Manual

About

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

tag_button

FMODB ID: 1J8KZ

Calculation Name: 1BVE-AB-NMR60-Model14

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 -2290492.707884
FMO2-HF: Nuclear repulsion 2214014.539029
FMO2-HF: Total energy -76478.168855
FMO2-MP2: Total energy -76703.941516


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.
-147.982-216.054278.414-88.562-121.778-0.053


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.
-147.982-216.054278.414-88.562-121.7780.053
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 : 0.051 / q_NPA : 0.010
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 10.8040.89418.5240.4510.4510.0000.0000.0000.000
2A2GLN 00.0620.06017.761-0.030-0.0300.0000.0000.0000.000
3A3VAL 00.0240.02013.1280.0400.0400.0000.0000.0000.000
4A4THR 00.013-0.00214.284-0.139-0.1390.0000.0000.0000.000
5A5LEU 00.0070.00614.081-0.062-0.0620.0000.0000.0000.000
6A6TRP 00.013-0.01113.350-0.002-0.0020.0000.0000.0000.000
7A7GLN 00.0650.03610.1170.0420.0420.0000.0000.0000.000
8A8ARG 10.9090.9616.7320.4680.4680.0000.0000.0000.000
9A9PRO 0-0.0040.0198.4940.2260.2260.0000.0000.0000.000
10A10LEU 00.0100.0027.523-0.018-0.0180.0000.0000.0000.000
11A11VAL 0-0.042-0.01311.2700.0230.0230.0000.0000.0000.000
12A12THR 00.0280.00413.5550.0400.0400.0000.0000.0000.000
13A13ILE 0-0.0070.01411.5550.0060.0060.0000.0000.0000.000
14A14LYS 10.9660.97515.4790.0190.0190.0000.0000.0000.000
15A15ILE 00.0480.02611.2750.0040.0040.0000.0000.0000.000
16A16GLY 00.008-0.00615.5590.0170.0170.0000.0000.0000.000
17A17GLY 0-0.041-0.01317.7730.0020.0020.0000.0000.0000.000
18A18GLN 0-0.051-0.02017.5150.0050.0050.0000.0000.0000.000
19A19LEU 0-0.001-0.01717.039-0.017-0.0170.0000.0000.0000.000
20A20LYS 10.8950.95511.697-0.206-0.2060.0000.0000.0000.000
21A21GLU -1-0.853-0.93410.382-0.118-0.1180.0000.0000.0000.000
22A22ALA 0-0.016-0.0119.1860.0800.0800.0000.0000.0000.000
23A23LEU 0-0.027-0.0073.689-0.932-0.0590.041-0.164-0.7500.001
24A24LEU 0-0.039-0.0116.1240.0350.0350.0000.0000.0000.000
25A25ASH 0-0.028-0.0941.309-15.907-63.17485.198-35.028-2.9020.046
26A26THR 0-0.031-0.0364.9520.4320.596-0.001-0.005-0.1580.000
27A27GLY 00.0450.0362.403-0.623-0.0240.888-0.652-0.8350.002
28A28ALA 0-0.043-0.0022.3240.0920.8878.376-2.231-6.9390.005
29A29ASP -1-0.862-0.9482.132-6.299-5.9624.652-1.588-3.4000.021
30A30ASP -1-0.861-0.9672.361-2.698-1.3812.150-0.998-2.4690.007
31A31THR 0-0.098-0.0283.166-3.694-2.4150.089-0.631-0.738-0.006
