FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: KRM43

Calculation Name: 1BVE-AB-NMR60-Model19

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 -2278947.640409
FMO2-HF: Nuclear repulsion 2202470.184642
FMO2-HF: Total energy -76477.455768
FMO2-MP2: Total energy -76703.204217


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.
-162.071-214.262258.382-75.988-130.2020.034


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.
-162.071-214.262258.382-75.988-130.202-0.034
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 : -0.034 / q_NPA : -0.099
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 10.8330.89418.0721.5091.5090.0000.0000.0000.000
2A2GLN 00.0650.06117.522-0.117-0.1170.0000.0000.0000.000
3A3VAL 0-0.0060.00213.5450.0780.0780.0000.0000.0000.000
4A4THR 00.0400.01114.775-0.166-0.1660.0000.0000.0000.000
5A5LEU 0-0.066-0.03013.846-0.092-0.0920.0000.0000.0000.000
6A6TRP 00.0410.01614.051-0.034-0.0340.0000.0000.0000.000
7A7GLN 00.0140.00311.1840.1370.1370.0000.0000.0000.000
8A8ARG 10.8630.9176.4981.7681.7680.0000.0000.0000.000
9A9PRO 00.0340.0288.1540.5520.5520.0000.0000.0000.000
10A10LEU 00.005-0.0038.406-0.500-0.5000.0000.0000.0000.000
11A11VAL 0-0.002-0.00311.6520.3780.3780.0000.0000.0000.000
12A12THR 0-0.018-0.02213.692-0.090-0.0900.0000.0000.0000.000
13A13ILE 00.0200.01011.4780.0670.0670.0000.0000.0000.000
14A14LYS 10.9160.95515.4190.9070.9070.0000.0000.0000.000
15A15ILE 00.0540.03011.0310.0180.0180.0000.0000.0000.000
16A16GLY 00.016-0.00115.3380.0640.0640.0000.0000.0000.000
17A17GLY 0-0.048-0.01117.6040.0520.0520.0000.0000.0000.000
18A18GLN 00.0300.01017.0850.0310.0310.0000.0000.0000.000
19A19LEU 0-0.041-0.03217.437-0.072-0.0720.0000.0000.0000.000
20A20LYS 10.9200.98212.2140.8080.8080.0000.0000.0000.000
21A21GLU -1-0.909-0.94510.672-1.359-1.3590.0000.0000.0000.000
22A22ALA 00.015-0.0159.344-0.017-0.0170.0000.0000.0000.000
23A23LEU 0-0.034-0.0103.6080.0750.7400.014-0.088-0.5920.000
24A24LEU 0-0.007-0.0215.892-2.159-2.1590.0000.0000.0000.000
25A25ASP -1-0.682-0.7791.346-72.584-120.24192.004-35.454-8.893-0.142
26A26THR 0-0.047-0.0514.3800.9481.186-0.001-0.029-0.2090.000
27A27GLY 00.0390.0392.8442.1942.9920.120-0.306-0.6110.001
28A28ALA 0-0.090-0.0282.0723.530-0.60214.346-3.830-6.3830.005
29A29ASP -1-0.873-0.9672.188-3.294-2.7733.213-1.167-2.5670.016
30A30ASP -1-0.860-0.9782.725-3.277-1.7020.323-0.636-1.2620.007
31A31THR 0-0.083-0.0193.568-3.465-2.8120.016-0.299-0.370-0.002
32A32VAL 0-0.009-0.0063.0010.1191.3260.095-0.237-1.0650.000
