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: JLMR9

Calculation Name: 1E6J-P-Xray372

Preferred Name: Gag-Pol polyprotein

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1E6J

Chain ID: P

ChEMBL ID: CHEMBL3638360

UniProt ID: P04585

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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2056506.536555
FMO2-HF: Nuclear repulsion 1973142.083098
FMO2-HF: Total energy -83364.453457
FMO2-MP2: Total energy -83602.210423


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(P:11:VAL)


Summations of interaction energy for fragment #1(P:11:VAL)
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.
-2.910.8950.122-1.779-2.1480.002
Interaction energy analysis for fragmet #1(P:11:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.006
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].
3P13GLN0-0.022-0.0152.981-1.8661.9050.123-1.773-2.1210.002
4P14ALA00.0280.0224.9000.0490.083-0.001-0.006-0.0270.000
5P15ILE00.0160.0118.4740.0250.0250.0000.0000.0000.000
6P16SER00.0020.00211.5340.1180.1180.0000.0000.0000.000
7P17PRO00.0670.01412.3990.0380.0380.0000.0000.0000.000
8P18ARG10.9340.97215.3270.2910.2910.0000.0000.0000.000
9P19THR00.0540.02214.5600.0420.0420.0000.0000.0000.000
10P20LEU00.0190.01416.3960.0240.0240.0000.0000.0000.000
11P21ASN0-0.013-0.01218.1070.0370.0370.0000.0000.0000.000
12P22ALA0-0.019-0.00920.2650.0240.0240.0000.0000.0000.000
13P23TRP00.010-0.00520.8430.0170.0170.0000.0000.0000.000
14P24VAL00.0210.01922.5500.0170.0170.0000.0000.0000.000
15P25LYS10.8150.88324.8380.1780.1780.0000.0000.0000.000
16P26VAL0-0.0070.00424.8250.0130.0130.0000.0000.0000.000
17P27VAL00.0040.00226.1160.0130.0130.0000.0000.0000.000
18P28GLU-1-0.873-0.90828.595-0.140-0.1400.0000.0000.0000.000
19P29GLU-1-0.926-0.95630.335-0.132-0.1320.0000.0000.0000.000
20P30LYS10.8010.89529.9700.1560.1560.0000.0000.0000.000
21P31ALA00.0140.01332.0990.0050.0050.0000.0000.0000.000
22P32PHE0-0.015-0.02230.151-0.012-0.0120.0000.0000.0000.000
23P33SER00.002-0.00733.4540.0020.0020.0000.0000.0000.000
24P34PRO00.022-0.01632.890-0.010-0.0100.0000.0000.0000.000
25P35GLU-1-0.865-0.90731.311-0.151-0.1510.0000.0000.0000.000
26P36VAL00.0200.00927.607-0.013-0.0130.0000.0000.0000.000
27P37ILE00.0140.01027.054-0.019-0.0190.0000.0000.0000.000
28P38PRO00.0180.00125.920-0.022-0.0220.0000.0000.0000.000
29P39MET00.0060.01324.229-0.019-0.0190.0000.0000.0000.000
30P40PHE00.0090.00521.557-0.031-0.0310.0000.0000.0000.000
31P41SER0-0.026-0.02121.163-0.038-0.0380.0000.0000.0000.000
32P42ALA0-0.013-0.00319.884-0.039-0.0390.0000.0000.0000.000
