FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 7J57K

Calculation Name: 1BVE-AB-NMR60-Model4

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:

Apendix: None


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 -2274838.902006
FMO2-HF: Nuclear repulsion 2198361.086334
FMO2-HF: Total energy -76477.815672
FMO2-MP2: Total energy -76703.485912


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.
-137.303-272.799381.937-125.281-121.158-0.057


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.
-137.303-272.799381.937-125.281-121.1580.057
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 : 0.055 / q_NPA : -0.011
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 10.7950.89518.2990.2980.2980.0000.0000.0000.000
2A2GLN 00.0220.04217.899-0.034-0.0340.0000.0000.0000.000
3A3VAL 00.0240.01313.7750.0430.0430.0000.0000.0000.000
4A4THR 00.0490.02414.763-0.084-0.0840.0000.0000.0000.000
5A5LEU 0-0.020-0.01314.098-0.027-0.0270.0000.0000.0000.000
6A6TRP 00.0680.03113.0800.0030.0030.0000.0000.0000.000
7A7GLN 0-0.061-0.05610.3700.1190.1190.0000.0000.0000.000
8A8ARG 10.8860.9313.1920.1850.6110.011-0.070-0.3680.000
9A9PRO 00.0240.0278.1540.1500.1500.0000.0000.0000.000
10A10LEU 0-0.0020.0007.8670.0060.0060.0000.0000.0000.000
11A11VAL 0-0.011-0.00711.180-0.004-0.0040.0000.0000.0000.000
12A12THR 00.000-0.00613.1680.0370.0370.0000.0000.0000.000
13A13ILE 0-0.001-0.00611.073-0.012-0.0120.0000.0000.0000.000
14A14LYS 10.9420.97015.107-0.094-0.0940.0000.0000.0000.000
15A15ILE 00.0340.03911.0600.0100.0100.0000.0000.0000.000
16A16GLY 00.0300.01015.3700.0100.0100.0000.0000.0000.000
17A17GLY 0-0.046-0.01917.815-0.009-0.0090.0000.0000.0000.000
18A18GLN 0-0.0040.00117.271-0.028-0.0280.0000.0000.0000.000
19A19LEU 0-0.008-0.02217.520-0.017-0.0170.0000.0000.0000.000
20A20LYS 10.8770.97011.824-0.428-0.4280.0000.0000.0000.000
21A21GLU -1-0.898-0.94810.7270.0440.0440.0000.0000.0000.000
22A22ALA 00.030-0.0169.2400.0840.0840.0000.0000.0000.000
23A23LEU 0-0.041-0.0173.249-1.075-0.0740.105-0.205-0.9000.001
24A24LEU 00.007-0.0105.965-0.159-0.1590.0000.0000.0000.000
25A25ASH 0-0.072-0.1011.313-13.453-68.42095.590-37.079-3.5450.046
26A26THR 0-0.010-0.0304.9900.2670.474-0.001-0.005-0.2010.000
27A27GLY 00.040-0.0082.536-0.9430.1880.723-1.006-0.847-0.002
28A28ALA 0-0.068-0.0192.090-0.030-4.65516.142-3.896-7.6210.006
29A29ASP -1-0.861-0.9571.9291.4700.3494.582-0.551-2.9090.006
30A30ASP -1-0.892-0.9862.520-1.973-0.3680.811-0.781-1.6350.010
31A31THR 0-0.070-0.0283.560-2.348-1.6490.019-0.299-0.418-0.002