33A33LEU 00.016-0.0074.715-0.519-0.440-0.001-0.009-0.0690.000
34A34GLU -1-0.864-0.9517.266-0.265-0.2650.0000.0000.0000.000
35A35GLU -1-0.884-0.9678.3110.2170.2170.0000.0000.0000.000
36A36MET 00.0090.01211.524-0.190-0.1900.0000.0000.0000.000
37A37SER 0-0.001-0.00314.6570.1290.1290.0000.0000.0000.000
38A38LEU 00.0050.01213.116-0.082-0.0820.0000.0000.0000.000
39A39PRO 00.0100.01716.4320.0480.0480.0000.0000.0000.000
40A40GLY 00.0270.00018.2420.0410.0410.0000.0000.0000.000
41A41ARG 10.9070.94318.150-0.011-0.0110.0000.0000.0000.000
42A42TRP 00.0280.04113.2390.0030.0030.0000.0000.0000.000
43A43LYS 10.9290.95912.719-0.309-0.3090.0000.0000.0000.000
44A44PRO 00.0090.00411.5920.0390.0390.0000.0000.0000.000
45A45LYS 10.9661.0015.211-1.762-1.7620.0000.0000.0000.000
46A46MET 0-0.016-0.0308.103-0.122-0.1220.0000.0000.0000.000
47A47ILE 0-0.0190.0202.604-3.718-0.8941.004-0.951-2.8770.011
48A48GLY 00.0530.0044.1750.3010.6760.000-0.067-0.3090.000
49A49GLY 0-0.016-0.0042.092-4.920-3.1054.865-3.241-3.4390.016
50A50ILE 0-0.040-0.0171.889-8.461-19.58033.053-3.745-18.1900.033
51A51GLY 00.029-0.0083.9360.6131.4280.006-0.161-0.6600.001
52A52GLY 00.0070.0136.199-2.078-2.0780.0000.0000.0000.000
53A53PHE 0-0.021-0.0056.2371.3771.3770.0000.0000.0000.000
54A54ILE 0-0.0060.0425.728-0.571-0.5710.0000.0000.0000.000
55A55LYS 10.9390.9468.537-1.410-1.4100.0000.0000.0000.000
56A56VAL 00.0270.0085.346-0.025-0.0250.0000.0000.0000.000
57A57ARG 10.8390.9218.569-0.328-0.3280.0000.0000.0000.000
58A58GLN 0-0.054-0.0277.9260.1710.1710.0000.0000.0000.000
59A59TYR 00.012-0.0059.8600.0250.0250.0000.0000.0000.000
60A60ASP -1-0.835-0.91311.5940.0820.0820.0000.0000.0000.000
61A61GLN 0-0.059-0.04513.476-0.052-0.0520.0000.0000.0000.000
62A62ILE 00.0140.00612.7700.0400.0400.0000.0000.0000.000
63A63LEU 0-0.037-0.03714.362-0.105-0.1050.0000.0000.0000.000
64A64ILE 00.0350.02110.9580.0270.0270.0000.0000.0000.000
65A65GLU -1-0.931-0.97914.789-0.844-0.8440.0000.0000.0000.000
66A66ILE 00.0310.02312.511-0.103-0.1030.0000.0000.0000.000
67A67CYS 0-0.047-0.03516.4900.0550.0550.0000.0000.0000.000
68A68GLY 0-0.0190.00919.1840.0820.0820.0000.0000.0000.000
69A69HIS 00.0380.02119.3660.0860.0860.0000.0000.0000.000
70A70LYS 10.9420.97219.0880.6010.6010.0000.0000.0000.000
71A71ALA 00.0210.00814.6810.0020.0020.0000.0000.0000.000
72A72ILE 0-0.0130.01914.831-0.023-0.0230.0000.0000.0000.000
73A73GLY 00.024-0.01211.418-0.085-0.0850.0000.0000.0000.000
74A74THR 0-0.022-0.0147.939-0.048-0.0480.0000.0000.0000.000
