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: N937Q

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 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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2055362.504865
FMO2-HF: Nuclear repulsion 1971999.23373
FMO2-HF: Total energy -83363.271135
FMO2-MP2: Total energy -83601.141924


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.
-1.9081.0470.108-1.268-1.795-0.004
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 : -0.013 / q_NPA : -0.025
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].
3P13GLN0-0.019-0.0123.161-1.8011.1180.109-1.263-1.765-0.004
4P14ALA00.0410.0304.9340.2030.239-0.001-0.005-0.0300.000
5P15ILE00.0250.0178.460-0.088-0.0880.0000.0000.0000.000
6P16SER00.0030.00011.5700.1070.1070.0000.0000.0000.000
7P17PRO00.0710.01612.4540.0520.0520.0000.0000.0000.000
8P18ARG10.9410.97615.3890.3650.3650.0000.0000.0000.000
9P19THR00.0480.02114.6860.0340.0340.0000.0000.0000.000
10P20LEU00.0160.01216.4510.0280.0280.0000.0000.0000.000
11P21ASN0-0.008-0.01418.1510.0430.0430.0000.0000.0000.000
12P22ALA0-0.018-0.01120.3380.0230.0230.0000.0000.0000.000
13P23TRP00.004-0.01320.8890.0150.0150.0000.0000.0000.000
14P24VAL00.0050.01622.5830.0180.0180.0000.0000.0000.000
15P25LYS10.9210.95824.8820.1600.1600.0000.0000.0000.000
16P26VAL0-0.0130.00624.4920.0100.0100.0000.0000.0000.000
17P27VAL0-0.009-0.00426.1270.0110.0110.0000.0000.0000.000
18P28GLU-1-0.964-0.98128.650-0.111-0.1110.0000.0000.0000.000
19P29GLU-1-0.975-0.97930.407-0.119-0.1190.0000.0000.0000.000
20P30LYS10.8490.91730.1540.1360.1360.0000.0000.0000.000
21P31ALA00.0180.01932.1690.0060.0060.0000.0000.0000.000
22P32PHE0-0.013-0.02329.938-0.005-0.0050.0000.0000.0000.000
23P33SER00.0190.02533.5200.0040.0040.0000.0000.0000.000
24P34PRO00.021-0.01232.980-0.007-0.0070.0000.0000.0000.000
25P35GLU-1-0.866-0.93932.023-0.124-0.1240.0000.0000.0000.000
26P36VAL00.0160.01327.652-0.013-0.0130.0000.0000.0000.000
27P37ILE00.0290.01127.117-0.015-0.0150.0000.0000.0000.000
28P38PRO0-0.002-0.00925.771-0.016-0.0160.0000.0000.0000.000
29P39MET00.0110.01124.601-0.023-0.0230.0000.0000.0000.000
30P40PHE00.0180.01021.845-0.029-0.0290.0000.0000.0000.000
31P41SER0-0.023-0.02021.227-0.023-0.0230.0000.0000.0000.000
32P42ALA0-0.002-0.00119.756-0.030-0.0300.0000.0000.0000.000
33P43LEU0-0.060-0.02818.541-0.045-0.0450.0000.0000.0000.000
34P44SER0-0.004-0.00516.789-0.040-0.0400.0000.0000.0000.000
35P45GLU-1-0.987-1.00215.677-0.451-0.4510.0000.0000.0000.000
36P46GLY00.0030.00712.148-0.077-0.0770.0000.0000.0000.000
37P47ALA0-0.0360.00611.141-0.093-0.0930.0000.0000.0000.000
38P48THR00.0120.0049.8240.1320.1320.0000.0000.0000.000
39P49PRO00.0610.01312.707-0.002-0.0020.0000.0000.0000.000
40P50GLN00.0160.02312.696-0.015-0.0150.0000.0000.0000.000
41P51ASP-1-0.838-0.92411.452-0.593-0.5930.0000.0000.0000.000
42P52LEU00.015-0.00114.7220.0190.0190.0000.0000.0000.000
43P53ASN0-0.025-0.02918.1080.0200.0200.0000.0000.0000.000
44P54THR0-0.042-0.00416.2570.0190.0190.0000.0000.0000.000
45P55MET0-0.0030.01017.7590.0070.0070.0000.0000.0000.000
46P56LEU00.0070.00520.1540.0160.0160.0000.0000.0000.000
47P57ASN0-0.035-0.02522.2720.0130.0130.0000.0000.0000.000
