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: V2JL1

Calculation Name: 1BVE-AB-NMR60-Model15

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 -2285453.210315
FMO2-HF: Nuclear repulsion 2208975.63472
FMO2-HF: Total energy -76477.575595
FMO2-MP2: Total energy -76703.419805


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.
-128.511-250.722386.791-126.915-137.6640.035


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.
-128.511-250.722386.791-126.915-137.664-0.035
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 : -0.034 / q_NPA : -0.161
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 10.8310.90518.0130.8970.8970.0000.0000.0000.000
2A2GLN 00.0480.05118.054-0.091-0.0910.0000.0000.0000.000
3A3VAL 00.0010.00814.4240.0510.0510.0000.0000.0000.000
4A4THR 00.0380.01015.881-0.107-0.1070.0000.0000.0000.000
5A5LEU 0-0.0170.00216.8200.0520.0520.0000.0000.0000.000
6A6TRP 00.022-0.01314.430-0.069-0.0690.0000.0000.0000.000
7A7GLN 0-0.026-0.01112.226-0.032-0.0320.0000.0000.0000.000
8A8ARG 10.9270.9457.8591.2611.2610.0000.0000.0000.000
9A9PRO 00.0040.0218.8300.1860.1860.0000.0000.0000.000
10A10LEU 00.032-0.0018.411-0.203-0.2030.0000.0000.0000.000
11A11VAL 0-0.043-0.02111.4270.1690.1690.0000.0000.0000.000
12A12THR 00.009-0.00713.607-0.057-0.0570.0000.0000.0000.000
13A13ILE 00.0150.02211.6280.0520.0520.0000.0000.0000.000
14A14LYS 10.9600.96914.9420.4630.4630.0000.0000.0000.000
15A15ILE 00.0240.01910.8450.0090.0090.0000.0000.0000.000
16A16GLY 00.0260.00915.2410.0540.0540.0000.0000.0000.000
17A17GLY 0-0.057-0.02417.2450.0290.0290.0000.0000.0000.000
18A18GLN 00.0210.00417.014-0.006-0.0060.0000.0000.0000.000
19A19LEU 0-0.039-0.02817.407-0.059-0.0590.0000.0000.0000.000
20A20LYS 10.9070.97710.9400.3240.3240.0000.0000.0000.000
21A21GLU -1-0.904-0.94511.490-0.742-0.7420.0000.0000.0000.000
22A22ALA 00.0080.0029.377-0.064-0.0640.0000.0000.0000.000
23A23LEU 0-0.0260.0043.551-0.7110.1420.020-0.141-0.7320.000
24A24LEU 0-0.002-0.0205.829-1.132-1.1320.0000.0000.0000.000
25A25ASP -1-0.642-0.7151.343-40.576-98.020107.247-43.659-6.144-0.112
26A26THR 0-0.040-0.0304.246-0.3760.053-0.001-0.088-0.3400.000
27A27GLY 0-0.012-0.0202.267-1.501-0.4791.598-1.429-1.191-0.007
28A28ALA 0-0.0190.0152.1671.589-2.97315.996-2.861-8.5730.001
29A29ASP -1-0.763-0.8892.654-5.200-3.1370.193-0.444-1.812-0.002
30A30ASP -1-0.869-0.9582.5091.1803.3121.340-1.105-2.3670.003
31A31THR 0-0.091-0.0532.972-5.203-3.4930.254-0.920-1.044-0.011
32A32VAL 0-0.045-0.0062.503-0.1771.7290.561-0.553-1.9150.001
