FMODB

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

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: Q893Y

Calculation Name: 2VH1-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2VH1

Chain ID: A

ChEMBL ID:

UniProt ID: P06136

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

Apendix: None


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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 205
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2144596.96977
FMO2-HF: Nuclear repulsion 2062652.559331
FMO2-HF: Total energy -81944.410439
FMO2-MP2: Total energy -82183.48663


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:57:ACE )


Summations of interaction energy for fragment #1(A:57:ACE )
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.
-1.9180.8940.809-1.691-1.932-0.011
Interaction energy analysis for fragmet #1(A:57:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.051 / q_NPA : 0.024
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].
3A59LYS 10.9230.9743.8690.9971.709-0.005-0.316-0.3920.001
4A60LEU 00.0270.0226.621-0.096-0.0960.0000.0000.0000.000
5A61VAL 0-0.044-0.0239.8630.1130.1130.0000.0000.0000.000
6A62LEU 00.0210.00812.277-0.012-0.0120.0000.0000.0000.000
7A63THR 0-0.047-0.04315.9050.0260.0260.0000.0000.0000.000
8A64GLY 00.0260.01718.719-0.009-0.0090.0000.0000.0000.000
9A65GLU -1-0.912-0.95922.444-0.039-0.0390.0000.0000.0000.000
10A66ARG 10.8830.94719.0840.0780.0780.0000.0000.0000.000
11A67HIS 0-0.030-0.00425.7360.0080.0080.0000.0000.0000.000
12A68TYR 0-0.003-0.01728.7490.0030.0030.0000.0000.0000.000
13A69THR 0-0.057-0.02722.618-0.005-0.0050.0000.0000.0000.000
14A70ARG 10.8650.91624.0680.0590.0590.0000.0000.0000.000
15A71ASN 00.028-0.01219.126-0.020-0.0200.0000.0000.0000.000
16A72ASP -1-0.856-0.93419.808-0.129-0.1290.0000.0000.0000.000
17A73ASP -1-0.739-0.81721.310-0.104-0.1040.0000.0000.0000.000
18A74ILE 00.025-0.00116.839-0.013-0.0130.0000.0000.0000.000
19A75ARG 10.9240.96413.6980.1470.1470.0000.0000.0000.000
20A76GLN 00.004-0.02917.878-0.031-0.0310.0000.0000.0000.000
21A77SER 0-0.046-0.01019.8000.0040.0040.0000.0000.0000.000
22A78ILE 0-0.003-0.01313.669-0.013-0.0130.0000.0000.0000.000
23A79LEU 0-0.011-0.00815.846-0.016-0.0160.0000.0000.0000.000
24A80ALA 0-0.0300.00718.1080.0090.0090.0000.0000.0000.000
25A81LEU 0-0.055-0.02917.7520.0110.0110.0000.0000.0000.000
26A82GLY 0-0.0070.00717.514-0.006-0.0060.0000.0000.0000.000
27A83GLU -1-0.901-0.93815.583-0.198-0.1980.0000.0000.0000.000
28A84PRO 00.0090.01312.918-0.084-0.0840.0000.0000.0000.000
29A85GLY 0-0.009-0.0139.0360.0320.0320.0000.0000.0000.000
30A86THR 00.0110.0029.296-0.137-0.1370.0000.0000.0000.000
