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: 2NY5R

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 OptH
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 -2137413.584449
FMO2-HF: Nuclear repulsion 2055640.017323
FMO2-HF: Total energy -81773.567127
FMO2-MP2: Total energy -82012.118677


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.
-11.267-6.59712.966-8.165-9.468-0.015
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 : 0.040 / q_NPA : 0.014
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].
3A60LEU00.0210.0183.794-1.2481.907-0.032-1.762-1.3610.009
4A61VAL0-0.043-0.0226.8780.0040.0040.0000.0000.0000.000
5A62LEU00.0230.0089.6700.2240.2240.0000.0000.0000.000
6A63THR0-0.049-0.04312.952-0.042-0.0420.0000.0000.0000.000
7A64GLY00.0250.01716.0910.0520.0520.0000.0000.0000.000
8A65GLU-1-0.912-0.96019.692-0.228-0.2280.0000.0000.0000.000
9A66ARG10.8850.94816.5910.4560.4560.0000.0000.0000.000
10A67HIS0-0.034-0.00422.596-0.006-0.0060.0000.0000.0000.000
11A68TYR0-0.002-0.01624.9510.0020.0020.0000.0000.0000.000
12A69THR0-0.057-0.02718.4320.0170.0170.0000.0000.0000.000
13A70ARG10.8660.91719.8420.1240.1240.0000.0000.0000.000
14A71ASN00.028-0.01215.068-0.007-0.0070.0000.0000.0000.000
15A72ASP-1-0.856-0.93415.078-0.098-0.0980.0000.0000.0000.000
16A73ASP-1-0.740-0.81816.110-0.058-0.0580.0000.0000.0000.000
17A74ILE00.024-0.00211.8990.0480.0480.0000.0000.0000.000
18A75ARG10.9250.9649.5660.4770.4770.0000.0000.0000.000
19A76GLN00.005-0.03012.4900.1550.1550.0000.0000.0000.000
20A77SER0-0.042-0.00914.4140.0640.0640.0000.0000.0000.000
21A78ILE0-0.008-0.0148.0930.0670.0670.0000.0000.0000.000
22A79LEU0-0.005-0.00610.4110.1270.1270.0000.0000.0000.000
23A80ALA0-0.0280.00712.5300.0400.0400.0000.0000.0000.000
24A81LEU0-0.059-0.03012.375-0.012-0.0120.0000.0000.0000.000
25A82GLY0-0.0090.00712.5520.0760.0760.0000.0000.0000.000
26A83GLU-1-0.900-0.93611.4500.6620.6620.0000.0000.0000.000
27A84PRO00.0090.0138.0470.3660.3660.0000.0000.0000.000
28A85GLY0-0.007-0.0135.202-0.135-0.1350.0000.0000.0000.000
29A86THR00.0100.0025.4831.3941.450-0.0010.000-0.0550.000
30A87PHE00.010-0.0032.384-0.103-0.1663.289-0.908-2.317-0.008
31A88MET00.0140.0251.981-2.865-4.3437.947-3.154-3.3150.004
32A89THR0-0.092-0.0555.209-1.219-1.176-0.001-0.001-0.0400.000
33A90GLN00.0280.0268.304-0.660-0.6600.0000.0000.0000.000
34A91ASP-1-0.829-0.91610.5230.6120.6120.0000.0000.0000.000
35A92VAL0-0.001-0.01611.159-0.070-0.0700.0000.0000.0000.000
36A93ASN00.0310.01213.474-0.126-0.1260.0000.0000.0000.000
37A94ILE00.0200.02215.465-0.059-0.0590.0000.0000.0000.000
38A95ILE0-0.013-0.01610.034-0.048-0.0480.0000.0000.0000.000
39A96GLN0-0.082-0.03714.348-0.061-0.0610.0000.0000.0000.000
40A97THR00.0300.01917.069-0.040-0.0400.0000.0000.0000.000
41A98GLN0-0.025-0.01716.210-0.062-0.0620.0000.0000.0000.000
42A99ILE0-0.017-0.02013.862-0.044-0.0440.0000.0000.0000.000
43A100GLU-1-0.887-0.94518.0960.0850.0850.0000.0000.0000.000
44A101GLN0-0.031-0.01921.489-0.013-0.0130.0000.0000.0000.000
45A102ARG10.8810.95718.193-0.147-0.1470.0000.0000.0000.000
46A103LEU0-0.055-0.02918.198-0.026-0.0260.0000.0000.0000.000
