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: 6YMRZ

Calculation Name: 2VH1-A-Xray372

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: 2023-09-24

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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2140147.996696
FMO2-HF: Nuclear repulsion 2058372.795633
FMO2-HF: Total energy -81775.201064
FMO2-MP2: Total energy -82013.694921


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:58:SER)


Summations of interaction energy for fragment #1(A:58: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.
-7.075-0.847.426-5.835-7.825-0.018
Interaction energy analysis for fragmet #1(A:58:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.009
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].
3A60LEU00.0220.0113.794-0.5321.637-0.031-1.147-0.9910.004
4A61VAL0-0.040-0.0226.860-0.034-0.0340.0000.0000.0000.000
5A62LEU00.0080.0089.6590.0840.0840.0000.0000.0000.000
6A63THR0-0.040-0.04312.947-0.021-0.0210.0000.0000.0000.000
7A64GLY00.0380.01916.0820.0140.0140.0000.0000.0000.000
8A65GLU-1-0.903-0.94119.6860.0080.0080.0000.0000.0000.000
9A66ARG10.8730.94916.2630.0420.0420.0000.0000.0000.000
10A67HIS0-0.027-0.01822.508-0.014-0.0140.0000.0000.0000.000
11A68TYR0-0.034-0.04124.839-0.008-0.0080.0000.0000.0000.000
12A69THR0-0.045-0.03918.3170.0010.0010.0000.0000.0000.000
13A70ARG10.8250.89619.759-0.003-0.0030.0000.0000.0000.000
14A71ASN00.036-0.01114.9070.0290.0290.0000.0000.0000.000
15A72ASP-1-0.823-0.91115.001-0.041-0.0410.0000.0000.0000.000
16A73ASP-1-0.715-0.79016.0470.0420.0420.0000.0000.0000.000
17A74ILE00.0290.00711.7890.0300.0300.0000.0000.0000.000
18A75ARG10.9140.9669.7700.3540.3540.0000.0000.0000.000
19A76GLN0-0.014-0.04512.4430.0780.0780.0000.0000.0000.000
20A77SER0-0.063-0.02714.3540.0250.0250.0000.0000.0000.000
21A78ILE00.006-0.0078.0200.0430.0430.0000.0000.0000.000
22A79LEU0-0.005-0.00510.2020.0640.0640.0000.0000.0000.000
23A80ALA0-0.0200.01112.5110.0040.0040.0000.0000.0000.000
24A81LEU0-0.055-0.02512.415-0.012-0.0120.0000.0000.0000.000
25A82GLY0-0.0080.00312.5820.0490.0490.0000.0000.0000.000
26A83GLU-1-0.879-0.92711.4130.2090.2090.0000.0000.0000.000
27A84PRO0-0.0090.0048.0460.2650.2650.0000.0000.0000.000
28A85GLY0-0.008-0.0145.151-0.212-0.2120.0000.0000.0000.000
29A86THR00.0100.0055.4960.7970.856-0.0010.000-0.0580.000
30A87PHE00.0180.0102.503-0.0650.1812.680-0.806-2.120-0.009
31A88MET00.0060.0182.075-3.044-1.9683.285-1.904-2.4560.002
32A89THR0-0.082-0.0574.990-1.201-1.152-0.001-0.002-0.0450.000
33A90GLN00.0280.0268.056-0.447-0.4470.0000.0000.0000.000
34A91ASP-1-0.783-0.88410.4910.5590.5590.0000.0000.0000.000
35A92VAL00.002-0.01211.326-0.030-0.0300.0000.0000.0000.000
36A93ASN0-0.015-0.01513.467-0.080-0.0800.0000.0000.0000.000
37A94ILE00.0250.02415.525-0.048-0.0480.0000.0000.0000.000
38A95ILE0-0.011-0.01410.045-0.033-0.0330.0000.0000.0000.000
39A96GLN0-0.093-0.05414.326-0.031-0.0310.0000.0000.0000.000
40A97THR00.0320.01717.036-0.040-0.0400.0000.0000.0000.000
41A98GLN0-0.011-0.00916.133-0.056-0.0560.0000.0000.0000.000
42A99ILE0-0.033-0.03313.708-0.034-0.0340.0000.0000.0000.000
43A100GLU-1-0.874-0.92318.0480.1620.1620.0000.0000.0000.000