31A87PHE 00.005-0.0047.403-0.074-0.0740.0000.0000.0000.000
32A88MET 00.0200.0285.9010.2110.2110.0000.0000.0000.000
33A89THR 0-0.092-0.0559.2670.1080.1080.0000.0000.0000.000
34A90GLN 00.0280.02611.9710.1330.1330.0000.0000.0000.000
35A91ASP -1-0.831-0.91714.776-0.291-0.2910.0000.0000.0000.000
36A92VAL 0-0.003-0.01614.8800.0100.0100.0000.0000.0000.000
37A93ASN 00.0340.01317.3360.0230.0230.0000.0000.0000.000
38A94ILE 00.0210.02220.1230.0200.0200.0000.0000.0000.000
39A95ILE 0-0.016-0.01814.8160.0080.0080.0000.0000.0000.000
40A96GLN 0-0.078-0.03619.2600.0050.0050.0000.0000.0000.000
41A97THR 00.0280.01921.6480.0190.0190.0000.0000.0000.000
42A98GLN 0-0.024-0.01721.5050.0210.0210.0000.0000.0000.000
43A99ILE 0-0.016-0.02018.7760.0120.0120.0000.0000.0000.000
44A100GLU -1-0.885-0.94423.208-0.119-0.1190.0000.0000.0000.000
45A101GLN 0-0.035-0.02026.4850.0130.0130.0000.0000.0000.000
46A102ARG 10.8800.95723.7040.1470.1470.0000.0000.0000.000
47A103LEU 0-0.057-0.03023.2750.0070.0070.0000.0000.0000.000
48A104PRO 00.0850.05627.6130.0000.0000.0000.0000.0000.000
49A105TRP 0-0.025-0.02626.7100.0060.0060.0000.0000.0000.000
50A106ILE 0-0.065-0.03724.6660.0030.0030.0000.0000.0000.000
51A107LYS 10.9660.99327.9990.0610.0610.0000.0000.0000.000
52A108GLN 0-0.020-0.01525.8000.0060.0060.0000.0000.0000.000
53A109VAL 00.0190.01220.8540.0000.0000.0000.0000.0000.000
54A110SER 0-0.074-0.02520.096-0.008-0.0080.0000.0000.0000.000
55A111VAL 00.0680.02715.578-0.014-0.0140.0000.0000.0000.000
56A112ARG 10.9360.96714.9060.2060.2060.0000.0000.0000.000
57A113LYS 10.9000.95110.6830.6260.6260.0000.0000.0000.000
58A114GLN 00.0080.00110.0720.0960.0960.0000.0000.0000.000
59A115TRP 00.0100.0458.382-0.166-0.1660.0000.0000.0000.000
60A116PRO 0-0.017-0.0145.1990.0500.0500.0000.0000.0000.000
61A117ASP -1-0.878-0.9632.925-3.587-1.4570.814-1.362-1.583-0.012
62A118GLU -1-0.946-0.9834.876-0.351-0.3810.000-0.0130.0430.000
63A119LEU 00.0290.0057.5420.0790.0790.0000.0000.0000.000
64A120LYS 10.8640.93410.5420.2610.2610.0000.0000.0000.000
65A121ILE 00.0060.01313.3950.0010.0010.0000.0000.0000.000
66A122HIS 0-0.0070.01016.4370.0190.0190.0000.0000.0000.000
67A123LEU 0-0.006-0.00619.513-0.003-0.0030.0000.0000.0000.000
68A124VAL 00.022-0.00122.6330.0110.0110.0000.0000.0000.000
69A125GLU -1-0.720-0.84126.281-0.071-0.0710.0000.0000.0000.000
70A126TYR 0-0.0030.00828.7690.0050.0050.0000.0000.0000.000
71A127VAL 00.0160.00332.4550.0010.0010.0000.0000.0000.000
72A128PRO 0-0.056-0.01534.6210.0020.0020.0000.0000.0000.000
73A129ILE 0-0.040-0.03637.8250.0030.0030.0000.0000.0000.000
74A130ALA 0-0.028-0.01941.2290.0030.0030.0000.0000.0000.000