33A33LEU 0-0.029-0.0224.185-0.554-0.3900.002-0.038-0.1280.000
34A34GLU -1-0.963-0.9837.8540.6840.6840.0000.0000.0000.000
35A35GLU -1-0.958-0.9938.7790.7540.7540.0000.0000.0000.000
36A36MET 0-0.0300.00212.125-0.109-0.1090.0000.0000.0000.000
37A37SER 0-0.022-0.00914.9740.0970.0970.0000.0000.0000.000
38A38LEU 00.0360.00712.461-0.076-0.0760.0000.0000.0000.000
39A39PRO 00.0330.03315.6550.0280.0280.0000.0000.0000.000
40A40GLY 00.0310.01817.1620.0620.0620.0000.0000.0000.000
41A41ARG 10.9180.95117.751-0.324-0.3240.0000.0000.0000.000
42A42TRP 00.0440.04312.6180.0330.0330.0000.0000.0000.000
43A43LYS 11.0110.98912.290-1.062-1.0620.0000.0000.0000.000
44A44PRO 00.0140.02611.0730.1730.1730.0000.0000.0000.000
45A45LYS 10.7880.8936.382-2.161-2.1610.0000.0000.0000.000
46A46MET 00.011-0.0167.978-0.184-0.1840.0000.0000.0000.000
47A47ILE 0-0.0120.0262.416-3.303-1.1573.410-1.093-4.4640.013
48A48GLY 00.067-0.0014.249-0.1200.2670.000-0.072-0.3160.000
49A49GLY 0-0.023-0.0141.990-4.496-3.6788.321-4.721-4.4180.017
50A50ILE 0-0.031-0.0101.863-4.849-21.79741.202-3.015-21.2400.031
51A51GLY 00.060-0.0053.7470.3861.4630.015-0.170-0.9220.001
52A52GLY 0-0.027-0.0036.192-2.058-2.0580.0000.0000.0000.000
53A53PHE 00.0030.0146.1461.4691.4690.0000.0000.0000.000
54A54ILE 0-0.0110.0315.626-0.709-0.7090.0000.0000.0000.000
55A55LYS 10.9650.9788.232-2.529-2.5290.0000.0000.0000.000
56A56VAL 00.0360.0175.395-0.063-0.0630.0000.0000.0000.000
57A57ARG 10.8750.9398.448-0.766-0.7660.0000.0000.0000.000
58A58GLN 0-0.056-0.0517.2290.1800.1800.0000.0000.0000.000
59A59TYR 0-0.012-0.0268.996-0.044-0.0440.0000.0000.0000.000
60A60ASP -1-0.805-0.91010.3860.4120.4120.0000.0000.0000.000
61A61GLN 0-0.047-0.02612.061-0.036-0.0360.0000.0000.0000.000
62A62ILE 00.0010.00112.3240.0350.0350.0000.0000.0000.000
63A63LEU 0-0.021-0.04013.811-0.099-0.0990.0000.0000.0000.000
64A64ILE 00.0260.00010.3560.0300.0300.0000.0000.0000.000
65A65GLU -1-0.997-0.99914.251-0.611-0.6110.0000.0000.0000.000
66A66ILE 00.0820.04511.786-0.059-0.0590.0000.0000.0000.000
67A67CYS 0-0.039-0.02615.8190.0260.0260.0000.0000.0000.000
68A68GLY 00.0370.02818.2470.0520.0520.0000.0000.0000.000
69A69HIS 0-0.022-0.00418.7760.0860.0860.0000.0000.0000.000
70A70LYS 10.9180.94317.9870.3340.3340.0000.0000.0000.000
71A71ALA 00.0780.04614.5700.0050.0050.0000.0000.0000.000
72A72ILE 0-0.0150.02214.6980.0180.0180.0000.0000.0000.000
73A73GLY 00.0180.00610.942-0.068-0.0680.0000.0000.0000.000
74A74THR 0-0.039-0.0137.358-0.019-0.0190.0000.0000.0000.000
