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: 2K8QR

Calculation Name: 1BVE-AB-NMR60-Model3

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 -2292291.493163
FMO2-HF: Nuclear repulsion 2215813.792854
FMO2-HF: Total energy -76477.700309
FMO2-MP2: Total energy -76703.419819


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.
-154.364-223.915281.781-90.212-122.0150.037


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.
-154.364-223.915281.781-90.212-122.015-0.037
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 : -0.038 / q_NPA : -0.145
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 10.8310.89617.2631.3741.3740.0000.0000.0000.000
2A2GLN 00.0540.05517.679-0.150-0.1500.0000.0000.0000.000
3A3VAL 0-0.0340.00113.5350.0570.0570.0000.0000.0000.000
4A4THR 00.0750.01815.556-0.181-0.1810.0000.0000.0000.000
5A5LEU 00.014-0.01710.859-0.166-0.1660.0000.0000.0000.000
6A6TRP 00.0490.02012.674-0.087-0.0870.0000.0000.0000.000
7A7GLN 00.051-0.0048.5470.2240.2240.0000.0000.0000.000
8A8ARG 10.8900.9636.3981.6181.6180.0000.0000.0000.000
9A9PRO 0-0.066-0.0257.6850.8270.8270.0000.0000.0000.000
10A10LEU 00.0160.0108.252-0.172-0.1720.0000.0000.0000.000
11A11VAL 0-0.042-0.01611.2330.3000.3000.0000.0000.0000.000
12A12THR 0-0.016-0.00613.4890.0250.0250.0000.0000.0000.000
13A13ILE 00.0150.00211.4830.0060.0060.0000.0000.0000.000
14A14LYS 10.9160.96115.5920.5860.5860.0000.0000.0000.000
15A15ILE 00.0500.04111.432-0.005-0.0050.0000.0000.0000.000
16A16GLY 00.0080.00715.9650.0760.0760.0000.0000.0000.000
17A17GLY 0-0.034-0.02718.5860.0000.0000.0000.0000.0000.000
18A18GLN 0-0.026-0.00716.6240.0710.0710.0000.0000.0000.000
19A19LEU 00.011-0.00617.232-0.055-0.0550.0000.0000.0000.000
20A20LYS 10.9120.98011.8490.3390.3390.0000.0000.0000.000
21A21GLU -1-0.892-0.94010.111-1.097-1.0970.0000.0000.0000.000
22A22ALA 0-0.022-0.0219.3160.0060.0060.0000.0000.0000.000
23A23LEU 00.0300.0243.537-0.2710.5220.026-0.132-0.6870.000
24A24LEU 0-0.034-0.0366.043-1.533-1.5330.0000.0000.0000.000
25A25ASP -1-0.645-0.7861.492-44.548-69.18850.215-16.579-8.995-0.099
26A26THR 0-0.019-0.0194.4630.5530.764-0.001-0.011-0.2000.000
27A27GLY 00.0250.0312.9391.5752.2610.123-0.387-0.4220.000
28A28ALA 0-0.073-0.0192.1041.211-2.41913.901-3.842-6.4290.006
29A29ASP -1-0.801-0.9342.244-0.7170.2981.267-0.440-1.8420.008
30A30ASP -1-0.863-0.9682.786-1.0370.8400.354-0.778-1.4530.007
31A31THR 0-0.098-0.0513.386-4.180-3.2510.039-0.450-0.518-0.004
32A32VAL 0-0.008-0.0103.004-0.0741.3440.158-0.293-1.2830.001
