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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: 9YK92

Calculation Name: 1BVE-AB-NMR60-Model7

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 -2277235.644179
FMO2-HF: Nuclear repulsion 2200758.496178
FMO2-HF: Total energy -76477.148
FMO2-MP2: Total energy -76702.882788


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.
-162.228-165.611177.292-51.927-121.9900.005


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.
-162.228-165.611177.292-51.927-121.99-0.005
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 : -0.005 / q_NPA : -0.056
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 10.8140.90018.3181.5161.5160.0000.0000.0000.000
2A2GLN 00.0730.06218.093-0.127-0.1270.0000.0000.0000.000
3A3VAL 00.0020.00913.5240.0760.0760.0000.0000.0000.000
4A4THR 0-0.015-0.01215.199-0.261-0.2610.0000.0000.0000.000
5A5LEU 00.0150.02214.4530.1340.1340.0000.0000.0000.000
6A6TRP 00.015-0.02014.159-0.073-0.0730.0000.0000.0000.000
7A7GLN 0-0.0100.00911.8710.1410.1410.0000.0000.0000.000
8A8ARG 10.9720.9728.3811.5551.5550.0000.0000.0000.000
9A9PRO 00.0140.0239.0220.5450.5450.0000.0000.0000.000
10A10LEU 00.0340.0028.345-0.425-0.4250.0000.0000.0000.000
11A11VAL 0-0.026-0.02411.7940.2830.2830.0000.0000.0000.000
12A12THR 00.009-0.00113.680-0.041-0.0410.0000.0000.0000.000
13A13ILE 00.0100.01811.0640.0840.0840.0000.0000.0000.000
14A14LYS 10.9630.97315.1580.6090.6090.0000.0000.0000.000
15A15ILE 00.0540.03410.8860.0050.0050.0000.0000.0000.000
16A16GLY 0-0.005-0.01215.2590.0580.0580.0000.0000.0000.000
17A17GLY 0-0.070-0.02317.4780.0380.0380.0000.0000.0000.000
18A18GLN 00.0430.01716.9670.0230.0230.0000.0000.0000.000
19A19LEU 0-0.034-0.02117.467-0.080-0.0800.0000.0000.0000.000
20A20LYS 10.8930.96111.2650.2800.2800.0000.0000.0000.000
21A21GLU -1-0.927-0.94711.262-0.972-0.9720.0000.0000.0000.000
22A22ALA 0-0.020-0.0139.4150.0410.0410.0000.0000.0000.000
23A23LEU 0-0.0270.0113.485-0.4160.4830.025-0.194-0.7300.001
24A24LEU 0-0.025-0.0116.558-1.239-1.2390.0000.0000.0000.000
25A25ASP -1-0.696-0.8722.235-43.179-36.9483.475-4.283-5.424-0.052
26A26THR 0-0.097-0.0304.8491.5511.675-0.001-0.007-0.1170.000
27A27GLY 00.0940.0342.9241.7972.5300.126-0.329-0.5310.001
28A28ALA 0-0.082-0.0192.1060.9021.9497.929-3.080-5.8960.003
29A29ASP -1-0.900-0.9652.057-3.087-2.4383.371-1.290-2.7300.014
30A30ASP -1-0.900-0.9972.273-2.672-1.7172.438-1.163-2.2300.012
31A31THR 0-0.079-0.0183.043-4.846-3.4040.152-0.722-0.872-0.007
