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: LL9K9

Calculation Name: 1BVE-AB-NMR60-Model28

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 -2268634.477596
FMO2-HF: Nuclear repulsion 2192156.764758
FMO2-HF: Total energy -76477.712839
FMO2-MP2: Total energy -76703.262546


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.
-165.526-221.116264.744-86.855-122.3090.054


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.
-165.526-221.116264.744-86.855-122.309-0.054
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 : -0.052 / q_NPA : -0.172
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 10.8440.90417.9261.2091.2090.0000.0000.0000.000
2A2GLN 00.0170.03317.979-0.087-0.0870.0000.0000.0000.000
3A3VAL 00.0060.01613.6840.0980.0980.0000.0000.0000.000
4A4THR 00.0500.02015.326-0.146-0.1460.0000.0000.0000.000
5A5LEU 0-0.031-0.02516.039-0.071-0.0710.0000.0000.0000.000
6A6TRP 00.0220.00414.4520.0090.0090.0000.0000.0000.000
7A7GLN 0-0.0020.00512.4970.0900.0900.0000.0000.0000.000
8A8ARG 10.9130.9565.6760.6870.6870.0000.0000.0000.000
9A9PRO 00.0450.0328.7560.3700.3700.0000.0000.0000.000
10A10LEU 0-0.021-0.0088.520-0.342-0.3420.0000.0000.0000.000
11A11VAL 0-0.020-0.00811.6950.2160.2160.0000.0000.0000.000
12A12THR 0-0.013-0.01313.5110.0270.0270.0000.0000.0000.000
13A13ILE 00.0070.01111.0430.0190.0190.0000.0000.0000.000
14A14LYS 10.9340.94814.8600.4760.4760.0000.0000.0000.000
15A15ILE 00.0490.03610.600-0.005-0.0050.0000.0000.0000.000
16A16GLY 00.0250.01114.8940.0770.0770.0000.0000.0000.000
17A17GLY 0-0.055-0.02417.2100.0300.0300.0000.0000.0000.000
18A18GLN 00.0490.01916.7710.0550.0550.0000.0000.0000.000
19A19LEU 0-0.043-0.02517.126-0.079-0.0790.0000.0000.0000.000
20A20LYS 10.9070.96112.298-0.139-0.1390.0000.0000.0000.000
21A21GLU -1-0.892-0.93510.784-0.686-0.6860.0000.0000.0000.000
22A22ALA 00.021-0.0039.3920.0660.0660.0000.0000.0000.000
23A23LEU 0-0.0160.0083.608-0.1340.5630.017-0.092-0.6220.000
24A24LEU 0-0.025-0.0206.003-1.567-1.5670.0000.0000.0000.000
25A25ASP -1-0.695-0.7831.345-51.355-90.55677.676-31.502-6.974-0.106
26A26THR 0-0.074-0.0104.4320.6600.883-0.001-0.028-0.1950.000
27A27GLY 00.0160.0212.3560.8141.7180.670-0.741-0.833-0.001
28A28ALA 0-0.0370.0082.0831.0690.9838.775-2.428-6.2610.003
29A29ASP -1-0.882-0.9572.649-6.896-4.7340.152-0.625-1.689-0.001
30A30ASP -1-0.879-0.9712.5991.1153.3171.101-1.114-2.1900.010
31A31THR 0-0.087-0.0453.108-5.264-3.8660.173-0.640-0.931-0.007
32A32VAL 0-0.0170.0052.396-0.9331.2381.558-0.819-2.9100.003
33A33LEU 0-0.014-0.0263.762-0.880-0.6810.014-0.028-0.1860.000
34A34GLU -1-0.952-0.9807.4941.7251.7250.0000.0000.0000.000
35A35GLU -1-0.927-0.9769.1441.4851.4850.0000.0000.0000.000
36A36MET 0-0.065-0.04012.317-0.181-0.1810.0000.0000.0000.000
37A37SER 0-0.043-0.01614.6480.0960.0960.0000.0000.0000.000
38A38LEU 00.0090.00511.625-0.079-0.0790.0000.0000.0000.000
39A39PRO 00.0020.01115.3970.0260.0260.0000.0000.0000.000
40A40GLY 00.029-0.01716.4690.0530.0530.0000.0000.0000.000
41A41ARG 10.9480.97817.088-0.266-0.2660.0000.0000.0000.000
42A42TRP 00.0580.06612.5380.0410.0410.0000.0000.0000.000
