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: MMJQZ

Calculation Name: 1BVE-AB-NMR60-Model26

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 -2270994.159351
FMO2-HF: Nuclear repulsion 2194517.075942
FMO2-HF: Total energy -76477.083409
FMO2-MP2: Total energy -76702.78887


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.
-166.076-167.931177.112-52.405-122.850-0.031


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.
-166.076-167.931177.112-52.405-122.850.031
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 : 0.029 / q_NPA : -0.054
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 10.8390.90918.6641.1381.1380.0000.0000.0000.000
2A2GLN 00.0390.04218.267-0.150-0.1500.0000.0000.0000.000
3A3VAL 00.0000.00614.2370.0960.0960.0000.0000.0000.000
4A4THR 00.0180.01314.973-0.215-0.2150.0000.0000.0000.000
5A5LEU 0-0.009-0.01714.826-0.125-0.1250.0000.0000.0000.000
6A6TRP 00.0170.00314.134-0.037-0.0370.0000.0000.0000.000
7A7GLN 00.0310.0129.704-0.117-0.1170.0000.0000.0000.000
8A8ARG 10.8240.9175.3852.8762.8760.0000.0000.0000.000
9A9PRO 0-0.0100.0198.4890.4070.4070.0000.0000.0000.000
10A10LEU 00.0320.0018.010-0.242-0.2420.0000.0000.0000.000
11A11VAL 0-0.022-0.02311.4870.1510.1510.0000.0000.0000.000
12A12THR 00.0100.00213.456-0.003-0.0030.0000.0000.0000.000
13A13ILE 0-0.0040.00911.4390.0250.0250.0000.0000.0000.000
14A14LYS 10.9730.96915.1280.3990.3990.0000.0000.0000.000
15A15ILE 00.0290.04211.5100.0030.0030.0000.0000.0000.000
16A16GLY 00.000-0.00815.7810.0570.0570.0000.0000.0000.000
17A17GLY 0-0.054-0.01918.0330.0280.0280.0000.0000.0000.000
18A18GLN 0-0.009-0.00617.2530.0170.0170.0000.0000.0000.000
19A19LEU 0-0.014-0.01217.041-0.066-0.0660.0000.0000.0000.000
20A20LYS 10.9490.98611.755-0.107-0.1070.0000.0000.0000.000
21A21GLU -1-0.882-0.94110.125-0.657-0.6570.0000.0000.0000.000
22A22ALA 0-0.041-0.0199.3090.1440.1440.0000.0000.0000.000
23A23LEU 00.000-0.0073.385-0.5700.1600.031-0.114-0.6460.000
24A24LEU 0-0.032-0.0216.174-1.370-1.3700.0000.0000.0000.000
25A25ASP -1-0.708-0.8471.770-51.737-54.22016.951-7.268-7.200-0.075
26A26THR 0-0.080-0.0624.7480.4080.557-0.001-0.007-0.1410.000
27A27GLY 00.0330.0262.8911.5442.2620.121-0.292-0.5470.002
28A28ALA 0-0.064-0.0082.1383.1650.88711.883-3.386-6.2200.001
29A29ASP -1-0.890-0.9582.231-3.218-2.6842.728-0.917-2.3450.012
30A30ASP -1-0.956-0.9982.631-2.927-1.1990.448-0.745-1.4310.009
31A31THR 0-0.082-0.0723.678-2.899-2.3480.011-0.218-0.343-0.001
32A32VAL 0-0.023-0.0053.014-0.1841.0760.091-0.258-1.0940.001
33A33LEU 00.002-0.0234.714-0.483-0.393-0.001-0.010-0.0800.000
34A34GLU -1-0.971-0.9986.9891.2111.2110.0000.0000.0000.000
35A35GLU -1-0.912-0.9788.1200.7940.7940.0000.0000.0000.000
36A36MET 00.0250.01511.556-0.158-0.1580.0000.0000.0000.000
37A37SER 0-0.017-0.00614.5100.0570.0570.0000.0000.0000.000
38A38LEU 00.0280.01613.580-0.091-0.0910.0000.0000.0000.000
39A39PRO 0-0.021-0.00817.5860.0270.0270.0000.0000.0000.000
40A40GLY 0-0.018-0.01719.271-0.008-0.0080.0000.0000.0000.000
41A41ARG 10.9480.96917.748-0.249-0.2490.0000.0000.0000.000
42A42TRP 00.0160.03213.1400.0400.0400.0000.0000.0000.000