75A131ARG 10.9110.96840.2170.0280.0280.0000.0000.0000.000
76A132TRP 00.022-0.00142.3460.0020.0020.0000.0000.0000.000
77A133ASN 00.0380.01943.8220.0000.0000.0000.0000.0000.000
78A134ASP -1-0.885-0.95545.098-0.031-0.0310.0000.0000.0000.000
79A135GLN 0-0.054-0.02841.049-0.001-0.0010.0000.0000.0000.000
80A136HIS 0-0.0010.01539.196-0.004-0.0040.0000.0000.0000.000
81A137MET 0-0.067-0.01537.3690.0030.0030.0000.0000.0000.000
82A138VAL 00.0320.01839.550-0.002-0.0020.0000.0000.0000.000
83A139ASP -1-0.737-0.85136.268-0.047-0.0470.0000.0000.0000.000
84A140ALA 0-0.016-0.00638.7660.0020.0020.0000.0000.0000.000
85A141GLU -1-0.900-0.96737.263-0.041-0.0410.0000.0000.0000.000
86A142GLY 0-0.066-0.02340.4300.0000.0000.0000.0000.0000.000
87A143ASN 0-0.090-0.05136.745-0.002-0.0020.0000.0000.0000.000
88A144THR 00.0160.00338.7420.0020.0020.0000.0000.0000.000
89A145PHE 0-0.003-0.00533.874-0.004-0.0040.0000.0000.0000.000
90A146SER 00.0170.01034.6810.0030.0030.0000.0000.0000.000
91A147VAL 00.0480.00332.665-0.005-0.0050.0000.0000.0000.000
92A148PRO 00.0040.02031.3540.0040.0040.0000.0000.0000.000
93A149PRO 00.0810.04234.5890.0020.0020.0000.0000.0000.000
94A150GLU -1-0.911-0.97733.964-0.046-0.0460.0000.0000.0000.000
95A151ARG 10.7150.85027.1020.0740.0740.0000.0000.0000.000
96A152THR 00.0420.00733.9560.0010.0010.0000.0000.0000.000
97A153SER 0-0.007-0.00136.8090.0020.0020.0000.0000.0000.000
98A154LYS 10.9340.96738.7910.0200.0200.0000.0000.0000.000
99A155GLN 00.0480.04036.2960.0000.0000.0000.0000.0000.000
100A156VAL 0-0.021-0.01840.6620.0000.0000.0000.0000.0000.000
101A157LEU 0-0.016-0.00439.6740.0000.0000.0000.0000.0000.000
102A158PRO 00.0140.02344.2490.0010.0010.0000.0000.0000.000
103A159MET 00.0120.01045.723-0.002-0.0020.0000.0000.0000.000
104A160LEU 0-0.031-0.01045.9680.0010.0010.0000.0000.0000.000
105A161TYR 0-0.038-0.03547.597-0.001-0.0010.0000.0000.0000.000
106A162GLY 0-0.005-0.01249.6600.0010.0010.0000.0000.0000.000
107A163PRO 0-0.068-0.01549.644-0.001-0.0010.0000.0000.0000.000
108A164GLU -1-0.904-0.95844.515-0.044-0.0440.0000.0000.0000.000
109A165GLY 00.0780.04745.6370.0010.0010.0000.0000.0000.000
110A166SER 0-0.064-0.05046.6890.0010.0010.0000.0000.0000.000
111A167ALA 00.0390.02743.8670.0010.0010.0000.0000.0000.000
112A168ASN 00.0760.01343.9210.0030.0030.0000.0000.0000.000
113A169GLU -1-0.813-0.86246.266-0.026-0.0260.0000.0000.0000.000
114A170VAL 0-0.003-0.01748.6680.0020.0020.0000.0000.0000.000
115A171LEU 00.0060.01843.5230.0020.0020.0000.0000.0000.000
116A172GLN 00.009-0.00546.6130.0020.0020.0000.0000.0000.000
117A173GLY 00.0290.03049.9870.0010.0010.0000.0000.0000.000
118A174TYR 0-0.005-0.01447.2600.0010.0010.0000.0000.0000.000
