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: ZVJGN

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2143913.448877
FMO2-HF: Nuclear repulsion 2062137.540426
FMO2-HF: Total energy -81775.90845
FMO2-MP2: Total energy -82014.382864


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.
-13.061-4.5119.344-8.5-9.393-0.029
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 : -0.009 / 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].
3A60LEU00.0190.0073.876-0.7491.200-0.019-1.073-0.8580.004
4A61VAL0-0.045-0.0287.0450.0260.0260.0000.0000.0000.000
5A62LEU00.0070.0119.8560.0670.0670.0000.0000.0000.000
6A63THR0-0.044-0.04513.076-0.008-0.0080.0000.0000.0000.000
7A64GLY00.0560.03116.0740.0090.0090.0000.0000.0000.000
8A65GLU-1-0.912-0.94019.7830.0040.0040.0000.0000.0000.000
9A66ARG10.8640.93016.7290.0420.0420.0000.0000.0000.000
10A67HIS0-0.009-0.00723.070-0.011-0.0110.0000.0000.0000.000
11A68TYR0-0.046-0.03725.346-0.006-0.0060.0000.0000.0000.000
12A69THR0-0.014-0.02018.887-0.001-0.0010.0000.0000.0000.000
13A70ARG10.8000.88020.1560.0100.0100.0000.0000.0000.000
14A71ASN00.036-0.00115.1120.0230.0230.0000.0000.0000.000
15A72ASP-1-0.816-0.91014.994-0.098-0.0980.0000.0000.0000.000
16A73ASP-1-0.728-0.81016.4030.0090.0090.0000.0000.0000.000
17A74ILE00.0440.02712.1570.0220.0220.0000.0000.0000.000
18A75ARG10.9280.97710.8900.3250.3250.0000.0000.0000.000
19A76GLN0-0.004-0.03412.8390.0560.0560.0000.0000.0000.000
20A77SER0-0.052-0.03214.9270.0220.0220.0000.0000.0000.000
21A78ILE0-0.021-0.0118.5480.0350.0350.0000.0000.0000.000
22A79LEU00.007-0.01110.5700.0450.0450.0000.0000.0000.000
23A80ALA0-0.0410.00013.0450.0080.0080.0000.0000.0000.000
24A81LEU0-0.032-0.00912.756-0.003-0.0030.0000.0000.0000.000
25A82GLY0-0.0060.00012.8320.0460.0460.0000.0000.0000.000
26A83GLU-1-0.874-0.92811.6080.1280.1280.0000.0000.0000.000
27A84PRO00.0050.0178.5270.1670.1670.0000.0000.0000.000
28A85GLY0-0.015-0.0065.107-0.113-0.1130.0000.0000.0000.000
29A86THR0-0.006-0.0265.0671.2621.333-0.0010.000-0.0690.000
30A87PHE00.0170.0142.532-0.0910.6111.642-0.655-1.689-0.007
31A88MET0-0.0010.0172.143-3.486-1.7632.565-1.756-2.5320.007
32A89THR0-0.036-0.0394.921-1.109-1.042-0.001-0.004-0.0620.000
33A90GLN00.0040.0087.897-0.364-0.3640.0000.0000.0000.000
34A91ASP-1-0.778-0.88010.4220.4880.4880.0000.0000.0000.000
35A92VAL0-0.008-0.00411.888-0.017-0.0170.0000.0000.0000.000
36A93ASN00.005-0.00913.609-0.071-0.0710.0000.0000.0000.000
37A94ILE00.0200.02315.580-0.038-0.0380.0000.0000.0000.000
38A95ILE00.005-0.0059.966-0.035-0.0350.0000.0000.0000.000
39A96GLN0-0.060-0.05014.211-0.029-0.0290.0000.0000.0000.000
40A97THR00.0320.00016.899-0.034-0.0340.0000.0000.0000.000
41A98GLN0-0.017-0.00116.222-0.047-0.0470.0000.0000.0000.000
42A99ILE0-0.040-0.02714.047-0.028-0.0280.0000.0000.0000.000
43A100GLU-1-0.859-0.93318.3600.1210.1210.0000.0000.0000.000
44A101GLN0-0.055-0.02621.451-0.018-0.0180.0000.0000.0000.000
45A102ARG10.8730.94918.536-0.083-0.0830.0000.0000.0000.000
46A103LEU0-0.062-0.01918.512-0.016-0.0160.0000.0000.0000.000
47A104PRO00.0640.03122.9130.0020.0020.0000.0000.0000.000