33A33LEU 0-0.027-0.0094.789-0.761-0.651-0.001-0.007-0.1020.000
34A34GLU -1-0.914-0.9607.0940.1790.1790.0000.0000.0000.000
35A35GLU -1-0.975-1.0048.0570.6480.6480.0000.0000.0000.000
36A36MET 0-0.045-0.01311.368-0.084-0.0840.0000.0000.0000.000
37A37SER 0-0.025-0.00514.1800.0900.0900.0000.0000.0000.000
38A38LEU 00.048-0.00113.211-0.089-0.0890.0000.0000.0000.000
39A39PRO 0-0.0270.00417.4770.0660.0660.0000.0000.0000.000
40A40GLY 00.0440.01119.434-0.041-0.0410.0000.0000.0000.000
41A41ARG 10.8990.94518.830-0.153-0.1530.0000.0000.0000.000
42A42TRP 00.0520.03813.8020.0380.0380.0000.0000.0000.000
43A43LYS 10.9800.97413.279-0.476-0.4760.0000.0000.0000.000
44A44PRO 0-0.0080.00312.0860.0420.0420.0000.0000.0000.000
45A45LYS 10.9660.9936.349-2.717-2.7170.0000.0000.0000.000
46A46MET 0-0.040-0.0337.738-0.131-0.1310.0000.0000.0000.000
47A47ILE 0-0.0120.0242.124-2.830-1.6155.851-1.547-5.5190.016
48A48GLY 00.060-0.0294.026-0.1370.3270.002-0.092-0.3740.000
49A49GLY 0-0.021-0.0162.140-5.137-2.9386.115-4.035-4.2790.011
50A50ILE 00.0040.0221.987-6.083-17.86531.576-2.108-17.6860.036
51A51GLY 0-0.014-0.0034.142-0.0370.5300.007-0.147-0.4270.001
52A52GLY 00.0200.0086.340-1.711-1.7110.0000.0000.0000.000
53A53PHE 0-0.0060.0376.0321.4821.4820.0000.0000.0000.000
54A54ILE 00.0080.0445.435-0.293-0.2930.0000.0000.0000.000
55A55LYS 10.9140.9517.472-1.938-1.9380.0000.0000.0000.000
56A56VAL 00.0360.0225.448-0.013-0.0130.0000.0000.0000.000
57A57ARG 10.8900.9468.660-0.855-0.8550.0000.0000.0000.000
58A58GLN 00.0190.0007.5470.2820.2820.0000.0000.0000.000
59A59TYR 00.0220.0199.778-0.025-0.0250.0000.0000.0000.000
60A60ASP -1-0.897-0.95211.8230.4010.4010.0000.0000.0000.000
61A61GLN 0-0.035-0.03313.474-0.025-0.0250.0000.0000.0000.000
62A62ILE 00.0130.01013.0690.0000.0000.0000.0000.0000.000
63A63LEU 0-0.044-0.04114.486-0.097-0.0970.0000.0000.0000.000
64A64ILE 00.0670.01511.0740.0280.0280.0000.0000.0000.000
65A65GLU -1-0.985-0.99714.914-0.769-0.7690.0000.0000.0000.000
66A66ILE 00.0840.04111.985-0.043-0.0430.0000.0000.0000.000
67A67CYS 0-0.054-0.02616.1560.0380.0380.0000.0000.0000.000
68A68GLY 00.0550.03018.3230.0500.0500.0000.0000.0000.000
69A69HIS 10.8340.92118.1861.1231.1230.0000.0000.0000.000
70A70LYS 10.9780.98718.0930.4400.4400.0000.0000.0000.000
71A71ALA 00.0630.03414.676-0.006-0.0060.0000.0000.0000.000
72A72ILE 0-0.0020.02214.702-0.027-0.0270.0000.0000.0000.000
73A73GLY 00.0370.01111.581-0.075-0.0750.0000.0000.0000.000
74A74THR 00.0120.0038.260-0.060-0.0600.0000.0000.0000.000
