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: LJ5L9

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 OptHSide
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 -2559889.505125
FMO2-HF: Nuclear repulsion 2474317.510853
FMO2-HF: Total energy -85571.994273
FMO2-MP2: Total energy -85825.177763


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.
0.9744.9420.673-1.968-2.6730.001
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 : 0.073 / q_NPA : 0.024
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].
3A51ASN0-0.064-0.0493.297-0.3521.8170.011-1.098-1.0820.003
4A52PRO0-0.0190.0565.1330.2330.280-0.001-0.011-0.0350.000
5A53ARG10.9660.9597.8400.8110.8110.0000.0000.0000.000
6A54GLY00.0000.0139.844-0.064-0.0640.0000.0000.0000.000
7A55LEU00.0150.00010.992-0.029-0.0290.0000.0000.0000.000
8A56GLY00.0150.00213.7450.0300.0300.0000.0000.0000.000
9A57PRO0-0.037-0.02816.762-0.016-0.0160.0000.0000.0000.000
10A58LEU0-0.056-0.02519.2410.0080.0080.0000.0000.0000.000
11A59GLN00.0270.03114.532-0.024-0.0240.0000.0000.0000.000
12A60ILE00.0310.00210.5240.0180.0180.0000.0000.0000.000
13A61TRP0-0.0100.00914.603-0.025-0.0250.0000.0000.0000.000
14A62GLN00.0060.01911.5370.0280.0280.0000.0000.0000.000
15A63THR0-0.008-0.00215.9900.0090.0090.0000.0000.0000.000
16A64ASP-1-0.795-0.88418.190-0.111-0.1110.0000.0000.0000.000
17A65PHE00.0130.00620.4550.0080.0080.0000.0000.0000.000
18A66THR00.0270.02623.1890.0000.0000.0000.0000.0000.000
19A67LEU00.0110.01025.2570.0050.0050.0000.0000.0000.000
20A68GLU-1-0.793-0.88828.739-0.066-0.0660.0000.0000.0000.000
21A69PRO00.0340.00831.1340.0040.0040.0000.0000.0000.000
22A70ARG10.8710.92634.2070.0540.0540.0000.0000.0000.000
23A71MET0-0.030-0.00833.2110.0020.0020.0000.0000.0000.000
24A72ALA00.0180.03835.9230.0020.0020.0000.0000.0000.000
25A73PRO00.0460.01037.5540.0000.0000.0000.0000.0000.000
26A74ARG10.8860.94135.6390.0330.0330.0000.0000.0000.000
27A75SER00.0470.02933.055-0.001-0.0010.0000.0000.0000.000
28A76TRP00.0090.02326.616-0.005-0.0050.0000.0000.0000.000
29A77LEU00.001-0.00427.7910.0030.0030.0000.0000.0000.000
30A78ALA00.0110.02325.240-0.004-0.0040.0000.0000.0000.000
31A79VAL00.009-0.01821.8970.0000.0000.0000.0000.0000.000
32A80THR00.0210.01920.412-0.009-0.0090.0000.0000.0000.000
33A81VAL0-0.011-0.00717.4480.0040.0040.0000.0000.0000.000
34A82ASP-1-0.705-0.83417.406-0.204-0.2040.0000.0000.0000.000
35A83THR0-0.067-0.09112.571-0.032-0.0320.0000.0000.0000.000
36A84ALA00.0040.03013.991-0.047-0.0470.0000.0000.0000.000
37A85SER0-0.018-0.02215.8140.0020.0020.0000.0000.0000.000
38A86SER0-0.041-0.03918.2840.0120.0120.0000.0000.0000.000
39A87ALA00.0090.01619.1770.0110.0110.0000.0000.0000.000
40A88ILE0-0.042-0.03421.215-0.011-0.0110.0000.0000.0000.000
