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: 6382Z

Calculation Name: 1BVE-AB-NMR60-Model2

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 -2272156.49014
FMO2-HF: Nuclear repulsion 2195679.044398
FMO2-HF: Total energy -76477.445742
FMO2-MP2: Total energy -76703.07452


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.
-154.942-237.821299.422-93.408-123.1370.070


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.
-154.942-237.821299.422-93.408-123.137-0.07
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 : -0.068 / q_NPA : -0.174
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 10.7970.88917.8771.2111.2110.0000.0000.0000.000
2A2GLN 00.0440.04417.668-0.158-0.1580.0000.0000.0000.000
3A3VAL 00.0190.02013.5620.1080.1080.0000.0000.0000.000
4A4THR 00.0500.01814.855-0.161-0.1610.0000.0000.0000.000
5A5LEU 0-0.027-0.01814.859-0.081-0.0810.0000.0000.0000.000
6A6TRP 00.0580.01912.8350.0060.0060.0000.0000.0000.000
7A7GLN 0-0.007-0.01311.0360.1030.1030.0000.0000.0000.000
8A8ARG 10.9400.9636.3840.4420.4420.0000.0000.0000.000
9A9PRO 00.0400.0328.1660.4090.4090.0000.0000.0000.000
10A10LEU 00.026-0.0088.384-0.294-0.2940.0000.0000.0000.000
11A11VAL 0-0.030-0.02311.4000.1430.1430.0000.0000.0000.000
12A12THR 00.000-0.00513.383-0.037-0.0370.0000.0000.0000.000
13A13ILE 00.0270.02210.810-0.008-0.0080.0000.0000.0000.000
14A14LYS 10.9560.96914.4950.4210.4210.0000.0000.0000.000
15A15ILE 00.0320.03510.578-0.024-0.0240.0000.0000.0000.000
16A16GLY 00.0160.01114.8870.0900.0900.0000.0000.0000.000
17A17GLY 0-0.070-0.03117.3430.0360.0360.0000.0000.0000.000
18A18GLN 00.013-0.00216.5790.0370.0370.0000.0000.0000.000
19A19LEU 0-0.019-0.03216.913-0.085-0.0850.0000.0000.0000.000
20A20LYS 10.9260.98312.883-0.289-0.2890.0000.0000.0000.000
21A21GLU -1-0.883-0.93311.793-0.419-0.4190.0000.0000.0000.000
22A22ALA 0-0.023-0.0059.3900.0870.0870.0000.0000.0000.000
23A23LEU 0-0.032-0.0123.358-0.3160.4870.025-0.112-0.7150.000
24A24LEU 0-0.040-0.0315.977-1.574-1.5740.0000.0000.0000.000
25A25ASP -1-0.692-0.8001.388-38.010-85.38183.950-28.448-8.131-0.102
26A26THR 0-0.084-0.0684.3880.1280.396-0.001-0.026-0.2410.000
27A27GLY 00.0190.0012.4580.5411.4590.543-0.708-0.753-0.002
28A28ALA 0-0.0210.0112.0390.531-0.06610.123-2.667-6.8590.005
29A29ASP -1-0.850-0.9333.125-9.146-6.8150.083-0.658-1.757-0.002
30A30ASP -1-0.896-0.9842.7501.0132.7490.217-0.666-1.2870.002
31A31THR 0-0.046-0.0133.020-5.036-3.4520.199-0.836-0.947-0.009
32A32VAL 0-0.017-0.0042.0500.1541.1372.933-1.011-2.9050.003
