FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: M9N2Z

Calculation Name: 2HIV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HIV

Chain ID: A

ChEMBL ID:

UniProt ID: Q980T8

Base Structure: X-ray

Registration Date: 2023-09-27

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 577
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -11653487.476236
FMO2-HF: Nuclear repulsion 11425815.644175
FMO2-HF: Total energy -227671.83206
FMO2-MP2: Total energy -228341.462674


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-12.108-14.46326.958-4.709-19.894-0.019
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : 0.041
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].
3A3PHE0-0.022-0.0333.000-3.935-1.3450.196-1.373-1.413-0.006
4A4LYS10.8920.9525.1020.5870.721-0.001-0.005-0.1270.000
5A5VAL00.0090.0113.314-0.1590.4100.026-0.091-0.5040.000
6A6ILE00.0280.0102.673-0.5580.1850.496-0.153-1.0870.000
7A7ALA0-0.026-0.0015.2350.4540.504-0.001-0.001-0.0470.000
8A8GLU-1-0.821-0.9178.289-0.562-0.5620.0000.0000.0000.000
9A9TYR0-0.023-0.0237.0910.2100.2100.0000.0000.0000.000
10A10PHE00.010-0.0088.8740.1830.1830.0000.0000.0000.000
11A11ASP-1-0.823-0.89511.296-0.432-0.4320.0000.0000.0000.000
12A12LYS10.8460.91112.0060.8570.8570.0000.0000.0000.000
13A13LEU00.0000.00712.4110.0760.0760.0000.0000.0000.000
14A14GLU-1-0.874-0.92014.630-0.345-0.3450.0000.0000.0000.000
15A15LYS10.7410.84716.9680.5150.5150.0000.0000.0000.000
16A16ILE0-0.0200.01915.1480.0330.0330.0000.0000.0000.000
17A17SER00.007-0.01418.9160.0260.0260.0000.0000.0000.000
18A18SER0-0.0260.00620.6600.0210.0210.0000.0000.0000.000
19A19ARG10.8850.89917.0380.2600.2600.0000.0000.0000.000
20A20LEU00.0300.02518.288-0.022-0.0220.0000.0000.0000.000
21A21GLN00.0560.00516.919-0.023-0.0230.0000.0000.0000.000
22A22LEU00.0310.02313.396-0.068-0.0680.0000.0000.0000.000
23A23THR00.007-0.00113.238-0.075-0.0750.0000.0000.0000.000
24A24ALA0-0.0150.00012.985-0.045-0.0450.0000.0000.0000.000
25A25LEU0-0.0060.0019.372-0.075-0.0750.0000.0000.0000.000
26A26LEU00.0130.0018.658-0.247-0.2470.0000.0000.0000.000
27A27ALA00.0340.0158.070-0.172-0.1720.0000.0000.0000.000
28A28ASP-1-0.829-0.8808.803-0.956-0.9560.0000.0000.0000.000
29A29LEU0-0.011-0.0043.045-0.694-0.1830.089-0.101-0.4990.000
30A30LEU0-0.026-0.0093.878-1.100-0.8180.003-0.079-0.2060.000
31A31SER0-0.037-0.0425.8630.6080.6080.0000.0000.0000.000
32A32LYS10.7870.8905.1211.2831.2830.0000.0000.0000.000
33A33SER0-0.033-0.0492.301-3.620-5.2449.188-3.510-4.054-0.014
34A34ASP-1-0.828-0.9182.3982.027-6.31910.6682.488-4.8110.002
35A35LYS10.9900.9823.488-0.387-0.2880.0160.234-0.3500.001
