FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: YQJ82

Calculation Name: 1BVE-AB-NMR60-Model16

Preferred Name: Gag-Pol polyprotein

Target Type: SINGLE PROTEIN

Ligand Name: [4-r-(-4-alpha,5-alpha,6-beta,7-beta)]-hexahydro-5,6-bis(hydroxy)-[1,3-bis([4-hydroxymethyl-phenyl]methyl)-4,7-bis(phen ylmethyl)]-2h-1,3-diazepinone

ligand 3-letter code: DMP

PDB ID: 1BVE

Chain ID: AB

ChEMBL ID: CHEMBL3638360

UniProt ID: P04585

Base Structure: NMR

Registration Date: 2019-08-16

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 199
LigandResidueName DMP
LigandFragmentNumber 199
LigandCharge
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2273881.562094
FMO2-HF: Nuclear repulsion 2197404.007475
FMO2-HF: Total energy -76477.554618
FMO2-MP2: Total energy -76703.262388


3D Structure
Snapshot
 
Ligand structure

DMP

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.
-164.917-188.936209.035-71.521-113.500-0.026


Interactive mode: IFIE and PIEDA for fragment #199(B:100:DMP )


Summations of interaction energy for fragment #199(B:100:DMP )
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.
-164.917-188.936209.035-71.521-113.50.026
Interaction energy analysis for fragmet #199(B:100:DMP )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : -0.061
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].
1A1PRO 10.8430.91218.8640.4180.4180.0000.0000.0000.000
2A2GLN 00.0650.05818.155-0.080-0.0800.0000.0000.0000.000
3A3VAL 0-0.023-0.00714.1660.0490.0490.0000.0000.0000.000
4A4THR 00.0460.01915.083-0.122-0.1220.0000.0000.0000.000
5A5LEU 00.009-0.00914.876-0.084-0.0840.0000.0000.0000.000
6A6TRP 00.001-0.00815.263-0.029-0.0290.0000.0000.0000.000
7A7GLN 00.0020.00111.7640.0250.0250.0000.0000.0000.000
8A8ARG 10.9420.9747.6171.1191.1190.0000.0000.0000.000
9A9PRO 00.0030.0268.5990.2560.2560.0000.0000.0000.000
10A10LEU 00.022-0.0058.954-0.003-0.0030.0000.0000.0000.000
11A11VAL 0-0.023-0.00912.0100.0710.0710.0000.0000.0000.000
12A12THR 0-0.013-0.01914.0820.0450.0450.0000.0000.0000.000
13A13ILE 00.0150.02311.9990.0260.0260.0000.0000.0000.000
14A14LYS 10.9360.96015.5190.0100.0100.0000.0000.0000.000
15A15ILE 00.0430.02611.3800.0240.0240.0000.0000.0000.000
16A16GLY 0-0.005-0.00615.8540.0140.0140.0000.0000.0000.000
17A17GLY 0-0.023-0.00718.518-0.008-0.0080.0000.0000.0000.000
18A18GLN 00.0110.00117.244-0.017-0.0170.0000.0000.0000.000
19A19LEU 0-0.012-0.01717.674-0.016-0.0160.0000.0000.0000.000
20A20LYS 10.9100.97712.646-0.321-0.3210.0000.0000.0000.000
21A21GLU -1-0.906-0.94312.072-0.374-0.3740.0000.0000.0000.000
22A22ALA 00.003-0.0039.6800.0720.0720.0000.0000.0000.000
