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: GQZG1

Calculation Name: 1BVE-AB-NMR60-Model13

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 -2298763.328919
FMO2-HF: Nuclear repulsion 2222286.217456
FMO2-HF: Total energy -76477.111463
FMO2-MP2: Total energy -76702.933907


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.
-156.496-208.322258.727-66.207-140.6980.041


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.
-156.496-208.322258.727-66.207-140.698-0.041
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 : -0.043 / q_NPA : -0.082
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 10.8260.90217.7341.3981.3980.0000.0000.0000.000
2A2GLN 00.0610.05817.580-0.121-0.1210.0000.0000.0000.000
3A3VAL 00.0060.01212.7780.0490.0490.0000.0000.0000.000
4A4THR 00.0540.01913.995-0.254-0.2540.0000.0000.0000.000
5A5LEU 0-0.012-0.02612.868-0.184-0.1840.0000.0000.0000.000
6A6TRP 00.0420.03411.878-0.022-0.0220.0000.0000.0000.000
7A7GLN 00.0290.0158.7420.1820.1820.0000.0000.0000.000
8A8ARG 10.9620.9975.5881.8861.8860.0000.0000.0000.000
9A9PRO 0-0.0160.0137.4510.7140.7140.0000.0000.0000.000
10A10LEU 0-0.036-0.0176.687-0.321-0.3210.0000.0000.0000.000
11A11VAL 0-0.009-0.00410.5190.3010.3010.0000.0000.0000.000
12A12THR 0-0.016-0.00112.918-0.042-0.0420.0000.0000.0000.000
13A13ILE 00.009-0.00511.698-0.034-0.0340.0000.0000.0000.000
14A14LYS 10.9670.97415.5680.6150.6150.0000.0000.0000.000
15A15ILE 00.0580.02411.626-0.005-0.0050.0000.0000.0000.000
16A16GLY 00.0160.00215.9290.0760.0760.0000.0000.0000.000
17A17GLY 0-0.062-0.01917.9820.0510.0510.0000.0000.0000.000
18A18GLN 00.0240.00116.5530.0290.0290.0000.0000.0000.000
19A19LEU 0-0.032-0.01716.746-0.080-0.0800.0000.0000.0000.000
20A20LYS 10.8770.96311.6120.3880.3880.0000.0000.0000.000
21A21GLU -1-0.881-0.9459.308-0.885-0.8850.0000.0000.0000.000
22A22ALA 00.022-0.0189.0590.0550.0550.0000.0000.0000.000
23A23LEU 0-0.047-0.0083.080-1.2450.4430.274-0.480-1.4820.003
24A24LEU 0-0.027-0.0285.822-1.729-1.7290.0000.0000.0000.000
25A25ASP -1-0.689-0.8311.869-45.590-64.83341.036-11.178-10.616-0.102
26A26THR 0-0.069-0.0684.4620.1610.411-0.001-0.042-0.2070.000
27A27GLY 00.0360.0252.6301.8462.9680.444-0.656-0.9110.003
28A28ALA 0-0.097-0.0312.0913.3790.66513.255-3.793-6.748-0.002
29A29ASP -1-0.821-0.9352.0541.9140.9532.4020.688-2.1290.005
30A30ASP -1-0.901-0.9903.000-0.8350.5420.121-0.532-0.9660.005
31A31THR 0-0.049-0.0173.972-3.203-2.8480.003-0.108-0.250-0.001
32A32VAL 0-0.026-0.0042.719-0.3661.4880.357-0.475-1.7360.001
33A33LEU 00.023-0.0014.509-0.702-0.5720.000-0.017-0.1130.000
