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: 6381Z

Calculation Name: 1BVE-AB-NMR60-Model23

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 -2276124.316185
FMO2-HF: Nuclear repulsion 2199646.46345
FMO2-HF: Total energy -76477.852736
FMO2-MP2: Total energy -76703.4948


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.
-153.877-231.388300.128-99.655-122.9730.043


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.
-153.877-231.388300.128-99.655-122.973-0.043
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 : -0.044 / q_NPA : -0.168
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 10.8460.91118.1401.3621.3620.0000.0000.0000.000
2A2GLN 00.0610.05917.928-0.084-0.0840.0000.0000.0000.000
3A3VAL 00.0170.01213.5340.0660.0660.0000.0000.0000.000
4A4THR 00.027-0.00315.335-0.085-0.0850.0000.0000.0000.000
5A5LEU 0-0.019-0.01114.953-0.135-0.1350.0000.0000.0000.000
6A6TRP 00.0370.00913.5670.0160.0160.0000.0000.0000.000
7A7GLN 0-0.021-0.02011.1350.1150.1150.0000.0000.0000.000
8A8ARG 10.9000.9556.9941.4991.4990.0000.0000.0000.000
9A9PRO 00.0070.0318.1920.5520.5520.0000.0000.0000.000
10A10LEU 00.036-0.0027.717-0.388-0.3880.0000.0000.0000.000
11A11VAL 0-0.034-0.02111.2030.3790.3790.0000.0000.0000.000
12A12THR 00.004-0.01613.162-0.120-0.1200.0000.0000.0000.000
13A13ILE 0-0.0070.01011.0160.0920.0920.0000.0000.0000.000
14A14LYS 10.9400.96514.8290.7660.7660.0000.0000.0000.000
15A15ILE 00.0320.03611.0860.0370.0370.0000.0000.0000.000
16A16GLY 00.0530.00615.4840.0700.0700.0000.0000.0000.000
17A17GLY 0-0.071-0.03118.2710.0530.0530.0000.0000.0000.000
18A18GLN 0-0.011-0.00316.5900.0440.0440.0000.0000.0000.000
19A19LEU 00.019-0.00517.006-0.086-0.0860.0000.0000.0000.000
20A20LYS 10.9040.96910.3541.0141.0140.0000.0000.0000.000
21A21GLU -1-0.900-0.94210.335-1.314-1.3140.0000.0000.0000.000
22A22ALA 0-0.054-0.0249.224-0.053-0.0530.0000.0000.0000.000
23A23LEU 00.0090.0063.166-0.4540.7790.105-0.244-1.0940.001
24A24LEU 0-0.024-0.0215.879-1.812-1.8120.0000.0000.0000.000
25A25ASP -1-0.683-0.7671.296-57.549-95.93580.297-35.471-6.441-0.107
26A26THR 0-0.071-0.0614.5671.1621.362-0.001-0.013-0.1870.000
27A27GLY 00.0710.0272.9851.2801.9200.105-0.291-0.4540.000
28A28ALA 0-0.114-0.0312.0900.606-2.48812.806-3.597-6.1160.004
29A29ASP -1-0.817-0.9222.301-0.5900.5950.861-0.282-1.7640.000
30A30ASP -1-0.868-0.9692.700-1.7080.1800.426-0.815-1.4990.009
31A31THR 0-0.096-0.0363.359-4.078-3.1240.044-0.472-0.526-0.004
32A32VAL 00.0000.0083.0210.0021.3610.115-0.290-1.1850.001