48A105TRP0-0.008-0.02122.2370.0000.0000.0000.0000.0000.000
49A106ILE0-0.063-0.03620.751-0.004-0.0040.0000.0000.0000.000
50A107LYS10.7890.87024.085-0.045-0.0450.0000.0000.0000.000
51A108GLN0-0.018-0.01322.318-0.003-0.0030.0000.0000.0000.000
52A109VAL0-0.005-0.01017.890-0.007-0.0070.0000.0000.0000.000
53A110SER0-0.055-0.00917.5010.0040.0040.0000.0000.0000.000
54A111VAL00.0070.01511.867-0.006-0.0060.0000.0000.0000.000
55A112ARG10.9100.93811.952-0.261-0.2610.0000.0000.0000.000
56A113LYS10.8710.9267.885-1.358-1.3580.0000.0000.0000.000
57A114GLN00.0050.0117.562-0.190-0.1900.0000.0000.0000.000
58A115TRP00.0700.0597.0100.1910.1910.0000.0000.0000.000
59A116PRO0-0.023-0.0066.208-0.088-0.0880.0000.0000.0000.000
60A117ASP-1-0.832-0.9442.169-6.147-3.6493.178-3.114-2.563-0.012
61A118GLU-1-0.817-0.9002.489-1.2430.2301.981-1.897-1.556-0.021
62A119LEU00.0230.0085.1250.0620.129-0.001-0.001-0.0640.000
63A120LYS10.7870.8997.052-0.499-0.4990.0000.0000.0000.000
64A121ILE00.0090.00210.0550.0420.0420.0000.0000.0000.000
65A122HIS00.0280.04212.938-0.041-0.0410.0000.0000.0000.000
66A123LEU00.015-0.00816.3590.0120.0120.0000.0000.0000.000
67A124VAL00.003-0.00319.454-0.006-0.0060.0000.0000.0000.000
68A125GLU-1-0.693-0.80223.2480.0190.0190.0000.0000.0000.000
69A126TYR00.0060.01025.5130.0000.0000.0000.0000.0000.000
70A127VAL00.004-0.00129.167-0.004-0.0040.0000.0000.0000.000
71A128PRO0-0.052-0.02231.6170.0010.0010.0000.0000.0000.000
72A129ILE0-0.028-0.02134.560-0.002-0.0020.0000.0000.0000.000
73A130ALA0-0.010-0.00438.052-0.002-0.0020.0000.0000.0000.000
74A131ARG10.8650.93336.115-0.008-0.0080.0000.0000.0000.000
75A132TRP00.0200.00538.169-0.001-0.0010.0000.0000.0000.000
76A133ASN00.0260.00339.4450.0000.0000.0000.0000.0000.000
77A134ASP-1-0.829-0.91340.5210.0160.0160.0000.0000.0000.000
78A135GLN0-0.092-0.02736.0960.0000.0000.0000.0000.0000.000
79A136HIS00.0160.01834.7770.0020.0020.0000.0000.0000.000
80A137MET0-0.069-0.01933.472-0.003-0.0030.0000.0000.0000.000
81A138VAL00.0220.02235.6500.0030.0030.0000.0000.0000.000
82A139ASP-1-0.739-0.84532.7330.0390.0390.0000.0000.0000.000
83A140ALA00.0240.01435.411-0.001-0.0010.0000.0000.0000.000
84A141GLU-1-0.805-0.89233.3270.0420.0420.0000.0000.0000.000
85A142GLY00.0070.00537.3560.0010.0010.0000.0000.0000.000
86A143ASN0-0.072-0.03832.8410.0030.0030.0000.0000.0000.000
87A144THR0-0.036-0.03234.550-0.003-0.0030.0000.0000.0000.000
88A145PHE00.0220.01029.7960.0030.0030.0000.0000.0000.000
89A146SER00.0320.00930.354-0.003-0.0030.0000.0000.0000.000
90A147VAL00.015-0.00527.5590.0020.0020.0000.0000.0000.000
91A148PRO00.0010.01426.736-0.001-0.0010.0000.0000.0000.000
92A149PRO00.0690.02830.020-0.003-0.0030.0000.0000.0000.000
93A150GLU-1-0.848-0.94629.041-0.002-0.0020.0000.0000.0000.000
94A151ARG10.7320.83422.618-0.001-0.0010.0000.0000.0000.000
95A152THR00.0310.00729.8880.0010.0010.0000.0000.0000.000
96A153SER0-0.054-0.02133.0610.0000.0000.0000.0000.0000.000
97A154LYS10.9250.96435.2410.0100.0100.0000.0000.0000.000
98A155GLN00.0420.05732.6870.0010.0010.0000.0000.0000.000
99A156VAL00.0210.00637.0480.0010.0010.0000.0000.0000.000
100A157LEU0-0.0010.00036.1090.0010.0010.0000.0000.0000.000