43A43LYS 10.9370.94612.337-0.880-0.8800.0000.0000.0000.000
44A44PRO 0-0.0240.01111.4010.1660.1660.0000.0000.0000.000
45A45LYS 10.9040.9577.350-2.166-2.1660.0000.0000.0000.000
46A46MET 0-0.005-0.0308.236-0.189-0.1890.0000.0000.0000.000
47A47ILE 0-0.0110.0252.683-3.768-1.0101.717-0.974-3.5010.013
48A48GLY 00.0410.0054.3150.1640.5130.000-0.061-0.2880.000
49A49GLY 0-0.0070.0002.039-4.962-4.0608.397-4.690-4.6090.020
50A50ILE 0-0.022-0.0051.975-5.352-21.18437.962-1.973-20.1580.030
51A51GLY 00.021-0.0073.9110.4301.2830.010-0.170-0.6920.001
52A52GLY 0-0.0020.0066.181-2.310-2.3100.0000.0000.0000.000
53A53PHE 0-0.009-0.0176.2761.5651.5650.0000.0000.0000.000
54A54ILE 00.0060.0395.639-0.778-0.7780.0000.0000.0000.000
55A55LYS 10.9540.9778.328-2.370-2.3700.0000.0000.0000.000
56A56VAL 00.0260.0085.4680.0700.0700.0000.0000.0000.000
57A57ARG 10.9090.9528.559-1.312-1.3120.0000.0000.0000.000
58A58GLN 00.0370.0106.3070.3510.3510.0000.0000.0000.000
59A59TYR 00.011-0.0058.918-0.140-0.1400.0000.0000.0000.000
60A60ASP -1-0.840-0.93410.7330.7920.7920.0000.0000.0000.000
61A61GLN 0-0.045-0.03412.111-0.025-0.0250.0000.0000.0000.000
62A62ILE 0-0.020-0.00711.7130.0060.0060.0000.0000.0000.000
63A63LEU 0-0.070-0.05313.494-0.097-0.0970.0000.0000.0000.000
64A64ILE 00.0220.01310.1420.0540.0540.0000.0000.0000.000
65A65GLU -1-0.933-0.97313.916-0.696-0.6960.0000.0000.0000.000
66A66ILE 00.0460.01711.423-0.042-0.0420.0000.0000.0000.000
67A67CYS 0-0.052-0.02915.770-0.013-0.0130.0000.0000.0000.000
68A68GLY 0-0.0210.00418.8880.0260.0260.0000.0000.0000.000
69A69HIS 00.0590.04018.3400.0650.0650.0000.0000.0000.000
70A70LYS 10.9190.94517.7140.3050.3050.0000.0000.0000.000
71A71ALA 00.0370.02613.583-0.030-0.0300.0000.0000.0000.000
72A72ILE 0-0.0320.00013.9750.0520.0520.0000.0000.0000.000
73A73GLY 00.0400.01210.397-0.132-0.1320.0000.0000.0000.000
74A74THR 0-0.030-0.0087.306-0.116-0.1160.0000.0000.0000.000
75A75VAL 00.0010.0066.7370.1200.1200.0000.0000.0000.000
76A76LEU 0-0.027-0.0152.888-0.4700.1700.088-0.106-0.6220.000
77A77VAL 0-0.0020.0106.141-0.190-0.1900.0000.0000.0000.000
78A78GLY 00.018-0.0038.5210.1580.1580.0000.0000.0000.000
79A79PRO 0-0.0120.0249.136-0.268-0.2680.0000.0000.0000.000
80A80THR 0-0.096-0.0144.2040.8571.1590.000-0.036-0.2670.000
81A81PRO 00.0740.0321.978-1.098-1.3002.654-0.586-1.866-0.001
82A82VAL 00.0400.0053.499-1.919-0.3970.119-0.360-1.2810.003
83A83ASN 0-0.011-0.0195.374-0.0980.032-0.001-0.004-0.1250.000
84A84ILE 00.0040.0012.077-3.251-0.9464.517-1.417-5.4050.000
85A85ILE 00.0140.0164.6780.5510.819-0.001-0.014-0.2540.000
86A86GLY 00.1150.0204.148-1.085-0.9470.000-0.029-0.1080.000
87A87ARG 10.8870.9464.9593.7083.829-0.001-0.004-0.1160.000
88A88ASN 00.0260.0865.790-0.289-0.2890.0000.0000.0000.000
89A89LEU 00.008-0.0057.5780.3130.3130.0000.0000.0000.000
90A90LEU 0-0.0210.0008.3970.2810.2810.0000.0000.0000.000
91A91THR 0-0.054-0.04410.8430.2340.2340.0000.0000.0000.000
92A92GLN 0-0.066-0.01712.3370.2800.2800.0000.0000.0000.000
93A93ILE 0-0.017-0.00613.1950.1180.1180.0000.0000.0000.000
94A94GLY 0-0.0050.01115.3270.0560.0560.0000.0000.0000.000
95A95ALA 00.008-0.01513.0070.0180.0180.0000.0000.0000.000