48P58THR0-0.047-0.03220.8270.0010.0010.0000.0000.0000.000
49P59VAL0-0.049-0.01523.3310.0000.0000.0000.0000.0000.000
50P60GLY00.0260.02726.5770.0110.0110.0000.0000.0000.000
51P61GLY0-0.001-0.01129.464-0.001-0.0010.0000.0000.0000.000
52P62HIS00.0360.00231.6120.0020.0020.0000.0000.0000.000
53P63GLN00.0280.00533.3640.0000.0000.0000.0000.0000.000
54P64ALA0-0.0130.00134.4000.0020.0020.0000.0000.0000.000
55P65ALA00.0530.02733.2290.0020.0020.0000.0000.0000.000
56P66MET00.0110.00427.1090.0000.0000.0000.0000.0000.000
57P67GLN0-0.043-0.01331.7100.0040.0040.0000.0000.0000.000
58P68MET00.0240.01734.0330.0030.0030.0000.0000.0000.000
59P69LEU00.0410.01627.1260.0020.0020.0000.0000.0000.000
60P70LYS10.9490.97929.2610.0280.0280.0000.0000.0000.000
61P71GLU-1-0.938-0.96830.216-0.030-0.0300.0000.0000.0000.000
62P72THR00.001-0.00129.9960.0030.0030.0000.0000.0000.000
63P73ILE0-0.032-0.00325.0920.0010.0010.0000.0000.0000.000
64P74ASN0-0.048-0.04128.2420.0030.0030.0000.0000.0000.000
65P75GLU-1-0.909-0.94830.310-0.026-0.0260.0000.0000.0000.000
66P76GLU-1-0.910-0.96227.843-0.036-0.0360.0000.0000.0000.000
67P77ALA0-0.054-0.02626.7730.0070.0070.0000.0000.0000.000
68P78ALA00.0110.00027.7940.0090.0090.0000.0000.0000.000
69P79GLU-1-0.867-0.92330.4670.0010.0010.0000.0000.0000.000
70P80TRP0-0.042-0.03422.909-0.004-0.0040.0000.0000.0000.000
71P81ASP-1-0.830-0.94027.9520.0440.0440.0000.0000.0000.000
72P82ARG10.7950.91629.7040.0030.0030.0000.0000.0000.000
73P83VAL0-0.062-0.02829.1530.0040.0040.0000.0000.0000.000
74P84HIS10.8510.92826.472-0.027-0.0270.0000.0000.0000.000
75P85PRO00.0540.03528.2390.0070.0070.0000.0000.0000.000
76P86VAL0-0.052-0.02725.4050.0050.0050.0000.0000.0000.000
77P87HIS00.0560.01928.392-0.003-0.0030.0000.0000.0000.000
78P88ALA0-0.064-0.03628.9390.0100.0100.0000.0000.0000.000
79P89GLY00.0100.02429.311-0.004-0.0040.0000.0000.0000.000
80P90PRO0-0.006-0.01125.817-0.004-0.0040.0000.0000.0000.000
81P91ILE0-0.0020.00328.5060.0110.0110.0000.0000.0000.000
82P92ALA0-0.017-0.00729.990-0.001-0.0010.0000.0000.0000.000
83P93PRO00.003-0.00224.7580.0010.0010.0000.0000.0000.000
84P94GLY00.0390.01224.077-0.011-0.0110.0000.0000.0000.000
85P95GLN0-0.016-0.01419.8410.0210.0210.0000.0000.0000.000
86P96MET0-0.037-0.00514.1390.0480.0480.0000.0000.0000.000
87P97ARG10.7960.91219.418-0.225-0.2250.0000.0000.0000.000
88P98GLU-1-0.865-0.94820.0320.1660.1660.0000.0000.0000.000
89P99PRO0-0.057-0.01018.975-0.006-0.0060.0000.0000.0000.000
90P100ARG11.0051.00321.073-0.101-0.1010.0000.0000.0000.000
91P101GLY00.0940.04122.931-0.004-0.0040.0000.0000.0000.000
92P102SER0-0.016-0.01523.554-0.011-0.0110.0000.0000.0000.000
93P103ASP-1-0.840-0.92019.8730.1150.1150.0000.0000.0000.000
94P104ILE00.0040.02319.106-0.006-0.0060.0000.0000.0000.000
95P105ALA00.000-0.02119.322-0.023-0.0230.0000.0000.0000.000
96P106GLY0-0.0130.00018.764-0.020-0.0200.0000.0000.0000.000
97P107THR0-0.073-0.02819.5280.0060.0060.0000.0000.0000.000
98P108THR0-0.032-0.02722.1620.0000.0000.0000.0000.0000.000
99P109SER0-0.010-0.00917.3120.0120.0120.0000.0000.0000.000
100P110THR0-0.0270.00014.7060.0030.0030.0000.0000.0000.000
101P111LEU00.0490.0238.4270.0350.0350.0000.0000.0000.000
102P112GLN00.043-0.0079.719-0.101-0.1010.0000.0000.0000.000