33P43LEU0-0.057-0.02918.404-0.040-0.0400.0000.0000.0000.000
34P44SER0-0.026-0.01916.684-0.053-0.0530.0000.0000.0000.000
35P45GLU-1-0.956-0.97715.169-0.529-0.5290.0000.0000.0000.000
36P46GLY0-0.023-0.01212.289-0.069-0.0690.0000.0000.0000.000
37P47ALA0-0.051-0.00311.345-0.188-0.1880.0000.0000.0000.000
38P48THR0-0.011-0.0439.8600.0960.0960.0000.0000.0000.000
39P49PRO00.0660.01012.8950.0650.0650.0000.0000.0000.000
40P50GLN00.0150.02213.1620.0070.0070.0000.0000.0000.000
41P51ASP-1-0.796-0.87211.610-1.016-1.0160.0000.0000.0000.000
42P52LEU00.0230.01014.7340.0740.0740.0000.0000.0000.000
43P53ASN0-0.018-0.01318.1000.0840.0840.0000.0000.0000.000
44P54THR0-0.046-0.00616.3820.0460.0460.0000.0000.0000.000
45P55MET00.0040.01617.7010.0260.0260.0000.0000.0000.000
46P56LEU00.0000.00420.1450.0370.0370.0000.0000.0000.000
47P57ASN0-0.053-0.03122.2940.0380.0380.0000.0000.0000.000
48P58THR0-0.043-0.04020.9020.0140.0140.0000.0000.0000.000
49P59VAL0-0.036-0.00723.3440.0150.0150.0000.0000.0000.000
50P60GLY00.0270.02826.5750.0080.0080.0000.0000.0000.000
51P61GLY00.001-0.01129.4740.0040.0040.0000.0000.0000.000
52P62HIS00.025-0.00531.677-0.001-0.0010.0000.0000.0000.000
53P63GLN00.0230.00433.376-0.006-0.0060.0000.0000.0000.000
54P64ALA0-0.0100.00234.418-0.001-0.0010.0000.0000.0000.000
55P65ALA00.0600.02833.1840.0000.0000.0000.0000.0000.000
56P66MET00.0090.00226.932-0.005-0.0050.0000.0000.0000.000
57P67GLN0-0.074-0.03031.726-0.008-0.0080.0000.0000.0000.000
58P68MET00.0160.01234.1210.0000.0000.0000.0000.0000.000
59P69LEU00.0320.01727.362-0.003-0.0030.0000.0000.0000.000
60P70LYS10.9540.98329.2980.1390.1390.0000.0000.0000.000
61P71GLU-1-0.876-0.92930.209-0.127-0.1270.0000.0000.0000.000
62P72THR00.000-0.01030.4310.0050.0050.0000.0000.0000.000
63P73ILE0-0.0160.01425.453-0.004-0.0040.0000.0000.0000.000
64P74ASN0-0.058-0.04228.268-0.003-0.0030.0000.0000.0000.000
65P75GLU-1-0.836-0.89230.182-0.131-0.1310.0000.0000.0000.000
66P76GLU-1-0.886-0.95527.797-0.174-0.1740.0000.0000.0000.000
67P77ALA0-0.055-0.02226.564-0.001-0.0010.0000.0000.0000.000
68P78ALA00.005-0.00627.6180.0040.0040.0000.0000.0000.000
69P79GLU-1-0.788-0.85230.729-0.114-0.1140.0000.0000.0000.000
70P80TRP0-0.057-0.03822.3820.0000.0000.0000.0000.0000.000
71P81ASP-1-0.816-0.92927.192-0.155-0.1550.0000.0000.0000.000
72P82ARG10.7320.85229.3280.1170.1170.0000.0000.0000.000
73P83VAL0-0.031-0.01628.6990.0080.0080.0000.0000.0000.000
74P84HIS10.8400.92225.9730.1580.1580.0000.0000.0000.000
75P85PRO00.0570.03827.764-0.006-0.0060.0000.0000.0000.000
76P86VAL0-0.047-0.03024.8460.0080.0080.0000.0000.0000.000
77P87HIS00.0510.02027.6900.0100.0100.0000.0000.0000.000