32A32VAL 0-0.0010.0013.239-0.7510.3610.051-0.210-0.9520.001
33A33LEU 0-0.032-0.0265.072-0.0700.020-0.001-0.004-0.0860.000
34A34GLU -1-0.870-0.9576.5890.5430.5430.0000.0000.0000.000
35A35GLU -1-0.972-1.0057.9540.6120.6120.0000.0000.0000.000
36A36MET 0-0.037-0.00511.428-0.082-0.0820.0000.0000.0000.000
37A37SER 0-0.014-0.00114.1050.0290.0290.0000.0000.0000.000
38A38LEU 00.032-0.00313.114-0.037-0.0370.0000.0000.0000.000
39A39PRO 00.0230.03817.0940.0090.0090.0000.0000.0000.000
40A40GLY 00.0680.04817.7650.0360.0360.0000.0000.0000.000
41A41ARG 10.9320.94917.824-0.224-0.2240.0000.0000.0000.000
42A42TRP 00.0160.05213.1970.0180.0180.0000.0000.0000.000
43A43LYS 10.9330.95712.355-0.369-0.3690.0000.0000.0000.000
44A44PRO 00.0240.01711.5480.0580.0580.0000.0000.0000.000
45A45LYS 10.9450.9834.940-0.752-0.7520.0000.0000.0000.000
46A46MET 0-0.003-0.0108.235-0.017-0.0170.0000.0000.0000.000
47A47ILE 0-0.0020.0172.434-3.570-0.9750.791-0.850-2.5360.006
48A48GLY 00.075-0.0074.5630.5420.810-0.001-0.036-0.2320.000
49A49GLY 0-0.033-0.0102.094-4.502-3.2335.515-3.301-3.4820.016
50A50ILE 0-0.020-0.0051.951-7.423-21.52238.242-4.184-19.9590.035
51A51GLY 00.016-0.0243.8610.2030.9720.008-0.124-0.6530.001
52A52GLY 00.0150.0086.063-1.925-1.9250.0000.0000.0000.000
53A53PHE 0-0.0150.0196.1191.5541.5540.0000.0000.0000.000
54A54ILE 0-0.0140.0335.923-0.323-0.3230.0000.0000.0000.000
55A55LYS 10.9000.9388.572-1.390-1.3900.0000.0000.0000.000
56A56VAL 00.0340.0095.7100.0580.0580.0000.0000.0000.000
57A57ARG 10.9130.9638.879-0.708-0.7080.0000.0000.0000.000
58A58GLN 0-0.011-0.0347.246-0.040-0.0400.0000.0000.0000.000
59A59TYR 0-0.058-0.0809.231-0.051-0.0510.0000.0000.0000.000
60A60ASP -1-0.807-0.88011.1690.5710.5710.0000.0000.0000.000
61A61GLN 0-0.056-0.04312.612-0.024-0.0240.0000.0000.0000.000
62A62ILE 0-0.012-0.01212.738-0.026-0.0260.0000.0000.0000.000
63A63LEU 0-0.069-0.03414.113-0.012-0.0120.0000.0000.0000.000
64A64ILE 00.045-0.00411.3050.0180.0180.0000.0000.0000.000
65A65GLU -1-0.988-0.99015.249-0.098-0.0980.0000.0000.0000.000
66A66ILE 00.0440.03212.124-0.002-0.0020.0000.0000.0000.000
67A67CYS 0-0.036-0.02616.341-0.038-0.0380.0000.0000.0000.000
68A68GLY 00.0460.01918.7370.0270.0270.0000.0000.0000.000
69A69HIS 0-0.0150.00518.8740.0090.0090.0000.0000.0000.000
70A70LYS 10.9510.96818.4360.0240.0240.0000.0000.0000.000
71A71ALA 00.0590.03214.902-0.012-0.0120.0000.0000.0000.000
72A72ILE 0-0.0220.01915.1570.0230.0230.0000.0000.0000.000
73A73GLY 00.0290.01311.260-0.018-0.0180.0000.0000.0000.000