96A96THR 0-0.087-0.08014.9560.0610.0610.0000.0000.0000.000
97A97LEU 0-0.0090.0109.8510.0100.0100.0000.0000.0000.000
98A98ASN 0-0.006-0.01914.297-0.001-0.0010.0000.0000.0000.000
99A99PHE -1-0.820-0.89213.165-1.470-1.4700.0000.0000.0000.000
100B1PRO 10.8150.89718.4551.4181.4180.0000.0000.0000.000
101B2GLN 00.0620.05518.228-0.115-0.1150.0000.0000.0000.000
102B3VAL 00.0150.02113.8530.0650.0650.0000.0000.0000.000
103B4THR 00.0160.01214.942-0.152-0.1520.0000.0000.0000.000
104B5LEU 00.024-0.01015.548-0.111-0.1110.0000.0000.0000.000
105B6TRP 00.018-0.00515.182-0.051-0.0510.0000.0000.0000.000
106B7GLN 00.0250.00911.609-0.051-0.0510.0000.0000.0000.000
107B8ARG 10.9180.9767.4232.2982.2980.0000.0000.0000.000
108B9PRO 00.0220.0198.6200.4500.4500.0000.0000.0000.000
109B10LEU 00.0250.0029.322-0.327-0.3270.0000.0000.0000.000
110B11VAL 0-0.007-0.00711.8020.3490.3490.0000.0000.0000.000
111B12THR 00.010-0.00714.156-0.082-0.0820.0000.0000.0000.000
112B13ILE 00.0120.01611.7400.0790.0790.0000.0000.0000.000
113B14LYS 10.9490.96815.1980.9530.9530.0000.0000.0000.000
114B15ILE 00.0600.03511.023-0.026-0.0260.0000.0000.0000.000
115B16GLY 00.017-0.00315.5050.1010.1010.0000.0000.0000.000
116B17GLY 0-0.058-0.02018.2200.0880.0880.0000.0000.0000.000
117B18GLN 0-0.047-0.01917.6330.0450.0450.0000.0000.0000.000
118B19LEU 00.013-0.01117.491-0.062-0.0620.0000.0000.0000.000
119B20LYS 10.8980.96212.9950.8300.8300.0000.0000.0000.000
120B21GLU -1-0.887-0.94311.770-1.450-1.4500.0000.0000.0000.000
121B22ALA 0-0.030-0.0159.688-0.059-0.0590.0000.0000.0000.000
122B23LEU 0-0.0090.0014.4200.3390.6350.000-0.013-0.2830.000
123B24LEU 0-0.016-0.0256.259-1.443-1.4430.0000.0000.0000.000
124B25ASP -1-0.688-0.7971.438-47.840-70.60648.779-18.284-7.729-0.095
125B26THR 0-0.083-0.0944.5561.2641.434-0.001-0.011-0.1590.000
126B27GLY 00.0140.0092.5060.8261.7310.480-0.660-0.725-0.002
127B28ALA 0-0.0380.0032.0860.565-0.76511.964-3.618-7.0170.001
128B29ASP -1-0.834-0.9392.395-4.969-3.4191.963-1.007-2.5070.011
129B30ASP -1-0.933-1.0041.978-11.079-10.1095.352-2.818-3.5050.003
130B31THR 0-0.0320.0023.161-0.7320.1320.093-0.245-0.712-0.005
131B32VAL 0-0.0120.0123.036-0.0171.3800.127-0.320-1.2030.001
132B33LEU 0-0.005-0.0284.668-0.474-0.3770.000-0.010-0.0860.000
133B34GLU -1-0.899-0.9747.1310.3660.3660.0000.0000.0000.000
134B35GLU -1-0.992-0.9998.1200.3750.3750.0000.0000.0000.000
135B36MET 00.008-0.00111.303-0.172-0.1720.0000.0000.0000.000
136B37SER 0-0.029-0.02014.4450.0500.0500.0000.0000.0000.000
137B38LEU 0-0.0040.00513.526-0.069-0.0690.0000.0000.0000.000
138B39PRO 00.0080.02017.0880.0620.0620.0000.0000.0000.000
139B40GLY 00.0720.02218.447-0.065-0.0650.0000.0000.0000.000
140B41ARG 10.9080.94717.9320.1310.1310.0000.0000.0000.000
141B42TRP 00.0280.02913.376-0.020-0.0200.0000.0000.0000.000
142B43LYS 10.9650.96912.9800.2460.2460.0000.0000.0000.000
143B44PRO 00.0000.01611.818-0.071-0.0710.0000.0000.0000.000
144B45LYS 10.9400.9836.4780.2840.2840.0000.0000.0000.000
145B46MET 0-0.010-0.0348.530-0.059-0.0590.0000.0000.0000.000
146B47ILE 0-0.0230.0142.628-3.821-1.0910.597-0.923-2.4030.009
