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: 9G5Y2

Calculation Name: 1C0M-A-Xray372

Preferred Name: Rous sarcoma virus integrase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1C0M

Chain ID: A

ChEMBL ID: CHEMBL2750

UniProt ID: P03354

Base Structure: X-ray

Registration Date: 2023-06-21

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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2560426.06304
FMO2-HF: Nuclear repulsion 2474853.241541
FMO2-HF: Total energy -85572.8215
FMO2-MP2: Total energy -85825.87374


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:49:GLY)


Summations of interaction energy for fragment #1(A:49:GLY)
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.
0.2943.8811.037-1.936-2.687-0.009
Interaction energy analysis for fragmet #1(A:49:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.075 / 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].
3A51ASN0-0.040-0.0193.8690.5821.692-0.002-0.466-0.6410.001
4A52PRO0-0.0170.0185.5690.2530.2530.0000.0000.0000.000
5A53ARG10.9430.9488.2400.8860.8860.0000.0000.0000.000
6A54GLY00.0060.0219.895-0.093-0.0930.0000.0000.0000.000
7A55LEU00.0260.00310.811-0.052-0.0520.0000.0000.0000.000
8A56GLY00.007-0.00813.6510.0370.0370.0000.0000.0000.000
9A57PRO0-0.017-0.01216.776-0.015-0.0150.0000.0000.0000.000
10A58LEU0-0.066-0.02219.3440.0080.0080.0000.0000.0000.000
11A59GLN00.0110.01814.495-0.028-0.0280.0000.0000.0000.000
12A60ILE00.0420.01510.7440.0280.0280.0000.0000.0000.000
13A61TRP0-0.0180.00714.843-0.026-0.0260.0000.0000.0000.000
14A62GLN00.0070.00311.8000.0350.0350.0000.0000.0000.000
15A63THR0-0.018-0.01216.0830.0060.0060.0000.0000.0000.000
16A64ASP-1-0.783-0.87318.590-0.084-0.0840.0000.0000.0000.000
17A65PHE0-0.018-0.02420.6710.0070.0070.0000.0000.0000.000
18A66THR00.0270.03323.9760.0040.0040.0000.0000.0000.000
19A67LEU00.0220.01725.5830.0040.0040.0000.0000.0000.000
20A68GLU-1-0.819-0.90229.048-0.065-0.0650.0000.0000.0000.000
21A69PRO00.0470.00931.4060.0030.0030.0000.0000.0000.000
22A70ARG10.8310.90034.6450.0560.0560.0000.0000.0000.000
23A71MET0-0.014-0.00533.2610.0020.0020.0000.0000.0000.000
24A72ALA00.0260.03536.0010.0020.0020.0000.0000.0000.000
25A73PRO00.0360.00737.661-0.001-0.0010.0000.0000.0000.000
26A74ARG10.8510.92235.9880.0330.0330.0000.0000.0000.000
27A75SER00.0630.03433.238-0.002-0.0020.0000.0000.0000.000
28A76TRP0-0.0120.00926.794-0.005-0.0050.0000.0000.0000.000
29A77LEU00.0230.00228.0280.0020.0020.0000.0000.0000.000
30A78ALA00.0250.03125.602-0.003-0.0030.0000.0000.0000.000
31A79VAL0-0.007-0.01922.143-0.003-0.0030.0000.0000.0000.000
32A80THR00.0340.01820.592-0.004-0.0040.0000.0000.0000.000
33A81VAL0-0.012-0.01217.6730.0000.0000.0000.0000.0000.000
34A82ASP-1-0.692-0.83717.925-0.227-0.2270.0000.0000.0000.000