47A104PRO00.0810.05422.482-0.009-0.0090.0000.0000.0000.000
48A105TRP0-0.020-0.02521.9570.0050.0050.0000.0000.0000.000
49A106ILE0-0.067-0.03820.561-0.023-0.0230.0000.0000.0000.000
50A107LYS10.9660.99323.6850.0690.0690.0000.0000.0000.000
51A108GLN0-0.018-0.01422.4130.0140.0140.0000.0000.0000.000
52A109VAL00.0210.01216.774-0.037-0.0370.0000.0000.0000.000
53A110SER0-0.076-0.02616.8800.0330.0330.0000.0000.0000.000
54A111VAL00.0700.02711.709-0.062-0.0620.0000.0000.0000.000
55A112ARG10.9330.96611.9080.3040.3040.0000.0000.0000.000
56A113LYS10.9020.9527.753-1.897-1.8970.0000.0000.0000.000
57A114GLN00.0090.0017.7360.0450.0450.0000.0000.0000.000
58A115TRP00.0090.0457.284-0.196-0.1960.0000.0000.0000.000
59A116PRO0-0.015-0.0126.0480.0820.0820.0000.0000.0000.000
60A117ASP-1-0.880-0.9672.385-2.072-1.1721.304-0.889-1.315-0.006
61A118GLU-1-0.945-0.9832.874-6.533-4.5400.461-1.451-1.003-0.014
62A119LEU00.0280.0055.1360.8370.901-0.0010.000-0.0620.000
63A120LYS10.8640.9346.9230.4350.4350.0000.0000.0000.000
64A121ILE00.0070.01410.2790.1900.1900.0000.0000.0000.000
65A122HIS0-0.0090.00912.885-0.132-0.1320.0000.0000.0000.000
66A123LEU0-0.005-0.00516.2880.0620.0620.0000.0000.0000.000
67A124VAL00.020-0.00219.205-0.028-0.0280.0000.0000.0000.000
68A125GLU-1-0.721-0.84122.922-0.132-0.1320.0000.0000.0000.000
69A126TYR0-0.0010.00925.124-0.003-0.0030.0000.0000.0000.000
70A127VAL00.0150.00228.691-0.009-0.0090.0000.0000.0000.000
71A128PRO0-0.056-0.01531.1100.0080.0080.0000.0000.0000.000
72A129ILE0-0.038-0.03634.056-0.006-0.0060.0000.0000.0000.000
73A130ALA0-0.024-0.01837.5570.0000.0000.0000.0000.0000.000
74A131ARG10.9130.96935.9840.0510.0510.0000.0000.0000.000
75A132TRP00.018-0.00337.7210.0000.0000.0000.0000.0000.000
76A133ASN00.0390.01939.0080.0010.0010.0000.0000.0000.000
77A134ASP-1-0.886-0.95540.039-0.011-0.0110.0000.0000.0000.000
78A135GLN0-0.054-0.02935.865-0.003-0.0030.0000.0000.0000.000
79A136HIS00.0010.01634.000-0.004-0.0040.0000.0000.0000.000
80A137MET0-0.069-0.01633.050-0.007-0.0070.0000.0000.0000.000
81A138VAL00.0320.01935.0900.0060.0060.0000.0000.0000.000
82A139ASP-1-0.738-0.85232.638-0.044-0.0440.0000.0000.0000.000
83A140ALA0-0.014-0.00535.1180.0050.0050.0000.0000.0000.000
84A141GLU-1-0.903-0.96834.008-0.049-0.0490.0000.0000.0000.000
85A142GLY0-0.064-0.02336.9400.0060.0060.0000.0000.0000.000
86A143ASN0-0.091-0.05132.6520.0140.0140.0000.0000.0000.000
87A144THR00.0170.00334.190-0.009-0.0090.0000.0000.0000.000
88A145PHE0-0.003-0.00629.3680.0030.0030.0000.0000.0000.000
89A146SER00.0170.00929.869-0.002-0.0020.0000.0000.0000.000
90A147VAL00.0450.00328.027-0.004-0.0040.0000.0000.0000.000
91A148PRO00.0070.02226.2550.0020.0020.0000.0000.0000.000
92A149PRO00.0810.04129.548-0.012-0.0120.0000.0000.0000.000
93A150GLU-1-0.912-0.97828.950-0.047-0.0470.0000.0000.0000.000
94A151ARG10.7160.84922.1300.0790.0790.0000.0000.0000.000
95A152THR00.0430.00829.531-0.007-0.0070.0000.0000.0000.000
96A153SER0-0.010-0.00232.5700.0000.0000.0000.0000.0000.000
97A154LYS10.9350.96734.9620.0910.0910.0000.0000.0000.000
98A155GLN00.0470.04032.596-0.004-0.0040.0000.0000.0000.000
99A156VAL0-0.020-0.01836.9250.0070.0070.0000.0000.0000.000
