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

tag_button

FMODB ID: Z23QN

Calculation Name: 2VH1-A-Xray307

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:


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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 205
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2144596.541277
FMO2-HF: Nuclear repulsion 2062652.130751
FMO2-HF: Total energy -81944.410526
FMO2-MP2: Total energy -82183.486498


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.
-2.0670.7830.833-1.728-1.956-0.012
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 : 0.050 / 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 10.9230.9743.8680.9941.709-0.005-0.317-0.3930.001
4A60LEU 00.0270.0226.599-0.096-0.0960.0000.0000.0000.000
5A61VAL 0-0.044-0.0239.8550.1140.1140.0000.0000.0000.000
6A62LEU 00.0210.00812.265-0.012-0.0120.0000.0000.0000.000
7A63THR 0-0.047-0.04315.8910.0260.0260.0000.0000.0000.000
8A64GLY 00.0260.01718.708-0.009-0.0090.0000.0000.0000.000
9A65GLU -1-0.912-0.95922.434-0.038-0.0380.0000.0000.0000.000
10A66ARG 10.8830.94719.0600.0770.0770.0000.0000.0000.000
11A67HIS 0-0.030-0.00425.7180.0080.0080.0000.0000.0000.000
12A68TYR 0-0.003-0.01728.7300.0030.0030.0000.0000.0000.000
13A69THR 0-0.057-0.02722.596-0.005-0.0050.0000.0000.0000.000
14A70ARG 10.8650.91624.0410.0590.0590.0000.0000.0000.000
15A71ASN 00.028-0.01219.095-0.020-0.0200.0000.0000.0000.000
16A72ASP -1-0.856-0.93419.782-0.129-0.1290.0000.0000.0000.000
17A73ASP -1-0.739-0.81721.312-0.103-0.1030.0000.0000.0000.000
18A74ILE 00.025-0.00116.822-0.013-0.0130.0000.0000.0000.000
19A75ARG 10.9240.96413.7160.1460.1460.0000.0000.0000.000
20A76GLN 00.004-0.02917.876-0.031-0.0310.0000.0000.0000.000
21A77SER 0-0.045-0.01019.7980.0040.0040.0000.0000.0000.000
22A78ILE 0-0.004-0.01313.668-0.013-0.0130.0000.0000.0000.000
23A79LEU 0-0.011-0.00815.849-0.017-0.0170.0000.0000.0000.000
24A80ALA 0-0.0300.00718.1070.0090.0090.0000.0000.0000.000
25A81LEU 0-0.055-0.02917.7510.0110.0110.0000.0000.0000.000
26A82GLY 0-0.0070.00717.513-0.007-0.0070.0000.0000.0000.000
27A83GLU -1-0.901-0.93815.564-0.198-0.1980.0000.0000.0000.000
28A84PRO 00.0090.01312.916-0.084-0.0840.0000.0000.0000.000
29A85GLY 0-0.009-0.0139.0240.0320.0320.0000.0000.0000.000
30A86THR 00.0110.0019.275-0.138-0.1380.0000.0000.0000.000
31A87PHE 00.005-0.0047.402-0.075-0.0750.0000.0000.0000.000
32A88MET 00.0200.0285.8990.2120.2120.0000.0000.0000.000
33A89THR 0-0.092-0.0559.2660.1080.1080.0000.0000.0000.000
34A90GLN 00.0280.02611.9750.1330.1330.0000.0000.0000.000
35A91ASP -1-0.831-0.91714.775-0.292-0.2920.0000.0000.0000.000
36A92VAL 0-0.003-0.01614.8780.0100.0100.0000.0000.0000.000
37A93ASN 00.0340.01317.3350.0230.0230.0000.0000.0000.000
38A94ILE 00.0210.02220.1220.0200.0200.0000.0000.0000.000
39A95ILE 0-0.016-0.01814.8150.0080.0080.0000.0000.0000.000
40A96GLN 0-0.078-0.03619.2590.0050.0050.0000.0000.0000.000
41A97THR 00.0280.01921.6460.0190.0190.0000.0000.0000.000
42A98GLN 0-0.024-0.01721.5040.0210.0210.0000.0000.0000.000
43A99ILE 0-0.016-0.02018.7690.0120.0120.0000.0000.0000.000
44A100GLU -1-0.885-0.94423.206-0.119-0.1190.0000.0000.0000.000
45A101GLN 0-0.035-0.02026.4830.0130.0130.0000.0000.0000.000