74A74THR 0-0.022-0.0307.607-0.098-0.0980.0000.0000.0000.000
75A75VAL 0-0.0030.0067.2540.1310.1310.0000.0000.0000.000
76A76LEU 0-0.028-0.0233.792-0.1860.1140.004-0.040-0.2640.000
77A77VAL 00.0170.0267.3210.0060.0060.0000.0000.0000.000
78A78GLY 00.0410.0079.2750.0420.0420.0000.0000.0000.000
79A79PRO 0-0.0320.0098.531-0.158-0.1580.0000.0000.0000.000
80A80THR 0-0.0580.0073.306-0.6870.3600.043-0.420-0.670-0.003
81A81PRO 00.0420.0212.109-1.170-1.0823.188-0.664-2.6120.001
82A82VAL 00.0240.0012.286-2.784-1.2643.436-1.066-3.8900.003
83A83ASN 0-0.0270.0074.377-0.1510.0460.000-0.016-0.1810.000
84A84ILE 0-0.007-0.0212.140-1.578-2.0326.778-1.097-5.228-0.001
85A85ILE 0-0.0070.0215.938-0.072-0.0720.0000.0000.0000.000
86A86GLY 00.1060.0354.463-0.545-0.413-0.001-0.019-0.1130.000
87A87ARG 10.8840.9295.3010.2480.386-0.001-0.003-0.1340.000
88A88ASN 00.0070.0346.142-0.299-0.2990.0000.0000.0000.000
89A89LEU 0-0.015-0.0248.150-0.218-0.2180.0000.0000.0000.000
90A90LEU 0-0.053-0.0068.179-0.213-0.2130.0000.0000.0000.000
91A91THR 0-0.012-0.00811.121-0.105-0.1050.0000.0000.0000.000
92A92GLN 0-0.043-0.00913.004-0.029-0.0290.0000.0000.0000.000
93A93ILE 0-0.046-0.01713.787-0.015-0.0150.0000.0000.0000.000
94A94GLY 00.0460.02716.052-0.024-0.0240.0000.0000.0000.000
95A95ALA 0-0.016-0.02013.114-0.053-0.0530.0000.0000.0000.000
96A96THR 0-0.083-0.03915.149-0.029-0.0290.0000.0000.0000.000
97A97LEU 0-0.021-0.0239.108-0.049-0.0490.0000.0000.0000.000
98A98ASN 00.031-0.00613.689-0.032-0.0320.0000.0000.0000.000
99A99PHE -1-0.867-0.90512.355-1.127-1.1270.0000.0000.0000.000
100B1PRO 10.8090.88317.3431.0431.0430.0000.0000.0000.000
101B2GLN 00.0710.06117.212-0.064-0.0640.0000.0000.0000.000
102B3VAL 00.0000.00512.7940.0220.0220.0000.0000.0000.000
103B4THR 00.0560.01814.428-0.107-0.1070.0000.0000.0000.000
104B5LEU 0-0.016-0.02111.8410.1330.1330.0000.0000.0000.000
105B6TRP 00.0280.03111.391-0.018-0.0180.0000.0000.0000.000
106B7GLN 0-0.028-0.0089.0560.2210.2210.0000.0000.0000.000
107B8ARG 11.0101.0066.1851.5661.5660.0000.0000.0000.000
108B9PRO 0-0.0080.0027.7010.2650.2650.0000.0000.0000.000
109B10LEU 00.007-0.0047.371-0.518-0.5180.0000.0000.0000.000
110B11VAL 0-0.014-0.01410.6460.3840.3840.0000.0000.0000.000
111B12THR 00.009-0.01012.733-0.122-0.1220.0000.0000.0000.000
112B13ILE 0-0.0040.00110.9580.1190.1190.0000.0000.0000.000
113B14LYS 10.9680.97115.0340.7100.7100.0000.0000.0000.000
114B15ILE 00.0300.03611.3110.0340.0340.0000.0000.0000.000
115B16GLY 0-0.0040.00115.7570.0680.0680.0000.0000.0000.000
