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FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: LL949

Calculation Name: 1BVE-AB-NMR60-Model8

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
LigandCharge
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2286989.115391
FMO2-HF: Nuclear repulsion 2210511.51699
FMO2-HF: Total energy -76477.5984
FMO2-MP2: Total energy -76703.292262


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.
-159.494-191.152229.052-69.544-127.8490.026


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.
-159.494-191.152229.052-69.544-127.849-0.026
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 : -0.026 / q_NPA : -0.098
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 10.8580.91017.7961.3541.3540.0000.0000.0000.000
2A2GLN 00.0480.05417.656-0.105-0.1050.0000.0000.0000.000
3A3VAL 00.0030.01312.6000.0910.0910.0000.0000.0000.000
4A4THR 00.0550.01014.202-0.351-0.3510.0000.0000.0000.000
5A5LEU 0-0.0140.00214.7730.1140.1140.0000.0000.0000.000
6A6TRP 0-0.010-0.02612.498-0.091-0.0910.0000.0000.0000.000
7A7GLN 0-0.0010.0129.9550.1540.1540.0000.0000.0000.000
8A8ARG 10.8660.9124.8800.1190.1190.0000.0000.0000.000
9A9PRO 0-0.0030.0117.9920.5360.5360.0000.0000.0000.000
10A10LEU 00.0100.0108.903-0.224-0.2240.0000.0000.0000.000
11A11VAL 0-0.030-0.02011.5180.1250.1250.0000.0000.0000.000
12A12THR 00.000-0.00913.3920.0490.0490.0000.0000.0000.000
13A13ILE 00.006-0.00310.790-0.046-0.0460.0000.0000.0000.000
14A14LYS 10.9450.96414.8730.3550.3550.0000.0000.0000.000
15A15ILE 00.0680.03710.710-0.023-0.0230.0000.0000.0000.000
16A16GLY 00.008-0.01015.1000.0770.0770.0000.0000.0000.000
17A17GLY 0-0.033-0.00317.3790.0310.0310.0000.0000.0000.000
18A18GLN 0-0.063-0.03716.6480.1190.1190.0000.0000.0000.000
19A19LEU 0-0.009-0.02217.408-0.081-0.0810.0000.0000.0000.000
20A20LYS 10.9320.99012.952-0.220-0.2200.0000.0000.0000.000
21A21GLU -1-0.875-0.92211.297-0.309-0.3090.0000.0000.0000.000
22A22ALA 00.031-0.0169.4510.0830.0830.0000.0000.0000.000
23A23LEU 0-0.0580.0103.495-0.8440.1010.031-0.198-0.7780.001
24A24LEU 0-0.017-0.0296.394-1.163-1.1630.0000.0000.0000.000
25A25ASP -1-0.686-0.8562.219-33.376-33.85212.180-4.396-7.308-0.047
26A26THR 0-0.100-0.0694.6670.3030.497-0.001-0.004-0.1890.000
27A27GLY 00.0460.0162.4870.9741.8380.503-0.670-0.698-0.002
28A28ALA 0-0.0370.0072.0574.196-0.89116.578-4.041-7.4500.000
29A29ASP -1-0.864-0.9572.688-6.097-3.8820.199-0.641-1.773-0.004
30A30ASP -1-0.870-0.9752.6641.8193.8760.464-0.873-1.6490.005
