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: 39N4L

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 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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2066336.033987
FMO2-HF: Nuclear repulsion 1982971.079793
FMO2-HF: Total energy -83364.954195
FMO2-MP2: Total energy -83602.68464


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.
-3.0930.5570.545-1.869-2.326-0.003
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 : 0.008
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].
3P13GLN0-0.016-0.0222.790-2.2281.3940.546-1.864-2.304-0.003
4P14ALA00.0170.0234.9420.1050.133-0.001-0.005-0.0220.000
5P15ILE00.003-0.0028.6900.0070.0070.0000.0000.0000.000
6P16SER00.0020.00711.6620.1100.1100.0000.0000.0000.000
7P17PRO00.0590.00712.4020.0450.0450.0000.0000.0000.000
8P18ARG10.9260.97015.2620.3190.3190.0000.0000.0000.000
9P19THR00.0600.02714.5100.0430.0430.0000.0000.0000.000
10P20LEU00.0230.02416.4940.0240.0240.0000.0000.0000.000
11P21ASN0-0.012-0.01118.2070.0390.0390.0000.0000.0000.000
12P22ALA0-0.016-0.00620.1520.0230.0230.0000.0000.0000.000
13P23TRP00.015-0.00220.6040.0170.0170.0000.0000.0000.000
14P24VAL00.0160.00922.2660.0190.0190.0000.0000.0000.000
15P25LYS10.7920.87224.5190.1790.1790.0000.0000.0000.000
16P26VAL00.0000.00324.6160.0140.0140.0000.0000.0000.000
17P27VAL0-0.009-0.00326.0510.0130.0130.0000.0000.0000.000
18P28GLU-1-0.867-0.91128.459-0.139-0.1390.0000.0000.0000.000
19P29GLU-1-0.923-0.94930.133-0.139-0.1390.0000.0000.0000.000
20P30LYS10.8030.89029.8470.1640.1640.0000.0000.0000.000
21P31ALA00.0100.01332.0320.0070.0070.0000.0000.0000.000
22P32PHE0-0.030-0.02429.646-0.012-0.0120.0000.0000.0000.000
23P33SER00.019-0.01233.3060.0030.0030.0000.0000.0000.000
24P34PRO00.032-0.01032.606-0.010-0.0100.0000.0000.0000.000
25P35GLU-1-0.850-0.89330.916-0.158-0.1580.0000.0000.0000.000
26P36VAL00.0220.00827.532-0.015-0.0150.0000.0000.0000.000
27P37ILE00.0130.01526.757-0.019-0.0190.0000.0000.0000.000
28P38PRO00.0050.00325.784-0.023-0.0230.0000.0000.0000.000
29P39MET0-0.0070.00924.013-0.020-0.0200.0000.0000.0000.000
30P40PHE00.0170.00421.010-0.028-0.0280.0000.0000.0000.000
31P41SER0-0.034-0.04120.967-0.037-0.0370.0000.0000.0000.000
32P42ALA0-0.0020.00120.121-0.037-0.0370.0000.0000.0000.000
33P43LEU0-0.056-0.03118.155-0.049-0.0490.0000.0000.0000.000
34P44SER0-0.004-0.00516.745-0.040-0.0400.0000.0000.0000.000
35P45GLU-1-0.957-0.97615.794-0.523-0.5230.0000.0000.0000.000
36P46GLY0-0.035-0.01512.851-0.070-0.0700.0000.0000.0000.000
37P47ALA0-0.0360.00111.970-0.166-0.1660.0000.0000.0000.000
38P48THR0-0.016-0.04810.2800.1110.1110.0000.0000.0000.000
39P49PRO00.0640.01513.3050.0560.0560.0000.0000.0000.000
40P50GLN00.0130.02013.2290.0090.0090.0000.0000.0000.000
41P51ASP-1-0.793-0.84711.592-0.980-0.9800.0000.0000.0000.000
42P52LEU00.0230.00914.6370.0670.0670.0000.0000.0000.000
43P53ASN0-0.022-0.01118.0340.0750.0750.0000.0000.0000.000
44P54THR0-0.045-0.02016.1720.0460.0460.0000.0000.0000.000
45P55MET0-0.035-0.00717.4670.0220.0220.0000.0000.0000.000
46P56LEU00.0020.00719.9010.0360.0360.0000.0000.0000.000
47P57ASN0-0.054-0.03022.1060.0300.0300.0000.0000.0000.000
48P58THR0-0.014-0.01920.7350.0180.0180.0000.0000.0000.000