116B17GLY 00.003-0.00918.6680.0320.0320.0000.0000.0000.000
117B18GLN 0-0.083-0.03117.3560.0160.0160.0000.0000.0000.000
118B19LEU 0-0.004-0.01317.007-0.040-0.0400.0000.0000.0000.000
119B20LYS 10.9650.99411.3200.8580.8580.0000.0000.0000.000
120B21GLU -1-0.901-0.95410.025-1.535-1.5350.0000.0000.0000.000
121B22ALA 00.002-0.0318.706-0.113-0.1130.0000.0000.0000.000
122B23LEU 0-0.0300.0153.207-0.8610.6910.180-0.398-1.3330.002
123B24LEU 00.008-0.0185.399-2.457-2.4570.0000.0000.0000.000
124B25ASP -1-0.642-0.7701.621-66.719-92.23755.495-19.263-10.714-0.146
125B26THR 0-0.074-0.0654.2600.5420.747-0.001-0.032-0.1730.000
126B27GLY 00.0330.0083.4091.1731.9940.034-0.361-0.4930.001
127B28ALA 0-0.076-0.0112.0860.765-0.28310.549-3.384-6.1180.003
128B29ASP -1-0.850-0.9502.283-0.6370.9810.903-0.688-1.8320.003
129B30ASP -1-0.930-0.9862.701-1.5470.2440.487-0.765-1.5120.008
130B31THR 0-0.068-0.0603.541-4.030-3.2930.026-0.329-0.435-0.002
131B32VAL 0-0.043-0.0042.969-0.2571.4180.210-0.394-1.4910.001
132B33LEU 0-0.008-0.0184.536-0.445-0.3350.000-0.016-0.0940.000
133B34GLU -1-0.921-0.9767.5380.0000.0000.0000.0000.0000.000
134B35GLU -1-0.924-0.9638.431-0.068-0.0680.0000.0000.0000.000
135B36MET 0-0.037-0.02411.875-0.158-0.1580.0000.0000.0000.000
136B37SER 0-0.0060.00914.8250.1020.1020.0000.0000.0000.000
137B38LEU 0-0.030-0.01312.136-0.019-0.0190.0000.0000.0000.000
138B39PRO 00.0380.02215.8950.0600.0600.0000.0000.0000.000
139B40GLY 00.0350.00817.1920.0200.0200.0000.0000.0000.000
140B41ARG 10.9170.95117.0120.1270.1270.0000.0000.0000.000
141B42TRP 00.0000.02812.2970.0030.0030.0000.0000.0000.000
142B43LYS 10.9490.97111.710-0.132-0.1320.0000.0000.0000.000
143B44PRO 00.0230.01710.9200.0380.0380.0000.0000.0000.000
144B45LYS 10.9220.9756.296-1.273-1.2730.0000.0000.0000.000
145B46MET 0-0.023-0.0278.035-0.077-0.0770.0000.0000.0000.000
146B47ILE 0-0.0270.0222.483-3.353-0.5771.237-0.984-3.0290.009
147B48GLY 00.0390.0153.9150.2130.7080.003-0.103-0.3950.000
148B49GLY 0-0.007-0.0081.980-5.438-4.79210.242-5.691-5.1980.016
149B50ILE 00.0060.0091.951-4.287-18.35131.1140.442-17.4920.023
150B51GLY 0-0.006-0.0194.0780.4211.0530.009-0.146-0.4940.001
151B52GLY 00.0080.0046.002-1.900-1.9000.0000.0000.0000.000
152B53PHE 00.030-0.0115.7421.5011.5010.0000.0000.0000.000
153B54ILE 0-0.0170.0515.467-0.458-0.4580.0000.0000.0000.000
154B55LYS 10.9420.9607.702-1.170-1.1700.0000.0000.0000.000
155B56VAL 00.007-0.0225.397-0.016-0.0160.0000.0000.0000.000
156B57ARG 10.9480.9728.478-0.096-0.0960.0000.0000.0000.000
157B58GLN 0-0.051-0.0417.8550.0050.0050.0000.0000.0000.000