36A36THR0-0.070-0.0506.563-0.261-0.2610.0000.0000.0000.000
37A37ILE0-0.042-0.0182.584-1.370-0.5330.633-0.283-1.1860.000
38A38ILE00.0300.0185.2010.2270.2270.0000.0000.0000.000
39A39ASP-1-0.842-0.9326.8440.3940.3940.0000.0000.0000.000
40A40LYS10.8100.9046.842-0.995-0.9950.0000.0000.0000.000
41A41VAL00.0010.0002.653-1.356-0.5431.144-0.363-1.594-0.003
42A42VAL00.006-0.0015.083-0.509-0.489-0.001-0.001-0.0180.000
43A43TYR0-0.015-0.0308.044-0.079-0.0790.0000.0000.0000.000
44A44ILE00.0290.0165.856-0.084-0.0840.0000.0000.0000.000
45A45ILE0-0.020-0.0105.327-0.097-0.0970.0000.0000.0000.000
46A46GLN0-0.038-0.0248.0320.0480.0480.0000.0000.0000.000
47A47GLY0-0.015-0.00210.8300.0420.0420.0000.0000.0000.000
48A48LYS10.8220.90111.7500.2120.2120.0000.0000.0000.000
49A49LEU00.010-0.00511.278-0.016-0.0160.0000.0000.0000.000
50A50TRP0-0.021-0.00912.9430.0910.0910.0000.0000.0000.000
51A51PRO00.0160.03014.837-0.042-0.0420.0000.0000.0000.000
52A52ASP-1-0.779-0.88016.879-0.086-0.0860.0000.0000.0000.000
53A53PHE00.0360.01918.8970.0080.0080.0000.0000.0000.000
54A54LEU0-0.032-0.01717.8810.0080.0080.0000.0000.0000.000
55A55GLY0-0.031-0.01921.7620.0050.0050.0000.0000.0000.000
56A56TYR0-0.056-0.02118.5780.0000.0000.0000.0000.0000.000
57A57PRO0-0.001-0.00521.588-0.010-0.0100.0000.0000.0000.000
58A58GLU-1-0.882-0.93620.200-0.092-0.0920.0000.0000.0000.000
59A59LEU0-0.056-0.03414.8970.0070.0070.0000.0000.0000.000
60A60GLY00.0490.03419.009-0.020-0.0200.0000.0000.0000.000
61A61ILE0-0.080-0.04121.4160.0180.0180.0000.0000.0000.000
62A62GLY00.0430.02523.938-0.007-0.0070.0000.0000.0000.000
63A63GLU-1-0.760-0.86325.721-0.131-0.1310.0000.0000.0000.000
64A64LYS11.0050.98926.5590.0660.0660.0000.0000.0000.000
65A65PHE0-0.004-0.00226.4560.0040.0040.0000.0000.0000.000
66A66LEU00.0550.03120.0500.0020.0020.0000.0000.0000.000
67A67ILE00.0200.01523.703-0.007-0.0070.0000.0000.0000.000
68A68LYS10.8200.88926.2100.0620.0620.0000.0000.0000.000
69A69ALA0-0.011-0.00821.7430.0050.0050.0000.0000.0000.000
70A70ILE00.0220.00421.223-0.002-0.0020.0000.0000.0000.000
71A71SER0-0.066-0.04623.1840.0060.0060.0000.0000.0000.000
72A72ILE0-0.012-0.01924.0780.0070.0070.0000.0000.0000.000
73A73ALA0-0.052-0.01920.1250.0080.0080.0000.0000.0000.000
74A74THR00.0200.00821.581-0.005-0.0050.0000.0000.0000.000
75A75ASN0-0.088-0.03123.8440.0110.0110.0000.0000.0000.000
76A76THR00.0430.01927.2160.0020.0020.0000.0000.0000.000
77A77ASP-1-0.787-0.85929.329-0.075-0.0750.0000.0000.0000.000
78A78GLU-1-0.758-0.87329.545-0.074-0.0740.0000.0000.0000.000
79A79ASN0-0.0050.00231.051-0.006-0.0060.0000.0000.0000.000
80A80SER0-0.013-0.00730.972-0.006-0.0060.0000.0000.0000.000