75A75VAL 00.0140.0077.700-0.082-0.0820.0000.0000.0000.000
76A76LEU 0-0.027-0.0174.0750.0550.2860.001-0.023-0.2090.000
77A77VAL 00.0260.0277.164-0.200-0.2000.0000.0000.0000.000
78A78GLY 00.0480.0038.9620.2290.2290.0000.0000.0000.000
79A79PRO 0-0.0390.0098.596-0.301-0.3010.0000.0000.0000.000
80A80THR 0-0.078-0.0304.1240.2620.6320.001-0.059-0.3120.000
81A81PRO 00.0380.0112.057-1.211-1.0252.506-0.509-2.1820.000
82A82VAL 00.0550.0202.841-3.013-0.6371.019-0.703-2.6910.004
83A83ASN 00.0090.0114.614-0.328-0.1540.000-0.009-0.1660.000
84A84ILE 00.0000.0022.246-3.130-0.8682.638-0.836-4.0640.001
85A85ILE 0-0.0240.0075.5561.0921.0920.0000.0000.0000.000
86A86GLY 00.1000.0414.657-1.001-0.908-0.001-0.014-0.0780.000
87A87ARG 10.8380.8995.5774.2954.2950.0000.0000.0000.000
88A88ASN 00.0210.0646.366-0.390-0.3900.0000.0000.0000.000
89A89LEU 0-0.012-0.0098.3580.0840.0840.0000.0000.0000.000
90A90LEU 0-0.051-0.0168.4350.0970.0970.0000.0000.0000.000
91A91THR 0-0.002-0.03011.0800.1560.1560.0000.0000.0000.000
92A92GLN 0-0.098-0.03213.2200.1490.1490.0000.0000.0000.000
93A93ILE 0-0.084-0.03313.0210.0560.0560.0000.0000.0000.000
94A94GLY 00.0380.02515.8030.0240.0240.0000.0000.0000.000
95A95ALA 0-0.020-0.02312.760-0.021-0.0210.0000.0000.0000.000
96A96THR 0-0.074-0.03914.7370.0370.0370.0000.0000.0000.000
97A97LEU 00.007-0.0099.294-0.061-0.0610.0000.0000.0000.000
98A98ASN 0-0.017-0.03013.7980.1020.1020.0000.0000.0000.000
99A99PHE -1-0.841-0.90212.292-1.558-1.5580.0000.0000.0000.000
100B1PRO 10.8360.90317.3481.3671.3670.0000.0000.0000.000
101B2GLN 00.0470.04917.382-0.126-0.1260.0000.0000.0000.000
102B3VAL 00.0120.01212.9970.0790.0790.0000.0000.0000.000
103B4THR 00.0450.01414.729-0.171-0.1710.0000.0000.0000.000
104B5LEU 0-0.008-0.02711.4640.1480.1480.0000.0000.0000.000
105B6TRP 00.0220.03210.972-0.170-0.1700.0000.0000.0000.000
106B7GLN 0-0.0330.0028.6420.3030.3030.0000.0000.0000.000
107B8ARG 10.9910.9854.718-0.1200.064-0.001-0.005-0.1780.000
108B9PRO 0-0.022-0.0047.9370.4480.4480.0000.0000.0000.000
109B10LEU 0-0.012-0.0017.490-0.392-0.3920.0000.0000.0000.000
110B11VAL 0-0.011-0.00510.6030.2790.2790.0000.0000.0000.000
111B12THR 0-0.021-0.01313.079-0.036-0.0360.0000.0000.0000.000
112B13ILE 00.0020.00411.7300.0290.0290.0000.0000.0000.000
113B14LYS 10.9550.97015.1720.7190.7190.0000.0000.0000.000
114B15ILE 00.0540.03311.299-0.001-0.0010.0000.0000.0000.000
115B16GLY 0-0.004-0.00115.5980.0910.0910.0000.0000.0000.000
116B17GLY 0-0.054-0.02718.1520.0540.0540.0000.0000.0000.000