49P59VAL0-0.022-0.00823.3750.0120.0120.0000.0000.0000.000
50P60GLY00.0240.02326.4320.0120.0120.0000.0000.0000.000
51P61GLY00.005-0.00229.1300.0020.0020.0000.0000.0000.000
52P62HIS00.027-0.01431.1480.0020.0020.0000.0000.0000.000
53P63GLN00.0100.00633.074-0.003-0.0030.0000.0000.0000.000
54P64ALA00.0000.00434.117-0.002-0.0020.0000.0000.0000.000
55P65ALA00.0520.02832.9950.0000.0000.0000.0000.0000.000
56P66MET00.0140.01126.714-0.005-0.0050.0000.0000.0000.000
57P67GLN0-0.029-0.01531.092-0.008-0.0080.0000.0000.0000.000
58P68MET00.0330.01933.589-0.001-0.0010.0000.0000.0000.000
59P69LEU0-0.0020.01627.077-0.003-0.0030.0000.0000.0000.000
60P70LYS10.8970.94529.1960.1280.1280.0000.0000.0000.000
61P71GLU-1-0.877-0.92630.232-0.124-0.1240.0000.0000.0000.000
62P72THR0-0.002-0.01830.5890.0060.0060.0000.0000.0000.000
63P73ILE0-0.0120.00625.459-0.006-0.0060.0000.0000.0000.000
64P74ASN0-0.061-0.03528.3760.0010.0010.0000.0000.0000.000
65P75GLU-1-0.835-0.89430.569-0.130-0.1300.0000.0000.0000.000
66P76GLU-1-0.872-0.94427.848-0.176-0.1760.0000.0000.0000.000
67P77ALA0-0.039-0.00826.724-0.002-0.0020.0000.0000.0000.000
68P78ALA00.0150.00227.8130.0050.0050.0000.0000.0000.000
69P79GLU-1-0.779-0.84331.023-0.111-0.1110.0000.0000.0000.000
70P80TRP0-0.051-0.04222.534-0.002-0.0020.0000.0000.0000.000
71P81ASP-1-0.795-0.91327.060-0.150-0.1500.0000.0000.0000.000
72P82ARG10.7290.83329.2060.1150.1150.0000.0000.0000.000
73P83VAL0-0.045-0.02028.9390.0080.0080.0000.0000.0000.000
74P84HIS10.8320.92326.1370.1570.1570.0000.0000.0000.000
75P85PRO00.0590.03428.012-0.003-0.0030.0000.0000.0000.000
76P86VAL0-0.065-0.03825.5260.0060.0060.0000.0000.0000.000
77P87HIS00.0600.03228.0540.0110.0110.0000.0000.0000.000
78P88ALA0-0.0080.00028.339-0.005-0.0050.0000.0000.0000.000
79P89GLY00.0330.00229.353-0.003-0.0030.0000.0000.0000.000
80P90PRO0-0.0420.00725.0170.0070.0070.0000.0000.0000.000
81P91ILE00.000-0.01227.2240.0060.0060.0000.0000.0000.000
82P92ALA0-0.024-0.01329.067-0.001-0.0010.0000.0000.0000.000
83P93PRO00.0090.01423.527-0.005-0.0050.0000.0000.0000.000
84P94GLY00.0250.00523.2960.0090.0090.0000.0000.0000.000
85P95GLN00.010-0.00318.7170.0120.0120.0000.0000.0000.000
86P96MET0-0.058-0.01513.8470.0050.0050.0000.0000.0000.000
87P97ARG10.7630.87618.7240.1780.1780.0000.0000.0000.000
88P98GLU-1-0.848-0.93519.363-0.195-0.1950.0000.0000.0000.000
89P99PRO0-0.069-0.01518.7660.0060.0060.0000.0000.0000.000
90P100ARG10.9590.96920.7890.1190.1190.0000.0000.0000.000
91P101GLY00.0510.00822.849-0.025-0.0250.0000.0000.0000.000
92P102SER0-0.021-0.03323.818-0.014-0.0140.0000.0000.0000.000
93P103ASP-1-0.798-0.84119.408-0.212-0.2120.0000.0000.0000.000
94P104ILE00.0080.01618.949-0.051-0.0510.0000.0000.0000.000
95P105ALA00.0150.00519.565-0.037-0.0370.0000.0000.0000.000
96P106GLY0-0.0080.00018.446-0.007-0.0070.0000.0000.0000.000
97P107THR0-0.070-0.02619.2540.0110.0110.0000.0000.0000.000
98P108THR0-0.041-0.03821.5770.0200.0200.0000.0000.0000.000
99P109SER0-0.038-0.02116.7360.0060.0060.0000.0000.0000.000
100P110THR0-0.017-0.03314.408-0.037-0.0370.0000.0000.0000.000
101P111LEU00.0250.0218.329-0.016-0.0160.0000.0000.0000.000
102P112GLN00.0580.0059.419-0.214-0.2140.0000.0000.0000.000