81A81VAL0-0.015-0.00726.047-0.007-0.0070.0000.0000.0000.000
82A82GLU-1-0.814-0.90528.728-0.105-0.1050.0000.0000.0000.000
83A83ASN0-0.048-0.04130.993-0.002-0.0020.0000.0000.0000.000
84A84LEU00.0050.00327.551-0.003-0.0030.0000.0000.0000.000
85A85TYR0-0.051-0.04226.110-0.012-0.0120.0000.0000.0000.000
86A86LYS10.8250.90128.6640.0920.0920.0000.0000.0000.000
87A87THR0-0.030-0.01031.0330.0000.0000.0000.0000.0000.000
88A88ILE0-0.088-0.03624.856-0.007-0.0070.0000.0000.0000.000
89A89GLY00.0080.01426.704-0.010-0.0100.0000.0000.0000.000
90A90ASP-1-0.767-0.87020.817-0.297-0.2970.0000.0000.0000.000
91A91LEU00.0160.00722.1610.0000.0000.0000.0000.0000.000
92A92GLY00.0530.03618.651-0.004-0.0040.0000.0000.0000.000
93A93GLU-1-0.741-0.84319.249-0.291-0.2910.0000.0000.0000.000
94A94VAL0-0.035-0.00721.2170.0110.0110.0000.0000.0000.000
95A95ALA00.0210.00819.3630.0120.0120.0000.0000.0000.000
96A96ARG10.8390.91018.0780.2900.2900.0000.0000.0000.000
97A97ARG10.8810.91919.7770.2080.2080.0000.0000.0000.000
98A98LEU0-0.029-0.01723.4260.0170.0170.0000.0000.0000.000
99A99LYS10.8360.91117.2130.2260.2260.0000.0000.0000.000
100A100SER00.001-0.01521.2670.0090.0090.0000.0000.0000.000
101A101LYS10.8050.93822.4290.1200.1200.0000.0000.0000.000
102A102GLN0-0.035-0.00822.2130.0040.0040.0000.0000.0000.000
103A116LYS10.8240.85813.371-0.379-0.3790.0000.0000.0000.000
104A117GLU-1-0.828-0.8719.7880.4880.4880.0000.0000.0000.000
105A118SER00.014-0.0187.9060.0110.0110.0000.0000.0000.000
106A119LEU0-0.064-0.0228.5810.1850.1850.0000.0000.0000.000
107A120THR00.021-0.0054.083-0.756-0.500-0.001-0.074-0.1820.000
108A121VAL00.018-0.0142.335-1.515-1.0954.504-1.376-3.5480.001
109A122ASP-1-0.761-0.8694.8240.7411.032-0.001-0.021-0.2680.000
110A123GLU-1-0.768-0.8226.5840.0360.0360.0000.0000.0000.000
111A124VAL00.0290.0238.1010.0780.0780.0000.0000.0000.000
112A125TYR00.0170.0008.4880.0840.0840.0000.0000.0000.000
113A126SER0-0.012-0.01710.141-0.021-0.0210.0000.0000.0000.000
114A127THR0-0.060-0.04312.2750.0130.0130.0000.0000.0000.000
115A128LEU00.0180.00011.4430.0030.0030.0000.0000.0000.000
116A129SER00.019-0.00213.5200.0100.0100.0000.0000.0000.000
117A130LYS10.9200.96415.802-0.061-0.0610.0000.0000.0000.000
118A131VAL0-0.023-0.00917.8480.0010.0010.0000.0000.0000.000
119A132ALA00.0180.01418.284-0.002-0.0020.0000.0000.0000.000
120A133LEU0-0.002-0.00218.7150.0020.0020.0000.0000.0000.000
121A134THR0-0.075-0.01521.9510.0020.0020.0000.0000.0000.000
122A135THR00.040-0.00324.020-0.010-0.0100.0000.0000.0000.000
123A136GLY00.0650.03627.7440.0060.0060.0000.0000.0000.000
124A137GLU-1-0.849-0.90730.804-0.005-0.0050.0000.0000.0000.000