75A75VAL 00.0180.0157.008-0.253-0.2530.0000.0000.0000.000
76A76LEU 0-0.038-0.0222.705-0.2470.4210.187-0.124-0.7310.000
77A77VAL 00.0330.0276.229-0.271-0.2710.0000.0000.0000.000
78A78GLY 00.001-0.0218.8440.2560.2560.0000.0000.0000.000
79A79PRO 00.0130.0288.755-0.279-0.2790.0000.0000.0000.000
80A80THR 0-0.082-0.0123.8170.5781.0070.003-0.077-0.3550.000
81A81PRO 00.0770.0331.959-0.881-1.2963.282-0.710-2.157-0.001
82A82VAL 00.0880.0283.465-1.993-0.4390.130-0.361-1.3220.003
83A83ASN 0-0.028-0.0385.364-0.268-0.119-0.001-0.006-0.1420.000
84A84ILE 00.0320.0252.482-4.228-0.8475.045-2.182-6.244-0.001
85A85ILE 0-0.0100.0045.1680.0090.266-0.001-0.008-0.2480.000
86A86GLY 00.1110.0304.359-0.478-0.388-0.001-0.020-0.0690.000
87A87ARG 10.8890.9325.2703.0433.157-0.001-0.002-0.1110.000
88A88ASN 00.0500.0735.809-0.262-0.2620.0000.0000.0000.000
89A89LEU 0-0.002-0.0057.8160.3630.3630.0000.0000.0000.000
90A90LEU 0-0.043-0.0038.4100.2370.2370.0000.0000.0000.000
91A91THR 0-0.035-0.01611.0190.2050.2050.0000.0000.0000.000
92A92GLN 0-0.077-0.02512.7440.2190.2190.0000.0000.0000.000
93A93ILE 0-0.048-0.01213.2730.0730.0730.0000.0000.0000.000
94A94GLY 00.0540.03315.2910.0440.0440.0000.0000.0000.000
95A95ALA 0-0.027-0.03212.7920.0260.0260.0000.0000.0000.000
96A96THR 0-0.080-0.04114.069-0.058-0.0580.0000.0000.0000.000
97A97LEU 0-0.015-0.0189.347-0.044-0.0440.0000.0000.0000.000
98A98ASN 0-0.019-0.02113.7700.0870.0870.0000.0000.0000.000
99A99PHE -1-0.816-0.89812.163-1.038-1.0380.0000.0000.0000.000
100B1PRO 10.7970.88817.5970.9450.9450.0000.0000.0000.000
101B2GLN 00.0850.06317.302-0.086-0.0860.0000.0000.0000.000
102B3VAL 0-0.0030.00312.7010.0420.0420.0000.0000.0000.000
103B4THR 00.0410.01614.249-0.111-0.1110.0000.0000.0000.000
104B5LEU 00.008-0.01612.931-0.102-0.1020.0000.0000.0000.000
105B6TRP 00.0110.00512.786-0.027-0.0270.0000.0000.0000.000
106B7GLN 00.0190.0269.082-0.063-0.0630.0000.0000.0000.000
107B8ARG 10.8790.9203.8301.1211.6130.012-0.099-0.404-0.001
108B9PRO 0-0.0040.0157.2100.3430.3430.0000.0000.0000.000
109B10LEU 0-0.015-0.0147.211-0.157-0.1570.0000.0000.0000.000
110B11VAL 00.0000.00110.4080.1580.1580.0000.0000.0000.000
111B12THR 0-0.006-0.00613.1470.0240.0240.0000.0000.0000.000
112B13ILE 0-0.0120.00411.7620.0010.0010.0000.0000.0000.000
113B14LYS 10.9350.95214.9780.6180.6180.0000.0000.0000.000
114B15ILE 00.0380.01011.394-0.025-0.0250.0000.0000.0000.000
115B16GLY 0-0.0170.00215.8770.0800.0800.0000.0000.0000.000
116B17GLY 0-0.018-0.00818.5300.0560.0560.0000.0000.0000.000
