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: L7N69

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 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 577
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -11660797.573613
FMO2-HF: Nuclear repulsion 11433131.9965
FMO2-HF: Total energy -227665.577113
FMO2-MP2: Total energy -228335.477627


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.
-11.753-8.46220.385-6.032-17.645-0.011
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 : 0.026 / q_NPA : 0.030
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].
3A3PHE0-0.015-0.0343.161-2.945-0.5400.120-1.158-1.367-0.002
4A4LYS10.9340.9745.0340.7380.878-0.001-0.006-0.1330.000
5A5VAL00.0160.0123.056-0.3650.4140.106-0.148-0.7370.000
6A6ILE00.0210.0102.569-0.4880.1880.517-0.155-1.0380.000
7A7ALA0-0.0080.0045.2160.3890.445-0.001-0.002-0.0530.000
8A8GLU-1-0.869-0.9418.091-0.459-0.4590.0000.0000.0000.000
9A9TYR0-0.048-0.0277.0740.2210.2210.0000.0000.0000.000
10A10PHE0-0.004-0.0198.7480.1720.1720.0000.0000.0000.000
11A11ASP-1-0.883-0.95911.169-0.354-0.3540.0000.0000.0000.000
12A12LYS10.8430.90710.8940.7240.7240.0000.0000.0000.000
13A13LEU00.0100.00412.3750.0810.0810.0000.0000.0000.000
14A14GLU-1-0.890-0.91914.449-0.325-0.3250.0000.0000.0000.000
15A15LYS10.8550.93416.9540.4250.4250.0000.0000.0000.000
16A16ILE0-0.0540.00615.3230.0370.0370.0000.0000.0000.000
17A17SER00.0640.01918.8390.0080.0080.0000.0000.0000.000
18A18SER0-0.0510.00220.1390.0180.0180.0000.0000.0000.000
19A19ARG10.9940.97716.7490.1850.1850.0000.0000.0000.000
20A20LEU00.0300.01718.142-0.015-0.0150.0000.0000.0000.000
21A21GLN00.042-0.01616.940-0.030-0.0300.0000.0000.0000.000
22A22LEU00.0280.03413.296-0.046-0.0460.0000.0000.0000.000
23A23THR00.0110.01013.050-0.068-0.0680.0000.0000.0000.000
24A24ALA0-0.018-0.00512.878-0.020-0.0200.0000.0000.0000.000
25A25LEU0-0.014-0.0099.436-0.031-0.0310.0000.0000.0000.000
26A26LEU0-0.005-0.0048.613-0.174-0.1740.0000.0000.0000.000
27A27ALA00.0210.0188.065-0.095-0.0950.0000.0000.0000.000
28A28ASP-1-0.848-0.9118.450-0.449-0.4490.0000.0000.0000.000
29A29LEU00.0140.0113.064-0.5100.0030.115-0.106-0.5230.000
30A30LEU0-0.0270.0014.180-0.557-0.3510.000-0.035-0.1710.000
31A31SER0-0.040-0.0225.9570.6380.6380.0000.0000.0000.000
32A32LYS10.8100.9005.6130.5070.5070.0000.0000.0000.000
33A33SER0-0.046-0.0662.811-2.755-2.4065.008-2.590-2.766-0.009
34A34ASP-1-0.853-0.9372.116-2.051-6.4458.824-0.097-4.3330.001
35A35LYS10.9690.9663.638-0.917-0.7810.0100.144-0.2910.000
36A36THR0-0.041-0.0176.574-0.246-0.2460.0000.0000.0000.000