125A138GLY0-0.025-0.01730.259-0.005-0.0050.0000.0000.0000.000
126A139SER0-0.070-0.04326.535-0.005-0.0050.0000.0000.0000.000
127A140ARG10.9000.94526.1100.0260.0260.0000.0000.0000.000
128A141ASP-1-0.802-0.91126.674-0.038-0.0380.0000.0000.0000.000
129A142LEU0-0.061-0.02522.619-0.002-0.0020.0000.0000.0000.000
130A143LYS10.8930.94022.0130.0430.0430.0000.0000.0000.000
131A144ILE0-0.0110.00021.817-0.014-0.0140.0000.0000.0000.000
132A145ARG10.9340.96422.5950.0060.0060.0000.0000.0000.000
133A146LEU0-0.026-0.00418.106-0.001-0.0010.0000.0000.0000.000
134A147LEU00.0390.02217.233-0.018-0.0180.0000.0000.0000.000
135A148ALA00.0020.00618.325-0.025-0.0250.0000.0000.0000.000
136A149GLY0-0.022-0.01018.073-0.005-0.0050.0000.0000.0000.000
137A150LEU0-0.009-0.00212.267-0.006-0.0060.0000.0000.0000.000
138A151LEU00.0170.00714.757-0.039-0.0390.0000.0000.0000.000
139A152LYS10.9680.99216.9090.0360.0360.0000.0000.0000.000
140A153LYS10.7610.8699.479-0.055-0.0550.0000.0000.0000.000
141A154ALA0-0.0030.01312.591-0.010-0.0100.0000.0000.0000.000
142A155ASP-1-0.744-0.87712.609-0.489-0.4890.0000.0000.0000.000
143A156PRO0-0.027-0.03114.391-0.026-0.0260.0000.0000.0000.000
144A157LEU0-0.0040.00411.9140.0300.0300.0000.0000.0000.000
145A158GLU-1-0.794-0.9288.595-0.958-0.9580.0000.0000.0000.000
146A159ALA0-0.001-0.00611.7780.0230.0230.0000.0000.0000.000
147A160LYS10.8360.93615.1650.4010.4010.0000.0000.0000.000
148A161PHE00.003-0.01211.4270.0420.0420.0000.0000.0000.000
149A162LEU00.0100.00710.8730.0290.0290.0000.0000.0000.000
150A163VAL0-0.045-0.02213.4250.0530.0530.0000.0000.0000.000
151A164ARG10.8310.86915.6570.3850.3850.0000.0000.0000.000
152A165PHE0-0.039-0.0119.7340.0160.0160.0000.0000.0000.000
153A166VAL0-0.024-0.00814.8850.0420.0420.0000.0000.0000.000
154A167GLU-1-0.832-0.93917.850-0.208-0.2080.0000.0000.0000.000
155A168GLY00.0680.05518.6410.0160.0160.0000.0000.0000.000
156A169ARG10.7170.82018.5950.1900.1900.0000.0000.0000.000
157A170LEU00.0030.01712.304-0.009-0.0090.0000.0000.0000.000
158A171ARG10.8640.94516.2580.2540.2540.0000.0000.0000.000
159A172VAL00.0180.00612.5540.0020.0020.0000.0000.0000.000
160A173GLY00.0270.01615.465-0.010-0.0100.0000.0000.0000.000
161A174ILE0-0.065-0.02711.2540.0170.0170.0000.0000.0000.000
162A175GLY00.0510.02115.4080.0130.0130.0000.0000.0000.000
163A176ASP-1-0.776-0.87114.472-0.147-0.1470.0000.0000.0000.000
164A177ALA00.0290.01515.099-0.007-0.0070.0000.0000.0000.000
165A178THR0-0.001-0.01014.4700.0200.0200.0000.0000.0000.000
166A179VAL00.0150.0149.710-0.051-0.0510.0000.0000.0000.000
167A180LEU00.0000.00112.2600.0130.0130.0000.0000.0000.000
168A181ASP-1-0.744-0.84014.828-0.257-0.2570.0000.0000.0000.000