43A43LYS 10.9790.98212.928-0.686-0.6860.0000.0000.0000.000
44A44PRO 0-0.0150.00112.1320.0950.0950.0000.0000.0000.000
45A45LYS 10.9470.9766.581-1.561-1.5610.0000.0000.0000.000
46A46MET 0-0.009-0.0088.383-0.101-0.1010.0000.0000.0000.000
47A47ILE 00.0070.0202.883-3.691-0.9510.763-0.896-2.6070.010
48A48GLY 00.053-0.0094.6010.5090.760-0.001-0.035-0.2140.000
49A49GLY 0-0.0090.0042.216-4.660-2.6493.197-2.381-2.8260.015
50A50ILE 0-0.019-0.0042.004-9.703-20.18334.205-5.049-18.6760.039
51A51GLY 00.017-0.0063.9880.4661.2010.006-0.151-0.5890.001
52A52GLY 00.0180.0146.251-2.340-2.3400.0000.0000.0000.000
53A53PHE 0-0.0380.0076.3841.4471.4470.0000.0000.0000.000
54A54ILE 00.0220.0535.731-0.593-0.5930.0000.0000.0000.000
55A55LYS 10.9380.9468.498-2.092-2.0920.0000.0000.0000.000
56A56VAL 00.012-0.0036.2080.0910.0910.0000.0000.0000.000
57A57ARG 10.8500.9239.288-1.295-1.2950.0000.0000.0000.000
58A58GLN 0-0.043-0.0238.3180.1330.1330.0000.0000.0000.000
59A59TYR 00.0420.0259.555-0.101-0.1010.0000.0000.0000.000
60A60ASP -1-0.808-0.90711.1340.5460.5460.0000.0000.0000.000
61A61GLN 0-0.050-0.04313.267-0.064-0.0640.0000.0000.0000.000
62A62ILE 0-0.011-0.01012.8090.0120.0120.0000.0000.0000.000
63A63LEU 0-0.055-0.03414.308-0.073-0.0730.0000.0000.0000.000
64A64ILE 00.0390.00110.6610.0280.0280.0000.0000.0000.000
65A65GLU -1-0.955-0.97114.627-0.518-0.5180.0000.0000.0000.000
66A66ILE 00.0810.03212.090-0.031-0.0310.0000.0000.0000.000
67A67CYS 0-0.047-0.01716.089-0.033-0.0330.0000.0000.0000.000
68A68GLY 00.0290.01618.8830.0410.0410.0000.0000.0000.000
69A69HIS 0-0.036-0.01518.9930.0800.0800.0000.0000.0000.000
70A70LYS 10.9260.95118.3860.2800.2800.0000.0000.0000.000
71A71ALA 00.0620.04014.876-0.013-0.0130.0000.0000.0000.000
72A72ILE 0-0.0260.00715.1040.0440.0440.0000.0000.0000.000
73A73GLY 00.0460.00311.337-0.091-0.0910.0000.0000.0000.000
74A74THR 0-0.027-0.0167.929-0.087-0.0870.0000.0000.0000.000
75A75VAL 00.0180.0137.618-0.059-0.0590.0000.0000.0000.000
76A76LEU 0-0.030-0.0153.576-0.1200.2540.012-0.057-0.3290.000
77A77VAL 00.0250.0257.118-0.082-0.0820.0000.0000.0000.000
78A78GLY 0-0.012-0.0219.4810.1040.1040.0000.0000.0000.000
79A79PRO 0-0.0340.0108.527-0.280-0.2800.0000.0000.0000.000
80A80THR 0-0.0620.0163.6480.4361.1720.017-0.251-0.501-0.001
81A81PRO 00.0460.0171.968-1.098-1.8184.140-0.732-2.6890.000
82A82VAL 00.0420.0112.801-4.096-1.2612.248-1.095-3.9870.007
83A83ASN 0-0.0290.0074.507-0.406-0.1740.000-0.018-0.2140.000
84A84ILE 0-0.007-0.0132.238-2.761-0.4322.823-0.896-4.2560.000
85A85ILE 0-0.0070.0135.4040.7440.7440.0000.0000.0000.000
86A86GLY 00.1260.0494.824-1.120-1.1200.0000.0000.0000.000
87A87ARG 10.9560.9455.7361.2971.2970.0000.0000.0000.000
88A88ASN 0-0.0300.0456.638-0.338-0.3380.0000.0000.0000.000
89A89LEU 00.0150.0018.5150.1000.1000.0000.0000.0000.000
90A90LEU 0-0.0350.0118.0830.0660.0660.0000.0000.0000.000
91A91THR 0-0.065-0.03211.4960.0980.0980.0000.0000.0000.000
92A92GLN 0-0.045-0.01313.4530.0960.0960.0000.0000.0000.000
93A93ILE 0-0.044-0.01013.8200.0620.0620.0000.0000.0000.000
94A94GLY 00.0050.01316.2890.0150.0150.0000.0000.0000.000
95A95ALA 00.009-0.02613.304-0.014-0.0140.0000.0000.0000.000