33A33LEU 0-0.004-0.0174.699-0.561-0.481-0.001-0.009-0.0710.000
34A34GLU -1-0.887-0.9535.726-0.127-0.1270.0000.0000.0000.000
35A35GLU -1-0.987-0.9947.9030.2920.2920.0000.0000.0000.000
36A36MET 0-0.029-0.01011.173-0.125-0.1250.0000.0000.0000.000
37A37SER 00.0010.00914.0930.0950.0950.0000.0000.0000.000
38A38LEU 00.0580.01213.482-0.084-0.0840.0000.0000.0000.000
39A39PRO 0-0.047-0.00316.8930.0760.0760.0000.0000.0000.000
40A40GLY 00.0710.02317.933-0.048-0.0480.0000.0000.0000.000
41A41ARG 10.9260.95717.550-0.131-0.1310.0000.0000.0000.000
42A42TRP 00.0210.01913.3550.0160.0160.0000.0000.0000.000
43A43LYS 10.9150.95812.023-0.400-0.4000.0000.0000.0000.000
44A44PRO 00.0070.00711.3640.0740.0740.0000.0000.0000.000
45A45LYS 10.9200.9716.478-1.923-1.9230.0000.0000.0000.000
46A46MET 00.025-0.0018.135-0.198-0.1980.0000.0000.0000.000
47A47ILE 0-0.0180.0132.705-3.683-0.9651.705-1.017-3.4070.013
48A48GLY 00.060-0.0154.2080.0630.4020.000-0.059-0.2790.000
49A49GLY 0-0.019-0.0132.081-4.137-3.3248.054-4.387-4.4810.015
50A50ILE 0-0.0040.0092.002-4.504-19.94536.254-1.271-19.5430.028
51A51GLY 0-0.019-0.0194.036-0.2970.4070.010-0.174-0.5410.001
52A52GLY 00.0270.0096.340-1.825-1.8250.0000.0000.0000.000
53A53PHE 0-0.0050.0286.2311.6361.6360.0000.0000.0000.000
54A54ILE 00.0040.0685.654-0.577-0.5770.0000.0000.0000.000
55A55LYS 10.9460.9518.355-1.629-1.6290.0000.0000.0000.000
56A56VAL 0-0.022-0.0025.628-0.057-0.0570.0000.0000.0000.000
57A57ARG 10.9080.9638.923-0.719-0.7190.0000.0000.0000.000
58A58GLN 00.0090.0008.1930.2890.2890.0000.0000.0000.000
59A59TYR 00.0190.0179.8210.0400.0400.0000.0000.0000.000
60A60ASP -1-0.860-0.94311.6090.2030.2030.0000.0000.0000.000
61A61GLN 0-0.032-0.02913.273-0.059-0.0590.0000.0000.0000.000
62A62ILE 0-0.011-0.00712.9540.0270.0270.0000.0000.0000.000
63A63LEU 0-0.015-0.00814.248-0.095-0.0950.0000.0000.0000.000
64A64ILE 00.0040.00010.5030.0130.0130.0000.0000.0000.000
65A65GLU -1-0.921-0.97114.441-0.824-0.8240.0000.0000.0000.000
66A66ILE 00.0560.02511.823-0.095-0.0950.0000.0000.0000.000
67A67CYS 0-0.009-0.01615.8990.0680.0680.0000.0000.0000.000
68A68GLY 00.0060.01718.5050.0840.0840.0000.0000.0000.000
69A69HIS 0-0.035-0.02117.7490.1010.1010.0000.0000.0000.000
70A70LYS 10.9110.93017.7330.5950.5950.0000.0000.0000.000
71A71ALA 00.0660.05714.5950.0370.0370.0000.0000.0000.000
72A72ILE 0-0.0010.01315.0230.0080.0080.0000.0000.0000.000
73A73GLY 00.0230.01011.297-0.075-0.0750.0000.0000.0000.000
74A74THR 0-0.049-0.0188.055-0.008-0.0080.0000.0000.0000.000