37A37ILE0-0.003-0.0032.815-1.188-0.5680.898-0.292-1.2270.002
38A38ILE00.0280.0185.7600.2040.2040.0000.0000.0000.000
39A39ASP-1-0.935-0.9717.1350.0610.0610.0000.0000.0000.000
40A40LYS10.8820.9587.327-0.260-0.2600.0000.0000.0000.000
41A41VAL00.0060.0052.795-1.218-0.4350.643-0.275-1.151-0.002
42A42VAL00.001-0.0055.349-0.415-0.401-0.0010.000-0.0120.000
43A43TYR00.0200.0138.298-0.053-0.0530.0000.0000.0000.000
44A44ILE00.0490.0316.341-0.079-0.0790.0000.0000.0000.000
45A45ILE0-0.0010.0015.658-0.050-0.0500.0000.0000.0000.000
46A46GLN0-0.027-0.0178.3390.0560.0560.0000.0000.0000.000
47A47GLY0-0.066-0.03710.9950.0540.0540.0000.0000.0000.000
48A48LYS10.9030.96611.8880.2520.2520.0000.0000.0000.000
49A49LEU0-0.002-0.01111.379-0.048-0.0480.0000.0000.0000.000
50A50TRP0-0.007-0.01212.7640.0470.0470.0000.0000.0000.000
51A51PRO0-0.0060.01414.879-0.027-0.0270.0000.0000.0000.000
52A52ASP-1-0.804-0.90917.160-0.138-0.1380.0000.0000.0000.000
53A53PHE0-0.040-0.01919.0020.0050.0050.0000.0000.0000.000
54A54LEU0-0.021-0.02417.9390.0100.0100.0000.0000.0000.000
55A55GLY0-0.017-0.00721.9950.0050.0050.0000.0000.0000.000
56A56TYR0-0.076-0.03018.7790.0060.0060.0000.0000.0000.000
57A57PRO00.014-0.00122.238-0.005-0.0050.0000.0000.0000.000
58A58GLU-1-0.892-0.94220.227-0.155-0.1550.0000.0000.0000.000
59A59LEU0-0.053-0.02814.8350.0030.0030.0000.0000.0000.000
60A60GLY00.0830.05219.055-0.006-0.0060.0000.0000.0000.000
61A61ILE0-0.115-0.06321.4200.0150.0150.0000.0000.0000.000
62A62GLY00.0450.02423.670-0.002-0.0020.0000.0000.0000.000
63A63GLU-1-0.768-0.90325.503-0.171-0.1710.0000.0000.0000.000
64A64LYS11.0020.99626.5740.0960.0960.0000.0000.0000.000
65A65PHE0-0.031-0.01326.0720.0030.0030.0000.0000.0000.000
66A66LEU00.0670.03219.714-0.004-0.0040.0000.0000.0000.000
67A67ILE00.0230.01923.573-0.011-0.0110.0000.0000.0000.000
68A68LYS10.9470.98626.0560.1120.1120.0000.0000.0000.000
69A69ALA0-0.018-0.01321.4610.0030.0030.0000.0000.0000.000
70A70ILE00.0470.01620.946-0.005-0.0050.0000.0000.0000.000
71A71SER0-0.0260.01322.8810.0040.0040.0000.0000.0000.000
72A72ILE0-0.032-0.02823.5540.0090.0090.0000.0000.0000.000
73A73ALA0-0.069-0.03219.9070.0080.0080.0000.0000.0000.000
74A74THR0-0.042-0.02221.8340.0040.0040.0000.0000.0000.000
75A75ASN0-0.077-0.02923.6960.0130.0130.0000.0000.0000.000
76A76THR0-0.012-0.00426.4500.0120.0120.0000.0000.0000.000
77A77ASP-1-0.850-0.93328.736-0.103-0.1030.0000.0000.0000.000
78A78GLU-1-0.878-0.97029.674-0.117-0.1170.0000.0000.0000.000
79A79ASN00.0300.03031.026-0.005-0.0050.0000.0000.0000.000
80A80SER0-0.035-0.00930.742-0.005-0.0050.0000.0000.0000.000
81A81VAL00.0040.00126.047-0.006-0.0060.0000.0000.0000.000