32A32VAL 0-0.022-0.0072.960-0.7790.4090.103-0.239-1.0520.000
33A33LEU 00.007-0.0114.654-0.234-0.155-0.001-0.010-0.0690.000
34A34GLU -1-0.943-0.9727.7510.6570.6570.0000.0000.0000.000
35A35GLU -1-0.971-1.0038.8280.6380.6380.0000.0000.0000.000
36A36MET 00.0010.00012.122-0.093-0.0930.0000.0000.0000.000
37A37SER 0-0.017-0.00915.1580.0390.0390.0000.0000.0000.000
38A38LEU 00.0480.01412.859-0.038-0.0380.0000.0000.0000.000
39A39PRO 00.0100.02116.6870.0350.0350.0000.0000.0000.000
40A40GLY 0-0.016-0.01718.2520.0030.0030.0000.0000.0000.000
41A41ARG 10.9960.98717.883-0.401-0.4010.0000.0000.0000.000
42A42TRP 0-0.0060.00513.3270.0600.0600.0000.0000.0000.000
43A43LYS 10.9830.98912.716-0.762-0.7620.0000.0000.0000.000
44A44PRO 00.0090.00611.7290.0890.0890.0000.0000.0000.000
45A45LYS 10.9830.9954.733-2.278-2.191-0.001-0.002-0.0840.000
46A46MET 0-0.037-0.0277.732-0.106-0.1060.0000.0000.0000.000
47A47ILE 0-0.043-0.0062.036-2.831-1.6764.582-1.467-4.2710.012
48A48GLY 00.0700.0064.1670.2290.6540.001-0.076-0.3490.000
49A49GLY 0-0.040-0.0121.988-4.736-3.5626.567-3.979-3.7620.019
50A50ILE 0-0.030-0.0121.936-6.076-20.08136.857-3.423-19.4280.028
51A51GLY 00.026-0.0083.8880.2011.0060.008-0.150-0.6630.001
52A52GLY 00.0240.0166.057-1.741-1.7410.0000.0000.0000.000
53A53PHE 0-0.0130.0086.0231.2631.2630.0000.0000.0000.000
54A54ILE 00.0070.0355.884-0.476-0.4760.0000.0000.0000.000
55A55LYS 10.9530.9618.231-1.240-1.2400.0000.0000.0000.000
56A56VAL 00.000-0.0025.470-0.010-0.0100.0000.0000.0000.000
57A57ARG 10.9130.9668.793-0.827-0.8270.0000.0000.0000.000
58A58GLN 0-0.091-0.0468.2180.1670.1670.0000.0000.0000.000
59A59TYR 00.0440.0279.976-0.085-0.0850.0000.0000.0000.000
60A60ASP -1-0.827-0.93111.7450.8560.8560.0000.0000.0000.000
61A61GLN 0-0.068-0.04313.387-0.102-0.1020.0000.0000.0000.000
62A62ILE 00.0130.00112.929-0.051-0.0510.0000.0000.0000.000
63A63LEU 0-0.045-0.04514.1630.0020.0020.0000.0000.0000.000
64A64ILE 00.0610.02210.901-0.009-0.0090.0000.0000.0000.000
65A65GLU -1-0.960-0.99114.6730.0620.0620.0000.0000.0000.000
66A66ILE 00.0320.01611.820-0.005-0.0050.0000.0000.0000.000
67A67CYS 0-0.049-0.01115.993-0.039-0.0390.0000.0000.0000.000
68A68GLY 00.0100.00918.739-0.009-0.0090.0000.0000.0000.000
69A69HIS 00.0240.01518.345-0.001-0.0010.0000.0000.0000.000
70A70LYS 10.9360.96517.970-0.121-0.1210.0000.0000.0000.000
71A71ALA 00.0360.02614.370-0.017-0.0170.0000.0000.0000.000
72A72ILE 0-0.0490.01214.5440.0380.0380.0000.0000.0000.000
73A73GLY 00.0470.00811.338-0.017-0.0170.0000.0000.0000.000