46A102ARG 10.8800.95723.7030.1470.1470.0000.0000.0000.000
47A103LEU 0-0.056-0.03023.2590.0070.0070.0000.0000.0000.000
48A104PRO 00.0850.05627.6000.0000.0000.0000.0000.0000.000
49A105TRP 0-0.025-0.02626.6930.0060.0060.0000.0000.0000.000
50A106ILE 0-0.065-0.03724.6550.0030.0030.0000.0000.0000.000
51A107LYS 10.9660.99327.9910.0610.0610.0000.0000.0000.000
52A108GLN 0-0.020-0.01525.8070.0060.0060.0000.0000.0000.000
53A109VAL 00.0190.01220.8550.0000.0000.0000.0000.0000.000
54A110SER 0-0.074-0.02520.104-0.008-0.0080.0000.0000.0000.000
55A111VAL 00.0680.02715.587-0.014-0.0140.0000.0000.0000.000
56A112ARG 10.9360.96714.9250.2060.2060.0000.0000.0000.000
57A113LYS 10.9000.95110.6640.6280.6280.0000.0000.0000.000
58A114GLN 00.0080.00110.0930.0960.0960.0000.0000.0000.000
59A115TRP 00.0100.0458.350-0.166-0.1660.0000.0000.0000.000
60A116PRO 0-0.017-0.0145.2340.0500.0500.0000.0000.0000.000
61A117ASP -1-0.878-0.9632.888-3.736-1.5710.838-1.398-1.606-0.013
62A118GLU -1-0.946-0.9834.884-0.345-0.3750.000-0.0130.0430.000
63A119LEU 00.0290.0057.5510.0780.0780.0000.0000.0000.000
64A120LYS 10.8640.93410.5460.2610.2610.0000.0000.0000.000
65A121ILE 00.0060.01313.3970.0010.0010.0000.0000.0000.000
66A122HIS 0-0.0070.01016.4350.0190.0190.0000.0000.0000.000
67A123LEU 0-0.006-0.00619.511-0.003-0.0030.0000.0000.0000.000
68A124VAL 00.022-0.00122.6270.0110.0110.0000.0000.0000.000
69A125GLU -1-0.720-0.84126.275-0.071-0.0710.0000.0000.0000.000
70A126TYR 0-0.0030.00828.7590.0050.0050.0000.0000.0000.000
71A127VAL 00.0160.00332.4460.0010.0010.0000.0000.0000.000
72A128PRO 0-0.056-0.01534.6100.0020.0020.0000.0000.0000.000
73A129ILE 0-0.040-0.03637.8120.0030.0030.0000.0000.0000.000
74A130ALA 0-0.028-0.01941.2160.0030.0030.0000.0000.0000.000
75A131ARG 10.9110.96840.1950.0280.0280.0000.0000.0000.000
76A132TRP 00.022-0.00142.3340.0020.0020.0000.0000.0000.000
77A133ASN 00.0380.01943.8080.0000.0000.0000.0000.0000.000
78A134ASP -1-0.885-0.95545.082-0.031-0.0310.0000.0000.0000.000
79A135GLN 0-0.054-0.02841.032-0.001-0.0010.0000.0000.0000.000
80A136HIS 00.0000.01539.195-0.004-0.0040.0000.0000.0000.000
81A137MET 0-0.067-0.01437.3520.0030.0030.0000.0000.0000.000
82A138VAL 00.0320.01839.539-0.002-0.0020.0000.0000.0000.000
83A139ASP -1-0.737-0.85136.263-0.047-0.0470.0000.0000.0000.000
84A140ALA 0-0.016-0.00638.7590.0020.0020.0000.0000.0000.000
85A141GLU -1-0.900-0.96737.262-0.041-0.0410.0000.0000.0000.000
86A142GLY 0-0.066-0.02340.4280.0000.0000.0000.0000.0000.000
87A143ASN 0-0.090-0.05136.742-0.002-0.0020.0000.0000.0000.000
88A144THR 00.0160.00338.7370.0020.0020.0000.0000.0000.000
89A145PHE 0-0.003-0.00533.861-0.004-0.0040.0000.0000.0000.000
90A146SER 00.0170.01034.6690.0030.0030.0000.0000.0000.000
91A147VAL 00.0480.00332.647-0.005-0.0050.0000.0000.0000.000
92A148PRO 00.0040.02031.3330.0040.0040.0000.0000.0000.000
93A149PRO 00.0810.04234.5670.0020.0020.0000.0000.0000.000
94A150GLU -1-0.912-0.97733.972-0.046-0.0460.0000.0000.0000.000
95A151ARG 10.7150.84927.0780.0740.0740.0000.0000.0000.000
96A152THR 00.0410.00733.9300.0010.0010.0000.0000.0000.000
97A153SER 0-0.007-0.00136.7850.0020.0020.0000.0000.0000.000
98A154LYS 10.9340.96738.7620.0190.0190.0000.0000.0000.000
99A155GLN 00.0480.04036.2760.0000.0000.0000.0000.0000.000