103P113GLU-1-0.809-0.88911.1350.3410.3410.0000.0000.0000.000
104P114GLN00.0230.00412.531-0.053-0.0530.0000.0000.0000.000
105P115ILE0-0.008-0.0106.355-0.072-0.0720.0000.0000.0000.000
106P116GLY00.0080.0099.4890.0780.0780.0000.0000.0000.000
107P117TRP0-0.011-0.02111.353-0.033-0.0330.0000.0000.0000.000
108P118MET0-0.058-0.01610.125-0.097-0.0970.0000.0000.0000.000
109P119THR0-0.079-0.0386.9760.0420.0420.0000.0000.0000.000
110P120ASN00.0150.01010.3080.1080.1080.0000.0000.0000.000
111P121ASN0-0.078-0.01213.670-0.068-0.0680.0000.0000.0000.000
112P122PRO00.040-0.00616.7000.0070.0070.0000.0000.0000.000
113P123PRO00.0260.02713.9270.0190.0190.0000.0000.0000.000
114P124ILE00.0260.00915.429-0.043-0.0430.0000.0000.0000.000
115P125PRO00.0090.01214.7840.0070.0070.0000.0000.0000.000
116P126VAL00.018-0.01914.784-0.034-0.0340.0000.0000.0000.000
117P127GLY00.0480.01414.468-0.008-0.0080.0000.0000.0000.000
118P128GLU-1-0.883-0.95115.464-0.295-0.2950.0000.0000.0000.000
119P129ILE0-0.094-0.04517.7370.0080.0080.0000.0000.0000.000
120P130TYR00.0390.02519.1050.0080.0080.0000.0000.0000.000
121P131LYS10.9160.97717.5870.3090.3090.0000.0000.0000.000
122P132ARG10.9250.95720.8330.0940.0940.0000.0000.0000.000
123P133TRP00.0550.02623.7520.0050.0050.0000.0000.0000.000
124P134ILE00.0300.01621.4960.0040.0040.0000.0000.0000.000
125P135ILE0-0.054-0.01423.1260.0030.0030.0000.0000.0000.000
126P136LEU00.0160.01326.6050.0050.0050.0000.0000.0000.000
127P137GLY00.0300.01128.7110.0060.0060.0000.0000.0000.000
128P138LEU0-0.002-0.00826.1170.0040.0040.0000.0000.0000.000
129P139ASN0-0.052-0.02930.1780.0020.0020.0000.0000.0000.000
130P140LYS10.8920.95332.6290.0510.0510.0000.0000.0000.000
131P141ILE00.0110.01131.0490.0040.0040.0000.0000.0000.000
132P142VAL00.0280.00933.0840.0030.0030.0000.0000.0000.000
133P143ARG10.9260.97535.7750.0600.0600.0000.0000.0000.000
134P144MET0-0.045-0.01037.8530.0030.0030.0000.0000.0000.000
135P145TYR0-0.015-0.01736.9450.0010.0010.0000.0000.0000.000
136P146SER0-0.090-0.03539.106-0.002-0.0020.0000.0000.0000.000
137P147PRO0-0.021-0.00541.3760.0030.0030.0000.0000.0000.000
138P148THR0-0.010-0.01545.0370.0000.0000.0000.0000.0000.000
139P149SER00.0600.04647.3190.0010.0010.0000.0000.0000.000
140P150ILE00.0450.00148.9970.0020.0020.0000.0000.0000.000
141P151LEU0-0.050-0.02250.1430.0020.0020.0000.0000.0000.000
142P152ASP-1-0.924-0.95747.647-0.045-0.0450.0000.0000.0000.000
143P153ILE0-0.085-0.03350.5660.0020.0020.0000.0000.0000.000
144P154ARG10.9530.97951.9540.0350.0350.0000.0000.0000.000
145P155GLN00.0260.01955.2250.0000.0000.0000.0000.0000.000
146P156GLY0-0.0050.00056.5180.0000.0000.0000.0000.0000.000
147P157PRO00.004-0.02256.5990.0010.0010.0000.0000.0000.000
148P158LYS10.9560.97259.3660.0150.0150.0000.0000.0000.000
149P159GLU-1-0.819-0.89657.971-0.023-0.0230.0000.0000.0000.000
150P160PRO00.0250.02560.5980.0000.0000.0000.0000.0000.000
151P161PHE00.0830.02562.691-0.001-0.0010.0000.0000.0000.000
152P162ARG10.8880.93663.6490.0190.0190.0000.0000.0000.000
153P163ASP-1-0.830-0.92260.070-0.019-0.0190.0000.0000.0000.000
154P164TYR0-0.056-0.03857.452-0.002-0.0020.0000.0000.0000.000
155P165VAL00.0340.01959.409-0.002-0.0020.0000.0000.0000.000