74A74THR 0-0.068-0.0348.535-0.188-0.1880.0000.0000.0000.000
75A75VAL 00.0270.0327.6710.2100.2100.0000.0000.0000.000
76A76LEU 0-0.030-0.0263.951-0.1260.1310.002-0.032-0.2280.000
77A77VAL 0-0.0080.0147.425-0.113-0.1130.0000.0000.0000.000
78A78GLY 00.030-0.0129.4020.0470.0470.0000.0000.0000.000
79A79PRO 0-0.0100.0249.080-0.147-0.1470.0000.0000.0000.000
80A80THR 0-0.070-0.0134.3150.1120.3800.000-0.024-0.2440.000
81A81PRO 00.0510.0201.974-0.686-0.7852.353-0.521-1.734-0.002
82A82VAL 00.0640.0173.302-1.893-0.1500.219-0.423-1.5400.004
83A83ASN 0-0.0100.0145.198-0.247-0.104-0.001-0.004-0.1380.000
84A84ILE 0-0.037-0.0232.210-3.170-0.7502.367-0.804-3.9830.001
85A85ILE 00.0290.0325.1980.0900.240-0.001-0.004-0.1440.000
86A86GLY 00.1070.0294.820-0.438-0.4380.0000.0000.0000.000
87A87ARG 10.9590.9645.630-0.701-0.7010.0000.0000.0000.000
88A88ASN 0-0.0230.0376.531-0.214-0.2140.0000.0000.0000.000
89A89LEU 00.0280.0088.567-0.161-0.1610.0000.0000.0000.000
90A90LEU 00.0060.0318.456-0.102-0.1020.0000.0000.0000.000
91A91THR 0-0.056-0.03311.544-0.063-0.0630.0000.0000.0000.000
92A92GLN 0-0.043-0.01713.287-0.026-0.0260.0000.0000.0000.000
93A93ILE 0-0.047-0.01113.302-0.017-0.0170.0000.0000.0000.000
94A94GLY 00.0030.01516.274-0.030-0.0300.0000.0000.0000.000
95A95ALA 00.004-0.00613.500-0.035-0.0350.0000.0000.0000.000
96A96THR 0-0.055-0.04515.331-0.006-0.0060.0000.0000.0000.000
97A97LEU 0-0.0200.0099.980-0.017-0.0170.0000.0000.0000.000
98A98ASN 00.013-0.01714.496-0.012-0.0120.0000.0000.0000.000
99A99PHE -1-0.850-0.90314.599-0.765-0.7650.0000.0000.0000.000
100B1PRO 10.8360.90718.0840.7570.7570.0000.0000.0000.000
101B2GLN 00.0750.06217.805-0.055-0.0550.0000.0000.0000.000
102B3VAL 0-0.047-0.01914.3600.0120.0120.0000.0000.0000.000
103B4THR 00.0420.01915.307-0.044-0.0440.0000.0000.0000.000
104B5LEU 0-0.017-0.02115.186-0.006-0.0060.0000.0000.0000.000
105B6TRP 00.0240.01314.4310.0280.0280.0000.0000.0000.000
106B7GLN 0-0.045-0.01911.1880.2500.2500.0000.0000.0000.000
107B8ARG 10.9150.9625.8461.3041.3040.0000.0000.0000.000
108B9PRO 00.0440.0398.6280.1830.1830.0000.0000.0000.000
109B10LEU 0-0.021-0.0158.196-0.278-0.2780.0000.0000.0000.000
110B11VAL 0-0.0090.00611.7620.2870.2870.0000.0000.0000.000
111B12THR 0-0.010-0.01913.919-0.130-0.1300.0000.0000.0000.000
112B13ILE 00.0240.02012.0130.0790.0790.0000.0000.0000.000
113B14LYS 10.9340.96615.7090.6310.6310.0000.0000.0000.000
114B15ILE 00.0420.01711.8380.0170.0170.0000.0000.0000.000
115B16GLY 00.0220.00916.1660.0400.0400.0000.0000.0000.000