82A82GLU-1-0.921-0.97028.745-0.129-0.1290.0000.0000.0000.000
83A83ASN0-0.035-0.05130.929-0.002-0.0020.0000.0000.0000.000
84A84LEU0-0.037-0.01527.1770.0010.0010.0000.0000.0000.000
85A85TYR0-0.040-0.01425.368-0.011-0.0110.0000.0000.0000.000
86A86LYS10.9360.98128.5400.1030.1030.0000.0000.0000.000
87A87THR0-0.050-0.01930.909-0.002-0.0020.0000.0000.0000.000
88A88ILE0-0.064-0.02724.855-0.003-0.0030.0000.0000.0000.000
89A89GLY00.0200.01726.958-0.007-0.0070.0000.0000.0000.000
90A90ASP-1-0.818-0.91620.491-0.309-0.3090.0000.0000.0000.000
91A91LEU00.0530.01522.314-0.002-0.0020.0000.0000.0000.000
92A92GLY00.0610.04518.684-0.007-0.0070.0000.0000.0000.000
93A93GLU-1-0.830-0.92519.251-0.296-0.2960.0000.0000.0000.000
94A94VAL0-0.017-0.00121.0850.0090.0090.0000.0000.0000.000
95A95ALA00.0230.00819.1750.0110.0110.0000.0000.0000.000
96A96ARG10.8940.95517.5050.2970.2970.0000.0000.0000.000
97A97ARG10.8890.94819.5910.2020.2020.0000.0000.0000.000
98A98LEU0-0.018-0.02323.2050.0170.0170.0000.0000.0000.000
99A99LYS10.8290.90316.9040.3120.3120.0000.0000.0000.000
100A100SER0-0.035-0.02420.6390.0070.0070.0000.0000.0000.000
101A101LYS10.8920.97521.9430.1460.1460.0000.0000.0000.000
102A102GLN0-0.048-0.00922.293-0.005-0.0050.0000.0000.0000.000
103A116LYS10.9150.94413.069-0.322-0.3220.0000.0000.0000.000
104A117GLU-1-0.936-0.9679.0830.6730.6730.0000.0000.0000.000
105A118SER00.0350.0218.073-0.101-0.1010.0000.0000.0000.000
106A119LEU0-0.0090.0067.9840.0880.0880.0000.0000.0000.000
107A120THR00.0480.0363.589-0.771-0.4600.001-0.081-0.2310.000
108A121VAL00.008-0.0112.174-0.530-0.2174.147-1.204-3.256-0.001
109A122ASP-1-0.796-0.9034.599-0.1590.225-0.001-0.027-0.3560.000
110A123GLU-1-0.837-0.9146.400-0.155-0.1550.0000.0000.0000.000
111A124VAL00.0230.0247.6860.2370.2370.0000.0000.0000.000
112A125TYR00.0220.0168.5330.1720.1720.0000.0000.0000.000
113A126SER0-0.026-0.00410.1310.1170.1170.0000.0000.0000.000
114A127THR0-0.057-0.04812.2410.0940.0940.0000.0000.0000.000
115A128LEU00.004-0.01011.3760.0610.0610.0000.0000.0000.000
116A129SER00.014-0.00413.4540.0510.0510.0000.0000.0000.000
117A130LYS10.9350.96615.9960.1840.1840.0000.0000.0000.000
118A131VAL0-0.061-0.03317.7860.0260.0260.0000.0000.0000.000
119A132ALA0-0.020-0.00718.0360.0150.0150.0000.0000.0000.000
120A133LEU00.0060.00419.1240.0160.0160.0000.0000.0000.000
121A134THR0-0.091-0.02122.0020.0200.0200.0000.0000.0000.000
122A135THR00.041-0.00724.004-0.002-0.0020.0000.0000.0000.000
123A136GLY00.0130.01427.6840.0050.0050.0000.0000.0000.000
124A137GLU-1-0.895-0.93330.867-0.065-0.0650.0000.0000.0000.000