117B18GLN 00.0400.01917.3320.0220.0220.0000.0000.0000.000
118B19LEU 0-0.044-0.02617.148-0.083-0.0830.0000.0000.0000.000
119B20LYS 10.9300.97912.1540.4410.4410.0000.0000.0000.000
120B21GLU -1-0.902-0.9399.435-0.814-0.8140.0000.0000.0000.000
121B22ALA 00.000-0.0158.918-0.098-0.0980.0000.0000.0000.000
122B23LEU 0-0.0320.0052.991-0.8770.5820.289-0.325-1.4230.001
123B24LEU 0-0.012-0.0235.928-1.534-1.5340.0000.0000.0000.000
124B25ASP -1-0.688-0.8091.395-52.083-105.946101.148-39.775-7.510-0.099
125B26THR 0-0.076-0.0684.0880.0770.385-0.001-0.053-0.2530.000
126B27GLY 00.0210.0072.3020.3691.4461.083-0.961-1.1990.002
127B28ALA 0-0.0550.0062.1833.0301.62311.507-2.574-7.5260.003
128B29ASP -1-0.838-0.9233.185-7.458-5.3540.126-0.588-1.642-0.003
129B30ASP -1-0.873-0.9802.8460.6872.3190.181-0.588-1.2250.001
130B31THR 0-0.051-0.0253.225-4.617-3.3710.082-0.653-0.675-0.006
131B32VAL 0-0.0140.0032.258-0.0701.4841.445-0.580-2.4190.001
132B33LEU 0-0.021-0.0134.417-0.587-0.4400.001-0.025-0.1220.000
133B34GLU -1-0.918-0.9767.5470.5840.5840.0000.0000.0000.000
134B35GLU -1-0.939-0.9638.6500.8480.8480.0000.0000.0000.000
135B36MET 0-0.042-0.03511.853-0.138-0.1380.0000.0000.0000.000
136B37SER 0-0.038-0.00914.3780.0630.0630.0000.0000.0000.000
137B38LEU 00.0530.01612.077-0.098-0.0980.0000.0000.0000.000
138B39PRO 00.0160.01216.0720.0690.0690.0000.0000.0000.000
139B40GLY 0-0.034-0.03317.644-0.001-0.0010.0000.0000.0000.000
140B41ARG 10.9710.97516.3890.0670.0670.0000.0000.0000.000
141B42TRP 00.0110.04112.339-0.014-0.0140.0000.0000.0000.000
142B43LYS 10.9520.96811.804-0.386-0.3860.0000.0000.0000.000
143B44PRO 00.0140.01510.9660.0800.0800.0000.0000.0000.000
144B45LYS 10.9660.9935.874-3.042-3.0420.0000.0000.0000.000
145B46MET 0-0.011-0.0177.947-0.030-0.0300.0000.0000.0000.000
146B47ILE 0-0.0300.0072.529-3.977-0.8892.020-1.144-3.9640.014
147B48GLY 00.0750.0004.345-0.2060.1550.000-0.051-0.3100.000
148B49GLY 0-0.026-0.0082.113-4.199-2.6405.853-3.586-3.8260.019
149B50ILE 0-0.017-0.0081.989-7.687-21.12037.260-3.926-19.9010.039
150B51GLY 00.005-0.0183.9420.3351.0750.008-0.145-0.6030.001
151B52GLY 0-0.003-0.0036.069-2.169-2.1690.0000.0000.0000.000
152B53PHE 0-0.0220.0106.0831.5621.5620.0000.0000.0000.000
153B54ILE 00.0100.0195.658-0.519-0.5190.0000.0000.0000.000
154B55LYS 10.9340.9548.311-1.650-1.6500.0000.0000.0000.000
155B56VAL 00.0250.0175.038-0.053-0.0530.0000.0000.0000.000
156B57ARG 10.9030.9448.166-0.507-0.5070.0000.0000.0000.000
157B58GLN 0-0.028-0.0347.7590.1530.1530.0000.0000.0000.000