44A101GLN0-0.037-0.02421.317-0.023-0.0230.0000.0000.0000.000
45A102ARG10.8740.95217.942-0.147-0.1470.0000.0000.0000.000
46A103LEU0-0.061-0.02918.035-0.020-0.0200.0000.0000.0000.000
47A104PRO00.0820.05022.4230.0030.0030.0000.0000.0000.000
48A105TRP0-0.020-0.02621.656-0.003-0.0030.0000.0000.0000.000
49A106ILE0-0.073-0.04520.414-0.005-0.0050.0000.0000.0000.000
50A107LYS10.8200.90023.619-0.064-0.0640.0000.0000.0000.000
51A108GLN0-0.003-0.00422.082-0.002-0.0020.0000.0000.0000.000
52A109VAL00.0150.00617.131-0.009-0.0090.0000.0000.0000.000
53A110SER0-0.068-0.01717.2760.0160.0160.0000.0000.0000.000
54A111VAL00.0380.00611.9130.0020.0020.0000.0000.0000.000
55A112ARG10.9190.94911.907-0.319-0.3190.0000.0000.0000.000
56A113LYS10.8730.9267.941-1.477-1.4770.0000.0000.0000.000
57A114GLN00.0220.0077.724-0.200-0.2000.0000.0000.0000.000
58A115TRP00.0250.0557.2660.2390.2390.0000.0000.0000.000
59A116PRO0-0.018-0.0176.664-0.108-0.1080.0000.0000.0000.000
60A117ASP-1-0.849-0.9602.472-1.089-0.1391.004-0.775-1.180-0.003
61A118GLU-1-0.844-0.9202.844-0.2831.3350.491-1.201-0.908-0.012
62A119LEU00.0180.0095.1190.0450.113-0.0010.000-0.0670.000
63A120LYS10.8110.9186.928-0.590-0.5900.0000.0000.0000.000
64A121ILE00.0260.01410.2340.0480.0480.0000.0000.0000.000
65A122HIS00.0000.02012.889-0.050-0.0500.0000.0000.0000.000
66A123LEU00.004-0.00416.2550.0150.0150.0000.0000.0000.000
67A124VAL00.0220.00019.208-0.013-0.0130.0000.0000.0000.000
68A125GLU-1-0.684-0.79622.8150.0380.0380.0000.0000.0000.000
69A126TYR00.0140.01425.048-0.003-0.0030.0000.0000.0000.000
70A127VAL00.0070.00128.618-0.005-0.0050.0000.0000.0000.000
71A128PRO0-0.048-0.01431.0400.0010.0010.0000.0000.0000.000
72A129ILE0-0.044-0.03433.978-0.003-0.0030.0000.0000.0000.000
73A130ALA0-0.021-0.01537.478-0.003-0.0030.0000.0000.0000.000
74A131ARG10.8900.95236.046-0.014-0.0140.0000.0000.0000.000
75A132TRP00.013-0.00737.670-0.001-0.0010.0000.0000.0000.000
76A133ASN00.0320.01738.9440.0000.0000.0000.0000.0000.000
77A134ASP-1-0.864-0.92939.9450.0240.0240.0000.0000.0000.000
78A135GLN0-0.063-0.02935.7540.0000.0000.0000.0000.0000.000
79A136HIS00.0070.02234.4080.0030.0030.0000.0000.0000.000
80A137MET0-0.064-0.01233.079-0.004-0.0040.0000.0000.0000.000
81A138VAL00.0140.00535.0230.0040.0040.0000.0000.0000.000
82A139ASP-1-0.704-0.82732.4310.0530.0530.0000.0000.0000.000
83A140ALA00.0090.00235.046-0.001-0.0010.0000.0000.0000.000
84A141GLU-1-0.859-0.92733.1150.0550.0550.0000.0000.0000.000
85A142GLY0-0.029-0.01036.9450.0010.0010.0000.0000.0000.000
86A143ASN0-0.075-0.03832.5570.0040.0040.0000.0000.0000.000
87A144THR00.003-0.00334.315-0.004-0.0040.0000.0000.0000.000
88A145PHE00.0250.00529.2460.0050.0050.0000.0000.0000.000
89A146SER00.0210.01229.809-0.004-0.0040.0000.0000.0000.000
90A147VAL00.032-0.00227.2430.0040.0040.0000.0000.0000.000
91A148PRO00.0070.02126.214-0.002-0.0020.0000.0000.0000.000
92A149PRO00.0830.03829.481-0.004-0.0040.0000.0000.0000.000
93A150GLU-1-0.901-0.97228.5750.0100.0100.0000.0000.0000.000
94A151ARG10.6950.82022.140-0.022-0.0220.0000.0000.0000.000
95A152THR00.029-0.00529.4520.0000.0000.0000.0000.0000.000
96A153SER0-0.014-0.00332.4900.0000.0000.0000.0000.0000.000
97A154LYS10.9330.96934.8810.0100.0100.0000.0000.0000.000