33A33LEU 0-0.009-0.0243.547-0.821-0.6370.0270.000-0.2110.000
34A34GLU -1-0.945-0.9837.1761.8441.8440.0000.0000.0000.000
35A35GLU -1-0.980-0.9859.1251.2921.2920.0000.0000.0000.000
36A36MET 0-0.022-0.01511.908-0.185-0.1850.0000.0000.0000.000
37A37SER 0-0.046-0.01514.2690.0930.0930.0000.0000.0000.000
38A38LEU 00.0300.01911.623-0.104-0.1040.0000.0000.0000.000
39A39PRO 00.0260.01815.4110.0200.0200.0000.0000.0000.000
40A40GLY 00.0370.02616.9530.0880.0880.0000.0000.0000.000
41A41ARG 10.9180.95816.241-0.250-0.2500.0000.0000.0000.000
42A42TRP 00.0280.03112.3360.0490.0490.0000.0000.0000.000
43A43LYS 10.9570.96412.179-0.825-0.8250.0000.0000.0000.000
44A44PRO 0-0.0040.01211.5200.2130.2130.0000.0000.0000.000
45A45LYS 10.9310.9656.158-2.843-2.8430.0000.0000.0000.000
46A46MET 0-0.009-0.0198.3120.0500.0500.0000.0000.0000.000
47A47ILE 0-0.0340.0072.756-3.444-0.9671.456-0.855-3.0780.011
48A48GLY 00.058-0.0024.3640.0700.3770.000-0.054-0.2530.000
49A49GLY 0-0.0150.0012.095-5.063-3.7156.889-4.057-4.1800.020
50A50ILE 0-0.0090.0051.934-5.978-21.94139.943-3.286-20.6930.032
51A51GLY 00.017-0.0183.8710.3421.1830.009-0.153-0.6970.001
52A52GLY 0-0.018-0.0106.097-2.439-2.4390.0000.0000.0000.000
53A53PHE 00.0070.0066.1921.7231.7230.0000.0000.0000.000
54A54ILE 00.0100.0405.762-0.835-0.8350.0000.0000.0000.000
55A55LYS 10.9310.9658.413-2.381-2.3810.0000.0000.0000.000
56A56VAL 00.0170.0015.578-0.019-0.0190.0000.0000.0000.000
57A57ARG 10.9080.9518.631-1.603-1.6030.0000.0000.0000.000
58A58GLN 00.0570.0136.2010.3350.3350.0000.0000.0000.000
59A59TYR 0-0.009-0.0258.816-0.246-0.2460.0000.0000.0000.000
60A60ASP -1-0.836-0.92710.1270.7200.7200.0000.0000.0000.000
61A61GLN 0-0.070-0.06212.333-0.081-0.0810.0000.0000.0000.000
62A62ILE 0-0.044-0.00610.9710.0620.0620.0000.0000.0000.000
63A63LEU 0-0.081-0.03613.586-0.114-0.1140.0000.0000.0000.000
64A64ILE 00.0400.00110.0940.0780.0780.0000.0000.0000.000
65A65GLU -1-0.951-0.98313.953-0.709-0.7090.0000.0000.0000.000
66A66ILE 00.0460.00311.233-0.028-0.0280.0000.0000.0000.000
67A67CYS 0-0.075-0.03715.5280.0080.0080.0000.0000.0000.000
68A68GLY 00.0160.02818.4570.0230.0230.0000.0000.0000.000
69A69HIS 00.0240.02017.1100.0480.0480.0000.0000.0000.000
70A70LYS 10.9640.98117.2510.3870.3870.0000.0000.0000.000
71A71ALA 00.0420.02413.650-0.021-0.0210.0000.0000.0000.000
72A72ILE 0-0.058-0.00214.3130.0760.0760.0000.0000.0000.000
73A73GLY 00.0340.02010.552-0.096-0.0960.0000.0000.0000.000
74A74THR 0-0.036-0.0217.467-0.035-0.0350.0000.0000.0000.000