158B59TYR 00.0040.0128.695-0.018-0.0180.0000.0000.0000.000
159B60ASP -1-0.836-0.90910.4390.0090.0090.0000.0000.0000.000
160B61GLN 0-0.035-0.04712.626-0.058-0.0580.0000.0000.0000.000
161B62ILE 0-0.025-0.01612.1640.0740.0740.0000.0000.0000.000
162B63LEU 0-0.080-0.02513.795-0.152-0.1520.0000.0000.0000.000
163B64ILE 00.0520.00910.6840.0950.0950.0000.0000.0000.000
164B65GLU -1-0.989-0.99314.428-0.936-0.9360.0000.0000.0000.000
165B66ILE 00.0890.03312.011-0.044-0.0440.0000.0000.0000.000
166B67CYS 0-0.061-0.02315.4740.0360.0360.0000.0000.0000.000
167B68GLY 00.0460.04218.2960.0800.0800.0000.0000.0000.000
168B69HIS 0-0.001-0.01218.1570.0570.0570.0000.0000.0000.000
169B70LYS 10.9160.94017.7370.6610.6610.0000.0000.0000.000
170B71ALA 00.0960.04814.3990.0170.0170.0000.0000.0000.000
171B72ILE 0-0.0340.01014.254-0.051-0.0510.0000.0000.0000.000
172B73GLY 00.0510.02311.109-0.105-0.1050.0000.0000.0000.000
173B74THR 0-0.009-0.0067.9530.0950.0950.0000.0000.0000.000
174B75VAL 00.0140.0017.143-0.333-0.3330.0000.0000.0000.000
175B76LEU 0-0.022-0.0152.958-0.3520.5030.127-0.193-0.7880.000
176B77VAL 0-0.0040.0056.101-0.248-0.2480.0000.0000.0000.000
177B78GLY 00.0320.0008.1680.3070.3070.0000.0000.0000.000
178B79PRO 0-0.0330.0168.962-0.296-0.2960.0000.0000.0000.000
179B80THR 0-0.080-0.0153.9410.4210.8860.003-0.102-0.3660.000
180B81PRO 00.0470.0202.024-1.015-0.8191.920-0.434-1.683-0.002
181B82VAL 00.0580.0143.049-2.298-0.3000.540-0.510-2.0280.004
182B83ASN 0-0.044-0.0184.924-0.273-0.109-0.001-0.007-0.1560.000
183B84ILE 0-0.010-0.0122.211-3.410-0.7152.396-0.980-4.1110.000
184B85ILE 0-0.0260.0075.3190.5580.754-0.001-0.006-0.1890.000
185B86GLY 00.1470.0474.807-0.754-0.7540.0000.0000.0000.000
186B87ARG 10.8580.9465.6164.9674.9670.0000.0000.0000.000
187B88ASN 00.0170.0556.117-0.184-0.1840.0000.0000.0000.000
188B89LEU 0-0.033-0.0148.1740.5830.5830.0000.0000.0000.000
189B90LEU 0-0.0140.0057.9430.4450.4450.0000.0000.0000.000
190B91THR 00.0300.01011.6690.2960.2960.0000.0000.0000.000
191B92GLN 0-0.112-0.04812.7730.2940.2940.0000.0000.0000.000
192B93ILE 0-0.106-0.02913.2980.1650.1650.0000.0000.0000.000
193B94GLY 00.0210.01716.3560.0560.0560.0000.0000.0000.000
194B95ALA 00.001-0.00413.3290.0290.0290.0000.0000.0000.000
195B96THR 0-0.056-0.03915.3600.0480.0480.0000.0000.0000.000
196B97LEU 0-0.017-0.0049.400-0.017-0.0170.0000.0000.0000.000
197B98ASN 0-0.023-0.03813.9620.0240.0240.0000.0000.0000.000
198B99PHE -1-0.875-0.90613.866-1.339-1.3390.0000.0000.0000.000