34A34GLU -1-0.871-0.9347.3420.3270.3270.0000.0000.0000.000
35A35GLU -1-0.965-1.0168.4310.6760.6760.0000.0000.0000.000
36A36MET 0-0.018-0.00411.944-0.084-0.0840.0000.0000.0000.000
37A37SER 0-0.034-0.01514.7460.0770.0770.0000.0000.0000.000
38A38LEU 00.0290.00512.477-0.099-0.0990.0000.0000.0000.000
39A39PRO 00.0070.01515.8690.0710.0710.0000.0000.0000.000
40A40GLY 00.0430.01117.674-0.052-0.0520.0000.0000.0000.000
41A41ARG 10.9120.94616.747-0.207-0.2070.0000.0000.0000.000
42A42TRP 00.0640.04212.7770.0160.0160.0000.0000.0000.000
43A43LYS 10.9500.97211.066-0.742-0.7420.0000.0000.0000.000
44A44PRO 00.0030.01010.4350.1090.1090.0000.0000.0000.000
45A45LYS 11.0031.0013.147-6.194-5.7530.010-0.107-0.3440.001
46A46MET 0-0.0550.0127.728-0.017-0.0170.0000.0000.0000.000
47A47ILE 0-0.0200.0012.115-3.953-1.6913.905-1.444-4.7220.014
48A48GLY 00.078-0.0233.819-0.2450.3270.004-0.119-0.4580.000
49A49GLY 0-0.024-0.0231.975-5.262-5.86913.966-7.134-6.2240.016
50A50ILE 00.0120.0101.999-2.868-21.74737.0242.052-20.1970.036
51A51GLY 0-0.018-0.0144.007-0.0370.6610.011-0.175-0.5340.001
52A52GLY 00.0150.0015.967-2.228-2.2280.0000.0000.0000.000
53A53PHE 0-0.0090.0475.6671.8991.8990.0000.0000.0000.000
54A54ILE 0-0.0100.0285.656-0.646-0.6460.0000.0000.0000.000
55A55LYS 10.9600.9417.417-2.198-2.1980.0000.0000.0000.000
56A56VAL 0-0.0040.0054.744-0.215-0.104-0.001-0.003-0.1070.000
57A57ARG 10.8670.9478.168-0.783-0.7830.0000.0000.0000.000
58A58GLN 0-0.024-0.0077.7530.4060.4060.0000.0000.0000.000
59A59TYR 00.0000.0099.2580.0420.0420.0000.0000.0000.000
60A60ASP -1-0.854-0.94311.5770.2740.2740.0000.0000.0000.000
61A61GLN 0-0.060-0.03613.338-0.073-0.0730.0000.0000.0000.000
62A62ILE 00.0190.00712.9050.0320.0320.0000.0000.0000.000
63A63LEU 0-0.059-0.03014.819-0.117-0.1170.0000.0000.0000.000
64A64ILE 00.0360.00911.4760.0490.0490.0000.0000.0000.000
65A65GLU -1-0.985-0.99315.309-0.769-0.7690.0000.0000.0000.000
66A66ILE 00.0440.02812.881-0.041-0.0410.0000.0000.0000.000
67A67CYS 0-0.042-0.03116.5810.0180.0180.0000.0000.0000.000
68A68GLY 00.0330.02818.6240.0780.0780.0000.0000.0000.000
69A69HIS 0-0.027-0.00819.6520.0690.0690.0000.0000.0000.000
70A70LYS 10.9250.94619.0290.4850.4850.0000.0000.0000.000
71A71ALA 00.0520.02915.286-0.005-0.0050.0000.0000.0000.000
72A72ILE 0-0.0370.00015.228-0.026-0.0260.0000.0000.0000.000
73A73GLY 00.0760.03312.112-0.070-0.0700.0000.0000.0000.000
74A74THR 0-0.048-0.0188.800-0.015-0.0150.0000.0000.0000.000
75A75VAL 00.0400.0777.959-0.141-0.1410.0000.0000.0000.000
76A76LEU 00.013-0.0143.8000.3520.6160.003-0.034-0.2330.000
77A77VAL 0-0.071-0.0037.595-0.197-0.1970.0000.0000.0000.000