117B18GLN 00.0340.01117.6660.0660.0660.0000.0000.0000.000
118B19LEU 0-0.029-0.02417.535-0.073-0.0730.0000.0000.0000.000
119B20LYS 10.9150.98612.3930.5780.5780.0000.0000.0000.000
120B21GLU -1-0.859-0.94510.188-0.402-0.4020.0000.0000.0000.000
121B22ALA 00.034-0.0409.635-0.037-0.0370.0000.0000.0000.000
122B23LEU 0-0.0450.0193.175-1.414-0.0620.093-0.283-1.1620.000
123B24LEU 00.003-0.0136.046-0.984-0.9840.0000.0000.0000.000
124B25ASH 0-0.0500.0071.341-21.393-75.375103.556-42.092-7.482-0.020
125B26THR 0-0.013-0.0374.411-0.0680.201-0.001-0.029-0.2390.000
126B27GLY 00.0310.0082.863-0.6840.1430.194-0.473-0.548-0.001
127B28ALA 0-0.048-0.0072.0810.225-3.99715.222-3.860-7.1400.004
128B29ASP -1-0.825-0.9262.851-5.767-3.5460.360-0.749-1.8320.008
129B30ASP -1-0.893-0.9941.902-10.914-9.1354.152-2.645-3.286-0.008
130B31THR 0-0.086-0.0352.937-0.7870.3870.280-0.395-1.058-0.011
131B32VAL 0-0.052-0.0012.819-0.8710.9450.334-0.471-1.6790.001
132B33LEU 0-0.006-0.0174.335-0.182-0.0500.001-0.029-0.1040.000
133B34GLU -1-0.927-0.9747.7180.4250.4250.0000.0000.0000.000
134B35GLU -1-0.948-0.9928.7160.2460.2460.0000.0000.0000.000
135B36MET 00.0270.01912.175-0.128-0.1280.0000.0000.0000.000
136B37SER 0-0.020-0.00115.0100.0660.0660.0000.0000.0000.000
137B38LEU 0-0.009-0.00612.193-0.080-0.0800.0000.0000.0000.000
138B39PRO 00.0380.01816.5420.0770.0770.0000.0000.0000.000
139B40GLY 0-0.042-0.03718.098-0.005-0.0050.0000.0000.0000.000
140B41ARG 10.9430.96517.2670.1770.1770.0000.0000.0000.000
141B42TRP 00.0350.05013.030-0.057-0.0570.0000.0000.0000.000
142B43LYS 10.9350.94912.7010.2510.2510.0000.0000.0000.000
143B44PRO 00.0010.01211.672-0.071-0.0710.0000.0000.0000.000
144B45LYS 10.9030.9875.6450.4070.4070.0000.0000.0000.000
145B46MET 00.011-0.0297.984-0.117-0.1170.0000.0000.0000.000
146B47ILE 0-0.0130.0142.330-3.771-1.4353.457-1.270-4.5230.016
147B48GLY 00.057-0.0083.8990.1860.6410.002-0.096-0.3610.000
148B49GLY 0-0.017-0.0131.989-4.766-4.36510.185-5.564-5.0210.016
149B50ILE 0-0.0210.0021.991-3.538-20.93438.997-1.069-20.5320.031
150B51GLY 0-0.001-0.0213.8200.2280.9500.011-0.100-0.6330.001
151B52GLY 00.0120.0136.128-2.011-2.0110.0000.0000.0000.000
152B53PHE 00.0090.0235.9281.6931.6930.0000.0000.0000.000
153B54ILE 0-0.0140.0415.624-0.633-0.6330.0000.0000.0000.000
154B55LYS 10.9440.9667.705-2.286-2.2860.0000.0000.0000.000
155B56VAL 0-0.003-0.0015.6890.0150.0150.0000.0000.0000.000
156B57ARG 10.9190.9568.954-0.192-0.1920.0000.0000.0000.000
157B58GLN 0-0.064-0.0618.1340.0180.0180.0000.0000.0000.000