23A23LEU 00.0090.0033.729-0.643-0.0410.006-0.091-0.5170.000
24A24LEU 0-0.040-0.0176.545-0.047-0.0470.0000.0000.0000.000
25A25ASH 00.0820.0241.658-20.115-24.91518.421-8.111-5.5100.034
26A26THR 0-0.0050.0295.0760.7070.874-0.001-0.007-0.1590.000
27A27GLY 0-0.0020.0092.228-0.841-0.1901.621-1.165-1.107-0.004
28A28ALA 0-0.041-0.0022.209-2.245-2.88511.848-3.091-8.118-0.005
29A29ASP -1-0.880-0.9662.058-6.543-7.0076.322-2.024-3.8340.026
30A30ASP -1-0.875-0.9742.255-2.909-2.1792.418-0.885-2.2640.009
31A31THR 0-0.058-0.0343.294-3.084-2.0030.056-0.524-0.613-0.004
32A32VAL 0-0.023-0.0253.071-1.0400.2360.083-0.268-1.0920.001
33A33LEU 0-0.028-0.0244.841-0.231-0.147-0.001-0.006-0.0770.000
34A34GLU -1-0.965-1.0097.2010.6730.6730.0000.0000.0000.000
35A35GLU -1-0.966-0.9908.3390.6240.6240.0000.0000.0000.000
36A36MET 00.0140.00511.717-0.089-0.0890.0000.0000.0000.000
37A37SER 00.0240.02014.5470.0150.0150.0000.0000.0000.000
38A38LEU 0-0.039-0.01612.719-0.037-0.0370.0000.0000.0000.000
39A39PRO 00.0550.03216.718-0.009-0.0090.0000.0000.0000.000
40A40GLY 00.0190.02717.6320.0500.0500.0000.0000.0000.000
41A41ARG 10.9200.95817.857-0.354-0.3540.0000.0000.0000.000
42A42TRP 00.0540.00612.7250.0490.0490.0000.0000.0000.000
43A43LYS 10.9570.96011.980-0.607-0.6070.0000.0000.0000.000
44A44PRO 00.0050.00710.9110.1190.1190.0000.0000.0000.000
45A45LYS 10.8600.9475.320-1.523-1.5230.0000.0000.0000.000
46A46MET 0-0.030-0.0278.4110.0220.0220.0000.0000.0000.000
47A47ILE 0-0.0160.0152.637-3.360-0.7960.597-0.807-2.3540.007
48A48GLY 00.080-0.0154.1990.5390.8540.000-0.052-0.2630.000
49A49GLY 0-0.029-0.0102.227-5.321-3.1774.272-2.976-3.4400.013
50A50ILE 00.0030.0111.914-8.990-14.87823.800-2.246-15.6670.027
51A51GLY 0-0.009-0.0064.1680.3880.9710.006-0.133-0.4560.001
52A52GLY 00.0080.0026.262-1.758-1.7580.0000.0000.0000.000
53A53PHE 00.0070.0356.0601.4721.4720.0000.0000.0000.000
54A54ILE 0-0.0100.0485.753-0.405-0.4050.0000.0000.0000.000
55A55LYS 10.9550.9678.221-1.530-1.5300.0000.0000.0000.000
56A56VAL 00.0430.0245.217-0.037-0.0370.0000.0000.0000.000
57A57ARG 10.9280.9728.629-1.027-1.0270.0000.0000.0000.000
58A58GLN 0-0.020-0.0147.6640.0260.0260.0000.0000.0000.000
59A59TYR 0-0.015-0.0119.621-0.121-0.1210.0000.0000.0000.000
60A60ASP -1-0.849-0.92811.2060.9390.9390.0000.0000.0000.000
61A61GLN 0-0.042-0.03513.060-0.107-0.1070.0000.0000.0000.000
62A62ILE 00.000-0.00112.708-0.055-0.0550.0000.0000.0000.000
63A63LEU 0-0.069-0.05014.427-0.009-0.0090.0000.0000.0000.000
64A64ILE 00.0310.01111.361-0.017-0.0170.0000.0000.0000.000
65A65GLU -1-0.960-0.97715.039-0.097-0.0970.0000.0000.0000.000
66A66ILE 00.0630.03112.369-0.014-0.0140.0000.0000.0000.000