78P88ALA0-0.063-0.02628.114-0.004-0.0040.0000.0000.0000.000
79P89GLY00.0150.02328.4350.0060.0060.0000.0000.0000.000
80P90PRO0-0.004-0.01224.8010.0060.0060.0000.0000.0000.000
81P91ILE0-0.0080.00027.5000.0050.0050.0000.0000.0000.000
82P92ALA0-0.016-0.00529.0100.0020.0020.0000.0000.0000.000
83P93PRO00.005-0.00223.684-0.005-0.0050.0000.0000.0000.000
84P94GLY00.0360.01023.1000.0060.0060.0000.0000.0000.000
85P95GLN0-0.004-0.00618.8010.0070.0070.0000.0000.0000.000
86P96MET0-0.057-0.01213.4510.0050.0050.0000.0000.0000.000
87P97ARG10.7640.88018.4440.2010.2010.0000.0000.0000.000
88P98GLU-1-0.851-0.94019.235-0.196-0.1960.0000.0000.0000.000
89P99PRO0-0.073-0.01718.4470.0060.0060.0000.0000.0000.000
90P100ARG10.9910.98020.5060.1390.1390.0000.0000.0000.000
91P101GLY00.0710.02322.495-0.026-0.0260.0000.0000.0000.000
92P102SER0-0.029-0.03523.239-0.017-0.0170.0000.0000.0000.000
93P103ASP-1-0.785-0.86419.223-0.234-0.2340.0000.0000.0000.000
94P104ILE0-0.0010.01818.831-0.052-0.0520.0000.0000.0000.000
95P105ALA00.001-0.00819.161-0.039-0.0390.0000.0000.0000.000
96P106GLY0-0.0050.00518.419-0.016-0.0160.0000.0000.0000.000
97P107THR0-0.069-0.02719.2010.0090.0090.0000.0000.0000.000
98P108THR0-0.046-0.02521.6240.0200.0200.0000.0000.0000.000
99P109SER0-0.016-0.01016.758-0.004-0.0040.0000.0000.0000.000
100P110THR0-0.036-0.02614.543-0.034-0.0340.0000.0000.0000.000
101P111LEU00.0340.0178.524-0.017-0.0170.0000.0000.0000.000
102P112GLN00.048-0.0029.554-0.195-0.1950.0000.0000.0000.000
103P113GLU-1-0.765-0.84110.435-0.299-0.2990.0000.0000.0000.000
104P114GLN00.0080.00012.140-0.089-0.0890.0000.0000.0000.000
105P115ILE00.003-0.0105.716-0.059-0.0590.0000.0000.0000.000
106P116GLY00.0130.0108.969-0.010-0.0100.0000.0000.0000.000
107P117TRP0-0.012-0.02910.5690.0290.0290.0000.0000.0000.000
108P118MET0-0.053-0.00910.1340.0570.0570.0000.0000.0000.000
109P119THR0-0.083-0.0336.869-0.003-0.0030.0000.0000.0000.000
110P120ASN00.0320.0209.9760.1510.1510.0000.0000.0000.000
111P121ASN0-0.076-0.01313.159-0.016-0.0160.0000.0000.0000.000
112P122PRO00.042-0.00616.3070.0250.0250.0000.0000.0000.000
113P123PRO00.0140.01913.796-0.005-0.0050.0000.0000.0000.000
114P124ILE00.0290.00815.1820.0240.0240.0000.0000.0000.000
115P125PRO0-0.0010.00714.876-0.064-0.0640.0000.0000.0000.000
116P126VAL00.018-0.01814.5880.0120.0120.0000.0000.0000.000
117P127GLY00.0500.01414.6900.0240.0240.0000.0000.0000.000
118P128GLU-1-0.832-0.90515.643-0.449-0.4490.0000.0000.0000.000
119P129ILE0-0.084-0.04117.9850.0480.0480.0000.0000.0000.000
120P130TYR00.0340.00118.9530.0420.0420.0000.0000.0000.000
121P131LYS10.8780.93117.5640.5140.5140.0000.0000.0000.000