100A157LEU0-0.017-0.00335.764-0.003-0.0030.0000.0000.0000.000
101A158PRO00.0160.02440.4280.0030.0030.0000.0000.0000.000
102A159MET00.0060.00741.641-0.002-0.0020.0000.0000.0000.000
103A160LEU0-0.024-0.00741.9010.0010.0010.0000.0000.0000.000
104A161TYR0-0.042-0.03643.0480.0010.0010.0000.0000.0000.000
105A162GLY0-0.006-0.01344.905-0.001-0.0010.0000.0000.0000.000
106A163PRO0-0.065-0.01344.8000.0020.0020.0000.0000.0000.000
107A164GLU-1-0.906-0.96039.5850.0240.0240.0000.0000.0000.000
108A165GLY00.0770.04741.0120.0020.0020.0000.0000.0000.000
109A166SER0-0.063-0.04942.041-0.003-0.0030.0000.0000.0000.000
110A167ALA00.0390.02739.564-0.003-0.0030.0000.0000.0000.000
111A168ASN00.0750.01340.282-0.008-0.0080.0000.0000.0000.000
112A169GLU-1-0.816-0.86342.294-0.002-0.0020.0000.0000.0000.000
113A170VAL00.000-0.01644.441-0.002-0.0020.0000.0000.0000.000
114A171LEU00.0030.01839.925-0.003-0.0030.0000.0000.0000.000
115A172GLN00.010-0.00543.121-0.006-0.0060.0000.0000.0000.000
116A173GLY00.0270.03046.419-0.001-0.0010.0000.0000.0000.000
117A174TYR0-0.003-0.01343.809-0.002-0.0020.0000.0000.0000.000
118A175ARG10.8760.93739.9080.0360.0360.0000.0000.0000.000
119A176GLU-1-0.940-0.96347.170-0.022-0.0220.0000.0000.0000.000
120A177MET0-0.036-0.03250.7890.0000.0000.0000.0000.0000.000
121A178GLY00.0310.00349.213-0.001-0.0010.0000.0000.0000.000
122A179GLN0-0.047-0.02347.426-0.004-0.0040.0000.0000.0000.000
123A180MET0-0.061-0.01451.2840.0000.0000.0000.0000.0000.000
124A181LEU00.0030.00053.0240.0000.0000.0000.0000.0000.000
125A182ALA00.024-0.00150.9980.0000.0000.0000.0000.0000.000
126A183LYS10.8860.95753.0970.0360.0360.0000.0000.0000.000
127A184ASP-1-0.876-0.92955.697-0.032-0.0320.0000.0000.0000.000
128A185ARG10.9330.95255.2450.0340.0340.0000.0000.0000.000
129A186PHE0-0.079-0.02454.538-0.001-0.0010.0000.0000.0000.000
130A187THR00.0090.00648.593-0.002-0.0020.0000.0000.0000.000
131A188LEU0-0.042-0.01648.3570.0020.0020.0000.0000.0000.000
132A189LYS10.9310.96847.0990.0380.0380.0000.0000.0000.000
133A190GLU-1-0.899-0.95846.396-0.026-0.0260.0000.0000.0000.000
134A191ALA0-0.011-0.01247.2640.0010.0010.0000.0000.0000.000
135A192ALA00.0120.01747.3940.0010.0010.0000.0000.0000.000
136A193MET0-0.0110.01748.3450.0000.0000.0000.0000.0000.000
137A194THR0-0.128-0.08449.3910.0020.0020.0000.0000.0000.000
138A195ALA00.1300.04550.8110.0000.0000.0000.0000.0000.000
139A196ARG10.9720.98751.748-0.006-0.0060.0000.0000.0000.000
140A197ARG10.8390.89448.428-0.005-0.0050.0000.0000.0000.000
141A198SER0-0.047-0.02854.272-0.002-0.0020.0000.0000.0000.000
142A199TRP00.0600.02948.6860.0000.0000.0000.0000.0000.000
143A200GLN0-0.042-0.03053.0980.0010.0010.0000.0000.0000.000
144A201LEU00.0130.01251.571-0.001-0.0010.0000.0000.0000.000
145A202THR00.0160.02450.6020.0020.0020.0000.0000.0000.000
146A203LEU00.0100.00451.237-0.002-0.0020.0000.0000.0000.000
147A204ASN00.0500.02351.7590.0000.0000.0000.0000.0000.000
148A205ASN0-0.027-0.02252.284-0.002-0.0020.0000.0000.0000.000
149A206ASP-1-0.895-0.94152.863-0.025-0.0250.0000.0000.0000.000
150A207ILE0-0.089-0.04454.8510.0020.0020.0000.0000.0000.000
151A208LYS10.9791.00153.3240.0180.0180.0000.0000.0000.000