32A32VAL 0-0.0120.0042.979-0.2211.2580.170-0.335-1.3140.001
33A33LEU 0-0.009-0.0224.569-0.626-0.5300.000-0.013-0.0830.000
34A34GLU -1-0.957-1.0077.8860.9160.9160.0000.0000.0000.000
35A35GLU -1-0.964-0.9828.7410.7300.7300.0000.0000.0000.000
36A36MET 0-0.0050.00011.948-0.136-0.1360.0000.0000.0000.000
37A37SER 0-0.0020.00715.0130.0790.0790.0000.0000.0000.000
38A38LEU 0-0.006-0.00412.436-0.100-0.1000.0000.0000.0000.000
39A39PRO 00.0030.02016.1700.0750.0750.0000.0000.0000.000
40A40GLY 00.0210.00117.563-0.041-0.0410.0000.0000.0000.000
41A41ARG 10.9170.94917.886-0.110-0.1100.0000.0000.0000.000
42A42TRP 00.0200.03213.2590.0340.0340.0000.0000.0000.000
43A43LYS 10.9510.95912.720-0.570-0.5700.0000.0000.0000.000
44A44PRO 00.0130.01911.7890.0810.0810.0000.0000.0000.000
45A45LYS 10.9530.9844.859-2.344-2.3440.0000.0000.0000.000
46A46MET 00.000-0.0118.017-0.009-0.0090.0000.0000.0000.000
47A47ILE 0-0.0090.0122.653-3.927-0.9650.842-0.965-2.8390.011
48A48GLY 00.055-0.0164.2770.5100.8510.000-0.054-0.2870.000
49A49GLY 0-0.027-0.0102.055-5.005-3.7286.657-3.913-4.0220.019
50A50ILE 0-0.0190.0031.990-6.500-21.11637.280-2.975-19.6890.036
51A51GLY 0-0.008-0.0183.9410.2571.0430.008-0.159-0.6360.001
52A52GLY 00.0390.0146.133-2.320-2.3200.0000.0000.0000.000
53A53PHE 0-0.0100.0316.1311.6411.6410.0000.0000.0000.000
54A54ILE 0-0.0350.0205.649-0.737-0.7370.0000.0000.0000.000
55A55LYS 10.9390.9498.276-2.748-2.7480.0000.0000.0000.000
56A56VAL 00.0290.0275.498-0.004-0.0040.0000.0000.0000.000
57A57ARG 10.9190.9618.830-1.226-1.2260.0000.0000.0000.000
58A58GLN 0-0.058-0.0658.3010.1710.1710.0000.0000.0000.000
59A59TYR 00.0280.0079.268-0.071-0.0710.0000.0000.0000.000
60A60ASP -1-0.812-0.86411.1010.5640.5640.0000.0000.0000.000
61A61GLN 0-0.047-0.04412.759-0.092-0.0920.0000.0000.0000.000
62A62ILE 0-0.001-0.00212.5200.0040.0040.0000.0000.0000.000
63A63LEU 0-0.040-0.02513.907-0.088-0.0880.0000.0000.0000.000
64A64ILE 00.016-0.00310.3160.0290.0290.0000.0000.0000.000
65A65GLU -1-0.985-1.00514.243-0.844-0.8440.0000.0000.0000.000
66A66ILE 00.0760.03811.265-0.053-0.0530.0000.0000.0000.000
67A67CYS 0-0.057-0.02015.488-0.029-0.0290.0000.0000.0000.000
68A68GLY 00.0470.03518.5070.0550.0550.0000.0000.0000.000
69A69HIS 0-0.009-0.00517.6960.1300.1300.0000.0000.0000.000
70A70LYS 10.9090.92117.6020.4610.4610.0000.0000.0000.000
71A71ALA 00.0750.06214.3460.0180.0180.0000.0000.0000.000
72A72ILE 0-0.0370.01414.6800.0690.0690.0000.0000.0000.000
73A73GLY 00.010-0.00510.816-0.093-0.0930.0000.0000.0000.000