75A75VAL 00.0020.0036.896-0.069-0.0690.0000.0000.0000.000
76A76LEU 0-0.028-0.0042.481-0.6410.2610.480-0.274-1.1080.001
77A77VAL 00.0640.0286.006-0.218-0.2180.0000.0000.0000.000
78A78GLY 0-0.020-0.0178.5350.1870.1870.0000.0000.0000.000
79A79PRO 0-0.0050.0249.133-0.302-0.3020.0000.0000.0000.000
80A80THR 0-0.0620.0024.0460.9151.2620.001-0.048-0.2990.000
81A81PRO 00.0760.0352.083-1.412-1.0981.822-0.487-1.6490.000
82A82VAL 00.0640.0153.512-1.998-0.4280.112-0.379-1.3040.003
83A83ASN 0-0.058-0.0225.439-0.135-0.1350.0000.0000.0000.000
84A84ILE 0-0.020-0.0182.077-3.374-0.8073.627-1.251-4.944-0.001
85A85ILE 0-0.0090.0164.5920.6890.934-0.001-0.013-0.2300.000
86A86GLY 00.1450.0504.452-0.946-0.818-0.001-0.019-0.1080.000
87A87ARG 10.9320.9435.1824.5074.598-0.001-0.002-0.0890.000
88A88ASN 00.0090.0535.914-0.145-0.1450.0000.0000.0000.000
89A89LEU 00.010-0.0187.9110.5260.5260.0000.0000.0000.000
90A90LEU 0-0.0210.0198.1540.3710.3710.0000.0000.0000.000
91A91THR 0-0.062-0.03811.2930.2780.2780.0000.0000.0000.000
92A92GLN 0-0.012-0.00412.0330.2610.2610.0000.0000.0000.000
93A93ILE 0-0.052-0.01013.0870.1220.1220.0000.0000.0000.000
94A94GLY 00.0010.01116.0120.0520.0520.0000.0000.0000.000
95A95ALA 0-0.005-0.01413.9460.0330.0330.0000.0000.0000.000
96A96THR 0-0.050-0.05115.9250.0230.0230.0000.0000.0000.000
97A97LEU 0-0.038-0.01110.139-0.058-0.0580.0000.0000.0000.000
98A98ASN 0-0.002-0.00914.7050.0040.0040.0000.0000.0000.000
99A99PHE -1-0.843-0.90312.766-1.576-1.5760.0000.0000.0000.000
100B1PRO 10.8360.90418.0151.4971.4970.0000.0000.0000.000
101B2GLN 00.0590.05118.406-0.063-0.0630.0000.0000.0000.000
102B3VAL 0-0.0150.00114.5210.0830.0830.0000.0000.0000.000
103B4THR 00.0710.01616.517-0.153-0.1530.0000.0000.0000.000
104B5LEU 0-0.031-0.00317.5570.1170.1170.0000.0000.0000.000
105B6TRP 00.002-0.01315.522-0.084-0.0840.0000.0000.0000.000
106B7GLN 00.0120.01113.1610.1780.1780.0000.0000.0000.000
107B8ARG 10.8560.9205.7783.3953.3950.0000.0000.0000.000
108B9PRO 00.0080.0188.7640.4980.4980.0000.0000.0000.000
109B10LEU 00.0170.0058.987-0.261-0.2610.0000.0000.0000.000
110B11VAL 0-0.010-0.00312.0900.3530.3530.0000.0000.0000.000
111B12THR 0-0.005-0.01514.146-0.089-0.0890.0000.0000.0000.000
112B13ILE 00.0080.01711.6820.0890.0890.0000.0000.0000.000
113B14LYS 10.9500.96315.8451.0101.0100.0000.0000.0000.000
114B15ILE 00.0540.02812.111-0.024-0.0240.0000.0000.0000.000
115B16GLY 00.013-0.01915.6370.1110.1110.0000.0000.0000.000
116B17GLY 0-0.035-0.00918.0460.0920.0920.0000.0000.0000.000