35A83THR0-0.074-0.07512.861-0.038-0.0380.0000.0000.0000.000
36A84ALA00.0060.02213.875-0.068-0.0680.0000.0000.0000.000
37A85SER00.015-0.00315.7700.0050.0050.0000.0000.0000.000
38A86SER0-0.085-0.04918.1800.0150.0150.0000.0000.0000.000
39A87ALA00.0580.03119.1570.0140.0140.0000.0000.0000.000
40A88ILE0-0.040-0.02621.390-0.011-0.0110.0000.0000.0000.000
41A89VAL00.0360.01523.5640.0110.0110.0000.0000.0000.000
42A90VAL00.005-0.00425.086-0.004-0.0040.0000.0000.0000.000
43A91THR0-0.001-0.00627.6230.0030.0030.0000.0000.0000.000
44A92GLN0-0.0080.00229.865-0.001-0.0010.0000.0000.0000.000
45A93HIS00.0200.02129.9700.0010.0010.0000.0000.0000.000
46A94GLY00.0420.01433.408-0.001-0.0010.0000.0000.0000.000
47A95ARG10.9580.97032.9370.0040.0040.0000.0000.0000.000
48A96VAL00.0420.03726.6570.0000.0000.0000.0000.0000.000
49A97THR0-0.012-0.00829.2770.0050.0050.0000.0000.0000.000
50A98SER00.0820.04026.994-0.003-0.0030.0000.0000.0000.000
51A99VAL00.0070.01428.720-0.003-0.0030.0000.0000.0000.000
52A100ALA0-0.014-0.00129.871-0.003-0.0030.0000.0000.0000.000
53A101VAL00.0470.02224.219-0.006-0.0060.0000.0000.0000.000
54A102GLN00.0480.03626.8240.0000.0000.0000.0000.0000.000
55A103HIS00.0230.02128.692-0.001-0.0010.0000.0000.0000.000
56A104HIS0-0.048-0.02124.462-0.009-0.0090.0000.0000.0000.000
57A105TRP00.024-0.02220.5380.0010.0010.0000.0000.0000.000
58A106ALA00.0000.00826.330-0.004-0.0040.0000.0000.0000.000
59A107THR0-0.016-0.01429.759-0.002-0.0020.0000.0000.0000.000
60A108ALA0-0.019-0.01624.994-0.004-0.0040.0000.0000.0000.000
61A109ILE0-0.031-0.01925.335-0.007-0.0070.0000.0000.0000.000
62A110ALA0-0.024-0.00527.417-0.002-0.0020.0000.0000.0000.000
63A111VAL0-0.033-0.00228.4170.0000.0000.0000.0000.0000.000
64A112LEU0-0.035-0.02023.202-0.007-0.0070.0000.0000.0000.000
65A113GLY00.0560.04125.567-0.007-0.0070.0000.0000.0000.000
66A114ARG10.8640.91623.3640.0190.0190.0000.0000.0000.000
67A115PRO0-0.0140.01019.452-0.003-0.0030.0000.0000.0000.000
68A116LYS10.9470.96817.4940.0800.0800.0000.0000.0000.000
69A117ALA00.0330.01815.0930.0300.0300.0000.0000.0000.000
70A118ILE0-0.019-0.00716.648-0.039-0.0390.0000.0000.0000.000
71A119LYS10.8020.94710.085-0.030-0.0300.0000.0000.0000.000
72A120THR0-0.0030.00214.608-0.022-0.0220.0000.0000.0000.000
73A121ASP-1-0.758-0.89015.0850.0110.0110.0000.0000.0000.000
74A122ASN00.020-0.02216.083-0.002-0.0020.0000.0000.0000.000
75A123GLY00.0700.04819.1500.0050.0050.0000.0000.0000.000
76A124SER00.0300.01422.3950.0000.0000.0000.0000.0000.000
77A125CYS0-0.065-0.02323.8100.0020.0020.0000.0000.0000.000
78A126PHE00.0450.01220.833-0.005-0.0050.0000.0000.0000.000
79A127THR0-0.026-0.03120.3910.0060.0060.0000.0000.0000.000
80A128SER0-0.022-0.00922.8700.0110.0110.0000.0000.0000.000
81A129LYS11.0051.00026.110-0.044-0.0440.0000.0000.0000.000
82A130SER0-0.049-0.02728.260-0.001-0.0010.0000.0000.0000.000