158B59TYR 00.008-0.0178.7990.0580.0580.0000.0000.0000.000
159B60ASP -1-0.819-0.89310.890-0.009-0.0090.0000.0000.0000.000
160B61GLN 0-0.021-0.01712.588-0.002-0.0020.0000.0000.0000.000
161B62ILE 0-0.016-0.00512.4770.0310.0310.0000.0000.0000.000
162B63LEU 0-0.026-0.03214.098-0.084-0.0840.0000.0000.0000.000
163B64ILE 00.0300.01310.5090.0160.0160.0000.0000.0000.000
164B65GLU -1-0.932-0.96814.311-0.765-0.7650.0000.0000.0000.000
165B66ILE 00.0500.01311.999-0.167-0.1670.0000.0000.0000.000
166B67CYS 0-0.055-0.01915.2260.1190.1190.0000.0000.0000.000
167B68GLY 00.0300.02418.0090.0870.0870.0000.0000.0000.000
168B69HIS 10.8910.93618.1740.9570.9570.0000.0000.0000.000
169B70LYS 11.0031.00117.8290.4240.4240.0000.0000.0000.000
170B71ALA 00.0250.02014.3670.0200.0200.0000.0000.0000.000
171B72ILE 0-0.0070.00914.337-0.054-0.0540.0000.0000.0000.000
172B73GLY 00.023-0.00111.157-0.057-0.0570.0000.0000.0000.000
173B74THR 0-0.002-0.0117.699-0.040-0.0400.0000.0000.0000.000
174B75VAL 00.0120.0057.276-0.119-0.1190.0000.0000.0000.000
175B76LEU 0-0.011-0.0233.105-0.0390.4870.050-0.088-0.4870.000
176B77VAL 00.0280.0216.583-0.356-0.3560.0000.0000.0000.000
177B78GLY 0-0.014-0.0058.8340.3070.3070.0000.0000.0000.000
178B79PRO 0-0.0150.0218.586-0.294-0.2940.0000.0000.0000.000
179B80THR 0-0.0440.0113.743-0.1260.5440.011-0.218-0.463-0.001
180B81PRO 00.0420.0211.980-0.783-1.2593.704-0.693-2.535-0.003
181B82VAL 00.0250.0012.792-3.506-0.7861.531-0.887-3.3640.006
182B83ASN 0-0.0400.0144.552-0.230-0.0180.000-0.013-0.1980.000
183B84ILE 0-0.042-0.0322.204-3.376-0.8403.187-1.203-4.521-0.003
184B85ILE 00.0110.0295.1671.2701.447-0.001-0.006-0.1700.000
185B86GLY 00.1460.0374.754-1.087-1.021-0.001-0.011-0.0540.000
186B87ARG 10.8870.9225.6783.0023.0020.0000.0000.0000.000
187B88ASN 00.0980.1046.343-0.326-0.3260.0000.0000.0000.000
188B89LEU 0-0.039-0.0188.1480.1940.1940.0000.0000.0000.000
189B90LEU 0-0.064-0.0027.9790.1960.1960.0000.0000.0000.000
190B91THR 0-0.045-0.01211.4680.2310.2310.0000.0000.0000.000
191B92GLN 0-0.014-0.00313.2380.1480.1480.0000.0000.0000.000
192B93ILE 0-0.073-0.02512.5070.0920.0920.0000.0000.0000.000
193B94GLY 00.0410.03015.8270.0510.0510.0000.0000.0000.000
194B95ALA 0-0.009-0.02812.2520.0270.0270.0000.0000.0000.000
195B96THR 0-0.061-0.04614.2310.1030.1030.0000.0000.0000.000
196B97LEU 0-0.0190.0059.094-0.022-0.0220.0000.0000.0000.000
197B98ASN 0-0.024-0.02913.6550.1380.1380.0000.0000.0000.000
198B99PHE -1-0.800-0.87613.950-0.449-0.4490.0000.0000.0000.000