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: 3Q2NL

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 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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2562104.442932
FMO2-HF: Nuclear repulsion 2476534.169603
FMO2-HF: Total energy -85570.273329
FMO2-MP2: Total energy -85823.714833


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.
0.6234.6490.38-1.891-2.5140
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 : 0.069 / 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].
3A51ASN0-0.029-0.0583.329-0.6901.4710.009-1.132-1.0380.003
4A52PRO0-0.0900.0545.1300.1940.244-0.001-0.011-0.0380.000
5A53ARG10.9630.9577.7760.7530.7530.0000.0000.0000.000
6A54GLY0-0.0070.0119.844-0.061-0.0610.0000.0000.0000.000
7A55LEU00.014-0.00511.474-0.030-0.0300.0000.0000.0000.000
8A56GLY00.0040.00213.7450.0260.0260.0000.0000.0000.000
9A57PRO0-0.030-0.02716.762-0.014-0.0140.0000.0000.0000.000
10A58LEU0-0.047-0.01919.2410.0080.0080.0000.0000.0000.000
11A59GLN00.0220.03214.428-0.025-0.0250.0000.0000.0000.000
12A60ILE00.0410.01110.3870.0200.0200.0000.0000.0000.000
13A61TRP00.0030.02714.603-0.025-0.0250.0000.0000.0000.000
14A62GLN00.0320.03411.3640.0480.0480.0000.0000.0000.000
15A63THR0-0.024-0.00516.0370.0080.0080.0000.0000.0000.000
16A64ASP-1-0.764-0.88418.231-0.094-0.0940.0000.0000.0000.000
17A65PHE0-0.030-0.01520.4900.0070.0070.0000.0000.0000.000
18A66THR00.0400.03123.212-0.001-0.0010.0000.0000.0000.000
19A67LEU00.0100.00425.2780.0040.0040.0000.0000.0000.000
20A68GLU-1-0.855-0.92128.755-0.057-0.0570.0000.0000.0000.000
21A69PRO00.0480.01331.1490.0030.0030.0000.0000.0000.000
22A70ARG10.9170.96533.7530.0490.0490.0000.0000.0000.000
23A71MET0-0.024-0.00433.2100.0020.0020.0000.0000.0000.000
24A72ALA00.0070.03335.9430.0020.0020.0000.0000.0000.000
25A73PRO00.029-0.00437.5740.0000.0000.0000.0000.0000.000
26A74ARG10.9280.96635.7060.0270.0270.0000.0000.0000.000
27A75SER00.0530.02732.722-0.001-0.0010.0000.0000.0000.000
28A76TRP00.0120.02626.788-0.004-0.0040.0000.0000.0000.000
29A77LEU00.003-0.00327.7800.0020.0020.0000.0000.0000.000
30A78ALA00.0050.02025.276-0.003-0.0030.0000.0000.0000.000
31A79VAL00.015-0.01221.610-0.001-0.0010.0000.0000.0000.000
32A80THR00.0050.01420.455-0.010-0.0100.0000.0000.0000.000
33A81VAL00.001-0.01217.5470.0010.0010.0000.0000.0000.000
34A82ASP-1-0.708-0.84517.404-0.179-0.1790.0000.0000.0000.000
35A83THR0-0.063-0.11312.539-0.027-0.0270.0000.0000.0000.000
36A84ALA00.0190.04013.990-0.044-0.0440.0000.0000.0000.000
37A85SER0-0.038-0.02715.8130.0000.0000.0000.0000.0000.000
38A86SER0-0.082-0.08818.3080.0110.0110.0000.0000.0000.000
39A87ALA00.0250.05019.1760.0090.0090.0000.0000.0000.000