74A74THR 0-0.039-0.0287.576-0.055-0.0550.0000.0000.0000.000
75A75VAL 00.0030.0047.2160.0660.0660.0000.0000.0000.000
76A76LEU 0-0.051-0.0263.072-0.1770.3580.044-0.095-0.4840.000
77A77VAL 00.0380.0266.751-0.130-0.1300.0000.0000.0000.000
78A78GLY 00.012-0.0349.3080.1340.1340.0000.0000.0000.000
79A79PRO 0-0.0240.0168.918-0.257-0.2570.0000.0000.0000.000
80A80THR 0-0.0710.0144.1680.9251.2220.000-0.039-0.2590.000
81A81PRO 00.0540.0221.938-0.953-1.4163.101-0.628-2.011-0.001
82A82VAL 00.0850.0313.250-2.589-0.6630.289-0.484-1.7310.005
83A83ASN 0-0.053-0.0325.105-0.218-0.066-0.001-0.007-0.1450.000
84A84ILE 00.000-0.0012.076-2.835-0.3312.779-1.042-4.240-0.005
85A85ILE 00.0170.0224.9751.0421.213-0.001-0.007-0.1640.000
86A86GLY 00.1250.0314.225-1.561-1.4090.000-0.023-0.1280.000
87A87ARG 10.8600.8975.0583.6093.739-0.001-0.004-0.1260.000
88A88ASN 00.0310.0456.122-0.376-0.3760.0000.0000.0000.000
89A89LEU 00.012-0.0017.8500.0480.0480.0000.0000.0000.000
90A90LEU 0-0.0460.0297.8610.0970.0970.0000.0000.0000.000
91A91THR 0-0.058-0.02611.2560.1730.1730.0000.0000.0000.000
92A92GLN 0-0.007-0.00212.6590.1280.1280.0000.0000.0000.000
93A93ILE 0-0.063-0.02312.8840.0590.0590.0000.0000.0000.000
94A94GLY 00.0410.02315.3310.0630.0630.0000.0000.0000.000
95A95ALA 0-0.030-0.04212.538-0.035-0.0350.0000.0000.0000.000
96A96THR 0-0.073-0.03614.6350.0230.0230.0000.0000.0000.000
97A97LEU 00.016-0.0059.375-0.124-0.1240.0000.0000.0000.000
98A98ASN 00.021-0.00913.9210.0870.0870.0000.0000.0000.000
99A99PHE -1-0.813-0.89312.418-1.845-1.8450.0000.0000.0000.000
100B1PRO 10.8210.89917.7851.6831.6830.0000.0000.0000.000
101B2GLN 00.0560.05317.626-0.171-0.1710.0000.0000.0000.000
102B3VAL 0-0.010-0.00313.8250.1230.1230.0000.0000.0000.000
103B4THR 00.0450.02214.911-0.193-0.1930.0000.0000.0000.000
104B5LEU 0-0.023-0.02315.267-0.112-0.1120.0000.0000.0000.000
105B6TRP 00.040-0.00313.6330.0190.0190.0000.0000.0000.000
106B7GLN 0-0.0070.02011.4620.1750.1750.0000.0000.0000.000
107B8ARG 10.9860.9857.3281.0921.0920.0000.0000.0000.000
108B9PRO 00.0070.0278.4300.5210.5210.0000.0000.0000.000
109B10LEU 0-0.011-0.0108.274-0.445-0.4450.0000.0000.0000.000
110B11VAL 00.0050.00611.3730.3200.3200.0000.0000.0000.000
111B12THR 0-0.002-0.01113.259-0.018-0.0180.0000.0000.0000.000
112B13ILE 00.0080.00211.4980.0160.0160.0000.0000.0000.000
113B14LYS 10.9490.95915.1900.8070.8070.0000.0000.0000.000
114B15ILE 00.0510.05110.917-0.014-0.0140.0000.0000.0000.000
115B16GLY 00.012-0.00815.3450.1020.1020.0000.0000.0000.000
