Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: V5VL1

Calculation Name: 1HAR-A-Xray372

Preferred Name: Gag-Pol polyprotein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1HAR

Chain ID: A

ChEMBL ID: CHEMBL5823

UniProt ID: P03366

Base Structure: X-ray

Registration Date: 2023-06-22

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 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2134794.201982
FMO2-HF: Nuclear repulsion 2058153.667293
FMO2-HF: Total energy -76640.534689
FMO2-MP2: Total energy -76866.555122


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:PRO)


Summations of interaction energy for fragment #1(A:1:PRO)
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.
-3.6941.823.932-3.401-6.044-0.015
Interaction energy analysis for fragmet #1(A:1:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : -0.001
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].
3A3SER0-0.031-0.0213.861-0.0721.928-0.001-0.935-1.0640.003
4A4PRO0-0.035-0.0075.3280.1780.240-0.001-0.002-0.0590.000
5A5ILE0-0.037-0.0298.0380.1370.1370.0000.0000.0000.000
6A6GLU-1-0.895-0.95510.792-0.329-0.3290.0000.0000.0000.000
7A7THR0-0.023-0.00113.632-0.044-0.0440.0000.0000.0000.000
8A8VAL00.0080.00514.9320.0640.0640.0000.0000.0000.000
9A9PRO0-0.021-0.00417.774-0.010-0.0100.0000.0000.0000.000
10A10VAL0-0.035-0.02619.055-0.002-0.0020.0000.0000.0000.000
11A11LYS10.8540.91822.0270.1980.1980.0000.0000.0000.000
12A12LEU00.0090.00925.258-0.010-0.0100.0000.0000.0000.000
13A13LYS10.8430.93627.5690.1520.1520.0000.0000.0000.000
14A14PRO00.032-0.00630.9160.0040.0040.0000.0000.0000.000
15A15GLY0-0.0030.00734.0460.0020.0020.0000.0000.0000.000
16A16MET0-0.0570.00430.6320.0070.0070.0000.0000.0000.000
17A17ASP-1-0.723-0.84129.900-0.093-0.0930.0000.0000.0000.000
18A18GLY00.0180.00326.888-0.004-0.0040.0000.0000.0000.000
19A19PRO0-0.049-0.01624.4400.0120.0120.0000.0000.0000.000
20A20LYS10.9070.94027.0840.0750.0750.0000.0000.0000.000
21A21VAL0-0.0170.01027.9360.0080.0080.0000.0000.0000.000
22A22ALA00.0370.01828.2910.0000.0000.0000.0000.0000.000
23A23GLN0-0.009-0.00824.658-0.016-0.0160.0000.0000.0000.000
24A24TRP00.0000.00526.2250.0070.0070.0000.0000.0000.000
25A25PRO00.0660.03128.1590.0020.0020.0000.0000.0000.000
26A26LEU0-0.034-0.01124.134-0.006-0.0060.0000.0000.0000.000
27A27THR00.0200.00327.9110.0050.0050.0000.0000.0000.000
28A28ALA00.0770.03627.1190.0010.0010.0000.0000.0000.000
29A29ALA00.0160.00926.0450.0070.0070.0000.0000.0000.000
30A30LYS10.8920.94523.2560.0450.0450.0000.0000.0000.000
31A31ILE00.0020.01522.313-0.001-0.0010.0000.0000.0000.000
32A32ALA00.0220.00822.1310.0080.0080.0000.0000.0000.000
33A33ALA00.0040.00419.7760.0210.0210.0000.0000.0000.000
34A34LEU00.007-0.00117.9960.0090.0090.0000.0000.0000.000
35A35VAL00.0310.02017.3920.0070.0070.0000.0000.0000.000
36A36ALA0-0.0050.01917.1090.0330.0330.0000.0000.0000.000
37A37ILE00.008-0.00212.7770.0520.0520.0000.0000.0000.000
38A38CYS0-0.044-0.03012.544-0.002-0.0020.0000.0000.0000.000
39A39THR0-0.003-0.00913.3240.0180.0180.0000.0000.0000.000
40A40GLU-1-0.835-0.90010.2320.9310.9310.0000.0000.0000.000