31A31THR 0-0.078-0.0053.120-5.104-3.6940.128-0.726-0.812-0.007
32A32VAL 0-0.035-0.0022.559-0.2661.5000.647-0.476-1.9370.001
33A33LEU 0-0.014-0.0294.196-0.684-0.5230.003-0.040-0.1240.000
34A34GLU -1-0.923-0.9597.3981.6351.6350.0000.0000.0000.000
35A35GLU -1-0.901-0.9659.2681.0631.0630.0000.0000.0000.000
36A36MET 0-0.053-0.02212.528-0.199-0.1990.0000.0000.0000.000
37A37SER 00.0020.01315.2040.0730.0730.0000.0000.0000.000
38A38LEU 00.0190.02012.083-0.113-0.1130.0000.0000.0000.000
39A39PRO 00.0180.05115.9120.0880.0880.0000.0000.0000.000
40A40GLY 00.0400.01017.330-0.051-0.0510.0000.0000.0000.000
41A41ARG 10.9360.95916.860-0.225-0.2250.0000.0000.0000.000
42A42TRP 00.0300.02912.5110.0970.0970.0000.0000.0000.000
43A43LYS 10.9660.96712.316-1.021-1.0210.0000.0000.0000.000
44A44PRO 0-0.0120.01511.5040.1900.1900.0000.0000.0000.000
45A45LYS 10.9750.9905.560-3.930-3.9300.0000.0000.0000.000
46A46MET 0-0.053-0.0188.0630.0020.0020.0000.0000.0000.000
47A47ILE 0-0.0200.0122.509-3.397-0.8161.450-0.965-3.0660.012
48A48GLY 00.0420.0294.246-0.0160.3550.000-0.070-0.3020.000
49A49GLY 0-0.017-0.0032.056-4.868-3.4886.829-4.074-4.1340.020
50A50ILE 0-0.024-0.0041.973-7.008-21.00436.963-2.915-20.0520.034
51A51GLY 00.034-0.0093.9120.5121.3220.009-0.159-0.6600.001
52A52GLY 0-0.005-0.0025.944-2.512-2.5120.0000.0000.0000.000
53A53PHE 00.013-0.0315.7961.8801.8800.0000.0000.0000.000
54A54ILE 0-0.0100.0395.894-0.902-0.9020.0000.0000.0000.000
55A55LYS 10.9820.9497.700-2.434-2.4340.0000.0000.0000.000
56A56VAL 0-0.015-0.0145.2890.0480.0480.0000.0000.0000.000
57A57ARG 10.8590.9368.303-1.638-1.6380.0000.0000.0000.000
58A58GLN 0-0.022-0.0117.5250.2120.2120.0000.0000.0000.000
59A59TYR 0-0.015-0.0388.834-0.189-0.1890.0000.0000.0000.000
60A60ASP -1-0.863-0.93210.2860.9130.9130.0000.0000.0000.000
61A61GLN 0-0.075-0.06312.706-0.035-0.0350.0000.0000.0000.000
62A62ILE 00.0140.00312.2500.0100.0100.0000.0000.0000.000
63A63LEU 0-0.033-0.03813.741-0.107-0.1070.0000.0000.0000.000
64A64ILE 00.0290.01210.0780.0760.0760.0000.0000.0000.000
65A65GLU -1-0.957-0.96813.955-0.556-0.5560.0000.0000.0000.000
66A66ILE 00.0480.01411.678-0.030-0.0300.0000.0000.0000.000
67A67CYS 0-0.052-0.01715.5450.0010.0010.0000.0000.0000.000
68A68GLY 00.0180.01818.4760.0420.0420.0000.0000.0000.000
69A69HIS 0-0.0030.00017.4660.0640.0640.0000.0000.0000.000
70A70LYS 10.9810.98317.1500.3890.3890.0000.0000.0000.000
71A71ALA 00.0230.01113.862-0.036-0.0360.0000.0000.0000.000
72A72ILE 0-0.0210.02413.8940.0420.0420.0000.0000.0000.000
73A73GLY 00.0410.02910.806-0.169-0.1690.0000.0000.0000.000