119A175ARG 10.8770.93743.2360.0300.0300.0000.0000.0000.000
120A176GLU -1-0.939-0.96350.508-0.018-0.0180.0000.0000.0000.000
121A177MET 0-0.039-0.03454.1040.0010.0010.0000.0000.0000.000
122A178GLY 00.0340.00452.5500.0010.0010.0000.0000.0000.000
123A179GLN 0-0.049-0.02450.4710.0000.0000.0000.0000.0000.000
124A180MET 0-0.059-0.01454.3550.0010.0010.0000.0000.0000.000
125A181LEU 00.000-0.00156.4620.0010.0010.0000.0000.0000.000
126A182ALA 00.0310.00253.9830.0010.0010.0000.0000.0000.000
127A183LYS 10.8800.95656.0460.0130.0130.0000.0000.0000.000
128A184ASP -1-0.874-0.92958.539-0.010-0.0100.0000.0000.0000.000
129A185ARG 10.9310.95158.1230.0110.0110.0000.0000.0000.000
130A186PHE 0-0.081-0.02557.6360.0000.0000.0000.0000.0000.000
131A187THR 00.0110.00751.9550.0000.0000.0000.0000.0000.000
132A188LEU 0-0.038-0.01452.1660.0000.0000.0000.0000.0000.000
133A189LYS 10.9300.96850.9740.0150.0150.0000.0000.0000.000
134A190GLU -1-0.903-0.95950.415-0.022-0.0220.0000.0000.0000.000
135A191ALA 0-0.013-0.01351.5160.0010.0010.0000.0000.0000.000
136A192ALA 00.0160.01951.747-0.001-0.0010.0000.0000.0000.000
137A193MET 0-0.0130.01652.8020.0010.0010.0000.0000.0000.000
138A194THR 0-0.129-0.08554.058-0.001-0.0010.0000.0000.0000.000
139A195ALA 00.1300.04455.6120.0000.0000.0000.0000.0000.000
140A196ARG 10.9720.98756.5570.0200.0200.0000.0000.0000.000
141A197ARG 10.8410.89652.9440.0270.0270.0000.0000.0000.000
142A198SER 0-0.051-0.02958.7180.0010.0010.0000.0000.0000.000
143A199TRP 00.0620.02952.737-0.001-0.0010.0000.0000.0000.000
144A200GLN 0-0.044-0.03057.4990.0020.0020.0000.0000.0000.000
145A201LEU 00.0130.01155.557-0.001-0.0010.0000.0000.0000.000
146A202THR 00.0170.02454.7600.0010.0010.0000.0000.0000.000
147A203LEU 00.0090.00355.1900.0000.0000.0000.0000.0000.000
148A204ASN 00.0490.02455.3910.0000.0000.0000.0000.0000.000
149A205ASN 0-0.026-0.02256.0150.0000.0000.0000.0000.0000.000
150A206ASP -1-0.893-0.93957.111-0.016-0.0160.0000.0000.0000.000
151A207ILE 0-0.092-0.04458.9400.0000.0000.0000.0000.0000.000
152A208LYS 10.9791.00157.8990.0170.0170.0000.0000.0000.000
153A209LEU 00.0110.00260.3560.0010.0010.0000.0000.0000.000
154A210ASN 0-0.020-0.02661.105-0.001-0.0010.0000.0000.0000.000
155A211LEU 00.0580.02759.8000.0010.0010.0000.0000.0000.000
156A212GLY 00.0190.01562.7250.0000.0000.0000.0000.0000.000
157A213ARG 10.9140.94861.9590.0190.0190.0000.0000.0000.000
158A214GLY 0-0.023-0.00763.4450.0000.0000.0000.0000.0000.000
159A215ASP -1-0.842-0.91163.609-0.016-0.0160.0000.0000.0000.000
160A216THR 0-0.019-0.02459.5990.0010.0010.0000.0000.0000.000
161A217MET 00.0710.04657.5140.0010.0010.0000.0000.0000.000