100A156VAL 0-0.021-0.01840.6390.0000.0000.0000.0000.0000.000
101A157LEU 0-0.016-0.00439.6550.0000.0000.0000.0000.0000.000
102A158PRO 00.0140.02444.2310.0010.0010.0000.0000.0000.000
103A159MET 00.0110.01045.707-0.002-0.0020.0000.0000.0000.000
104A160LEU 0-0.031-0.01045.9570.0010.0010.0000.0000.0000.000
105A161TYR 0-0.038-0.03547.584-0.001-0.0010.0000.0000.0000.000
106A162GLY 0-0.005-0.01249.6490.0010.0010.0000.0000.0000.000
107A163PRO 0-0.068-0.01549.635-0.001-0.0010.0000.0000.0000.000
108A164GLU -1-0.904-0.95844.511-0.044-0.0440.0000.0000.0000.000
109A165GLY 00.0780.04745.6340.0010.0010.0000.0000.0000.000
110A166SER 0-0.064-0.05046.6860.0010.0010.0000.0000.0000.000
111A167ALA 00.0390.02743.8600.0010.0010.0000.0000.0000.000
112A168ASN 00.0760.01243.9140.0030.0030.0000.0000.0000.000
113A169GLU -1-0.814-0.86246.263-0.026-0.0260.0000.0000.0000.000
114A170VAL 0-0.003-0.01748.6610.0020.0020.0000.0000.0000.000
115A171LEU 00.0060.01843.5170.0020.0020.0000.0000.0000.000
116A172GLN 00.009-0.00546.6100.0020.0020.0000.0000.0000.000
117A173GLY 00.0290.03049.9830.0010.0010.0000.0000.0000.000
118A174TYR 0-0.005-0.01447.2490.0010.0010.0000.0000.0000.000
119A175ARG 10.8770.93743.2310.0300.0300.0000.0000.0000.000
120A176GLU -1-0.939-0.96350.501-0.018-0.0180.0000.0000.0000.000
121A177MET 0-0.039-0.03454.0980.0010.0010.0000.0000.0000.000
122A178GLY 00.0340.00452.5390.0010.0010.0000.0000.0000.000
123A179GLN 0-0.049-0.02450.4640.0000.0000.0000.0000.0000.000
124A180MET 0-0.059-0.01454.3460.0010.0010.0000.0000.0000.000
125A181LEU 00.000-0.00156.4490.0010.0010.0000.0000.0000.000
126A182ALA 00.0310.00253.9700.0010.0010.0000.0000.0000.000
127A183LYS 10.8800.95656.0320.0130.0130.0000.0000.0000.000
128A184ASP -1-0.874-0.92958.527-0.010-0.0100.0000.0000.0000.000
129A185ARG 10.9310.95158.1060.0110.0110.0000.0000.0000.000
130A186PHE 0-0.081-0.02557.6190.0000.0000.0000.0000.0000.000
131A187THR 00.0110.00751.9370.0000.0000.0000.0000.0000.000
132A188LEU 0-0.038-0.01452.1530.0000.0000.0000.0000.0000.000
133A189LYS 10.9300.96850.9550.0150.0150.0000.0000.0000.000
134A190GLU -1-0.903-0.95950.398-0.022-0.0220.0000.0000.0000.000
135A191ALA 0-0.013-0.01351.5020.0010.0010.0000.0000.0000.000
136A192ALA 00.0160.01951.735-0.001-0.0010.0000.0000.0000.000
137A193MET 0-0.0130.01652.7960.0010.0010.0000.0000.0000.000
138A194THR 0-0.129-0.08554.049-0.001-0.0010.0000.0000.0000.000
139A195ALA 00.1300.04455.6060.0000.0000.0000.0000.0000.000
140A196ARG 10.9720.98756.5510.0200.0200.0000.0000.0000.000
141A197ARG 10.8410.89652.9410.0270.0270.0000.0000.0000.000
142A198SER 0-0.051-0.02958.7120.0010.0010.0000.0000.0000.000
143A199TRP 00.0620.02952.730-0.001-0.0010.0000.0000.0000.000
144A200GLN 0-0.044-0.03057.4870.0020.0020.0000.0000.0000.000
145A201LEU 00.0130.01155.544-0.001-0.0010.0000.0000.0000.000
146A202THR 00.0170.02454.7420.0010.0010.0000.0000.0000.000
147A203LEU 00.0080.00355.1730.0000.0000.0000.0000.0000.000
148A204ASN 00.0500.02455.3710.0000.0000.0000.0000.0000.000
149A205ASN 0-0.026-0.02255.9940.0000.0000.0000.0000.0000.000
150A206ASP -1-0.893-0.93957.089-0.016-0.0160.0000.0000.0000.000
151A207ILE 0-0.092-0.04458.9180.0000.0000.0000.0000.0000.000
152A208LYS 10.9791.00157.8790.0170.0170.0000.0000.0000.000