98A155GLN00.0620.07132.5650.0000.0000.0000.0000.0000.000
99A156VAL00.017-0.00136.8390.0010.0010.0000.0000.0000.000
100A157LEU0-0.013-0.00135.6410.0010.0010.0000.0000.0000.000
101A158PRO00.0200.02940.347-0.001-0.0010.0000.0000.0000.000
102A159MET00.0130.00741.5640.0020.0020.0000.0000.0000.000
103A160LEU0-0.027-0.00742.090-0.001-0.0010.0000.0000.0000.000
104A161TYR0-0.051-0.06042.9800.0010.0010.0000.0000.0000.000
105A162GLY00.010-0.00644.766-0.001-0.0010.0000.0000.0000.000
106A163PRO0-0.064-0.01344.7420.0010.0010.0000.0000.0000.000
107A164GLU-1-0.857-0.92939.7210.0520.0520.0000.0000.0000.000
108A165GLY00.0510.04240.9600.0000.0000.0000.0000.0000.000
109A166SER0-0.070-0.06541.990-0.001-0.0010.0000.0000.0000.000
110A167ALA00.0360.02539.455-0.002-0.0020.0000.0000.0000.000
111A168ASN00.0550.00139.576-0.004-0.0040.0000.0000.0000.000
112A169GLU-1-0.828-0.86442.2320.0320.0320.0000.0000.0000.000
113A170VAL00.010-0.01544.433-0.002-0.0020.0000.0000.0000.000
114A171LEU00.0040.02239.931-0.002-0.0020.0000.0000.0000.000
115A172GLN00.0470.01842.752-0.002-0.0020.0000.0000.0000.000
116A173GLY00.0180.02746.351-0.001-0.0010.0000.0000.0000.000
117A174TYR0-0.008-0.01744.165-0.002-0.0020.0000.0000.0000.000
118A175ARG10.8110.88840.185-0.037-0.0370.0000.0000.0000.000
119A176GLU-1-0.914-0.95447.0950.0220.0220.0000.0000.0000.000
120A177MET0-0.019-0.02250.748-0.002-0.0020.0000.0000.0000.000
121A178GLY00.0220.00549.134-0.001-0.0010.0000.0000.0000.000
122A179GLN0-0.042-0.02347.431-0.001-0.0010.0000.0000.0000.000
123A180MET0-0.053-0.00951.284-0.001-0.0010.0000.0000.0000.000
124A181LEU0-0.004-0.00252.855-0.001-0.0010.0000.0000.0000.000
125A182ALA00.017-0.00550.914-0.001-0.0010.0000.0000.0000.000
126A183LYS10.8790.95753.027-0.015-0.0150.0000.0000.0000.000
127A184ASP-1-0.875-0.92855.6940.0100.0100.0000.0000.0000.000
128A185ARG10.9280.95355.126-0.008-0.0080.0000.0000.0000.000
129A186PHE0-0.088-0.03154.452-0.001-0.0010.0000.0000.0000.000
130A187THR00.0240.01048.5010.0000.0000.0000.0000.0000.000
131A188LEU0-0.037-0.01548.5420.0000.0000.0000.0000.0000.000
132A189LYS10.8340.92247.050-0.009-0.0090.0000.0000.0000.000
133A190GLU-1-0.832-0.89846.3170.0150.0150.0000.0000.0000.000
134A191ALA0-0.002-0.01047.190-0.001-0.0010.0000.0000.0000.000
135A192ALA00.0110.01747.3240.0010.0010.0000.0000.0000.000
136A193MET0-0.0040.02648.029-0.001-0.0010.0000.0000.0000.000
137A194THR0-0.090-0.06149.3300.0000.0000.0000.0000.0000.000
138A195ALA00.0940.03650.7760.0010.0010.0000.0000.0000.000
139A196ARG10.9540.97751.694-0.022-0.0220.0000.0000.0000.000
140A197ARG10.8550.88148.652-0.033-0.0330.0000.0000.0000.000
141A198SER0-0.046-0.02754.213-0.001-0.0010.0000.0000.0000.000
142A199TRP00.0510.02448.6430.0010.0010.0000.0000.0000.000
143A200GLN0-0.032-0.02353.038-0.001-0.0010.0000.0000.0000.000
144A201LEU00.0150.01251.3730.0010.0010.0000.0000.0000.000
145A202THR0-0.042-0.02950.559-0.001-0.0010.0000.0000.0000.000
146A203LEU00.0120.00551.1580.0000.0000.0000.0000.0000.000
147A204ASN00.0900.04151.6750.0000.0000.0000.0000.0000.000
148A205ASN00.0320.01652.200-0.001-0.0010.0000.0000.0000.000
149A206ASP-1-0.867-0.93353.1610.0100.0100.0000.0000.0000.000
150A207ILE0-0.054-0.03054.7710.0000.0000.0000.0000.0000.000