75A75VAL 00.0190.0137.571-0.070-0.0700.0000.0000.0000.000
76A76LEU 0-0.018-0.0223.5910.0650.3900.007-0.048-0.2840.000
77A77VAL 0-0.0100.0077.118-0.294-0.2940.0000.0000.0000.000
78A78GLY 0-0.024-0.0509.4100.2880.2880.0000.0000.0000.000
79A79PRO 0-0.0230.0208.702-0.343-0.3430.0000.0000.0000.000
80A80THR 0-0.107-0.0183.6410.0850.7940.012-0.232-0.490-0.001
81A81PRO 00.0780.0341.982-1.053-1.2753.326-0.642-2.4620.002
82A82VAL 00.0560.0182.550-3.884-1.3442.832-1.198-4.1750.003
83A83ASN 0-0.027-0.0124.2380.0150.2560.000-0.008-0.2320.000
84A84ILE 0-0.016-0.0152.255-3.885-1.0782.971-1.064-4.7140.000
85A85ILE 0-0.0210.0075.0711.1891.385-0.001-0.007-0.1890.000
86A86GLY 00.1160.0434.520-1.059-0.970-0.001-0.015-0.0720.000
87A87ARG 10.9750.9635.3723.7693.872-0.001-0.002-0.1000.000
88A88ASN 00.0110.0806.357-0.362-0.3620.0000.0000.0000.000
89A89LEU 00.022-0.0028.1800.1640.1640.0000.0000.0000.000
90A90LEU 0-0.056-0.0028.5940.2180.2180.0000.0000.0000.000
91A91THR 0-0.024-0.05011.0150.2120.2120.0000.0000.0000.000
92A92GLN 0-0.084-0.03013.0480.2150.2150.0000.0000.0000.000
93A93ILE 0-0.056-0.01713.5010.0900.0900.0000.0000.0000.000
94A94GLY 00.0190.02115.8940.0530.0530.0000.0000.0000.000
95A95ALA 0-0.014-0.01613.6110.0010.0010.0000.0000.0000.000
96A96THR 0-0.061-0.03215.5720.0570.0570.0000.0000.0000.000
97A97LEU 0-0.015-0.0119.511-0.057-0.0570.0000.0000.0000.000
98A98ASN 00.024-0.01214.0900.0800.0800.0000.0000.0000.000
99A99PHE -1-0.824-0.90312.331-1.295-1.2950.0000.0000.0000.000
100B1PRO 10.7600.87117.7131.2631.2630.0000.0000.0000.000
101B2GLN 00.0590.05417.769-0.141-0.1410.0000.0000.0000.000
102B3VAL 00.0010.00813.7860.0980.0980.0000.0000.0000.000
103B4THR 00.0610.01715.407-0.173-0.1730.0000.0000.0000.000
104B5LEU 0-0.048-0.03812.8920.0630.0630.0000.0000.0000.000
105B6TRP 00.0180.03412.378-0.167-0.1670.0000.0000.0000.000
106B7GLN 0-0.036-0.01310.0630.0810.0810.0000.0000.0000.000
107B8ARG 10.9610.9643.8961.2501.5520.001-0.036-0.2670.000
108B9PRO 0-0.0030.0068.6710.4900.4900.0000.0000.0000.000
109B10LEU 00.0060.0097.509-0.403-0.4030.0000.0000.0000.000
110B11VAL 0-0.026-0.01010.9710.2800.2800.0000.0000.0000.000
111B12THR 0-0.014-0.01813.2230.0310.0310.0000.0000.0000.000
112B13ILE 00.0080.00912.3160.0010.0010.0000.0000.0000.000
113B14LYS 10.9410.96315.4070.4100.4100.0000.0000.0000.000
114B15ILE 00.0740.03811.532-0.012-0.0120.0000.0000.0000.000
115B16GLY 00.003-0.00816.0140.0740.0740.0000.0000.0000.000
116B17GLY 00.0050.00718.471-0.019-0.0190.0000.0000.0000.000