117B18GLN 0-0.017-0.00717.3590.0530.0530.0000.0000.0000.000
118B19LEU 0-0.031-0.02417.621-0.074-0.0740.0000.0000.0000.000
119B20LYS 10.9110.97012.3170.7590.7590.0000.0000.0000.000
120B21GLU -1-0.887-0.93810.782-1.560-1.5600.0000.0000.0000.000
121B22ALA 0-0.007-0.0129.7520.0010.0010.0000.0000.0000.000
122B23LEU 0-0.0110.0283.953-0.0800.4770.004-0.061-0.5000.000
123B24LEU 0-0.031-0.0276.330-1.301-1.3010.0000.0000.0000.000
124B25ASP -1-0.664-0.7901.357-55.194-91.60673.680-28.830-8.438-0.111
125B26THR 0-0.073-0.0554.3460.9581.168-0.001-0.017-0.1920.000
126B27GLY 00.0270.0222.5020.6501.6580.609-0.737-0.8800.000
127B28ALA 0-0.055-0.0082.0773.893-1.12116.475-4.104-7.3570.002
128B29ASP -1-0.879-0.9522.292-5.695-4.0232.342-1.262-2.7520.015
129B30ASP -1-0.929-1.0012.397-8.599-6.1060.882-1.298-2.0770.002
130B31THR 0-0.082-0.0263.495-1.247-0.4800.027-0.342-0.451-0.003
131B32VAL 0-0.0070.0083.107-0.0581.2030.074-0.271-1.0630.001
132B33LEU 0-0.020-0.0244.910-0.511-0.422-0.001-0.006-0.0830.000
133B34GLU -1-0.891-0.9436.2470.0560.0560.0000.0000.0000.000
134B35GLU -1-0.996-0.9847.9990.2550.2550.0000.0000.0000.000
135B36MET 0-0.041-0.01711.241-0.136-0.1360.0000.0000.0000.000
136B37SER 0-0.032-0.02413.9920.0810.0810.0000.0000.0000.000
137B38LEU 00.0420.03713.026-0.101-0.1010.0000.0000.0000.000
138B39PRO 00.0390.08016.8000.0720.0720.0000.0000.0000.000
139B40GLY 00.0740.01817.978-0.073-0.0730.0000.0000.0000.000
140B41ARG 10.8810.93417.4740.1630.1630.0000.0000.0000.000
141B42TRP 00.0620.05413.067-0.014-0.0140.0000.0000.0000.000
142B43LYS 10.9610.96312.1350.3150.3150.0000.0000.0000.000
143B44PRO 0-0.0230.00111.489-0.049-0.0490.0000.0000.0000.000
144B45LYS 10.9370.9805.728-0.170-0.1700.0000.0000.0000.000
145B46MET 00.014-0.0158.504-0.162-0.1620.0000.0000.0000.000
146B47ILE 0-0.0220.0042.569-3.407-0.9490.544-0.860-2.1430.007
147B48GLY 00.0550.0023.735-0.2240.1920.003-0.077-0.3410.000
148B49GLY 0-0.015-0.0072.008-4.299-2.9806.827-4.170-3.9760.015
149B50ILE 0-0.0220.0062.034-6.377-20.11635.623-2.461-19.4230.040
150B51GLY 0-0.005-0.0063.938-0.3290.3610.010-0.145-0.5550.001
151B52GLY 00.0150.0026.162-2.361-2.3610.0000.0000.0000.000
152B53PHE 00.0090.0246.0421.8331.8330.0000.0000.0000.000
153B54ILE 0-0.0170.0365.976-0.679-0.6790.0000.0000.0000.000
154B55LYS 10.9340.9558.568-1.615-1.6150.0000.0000.0000.000
155B56VAL 00.0430.0195.753-0.056-0.0560.0000.0000.0000.000
156B57ARG 10.9070.9538.922-0.107-0.1070.0000.0000.0000.000
157B58GLN 0-0.036-0.0297.8050.0000.0000.0000.0000.0000.000