41A89VAL00.0410.01423.4200.0100.0100.0000.0000.0000.000
42A90VAL00.003-0.00225.175-0.003-0.0030.0000.0000.0000.000
43A91THR00.0160.00327.6510.0030.0030.0000.0000.0000.000
44A92GLN0-0.013-0.00929.696-0.001-0.0010.0000.0000.0000.000
45A93HIS00.0130.01429.4230.0000.0000.0000.0000.0000.000
46A94GLY00.0170.00032.772-0.001-0.0010.0000.0000.0000.000
47A95ARG10.9580.97132.6720.0130.0130.0000.0000.0000.000
48A96VAL00.0330.03826.1550.0000.0000.0000.0000.0000.000
49A97THR0-0.005-0.00329.1500.0050.0050.0000.0000.0000.000
50A98SER00.0960.04526.762-0.002-0.0020.0000.0000.0000.000
51A99VAL00.0180.02128.420-0.002-0.0020.0000.0000.0000.000
52A100ALA0-0.033-0.00629.711-0.002-0.0020.0000.0000.0000.000
53A101VAL00.0510.01623.864-0.004-0.0040.0000.0000.0000.000
54A102GLN00.0280.01426.5540.0000.0000.0000.0000.0000.000
55A103HIS00.0210.01528.245-0.002-0.0020.0000.0000.0000.000
56A104HIS0-0.044-0.03624.280-0.008-0.0080.0000.0000.0000.000
57A105TRP00.031-0.01320.2780.0010.0010.0000.0000.0000.000
58A106ALA00.0020.01125.974-0.003-0.0030.0000.0000.0000.000
59A107THR0-0.025-0.01129.2100.0000.0000.0000.0000.0000.000
60A108ALA0-0.001-0.00524.688-0.003-0.0030.0000.0000.0000.000
61A109ILE0-0.041-0.01225.079-0.005-0.0050.0000.0000.0000.000
62A110ALA0-0.0280.00227.060-0.001-0.0010.0000.0000.0000.000
63A111VAL0-0.044-0.01428.0210.0000.0000.0000.0000.0000.000
64A112LEU0-0.040-0.03022.845-0.004-0.0040.0000.0000.0000.000
65A113GLY00.0620.03425.266-0.005-0.0050.0000.0000.0000.000
66A114ARG10.8790.93123.6700.0130.0130.0000.0000.0000.000
67A115PRO0-0.0100.01519.223-0.002-0.0020.0000.0000.0000.000
68A116LYS10.9440.96417.2180.0560.0560.0000.0000.0000.000
69A117ALA00.0220.01114.8390.0280.0280.0000.0000.0000.000
70A118ILE0-0.0150.00016.426-0.038-0.0380.0000.0000.0000.000
71A119LYS10.8440.9469.3660.1290.1290.0000.0000.0000.000
72A120THR00.0270.01814.138-0.015-0.0150.0000.0000.0000.000
73A121ASP-1-0.757-0.88714.536-0.038-0.0380.0000.0000.0000.000
74A122ASN00.018-0.02915.555-0.003-0.0030.0000.0000.0000.000
75A123GLY00.0620.04818.5820.0060.0060.0000.0000.0000.000
76A124SER00.0340.00521.7290.0030.0030.0000.0000.0000.000
77A125CYS0-0.077-0.03323.4020.0030.0030.0000.0000.0000.000
78A126PHE00.0420.00520.084-0.002-0.0020.0000.0000.0000.000
79A127THR0-0.036-0.01619.6720.0070.0070.0000.0000.0000.000
80A128SER00.0050.01222.2230.0090.0090.0000.0000.0000.000
81A129LYS10.9990.99625.669-0.033-0.0330.0000.0000.0000.000
82A130SER0-0.024-0.01327.5280.0000.0000.0000.0000.0000.000
83A131THR00.0240.00023.697-0.004-0.0040.0000.0000.0000.000
84A132ARG10.8940.95518.542-0.065-0.0650.0000.0000.0000.000
85A133GLU-1-0.825-0.90724.2930.0290.0290.0000.0000.0000.000
86A134TRP0-0.012-0.00524.757-0.002-0.0020.0000.0000.0000.000