67A67CYS 0-0.043-0.02616.534-0.034-0.0340.0000.0000.0000.000
68A68GLY 00.0410.01219.454-0.004-0.0040.0000.0000.0000.000
69A69HIS 00.0070.01319.2160.0000.0000.0000.0000.0000.000
70A70LYS 10.9050.95218.756-0.029-0.0290.0000.0000.0000.000
71A71ALA 00.0610.02814.846-0.019-0.0190.0000.0000.0000.000
72A72ILE 0-0.0120.01715.0860.0350.0350.0000.0000.0000.000
73A73GLY 00.0340.01411.556-0.017-0.0170.0000.0000.0000.000
74A74THR 0-0.040-0.0087.749-0.145-0.1450.0000.0000.0000.000
75A75VAL 0-0.0010.0157.5040.2550.2550.0000.0000.0000.000
76A76LEU 00.0200.0023.872-0.1820.1030.003-0.038-0.2510.000
77A77VAL 00.0170.0107.602-0.107-0.1070.0000.0000.0000.000
78A78GLY 0-0.008-0.0289.4540.0170.0170.0000.0000.0000.000
79A79PRO 0-0.0140.0268.463-0.174-0.1740.0000.0000.0000.000
80A80THR 0-0.0670.0153.8630.1170.6080.005-0.127-0.370-0.001
81A81PRO 00.0540.0221.957-0.611-1.3544.078-0.762-2.572-0.003
82A82VAL 00.0790.0293.136-2.816-0.6390.480-0.548-2.1090.005
83A83ASN 0-0.060-0.0224.938-0.220-0.048-0.001-0.009-0.1630.000
84A84ILE 00.008-0.0072.323-2.825-0.4651.343-0.603-3.0990.001
85A85ILE 00.0140.0215.6810.3040.3040.0000.0000.0000.000
86A86GLY 00.1100.0394.663-0.521-0.408-0.001-0.015-0.0970.000
87A87ARG 10.9340.9675.551-1.992-1.9920.0000.0000.0000.000
88A88ASN 0-0.0410.0496.304-0.325-0.3250.0000.0000.0000.000
89A89LEU 00.014-0.0108.360-0.282-0.2820.0000.0000.0000.000
90A90LEU 0-0.034-0.0028.432-0.230-0.2300.0000.0000.0000.000
91A91THR 0-0.019-0.03611.036-0.090-0.0900.0000.0000.0000.000
92A92GLN 0-0.089-0.02812.722-0.078-0.0780.0000.0000.0000.000
93A93ILE 0-0.057-0.01913.313-0.035-0.0350.0000.0000.0000.000
94A94GLY 00.0470.02915.946-0.042-0.0420.0000.0000.0000.000
95A95ALA 0-0.026-0.02513.361-0.070-0.0700.0000.0000.0000.000
96A96THR 0-0.042-0.02615.0200.0360.0360.0000.0000.0000.000
97A97LEU 00.0220.0019.296-0.022-0.0220.0000.0000.0000.000
98A98ASN 00.040-0.02213.736-0.056-0.0560.0000.0000.0000.000
99A99PHE -1-0.871-0.90512.928-1.041-1.0410.0000.0000.0000.000
100B1PRO 10.8100.89617.3981.0301.0300.0000.0000.0000.000
101B2GLN 00.0360.04117.342-0.104-0.1040.0000.0000.0000.000
102B3VAL 0-0.0090.00712.8350.0000.0000.0000.0000.0000.000
103B4THR 00.0350.02613.952-0.083-0.0830.0000.0000.0000.000
104B5LEU 0-0.003-0.02113.586-0.008-0.0080.0000.0000.0000.000
105B6TRP 00.0140.00913.6960.0660.0660.0000.0000.0000.000
106B7GLN 0-0.024-0.01610.5260.0630.0630.0000.0000.0000.000
107B8ARG 10.9650.9804.6471.9432.045-0.001-0.002-0.0990.000
108B9PRO 00.0250.0337.9610.2680.2680.0000.0000.0000.000
109B10LEU 00.020-0.0048.093-0.532-0.5320.0000.0000.0000.000
110B11VAL 0-0.030-0.01211.3680.3400.3400.0000.0000.0000.000
111B12THR 0-0.029-0.01213.493-0.096-0.0960.0000.0000.0000.000