96A96THR 0-0.077-0.05115.2430.0830.0830.0000.0000.0000.000
97A97LEU 00.0040.0179.902-0.015-0.0150.0000.0000.0000.000
98A98ASN 0-0.005-0.02914.3080.0880.0880.0000.0000.0000.000
99A99PHE -1-0.814-0.88314.594-1.553-1.5530.0000.0000.0000.000
100B1PRO 10.7770.87818.4031.4431.4430.0000.0000.0000.000
101B2GLN 00.0680.05518.032-0.125-0.1250.0000.0000.0000.000
102B3VAL 0-0.0090.00714.1970.0930.0930.0000.0000.0000.000
103B4THR 00.0510.00815.638-0.103-0.1030.0000.0000.0000.000
104B5LEU 0-0.061-0.03316.015-0.073-0.0730.0000.0000.0000.000
105B6TRP 00.0530.03213.1870.0370.0370.0000.0000.0000.000
106B7GLN 00.023-0.00211.9310.1320.1320.0000.0000.0000.000
107B8ARG 10.9610.9987.7500.9810.9810.0000.0000.0000.000
108B9PRO 00.0330.0338.4040.4510.4510.0000.0000.0000.000
109B10LEU 00.0150.0008.235-0.473-0.4730.0000.0000.0000.000
110B11VAL 0-0.041-0.01411.6000.2540.2540.0000.0000.0000.000
111B12THR 00.018-0.00513.661-0.031-0.0310.0000.0000.0000.000
112B13ILE 0-0.0110.01211.1680.0190.0190.0000.0000.0000.000
113B14LYS 10.9280.96415.2130.9370.9370.0000.0000.0000.000
114B15ILE 00.0650.03511.008-0.023-0.0230.0000.0000.0000.000
115B16GLY 00.0360.01215.2960.1020.1020.0000.0000.0000.000
116B17GLY 0-0.047-0.02117.5850.0660.0660.0000.0000.0000.000
117B18GLN 0-0.007-0.01416.5720.0640.0640.0000.0000.0000.000
118B19LEU 0-0.023-0.01116.742-0.123-0.1230.0000.0000.0000.000
119B20LYS 10.9290.96311.8640.5180.5180.0000.0000.0000.000
120B21GLU -1-0.925-0.96011.631-1.202-1.2020.0000.0000.0000.000
121B22ALA 0-0.020-0.0379.3160.0320.0320.0000.0000.0000.000
122B23LEU 0-0.014-0.0033.889-0.0720.5140.008-0.075-0.5200.000
123B24LEU 0-0.058-0.0286.156-1.363-1.3630.0000.0000.0000.000
124B25ASP -1-0.666-0.8401.888-49.437-54.00122.112-8.181-9.367-0.092
125B26THR 0-0.085-0.0594.1890.5170.803-0.001-0.097-0.1890.000
126B27GLY 00.0640.0292.4082.4803.4921.372-1.056-1.3300.006
127B28ALA 0-0.058-0.0082.1386.1823.30714.441-3.542-8.0240.001
128B29ASP -1-0.840-0.9372.231-5.776-4.9803.232-1.060-2.9680.013
129B30ASP -1-0.966-0.9922.162-11.498-9.5092.878-1.980-2.8880.007
130B31THR 0-0.039-0.0463.418-0.6170.0940.035-0.220-0.526-0.002
131B32VAL 0-0.0060.0033.057-0.0591.2860.095-0.332-1.1080.001
132B33LEU 00.008-0.0204.584-0.313-0.2130.000-0.010-0.0890.000
133B34GLU -1-0.903-0.9857.0060.7970.7970.0000.0000.0000.000
134B35GLU -1-0.945-0.9868.0570.1070.1070.0000.0000.0000.000
135B36MET 0-0.023-0.00511.362-0.112-0.1120.0000.0000.0000.000
136B37SER 0-0.025-0.01014.4390.0800.0800.0000.0000.0000.000
137B38LEU 00.0690.03013.073-0.082-0.0820.0000.0000.0000.000
138B39PRO 00.0080.01116.7900.0920.0920.0000.0000.0000.000
139B40GLY 0-0.022-0.01719.1860.0110.0110.0000.0000.0000.000
140B41ARG 10.9160.94418.0420.1840.1840.0000.0000.0000.000
141B42TRP 00.0460.03213.403-0.029-0.0290.0000.0000.0000.000
142B43LYS 10.9630.97112.0710.5630.5630.0000.0000.0000.000
143B44PRO 0-0.039-0.00610.994-0.092-0.0920.0000.0000.0000.000
144B45LYS 10.8880.9725.5470.3250.3250.0000.0000.0000.000
145B46MET 0-0.020-0.0318.232-0.101-0.1010.0000.0000.0000.000
146B47ILE 00.0190.0312.420-4.591-1.5421.357-1.185-3.2200.014