83A131THR00.0490.01724.498-0.005-0.0050.0000.0000.0000.000
84A132ARG10.8510.93319.430-0.092-0.0920.0000.0000.0000.000
85A133GLU-1-0.817-0.90124.8800.0370.0370.0000.0000.0000.000
86A134TRP0-0.018-0.00725.449-0.003-0.0030.0000.0000.0000.000
87A135LEU0-0.005-0.01521.344-0.006-0.0060.0000.0000.0000.000
88A136ALA00.0030.00924.588-0.003-0.0030.0000.0000.0000.000
89A137ARG10.8810.92025.849-0.021-0.0210.0000.0000.0000.000
90A138TRP00.0210.01326.162-0.006-0.0060.0000.0000.0000.000
91A139GLY00.0050.01625.128-0.007-0.0070.0000.0000.0000.000
92A140ILE0-0.093-0.03820.327-0.010-0.0100.0000.0000.0000.000
93A141ALA00.0340.01917.0620.0140.0140.0000.0000.0000.000
94A142HIS00.031-0.00117.665-0.007-0.0070.0000.0000.0000.000
95A143THR0-0.018-0.01611.3090.0510.0510.0000.0000.0000.000
96A144THR00.0250.02514.649-0.044-0.0440.0000.0000.0000.000
97A145GLY0-0.017-0.01512.1270.0470.0470.0000.0000.0000.000
98A146ILE00.0240.02612.7900.0310.0310.0000.0000.0000.000
99A147PRO0-0.002-0.00515.007-0.033-0.0330.0000.0000.0000.000
100A148GLY00.0820.05516.7500.0070.0070.0000.0000.0000.000
101A149ASN0-0.093-0.05214.360-0.014-0.0140.0000.0000.0000.000
102A150SER00.0200.01310.761-0.047-0.0470.0000.0000.0000.000
103A151GLN0-0.010-0.0313.297-0.588-0.3980.006-0.091-0.1060.000
104A152GLY0-0.016-0.0517.6880.1680.1680.0000.0000.0000.000
105A153GLN00.037-0.0089.928-0.002-0.0020.0000.0000.0000.000
106A154ALA00.0180.01011.7340.0120.0120.0000.0000.0000.000
107A155MET0-0.097-0.01713.140-0.016-0.0160.0000.0000.0000.000
108A156VAL00.0140.00814.8220.0260.0260.0000.0000.0000.000
109A157GLU-1-0.794-0.87416.585-0.109-0.1090.0000.0000.0000.000
110A158ARG10.8790.93717.3960.2390.2390.0000.0000.0000.000
111A159ALA0-0.008-0.00219.2100.0160.0160.0000.0000.0000.000
112A160ASN0-0.016-0.03420.9030.0190.0190.0000.0000.0000.000
113A161ARG10.9000.94722.1490.1320.1320.0000.0000.0000.000
114A162LEU0-0.005-0.01222.0030.0090.0090.0000.0000.0000.000
115A163LEU00.0010.01025.1200.0100.0100.0000.0000.0000.000
116A164LYS10.8450.89825.8900.0810.0810.0000.0000.0000.000
117A165ASP-1-0.801-0.88127.105-0.097-0.0970.0000.0000.0000.000
118A166ARG10.8750.93829.2610.0980.0980.0000.0000.0000.000
119A167ILE00.0090.00230.4610.0060.0060.0000.0000.0000.000
120A168ARG10.8460.91530.4940.0820.0820.0000.0000.0000.000
121A169VAL00.0050.00133.3640.0040.0040.0000.0000.0000.000
122A170LEU0-0.033-0.01734.1220.0030.0030.0000.0000.0000.000
123A171ALA00.0060.00636.8220.0030.0030.0000.0000.0000.000
124A172GLU-1-0.820-0.91037.774-0.051-0.0510.0000.0000.0000.000
125A173GLY00.0050.01539.6950.0020.0020.0000.0000.0000.000
126A174ASP-1-0.898-0.94941.483-0.042-0.0420.0000.0000.0000.000
127A175GLY00.0360.02843.3360.0030.0030.0000.0000.0000.000
128A176PHE0-0.042-0.04840.9060.0030.0030.0000.0000.0000.000