74A74THR 0-0.033-0.0067.286-0.046-0.0460.0000.0000.0000.000
75A75VAL 0-0.005-0.0017.074-0.068-0.0680.0000.0000.0000.000
76A76LEU 0-0.024-0.0152.675-0.5920.2940.343-0.242-0.9870.000
77A77VAL 00.0250.0266.005-0.060-0.0600.0000.0000.0000.000
78A78GLY 00.025-0.0038.4590.1660.1660.0000.0000.0000.000
79A79PRO 0-0.0390.0109.163-0.327-0.3270.0000.0000.0000.000
80A80THR 0-0.069-0.0224.0370.9641.2790.000-0.037-0.2790.000
81A81PRO 00.0660.0322.091-1.334-0.9651.549-0.400-1.517-0.001
82A82VAL 00.0770.0183.437-1.937-0.3750.138-0.385-1.3150.003
83A83ASN 0-0.046-0.0275.340-0.345-0.218-0.001-0.004-0.1220.000
84A84ILE 00.0490.0222.489-3.025-0.8553.685-0.966-4.8900.000
85A85ILE 0-0.018-0.0075.3340.4180.4180.0000.0000.0000.000
86A86GLY 00.1270.0384.446-1.265-1.137-0.001-0.018-0.1090.000
87A87ARG 10.8860.9375.2454.4034.499-0.001-0.002-0.0930.000
88A88ASN 0-0.0050.0566.026-0.217-0.2170.0000.0000.0000.000
89A89LEU 00.005-0.0168.0110.4000.4000.0000.0000.0000.000
90A90LEU 0-0.053-0.0058.2290.2890.2890.0000.0000.0000.000
91A91THR 0-0.045-0.03911.1290.2210.2210.0000.0000.0000.000
92A92GLN 0-0.066-0.04012.3230.2020.2020.0000.0000.0000.000
93A93ILE 0-0.088-0.03913.4870.1400.1400.0000.0000.0000.000
94A94GLY 00.0440.02415.5350.0870.0870.0000.0000.0000.000
95A95ALA 0-0.030-0.02513.316-0.014-0.0140.0000.0000.0000.000
96A96THR 0-0.034-0.02715.3450.0290.0290.0000.0000.0000.000
97A97LEU 0-0.062-0.0239.500-0.053-0.0530.0000.0000.0000.000
98A98ASN 00.037-0.01013.9570.0420.0420.0000.0000.0000.000
99A99PHE -1-0.858-0.89313.158-2.022-2.0220.0000.0000.0000.000
100B1PRO 10.8350.89817.4781.8071.8070.0000.0000.0000.000
101B2GLN 00.0490.05417.624-0.141-0.1410.0000.0000.0000.000
102B3VAL 0-0.0020.01013.2140.0800.0800.0000.0000.0000.000
103B4THR 00.047-0.00315.252-0.259-0.2590.0000.0000.0000.000
104B5LEU 0-0.0230.00215.1910.1780.1780.0000.0000.0000.000
105B6TRP 00.016-0.00813.562-0.094-0.0940.0000.0000.0000.000
106B7GLN 0-0.019-0.00710.6640.2880.2880.0000.0000.0000.000
107B8ARG 10.9580.9866.7781.5411.5410.0000.0000.0000.000
108B9PRO 00.0010.0188.1620.6470.6470.0000.0000.0000.000
109B10LEU 00.0270.0077.823-0.451-0.4510.0000.0000.0000.000
110B11VAL 0-0.017-0.01311.3070.3960.3960.0000.0000.0000.000
111B12THR 0-0.012-0.01813.515-0.107-0.1070.0000.0000.0000.000
112B13ILE 0-0.0120.02111.2290.1220.1220.0000.0000.0000.000
113B14LYS 10.9350.96315.3381.1181.1180.0000.0000.0000.000
114B15ILE 00.0230.02311.189-0.059-0.0590.0000.0000.0000.000
115B16GLY 00.030-0.00415.6140.1340.1340.0000.0000.0000.000