75A75VAL 00.0210.0207.668-0.076-0.0760.0000.0000.0000.000
76A76LEU 0-0.037-0.0273.8200.2240.5280.004-0.041-0.2660.000
77A77VAL 00.0010.0297.205-0.279-0.2790.0000.0000.0000.000
78A78GLY 00.0370.0019.2180.2540.2540.0000.0000.0000.000
79A79PRO 0-0.053-0.0018.431-0.303-0.3030.0000.0000.0000.000
80A80THR 0-0.0650.0133.8850.4080.8950.004-0.121-0.370-0.001
81A81PRO 00.0350.0111.999-1.061-1.3413.370-0.658-2.432-0.002
82A82VAL 00.0340.0072.976-3.018-0.6260.810-0.659-2.5420.005
83A83ASN 0-0.055-0.0104.801-0.338-0.149-0.001-0.010-0.1780.000
84A84ILE 0-0.035-0.0282.234-3.370-0.8481.909-0.794-3.637-0.002
85A85ILE 00.0040.0205.3781.2611.429-0.001-0.005-0.1620.000
86A86GLY 00.1040.0314.755-1.323-1.245-0.001-0.015-0.0610.000
87A87ARG 10.9220.9605.5631.8411.8410.0000.0000.0000.000
88A88ASN 0-0.0300.0226.596-0.346-0.3460.0000.0000.0000.000
89A89LEU 0-0.011-0.0058.5030.1550.1550.0000.0000.0000.000
90A90LEU 0-0.063-0.0037.8820.1770.1770.0000.0000.0000.000
91A91THR 0-0.017-0.00911.6010.2080.2080.0000.0000.0000.000
92A92GLN 0-0.043-0.01313.2750.1720.1720.0000.0000.0000.000
93A93ILE 0-0.057-0.02314.0160.1050.1050.0000.0000.0000.000
94A94GLY 00.0240.02016.2830.0480.0480.0000.0000.0000.000
95A95ALA 0-0.005-0.03113.069-0.008-0.0080.0000.0000.0000.000
96A96THR 0-0.059-0.05114.7750.1280.1280.0000.0000.0000.000
97A97LEU 0-0.0220.0178.898-0.053-0.0530.0000.0000.0000.000
98A98ASN 0-0.002-0.02513.5040.1350.1350.0000.0000.0000.000
99A99PHE -1-0.850-0.89813.701-1.384-1.3840.0000.0000.0000.000
100B1PRO 10.8250.90117.6911.3201.3200.0000.0000.0000.000
101B2GLN 00.0630.05617.185-0.164-0.1640.0000.0000.0000.000
102B3VAL 0-0.027-0.01113.7430.1070.1070.0000.0000.0000.000
103B4THR 00.0500.03314.183-0.197-0.1970.0000.0000.0000.000
104B5LEU 0-0.022-0.03014.257-0.110-0.1100.0000.0000.0000.000
105B6TRP 00.0060.00213.0720.0330.0330.0000.0000.0000.000
106B7GLN 00.0290.01910.4410.2300.2300.0000.0000.0000.000
107B8ARG 10.9120.9444.4051.3051.431-0.001-0.004-0.1210.000
108B9PRO 00.0280.0418.2450.4720.4720.0000.0000.0000.000
109B10LEU 00.017-0.0037.598-0.399-0.3990.0000.0000.0000.000
110B11VAL 0-0.017-0.01111.2150.1880.1880.0000.0000.0000.000
111B12THR 0-0.011-0.01413.380-0.018-0.0180.0000.0000.0000.000
112B13ILE 00.0220.01911.2520.0110.0110.0000.0000.0000.000
113B14LYS 10.9650.97615.1520.4080.4080.0000.0000.0000.000
114B15ILE 00.0470.03610.977-0.005-0.0050.0000.0000.0000.000
115B16GLY 00.008-0.00615.2310.0830.0830.0000.0000.0000.000
116B17GLY 0-0.025-0.00717.410-0.019-0.0190.0000.0000.0000.000