87A135LEU00.006-0.01520.918-0.003-0.0030.0000.0000.0000.000
88A136ALA0-0.0040.00324.161-0.002-0.0020.0000.0000.0000.000
89A137ARG10.8960.94225.163-0.013-0.0130.0000.0000.0000.000
90A138TRP00.0040.00925.539-0.004-0.0040.0000.0000.0000.000
91A139GLY00.0180.01624.385-0.006-0.0060.0000.0000.0000.000
92A140ILE0-0.122-0.05519.775-0.005-0.0050.0000.0000.0000.000
93A141ALA00.0390.01916.4370.0110.0110.0000.0000.0000.000
94A142HIS00.012-0.01116.612-0.009-0.0090.0000.0000.0000.000
95A143THR0-0.012-0.00610.3600.0440.0440.0000.0000.0000.000
96A144THR0-0.033-0.01313.820-0.043-0.0430.0000.0000.0000.000
97A145GLY0-0.049-0.02811.6340.0390.0390.0000.0000.0000.000
98A146ILE00.0350.01212.2680.0260.0260.0000.0000.0000.000
99A147PRO00.004-0.00314.482-0.033-0.0330.0000.0000.0000.000
100A148GLY00.0480.03515.6860.0100.0100.0000.0000.0000.000
101A149ASN0-0.066-0.03713.933-0.024-0.0240.0000.0000.0000.000
102A150SER0-0.0010.01810.058-0.053-0.0530.0000.0000.0000.000
103A151GLN00.031-0.0182.379-0.0640.3480.431-0.330-0.5120.000
104A152GLY00.013-0.0577.4490.0450.0450.0000.0000.0000.000
105A153GLN00.010-0.0059.5630.0430.0430.0000.0000.0000.000
106A154ALA00.0280.02111.3990.0220.0220.0000.0000.0000.000
107A155MET0-0.088-0.02112.7240.0070.0070.0000.0000.0000.000
108A156VAL00.0240.00814.3750.0260.0260.0000.0000.0000.000
109A157GLU-1-0.825-0.90216.309-0.117-0.1170.0000.0000.0000.000
110A158ARG10.9120.95017.1060.2110.2110.0000.0000.0000.000
111A159ALA0-0.012-0.00818.7710.0170.0170.0000.0000.0000.000
112A160ASN00.0100.00020.7100.0200.0200.0000.0000.0000.000
113A161ARG10.9530.99422.0630.1270.1270.0000.0000.0000.000
114A162LEU00.007-0.00421.5780.0080.0080.0000.0000.0000.000
115A163LEU00.0030.00024.6520.0100.0100.0000.0000.0000.000
116A164LYS10.8290.88025.6310.0830.0830.0000.0000.0000.000
117A165ASP-1-0.842-0.90426.920-0.085-0.0850.0000.0000.0000.000
118A166ARG10.9360.96028.9380.0840.0840.0000.0000.0000.000
119A167ILE00.0080.00930.2680.0060.0060.0000.0000.0000.000
120A168ARG10.8310.90230.2840.0740.0740.0000.0000.0000.000
121A169VAL0-0.016-0.01133.1930.0030.0030.0000.0000.0000.000
122A170LEU0-0.031-0.01834.1370.0030.0030.0000.0000.0000.000
123A171ALA0-0.0010.00936.6020.0030.0030.0000.0000.0000.000
124A172GLU-1-0.817-0.91537.506-0.048-0.0480.0000.0000.0000.000
125A173GLY0-0.0170.01039.2880.0020.0020.0000.0000.0000.000
126A174ASP-1-0.922-0.95341.060-0.039-0.0390.0000.0000.0000.000
127A175GLY00.0100.00543.0240.0020.0020.0000.0000.0000.000
128A176PHE0-0.074-0.06940.9970.0030.0030.0000.0000.0000.000
129A177MET00.0350.01840.337-0.003-0.0030.0000.0000.0000.000
130A178LYS10.9130.96440.1430.0310.0310.0000.0000.0000.000
131A179ARG10.8520.91839.2800.0280.0280.0000.0000.0000.000