129A177MET00.0140.01940.156-0.003-0.0030.0000.0000.0000.000
130A178LYS10.8680.91940.4940.0350.0350.0000.0000.0000.000
131A179ARG10.8400.91339.3770.0270.0270.0000.0000.0000.000
132A180ILE00.0170.02838.0260.0010.0010.0000.0000.0000.000
133A181PRO00.0060.00240.9810.0010.0010.0000.0000.0000.000
134A182THR00.0360.00441.349-0.002-0.0020.0000.0000.0000.000
135A183SER00.0010.01542.013-0.001-0.0010.0000.0000.0000.000
136A184LYS10.9190.95842.4270.0380.0380.0000.0000.0000.000
137A185GLN0-0.063-0.02837.695-0.002-0.0020.0000.0000.0000.000
138A186GLY00.0280.01137.142-0.003-0.0030.0000.0000.0000.000
139A187GLU-1-0.781-0.88737.286-0.042-0.0420.0000.0000.0000.000
140A188LEU00.0050.00635.824-0.004-0.0040.0000.0000.0000.000
141A189LEU00.0050.00730.860-0.005-0.0050.0000.0000.0000.000
142A190ALA00.0310.01532.742-0.006-0.0060.0000.0000.0000.000
143A191LYS10.9530.97933.8110.0540.0540.0000.0000.0000.000
144A192ALA00.018-0.00331.049-0.004-0.0040.0000.0000.0000.000
145A193MET0-0.0030.01028.310-0.008-0.0080.0000.0000.0000.000
146A194TYR00.0350.02129.400-0.007-0.0070.0000.0000.0000.000
147A195ALA0-0.018-0.00330.889-0.006-0.0060.0000.0000.0000.000
148A196LEU0-0.0110.00225.955-0.006-0.0060.0000.0000.0000.000
149A197ASN0-0.009-0.01025.465-0.027-0.0270.0000.0000.0000.000
150A198HIS00.0500.00827.482-0.008-0.0080.0000.0000.0000.000
151A199LYS10.8540.92529.2260.1040.1040.0000.0000.0000.000
152A200GLU-1-0.807-0.89426.665-0.114-0.1140.0000.0000.0000.000
153A201ARG10.7660.86920.9850.1800.1800.0000.0000.0000.000
154A202GLY00.0280.01924.109-0.012-0.0120.0000.0000.0000.000
155A203GLU-1-0.880-0.92720.597-0.196-0.1960.0000.0000.0000.000
156A204ASN0-0.075-0.05320.027-0.023-0.0230.0000.0000.0000.000
157A205THR00.0730.03123.9260.0100.0100.0000.0000.0000.000
158A206LYS10.8760.94823.6410.1620.1620.0000.0000.0000.000
159A207THR00.0390.02025.037-0.013-0.0130.0000.0000.0000.000
160A208PRO0-0.022-0.01722.869-0.005-0.0050.0000.0000.0000.000
161A209ILE00.0420.02424.044-0.005-0.0050.0000.0000.0000.000
162A210GLN00.0160.01026.750-0.003-0.0030.0000.0000.0000.000
163A211LYS10.8020.90019.5630.2240.2240.0000.0000.0000.000
164A212HIS00.0040.01122.085-0.030-0.0300.0000.0000.0000.000
165A213TRP00.0270.01223.664-0.001-0.0010.0000.0000.0000.000
166A214ARG10.9250.97325.9970.0990.0990.0000.0000.0000.000
167A215PRO00.0410.03720.843-0.008-0.0080.0000.0000.0000.000
168A216THR0-0.058-0.05220.6170.0160.0160.0000.0000.0000.000
169A217VAL00.0090.00916.707-0.025-0.0250.0000.0000.0000.000
170A218LEU0-0.026-0.00116.8070.0260.0260.0000.0000.0000.000
171A219THR00.0150.00017.433-0.016-0.0160.0000.0000.0000.000
172A220GLU-1-0.782-0.87117.569-0.110-0.1100.0000.0000.0000.000
173A221GLY00.0200.01616.325-0.023-0.0230.0000.0000.0000.000
174A222PRO0-0.0040.00417.4270.0190.0190.0000.0000.0000.000