117B18GLN 0-0.045-0.01816.4640.0360.0360.0000.0000.0000.000
118B19LEU 0-0.006-0.01116.840-0.055-0.0550.0000.0000.0000.000
119B20LYS 10.8980.96010.9660.0090.0090.0000.0000.0000.000
120B21GLU -1-0.903-0.93810.634-0.899-0.8990.0000.0000.0000.000
121B22ALA 00.000-0.0078.9970.0800.0800.0000.0000.0000.000
122B23LEU 0-0.048-0.0183.152-0.6190.4170.105-0.231-0.9100.001
123B24LEU 0-0.029-0.0225.969-1.251-1.2510.0000.0000.0000.000
124B25ASP -1-0.681-0.8802.155-36.682-34.0218.911-4.577-6.995-0.054
125B26THR 0-0.054-0.0304.6050.6460.814-0.001-0.005-0.1630.000
126B27GLY 00.0330.0172.6431.5442.3050.310-0.507-0.563-0.001
127B28ALA 00.0140.0352.1921.3911.7309.436-2.573-7.2010.000
128B29ASP -1-0.905-0.9652.175-5.930-3.1371.392-1.187-2.9980.014
129B30ASP -1-0.910-0.9842.1871.7513.0852.334-1.105-2.5630.006
130B31THR 0-0.0410.0142.724-6.597-4.5920.573-1.128-1.449-0.016
131B32VAL 0-0.0410.0032.728-0.3521.5740.333-0.514-1.7460.002
132B33LEU 00.002-0.0164.392-0.652-0.4980.001-0.024-0.1310.000
133B34GLU -1-0.931-0.9787.2590.8340.8340.0000.0000.0000.000
134B35GLU -1-0.985-0.9858.0471.0701.0700.0000.0000.0000.000
135B36MET 0-0.0180.00411.531-0.123-0.1230.0000.0000.0000.000
136B37SER 0-0.038-0.02314.3200.0840.0840.0000.0000.0000.000
137B38LEU 00.0560.00611.693-0.081-0.0810.0000.0000.0000.000
138B39PRO 0-0.0010.00415.8220.0290.0290.0000.0000.0000.000
139B40GLY 0-0.029-0.02018.0430.0020.0020.0000.0000.0000.000
140B41ARG 10.9420.95316.723-0.290-0.2900.0000.0000.0000.000
141B42TRP 00.0390.03912.6310.0290.0290.0000.0000.0000.000
142B43LYS 10.9130.95811.889-0.783-0.7830.0000.0000.0000.000
143B44PRO 0-0.0020.00610.8410.1750.1750.0000.0000.0000.000
144B45LYS 10.9250.9835.847-3.044-3.0440.0000.0000.0000.000
145B46MET 0-0.015-0.0268.000-0.120-0.1200.0000.0000.0000.000
146B47ILE 00.0020.0242.413-3.665-1.7364.136-1.213-4.8520.015
147B48GLY 00.040-0.0094.019-0.0390.4000.001-0.084-0.3560.000
148B49GLY 0-0.008-0.0072.035-4.585-5.05512.636-6.334-5.8310.016
149B50ILE 0-0.0030.0062.013-3.786-22.22737.8770.900-20.3360.036
150B51GLY 00.011-0.0163.9740.1150.8010.009-0.147-0.5490.001
151B52GLY 0-0.0010.0106.369-1.502-1.5020.0000.0000.0000.000
152B53PHE 00.004-0.0066.0681.7891.7890.0000.0000.0000.000
153B54ILE 00.0050.0565.406-0.625-0.6250.0000.0000.0000.000
154B55LYS 10.9340.9547.952-2.120-2.1200.0000.0000.0000.000
155B56VAL 00.001-0.0095.0110.0300.0300.0000.0000.0000.000
156B57ARG 10.9130.9658.193-1.462-1.4620.0000.0000.0000.000
157B58GLN 00.013-0.0027.8210.1800.1800.0000.0000.0000.000