147B48GLY 00.0310.0134.1620.1990.5370.000-0.059-0.2790.000
148B49GLY 00.0090.0062.131-4.841-2.5704.693-3.427-3.5370.011
149B50ILE 0-0.0230.0081.990-7.489-20.42336.300-4.138-19.2290.044
150B51GLY 00.010-0.0073.8840.0880.7790.007-0.107-0.5900.001
151B52GLY 00.0100.0146.324-2.079-2.0790.0000.0000.0000.000
152B53PHE 00.024-0.0205.9741.7111.7110.0000.0000.0000.000
153B54ILE 0-0.0050.0425.717-0.706-0.7060.0000.0000.0000.000
154B55LYS 10.9450.9718.346-1.879-1.8790.0000.0000.0000.000
155B56VAL 0-0.007-0.0195.9080.0060.0060.0000.0000.0000.000
156B57ARG 10.9240.9569.138-0.235-0.2350.0000.0000.0000.000
157B58GLN 0-0.034-0.0188.5830.0000.0000.0000.0000.0000.000
158B59TYR 00.0150.0039.5440.2130.2130.0000.0000.0000.000
159B60ASP -1-0.810-0.86910.504-1.436-1.4360.0000.0000.0000.000
160B61GLN 0-0.081-0.04512.2590.1620.1620.0000.0000.0000.000
161B62ILE 00.0280.00612.9500.1470.1470.0000.0000.0000.000
162B63LEU 0-0.051-0.05513.987-0.129-0.1290.0000.0000.0000.000
163B64ILE 00.0200.01210.2260.0550.0550.0000.0000.0000.000
164B65GLU -1-0.955-0.98114.143-1.105-1.1050.0000.0000.0000.000
165B66ILE 00.0470.02111.543-0.074-0.0740.0000.0000.0000.000
166B67CYS 0-0.044-0.02915.4280.0920.0920.0000.0000.0000.000
167B68GLY 00.0200.01418.2570.1220.1220.0000.0000.0000.000
168B69HIS 00.0030.00518.0380.0690.0690.0000.0000.0000.000
169B70LYS 10.9430.98517.7010.7590.7590.0000.0000.0000.000
170B71ALA 00.0490.02013.9210.0200.0200.0000.0000.0000.000
171B72ILE 0-0.0520.02114.3270.0570.0570.0000.0000.0000.000
172B73GLY 00.0210.00510.473-0.094-0.0940.0000.0000.0000.000
173B74THR 0-0.038-0.0706.9700.2770.2770.0000.0000.0000.000
174B75VAL 0-0.0030.0077.118-0.648-0.6480.0000.0000.0000.000
175B76LEU 0-0.022-0.0223.2790.3300.7180.021-0.069-0.3410.000
176B77VAL 00.0140.0196.9800.0470.0470.0000.0000.0000.000
177B78GLY 0-0.001-0.0069.3250.2240.2240.0000.0000.0000.000
178B79PRO 0-0.0190.0158.302-0.293-0.2930.0000.0000.0000.000
179B80THR 0-0.0570.0103.4970.5931.3220.016-0.235-0.510-0.001
180B81PRO 00.0730.0371.964-0.414-2.3926.366-1.189-3.200-0.003
181B82VAL 00.0490.0173.326-2.289-0.5380.224-0.396-1.5790.004
182B83ASN 0-0.058-0.0215.189-0.182-0.038-0.001-0.006-0.1380.000
183B84ILE 0-0.002-0.0012.508-3.072-0.3462.171-0.846-4.0510.000
184B85ILE 0-0.040-0.0115.0350.2140.394-0.001-0.007-0.1720.000
185B86GLY 00.1130.0414.335-0.798-0.659-0.001-0.022-0.1160.000
186B87ARG 10.9090.9325.1592.0322.191-0.001-0.004-0.1550.000
187B88ASN 0-0.0120.0555.827-0.150-0.1500.0000.0000.0000.000
188B89LEU 00.007-0.0047.4940.4010.4010.0000.0000.0000.000
189B90LEU 00.0170.0218.6100.3850.3850.0000.0000.0000.000
190B91THR 0-0.044-0.05210.2780.2770.2770.0000.0000.0000.000
191B92GLN 0-0.093-0.03412.3550.2820.2820.0000.0000.0000.000
192B93ILE 0-0.057-0.02413.1360.1400.1400.0000.0000.0000.000
193B94GLY 00.0230.02815.2670.0950.0950.0000.0000.0000.000
194B95ALA 0-0.005-0.01813.7690.0600.0600.0000.0000.0000.000
195B96THR 0-0.084-0.04615.7560.1070.1070.0000.0000.0000.000
196B97LEU 0-0.0100.0019.680-0.023-0.0230.0000.0000.0000.000
197B98ASN 00.032-0.01414.0380.0850.0850.0000.0000.0000.000
198B99PHE -1-0.851-0.90212.948-1.403-1.4030.0000.0000.0000.000