175A223PRO00.0260.01516.716-0.027-0.0270.0000.0000.0000.000
176A224VAL0-0.064-0.04612.748-0.009-0.0090.0000.0000.0000.000
177A225LYN00.0230.02914.7020.0210.0210.0000.0000.0000.000
178A226ILE0-0.010-0.0168.266-0.049-0.0490.0000.0000.0000.000
179A227ARG10.8540.94011.6880.2120.2120.0000.0000.0000.000
180A228ILE00.0500.0339.956-0.049-0.0490.0000.0000.0000.000
181A229GLU-1-0.843-0.9248.110-0.124-0.1240.0000.0000.0000.000
182A230THR0-0.062-0.03611.532-0.005-0.0050.0000.0000.0000.000
183A231GLY0-0.016-0.00514.322-0.006-0.0060.0000.0000.0000.000
184A232GLU-1-0.862-0.91115.991-0.012-0.0120.0000.0000.0000.000
185A233TRP0-0.060-0.05914.164-0.024-0.0240.0000.0000.0000.000
186A234GLU-1-0.845-0.91112.5480.0570.0570.0000.0000.0000.000
187A235LYS10.8550.89114.5860.0370.0370.0000.0000.0000.000
188A236GLY00.0400.02014.6160.0130.0130.0000.0000.0000.000
189A237TRP00.0230.0147.3850.0300.0300.0000.0000.0000.000
190A238ASN0-0.0080.00712.4720.0340.0340.0000.0000.0000.000
191A239VAL0-0.049-0.01711.960-0.066-0.0660.0000.0000.0000.000
192A240LEU00.003-0.00411.3540.0420.0420.0000.0000.0000.000
193A241VAL00.000-0.00811.8880.0330.0330.0000.0000.0000.000
194A242TRP00.0260.01111.995-0.081-0.0810.0000.0000.0000.000
195A243GLY00.0220.01812.8990.0500.0500.0000.0000.0000.000
196A244ARG10.9770.97113.8970.1890.1890.0000.0000.0000.000
197A245GLY00.0110.01912.9830.0250.0250.0000.0000.0000.000
198A246TYR0-0.045-0.0205.787-0.038-0.0380.0000.0000.0000.000
199A247ALA00.0240.0178.5170.1130.1130.0000.0000.0000.000
200A248ALA0-0.0100.0167.531-0.238-0.2380.0000.0000.0000.000
201A249VAL00.014-0.0147.0730.2120.2120.0000.0000.0000.000
202A250LYS10.8250.9047.749-0.009-0.0090.0000.0000.0000.000
203A251ASN00.0120.0209.3950.0580.0580.0000.0000.0000.000
204A252ARG10.8870.91110.9210.1150.1150.0000.0000.0000.000
205A253ASP-1-0.910-0.93514.2350.0740.0740.0000.0000.0000.000
206A254THR0-0.014-0.03011.4990.0350.0350.0000.0000.0000.000
207A255ASP-1-0.866-0.91812.713-0.081-0.0810.0000.0000.0000.000
208A256LYS10.9380.9716.673-0.512-0.5120.0000.0000.0000.000
209A257VAL00.0040.0037.514-0.067-0.0670.0000.0000.0000.000
210A258ILE0-0.055-0.0212.570-0.782-0.3370.689-0.477-0.657-0.002
211A259TRP0-0.030-0.0243.2120.8761.3210.026-0.157-0.3140.000
212A260VAL00.0220.0102.870-2.072-0.6750.318-0.745-0.969-0.008
213A261PRO00.005-0.0125.5200.1000.1000.0000.0000.0000.000
214A262SER00.012-0.0058.6500.0600.0600.0000.0000.0000.000
215A263ARG10.9870.99011.7930.3690.3690.0000.0000.0000.000
216A264LYS10.7480.8507.4940.3070.3070.0000.0000.0000.000
217A265VAL00.0090.01810.5960.0170.0170.0000.0000.0000.000
218A266LYS10.9050.97412.4330.1310.1310.0000.0000.0000.000
219A267PRO00.0470.01016.130-0.004-0.0040.0000.0000.0000.000
220A268ASP-1-0.856-0.91818.041-0.077-0.0770.0000.0000.0000.000
221A269ILE00.0240.02619.8220.0020.0020.0000.0000.0000.000