158B59TYR 00.0380.0239.409-0.061-0.0610.0000.0000.0000.000
159B60ASP -1-0.834-0.93111.1380.6610.6610.0000.0000.0000.000
160B61GLN 0-0.066-0.04312.494-0.008-0.0080.0000.0000.0000.000
161B62ILE 0-0.016-0.00812.1520.0170.0170.0000.0000.0000.000
162B63LEU 0-0.045-0.03114.063-0.092-0.0920.0000.0000.0000.000
163B64ILE 00.005-0.00310.4090.0400.0400.0000.0000.0000.000
164B65GLU -1-0.960-0.98414.325-0.622-0.6220.0000.0000.0000.000
165B66ILE 00.0830.03312.021-0.047-0.0470.0000.0000.0000.000
166B67CYS 0-0.051-0.01616.081-0.016-0.0160.0000.0000.0000.000
167B68GLY 00.0080.01018.7010.0380.0380.0000.0000.0000.000
168B69HIS 00.0210.01318.9640.0730.0730.0000.0000.0000.000
169B70LYS 10.9310.95718.4650.3550.3550.0000.0000.0000.000
170B71ALA 00.0600.04114.652-0.024-0.0240.0000.0000.0000.000
171B72ILE 0-0.0100.01114.8250.0660.0660.0000.0000.0000.000
172B73GLY 00.020-0.00211.039-0.124-0.1240.0000.0000.0000.000
173B74THR 0-0.016-0.0087.586-0.056-0.0560.0000.0000.0000.000
174B75VAL 00.0190.0197.219-0.068-0.0680.0000.0000.0000.000
175B76LEU 0-0.011-0.0233.1350.0030.4900.036-0.077-0.4450.000
176B77VAL 00.0190.0026.504-0.228-0.2280.0000.0000.0000.000
177B78GLY 0-0.008-0.0108.8460.2300.2300.0000.0000.0000.000
178B79PRO 00.0360.0398.706-0.268-0.2680.0000.0000.0000.000
179B80THR 0-0.064-0.0013.4190.2091.0610.020-0.302-0.571-0.002
180B81PRO 00.0380.0171.963-1.082-1.6583.896-0.725-2.5950.002
181B82VAL 00.0550.0092.648-2.980-0.8091.677-0.845-3.0040.006
182B83ASN 0-0.037-0.0314.408-0.310-0.1350.000-0.012-0.1620.000
183B84ILE 00.0400.0302.0462.073-5.85619.551-2.704-8.918-0.006
184B85ILE 0-0.0130.0025.1550.2630.476-0.001-0.009-0.2030.000
185B86GLY 00.1450.0323.816-1.625-1.3950.001-0.048-0.1830.000
186B87ARG 10.8700.9104.7256.8437.066-0.001-0.010-0.2130.000
187B88ASN 00.0210.0535.689-0.216-0.2160.0000.0000.0000.000
188B89LEU 0-0.034-0.0147.5410.2190.2190.0000.0000.0000.000
189B90LEU 0-0.0160.0367.8090.2560.2560.0000.0000.0000.000
190B91THR 0-0.011-0.03110.6920.2760.2760.0000.0000.0000.000
191B92GLN 0-0.087-0.03112.3530.1740.1740.0000.0000.0000.000
192B93ILE 0-0.067-0.01812.5830.1000.1000.0000.0000.0000.000
193B94GLY 00.0410.02715.2610.0640.0640.0000.0000.0000.000
194B95ALA 0-0.016-0.03112.515-0.001-0.0010.0000.0000.0000.000
195B96THR 0-0.075-0.04714.4770.0250.0250.0000.0000.0000.000
196B97LEU 0-0.004-0.0039.4250.0040.0040.0000.0000.0000.000
197B98ASN 00.029-0.00413.7130.0320.0320.0000.0000.0000.000
198B99PHE -1-0.866-0.89713.179-1.515-1.5150.0000.0000.0000.000