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: N3JQQ

Calculation Name: 1BVE-AB-NMR60-Model11

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 -2282829.749869
FMO2-HF: Nuclear repulsion 2206352.603206
FMO2-HF: Total energy -76477.146662
FMO2-MP2: Total energy -76702.942341


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.
-156.724-258.917359.469-118.942-138.3410.100


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.
-156.724-258.917359.469-118.942-138.341-0.1
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 : -0.099 / q_NPA : -0.159
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 10.8420.90516.8161.2171.2170.0000.0000.0000.000
2A2GLN 00.0540.05316.835-0.138-0.1380.0000.0000.0000.000
3A3VAL 00.0210.01613.1640.0660.0660.0000.0000.0000.000
4A4THR 00.023-0.00614.657-0.162-0.1620.0000.0000.0000.000
5A5LEU 00.0070.00910.629-0.190-0.1900.0000.0000.0000.000
6A6TRP 00.0190.01010.940-0.126-0.1260.0000.0000.0000.000
7A7GLN 0-0.036-0.02110.9710.2170.2170.0000.0000.0000.000
8A8ARG 10.9300.9626.0791.1111.1110.0000.0000.0000.000
9A9PRO 00.0160.0148.7370.3360.3360.0000.0000.0000.000
10A10LEU 0-0.004-0.0037.444-0.332-0.3320.0000.0000.0000.000
11A11VAL 0-0.025-0.01410.8070.2100.2100.0000.0000.0000.000
12A12THR 0-0.005-0.01612.891-0.010-0.0100.0000.0000.0000.000
13A13ILE 0-0.011-0.00111.5910.0280.0280.0000.0000.0000.000
14A14LYS 10.9180.95515.1690.4540.4540.0000.0000.0000.000
15A15ILE 00.0440.04611.3570.0090.0090.0000.0000.0000.000
16A16GLY 00.0150.00415.5990.0760.0760.0000.0000.0000.000
17A17GLY 0-0.061-0.02818.2010.0360.0360.0000.0000.0000.000
18A18GLN 00.0170.00516.9290.0010.0010.0000.0000.0000.000
19A19LEU 00.002-0.01417.062-0.079-0.0790.0000.0000.0000.000
20A20LYS 10.8910.97711.6600.0250.0250.0000.0000.0000.000
21A21GLU -1-0.878-0.9369.765-0.658-0.6580.0000.0000.0000.000
22A22ALA 0-0.011-0.0179.2270.0710.0710.0000.0000.0000.000
23A23LEU 00.0020.0102.963-0.5820.5570.225-0.235-1.1290.001
24A24LEU 0-0.003-0.0165.799-1.654-1.6540.0000.0000.0000.000
25A25ASP -1-0.727-0.7941.347-66.220-159.924166.211-66.792-5.715-0.148
26A26THR 0-0.069-0.0573.9640.1340.536-0.002-0.046-0.3540.000
27A27GLY 00.0870.0352.3640.9702.0431.419-1.079-1.4140.006
28A28ALA 0-0.090-0.0212.0575.886-1.97320.942-4.673-8.4100.002
29A29ASP -1-0.821-0.9322.1130.5641.1161.775-0.123-2.2040.005
30A30ASP -1-0.895-0.9892.796-1.3340.3430.278-0.680-1.2750.007
31A31THR 0-0.076-0.0303.627-3.467-2.8760.014-0.251-0.355-0.002
32A32VAL 0-0.046-0.0062.953-0.2321.2330.159-0.311-1.3130.001
33A33LEU 0-0.014-0.0254.551-0.487-0.3910.000-0.015-0.0800.000
34A34GLU -1-0.902-0.9586.5101.0901.0900.0000.0000.0000.000
35A35GLU -1-0.952-0.9828.5301.0041.0040.0000.0000.0000.000
36A36MET 0-0.047-0.01311.881-0.133-0.1330.0000.0000.0000.000
37A37SER 0-0.035-0.00914.9120.0740.0740.0000.0000.0000.000
38A38LEU 00.0600.01712.448-0.083-0.0830.0000.0000.0000.000
39A39PRO 00.0050.01016.3510.0280.0280.0000.0000.0000.000
40A40GLY 0-0.043-0.03617.5950.0050.0050.0000.0000.0000.000
41A41ARG 10.9420.96217.271-0.429-0.4290.0000.0000.0000.000
42A42TRP 00.0510.04312.5190.0340.0340.0000.0000.0000.000