117B18GLN 0-0.065-0.02317.8210.0210.0210.0000.0000.0000.000
118B19LEU 00.006-0.00917.484-0.054-0.0540.0000.0000.0000.000
119B20LYS 10.9290.98212.3270.1640.1640.0000.0000.0000.000
120B21GLU -1-0.876-0.94310.483-0.989-0.9890.0000.0000.0000.000
121B22ALA 00.001-0.0149.1960.1320.1320.0000.0000.0000.000
122B23LEU 0-0.017-0.0033.023-0.9070.4100.252-0.320-1.2480.001
123B24LEU 0-0.053-0.0296.031-1.358-1.3580.0000.0000.0000.000
124B25ASP -1-0.650-0.7941.396-43.603-87.85482.947-30.445-8.250-0.095
125B26THR 0-0.100-0.0814.2630.0760.309-0.001-0.030-0.2020.000
126B27GLY 00.0220.0222.5291.1872.1750.361-0.671-0.678-0.003
127B28ALA 0-0.0330.0112.1702.6501.45412.000-3.359-7.4440.002
128B29ASP -1-0.809-0.9442.344-3.517-1.2910.493-0.777-1.9420.007
129B30ASP -1-0.908-0.9982.7380.9122.6660.263-0.665-1.3520.004
130B31THR 0-0.0470.0023.371-4.247-3.2480.043-0.493-0.549-0.004
131B32VAL 0-0.0210.0042.933-0.1861.5670.261-0.413-1.6010.001
132B33LEU 0-0.005-0.0284.637-0.615-0.5020.000-0.015-0.0980.000
133B34GLU -1-0.931-0.9457.3960.9450.9450.0000.0000.0000.000
134B35GLU -1-0.975-0.9818.4130.8040.8040.0000.0000.0000.000
135B36MET 00.0050.00011.779-0.143-0.1430.0000.0000.0000.000
136B37SER 0-0.032-0.01914.7760.0680.0680.0000.0000.0000.000
137B38LEU 00.0420.00111.681-0.088-0.0880.0000.0000.0000.000
138B39PRO 0-0.0350.00115.6330.0640.0640.0000.0000.0000.000
139B40GLY 00.0580.01517.006-0.056-0.0560.0000.0000.0000.000
140B41ARG 10.9300.95616.525-0.087-0.0870.0000.0000.0000.000
141B42TRP 00.0500.03912.2180.0330.0330.0000.0000.0000.000
142B43LYS 10.9540.96311.528-0.579-0.5790.0000.0000.0000.000
143B44PRO 0-0.0010.01810.6040.1600.1600.0000.0000.0000.000
144B45LYS 10.9350.9795.192-2.707-2.7070.0000.0000.0000.000
145B46MET 0-0.014-0.0338.040-0.105-0.1050.0000.0000.0000.000
146B47ILE 0-0.0330.0122.538-3.940-1.2412.185-1.068-3.8160.014
147B48GLY 00.0520.0034.3790.1830.5440.000-0.058-0.3040.000
148B49GLY 0-0.0130.0042.066-4.380-2.9976.002-3.672-3.7130.020
149B50ILE 0-0.015-0.0011.926-6.641-20.40136.969-3.471-19.7390.038
150B51GLY 00.022-0.0313.8380.8051.5790.008-0.116-0.6660.001
151B52GLY 0-0.0010.0006.031-2.169-2.1690.0000.0000.0000.000
152B53PHE 00.004-0.0016.0761.5401.5400.0000.0000.0000.000
153B54ILE 0-0.0020.0395.734-0.662-0.6620.0000.0000.0000.000
154B55LYS 10.9350.9628.210-1.794-1.7940.0000.0000.0000.000
155B56VAL 00.0090.0065.088-0.036-0.0360.0000.0000.0000.000
156B57ARG 10.9030.9408.352-0.816-0.8160.0000.0000.0000.000
157B58GLN 0-0.065-0.0687.203-0.011-0.0110.0000.0000.0000.000