156P166ASP-1-0.860-0.91460.483-0.022-0.0220.0000.0000.0000.000
157P167ARG10.7600.86753.6060.0260.0260.0000.0000.0000.000
158P168PHE00.0190.01456.312-0.002-0.0020.0000.0000.0000.000
159P169TYR00.0700.00557.246-0.001-0.0010.0000.0000.0000.000
160P170LYS10.8740.93954.8730.0260.0260.0000.0000.0000.000
161P171THR00.0260.00551.737-0.001-0.0010.0000.0000.0000.000
162P172LEU00.0230.03154.032-0.001-0.0010.0000.0000.0000.000
163P173ARG10.8560.93056.3420.0280.0280.0000.0000.0000.000
164P174ALA0-0.072-0.02051.2010.0000.0000.0000.0000.0000.000
165P175GLU-1-0.869-0.93951.292-0.046-0.0460.0000.0000.0000.000
166P176GLN0-0.047-0.02049.7440.0030.0030.0000.0000.0000.000
167P177ALA00.0190.00452.388-0.001-0.0010.0000.0000.0000.000
168P178SER00.0300.01455.1380.0010.0010.0000.0000.0000.000
169P179GLN00.0330.00058.3560.0000.0000.0000.0000.0000.000
170P180GLU-1-0.928-0.96561.594-0.034-0.0340.0000.0000.0000.000
171P181VAL00.0090.00556.3080.0010.0010.0000.0000.0000.000
172P182LYS10.9550.96957.3450.0360.0360.0000.0000.0000.000
173P183ASN00.0440.02860.2410.0010.0010.0000.0000.0000.000
174P184TRP00.0420.02756.1300.0000.0000.0000.0000.0000.000
175P185MET0-0.040-0.02756.1190.0010.0010.0000.0000.0000.000
176P186THR0-0.031-0.02360.1950.0010.0010.0000.0000.0000.000
177P187GLU-1-0.929-0.95663.035-0.026-0.0260.0000.0000.0000.000
178P188THR0-0.027-0.01162.7380.0010.0010.0000.0000.0000.000
179P189LEU0-0.053-0.01255.9040.0010.0010.0000.0000.0000.000
180P190LEU00.0580.03560.1520.0000.0000.0000.0000.0000.000
181P191VAL00.0390.02061.4610.0010.0010.0000.0000.0000.000
182P192GLN0-0.097-0.05158.5510.0010.0010.0000.0000.0000.000
183P193ASN0-0.036-0.02255.1090.0000.0000.0000.0000.0000.000
184P194ALA00.0370.03158.4560.0000.0000.0000.0000.0000.000
185P195ASN0-0.044-0.02260.3350.0000.0000.0000.0000.0000.000
186P196PRO00.005-0.03160.3300.0000.0000.0000.0000.0000.000
187P197ASP-1-0.850-0.90763.517-0.017-0.0170.0000.0000.0000.000
188P198CYS00.0110.00864.7550.0000.0000.0000.0000.0000.000
189P199LYS10.8940.95560.6830.0260.0260.0000.0000.0000.000
190P200THR0-0.022-0.02165.9030.0000.0000.0000.0000.0000.000
191P201ILE00.0050.01068.9080.0000.0000.0000.0000.0000.000
192P202LEU00.001-0.01065.8450.0000.0000.0000.0000.0000.000
193P203LYS10.8760.93665.9080.0230.0230.0000.0000.0000.000
194P204ALA0-0.025-0.00170.6080.0000.0000.0000.0000.0000.000
195P205LEU0-0.0150.00072.2910.0000.0000.0000.0000.0000.000
196P206GLY00.0080.02173.0840.0000.0000.0000.0000.0000.000
197P207PRO0-0.079-0.07970.2790.0000.0000.0000.0000.0000.000
198P208ALA00.0050.01070.709-0.001-0.0010.0000.0000.0000.000
199P209ALA00.0050.03771.9770.0000.0000.0000.0000.0000.000
200P210THR00.014-0.00671.530-0.001-0.0010.0000.0000.0000.000
201P211LEU00.0380.01066.1540.0000.0000.0000.0000.0000.000
202P212GLU-1-0.911-0.97369.806-0.019-0.0190.0000.0000.0000.000
203P213GLU-1-0.851-0.90872.390-0.017-0.0170.0000.0000.0000.000
204P214MET0-0.019-0.01368.1450.0000.0000.0000.0000.0000.000
205P215MET0-0.053-0.03167.7050.0000.0000.0000.0000.0000.000
206P216THR0-0.035-0.01770.0550.0010.0010.0000.0000.0000.000
207P217ALA0-0.040-0.01072.2560.0010.0010.0000.0000.0000.000
208P218CYS0-0.074-0.02667.9530.0000.0000.0000.0000.0000.000
209P219GLN0-0.031-0.00668.7190.0000.0000.0000.0000.0000.000