43A43LYS 10.9620.96711.742-0.680-0.6800.0000.0000.0000.000
44A44PRO 0-0.0240.00710.5100.1470.1470.0000.0000.0000.000
45A45LYS 10.9360.9894.624-3.269-3.159-0.001-0.003-0.1060.000
46A46MET 0-0.025-0.0257.579-0.034-0.0340.0000.0000.0000.000
47A47ILE 0-0.0240.0092.345-2.214-2.4057.579-1.347-6.0400.015
48A48GLY 00.063-0.0124.2670.2090.5640.000-0.066-0.2900.000
49A49GLY 0-0.019-0.0092.077-5.024-3.8288.016-4.576-4.6360.020
50A50ILE 0-0.0160.0001.976-5.512-19.92936.018-1.786-19.8150.039
51A51GLY 00.030-0.0123.9760.1270.8810.008-0.159-0.6030.001
52A52GLY 00.0020.0046.511-1.861-1.8610.0000.0000.0000.000
53A53PHE 00.0090.0296.1751.4811.4810.0000.0000.0000.000
54A54ILE 00.0110.0525.602-0.640-0.6400.0000.0000.0000.000
55A55LYS 10.9370.9537.741-2.217-2.2170.0000.0000.0000.000
56A56VAL 00.0110.0104.887-0.034-0.0340.0000.0000.0000.000
57A57ARG 10.8480.9198.196-1.464-1.4640.0000.0000.0000.000
58A58GLN 00.0040.0067.8850.2060.2060.0000.0000.0000.000
59A59TYR 00.0100.0068.727-0.114-0.1140.0000.0000.0000.000
60A60ASP -1-0.791-0.89010.8680.6830.6830.0000.0000.0000.000
61A61GLN 0-0.057-0.04813.034-0.068-0.0680.0000.0000.0000.000
62A62ILE 0-0.0190.00411.7210.0170.0170.0000.0000.0000.000
63A63LEU 0-0.042-0.04214.253-0.083-0.0830.0000.0000.0000.000
64A64ILE 00.0360.00010.6030.0320.0320.0000.0000.0000.000
65A65GLU -1-0.988-1.00014.555-0.559-0.5590.0000.0000.0000.000
66A66ILE 00.0740.04212.460-0.039-0.0390.0000.0000.0000.000
67A67CYS 0-0.043-0.02816.632-0.009-0.0090.0000.0000.0000.000
68A68GLY 00.0800.04819.2090.0890.0890.0000.0000.0000.000
69A69HIS 0-0.046-0.02818.048-0.022-0.0220.0000.0000.0000.000
70A70LYS 10.9360.96118.3890.2590.2590.0000.0000.0000.000
71A71ALA 00.0690.04714.8990.0120.0120.0000.0000.0000.000
72A72ILE 0-0.0100.02215.1130.0240.0240.0000.0000.0000.000
73A73GLY 00.0170.00611.389-0.058-0.0580.0000.0000.0000.000
74A74THR 0-0.047-0.0477.548-0.039-0.0390.0000.0000.0000.000
75A75VAL 00.0050.0017.403-0.047-0.0470.0000.0000.0000.000
76A76LEU 0-0.013-0.0103.219-0.3400.3420.069-0.120-0.6310.000
77A77VAL 00.0190.0186.708-0.185-0.1850.0000.0000.0000.000
78A78GLY 0-0.004-0.0288.9520.1810.1810.0000.0000.0000.000
79A79PRO 0-0.0260.0118.957-0.284-0.2840.0000.0000.0000.000
80A80THR 0-0.082-0.0073.9510.6741.1390.004-0.106-0.3630.000
81A81PRO 00.0420.0181.969-1.105-1.2452.660-0.511-2.010-0.002
82A82VAL 00.0980.0402.913-2.856-0.6330.824-0.646-2.4010.005
83A83ASN 0-0.039-0.0244.760-0.1150.079-0.001-0.009-0.1840.000
84A84ILE 00.0210.0042.043-2.832-2.0867.027-1.761-6.0120.004
85A85ILE 00.0140.0205.1830.8741.128-0.001-0.006-0.2470.000
86A86GLY 00.1260.0425.007-1.343-1.3430.0000.0000.0000.000
87A87ARG 10.9090.9415.8522.9002.9000.0000.0000.0000.000
88A88ASN 00.0090.0446.617-0.379-0.3790.0000.0000.0000.000
89A89LEU 00.015-0.0078.6090.1580.1580.0000.0000.0000.000
90A90LEU 0-0.0420.0127.6290.1070.1070.0000.0000.0000.000
91A91THR 0-0.062-0.03411.6980.1500.1500.0000.0000.0000.000
92A92GLN 0-0.046-0.01113.3690.1770.1770.0000.0000.0000.000
93A93ILE 0-0.061-0.01413.3180.0780.0780.0000.0000.0000.000
94A94GLY 00.0120.01116.6510.0180.0180.0000.0000.0000.000
95A95ALA 0-0.008-0.01112.932-0.021-0.0210.0000.0000.0000.000