112B13ILE 00.0340.01411.6290.0490.0490.0000.0000.0000.000
113B14LYS 10.9460.95814.7330.8030.8030.0000.0000.0000.000
114B15ILE 00.0680.03410.3010.0130.0130.0000.0000.0000.000
115B16GLY 00.008-0.03014.8410.0580.0580.0000.0000.0000.000
116B17GLY 0-0.047-0.01517.2150.0560.0560.0000.0000.0000.000
117B18GLN 0-0.015-0.00116.8940.0620.0620.0000.0000.0000.000
118B19LEU 0-0.006-0.01417.144-0.049-0.0490.0000.0000.0000.000
119B20LYS 10.9250.97512.8080.8580.8580.0000.0000.0000.000
120B21GLU -1-0.894-0.94110.979-1.285-1.2850.0000.0000.0000.000
121B22ALA 0-0.019-0.0109.486-0.124-0.1240.0000.0000.0000.000
122B23LEU 0-0.0010.0003.320-0.2020.8070.065-0.185-0.8880.000
123B24LEU 0-0.021-0.0215.956-2.021-2.0210.0000.0000.0000.000
124B25ASP -1-0.649-0.7451.361-70.263-104.03173.608-31.194-8.646-0.160
125B26THR 0-0.057-0.1114.4660.2670.472-0.001-0.021-0.1830.000
126B27GLY 00.043-0.0262.7431.7862.7740.292-0.495-0.7850.002
127B28ALA 0-0.100-0.0212.090-0.2291.2887.442-2.946-6.0130.005
128B29ASP -1-0.871-0.9542.356-5.136-2.7420.621-0.955-2.0600.006
129B30ASP -1-0.896-0.9592.510-2.211-0.3360.898-0.989-1.7840.012
130B31THR 0-0.064-0.0303.397-4.069-3.1450.047-0.418-0.553-0.003
131B32VAL 00.0050.0102.826-0.4381.2520.359-0.400-1.6490.000
132B33LEU 0-0.012-0.0364.317-0.487-0.3760.001-0.026-0.0870.000
133B34GLU -1-0.904-0.9547.944-0.249-0.2490.0000.0000.0000.000
134B35GLU -1-0.942-0.9778.972-0.096-0.0960.0000.0000.0000.000
135B36MET 00.0020.00812.290-0.059-0.0590.0000.0000.0000.000
136B37SER 0-0.031-0.01315.1530.0760.0760.0000.0000.0000.000
137B38LEU 00.0340.03011.772-0.060-0.0600.0000.0000.0000.000
138B39PRO 0-0.0070.01015.2730.0530.0530.0000.0000.0000.000
139B40GLY 00.0530.00816.521-0.041-0.0410.0000.0000.0000.000
140B41ARG 10.8950.94316.7840.1840.1840.0000.0000.0000.000
141B42TRP 00.0630.04312.925-0.005-0.0050.0000.0000.0000.000
142B43LYS 10.9080.94912.724-0.006-0.0060.0000.0000.0000.000
143B44PRO 00.0320.02411.8380.0070.0070.0000.0000.0000.000
144B45LYS 10.8830.9576.786-0.483-0.4830.0000.0000.0000.000
145B46MET 00.004-0.0178.297-0.039-0.0390.0000.0000.0000.000
146B47ILE 0-0.0130.0232.785-3.189-0.4590.967-0.845-2.8510.009
147B48GLY 00.063-0.0084.1580.4290.7850.000-0.059-0.2970.000
148B49GLY 0-0.021-0.0082.091-5.573-4.4988.221-4.626-4.6700.015
149B50ILE 0-0.015-0.0011.982-3.757-19.17736.578-1.729-19.4290.032
150B51GLY 00.014-0.0213.988-0.4660.2370.012-0.165-0.5500.001
151B52GLY 0-0.002-0.0056.257-1.900-1.9000.0000.0000.0000.000
152B53PHE 0-0.0050.0126.1641.3461.3460.0000.0000.0000.000
153B54ILE 0-0.0100.0275.916-0.477-0.4770.0000.0000.0000.000
154B55LYS 10.9370.9618.519-1.117-1.1170.0000.0000.0000.000