116B17GLY 0-0.073-0.02317.6380.0700.0700.0000.0000.0000.000
117B18GLN 00.0200.00216.9580.1050.1050.0000.0000.0000.000
118B19LEU 0-0.032-0.01617.519-0.090-0.0900.0000.0000.0000.000
119B20LYS 10.9080.97312.1100.4600.4600.0000.0000.0000.000
120B21GLU -1-0.886-0.94610.161-1.287-1.2870.0000.0000.0000.000
121B22ALA 00.029-0.0129.3010.0680.0680.0000.0000.0000.000
122B23LEU 0-0.0350.0043.780-0.3130.4270.018-0.130-0.6290.000
123B24LEU 0-0.029-0.0226.168-1.765-1.7650.0000.0000.0000.000
124B25ASP -1-0.684-0.8321.695-63.807-78.48436.945-12.018-10.250-0.111
125B26THR 0-0.123-0.0914.368-0.2100.012-0.001-0.029-0.1910.000
126B27GLY 00.0270.0172.5911.8062.7420.920-0.683-1.1720.004
127B28ALA 0-0.0160.0082.1284.3432.31312.997-3.308-7.659-0.006
128B29ASP -1-0.904-0.9662.557-5.029-3.1810.222-0.520-1.549-0.001
129B30ASP -1-0.890-0.9792.7510.8072.8610.875-0.952-1.9770.007
130B31THR 0-0.104-0.0423.228-5.634-4.3840.094-0.625-0.719-0.006
131B32VAL 0-0.035-0.0163.0060.3012.0360.194-0.437-1.4920.001
132B33LEU 00.004-0.0254.659-0.682-0.5610.000-0.014-0.1070.000
133B34GLU -1-0.970-0.9857.3980.8180.8180.0000.0000.0000.000
134B35GLU -1-0.890-0.9568.3880.3150.3150.0000.0000.0000.000
135B36MET 00.0170.01111.853-0.226-0.2260.0000.0000.0000.000
136B37SER 0-0.0030.01114.7180.1120.1120.0000.0000.0000.000
137B38LEU 00.0320.01612.418-0.114-0.1140.0000.0000.0000.000
138B39PRO 0-0.0070.00816.4970.0590.0590.0000.0000.0000.000
139B40GLY 0-0.026-0.02518.1860.0250.0250.0000.0000.0000.000
140B41ARG 10.9550.96917.754-0.074-0.0740.0000.0000.0000.000
141B42TRP 00.0450.04013.0260.0120.0120.0000.0000.0000.000
142B43LYS 10.9590.96812.644-0.508-0.5080.0000.0000.0000.000
143B44PRO 0-0.0120.00611.3630.0790.0790.0000.0000.0000.000
144B45LYS 10.9340.9845.804-2.647-2.6470.0000.0000.0000.000
145B46MET 0-0.014-0.0338.216-0.104-0.1040.0000.0000.0000.000
146B47ILE 0-0.0370.0042.727-3.688-0.8410.679-0.957-2.5700.011
147B48GLY 00.077-0.0164.052-0.0560.3480.001-0.068-0.3370.000
148B49GLY 0-0.008-0.0042.078-4.979-3.2526.696-4.207-4.2160.015
149B50ILE 0-0.0230.0042.004-6.877-20.52335.459-2.728-19.0850.040
150B51GLY 00.021-0.0103.919-0.0530.6630.007-0.131-0.5930.001
151B52GLY 0-0.0090.0106.488-1.925-1.9250.0000.0000.0000.000
152B53PHE 00.0010.0266.0101.9351.9350.0000.0000.0000.000
153B54ILE 00.0070.0475.809-0.858-0.8580.0000.0000.0000.000
154B55LYS 10.9350.9618.259-1.988-1.9880.0000.0000.0000.000
155B56VAL 00.015-0.0025.547-0.038-0.0380.0000.0000.0000.000
156B57ARG 10.8100.8928.821-0.793-0.7930.0000.0000.0000.000