41A41MET00.003-0.0078.5170.2280.2280.0000.0000.0000.000
42A42GLU-1-0.817-0.8719.0540.1440.1440.0000.0000.0000.000
43A43LYS10.7920.8869.118-1.133-1.1330.0000.0000.0000.000
44A44GLU-1-0.865-0.9224.4241.9762.120-0.001-0.011-0.1310.000
45A45GLY00.0140.0135.131-0.303-0.281-0.0010.000-0.0210.000
46A46LYS10.8280.9203.9070.4440.595-0.001-0.020-0.1300.000
47A47ILE0-0.041-0.0108.330-0.087-0.0870.0000.0000.0000.000
48A48SER00.003-0.00611.5830.0970.0970.0000.0000.0000.000
49A49LYS10.8520.91014.271-0.191-0.1910.0000.0000.0000.000
50A50ILE0-0.064-0.01318.001-0.013-0.0130.0000.0000.0000.000
51A51GLY00.0280.01020.8820.0150.0150.0000.0000.0000.000
52A52PRO0-0.041-0.02824.523-0.010-0.0100.0000.0000.0000.000
53A53GLU-1-0.846-0.91823.636-0.023-0.0230.0000.0000.0000.000
54A54ASN0-0.0050.00421.901-0.011-0.0110.0000.0000.0000.000
55A55PRO0-0.0020.00425.5870.0050.0050.0000.0000.0000.000
56A56TYR0-0.062-0.05424.490-0.001-0.0010.0000.0000.0000.000
57A57ASN0-0.020-0.02124.2940.0110.0110.0000.0000.0000.000
58A58THR00.0050.01321.921-0.004-0.0040.0000.0000.0000.000
59A59PRO0-0.023-0.00422.8810.0010.0010.0000.0000.0000.000
60A60VAL0-0.001-0.00719.367-0.021-0.0210.0000.0000.0000.000
61A61PHE00.006-0.00121.3560.0200.0200.0000.0000.0000.000
62A62ALA00.0610.03220.565-0.010-0.0100.0000.0000.0000.000
63A63ILE00.0270.02320.0720.0130.0130.0000.0000.0000.000
64A71TRP0-0.037-0.03318.677-0.010-0.0100.0000.0000.0000.000
65A72ALA00.0720.04316.1810.0100.0100.0000.0000.0000.000
66A73LYS10.8930.94914.7350.1750.1750.0000.0000.0000.000
67A74LEU00.0290.00916.697-0.037-0.0370.0000.0000.0000.000
68A75VAL00.001-0.00717.2550.0280.0280.0000.0000.0000.000
69A76ASP-1-0.777-0.84120.203-0.142-0.1420.0000.0000.0000.000
70A77PHE00.017-0.00517.1390.0160.0160.0000.0000.0000.000
71A78ARG10.8340.88622.8310.1110.1110.0000.0000.0000.000
72A79GLU-1-0.767-0.84926.428-0.105-0.1050.0000.0000.0000.000
73A80LEU00.0400.02120.8460.0060.0060.0000.0000.0000.000
74A81ASN00.0090.01222.251-0.015-0.0150.0000.0000.0000.000
75A82LYS10.8450.90225.2740.1090.1090.0000.0000.0000.000
76A83ARG10.8010.88127.5150.1100.1100.0000.0000.0000.000
77A84THR00.020-0.00722.894-0.002-0.0020.0000.0000.0000.000
78A85GLN00.0230.02224.8060.0090.0090.0000.0000.0000.000
79A86ASP-1-0.828-0.90726.205-0.179-0.1790.0000.0000.0000.000
80A87PHE00.0160.00222.192-0.006-0.0060.0000.0000.0000.000
81A88TRP00.0040.00925.1790.0200.0200.0000.0000.0000.000
82A89GLU-1-0.869-0.94323.024-0.322-0.3220.0000.0000.0000.000
83A90VAL0-0.049-0.01423.1170.0130.0130.0000.0000.0000.000
84A104LYS10.8000.86828.3940.1250.1250.0000.0000.0000.000
85A105SER0-0.045-0.01025.4900.0040.0040.0000.0000.0000.000
86A106VAL00.016-0.01223.662-0.009-0.0090.0000.0000.0000.000
87A107THR0-0.072-0.02918.3450.0170.0170.0000.0000.0000.000
88A108VAL00.0240.02018.136-0.006-0.0060.0000.0000.0000.000
89A109LEU0-0.048-0.01613.1440.0220.0220.0000.0000.0000.000
90A110ASP-1-0.842-0.91613.000-0.553-0.5530.0000.0000.0000.000
91A111VAL0-0.055-0.04210.285-0.086-0.0860.0000.0000.0000.000
92A112GLY00.0880.04410.647-0.159-0.1590.0000.0000.0000.000
93A113ASP-1-0.881-0.9548.301-0.838-0.8380.0000.0000.0000.000