40A88ILE0-0.039-0.03021.334-0.009-0.0090.0000.0000.0000.000
41A89VAL00.0350.02023.4180.0090.0090.0000.0000.0000.000
42A90VAL0-0.017-0.00725.173-0.003-0.0030.0000.0000.0000.000
43A91THR00.0340.01727.6480.0030.0030.0000.0000.0000.000
44A92GLN0-0.050-0.03829.734-0.002-0.0020.0000.0000.0000.000
45A93HIS00.0060.01029.2160.0010.0010.0000.0000.0000.000
46A94GLY00.005-0.00332.811-0.001-0.0010.0000.0000.0000.000
47A95ARG10.9590.96932.7300.0080.0080.0000.0000.0000.000
48A96VAL00.0490.04126.0640.0000.0000.0000.0000.0000.000
49A97THR0-0.016-0.00429.1870.0050.0050.0000.0000.0000.000
50A98SER00.0740.00727.407-0.004-0.0040.0000.0000.0000.000
51A99VAL00.0270.02728.473-0.002-0.0020.0000.0000.0000.000
52A100ALA0-0.042-0.01529.695-0.002-0.0020.0000.0000.0000.000
53A101VAL00.0540.01623.829-0.004-0.0040.0000.0000.0000.000
54A102GLN00.0350.01426.6100.0000.0000.0000.0000.0000.000
55A103HIS00.0130.00928.304-0.002-0.0020.0000.0000.0000.000
56A104HIS0-0.043-0.04024.335-0.007-0.0070.0000.0000.0000.000
57A105TRP00.041-0.01720.2310.0010.0010.0000.0000.0000.000
58A106ALA0-0.0030.00926.032-0.003-0.0030.0000.0000.0000.000
59A107THR0-0.019-0.00929.272-0.001-0.0010.0000.0000.0000.000
60A108ALA0-0.002-0.00524.668-0.002-0.0020.0000.0000.0000.000
61A109ILE0-0.037-0.01225.267-0.004-0.0040.0000.0000.0000.000
62A110ALA0-0.034-0.00427.060-0.001-0.0010.0000.0000.0000.000
63A111VAL0-0.044-0.01127.985-0.001-0.0010.0000.0000.0000.000
64A112LEU0-0.054-0.03522.749-0.004-0.0040.0000.0000.0000.000
65A113GLY00.0810.04225.266-0.005-0.0050.0000.0000.0000.000
66A114ARG10.9190.94823.6660.0060.0060.0000.0000.0000.000
67A115PRO0-0.0150.01019.278-0.001-0.0010.0000.0000.0000.000
68A116LYS10.9420.96317.2790.0390.0390.0000.0000.0000.000
69A117ALA00.0280.01114.8220.0270.0270.0000.0000.0000.000
70A118ILE0-0.0120.00716.512-0.037-0.0370.0000.0000.0000.000
71A119LYS10.8700.95310.4310.0370.0370.0000.0000.0000.000
72A120THR00.0110.01014.196-0.018-0.0180.0000.0000.0000.000
73A121ASP-1-0.737-0.88214.581-0.021-0.0210.0000.0000.0000.000
74A122ASN00.033-0.02016.292-0.002-0.0020.0000.0000.0000.000
75A123GLY00.0530.04618.6190.0050.0050.0000.0000.0000.000
76A124SER00.027-0.00121.7660.0030.0030.0000.0000.0000.000
77A125CYS0-0.039-0.00823.4780.0020.0020.0000.0000.0000.000
78A126PHE00.0240.00120.099-0.002-0.0020.0000.0000.0000.000
79A127THR0-0.040-0.02219.7140.0080.0080.0000.0000.0000.000
80A128SER00.0340.04722.2760.0070.0070.0000.0000.0000.000
81A129LYS10.9970.99125.729-0.036-0.0360.0000.0000.0000.000
82A130SER0-0.013-0.00327.5890.0000.0000.0000.0000.0000.000
83A131THR00.008-0.00423.480-0.002-0.0020.0000.0000.0000.000
84A132ARG10.9230.98218.779-0.074-0.0740.0000.0000.0000.000
85A133GLU-1-0.854-0.93224.3590.0350.0350.0000.0000.0000.000