169A182ALA0-0.020-0.00810.9460.0050.0050.0000.0000.0000.000
170A183MET0-0.0200.00010.2940.0310.0310.0000.0000.0000.000
171A184ALA00.0230.01812.4350.0490.0490.0000.0000.0000.000
172A185ILE0-0.056-0.02614.1070.0230.0230.0000.0000.0000.000
173A186ALA0-0.037-0.01210.0820.0170.0170.0000.0000.0000.000
174A187PHE0-0.036-0.0397.5870.0420.0420.0000.0000.0000.000
175A188GLY00.005-0.00713.6770.0400.0400.0000.0000.0000.000
176A189GLY0-0.0210.00916.5280.0110.0110.0000.0000.0000.000
177A190GLY00.001-0.01118.205-0.011-0.0110.0000.0000.0000.000
178A191GLN00.0080.00719.4320.0230.0230.0000.0000.0000.000
179A192SER0-0.0080.00320.8940.0030.0030.0000.0000.0000.000
180A193ALA0-0.0110.00918.8250.0130.0130.0000.0000.0000.000
181A194SER00.005-0.02419.4360.0090.0090.0000.0000.0000.000
182A195GLU-1-0.892-0.92720.459-0.022-0.0220.0000.0000.0000.000
183A196ILE0-0.030-0.01920.0570.0090.0090.0000.0000.0000.000
184A197ILE00.0170.00516.0120.0170.0170.0000.0000.0000.000
185A198GLU-1-0.925-0.96819.507-0.080-0.0800.0000.0000.0000.000
186A199ARG10.8610.93521.344-0.017-0.0170.0000.0000.0000.000
187A200ALA0-0.017-0.01420.3730.0060.0060.0000.0000.0000.000
188A201TYR00.001-0.03717.5800.0060.0060.0000.0000.0000.000
189A202ASN00.000-0.02620.326-0.004-0.0040.0000.0000.0000.000
190A203LEU0-0.021-0.00923.9040.0020.0020.0000.0000.0000.000
191A204ARG10.8130.89420.205-0.091-0.0910.0000.0000.0000.000
192A205ALA00.0350.03320.0440.0040.0040.0000.0000.0000.000
193A206ASP-1-0.832-0.91615.4310.1230.1230.0000.0000.0000.000
194A207LEU00.0150.00511.7420.0240.0240.0000.0000.0000.000
195A208GLY00.0250.02311.4650.0170.0170.0000.0000.0000.000
196A209ASN0-0.011-0.00212.4300.0580.0580.0000.0000.0000.000
197A210ILE00.0150.00115.3510.0230.0230.0000.0000.0000.000
198A211ALA00.0270.00510.0730.0080.0080.0000.0000.0000.000
199A212LYS10.8410.91410.477-0.645-0.6450.0000.0000.0000.000
200A213ILE0-0.028-0.01013.1080.0000.0000.0000.0000.0000.000
201A214ILE0-0.003-0.00213.655-0.004-0.0040.0000.0000.0000.000
202A215VAL0-0.024-0.0089.4740.0030.0030.0000.0000.0000.000
203A216GLU-1-0.890-0.92412.8770.5130.5130.0000.0000.0000.000
204A217LYS10.8120.89814.960-0.319-0.3190.0000.0000.0000.000
205A218GLY00.0340.03517.120-0.028-0.0280.0000.0000.0000.000
206A219ILE00.0360.00516.944-0.003-0.0030.0000.0000.0000.000
207A220GLU-1-0.795-0.88419.5810.0300.0300.0000.0000.0000.000
208A221ALA0-0.0050.00920.338-0.007-0.0070.0000.0000.0000.000
209A222LEU00.0040.00117.336-0.001-0.0010.0000.0000.0000.000
210A223LYS10.8130.88521.608-0.035-0.0350.0000.0000.0000.000
211A224THR0-0.019-0.01325.178-0.006-0.0060.0000.0000.0000.000
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