101A158PRO00.0130.02640.796-0.001-0.0010.0000.0000.0000.000
102A159MET0-0.0030.00841.9530.0010.0010.0000.0000.0000.000
103A160LEU0-0.011-0.00842.5910.0000.0000.0000.0000.0000.000
104A161TYR0-0.071-0.07143.5630.0010.0010.0000.0000.0000.000
105A162GLY00.0180.00545.363-0.001-0.0010.0000.0000.0000.000
106A163PRO0-0.055-0.01345.5780.0000.0000.0000.0000.0000.000
107A164GLU-1-0.806-0.89440.2160.0370.0370.0000.0000.0000.000
108A165GLY0-0.0150.00241.2840.0000.0000.0000.0000.0000.000
109A166SER0-0.087-0.07142.3090.0000.0000.0000.0000.0000.000
110A167ALA00.0600.03639.972-0.001-0.0010.0000.0000.0000.000
111A168ASN00.0600.00439.887-0.003-0.0030.0000.0000.0000.000
112A169GLU-1-0.817-0.85942.4410.0240.0240.0000.0000.0000.000
113A170VAL0-0.002-0.01844.858-0.002-0.0020.0000.0000.0000.000
114A171LEU00.0090.01840.128-0.002-0.0020.0000.0000.0000.000
115A172GLN00.0240.01242.991-0.002-0.0020.0000.0000.0000.000
116A173GLY00.0160.01746.664-0.001-0.0010.0000.0000.0000.000
117A174TYR0-0.032-0.03144.851-0.001-0.0010.0000.0000.0000.000
118A175ARG10.8120.89240.330-0.027-0.0270.0000.0000.0000.000
119A176GLU-1-0.902-0.94947.4240.0170.0170.0000.0000.0000.000
120A177MET0-0.013-0.01551.004-0.001-0.0010.0000.0000.0000.000
121A178GLY00.0170.01049.480-0.001-0.0010.0000.0000.0000.000
122A179GLN0-0.045-0.03347.4520.0000.0000.0000.0000.0000.000
123A180MET0-0.051-0.00451.211-0.001-0.0010.0000.0000.0000.000
124A181LEU0-0.012-0.01353.361-0.001-0.0010.0000.0000.0000.000
125A182ALA0-0.017-0.01951.043-0.001-0.0010.0000.0000.0000.000
126A183LYS10.8720.95653.133-0.012-0.0120.0000.0000.0000.000
127A184ASP-1-0.830-0.92955.9260.0080.0080.0000.0000.0000.000
128A185ARG10.8830.95555.341-0.007-0.0070.0000.0000.0000.000
129A186PHE0-0.048-0.02354.705-0.001-0.0010.0000.0000.0000.000
130A187THR00.0340.01248.7390.0000.0000.0000.0000.0000.000
131A188LEU0-0.015-0.00549.1790.0000.0000.0000.0000.0000.000
132A189LYS10.8160.92047.275-0.007-0.0070.0000.0000.0000.000
133A190GLU-1-0.753-0.86446.7300.0090.0090.0000.0000.0000.000
134A191ALA0-0.004-0.00647.6010.0000.0000.0000.0000.0000.000
135A192ALA00.0140.01247.7770.0010.0010.0000.0000.0000.000
136A193MET0-0.0080.02548.557-0.001-0.0010.0000.0000.0000.000
137A194THR0-0.023-0.03250.0560.0000.0000.0000.0000.0000.000
138A195ALA00.0660.02351.0870.0010.0010.0000.0000.0000.000
139A196ARG10.9340.97552.026-0.017-0.0170.0000.0000.0000.000
140A197ARG10.8650.90148.842-0.025-0.0250.0000.0000.0000.000
141A198SER0-0.043-0.04754.537-0.001-0.0010.0000.0000.0000.000
142A199TRP00.0310.01348.8070.0000.0000.0000.0000.0000.000
143A200GLN0-0.006-0.00853.664-0.001-0.0010.0000.0000.0000.000
144A201LEU00.0000.00651.6880.0010.0010.0000.0000.0000.000
145A202THR0-0.074-0.04751.422-0.001-0.0010.0000.0000.0000.000
146A203LEU00.0170.02551.6890.0000.0000.0000.0000.0000.000
147A204ASN00.0530.02351.8330.0000.0000.0000.0000.0000.000
148A205ASN00.0230.01052.428-0.001-0.0010.0000.0000.0000.000
149A206ASP-1-0.848-0.91553.7070.0070.0070.0000.0000.0000.000
150A207ILE0-0.015-0.00455.4050.0000.0000.0000.0000.0000.000
151A208LYS10.8160.89752.457-0.007-0.0070.0000.0000.0000.000