152A209LEU00.0080.00156.1610.0010.0010.0000.0000.0000.000
153A210ASN0-0.019-0.02556.8980.0010.0010.0000.0000.0000.000
154A211LEU00.0620.02855.8110.0000.0000.0000.0000.0000.000
155A212GLY00.0180.01658.3960.0010.0010.0000.0000.0000.000
156A213ARG10.9140.94757.670-0.002-0.0020.0000.0000.0000.000
157A214GLY0-0.025-0.00759.1110.0010.0010.0000.0000.0000.000
158A215ASP-1-0.842-0.91159.588-0.008-0.0080.0000.0000.0000.000
159A216THR0-0.016-0.02355.690-0.001-0.0010.0000.0000.0000.000
160A217MET00.0690.04653.927-0.002-0.0020.0000.0000.0000.000
161A218LYS10.9920.98958.6580.0110.0110.0000.0000.0000.000
162A219ARG10.8500.93761.1420.0080.0080.0000.0000.0000.000
163A220LEU00.0080.00555.4200.0000.0000.0000.0000.0000.000
164A221ALA00.0540.02759.694-0.001-0.0010.0000.0000.0000.000
165A222ARG10.9640.97161.7310.0130.0130.0000.0000.0000.000
166A223PHE0-0.018-0.01458.8140.0000.0000.0000.0000.0000.000
167A224VAL00.0060.00059.1970.0000.0000.0000.0000.0000.000
168A225GLU-1-0.955-0.96062.019-0.021-0.0210.0000.0000.0000.000
169A226LEU0-0.036-0.02765.6350.0000.0000.0000.0000.0000.000
170A227TYR0-0.023-0.00261.2410.0000.0000.0000.0000.0000.000
171A228PRO0-0.013-0.00964.1650.0000.0000.0000.0000.0000.000
172A229VAL00.0480.00966.0270.0000.0000.0000.0000.0000.000
173A230LEU00.0200.01466.6140.0000.0000.0000.0000.0000.000
174A231GLN0-0.0100.00063.3420.0000.0000.0000.0000.0000.000
175A232GLN0-0.007-0.00866.170-0.001-0.0010.0000.0000.0000.000
176A233GLN00.0070.01569.2160.0000.0000.0000.0000.0000.000
177A234ALA00.0040.00766.6110.0000.0000.0000.0000.0000.000
178A235GLN0-0.028-0.01265.226-0.001-0.0010.0000.0000.0000.000
179A236THR0-0.045-0.03068.331-0.001-0.0010.0000.0000.0000.000
180A237ASP-1-0.914-0.94371.420-0.019-0.0190.0000.0000.0000.000
181A238GLY0-0.034-0.01368.7920.0010.0010.0000.0000.0000.000
182A239LYS10.8500.92966.7260.0190.0190.0000.0000.0000.000
183A240ARG10.9550.96858.6360.0230.0230.0000.0000.0000.000
184A241ILE00.0340.00962.3860.0010.0010.0000.0000.0000.000
185A242SER0-0.071-0.03960.161-0.001-0.0010.0000.0000.0000.000
186A243TYR00.0130.00759.3900.0000.0000.0000.0000.0000.000
187A244VAL00.0270.01360.8330.0000.0000.0000.0000.0000.000
188A245ASP-1-0.781-0.87661.291-0.008-0.0080.0000.0000.0000.000
189A246LEU0-0.027-0.00761.4760.0000.0000.0000.0000.0000.000
190A247ARG10.8700.92160.7000.0060.0060.0000.0000.0000.000
191A248TYR0-0.044-0.03763.1340.0010.0010.0000.0000.0000.000
192A249ASP-1-0.847-0.91166.486-0.008-0.0080.0000.0000.0000.000
193A250SER0-0.107-0.06768.6650.0010.0010.0000.0000.0000.000
194A251GLY00.0250.01169.8660.0000.0000.0000.0000.0000.000
195A252ALA0-0.0130.00067.4660.0000.0000.0000.0000.0000.000
196A253ALA0-0.0080.01566.8320.0000.0000.0000.0000.0000.000
197A254VAL00.019-0.00465.769-0.001-0.0010.0000.0000.0000.000
198A255GLY00.0090.01865.0000.0010.0010.0000.0000.0000.000
199A256TRP00.006-0.00164.505-0.001-0.0010.0000.0000.0000.000
200A257ALA0-0.018-0.01162.5340.0010.0010.0000.0000.0000.000
201A258PRO00.0220.00363.903-0.001-0.0010.0000.0000.0000.000
202A259LEU0-0.0030.00662.750-0.001-0.0010.0000.0000.0000.000
203A260PRO00.0110.01758.7360.0000.0000.0000.0000.0000.000