122P132ARG10.9310.96321.0880.3050.3050.0000.0000.0000.000
123P133TRP00.0350.01723.7340.0100.0100.0000.0000.0000.000
124P134ILE00.0230.01321.6330.0200.0200.0000.0000.0000.000
125P135ILE0-0.029-0.00723.2730.0180.0180.0000.0000.0000.000
126P136LEU00.0170.01526.8340.0170.0170.0000.0000.0000.000
127P137GLY00.0230.00628.9670.0150.0150.0000.0000.0000.000
128P138LEU0-0.007-0.00726.0510.0140.0140.0000.0000.0000.000
129P139ASN0-0.047-0.02830.4070.0070.0070.0000.0000.0000.000
130P140LYS10.7870.87432.8470.1540.1540.0000.0000.0000.000
131P141ILE00.0060.00631.1710.0100.0100.0000.0000.0000.000
132P142VAL00.0300.01133.1170.0080.0080.0000.0000.0000.000
133P143ARG10.9280.98235.8230.1230.1230.0000.0000.0000.000
134P144MET0-0.053-0.01738.0440.0050.0050.0000.0000.0000.000
135P145TYR0-0.004-0.00736.8080.0040.0040.0000.0000.0000.000
136P146SER0-0.086-0.03839.2150.0020.0020.0000.0000.0000.000
137P147PRO0-0.017-0.00541.3040.0030.0030.0000.0000.0000.000
138P148THR0-0.029-0.02444.962-0.001-0.0010.0000.0000.0000.000
139P149SER00.0030.00147.5620.0040.0040.0000.0000.0000.000
140P150ILE00.050-0.00249.1780.0000.0000.0000.0000.0000.000
141P151LEU0-0.027-0.00550.2080.0030.0030.0000.0000.0000.000
142P152ASP-1-0.873-0.92048.272-0.076-0.0760.0000.0000.0000.000
143P153ILE0-0.062-0.02250.7600.0000.0000.0000.0000.0000.000
144P154ARG10.8850.95552.2830.0650.0650.0000.0000.0000.000
145P155GLN00.0330.01655.4360.0000.0000.0000.0000.0000.000
146P156GLY00.006-0.00256.7540.0000.0000.0000.0000.0000.000
147P157PRO00.005-0.01856.9020.0020.0020.0000.0000.0000.000
148P158LYS10.9490.96959.6120.0460.0460.0000.0000.0000.000
149P159GLU-1-0.814-0.86157.954-0.054-0.0540.0000.0000.0000.000
150P160PRO00.0400.03060.8480.0010.0010.0000.0000.0000.000
151P161PHE00.0730.02162.934-0.001-0.0010.0000.0000.0000.000
152P162ARG10.8630.90163.8810.0410.0410.0000.0000.0000.000
153P163ASP-1-0.850-0.93360.351-0.047-0.0470.0000.0000.0000.000
154P164TYR0-0.064-0.05957.773-0.002-0.0020.0000.0000.0000.000
155P165VAL00.0320.02159.633-0.002-0.0020.0000.0000.0000.000
156P166ASP-1-0.830-0.88060.595-0.047-0.0470.0000.0000.0000.000
157P167ARG10.7330.83254.0160.0560.0560.0000.0000.0000.000
158P168PHE00.0430.02256.532-0.002-0.0020.0000.0000.0000.000
159P169TYR00.0590.00557.422-0.001-0.0010.0000.0000.0000.000
160P170LYS10.8770.94554.8710.0570.0570.0000.0000.0000.000
161P171THR00.0360.01151.7400.0000.0000.0000.0000.0000.000
162P172LEU00.0320.03753.964-0.001-0.0010.0000.0000.0000.000
163P173ARG10.8820.93256.2690.0520.0520.0000.0000.0000.000
164P174ALA0-0.067-0.01751.1900.0000.0000.0000.0000.0000.000
165P175GLU-1-0.829-0.92251.460-0.070-0.0700.0000.0000.0000.000