116B17GLY 00.0090.01318.1820.0330.0330.0000.0000.0000.000
117B18GLN 0-0.024-0.02216.9930.1100.1100.0000.0000.0000.000
118B19LEU 0-0.018-0.01817.497-0.104-0.1040.0000.0000.0000.000
119B20LYS 10.8890.97412.4111.6411.6410.0000.0000.0000.000
120B21GLU -1-0.944-0.9528.873-1.639-1.6390.0000.0000.0000.000
121B22ALA 00.024-0.0149.2440.0270.0270.0000.0000.0000.000
122B23LEU 0-0.0170.0063.453-0.4520.6760.054-0.247-0.9350.001
123B24LEU 0-0.044-0.0255.998-1.796-1.7960.0000.0000.0000.000
124B25ASP -1-0.666-0.7871.376-66.081-99.26867.412-26.799-7.427-0.119
125B26THR 0-0.066-0.0704.5141.2201.408-0.001-0.016-0.1710.000
126B27GLY 00.0240.0022.7812.3223.1350.210-0.363-0.6600.002
127B28ALA 0-0.057-0.0082.1183.2121.59713.158-3.956-7.588-0.002
128B29ASP -1-0.802-0.8912.348-5.305-3.3802.727-1.355-3.2960.015
129B30ASP -1-0.972-1.0191.947-12.777-11.7145.463-2.701-3.824-0.004
130B31THR 0-0.023-0.0172.823-2.534-0.9400.394-0.769-1.219-0.013
131B32VAL 0-0.0270.0153.0810.0161.7750.170-0.454-1.4760.002
132B33LEU 00.001-0.0284.625-0.472-0.3510.000-0.016-0.1050.000
133B34GLU -1-0.893-0.9577.7010.6530.6530.0000.0000.0000.000
134B35GLU -1-0.964-0.9838.6680.2930.2930.0000.0000.0000.000
135B36MET 0-0.0300.01012.163-0.102-0.1020.0000.0000.0000.000
136B37SER 0-0.016-0.01014.9730.1200.1200.0000.0000.0000.000
137B38LEU 00.004-0.01113.090-0.145-0.1450.0000.0000.0000.000
138B39PRO 0-0.0070.01116.3060.0970.0970.0000.0000.0000.000
139B40GLY 00.029-0.00117.6490.0240.0240.0000.0000.0000.000
140B41ARG 10.9350.96517.1460.7540.7540.0000.0000.0000.000
141B42TRP 00.0340.03012.566-0.092-0.0920.0000.0000.0000.000
142B43LYS 10.9300.95212.3480.4880.4880.0000.0000.0000.000
143B44PRO 00.0240.02511.364-0.090-0.0900.0000.0000.0000.000
144B45LYS 10.9090.9705.1770.8160.8160.0000.0000.0000.000
145B46MET 0-0.013-0.0297.986-0.061-0.0610.0000.0000.0000.000
146B47ILE 0-0.0150.0202.389-4.163-1.8363.632-1.337-4.6220.018
147B48GLY 00.063-0.0274.0360.0460.4790.001-0.081-0.3530.000
148B49GLY 0-0.007-0.0121.993-4.341-3.4948.444-4.821-4.4690.017
149B50ILE 0-0.0040.0112.036-6.126-19.77734.512-1.295-19.5660.036
150B51GLY 0-0.009-0.0133.942-0.5010.1780.013-0.158-0.5340.001
151B52GLY 00.0080.0026.023-2.448-2.4480.0000.0000.0000.000
152B53PHE 0-0.0290.0375.8361.7841.7840.0000.0000.0000.000
153B54ILE 00.0110.0485.523-0.394-0.3940.0000.0000.0000.000
154B55LYS 10.9340.9598.342-1.927-1.9270.0000.0000.0000.000
155B56VAL 00.0120.0025.107-0.029-0.0290.0000.0000.0000.000
156B57ARG 10.9400.9678.325-0.166-0.1660.0000.0000.0000.000