86A134TRP0-0.020-0.00524.846-0.001-0.0010.0000.0000.0000.000
87A135LEU00.007-0.01821.053-0.004-0.0040.0000.0000.0000.000
88A136ALA0-0.0030.00624.232-0.002-0.0020.0000.0000.0000.000
89A137ARG10.9320.96325.237-0.017-0.0170.0000.0000.0000.000
90A138TRP0-0.0050.00525.568-0.005-0.0050.0000.0000.0000.000
91A139GLY0-0.0030.00524.462-0.005-0.0050.0000.0000.0000.000
92A140ILE0-0.124-0.04719.797-0.004-0.0040.0000.0000.0000.000
93A141ALA00.0300.01116.3800.0100.0100.0000.0000.0000.000
94A142HIS0-0.046-0.04316.470-0.013-0.0130.0000.0000.0000.000
95A143THR0-0.017-0.00310.5170.0250.0250.0000.0000.0000.000
96A144THR0-0.018-0.02513.886-0.041-0.0410.0000.0000.0000.000
97A145GLY0-0.092-0.05011.6730.0410.0410.0000.0000.0000.000
98A146ILE00.0530.02712.3040.0230.0230.0000.0000.0000.000
99A147PRO0-0.026-0.01514.497-0.030-0.0300.0000.0000.0000.000
100A148GLY00.0400.03215.6850.0090.0090.0000.0000.0000.000
101A149ASN00.0020.00013.924-0.019-0.0190.0000.0000.0000.000
102A150SER0-0.0080.01110.013-0.048-0.0480.0000.0000.0000.000
103A151GLN00.022-0.0032.806-0.0590.4390.149-0.229-0.417-0.001
104A152GLY00.032-0.0517.4750.0500.0500.0000.0000.0000.000
105A153GLN00.0530.0059.5960.0540.0540.0000.0000.0000.000
106A154ALA00.0520.03911.4370.0140.0140.0000.0000.0000.000
107A155MET0-0.120-0.02112.7390.0020.0020.0000.0000.0000.000
108A156VAL00.0170.01114.3730.0250.0250.0000.0000.0000.000
109A157GLU-1-0.870-0.93016.185-0.112-0.1120.0000.0000.0000.000
110A158ARG10.8970.94417.1120.1920.1920.0000.0000.0000.000
111A159ALA0-0.005-0.00118.7680.0150.0150.0000.0000.0000.000
112A160ASN00.0050.00320.5500.0190.0190.0000.0000.0000.000
113A161ARG10.9490.99321.9530.1190.1190.0000.0000.0000.000
114A162LEU00.016-0.00221.4370.0070.0070.0000.0000.0000.000
115A163LEU00.0030.00624.6500.0090.0090.0000.0000.0000.000
116A164LYS10.8720.91625.8680.0750.0750.0000.0000.0000.000
117A165ASP-1-0.860-0.91426.924-0.078-0.0780.0000.0000.0000.000
118A166ARG10.9290.95828.9100.0760.0760.0000.0000.0000.000
119A167ILE00.0110.01030.7420.0050.0050.0000.0000.0000.000
120A168ARG10.8610.91030.4120.0670.0670.0000.0000.0000.000
121A169VAL0-0.011-0.00732.9430.0030.0030.0000.0000.0000.000
122A170LEU0-0.034-0.02334.5600.0020.0020.0000.0000.0000.000
123A171ALA0-0.0030.01436.5990.0030.0030.0000.0000.0000.000
124A172GLU-1-0.911-0.97737.738-0.043-0.0430.0000.0000.0000.000
125A173GLY0-0.0200.01039.2850.0020.0020.0000.0000.0000.000
126A174ASP-1-0.944-0.96441.058-0.036-0.0360.0000.0000.0000.000
127A175GLY00.0150.00843.0240.0020.0020.0000.0000.0000.000
128A176PHE0-0.110-0.08040.9600.0030.0030.0000.0000.0000.000
129A177MET00.0720.04840.335-0.002-0.0020.0000.0000.0000.000
130A178LYS10.9420.96340.1400.0280.0280.0000.0000.0000.000
131A179ARG10.8620.92939.2920.0240.0240.0000.0000.0000.000