155B56VAL 00.0100.0125.391-0.049-0.0490.0000.0000.0000.000
156B57ARG 10.9150.9618.6440.0890.0890.0000.0000.0000.000
157B58GLN 00.0500.0166.9540.1470.1470.0000.0000.0000.000
158B59TYR 00.0260.0139.2190.0400.0400.0000.0000.0000.000
159B60ASP -1-0.881-0.94111.095-0.127-0.1270.0000.0000.0000.000
160B61GLN 0-0.067-0.04112.436-0.005-0.0050.0000.0000.0000.000
161B62ILE 0-0.0010.00311.9390.0270.0270.0000.0000.0000.000
162B63LEU 0-0.038-0.03913.292-0.104-0.1040.0000.0000.0000.000
163B64ILE 00.0210.00510.0780.0290.0290.0000.0000.0000.000
164B65GLU -1-0.991-0.99313.858-0.895-0.8950.0000.0000.0000.000
165B66ILE 00.0660.02311.387-0.128-0.1280.0000.0000.0000.000
166B67CYS 0-0.076-0.03415.3410.0960.0960.0000.0000.0000.000
167B68GLY 00.0720.03818.0910.0890.0890.0000.0000.0000.000
168B69HIS 0-0.0090.00318.2520.0680.0680.0000.0000.0000.000
169B70LYS 10.9330.95417.6010.5200.5200.0000.0000.0000.000
170B71ALA 00.0520.03213.0290.0030.0030.0000.0000.0000.000
171B72ILE 00.0000.03513.538-0.034-0.0340.0000.0000.0000.000
172B73GLY 00.0380.0019.789-0.056-0.0560.0000.0000.0000.000
173B74THR 0-0.016-0.0217.224-0.041-0.0410.0000.0000.0000.000
174B75VAL 00.0070.0066.6480.0370.0370.0000.0000.0000.000
175B76LEU 0-0.028-0.0182.773-0.3300.2550.147-0.100-0.6310.000
176B77VAL 00.0040.0126.437-0.235-0.2350.0000.0000.0000.000
177B78GLY 00.020-0.0169.0310.2260.2260.0000.0000.0000.000
178B79PRO 0-0.056-0.0059.347-0.209-0.2090.0000.0000.0000.000
179B80THR 0-0.080-0.0124.6740.4110.626-0.001-0.008-0.2070.000
180B81PRO 00.0530.0262.169-1.026-0.4641.049-0.296-1.316-0.002
181B82VAL 00.0540.0163.197-2.065-0.2960.293-0.436-1.6260.003
182B83ASN 0-0.006-0.0045.104-0.165-0.008-0.001-0.004-0.1510.000
183B84ILE 0-0.033-0.0162.080-3.915-1.4423.087-1.107-4.452-0.001
184B85ILE 0-0.0050.0124.8841.0751.288-0.001-0.008-0.2050.000
185B86GLY 00.1010.0244.389-1.514-1.417-0.001-0.017-0.0800.000
186B87ARG 10.7930.9355.2255.4795.638-0.001-0.002-0.1560.000
187B88ASN 00.0240.0436.552-0.410-0.4100.0000.0000.0000.000
188B89LEU 00.0510.0238.0870.1970.1970.0000.0000.0000.000
189B90LEU 0-0.049-0.0197.7970.2220.2220.0000.0000.0000.000
190B91THR 00.0430.01611.3250.2530.2530.0000.0000.0000.000
191B92GLN 0-0.106-0.02812.8420.1990.1990.0000.0000.0000.000
192B93ILE 0-0.056-0.01213.3560.0980.0980.0000.0000.0000.000
193B94GLY 00.0420.02615.5680.1040.1040.0000.0000.0000.000
194B95ALA 0-0.052-0.05112.5730.0510.0510.0000.0000.0000.000
195B96THR 0-0.070-0.02314.4650.0360.0360.0000.0000.0000.000
196B97LEU 0-0.009-0.0089.525-0.033-0.0330.0000.0000.0000.000
197B98ASN 00.006-0.02213.9710.0920.0920.0000.0000.0000.000
198B99PHE -1-0.879-0.91414.515-0.397-0.3970.0000.0000.0000.000