153A209LEU 00.0110.00260.3400.0010.0010.0000.0000.0000.000
154A210ASN 0-0.020-0.02661.091-0.001-0.0010.0000.0000.0000.000
155A211LEU 00.0590.02759.7900.0010.0010.0000.0000.0000.000
156A212GLY 00.0200.01662.7140.0000.0000.0000.0000.0000.000
157A213ARG 10.9140.94861.9510.0190.0190.0000.0000.0000.000
158A214GLY 0-0.023-0.00763.4380.0000.0000.0000.0000.0000.000
159A215ASP -1-0.842-0.91163.604-0.016-0.0160.0000.0000.0000.000
160A216THR 0-0.018-0.02459.5920.0010.0010.0000.0000.0000.000
161A217MET 00.0710.04657.5060.0010.0010.0000.0000.0000.000
162A218LYS 10.9920.98962.1940.0140.0140.0000.0000.0000.000
163A219ARG 10.8500.93865.0350.0160.0160.0000.0000.0000.000
164A220LEU 00.0090.00558.9050.0000.0000.0000.0000.0000.000
165A221ALA 00.0500.02663.3100.0000.0000.0000.0000.0000.000
166A222ARG 10.9670.97265.0870.0130.0130.0000.0000.0000.000
167A223PHE 0-0.017-0.01362.3600.0000.0000.0000.0000.0000.000
168A224VAL 00.0060.00062.4340.0000.0000.0000.0000.0000.000
169A225GLU -1-0.958-0.96065.335-0.009-0.0090.0000.0000.0000.000
170A226LEU 0-0.036-0.02768.8500.0000.0000.0000.0000.0000.000
171A227TYR 0-0.025-0.00464.6560.0000.0000.0000.0000.0000.000
172A228PRO 0-0.012-0.00967.4170.0000.0000.0000.0000.0000.000
173A229VAL 00.0470.00969.2660.0000.0000.0000.0000.0000.000
174A230LEU 00.0210.01470.3010.0000.0000.0000.0000.0000.000
175A231GLN 0-0.0090.00166.8110.0000.0000.0000.0000.0000.000
176A232GLN 0-0.008-0.00969.6470.0000.0000.0000.0000.0000.000
177A233GLN 00.0060.01572.5490.0000.0000.0000.0000.0000.000
178A234ALA 00.0040.00770.2760.0000.0000.0000.0000.0000.000
179A235GLN 0-0.028-0.01168.5600.0000.0000.0000.0000.0000.000
180A236THR 0-0.045-0.03071.8120.0000.0000.0000.0000.0000.000
181A237ASP -1-0.912-0.94275.028-0.007-0.0070.0000.0000.0000.000
182A238GLY 0-0.035-0.01472.4260.0000.0000.0000.0000.0000.000
183A239LYS 10.8500.92970.6280.0080.0080.0000.0000.0000.000
184A240ARG 10.9550.96762.8300.0120.0120.0000.0000.0000.000
185A241ILE 00.0370.00966.3230.0000.0000.0000.0000.0000.000
186A242SER 0-0.073-0.03964.2590.0000.0000.0000.0000.0000.000
187A243TYR 00.0120.00763.601-0.001-0.0010.0000.0000.0000.000
188A244VAL 00.0270.01165.0320.0010.0010.0000.0000.0000.000
189A245ASP -1-0.779-0.87565.502-0.015-0.0150.0000.0000.0000.000
190A246LEU 0-0.024-0.00665.3440.0010.0010.0000.0000.0000.000
191A247ARG 10.8630.92065.2150.0150.0150.0000.0000.0000.000
192A248TYR 0-0.042-0.03767.420-0.001-0.0010.0000.0000.0000.000
193A249ASP -1-0.845-0.91170.732-0.014-0.0140.0000.0000.0000.000
194A250SER 0-0.109-0.06772.7330.0000.0000.0000.0000.0000.000
195A251GLY 00.0250.01273.9550.0000.0000.0000.0000.0000.000
196A252ALA 0-0.012-0.00171.4970.0000.0000.0000.0000.0000.000
197A253ALA 0-0.0110.01471.1270.0000.0000.0000.0000.0000.000
198A254VAL 00.022-0.00269.9420.0000.0000.0000.0000.0000.000
199A255GLY 00.0070.01869.2140.0000.0000.0000.0000.0000.000
200A256TRP 00.004-0.00168.6720.0000.0000.0000.0000.0000.000
201A257ALA 0-0.018-0.01266.7030.0000.0000.0000.0000.0000.000
202A258PRO 00.0230.00368.1410.0000.0000.0000.0000.0000.000
203A259LEU 0-0.0030.00066.607-0.001-0.0010.0000.0000.0000.000
204A260PRO 0-0.035-0.01962.5330.0000.0000.0000.0000.0000.000
205A261NME 00.0450.04164.9820.0000.0000.0000.0000.0000.000