLY00.0470.02322.407-0.006-0.0060.0000.0000.0000.000
95A96LEU00.0270.02720.623-0.003-0.0030.0000.0000.0000.000
96A97ASN00.0040.00021.3370.0110.0110.0000.0000.0000.000
97A98PRO00.1210.03720.6550.0060.0060.0000.0000.0000.000
98A99LYS10.9760.99120.102-0.075-0.0750.0000.0000.0000.000
99A100ILE0-0.0130.00016.9980.0210.0210.0000.0000.0000.000
100A101VAL00.0310.01715.9730.0160.0160.0000.0000.0000.000
101A102LYS10.8620.92115.133-0.050-0.0500.0000.0000.0000.000
102A103LEU0-0.0010.00114.6320.0130.0130.0000.0000.0000.000
103A104CYS0-0.022-0.01511.3460.0720.0720.0000.0000.0000.000
104A105GLN0-0.021-0.00810.4880.0500.0500.0000.0000.0000.000
105A106ASP-1-0.822-0.89111.4200.1040.1040.0000.0000.0000.000
106A107LEU0-0.044-0.0119.9830.0810.0810.0000.0000.0000.000
107A108ASN0-0.030-0.0135.3750.0940.0940.0000.0000.0000.000
108A109PHE0-0.071-0.0415.6770.0790.0790.0000.0000.0000.000
109A110PRO00.0320.0135.7220.0450.0450.0000.0000.0000.000
110A111ILE00.0370.0138.7090.1240.1240.0000.0000.0000.000
111A112THR0-0.036-0.02712.355-0.055-0.0550.0000.0000.0000.000
112A113PRO00.0290.03014.9730.0280.0280.0000.0000.0000.000
113A114GLY00.0130.02418.281-0.020-0.0200.0000.0000.0000.000
114A115VAL0-0.029-0.02421.5550.0150.0150.0000.0000.0000.000
115A116ASN0-0.008-0.02124.645-0.003-0.0030.0000.0000.0000.000
116A117ASN0-0.031-0.01928.0400.0040.0040.0000.0000.0000.000
117A118PRO00.1170.03328.796-0.005-0.0050.0000.0000.0000.000
118A119MET00.0020.02329.419-0.001-0.0010.0000.0000.0000.000
119A120ALA0-0.020-0.01425.8740.0000.0000.0000.0000.0000.000
120A121ILE00.0110.00424.699-0.007-0.0070.0000.0000.0000.000
121A122GLU-1-0.839-0.90024.658-0.082-0.0820.0000.0000.0000.000
122A123ILE0-0.0120.00923.3130.0010.0010.0000.0000.0000.000
123A124ALA00.003-0.01220.5760.0000.0000.0000.0000.0000.000
124A125LEU0-0.033-0.00520.512-0.016-0.0160.0000.0000.0000.000
125A126GLU-1-0.915-0.94022.213-0.072-0.0720.0000.0000.0000.000
126A127MET0-0.108-0.04818.5700.0090.0090.0000.0000.0000.000
127A128GLY00.0200.01817.828-0.011-0.0110.0000.0000.0000.000
128A129ILE0-0.088-0.04915.591-0.048-0.0480.0000.0000.0000.000
129A130SER00.0460.01517.2870.0110.0110.0000.0000.0000.000
130A131ALA0-0.043-0.01615.3030.0060.0060.0000.0000.0000.000
131A132VAL00.0260.01216.9140.0010.0010.0000.0000.0000.000
132A133LYS10.8660.93215.4860.2440.2440.0000.0000.0000.000
133A134PHE0-0.0110.01020.2270.0150.0150.0000.0000.0000.000
134A135PHE0-0.0160.01023.7090.0020.0020.0000.0000.0000.000
135A136PRO0-0.040-0.02425.5630.0040.0040.0000.0000.0000.000
136A137ALA00.0540.00126.5460.0040.0040.0000.0000.0000.000
137A138GLU-1-0.782-0.86728.469-0.078-0.0780.0000.0000.0000.000
138A139ALA0-0.034-0.01831.9350.0030.0030.0000.0000.0000.000
139A140SER0-0.017-0.01330.2530.0060.0060.0000.0000.0000.000
140A141GLY0-0.010-0.01032.6180.0000.0000.0000.0000.0000.000
141A142GLY00.0080.00731.2410.0000.0000.0000.0000.0000.000
142A143VAL00.0290.00830.643-0.003-0.0030.0000.0000.0000.000
143A144LYS10.9430.97032.1130.0560.0560.0000.0000.0000.000
144A145MET00.0000.01431.2030.0000.0000.0000.0000.0000.000
145A146ILE00.0250.01226.597-0.002-0.0020.0000.0000.0000.000
146A147LYS10.9590.97630.0400.0950.0950.0000.0000.0000.000
147A148ALA0-0.0260.00132.3220.0000.0000.0000.0000.0000.000
148A149LEU00.005-0.00928.7690.0020.0020.0000.0000.0000.000
149A150LEU0-0.013-0.01026.214-0.004-0.0040.0000.0000.0000.000
150A151GLY0-0.0320.00230.059-0.003-0.0030.0000.0000.0000.000
151A152PRO0-0.040-0.01431.875-0.002-0.0020.0000.0000.0000.000
152A153TYR0-0.072-0.08026.965-0.004-0.0040.0000.0000.0000.000
153A154ALA00.0590.03827.139-0.012-0.0120.0000.0000.0000.000