152A209LEU00.0080.00956.5100.0000.0000.0000.0000.0000.000
153A210ASN00.0170.00057.1340.0010.0010.0000.0000.0000.000
154A211LEU00.0210.00956.2250.0000.0000.0000.0000.0000.000
155A212GLY00.0270.02058.9150.0000.0000.0000.0000.0000.000
156A213ARG10.9130.95457.857-0.016-0.0160.0000.0000.0000.000
157A214GLY00.0230.01859.4710.0000.0000.0000.0000.0000.000
158A215ASP-1-0.808-0.89359.5000.0140.0140.0000.0000.0000.000
159A216THR0-0.023-0.02255.797-0.001-0.0010.0000.0000.0000.000
160A217MET00.0670.04153.280-0.001-0.0010.0000.0000.0000.000
161A218LYS10.9080.94158.675-0.014-0.0140.0000.0000.0000.000
162A219ARG10.7690.87761.292-0.013-0.0130.0000.0000.0000.000
163A220LEU00.0200.01055.455-0.001-0.0010.0000.0000.0000.000
164A221ALA00.0590.02459.979-0.001-0.0010.0000.0000.0000.000
165A222ARG10.8670.91361.922-0.011-0.0110.0000.0000.0000.000
166A223PHE00.000-0.00759.086-0.001-0.0010.0000.0000.0000.000
167A224VAL0-0.028-0.01959.174-0.001-0.0010.0000.0000.0000.000
168A225GLU-1-0.950-0.96462.1250.0080.0080.0000.0000.0000.000
169A226LEU0-0.006-0.00265.7940.0000.0000.0000.0000.0000.000
170A227TYR0-0.037-0.03361.8570.0000.0000.0000.0000.0000.000
171A228PRO00.006-0.00664.487-0.001-0.0010.0000.0000.0000.000
172A229VAL00.0420.02166.3970.0000.0000.0000.0000.0000.000
173A230LEU00.0070.01066.5090.0000.0000.0000.0000.0000.000
174A231GLN0-0.0100.00962.8660.0000.0000.0000.0000.0000.000
175A232GLN00.0250.00966.4400.0000.0000.0000.0000.0000.000
176A233GLN0-0.041-0.01669.4640.0000.0000.0000.0000.0000.000
177A234ALA00.0140.00067.1500.0000.0000.0000.0000.0000.000
178A235GLN0-0.052-0.03265.8620.0000.0000.0000.0000.0000.000
179A236THR0-0.031-0.01768.6080.0000.0000.0000.0000.0000.000
180A237ASP-1-0.845-0.89471.8630.0030.0030.0000.0000.0000.000
181A238GLY0-0.0030.01669.4770.0000.0000.0000.0000.0000.000
182A239LYS10.7520.85767.117-0.002-0.0020.0000.0000.0000.000
183A240ARG10.8890.95058.744-0.004-0.0040.0000.0000.0000.000
184A241ILE00.0340.01562.5190.0000.0000.0000.0000.0000.000
185A242SER0-0.054-0.03060.3300.0000.0000.0000.0000.0000.000
186A243TYR0-0.038-0.03259.7060.0010.0010.0000.0000.0000.000
187A244VAL00.0230.00961.2100.0000.0000.0000.0000.0000.000
188A245ASP-1-0.777-0.83761.5140.0110.0110.0000.0000.0000.000
189A246LEU00.0290.00661.7970.0000.0000.0000.0000.0000.000
190A247ARG10.8260.89461.297-0.010-0.0100.0000.0000.0000.000
191A248TYR0-0.035-0.01963.0840.0010.0010.0000.0000.0000.000
192A249ASP-1-0.739-0.84366.4950.0110.0110.0000.0000.0000.000
193A250SER0-0.070-0.04069.0740.0000.0000.0000.0000.0000.000
194A251GLY00.0380.01970.6760.0000.0000.0000.0000.0000.000
195A252ALA0-0.025-0.00467.5280.0000.0000.0000.0000.0000.000
196A253ALA0-0.0080.00266.9520.0000.0000.0000.0000.0000.000
197A254VAL00.010-0.00665.9980.0000.0000.0000.0000.0000.000
198A255GLY00.0110.01665.2680.0000.0000.0000.0000.0000.000
199A256TRP00.0460.01664.7560.0000.0000.0000.0000.0000.000
200A257ALA0-0.031-0.01262.9090.0000.0000.0000.0000.0000.000
201A258PRO00.0610.01564.6230.0000.0000.0000.0000.0000.000
202A259LEU0-0.0270.00062.6570.0000.0000.0000.0000.0000.000
203A260PRO00.0280.01758.6590.0000.0000.0000.0000.0000.000