166P176GLN0-0.0180.00249.6510.0040.0040.0000.0000.0000.000
167P177ALA00.009-0.00152.289-0.001-0.0010.0000.0000.0000.000
168P178SER0-0.001-0.02655.0380.0010.0010.0000.0000.0000.000
169P179GLN00.022-0.00858.252-0.001-0.0010.0000.0000.0000.000
170P180GLU-1-0.858-0.90661.480-0.045-0.0450.0000.0000.0000.000
171P181VAL0-0.014-0.00856.2900.0000.0000.0000.0000.0000.000
172P182LYS10.8620.92155.7860.0560.0560.0000.0000.0000.000
173P183ASN0-0.017-0.00560.1450.0000.0000.0000.0000.0000.000
174P184TRP00.0490.03356.4970.0000.0000.0000.0000.0000.000
175P185MET0-0.043-0.02555.2110.0000.0000.0000.0000.0000.000
176P186THR0-0.019-0.02260.3590.0000.0000.0000.0000.0000.000
177P187GLU-1-0.891-0.93063.211-0.040-0.0400.0000.0000.0000.000
178P188THR0-0.0080.00162.3780.0010.0010.0000.0000.0000.000
179P189LEU0-0.063-0.01855.9800.0000.0000.0000.0000.0000.000
180P190LEU00.0620.04460.334-0.001-0.0010.0000.0000.0000.000
181P191VAL00.0430.03561.6510.0000.0000.0000.0000.0000.000
182P192GLN0-0.075-0.04058.7770.0010.0010.0000.0000.0000.000
183P193ASN0-0.037-0.01955.0410.0000.0000.0000.0000.0000.000
184P194ALA00.0370.03658.662-0.001-0.0010.0000.0000.0000.000
185P195ASN0-0.030-0.01860.4750.0010.0010.0000.0000.0000.000
186P196PRO00.017-0.02360.5750.0010.0010.0000.0000.0000.000
187P197ASP-1-0.888-0.92663.724-0.038-0.0380.0000.0000.0000.000
188P198CYS00.0200.01264.9710.0010.0010.0000.0000.0000.000
189P199LYS10.8730.93260.6110.0480.0480.0000.0000.0000.000
190P200THR0-0.016-0.01266.1030.0010.0010.0000.0000.0000.000
191P201ILE0-0.0070.00169.1060.0010.0010.0000.0000.0000.000
192P202LEU00.008-0.00966.1450.0010.0010.0000.0000.0000.000
193P203LYS10.8900.94166.3060.0390.0390.0000.0000.0000.000
194P204ALA0-0.030-0.00370.7910.0010.0010.0000.0000.0000.000
195P205LEU0-0.0150.00272.2410.0010.0010.0000.0000.0000.000
196P206GLY00.0120.02273.2680.0010.0010.0000.0000.0000.000
197P207PRO0-0.076-0.07670.454-0.001-0.0010.0000.0000.0000.000
198P208ALA0-0.0060.00470.871-0.001-0.0010.0000.0000.0000.000
199P209ALA00.0020.03472.1340.0000.0000.0000.0000.0000.000
200P210THR00.007-0.03571.712-0.001-0.0010.0000.0000.0000.000
201P211LEU00.0250.00666.3980.0000.0000.0000.0000.0000.000
202P212GLU-1-0.888-0.96670.007-0.036-0.0360.0000.0000.0000.000
203P213GLU-1-0.830-0.87272.603-0.031-0.0310.0000.0000.0000.000
204P214MET0-0.029-0.01068.3560.0000.0000.0000.0000.0000.000
205P215MET0-0.042-0.02667.912-0.001-0.0010.0000.0000.0000.000
206P216THR0-0.046-0.02570.2780.0000.0000.0000.0000.0000.000
207P217ALA0-0.036-0.01072.4910.0010.0010.0000.0000.0000.000
208P218CYS0-0.080-0.02768.1890.0000.0000.0000.0000.0000.000
209P219GLN0-0.038-0.00768.956-0.001-0.0010.0000.0000.0000.000