154A155GLN0-0.018-0.01023.8580.0030.0030.0000.0000.0000.000
155A156LEU00.0010.01322.348-0.023-0.0230.0000.0000.0000.000
156A157GLN0-0.0040.00016.430-0.010-0.0100.0000.0000.0000.000
157A158ILE00.010-0.00519.907-0.001-0.0010.0000.0000.0000.000
158A159MET00.0130.01515.682-0.025-0.0250.0000.0000.0000.000
159A160PRO00.0030.00720.1760.0180.0180.0000.0000.0000.000
160A161THR00.0680.02820.948-0.011-0.0110.0000.0000.0000.000
161A162GLY00.0340.01423.9190.0100.0100.0000.0000.0000.000
162A163GLY00.0070.00527.3220.0000.0000.0000.0000.0000.000
163A164ILE0-0.024-0.00825.0920.0000.0000.0000.0000.0000.000
164A165GLY00.031-0.00228.6470.0030.0030.0000.0000.0000.000
165A166LEU00.0160.00430.026-0.006-0.0060.0000.0000.0000.000
166A167HIS00.000-0.00131.692-0.003-0.0030.0000.0000.0000.000
167A168ASN00.0240.01930.896-0.003-0.0030.0000.0000.0000.000
168A169ILE00.0050.00624.799-0.006-0.0060.0000.0000.0000.000
169A170ARG10.8860.93328.2460.1030.1030.0000.0000.0000.000
170A171ASP-1-0.911-0.95230.378-0.097-0.0970.0000.0000.0000.000
171A172TYR0-0.106-0.09626.606-0.004-0.0040.0000.0000.0000.000
172A173LEU0-0.007-0.01223.304-0.009-0.0090.0000.0000.0000.000
173A174ALA0-0.0180.01426.713-0.007-0.0070.0000.0000.0000.000
174A175ILE0-0.075-0.03927.1600.0030.0030.0000.0000.0000.000
175A176PRO00.0670.02625.964-0.012-0.0120.0000.0000.0000.000
176A177ASN0-0.073-0.03723.559-0.012-0.0120.0000.0000.0000.000
177A178ILE0-0.079-0.03422.245-0.017-0.0170.0000.0000.0000.000
178A179VAL0-0.0170.00116.349-0.005-0.0050.0000.0000.0000.000
179A180ALA0-0.018-0.01917.799-0.008-0.0080.0000.0000.0000.000
180A181CYS0-0.050-0.00319.8850.0130.0130.0000.0000.0000.000
181A182GLY00.0500.03620.716-0.016-0.0160.0000.0000.0000.000
182A183GLY0-0.022-0.03021.3360.0150.0150.0000.0000.0000.000
183A184SER00.0140.00923.002-0.006-0.0060.0000.0000.0000.000
184A185TRP00.0100.00825.1530.0050.0050.0000.0000.0000.000
185A186PHE00.0580.02021.9590.0070.0070.0000.0000.0000.000
186A187VAL0-0.014-0.00422.332-0.001-0.0010.0000.0000.0000.000
187A188GLU-1-0.817-0.88025.548-0.025-0.0250.0000.0000.0000.000
188A189LYS10.8710.90527.3130.0020.0020.0000.0000.0000.000
189A190LYS10.8670.90828.5970.0320.0320.0000.0000.0000.000
190A191LEU00.0000.01029.5200.0030.0030.0000.0000.0000.000
191A192ILE00.0120.00924.1970.0010.0010.0000.0000.0000.000
192A193GLN00.0170.01928.0710.0030.0030.0000.0000.0000.000
193A194SER0-0.067-0.03330.6130.0020.0020.0000.0000.0000.000
194A195ASN0-0.058-0.04628.6710.0020.0020.0000.0000.0000.000
195A196ASN0-0.0110.00730.640-0.004-0.0040.0000.0000.0000.000
196A197TRP00.0660.00525.468-0.009-0.0090.0000.0000.0000.000
197A198ASP-1-0.894-0.94228.485-0.059-0.0590.0000.0000.0000.000
198A199GLU-1-0.841-0.89130.965-0.060-0.0600.0000.0000.0000.000
199A200ILE0-0.013-0.00225.299-0.006-0.0060.0000.0000.0000.000
200A201GLY00.035-0.00126.264-0.010-0.0100.0000.0000.0000.000
201A202ARG10.6920.81227.3070.0550.0550.0000.0000.0000.000
202A203LEU00.001-0.00228.725-0.005-0.0050.0000.0000.0000.000
203A204VAL0-0.019-0.00823.027-0.007-0.0070.0000.0000.0000.000
204A205ARG10.9460.96425.9610.0770.0770.0000.0000.0000.000
205A206GLU-1-0.830-0.89427.558-0.077-0.0770.0000.0000.0000.000
206A207VAL0-0.026-0.01625.096-0.002-0.0020.0000.0000.0000.000
207A208ILE0-0.029-0.02222.744-0.011-0.0110.0000.0000.0000.000
208A209ASP-1-0.868-0.93125.889-0.115-0.1150.0000.0000.0000.000
209A210ILE0-0.028-0.00329.3300.0000.0000.0000.0000.0000.000
210A211ILE0-0.031-0.02724.204-0.002-0.0020.0000.0000.0000.000
211A212LYS10.7900.90223.0960.1710.1710.0000.0000.0000.000
212A213GLU-1-0.930-0.94428.241-0.093-0.0930.0000.0000.0000.000