157B58GLN 00.000-0.0057.3990.1000.1000.0000.0000.0000.000
158B59TYR 00.0170.0128.9600.0200.0200.0000.0000.0000.000
159B60ASP -1-0.834-0.92410.690-0.001-0.0010.0000.0000.0000.000
160B61GLN 0-0.049-0.04612.9050.0230.0230.0000.0000.0000.000
161B62ILE 00.013-0.00312.3100.0800.0800.0000.0000.0000.000
162B63LEU 0-0.065-0.04313.946-0.141-0.1410.0000.0000.0000.000
163B64ILE 00.0440.00010.1660.0820.0820.0000.0000.0000.000
164B65GLU -1-0.956-0.98714.139-1.080-1.0800.0000.0000.0000.000
165B66ILE 00.0540.01211.689-0.043-0.0430.0000.0000.0000.000
166B67CYS 0-0.051-0.01315.589-0.008-0.0080.0000.0000.0000.000
167B68GLY 00.0280.02218.3350.0840.0840.0000.0000.0000.000
168B69HIS 0-0.0050.00418.5740.1440.1440.0000.0000.0000.000
169B70LYS 10.9260.96117.8320.6060.6060.0000.0000.0000.000
170B71ALA 00.0550.02914.302-0.008-0.0080.0000.0000.0000.000
171B72ILE 0-0.0210.01914.261-0.027-0.0270.0000.0000.0000.000
172B73GLY 00.007-0.01111.142-0.141-0.1410.0000.0000.0000.000
173B74THR 0-0.0060.0037.1730.0410.0410.0000.0000.0000.000
174B75VAL 00.0220.0217.113-0.265-0.2650.0000.0000.0000.000
175B76LEU 0-0.047-0.0153.3850.1890.6980.027-0.089-0.4470.000
176B77VAL 00.0340.0366.695-0.143-0.1430.0000.0000.0000.000
177B78GLY 00.002-0.0179.1700.2590.2590.0000.0000.0000.000
178B79PRO 0-0.0480.0078.585-0.330-0.3300.0000.0000.0000.000
179B80THR 0-0.0350.0053.5950.8441.4330.009-0.162-0.436-0.001
180B81PRO 00.0530.0271.961-1.027-1.6283.789-0.742-2.446-0.003
181B82VAL 00.0410.0022.974-2.775-0.5990.636-0.600-2.2110.006
182B83ASN 0-0.056-0.0214.940-0.0750.077-0.001-0.008-0.1430.000
183B84ILE 00.0380.0192.252-1.624-1.9939.045-1.695-6.981-0.001
184B85ILE 0-0.0100.0005.2200.5710.5710.0000.0000.0000.000
185B86GLY 00.1630.0474.497-1.853-1.748-0.001-0.013-0.0920.000
186B87ARG 10.8900.9325.4146.8776.8770.0000.0000.0000.000
187B88ASN 00.0670.0936.043-0.206-0.2060.0000.0000.0000.000
188B89LEU 0-0.035-0.0087.9330.5250.5250.0000.0000.0000.000
189B90LEU 0-0.039-0.0068.0370.3980.3980.0000.0000.0000.000
190B91THR 0-0.031-0.02611.3400.4190.4190.0000.0000.0000.000
191B92GLN 0-0.053-0.01412.8580.3090.3090.0000.0000.0000.000
192B93ILE 0-0.080-0.02412.7040.1420.1420.0000.0000.0000.000
193B94GLY 00.0190.02215.7000.0960.0960.0000.0000.0000.000
194B95ALA 0-0.012-0.01613.0500.0540.0540.0000.0000.0000.000
195B96THR 0-0.057-0.05915.1490.1260.1260.0000.0000.0000.000
196B97LEU 0-0.0160.0149.601-0.029-0.0290.0000.0000.0000.000
197B98ASN 0-0.040-0.04514.1430.2030.2030.0000.0000.0000.000
198B99PHE -1-0.828-0.89414.177-1.568-1.5680.0000.0000.0000.000