94A114ALA0-0.014-0.0016.474-0.372-0.3720.0000.0000.0000.000
95A115TYR0-0.031-0.0567.522-0.175-0.1750.0000.0000.0000.000
96A116PHE0-0.048-0.0336.6270.0980.0980.0000.0000.0000.000
97A117SER00.016-0.0022.8930.0680.6790.014-0.243-0.3820.000
98A118VAL0-0.009-0.0045.4280.2270.2270.0000.0000.0000.000
99A119PRO00.0160.0127.8830.1770.1770.0000.0000.0000.000
100A120LEU0-0.0180.00310.6140.0760.0760.0000.0000.0000.000
101A121ASP-1-0.813-0.91114.068-0.218-0.2180.0000.0000.0000.000
102A122GLU-1-0.800-0.89314.696-0.227-0.2270.0000.0000.0000.000
103A123ASP-1-0.835-0.89617.585-0.124-0.1240.0000.0000.0000.000
104A124PHE0-0.020-0.02119.1110.0240.0240.0000.0000.0000.000
105A125ARG10.7910.88913.5000.3150.3150.0000.0000.0000.000
106A126LYS10.8820.94718.0470.1470.1470.0000.0000.0000.000
107A127TYR00.0210.00721.2630.0210.0210.0000.0000.0000.000
108A128THR0-0.060-0.04316.874-0.003-0.0030.0000.0000.0000.000
109A129ALA0-0.0050.01018.915-0.003-0.0030.0000.0000.0000.000
110A130PHE00.001-0.01015.783-0.001-0.0010.0000.0000.0000.000
111A131THR00.022-0.00821.3820.0160.0160.0000.0000.0000.000
112A132ILE0-0.039-0.00718.396-0.009-0.0090.0000.0000.0000.000
113A133PRO00.009-0.01022.6350.0080.0080.0000.0000.0000.000
114A134SER00.018-0.00225.7420.0120.0120.0000.0000.0000.000
115A135ILE00.0160.00528.018-0.007-0.0070.0000.0000.0000.000
116A136ASN00.000-0.01629.737-0.001-0.0010.0000.0000.0000.000
117A137ASN0-0.072-0.03431.748-0.007-0.0070.0000.0000.0000.000
118A138GLU-1-0.942-0.94532.1190.0370.0370.0000.0000.0000.000
119A139THR00.013-0.00728.6260.0030.0030.0000.0000.0000.000
120A140PRO00.0140.00828.395-0.005-0.0050.0000.0000.0000.000
121A141GLY00.0270.04026.182-0.009-0.0090.0000.0000.0000.000
122A142ILE0-0.054-0.03220.0410.0040.0040.0000.0000.0000.000
123A143ARG10.8330.90321.5660.0330.0330.0000.0000.0000.000
124A144TYR0-0.001-0.04015.3110.0150.0150.0000.0000.0000.000
125A145GLN00.0320.01716.041-0.019-0.0190.0000.0000.0000.000
126A146TYR00.0360.01111.6450.0840.0840.0000.0000.0000.000
127A147ASN0-0.028-0.02810.0520.0570.0570.0000.0000.0000.000
128A148VAL0-0.0340.0057.163-0.023-0.0230.0000.0000.0000.000
129A149LEU0-0.024-0.01110.5160.2060.2060.0000.0000.0000.000
130A150PRO0-0.0040.00511.813-0.038-0.0380.0000.0000.0000.000
131A151GLN00.0390.03311.6190.1290.1290.0000.0000.0000.000
132A152GLY0-0.0020.00014.9780.0580.0580.0000.0000.0000.000
133A153TRP0-0.053-0.03016.8880.0450.0450.0000.0000.0000.000
134A154LYS10.7520.84818.8460.1680.1680.0000.0000.0000.000
135A155GLY00.0700.02819.9570.0030.0030.0000.0000.0000.000
136A156SER0-0.049-0.02714.943-0.031-0.0310.0000.0000.0000.000
137A157PRO00.0770.04216.035-0.060-0.0600.0000.0000.0000.000
138A158ALA00.0390.02617.872-0.027-0.0270.0000.0000.0000.000
139A159ILE0-0.009-0.01314.663-0.003-0.0030.0000.0000.0000.000
140A160PHE00.0410.0329.619-0.021-0.0210.0000.0000.0000.000
141A161GLN00.0570.04014.446-0.045-0.0450.0000.0000.0000.000
142A162SER0-0.049-0.01117.1250.0170.0170.0000.0000.0000.000
143A163SER0-0.017-0.02611.6430.0170.0170.0000.0000.0000.000
144A164MET00.0180.01410.6290.0010.0010.0000.0000.0000.000
145A165THR0-0.066-0.04613.6630.0660.0660.0000.0000.0000.000