157B58GLN 0-0.031-0.0226.835-0.142-0.1420.0000.0000.0000.000
158B59TYR 00.0220.0228.7970.2730.2730.0000.0000.0000.000
159B60ASP -1-0.853-0.93110.335-1.621-1.6210.0000.0000.0000.000
160B61GLN 0-0.053-0.05412.4970.2470.2470.0000.0000.0000.000
161B62ILE 00.0390.00412.9450.1950.1950.0000.0000.0000.000
162B63LEU 0-0.050-0.02714.222-0.176-0.1760.0000.0000.0000.000
163B64ILE 00.0330.01410.9550.1140.1140.0000.0000.0000.000
164B65GLU -1-0.989-0.99714.748-1.238-1.2380.0000.0000.0000.000
165B66ILE 00.0700.03711.882-0.013-0.0130.0000.0000.0000.000
166B67CYS 0-0.025-0.02016.0870.0500.0500.0000.0000.0000.000
167B68GLY 00.0480.03218.6170.1070.1070.0000.0000.0000.000
168B69HIS 0-0.024-0.01318.4060.1180.1180.0000.0000.0000.000
169B70LYS 10.8990.94017.9940.9700.9700.0000.0000.0000.000
170B71ALA 00.0790.03914.5280.0050.0050.0000.0000.0000.000
171B72ILE 0-0.0180.02514.445-0.105-0.1050.0000.0000.0000.000
172B73GLY 00.021-0.01311.154-0.090-0.0900.0000.0000.0000.000
173B74THR 0-0.024-0.0177.0510.3240.3240.0000.0000.0000.000
174B75VAL 00.0230.0147.445-0.765-0.7650.0000.0000.0000.000
175B76LEU 00.013-0.0033.0750.1870.7630.057-0.115-0.5170.000
176B77VAL 0-0.0100.0116.526-0.043-0.0430.0000.0000.0000.000
177B78GLY 0-0.003-0.0198.9480.2490.2490.0000.0000.0000.000
178B79PRO 00.0320.0479.003-0.272-0.2720.0000.0000.0000.000
179B80THR 0-0.074-0.0123.7560.9191.3840.004-0.107-0.3610.000
180B81PRO 00.0550.0231.932-1.040-1.4202.972-0.581-2.010-0.001
181B82VAL 00.0720.0212.737-2.688-0.6280.925-0.622-2.3620.004
182B83ASN 0-0.073-0.0464.676-0.233-0.079-0.001-0.007-0.1460.000
183B84ILE 00.0360.0192.366-1.364-1.4047.213-1.412-5.7610.001
184B85ILE 0-0.024-0.0075.3260.4790.4790.0000.0000.0000.000
185B86GLY 00.1330.0574.335-2.050-1.933-0.001-0.027-0.0890.000
186B87ARG 10.8900.9425.0674.6554.773-0.001-0.003-0.1140.000
187B88ASN 00.0440.0625.896-0.312-0.3120.0000.0000.0000.000
188B89LEU 0-0.0180.0047.6390.6590.6590.0000.0000.0000.000
189B90LEU 0-0.0520.0108.0590.4900.4900.0000.0000.0000.000
190B91THR 0-0.057-0.03710.2360.4320.4320.0000.0000.0000.000
191B92GLN 0-0.032-0.01012.4300.4200.4200.0000.0000.0000.000
192B93ILE 0-0.065-0.02913.4180.2130.2130.0000.0000.0000.000
193B94GLY 00.0110.02115.5190.1210.1210.0000.0000.0000.000
194B95ALA 0-0.006-0.02212.8840.0700.0700.0000.0000.0000.000
195B96THR 0-0.038-0.05614.5430.0570.0570.0000.0000.0000.000
196B97LEU 0-0.0330.0079.072-0.006-0.0060.0000.0000.0000.000
197B98ASN 00.011-0.02113.6400.1350.1350.0000.0000.0000.000
198B99PHE -1-0.861-0.90013.728-1.408-1.4080.0000.0000.0000.000