103P113GLU-1-0.775-0.84210.451-0.217-0.2170.0000.0000.0000.000
104P114GLN0-0.003-0.01112.431-0.090-0.0900.0000.0000.0000.000
105P115ILE00.008-0.0085.968-0.048-0.0480.0000.0000.0000.000
106P116GLY00.0290.0319.381-0.005-0.0050.0000.0000.0000.000
107P117TRP00.013-0.02510.7870.0260.0260.0000.0000.0000.000
108P118MET0-0.063-0.00310.7390.0700.0700.0000.0000.0000.000
109P119THR0-0.075-0.0467.043-0.049-0.0490.0000.0000.0000.000
110P120ASN00.0040.02510.3730.1560.1560.0000.0000.0000.000
111P121ASN0-0.069-0.03513.558-0.027-0.0270.0000.0000.0000.000
112P122PRO00.0490.00116.6330.0300.0300.0000.0000.0000.000
113P123PRO0-0.0110.02713.8430.0000.0000.0000.0000.0000.000
114P124ILE00.0340.00215.5760.0170.0170.0000.0000.0000.000
115P125PRO00.0000.00515.194-0.059-0.0590.0000.0000.0000.000
116P126VAL00.009-0.02214.7710.0050.0050.0000.0000.0000.000
117P127GLY00.0620.01815.2520.0310.0310.0000.0000.0000.000
118P128GLU-1-0.807-0.89616.258-0.420-0.4200.0000.0000.0000.000
119P129ILE0-0.091-0.04418.5120.0510.0510.0000.0000.0000.000
120P130TYR00.035-0.00219.2630.0370.0370.0000.0000.0000.000
121P131LYS10.8360.91318.7160.4880.4880.0000.0000.0000.000
122P132ARG10.9350.97021.5530.3140.3140.0000.0000.0000.000
123P133TRP00.0260.01323.8760.0100.0100.0000.0000.0000.000
124P134ILE00.0110.01121.7220.0200.0200.0000.0000.0000.000
125P135ILE0-0.019-0.00323.9570.0180.0180.0000.0000.0000.000
126P136LEU00.0270.01427.2990.0170.0170.0000.0000.0000.000
127P137GLY00.0220.00929.3110.0150.0150.0000.0000.0000.000
128P138LEU0-0.002-0.00826.0680.0140.0140.0000.0000.0000.000
129P139ASN0-0.055-0.03030.4200.0080.0080.0000.0000.0000.000
130P140LYS10.7990.87833.1830.1500.1500.0000.0000.0000.000
131P141ILE0-0.0020.00430.8950.0090.0090.0000.0000.0000.000
132P142VAL00.0300.00232.7660.0080.0080.0000.0000.0000.000
133P143ARG10.9060.97435.5180.1240.1240.0000.0000.0000.000
134P144MET0-0.035-0.01237.6090.0060.0060.0000.0000.0000.000
135P145TYR0-0.015-0.01036.2370.0050.0050.0000.0000.0000.000
136P146SER0-0.059-0.02639.1880.0010.0010.0000.0000.0000.000
137P147PRO0-0.0100.00341.2320.0030.0030.0000.0000.0000.000
138P148THR0-0.026-0.03144.8890.0000.0000.0000.0000.0000.000
139P149SER0-0.013-0.01647.3520.0040.0040.0000.0000.0000.000
140P150ILE00.040-0.01049.2260.0010.0010.0000.0000.0000.000
141P151LEU0-0.0100.00550.2890.0020.0020.0000.0000.0000.000
142P152ASP-1-0.860-0.89848.834-0.076-0.0760.0000.0000.0000.000
143P153ILE0-0.041-0.00451.3910.0000.0000.0000.0000.0000.000
144P154ARG10.8700.93052.1110.0680.0680.0000.0000.0000.000
145P155GLN00.0170.00855.893-0.001-0.0010.0000.0000.0000.000
146P156GLY00.0080.00257.349-0.001-0.0010.0000.0000.0000.000
147P157PRO00.000-0.02157.4640.0020.0020.0000.0000.0000.000
148P158LYS10.9310.96060.2050.0460.0460.0000.0000.0000.000
149P159GLU-1-0.777-0.83758.607-0.054-0.0540.0000.0000.0000.000
150P160PRO00.0520.03161.5390.0010.0010.0000.0000.0000.000
151P161PHE00.0710.01163.513-0.001-0.0010.0000.0000.0000.000
152P162ARG10.8750.92064.3050.0420.0420.0000.0000.0000.000
153P163ASP-1-0.854-0.93660.651-0.047-0.0470.0000.0000.0000.000
154P164TYR0-0.055-0.04558.308-0.003-0.0030.0000.0000.0000.000
155P165VAL00.0380.02659.714-0.002-0.0020.0000.0000.0000.000
156P166ASP-1-0.838-0.89760.413-0.047-0.0470.0000.0000.0000.000