125A138GLY00.0190.02029.893-0.003-0.0030.0000.0000.0000.000
126A139SER0-0.057-0.04626.545-0.010-0.0100.0000.0000.0000.000
127A140ARG10.9240.96626.0750.0780.0780.0000.0000.0000.000
128A141ASP-1-0.826-0.93426.453-0.106-0.1060.0000.0000.0000.000
129A142LEU0-0.039-0.00922.120-0.007-0.0070.0000.0000.0000.000
130A143LYS10.9640.98421.8780.1400.1400.0000.0000.0000.000
131A144ILE00.0040.00421.449-0.022-0.0220.0000.0000.0000.000
132A145ARG10.9500.97322.2500.0920.0920.0000.0000.0000.000
133A146LEU0-0.045-0.01617.830-0.008-0.0080.0000.0000.0000.000
134A147LEU00.0440.02017.357-0.033-0.0330.0000.0000.0000.000
135A148ALA00.0080.01917.861-0.030-0.0300.0000.0000.0000.000
136A149GLY0-0.023-0.01517.998-0.004-0.0040.0000.0000.0000.000
137A150LEU00.0260.00211.565-0.009-0.0090.0000.0000.0000.000
138A151LEU00.0000.00314.379-0.043-0.0430.0000.0000.0000.000
139A152LYS10.9520.99016.6000.1310.1310.0000.0000.0000.000
140A153LYS10.8400.92710.1190.2500.2500.0000.0000.0000.000
141A154ALA00.0030.01512.272-0.016-0.0160.0000.0000.0000.000
142A155ASP-1-0.785-0.89112.473-0.458-0.4580.0000.0000.0000.000
143A156PRO0-0.006-0.02714.338-0.035-0.0350.0000.0000.0000.000
144A157LEU00.0020.00111.6700.0120.0120.0000.0000.0000.000
145A158GLU-1-0.795-0.9108.596-1.060-1.0600.0000.0000.0000.000
146A159ALA00.0120.00411.7470.0010.0010.0000.0000.0000.000
147A160LYS10.8680.95015.0280.4000.4000.0000.0000.0000.000
148A161PHE00.007-0.01711.3680.0300.0300.0000.0000.0000.000
149A162LEU00.0110.00710.5850.0150.0150.0000.0000.0000.000
150A163VAL0-0.044-0.01613.3400.0480.0480.0000.0000.0000.000
151A164ARG10.8070.87115.2760.3860.3860.0000.0000.0000.000
152A165PHE0-0.0180.00110.0990.0290.0290.0000.0000.0000.000
153A166VAL0-0.027-0.01914.4890.0450.0450.0000.0000.0000.000
154A167GLU-1-0.940-0.98917.096-0.222-0.2220.0000.0000.0000.000
155A168GLY00.0320.03417.8980.0260.0260.0000.0000.0000.000
156A169ARG10.8410.90718.1850.2350.2350.0000.0000.0000.000
157A170LEU0-0.0060.03211.896-0.005-0.0050.0000.0000.0000.000
158A171ARG10.9020.95415.9740.2730.2730.0000.0000.0000.000
159A172VAL00.0220.01212.6630.0070.0070.0000.0000.0000.000
160A173GLY00.0140.01015.5470.0130.0130.0000.0000.0000.000
161A174ILE0-0.044-0.02511.2130.0160.0160.0000.0000.0000.000
162A175GLY00.0430.02615.470-0.004-0.0040.0000.0000.0000.000
163A176ASP-1-0.748-0.84214.954-0.153-0.1530.0000.0000.0000.000
164A177ALA00.0190.00715.4900.0040.0040.0000.0000.0000.000
165A178THR0-0.009-0.00314.1790.0250.0250.0000.0000.0000.000
166A179VAL00.0450.0239.839-0.019-0.0190.0000.0000.0000.000
167A180LEU0-0.004-0.02112.5820.0260.0260.0000.0000.0000.000
168A181ASP-1-0.878-0.94015.029-0.129-0.1290.0000.0000.0000.000