158B59TYR 00.0290.0109.0820.2350.2350.0000.0000.0000.000
159B60ASP -1-0.794-0.87210.007-1.420-1.4200.0000.0000.0000.000
160B61GLN 0-0.029-0.02511.6510.0990.0990.0000.0000.0000.000
161B62ILE 00.0300.00212.2630.1710.1710.0000.0000.0000.000
162B63LEU 0-0.067-0.03013.467-0.117-0.1170.0000.0000.0000.000
163B64ILE 00.0150.00810.4960.1160.1160.0000.0000.0000.000
164B65GLU -1-0.962-0.98314.204-0.702-0.7020.0000.0000.0000.000
165B66ILE 00.0530.01211.655-0.002-0.0020.0000.0000.0000.000
166B67CYS 0-0.074-0.03215.3920.0120.0120.0000.0000.0000.000
167B68GLY 00.0270.02518.4340.0620.0620.0000.0000.0000.000
168B69HIS 00.0430.02817.8120.0410.0410.0000.0000.0000.000
169B70LYS 10.9300.95017.1750.5280.5280.0000.0000.0000.000
170B71ALA 00.0550.03313.376-0.004-0.0040.0000.0000.0000.000
171B72ILE 0-0.0310.01313.424-0.063-0.0630.0000.0000.0000.000
172B73GLY 00.0540.0159.949-0.057-0.0570.0000.0000.0000.000
173B74THR 0-0.028-0.0256.5150.3120.3120.0000.0000.0000.000
174B75VAL 00.0070.0056.579-0.821-0.8210.0000.0000.0000.000
175B76LEU 0-0.078-0.0363.0250.4781.0760.049-0.121-0.5260.000
176B77VAL 00.0440.0326.3830.1270.1270.0000.0000.0000.000
177B78GLY 0-0.011-0.0309.1540.1260.1260.0000.0000.0000.000
178B79PRO 0-0.0250.0168.931-0.187-0.1870.0000.0000.0000.000
179B80THR 0-0.0630.0044.3560.7260.9950.000-0.020-0.2480.000
180B81PRO 00.0490.0281.911-0.804-1.2942.951-0.556-1.905-0.003
181B82VAL 00.0530.0032.2471.432-3.11811.394-1.770-5.074-0.005
182B83ASN 0-0.0060.0184.990-0.410-0.264-0.001-0.010-0.1350.000
183B84ILE 0-0.0020.0092.209-2.542-1.5236.744-1.379-6.3840.001
184B85ILE 00.0220.0115.017-0.655-0.436-0.001-0.008-0.2110.000
185B86GLY 00.0870.0184.167-0.0340.0760.000-0.025-0.0840.000
186B87ARG 10.9290.9895.0392.5552.667-0.001-0.003-0.1080.000
187B88ASN 00.0020.0505.725-0.076-0.0760.0000.0000.0000.000
188B89LEU 00.022-0.0027.4550.4480.4480.0000.0000.0000.000
189B90LEU 0-0.0280.0098.2500.3680.3680.0000.0000.0000.000
190B91THR 0-0.068-0.03410.6780.2680.2680.0000.0000.0000.000
191B92GLN 0-0.070-0.02611.7160.2790.2790.0000.0000.0000.000
192B93ILE 0-0.026-0.01313.1860.1180.1180.0000.0000.0000.000
193B94GLY 0-0.0010.01615.5140.0800.0800.0000.0000.0000.000
194B95ALA 0-0.003-0.01713.5350.0500.0500.0000.0000.0000.000
195B96THR 0-0.031-0.03715.5330.0510.0510.0000.0000.0000.000
196B97LEU 0-0.0220.0069.990-0.026-0.0260.0000.0000.0000.000
197B98ASN 00.033-0.01314.345-0.001-0.0010.0000.0000.0000.000
198B99PHE -1-0.853-0.89713.715-0.931-0.9310.0000.0000.0000.000