132A180ILE0-0.0120.00637.6630.0010.0010.0000.0000.0000.000
133A181PRO00.0180.01640.7180.0010.0010.0000.0000.0000.000
134A182THR00.0650.00541.506-0.002-0.0020.0000.0000.0000.000
135A183SER0-0.0130.00241.908-0.001-0.0010.0000.0000.0000.000
136A184LYS10.9130.95842.3120.0340.0340.0000.0000.0000.000
137A185GLN0-0.034-0.02037.432-0.002-0.0020.0000.0000.0000.000
138A186GLY00.0340.01737.043-0.003-0.0030.0000.0000.0000.000
139A187GLU-1-0.797-0.89936.743-0.038-0.0380.0000.0000.0000.000
140A188LEU00.0220.02335.320-0.003-0.0030.0000.0000.0000.000
141A189LEU00.0080.00130.711-0.004-0.0040.0000.0000.0000.000
142A190ALA00.0160.00332.520-0.005-0.0050.0000.0000.0000.000
143A191LYS10.9530.98133.6240.0460.0460.0000.0000.0000.000
144A192ALA00.0110.00230.724-0.004-0.0040.0000.0000.0000.000
145A193MET0-0.0160.01028.104-0.007-0.0070.0000.0000.0000.000
146A194TYR00.0100.00329.320-0.005-0.0050.0000.0000.0000.000
147A195ALA0-0.024-0.00530.934-0.004-0.0040.0000.0000.0000.000
148A196LEU00.0000.00425.513-0.005-0.0050.0000.0000.0000.000
149A197ASN00.0170.00525.477-0.022-0.0220.0000.0000.0000.000
150A198HIS00.003-0.01927.436-0.006-0.0060.0000.0000.0000.000
151A199LYS10.8790.92728.9640.0860.0860.0000.0000.0000.000
152A200GLU-1-0.827-0.89326.622-0.092-0.0920.0000.0000.0000.000
153A201ARG10.7820.88221.1730.1490.1490.0000.0000.0000.000
154A202GLY00.0120.00624.334-0.008-0.0080.0000.0000.0000.000
155A203GLU-1-0.927-0.95721.153-0.156-0.1560.0000.0000.0000.000
156A204ASN0-0.104-0.03820.361-0.010-0.0100.0000.0000.0000.000
157A205THR00.0850.04924.1130.0060.0060.0000.0000.0000.000
158A206LYS10.9110.94724.0110.1250.1250.0000.0000.0000.000
159A207THR00.0480.01125.156-0.010-0.0100.0000.0000.0000.000
160A208PRO0-0.025-0.01922.889-0.004-0.0040.0000.0000.0000.000
161A209ILE00.0450.02924.041-0.004-0.0040.0000.0000.0000.000
162A210GLN00.0220.01626.709-0.002-0.0020.0000.0000.0000.000
163A211LYS10.8140.90919.4980.1860.1860.0000.0000.0000.000
164A212HIS00.0030.01121.927-0.021-0.0210.0000.0000.0000.000
165A213TRP00.0280.01923.4790.0000.0000.0000.0000.0000.000
166A214ARG10.9290.97126.1070.0760.0760.0000.0000.0000.000
167A215PRO00.0180.02320.932-0.004-0.0040.0000.0000.0000.000
168A216THR0-0.038-0.02421.1300.0120.0120.0000.0000.0000.000
169A217VAL00.006-0.00417.024-0.022-0.0220.0000.0000.0000.000
170A218LEU0-0.027-0.00517.5200.0200.0200.0000.0000.0000.000
171A219THR00.0230.00518.164-0.009-0.0090.0000.0000.0000.000
172A220GLU-1-0.803-0.89818.421-0.065-0.0650.0000.0000.0000.000
173A221GLY00.0060.00516.785-0.016-0.0160.0000.0000.0000.000
174A222PRO0-0.009-0.00117.8690.0140.0140.0000.0000.0000.000
175A223PRO00.0380.02617.058-0.018-0.0180.0000.0000.0000.000
176A224VAL0-0.063-0.05713.283-0.007-0.0070.0000.0000.0000.000