116B17GLY 0-0.057-0.02418.4600.0470.0470.0000.0000.0000.000
117B18GLN 00.0070.00116.2730.0740.0740.0000.0000.0000.000
118B19LEU 0-0.023-0.02016.782-0.019-0.0190.0000.0000.0000.000
119B20LYS 10.9370.99411.0551.2861.2860.0000.0000.0000.000
120B21GLU -1-0.910-0.94810.203-1.197-1.1970.0000.0000.0000.000
121B22ALA 0-0.014-0.0119.389-0.166-0.1660.0000.0000.0000.000
122B23LEU 0-0.0450.0103.829-0.4350.3550.011-0.131-0.6700.000
123B24LEU 0-0.009-0.0106.151-1.418-1.4180.0000.0000.0000.000
124B25ASP -1-0.657-0.7521.350-67.154-133.143122.017-49.258-6.770-0.154
125B26THR 0-0.048-0.0304.257-0.313-0.016-0.001-0.072-0.2240.000
126B27GLY 00.0070.0072.4170.1591.4921.480-1.266-1.5480.010
127B28ALA 0-0.049-0.0022.0704.238-3.27920.263-4.538-8.207-0.001
128B29ASP -1-0.811-0.9142.262-4.698-3.3242.303-1.011-2.6660.019
129B30ASP -1-0.897-0.9662.688-4.266-2.4200.464-0.743-1.5660.006
130B31THR 0-0.094-0.0713.804-2.784-2.3050.007-0.157-0.329-0.001
131B32VAL 0-0.0460.0013.136-0.3521.1380.084-0.324-1.2500.001
132B33LEU 0-0.006-0.0204.837-0.293-0.197-0.001-0.007-0.0880.000
133B34GLU -1-0.950-0.9796.789-0.619-0.6190.0000.0000.0000.000
134B35GLU -1-0.966-0.9897.576-0.163-0.1630.0000.0000.0000.000
135B36MET 0-0.0310.00310.8460.0170.0170.0000.0000.0000.000
136B37SER 0-0.033-0.01613.8230.0760.0760.0000.0000.0000.000
137B38LEU 00.028-0.00313.516-0.039-0.0390.0000.0000.0000.000
138B39PRO 00.0040.00216.5240.0600.0600.0000.0000.0000.000
139B40GLY 0-0.0020.00317.986-0.007-0.0070.0000.0000.0000.000
140B41ARG 10.9230.94117.4350.3230.3230.0000.0000.0000.000
141B42TRP 00.0640.05812.662-0.018-0.0180.0000.0000.0000.000
142B43LYS 10.9730.96612.1300.3210.3210.0000.0000.0000.000
143B44PRO 0-0.0080.00610.953-0.087-0.0870.0000.0000.0000.000
144B45LYS 10.8760.9586.8660.5610.5610.0000.0000.0000.000
145B46MET 00.007-0.0218.4070.1080.1080.0000.0000.0000.000
146B47ILE 0-0.0110.0282.570-3.097-0.6160.740-0.787-2.4330.007
147B48GLY 00.0430.0124.2860.7781.0950.000-0.054-0.2630.000
148B49GLY 0-0.017-0.0072.165-4.830-2.9554.635-3.068-3.4420.011
149B50ILE 00.0010.0092.013-6.456-16.72831.160-3.067-17.8210.032
150B51GLY 0-0.014-0.0164.053-0.3780.1850.008-0.140-0.4310.001
151B52GLY 00.0190.0236.398-1.238-1.2380.0000.0000.0000.000
152B53PHE 00.038-0.0155.9801.2101.2100.0000.0000.0000.000
153B54ILE 0-0.0110.0455.825-0.220-0.2200.0000.0000.0000.000
154B55LYS 10.9250.9648.208-0.858-0.8580.0000.0000.0000.000
155B56VAL 00.017-0.0015.310-0.025-0.0250.0000.0000.0000.000
156B57ARG 10.9430.9568.5510.3770.3770.0000.0000.0000.000