132A180ILE0-0.0060.01737.7180.0010.0010.0000.0000.0000.000
133A181PRO0-0.0080.00240.7160.0010.0010.0000.0000.0000.000
134A182THR00.068-0.00141.617-0.002-0.0020.0000.0000.0000.000
135A183SER0-0.007-0.00141.937-0.001-0.0010.0000.0000.0000.000
136A184LYS11.0011.00742.3090.0280.0280.0000.0000.0000.000
137A185GLN0-0.036-0.00737.483-0.002-0.0020.0000.0000.0000.000
138A186GLY00.0430.01937.040-0.003-0.0030.0000.0000.0000.000
139A187GLU-1-0.881-0.94536.740-0.034-0.0340.0000.0000.0000.000
140A188LEU00.0180.02235.139-0.003-0.0030.0000.0000.0000.000
141A189LEU00.013-0.00230.964-0.004-0.0040.0000.0000.0000.000
142A190ALA00.0190.00532.518-0.005-0.0050.0000.0000.0000.000
143A191LYS10.9580.98333.6220.0410.0410.0000.0000.0000.000
144A192ALA00.002-0.00230.696-0.003-0.0030.0000.0000.0000.000
145A193MET0-0.0070.00128.379-0.005-0.0050.0000.0000.0000.000
146A194TYR00.0040.00529.319-0.005-0.0050.0000.0000.0000.000
147A195ALA0-0.024-0.00630.933-0.004-0.0040.0000.0000.0000.000
148A196LEU0-0.013-0.00825.290-0.005-0.0050.0000.0000.0000.000
149A197ASN00.0470.00325.396-0.021-0.0210.0000.0000.0000.000
150A198HIS0-0.007-0.01927.434-0.004-0.0040.0000.0000.0000.000
151A199LYS10.8880.92828.9670.0790.0790.0000.0000.0000.000
152A200GLU-1-0.831-0.89826.621-0.085-0.0850.0000.0000.0000.000
153A201ARG10.8210.91320.7480.1400.1400.0000.0000.0000.000
154A202GLY00.0110.00724.333-0.007-0.0070.0000.0000.0000.000
155A203GLU-1-0.927-0.95621.120-0.144-0.1440.0000.0000.0000.000
156A204ASN0-0.101-0.04220.225-0.003-0.0030.0000.0000.0000.000
157A205THR00.0950.05524.1130.0060.0060.0000.0000.0000.000
158A206LYS10.8820.94123.7440.1180.1180.0000.0000.0000.000
159A207THR00.0560.02125.156-0.009-0.0090.0000.0000.0000.000
160A208PRO0-0.025-0.01123.028-0.005-0.0050.0000.0000.0000.000
161A209ILE00.0370.02024.040-0.004-0.0040.0000.0000.0000.000
162A210GLN00.0330.02426.4630.0000.0000.0000.0000.0000.000
163A211LYS10.8390.91618.9530.1790.1790.0000.0000.0000.000
164A212HIS00.0070.00722.011-0.020-0.0200.0000.0000.0000.000
165A213TRP00.0240.02323.4780.0000.0000.0000.0000.0000.000
166A214ARG10.9160.96626.1030.0690.0690.0000.0000.0000.000
167A215PRO00.0000.00320.936-0.004-0.0040.0000.0000.0000.000
168A216THR0-0.031-0.01721.0490.0110.0110.0000.0000.0000.000
169A217VAL0-0.003-0.00917.123-0.021-0.0210.0000.0000.0000.000
170A218LEU0-0.034-0.01117.5450.0180.0180.0000.0000.0000.000
171A219THR00.0190.00718.164-0.008-0.0080.0000.0000.0000.000
172A220GLU-1-0.842-0.91718.470-0.063-0.0630.0000.0000.0000.000
173A221GLY0-0.012-0.01316.786-0.016-0.0160.0000.0000.0000.000
174A222PRO0-0.035-0.00617.6200.0130.0130.0000.0000.0000.000
175A223PRO00.0740.03317.058-0.018-0.0180.0000.0000.0000.000
176A224VAL0-0.051-0.05213.220-0.007-0.0070.0000.0000.0000.000