177A225LYN00.0280.02115.0110.0170.0170.0000.0000.0000.000
178A226ILE00.006-0.0218.328-0.035-0.0350.0000.0000.0000.000
179A227ARG10.8250.91612.1850.1430.1430.0000.0000.0000.000
180A228ILE00.0550.0319.959-0.030-0.0300.0000.0000.0000.000
181A229GLU-1-0.859-0.9428.661-0.058-0.0580.0000.0000.0000.000
182A230THR0-0.067-0.04711.883-0.011-0.0110.0000.0000.0000.000
183A231GLY0-0.049-0.02414.432-0.005-0.0050.0000.0000.0000.000
184A232GLU-1-0.864-0.90516.003-0.001-0.0010.0000.0000.0000.000
185A233TRP0-0.084-0.06214.848-0.012-0.0120.0000.0000.0000.000
186A234GLU-1-0.838-0.92312.8910.0550.0550.0000.0000.0000.000
187A235LYS10.8490.90914.7000.0190.0190.0000.0000.0000.000
188A236GLY00.0500.02715.3190.0120.0120.0000.0000.0000.000
189A237TRP00.009-0.0028.1060.0210.0210.0000.0000.0000.000
190A238ASN00.0310.04712.9210.0200.0200.0000.0000.0000.000
191A239VAL0-0.050-0.01812.386-0.041-0.0410.0000.0000.0000.000
192A240LEU00.002-0.00311.8400.0260.0260.0000.0000.0000.000
193A241VAL0-0.011-0.01212.1410.0210.0210.0000.0000.0000.000
194A242TRP00.0210.01712.397-0.057-0.0570.0000.0000.0000.000
195A243GLY00.0160.01712.9470.0350.0350.0000.0000.0000.000
196A244ARG10.9960.98214.3020.1640.1640.0000.0000.0000.000
197A245GLY0-0.0120.01112.8170.0120.0120.0000.0000.0000.000
198A246TYR0-0.033-0.0156.103-0.023-0.0230.0000.0000.0000.000
199A247ALA00.0290.0158.8870.0560.0560.0000.0000.0000.000
200A248ALA0-0.0290.0037.943-0.159-0.1590.0000.0000.0000.000
201A249VAL00.003-0.0177.3710.1530.1530.0000.0000.0000.000
202A250LYS10.9000.9538.021-0.017-0.0170.0000.0000.0000.000
203A251ASN0-0.018-0.0069.8400.0420.0420.0000.0000.0000.000
204A252ARG10.8950.91811.4660.0620.0620.0000.0000.0000.000
205A253ASP-1-0.898-0.93614.5800.0880.0880.0000.0000.0000.000
206A254THR0-0.024-0.02611.8030.0360.0360.0000.0000.0000.000
207A255ASP-1-0.894-0.94213.174-0.016-0.0160.0000.0000.0000.000
208A256LYS10.9340.9876.784-0.517-0.5170.0000.0000.0000.000
209A257VAL00.0090.0007.692-0.068-0.0680.0000.0000.0000.000
210A258ILE0-0.045-0.0222.835-0.734-0.2910.204-0.247-0.401-0.001
211A259TRP0-0.016-0.0073.6340.7601.0310.006-0.066-0.2110.000
212A260VAL00.0230.0143.526-0.4920.1340.022-0.216-0.432-0.001
213A261PRO0-0.011-0.0156.139-0.007-0.0070.0000.0000.0000.000
214A262SER00.035-0.0039.1070.0460.0460.0000.0000.0000.000
215A263ARG10.9990.99612.1320.2610.2610.0000.0000.0000.000
216A264LYS10.7820.9018.3330.1830.1830.0000.0000.0000.000
217A265VAL00.0110.02311.7040.0110.0110.0000.0000.0000.000
218A266LYS10.9160.98013.5780.0800.0800.0000.0000.0000.000
219A267PRO00.0430.00917.1440.0000.0000.0000.0000.0000.000
220A268ASP-1-0.848-0.90818.246-0.046-0.0460.0000.0000.0000.000
221A269ILE00.0190.01820.0740.0020.0020.0000.0000.0000.000