162A218LYS 10.9920.98962.2010.0140.0140.0000.0000.0000.000
163A219ARG 10.8500.93965.0440.0160.0160.0000.0000.0000.000
164A220LEU 00.0090.00558.9120.0000.0000.0000.0000.0000.000
165A221ALA 00.0500.02663.3200.0000.0000.0000.0000.0000.000
166A222ARG 10.9670.97165.0960.0130.0130.0000.0000.0000.000
167A223PHE 0-0.017-0.01362.3750.0000.0000.0000.0000.0000.000
168A224VAL 00.0060.00062.4460.0000.0000.0000.0000.0000.000
169A225GLU -1-0.958-0.96065.348-0.009-0.0090.0000.0000.0000.000
170A226LEU 0-0.035-0.02768.8630.0000.0000.0000.0000.0000.000
171A227TYR 0-0.026-0.00464.6740.0000.0000.0000.0000.0000.000
172A228PRO 0-0.012-0.00967.4320.0000.0000.0000.0000.0000.000
173A229VAL 00.0470.00969.2830.0000.0000.0000.0000.0000.000
174A230LEU 00.0210.01470.3180.0000.0000.0000.0000.0000.000
175A231GLN 0-0.0080.00166.8320.0000.0000.0000.0000.0000.000
176A232GLN 0-0.008-0.00969.6670.0000.0000.0000.0000.0000.000
177A233GLN 00.0060.01572.5690.0000.0000.0000.0000.0000.000
178A234ALA 00.0040.00770.2980.0000.0000.0000.0000.0000.000
179A235GLN 0-0.028-0.01168.5840.0000.0000.0000.0000.0000.000
180A236THR 0-0.045-0.03071.8350.0000.0000.0000.0000.0000.000
181A237ASP -1-0.912-0.94275.051-0.007-0.0070.0000.0000.0000.000
182A238GLY 0-0.035-0.01472.4510.0000.0000.0000.0000.0000.000
183A239LYS 10.8500.92970.6520.0080.0080.0000.0000.0000.000
184A240ARG 10.9550.96762.8520.0120.0120.0000.0000.0000.000
185A241ILE 00.0370.00966.3410.0000.0000.0000.0000.0000.000
186A242SER 0-0.073-0.03964.2790.0000.0000.0000.0000.0000.000
187A243TYR 00.0120.00763.621-0.001-0.0010.0000.0000.0000.000
188A244VAL 00.0270.01165.0480.0010.0010.0000.0000.0000.000
189A245ASP -1-0.779-0.87565.516-0.015-0.0150.0000.0000.0000.000
190A246LEU 0-0.024-0.00665.3560.0010.0010.0000.0000.0000.000
191A247ARG 10.8630.92065.2260.0150.0150.0000.0000.0000.000
192A248TYR 0-0.042-0.03667.431-0.001-0.0010.0000.0000.0000.000
193A249ASP -1-0.845-0.91170.742-0.014-0.0140.0000.0000.0000.000
194A250SER 0-0.109-0.06772.7410.0000.0000.0000.0000.0000.000
195A251GLY 00.0250.01273.9660.0000.0000.0000.0000.0000.000
196A252ALA 0-0.012-0.00171.5110.0000.0000.0000.0000.0000.000
197A253ALA 0-0.0110.01471.1410.0000.0000.0000.0000.0000.000
198A254VAL 00.022-0.00269.9590.0000.0000.0000.0000.0000.000
199A255GLY 00.0070.01869.2310.0000.0000.0000.0000.0000.000
200A256TRP 00.004-0.00168.6910.0000.0000.0000.0000.0000.000
201A257ALA 0-0.017-0.01266.7260.0000.0000.0000.0000.0000.000
202A258PRO 00.0230.00368.1660.0000.0000.0000.0000.0000.000
203A259LEU 0-0.0030.00066.632-0.001-0.0010.0000.0000.0000.000
204A260PRO 0-0.035-0.01962.5590.0000.0000.0000.0000.0000.000
205A261NME 00.0450.04165.0110.0000.0000.0000.0000.0000.000