177A225LYN00.0090.00114.9950.0170.0170.0000.0000.0000.000
178A226ILE0-0.008-0.0258.600-0.030-0.0300.0000.0000.0000.000
179A227ARG10.7840.90512.1840.1430.1430.0000.0000.0000.000
180A228ILE00.0230.0259.901-0.029-0.0290.0000.0000.0000.000
181A229GLU-1-0.865-0.9419.4370.0020.0020.0000.0000.0000.000
182A230THR0-0.077-0.04311.889-0.008-0.0080.0000.0000.0000.000
183A231GLY0-0.053-0.03214.439-0.003-0.0030.0000.0000.0000.000
184A232GLU-1-0.876-0.92515.930-0.012-0.0120.0000.0000.0000.000
185A233TRP0-0.092-0.05814.374-0.013-0.0130.0000.0000.0000.000
186A234GLU-1-0.799-0.90712.4640.0200.0200.0000.0000.0000.000
187A235LYS10.9290.96514.6990.0220.0220.0000.0000.0000.000
188A236GLY00.0580.03315.3180.0100.0100.0000.0000.0000.000
189A237TRP0-0.008-0.0118.2990.0100.0100.0000.0000.0000.000
190A238ASN00.0350.04612.9030.0180.0180.0000.0000.0000.000
191A239VAL0-0.044-0.01012.458-0.040-0.0400.0000.0000.0000.000
192A240LEU00.011-0.00112.0570.0260.0260.0000.0000.0000.000
193A241VAL0-0.008-0.00812.1110.0210.0210.0000.0000.0000.000
194A242TRP00.0070.01912.399-0.054-0.0540.0000.0000.0000.000
195A243GLY00.0060.01212.9480.0330.0330.0000.0000.0000.000
196A244ARG11.0110.99014.3030.1530.1530.0000.0000.0000.000
197A245GLY0-0.0160.01012.8170.0110.0110.0000.0000.0000.000
198A246TYR0-0.040-0.0206.853-0.026-0.0260.0000.0000.0000.000
199A247ALA00.0350.0188.8830.0510.0510.0000.0000.0000.000
200A248ALA0-0.0320.0017.945-0.147-0.1470.0000.0000.0000.000
201A249VAL00.003-0.0137.2940.1450.1450.0000.0000.0000.000
202A250LYS10.9910.9928.021-0.018-0.0180.0000.0000.0000.000
203A251ASN0-0.013-0.0159.9210.0520.0520.0000.0000.0000.000
204A252ARG10.8910.91611.4660.0660.0660.0000.0000.0000.000
205A253ASP-1-0.903-0.94514.6130.0720.0720.0000.0000.0000.000
206A254THR0-0.0140.00211.5830.0310.0310.0000.0000.0000.000
207A255ASP-1-0.946-0.96913.176-0.003-0.0030.0000.0000.0000.000
208A256LYS10.9571.0066.547-0.423-0.4230.0000.0000.0000.000
209A257VAL00.005-0.0017.439-0.074-0.0740.0000.0000.0000.000
210A258ILE0-0.057-0.0272.801-0.710-0.2930.195-0.239-0.373-0.001
211A259TRP00.0040.0013.6280.7511.0270.006-0.065-0.2160.000
212A260VAL00.0220.0163.528-0.4250.1990.022-0.215-0.432-0.001
213A261PRO0-0.025-0.0306.141-0.015-0.0150.0000.0000.0000.000
214A262SER00.026-0.0059.1090.0420.0420.0000.0000.0000.000
215A263ARG11.0281.00711.9960.2400.2400.0000.0000.0000.000
216A264LYS10.8660.9328.1310.2510.2510.0000.0000.0000.000
217A265VAL00.0310.03111.5630.0080.0080.0000.0000.0000.000
218A266LYS10.9120.97113.5810.0810.0810.0000.0000.0000.000
219A267PRO00.0420.00517.142-0.001-0.0010.0000.0000.0000.000
220A268ASP-1-0.939-0.95218.215-0.053-0.0530.0000.0000.0000.000
221A269ILE00.0240.01520.0730.0030.0030.0000.0000.0000.000