157B58GLN 0-0.069-0.0407.541-0.088-0.0880.0000.0000.0000.000
158B59TYR 00.0290.0208.8700.1560.1560.0000.0000.0000.000
159B60ASP -1-0.783-0.90311.120-0.552-0.5520.0000.0000.0000.000
160B61GLN 0-0.040-0.03713.1730.0240.0240.0000.0000.0000.000
161B62ILE 0-0.029-0.00312.0910.0350.0350.0000.0000.0000.000
162B63LEU 0-0.036-0.03514.645-0.059-0.0590.0000.0000.0000.000
163B64ILE 00.0090.00011.2680.0160.0160.0000.0000.0000.000
164B65GLU -1-0.970-0.99115.159-0.687-0.6870.0000.0000.0000.000
165B66ILE 00.0610.00712.938-0.159-0.1590.0000.0000.0000.000
166B67CYS 0-0.046-0.03016.8460.0740.0740.0000.0000.0000.000
167B68GLY 00.0380.05218.4490.0790.0790.0000.0000.0000.000
168B69HIS 0-0.033-0.01319.6160.0910.0910.0000.0000.0000.000
169B70LYS 10.9620.96419.3380.4750.4750.0000.0000.0000.000
170B71ALA 00.0450.03014.9730.0210.0210.0000.0000.0000.000
171B72ILE 0-0.0030.03115.026-0.061-0.0610.0000.0000.0000.000
172B73GLY 00.0190.00611.6930.0110.0110.0000.0000.0000.000
173B74THR 0-0.015-0.0158.144-0.017-0.0170.0000.0000.0000.000
174B75VAL 00.0160.0117.583-0.184-0.1840.0000.0000.0000.000
175B76LEU 0-0.006-0.0103.518-0.0250.3110.009-0.046-0.3000.000
176B77VAL 0-0.0130.0116.992-0.289-0.2890.0000.0000.0000.000
177B78GLY 00.006-0.0079.0750.2130.2130.0000.0000.0000.000
178B79PRO 00.0260.0418.006-0.204-0.2040.0000.0000.0000.000
179B80THR 0-0.062-0.0163.105-1.2730.4000.114-0.719-1.068-0.006
180B81PRO 00.0710.0361.950-0.015-2.5467.541-1.261-3.7480.003
181B82VAL 00.0390.0022.549-3.061-0.7932.330-0.990-3.6080.004
182B83ASN 0-0.019-0.0264.400-0.253-0.0280.000-0.014-0.2110.000
183B84ILE 00.0280.0092.3101.663-5.11317.736-2.578-8.382-0.003
184B85ILE 0-0.0150.0015.5070.3470.3470.0000.0000.0000.000
185B86GLY 00.1130.0244.819-0.678-0.6780.0000.0000.0000.000
186B87ARG 10.9460.9705.7590.8900.8900.0000.0000.0000.000
187B88ASN 00.0130.0836.483-0.397-0.3970.0000.0000.0000.000
188B89LEU 0-0.009-0.0108.3830.0930.0930.0000.0000.0000.000
189B90LEU 0-0.0470.0027.8190.1590.1590.0000.0000.0000.000
190B91THR 0-0.027-0.01711.3870.1650.1650.0000.0000.0000.000
191B92GLN 0-0.051-0.02113.3500.0980.0980.0000.0000.0000.000
192B93ILE 0-0.044-0.01113.7610.0670.0670.0000.0000.0000.000
193B94GLY 00.0200.02016.1490.0480.0480.0000.0000.0000.000
194B95ALA 0-0.010-0.02413.0230.0300.0300.0000.0000.0000.000
195B96THR 0-0.062-0.05114.9140.0530.0530.0000.0000.0000.000
196B97LEU 0-0.0120.0029.866-0.025-0.0250.0000.0000.0000.000
197B98ASN 00.047-0.01414.0130.0690.0690.0000.0000.0000.000
198B99PHE -1-0.808-0.90714.015-0.298-0.2980.0000.0000.0000.000