96A96THR 0-0.078-0.05714.8770.0910.0910.0000.0000.0000.000
97A97LEU 00.0080.0089.527-0.068-0.0680.0000.0000.0000.000
98A98ASN 0-0.017-0.02613.9200.0740.0740.0000.0000.0000.000
99A99PHE -1-0.841-0.89012.541-1.297-1.2970.0000.0000.0000.000
100B1PRO 10.8120.89817.7301.1891.1890.0000.0000.0000.000
101B2GLN 00.0770.06017.852-0.101-0.1010.0000.0000.0000.000
102B3VAL 00.0080.01513.6790.0860.0860.0000.0000.0000.000
103B4THR 00.0430.00115.722-0.117-0.1170.0000.0000.0000.000
104B5LEU 0-0.031-0.00415.8480.1010.1010.0000.0000.0000.000
105B6TRP 0-0.005-0.02613.242-0.071-0.0710.0000.0000.0000.000
106B7GLN 00.0070.00910.6600.1660.1660.0000.0000.0000.000
107B8ARG 10.9540.9857.012-0.008-0.0080.0000.0000.0000.000
108B9PRO 0-0.0200.0148.2140.3990.3990.0000.0000.0000.000
109B10LEU 00.0320.0027.207-0.312-0.3120.0000.0000.0000.000
110B11VAL 0-0.036-0.02010.9020.2160.2160.0000.0000.0000.000
111B12THR 0-0.022-0.01612.877-0.062-0.0620.0000.0000.0000.000
112B13ILE 00.0270.02111.4090.0220.0220.0000.0000.0000.000
113B14LYS 10.9770.96814.8270.6090.6090.0000.0000.0000.000
114B15ILE 00.0280.04211.477-0.027-0.0270.0000.0000.0000.000
115B16GLY 00.0090.00815.8130.0900.0900.0000.0000.0000.000
116B17GLY 0-0.060-0.03718.3840.0610.0610.0000.0000.0000.000
117B18GLN 0-0.010-0.00216.0620.1020.1020.0000.0000.0000.000
118B19LEU 0-0.024-0.02615.843-0.073-0.0730.0000.0000.0000.000
119B20LYS 10.8920.9809.3440.3340.3340.0000.0000.0000.000
120B21GLU -1-0.874-0.9408.581-0.617-0.6170.0000.0000.0000.000
121B22ALA 0-0.011-0.0048.7860.0420.0420.0000.0000.0000.000
122B23LEU 0-0.052-0.0062.925-1.4270.1780.326-0.471-1.4600.002
123B24LEU 0-0.033-0.0275.755-0.967-0.9670.0000.0000.0000.000
124B25ASP -1-0.588-0.8092.196-39.269-35.23323.801-12.811-15.026-0.134
125B26THR 0-0.055-0.0424.5060.4220.648-0.001-0.012-0.2130.000
126B27GLY 00.0020.0202.5980.9912.1350.386-0.908-0.622-0.003
127B28ALA 0-0.0260.0042.1282.523-1.04115.109-4.163-7.3830.001
128B29ASP -1-0.879-0.9592.271-6.095-4.7562.328-1.114-2.5540.013
129B30ASP -1-0.916-0.9862.555-8.153-5.7820.503-1.137-1.7370.004
130B31THR 0-0.090-0.0513.505-1.234-0.4520.025-0.350-0.457-0.003
131B32VAL 0-0.024-0.0012.994-0.5321.0600.134-0.392-1.3340.002
132B33LEU 0-0.001-0.0204.699-0.131-0.022-0.001-0.011-0.0970.000
133B34GLU -1-0.957-0.9705.9020.4580.4580.0000.0000.0000.000
134B35GLU -1-0.959-0.9907.7100.1270.1270.0000.0000.0000.000
135B36MET 0-0.010-0.00211.213-0.115-0.1150.0000.0000.0000.000
136B37SER 00.0000.00914.1100.0390.0390.0000.0000.0000.000
137B38LEU 00.0090.00613.122-0.086-0.0860.0000.0000.0000.000
138B39PRO 00.0200.00317.5360.0680.0680.0000.0000.0000.000
139B40GLY 0-0.030-0.02318.397-0.023-0.0230.0000.0000.0000.000
140B41ARG 10.9680.97817.3530.3430.3430.0000.0000.0000.000
141B42TRP 00.0320.04013.162-0.040-0.0400.0000.0000.0000.000
142B43LYS 10.9260.95312.1880.3530.3530.0000.0000.0000.000
143B44PRO 00.0000.00711.550-0.019-0.0190.0000.0000.0000.000
144B45LYS 10.9710.9846.1730.9330.9330.0000.0000.0000.000
145B46MET 0-0.073-0.0297.8180.2410.2410.0000.0000.0000.000
146B47ILE 00.0050.0272.765-3.808-1.0170.974-0.958-2.8060.011