157P167ARG10.6980.80954.2340.0570.0570.0000.0000.0000.000
158P168PHE00.0460.02156.319-0.002-0.0020.0000.0000.0000.000
159P169TYR00.041-0.01157.363-0.001-0.0010.0000.0000.0000.000
160P170LYS10.8460.93154.6360.0570.0570.0000.0000.0000.000
161P171THR00.0310.02151.7490.0000.0000.0000.0000.0000.000
162P172LEU00.0310.02154.066-0.001-0.0010.0000.0000.0000.000
163P173ARG10.8880.94056.6240.0520.0520.0000.0000.0000.000
164P174ALA0-0.019-0.00251.1350.0000.0000.0000.0000.0000.000
165P175GLU-1-0.834-0.90751.246-0.072-0.0720.0000.0000.0000.000
166P176GLN0-0.036-0.00549.5760.0040.0040.0000.0000.0000.000
167P177ALA00.0060.00451.955-0.001-0.0010.0000.0000.0000.000
168P178SER0-0.007-0.03054.7660.0010.0010.0000.0000.0000.000
169P179GLN00.015-0.00858.078-0.001-0.0010.0000.0000.0000.000
170P180GLU-1-0.816-0.89161.288-0.048-0.0480.0000.0000.0000.000
171P181VAL0-0.016-0.00556.1680.0000.0000.0000.0000.0000.000
172P182LYS10.8570.90555.4690.0570.0570.0000.0000.0000.000
173P183ASN0-0.034-0.01460.1470.0000.0000.0000.0000.0000.000
174P184TRP00.0730.04356.7920.0000.0000.0000.0000.0000.000
175P185MET0-0.049-0.02554.7730.0000.0000.0000.0000.0000.000
176P186THR0-0.0140.00060.2350.0000.0000.0000.0000.0000.000
177P187GLU-1-0.881-0.92563.343-0.041-0.0410.0000.0000.0000.000
178P188THR0-0.032-0.01262.4520.0010.0010.0000.0000.0000.000
179P189LEU0-0.063-0.01855.8720.0000.0000.0000.0000.0000.000
180P190LEU00.0650.04560.366-0.001-0.0010.0000.0000.0000.000
181P191VAL00.0470.03061.9280.0000.0000.0000.0000.0000.000
182P192GLN0-0.078-0.04459.0870.0010.0010.0000.0000.0000.000
183P193ASN0-0.039-0.02955.2050.0000.0000.0000.0000.0000.000
184P194ALA00.0360.03959.147-0.001-0.0010.0000.0000.0000.000
185P195ASN0-0.021-0.01361.2030.0010.0010.0000.0000.0000.000
186P196PRO00.025-0.00861.2830.0010.0010.0000.0000.0000.000
187P197ASP-1-0.875-0.91664.362-0.040-0.0400.0000.0000.0000.000
188P198CYS00.0110.01665.3500.0010.0010.0000.0000.0000.000
189P199LYS10.8720.92660.9500.0500.0500.0000.0000.0000.000
190P200THR0-0.040-0.02866.5420.0010.0010.0000.0000.0000.000
191P201ILE00.0000.00369.6360.0010.0010.0000.0000.0000.000
192P202LEU00.007-0.01366.4320.0010.0010.0000.0000.0000.000
193P203LYS10.8960.94166.8820.0410.0410.0000.0000.0000.000
194P204ALA0-0.033-0.00571.1920.0010.0010.0000.0000.0000.000
195P205LEU0-0.0250.00272.4250.0010.0010.0000.0000.0000.000
196P206GLY00.0230.02573.3110.0010.0010.0000.0000.0000.000
197P207PRO0-0.076-0.07470.7360.0000.0000.0000.0000.0000.000
198P208ALA0-0.017-0.00271.333-0.001-0.0010.0000.0000.0000.000
199P209ALA00.0010.03072.7590.0010.0010.0000.0000.0000.000
200P210THR0-0.002-0.03971.770-0.001-0.0010.0000.0000.0000.000
201P211LEU00.0350.01166.1390.0000.0000.0000.0000.0000.000
202P212GLU-1-0.870-0.95269.841-0.037-0.0370.0000.0000.0000.000
203P213GLU-1-0.820-0.85972.652-0.032-0.0320.0000.0000.0000.000
204P214MET0-0.039-0.01268.2800.0000.0000.0000.0000.0000.000
205P215MET0-0.034-0.02468.103-0.001-0.0010.0000.0000.0000.000
206P216THR0-0.053-0.03970.4910.0000.0000.0000.0000.0000.000
207P217ALA0-0.019-0.00573.2080.0010.0010.0000.0000.0000.000
208P218CYS0-0.039-0.00868.5840.0000.0000.0000.0000.0000.000
209P219GLN0-0.121-0.04769.5700.0000.0000.0000.0000.0000.000