151A208LYS10.8690.94052.721-0.011-0.0110.0000.0000.0000.000
152A209LEU00.0020.00456.088-0.001-0.0010.0000.0000.0000.000
153A210ASN0-0.014-0.01856.8250.0020.0020.0000.0000.0000.000
154A211LEU00.0280.01355.8710.0000.0000.0000.0000.0000.000
155A212GLY00.0270.01858.3300.0000.0000.0000.0000.0000.000
156A213ARG10.9230.95057.599-0.021-0.0210.0000.0000.0000.000
157A214GLY0-0.0220.00159.0490.0010.0010.0000.0000.0000.000
158A215ASP-1-0.793-0.88459.5240.0190.0190.0000.0000.0000.000
159A216THR00.016-0.00655.648-0.001-0.0010.0000.0000.0000.000
160A217MET00.0400.03053.208-0.001-0.0010.0000.0000.0000.000
161A218LYS10.9190.94658.587-0.018-0.0180.0000.0000.0000.000
162A219ARG10.7880.88761.045-0.017-0.0170.0000.0000.0000.000
163A220LEU00.0160.00655.159-0.001-0.0010.0000.0000.0000.000
164A221ALA00.0520.02559.619-0.001-0.0010.0000.0000.0000.000
165A222ARG10.9060.94361.655-0.014-0.0140.0000.0000.0000.000
166A223PHE0-0.013-0.01558.567-0.001-0.0010.0000.0000.0000.000
167A224VAL00.001-0.00558.927-0.001-0.0010.0000.0000.0000.000
168A225GLU-1-0.960-0.96561.9380.0100.0100.0000.0000.0000.000
169A226LEU0-0.032-0.02065.554-0.001-0.0010.0000.0000.0000.000
170A227TYR0-0.028-0.01761.3820.0000.0000.0000.0000.0000.000
171A228PRO0-0.011-0.01164.022-0.001-0.0010.0000.0000.0000.000
172A229VAL00.0420.00965.942-0.001-0.0010.0000.0000.0000.000
173A230LEU00.0140.01366.4030.0000.0000.0000.0000.0000.000
174A231GLN00.0030.01462.7430.0000.0000.0000.0000.0000.000
175A232GLN00.006-0.00566.0860.0000.0000.0000.0000.0000.000
176A233GLN0-0.038-0.00469.1300.0000.0000.0000.0000.0000.000
177A234ALA00.0040.00066.5390.0000.0000.0000.0000.0000.000
178A235GLN0-0.038-0.01665.3320.0000.0000.0000.0000.0000.000
179A236THR0-0.034-0.02368.245-0.001-0.0010.0000.0000.0000.000
180A237ASP-1-0.859-0.91071.3040.0040.0040.0000.0000.0000.000
181A238GLY0-0.036-0.02068.7060.0000.0000.0000.0000.0000.000
182A239LYS10.8420.92666.632-0.004-0.0040.0000.0000.0000.000
183A240ARG10.9220.95858.190-0.006-0.0060.0000.0000.0000.000
184A241ILE00.0260.00462.4300.0000.0000.0000.0000.0000.000
185A242SER0-0.029-0.01960.0780.0000.0000.0000.0000.0000.000
186A243TYR0-0.025-0.03459.2580.0010.0010.0000.0000.0000.000
187A244VAL00.0240.00960.758-0.001-0.0010.0000.0000.0000.000
188A245ASP-1-0.763-0.83261.2180.0150.0150.0000.0000.0000.000
189A246LEU0-0.0020.00761.6270.0000.0000.0000.0000.0000.000
190A247ARG10.8560.90060.897-0.014-0.0140.0000.0000.0000.000
191A248TYR0-0.024-0.02163.0660.0010.0010.0000.0000.0000.000
192A249ASP-1-0.790-0.87266.2910.0150.0150.0000.0000.0000.000
193A250SER0-0.065-0.04468.5970.0000.0000.0000.0000.0000.000
194A251GLY00.0240.01369.792-0.001-0.0010.0000.0000.0000.000
195A252ALA0-0.0140.00367.4130.0010.0010.0000.0000.0000.000
196A253ALA0-0.0070.01366.8110.0000.0000.0000.0000.0000.000
197A254VAL00.009-0.00765.6950.0000.0000.0000.0000.0000.000
198A255GLY00.0130.02164.9230.0000.0000.0000.0000.0000.000
199A256TRP00.0080.00564.4270.0000.0000.0000.0000.0000.000
200A257ALA0-0.018-0.01362.4550.0000.0000.0000.0000.0000.000
201A258PRO00.0460.01463.9890.0000.0000.0000.0000.0000.000
202A259LEU0-0.012-0.00162.6460.0000.0000.0000.0000.0000.000
203A260PRO00.0200.02358.548-0.001-0.0010.0000.0000.0000.000