147B48GLY 00.0730.0004.4600.3850.6430.000-0.039-0.2190.000
148B49GLY 0-0.020-0.0012.206-3.863-2.1454.533-2.917-3.3340.017
149B50ILE 0-0.016-0.0031.980-7.251-20.66136.716-4.030-19.2780.041
150B51GLY 00.005-0.0213.9450.0030.6610.007-0.129-0.5360.001
151B52GLY 00.0120.0076.270-2.095-2.0950.0000.0000.0000.000
152B53PHE 0-0.0160.0106.2351.6521.6520.0000.0000.0000.000
153B54ILE 00.0050.0475.582-0.723-0.7230.0000.0000.0000.000
154B55LYS 10.9550.9617.866-1.334-1.3340.0000.0000.0000.000
155B56VAL 00.0240.0165.5620.0250.0250.0000.0000.0000.000
156B57ARG 10.8910.9388.921-0.355-0.3550.0000.0000.0000.000
157B58GLN 0-0.024-0.0108.201-0.327-0.3270.0000.0000.0000.000
158B59TYR 00.0160.0159.2980.2340.2340.0000.0000.0000.000
159B60ASP -1-0.858-0.93011.330-1.302-1.3020.0000.0000.0000.000
160B61GLN 0-0.068-0.04913.3150.0950.0950.0000.0000.0000.000
161B62ILE 00.0100.00012.8160.1440.1440.0000.0000.0000.000
162B63LEU 0-0.044-0.05514.336-0.100-0.1000.0000.0000.0000.000
163B64ILE 00.0270.00810.7620.0840.0840.0000.0000.0000.000
164B65GLU -1-0.949-0.98614.694-0.756-0.7560.0000.0000.0000.000
165B66ILE 00.0530.02612.445-0.029-0.0290.0000.0000.0000.000
166B67CYS 0-0.070-0.04116.4340.0340.0340.0000.0000.0000.000
167B68GLY 00.0110.01618.6370.0750.0750.0000.0000.0000.000
168B69HIS 00.0080.01119.8160.0640.0640.0000.0000.0000.000
169B70LYS 10.9460.96718.9710.5110.5110.0000.0000.0000.000
170B71ALA 00.0330.03215.1060.0150.0150.0000.0000.0000.000
171B72ILE 0-0.0480.01115.2110.0690.0690.0000.0000.0000.000
172B73GLY 00.0660.04611.459-0.039-0.0390.0000.0000.0000.000
173B74THR 0-0.005-0.0077.9820.2900.2900.0000.0000.0000.000
174B75VAL 00.0110.0107.507-0.492-0.4920.0000.0000.0000.000
175B76LEU 0-0.042-0.0223.5770.1270.5610.014-0.076-0.3730.000
176B77VAL 00.0430.0407.0970.0990.0990.0000.0000.0000.000
177B78GLY 00.007-0.0319.4010.1110.1110.0000.0000.0000.000
178B79PRO 0-0.0260.0088.421-0.226-0.2260.0000.0000.0000.000
179B80THR 0-0.062-0.0203.3090.4441.4170.024-0.327-0.670-0.002
180B81PRO 00.0660.0331.969-0.704-2.1585.579-0.967-3.157-0.001
181B82VAL 00.0730.0292.582-3.058-0.8841.982-0.852-3.3040.003
182B83ASN 00.006-0.0404.408-0.1530.0460.000-0.012-0.1870.000
183B84ILE 00.0290.0262.2220.156-3.95813.809-1.943-7.752-0.006
184B85ILE 0-0.0140.0025.384-0.249-0.084-0.001-0.006-0.1590.000
185B86GLY 00.1210.0454.757-0.722-0.610-0.001-0.016-0.0960.000
186B87ARG 10.8690.9305.6464.4854.4850.0000.0000.0000.000
187B88ASN 00.0200.0726.462-0.056-0.0560.0000.0000.0000.000
188B89LEU 0-0.003-0.0108.1960.3980.3980.0000.0000.0000.000
189B90LEU 0-0.0270.0038.2570.3120.3120.0000.0000.0000.000
190B91THR 00.003-0.01811.0180.2150.2150.0000.0000.0000.000
191B92GLN 0-0.115-0.06313.1850.1420.1420.0000.0000.0000.000
192B93ILE 0-0.051-0.01513.5100.1290.1290.0000.0000.0000.000
193B94GLY 00.0370.02416.0880.0830.0830.0000.0000.0000.000
194B95ALA 00.007-0.02413.1680.0560.0560.0000.0000.0000.000
195B96THR 0-0.085-0.04315.1660.0490.0490.0000.0000.0000.000
196B97LEU 00.0090.0009.126-0.035-0.0350.0000.0000.0000.000
197B98ASN 0-0.018-0.02713.699-0.008-0.0080.0000.0000.0000.000
198B99PHE -1-0.831-0.90011.775-1.247-1.2470.0000.0000.0000.000