158B59TYR 0-0.0030.0228.361-0.041-0.0410.0000.0000.0000.000
159B60ASP -1-0.820-0.89310.6780.4860.4860.0000.0000.0000.000
160B61GLN 0-0.078-0.04412.594-0.002-0.0020.0000.0000.0000.000
161B62ILE 0-0.004-0.00912.2780.0290.0290.0000.0000.0000.000
162B63LEU 0-0.058-0.03614.338-0.106-0.1060.0000.0000.0000.000
163B64ILE 00.0280.01711.3160.0380.0380.0000.0000.0000.000
164B65GLU -1-0.959-0.99015.006-0.570-0.5700.0000.0000.0000.000
165B66ILE 00.0890.03412.650-0.023-0.0230.0000.0000.0000.000
166B67CYS 0-0.037-0.02016.7220.0050.0050.0000.0000.0000.000
167B68GLY 00.0230.01319.3880.0300.0300.0000.0000.0000.000
168B69HIS 10.8910.95118.9090.9060.9060.0000.0000.0000.000
169B70LYS 10.9610.98318.7010.3610.3610.0000.0000.0000.000
170B71ALA 00.0470.02414.923-0.025-0.0250.0000.0000.0000.000
171B72ILE 0-0.0270.01515.1340.0450.0450.0000.0000.0000.000
172B73GLY 00.0260.02011.287-0.094-0.0940.0000.0000.0000.000
173B74THR 0-0.025-0.0327.727-0.021-0.0210.0000.0000.0000.000
174B75VAL 00.0160.0187.317-0.114-0.1140.0000.0000.0000.000
175B76LEU 0-0.009-0.0133.085-0.0990.4890.051-0.101-0.5380.000
176B77VAL 0-0.0040.0146.562-0.219-0.2190.0000.0000.0000.000
177B78GLY 00.016-0.0168.8380.1890.1890.0000.0000.0000.000
178B79PRO 00.0000.0238.959-0.232-0.2320.0000.0000.0000.000
179B80THR 0-0.052-0.0223.6110.6541.1790.004-0.102-0.4280.000
180B81PRO 00.0570.0271.984-1.184-1.1852.558-0.556-2.002-0.002
181B82VAL 00.0230.0012.976-2.789-0.5540.773-0.641-2.3670.006
182B83ASN 0-0.029-0.0124.851-0.0960.062-0.001-0.008-0.1500.000
183B84ILE 00.0140.0142.530-2.304-1.0665.035-1.016-5.2570.002
184B85ILE 0-0.031-0.0045.5700.6230.6230.0000.0000.0000.000
185B86GLY 00.1150.0404.705-1.189-1.118-0.001-0.014-0.0560.000
186B87ARG 10.8910.9645.5882.8672.8670.0000.0000.0000.000
187B88ASN 00.0070.0386.310-0.143-0.1430.0000.0000.0000.000
188B89LEU 00.0100.0058.3520.2050.2050.0000.0000.0000.000
189B90LEU 0-0.0270.0178.1140.1440.1440.0000.0000.0000.000
190B91THR 0-0.051-0.03511.1980.2150.2150.0000.0000.0000.000
191B92GLN 0-0.021-0.01511.9850.2100.2100.0000.0000.0000.000
192B93ILE 0-0.078-0.02813.4260.1140.1140.0000.0000.0000.000
193B94GLY 00.0300.02116.1500.0310.0310.0000.0000.0000.000
194B95ALA 0-0.002-0.00912.9580.0260.0260.0000.0000.0000.000
195B96THR 0-0.066-0.04414.9810.0450.0450.0000.0000.0000.000
196B97LEU 0-0.013-0.0029.641-0.019-0.0190.0000.0000.0000.000
197B98ASN 0-0.004-0.01714.1690.0070.0070.0000.0000.0000.000
198B99PHE -1-0.852-0.91812.779-1.411-1.4110.0000.0000.0000.000