158B59TYR 0-0.070-0.0719.2770.2190.2190.0000.0000.0000.000
159B60ASP -1-0.811-0.91010.885-1.135-1.1350.0000.0000.0000.000
160B61GLN 0-0.049-0.04912.8740.1480.1480.0000.0000.0000.000
161B62ILE 00.003-0.00112.7210.1310.1310.0000.0000.0000.000
162B63LEU 0-0.050-0.03314.315-0.130-0.1300.0000.0000.0000.000
163B64ILE 00.0230.01411.3850.0660.0660.0000.0000.0000.000
164B65GLU -1-0.967-0.99115.070-0.999-0.9990.0000.0000.0000.000
165B66ILE 00.0610.02812.259-0.063-0.0630.0000.0000.0000.000
166B67CYS 0-0.049-0.02716.4720.0800.0800.0000.0000.0000.000
167B68GLY 00.0220.02118.9930.0700.0700.0000.0000.0000.000
168B69HIS 0-0.0040.00118.7860.1730.1730.0000.0000.0000.000
169B70LYS 10.9200.94718.6760.7700.7700.0000.0000.0000.000
170B71ALA 00.0600.04514.9220.0070.0070.0000.0000.0000.000
171B72ILE 0-0.0100.02014.5270.0350.0350.0000.0000.0000.000
172B73GLY 00.015-0.00811.013-0.108-0.1080.0000.0000.0000.000
173B74THR 0-0.035-0.0207.6050.3050.3050.0000.0000.0000.000
174B75VAL 00.0170.0137.434-0.526-0.5260.0000.0000.0000.000
175B76LEU 0-0.019-0.0073.6840.2560.6310.011-0.061-0.3250.000
176B77VAL 0-0.0150.0057.1500.1210.1210.0000.0000.0000.000
177B78GLY 00.0470.0119.2650.2000.2000.0000.0000.0000.000
178B79PRO 0-0.038-0.0058.415-0.288-0.2880.0000.0000.0000.000
179B80THR 0-0.058-0.0173.2780.9421.6940.017-0.229-0.541-0.001
180B81PRO 00.0740.0371.959-0.577-2.1335.600-0.992-3.053-0.005
181B82VAL 00.0550.0163.279-2.499-0.7030.269-0.407-1.6580.004
182B83ASN 0-0.033-0.0375.057-0.194-0.073-0.001-0.004-0.1160.000
183B84ILE 00.0450.0282.545-2.267-0.5073.994-1.047-4.7070.001
184B85ILE 0-0.036-0.0165.7450.6320.6320.0000.0000.0000.000
185B86GLY 00.1090.0324.515-0.719-0.634-0.001-0.017-0.0680.000
186B87ARG 10.8980.9615.4612.3862.3860.0000.0000.0000.000
187B88ASN 00.0060.0566.231-0.092-0.0920.0000.0000.0000.000
188B89LEU 0-0.022-0.0107.8940.4210.4210.0000.0000.0000.000
189B90LEU 00.0060.0208.0600.3610.3610.0000.0000.0000.000
190B91THR 0-0.052-0.04210.6780.3160.3160.0000.0000.0000.000
191B92GLN 0-0.051-0.01112.7350.2740.2740.0000.0000.0000.000
192B93ILE 0-0.060-0.02313.4890.1330.1330.0000.0000.0000.000
193B94GLY 00.0070.01315.6880.0940.0940.0000.0000.0000.000
194B95ALA 0-0.013-0.01713.2070.0520.0520.0000.0000.0000.000
195B96THR 0-0.064-0.04514.9390.0640.0640.0000.0000.0000.000
196B97LEU 0-0.0240.0029.715-0.038-0.0380.0000.0000.0000.000
197B98ASN 00.013-0.01514.1600.0750.0750.0000.0000.0000.000
198B99PHE -1-0.777-0.87912.420-1.315-1.3150.0000.0000.0000.000