169A182ALA00.005-0.00311.1180.0120.0120.0000.0000.0000.000
170A183MET0-0.0390.00510.8830.0470.0470.0000.0000.0000.000
171A184ALA00.0190.00712.5180.0560.0560.0000.0000.0000.000
172A185ILE0-0.075-0.03714.1750.0240.0240.0000.0000.0000.000
173A186ALA0-0.046-0.01910.1390.0140.0140.0000.0000.0000.000
174A187PHE0-0.032-0.0237.8990.0490.0490.0000.0000.0000.000
175A188GLY0-0.008-0.02313.7240.0200.0200.0000.0000.0000.000
176A189GLY0-0.0230.00416.693-0.004-0.0040.0000.0000.0000.000
177A190GLY00.0250.01118.209-0.012-0.0120.0000.0000.0000.000
178A191GLN00.0360.00519.2660.0110.0110.0000.0000.0000.000
179A192SER0-0.0200.01720.9140.0000.0000.0000.0000.0000.000
180A193ALA00.0120.02118.8230.0040.0040.0000.0000.0000.000
181A194SER00.008-0.03119.7020.0020.0020.0000.0000.0000.000
182A195GLU-1-0.894-0.93020.7420.0020.0020.0000.0000.0000.000
183A196ILE0-0.073-0.03519.7630.0030.0030.0000.0000.0000.000
184A197ILE00.0080.00116.0650.0080.0080.0000.0000.0000.000
185A198GLU-1-0.923-0.97019.613-0.049-0.0490.0000.0000.0000.000
186A199ARG10.8880.95521.470-0.034-0.0340.0000.0000.0000.000
187A200ALA0-0.012-0.01220.3520.0010.0010.0000.0000.0000.000
188A201TYR0-0.030-0.07717.5280.0000.0000.0000.0000.0000.000
189A202ASN00.002-0.02420.466-0.011-0.0110.0000.0000.0000.000
190A203LEU0-0.026-0.00324.040-0.003-0.0030.0000.0000.0000.000
191A204ARG10.8470.92620.808-0.063-0.0630.0000.0000.0000.000
192A205ALA00.0240.03520.1400.0060.0060.0000.0000.0000.000
193A206ASP-1-0.836-0.95116.0760.0250.0250.0000.0000.0000.000
194A207LEU00.017-0.01111.9450.0270.0270.0000.0000.0000.000
195A208GLY00.0120.01811.8090.0310.0310.0000.0000.0000.000
196A209ASN0-0.021-0.00812.8280.0760.0760.0000.0000.0000.000
197A210ILE00.014-0.00115.4900.0280.0280.0000.0000.0000.000
198A211ALA00.0370.01310.2380.0240.0240.0000.0000.0000.000
199A212LYS10.9220.96311.865-0.264-0.2640.0000.0000.0000.000
200A213ILE0-0.044-0.00113.2520.0160.0160.0000.0000.0000.000
201A214ILE0-0.0090.00113.7060.0060.0060.0000.0000.0000.000
202A215VAL0-0.036-0.0119.6540.0130.0130.0000.0000.0000.000
203A216GLU-1-0.961-0.98112.8950.3510.3510.0000.0000.0000.000
204A217LYS10.8880.93315.015-0.199-0.1990.0000.0000.0000.000
205A218GLY00.0470.03816.974-0.026-0.0260.0000.0000.0000.000
206A219ILE00.0640.01716.570-0.014-0.0140.0000.0000.0000.000
207A220GLU-1-0.901-0.95019.3710.0650.0650.0000.0000.0000.000
208A221ALA0-0.0200.00120.620-0.013-0.0130.0000.0000.0000.000
209A222LEU0-0.030-0.01717.742-0.009-0.0090.0000.0000.0000.000
210A223LYS10.9370.96721.977-0.064-0.0640.0000.0000.0000.000
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