147B48GLY 00.057-0.0144.1980.3460.7030.000-0.059-0.2980.000
148B49GLY 00.0000.0062.084-4.420-2.7625.838-3.715-3.7800.018
149B50ILE 0-0.0200.0032.013-9.243-19.32530.952-2.707-18.1640.044
150B51GLY 00.010-0.0223.982-0.0100.6270.007-0.132-0.5120.001
151B52GLY 0-0.0040.0036.290-2.242-2.2420.0000.0000.0000.000
152B53PHE 00.0040.0125.9842.0072.0070.0000.0000.0000.000
153B54ILE 0-0.0040.0445.597-0.827-0.8270.0000.0000.0000.000
154B55LYS 10.9290.9588.110-1.674-1.6740.0000.0000.0000.000
155B56VAL 00.0150.0145.634-0.098-0.0980.0000.0000.0000.000
156B57ARG 10.9080.9488.983-0.395-0.3950.0000.0000.0000.000
157B58GLN 00.0130.0006.698-0.005-0.0050.0000.0000.0000.000
158B59TYR 00.0340.0169.8370.2530.2530.0000.0000.0000.000
159B60ASP -1-0.811-0.91910.379-1.516-1.5160.0000.0000.0000.000
160B61GLN 0-0.080-0.05812.1780.1930.1930.0000.0000.0000.000
161B62ILE 0-0.001-0.00412.5680.1770.1770.0000.0000.0000.000
162B63LEU 0-0.058-0.04114.060-0.133-0.1330.0000.0000.0000.000
163B64ILE 00.0530.00710.8030.0980.0980.0000.0000.0000.000
164B65GLU -1-0.984-0.98714.630-1.013-1.0130.0000.0000.0000.000
165B66ILE 00.0980.04612.037-0.036-0.0360.0000.0000.0000.000
166B67CYS 0-0.049-0.01816.3560.0270.0270.0000.0000.0000.000
167B68GLY 00.0550.02619.2780.1000.1000.0000.0000.0000.000
168B69HIS 0-0.048-0.02319.1810.0660.0660.0000.0000.0000.000
169B70LYS 10.9080.94018.4410.7230.7230.0000.0000.0000.000
170B71ALA 00.0700.04614.8850.0290.0290.0000.0000.0000.000
171B72ILE 0-0.0320.02114.6400.0100.0100.0000.0000.0000.000
172B73GLY 0-0.026-0.00410.974-0.080-0.0800.0000.0000.0000.000
173B74THR 0-0.028-0.0056.9870.3190.3190.0000.0000.0000.000
174B75VAL 00.0390.0357.204-0.625-0.6250.0000.0000.0000.000
175B76LEU 0-0.055-0.0304.0250.4900.7050.000-0.020-0.1950.000
176B77VAL 0-0.0070.0277.3920.0010.0010.0000.0000.0000.000
177B78GLY 0-0.016-0.0459.5510.1670.1670.0000.0000.0000.000
178B79PRO 0-0.0200.0178.307-0.300-0.3000.0000.0000.0000.000
179B80THR 0-0.0690.0113.6310.2981.0840.019-0.278-0.526-0.002
180B81PRO 00.0660.0362.005-0.793-1.8054.692-0.793-2.887-0.001
181B82VAL 00.0710.0172.877-2.879-0.6371.104-0.697-2.6480.005
182B83ASN 0-0.0710.0024.634-0.442-0.2560.000-0.011-0.1750.000
183B84ILE 0-0.005-0.0112.210-1.212-2.5319.299-1.479-6.501-0.002
184B85ILE 00.0230.0215.2110.2770.2770.0000.0000.0000.000
185B86GLY 00.1420.0664.887-2.080-2.0800.0000.0000.0000.000
186B87ARG 10.8600.9135.8063.4253.4250.0000.0000.0000.000
187B88ASN 00.0590.0966.170-0.116-0.1160.0000.0000.0000.000
188B89LEU 00.0580.0087.8420.4800.4800.0000.0000.0000.000
189B90LEU 0-0.0350.0147.4990.3480.3480.0000.0000.0000.000
190B91THR 0-0.044-0.05210.7050.2500.2500.0000.0000.0000.000
191B92GLN 0-0.077-0.03011.1360.3360.3360.0000.0000.0000.000
192B93ILE 0-0.039-0.00913.4670.1550.1550.0000.0000.0000.000
193B94GLY 00.0500.02616.2750.0730.0730.0000.0000.0000.000
194B95ALA 0-0.008-0.01412.9210.0530.0530.0000.0000.0000.000
195B96THR 0-0.080-0.05314.9800.0500.0500.0000.0000.0000.000
196B97LEU 00.0070.0059.9670.0120.0120.0000.0000.0000.000
197B98ASN 00.024-0.01514.1710.0760.0760.0000.0000.0000.000
198B99PHE -1-0.853-0.89713.485-1.208-1.2080.0000.0000.0000.000