146A166LYS10.8880.93814.5410.4290.4290.0000.0000.0000.000
147A167ILE00.0160.0239.0590.0440.0440.0000.0000.0000.000
148A168LEU0-0.010-0.01013.0710.0620.0620.0000.0000.0000.000
149A169ALA0-0.0210.01315.7740.0490.0490.0000.0000.0000.000
150A170PRO00.003-0.00515.6500.0350.0350.0000.0000.0000.000
151A171PHE00.0200.01215.5050.0240.0240.0000.0000.0000.000
152A172LYS10.9020.93717.8990.3430.3430.0000.0000.0000.000
153A173ALA0-0.026-0.00420.9950.0200.0200.0000.0000.0000.000
154A174ALA0-0.028-0.01019.9560.0180.0180.0000.0000.0000.000
155A175ASN0-0.0170.00619.0570.0350.0350.0000.0000.0000.000
156A176PRO00.0310.01622.621-0.011-0.0110.0000.0000.0000.000
157A177ASP-1-0.888-0.93324.882-0.131-0.1310.0000.0000.0000.000
158A178ILE0-0.039-0.03220.7940.0020.0020.0000.0000.0000.000
159A179VAL0-0.0010.01023.476-0.011-0.0110.0000.0000.0000.000
160A180ILE0-0.002-0.00617.453-0.009-0.0090.0000.0000.0000.000
161A181TYR0-0.007-0.00520.596-0.009-0.0090.0000.0000.0000.000
162A182GLN00.010-0.01414.681-0.071-0.0710.0000.0000.0000.000
163A183TYR00.0110.02719.0330.0270.0270.0000.0000.0000.000
164A184MET0-0.017-0.01817.826-0.034-0.0340.0000.0000.0000.000
165A185ASP-1-0.809-0.88514.501-0.506-0.5060.0000.0000.0000.000
166A186ASP-1-0.832-0.89314.799-0.334-0.3340.0000.0000.0000.000
167A187LEU0-0.017-0.01813.3690.0280.0280.0000.0000.0000.000
168A188TYR0-0.057-0.04816.5100.0370.0370.0000.0000.0000.000
169A189VAL00.002-0.01016.945-0.006-0.0060.0000.0000.0000.000
170A190GLY00.003-0.00420.2990.0180.0180.0000.0000.0000.000
171A191SER0-0.004-0.00523.8920.0020.0020.0000.0000.0000.000
172A192ASP-1-0.804-0.89226.282-0.106-0.1060.0000.0000.0000.000
173A193LEU00.0130.02524.8010.0110.0110.0000.0000.0000.000
174A194ALA00.0420.01728.414-0.002-0.0020.0000.0000.0000.000
175A195ILE00.0640.02325.878-0.003-0.0030.0000.0000.0000.000
176A196GLY00.0190.01625.090-0.007-0.0070.0000.0000.0000.000
177A197ALA00.0280.02324.054-0.002-0.0020.0000.0000.0000.000
178A198HIS00.0420.02621.805-0.001-0.0010.0000.0000.0000.000
179A199ARG10.8260.87816.5830.1080.1080.0000.0000.0000.000
180A200THR0-0.001-0.01019.510-0.003-0.0030.0000.0000.0000.000
181A201LYS10.8370.90718.5540.1230.1230.0000.0000.0000.000
182A202ILE0-0.031-0.00716.165-0.030-0.0300.0000.0000.0000.000
183A203GLU-1-0.779-0.85713.988-0.202-0.2020.0000.0000.0000.000
184A204GLU-1-0.896-0.94313.634-0.160-0.1600.0000.0000.0000.000
185A205LEU0-0.0150.00113.556-0.031-0.0310.0000.0000.0000.000
186A206ARG10.8690.89510.7930.1830.1830.0000.0000.0000.000
187A207GLN00.008-0.0019.147-0.077-0.0770.0000.0000.0000.000
188A208HIS0-0.086-0.0489.2360.0170.0170.0000.0000.0000.000
189A209LEU00.002-0.0118.360-0.047-0.0470.0000.0000.0000.000
190A210LEU00.0130.0193.425-0.589-0.3140.010-0.052-0.2320.000
191A211ARG10.9120.9564.6780.0330.131-0.001-0.004-0.0930.000
192A212TRP0-0.0290.0026.7320.1270.1270.0000.0000.0000.000
193A213GLY00.0280.0162.634-0.678-0.1710.889-0.654-0.7420.001
194A214LEU0-0.002-0.0032.671-4.475-2.8050.903-0.934-1.639-0.020
195A215THR00.008-0.0042.3430.1500.1052.123-0.538-1.5400.001
196A216THR00.0130.0334.7330.3650.384-0.001-0.008-0.0110.000