78A78GLY 00.024-0.0229.1220.2200.2200.0000.0000.0000.000
79A79PRO 0-0.0150.0228.808-0.314-0.3140.0000.0000.0000.000
80A80THR 0-0.035-0.0163.6780.5151.1480.009-0.181-0.461-0.001
81A81PRO 00.0230.0162.056-1.355-1.0632.296-0.498-2.0900.000
82A82VAL 00.0360.0062.640-3.306-0.8801.736-0.923-3.2400.006
83A83ASN 0-0.0370.0044.493-0.274-0.0770.000-0.015-0.1820.000
84A84ILE 00.011-0.0121.949-1.047-2.95110.724-1.927-6.8940.001
85A85ILE 00.0070.0065.3750.7330.914-0.001-0.005-0.1750.000
86A86GLY 00.1080.0415.155-1.358-1.3580.0000.0000.0000.000
87A87ARG 10.9240.9496.0164.2434.2430.0000.0000.0000.000
88A88ASN 0-0.0270.0096.797-0.121-0.1210.0000.0000.0000.000
89A89LEU 00.0080.0058.8540.2320.2320.0000.0000.0000.000
90A90LEU 0-0.0520.0057.7000.3080.3080.0000.0000.0000.000
91A91THR 00.005-0.02411.7380.2340.2340.0000.0000.0000.000
92A92GLN 0-0.097-0.03413.4550.3010.3010.0000.0000.0000.000
93A93ILE 0-0.055-0.01513.9660.1180.1180.0000.0000.0000.000
94A94GLY 00.0150.01317.2140.0410.0410.0000.0000.0000.000
95A95ALA 0-0.013-0.00913.1330.0030.0030.0000.0000.0000.000
96A96THR 0-0.034-0.04114.9820.0660.0660.0000.0000.0000.000
97A97LEU 0-0.062-0.0179.496-0.038-0.0380.0000.0000.0000.000
98A98ASN 0-0.010-0.02313.8780.0760.0760.0000.0000.0000.000
99A99PHE -1-0.820-0.89712.361-1.452-1.4520.0000.0000.0000.000
100B1PRO 10.8120.89517.5401.3581.3580.0000.0000.0000.000
101B2GLN 00.0620.05517.560-0.147-0.1470.0000.0000.0000.000
102B3VAL 00.0080.01613.4820.0920.0920.0000.0000.0000.000
103B4THR 00.0890.01415.266-0.252-0.2520.0000.0000.0000.000
104B5LEU 0-0.048-0.01215.2130.1300.1300.0000.0000.0000.000
105B6TRP 00.0230.00312.269-0.023-0.0230.0000.0000.0000.000
106B7GLN 0-0.0050.00510.3540.1900.1900.0000.0000.0000.000
107B8ARG 10.9490.9676.912-0.028-0.0280.0000.0000.0000.000
108B9PRO 0-0.0360.0088.0130.5760.5760.0000.0000.0000.000
109B10LEU 00.0090.0017.588-0.415-0.4150.0000.0000.0000.000
110B11VAL 0-0.015-0.00810.9770.2790.2790.0000.0000.0000.000
111B12THR 0-0.018-0.02912.790-0.029-0.0290.0000.0000.0000.000
112B13ILE 0-0.0020.02611.8510.0280.0280.0000.0000.0000.000
113B14LYS 10.9250.95014.9800.6270.6270.0000.0000.0000.000
114B15ILE 00.0520.03711.160-0.009-0.0090.0000.0000.0000.000
115B16GLY 00.005-0.00315.5810.0810.0810.0000.0000.0000.000
116B17GLY 0-0.038-0.01218.3140.0490.0490.0000.0000.0000.000
117B18GLN 00.0290.00615.8510.0290.0290.0000.0000.0000.000
118B19LEU 0-0.022-0.01816.559-0.076-0.0760.0000.0000.0000.000
119B20LYS 10.8880.96811.1220.2120.2120.0000.0000.0000.000
120B21GLU -1-0.930-0.9538.359-0.828-0.8280.0000.0000.0000.000
121B22ALA 00.062-0.0208.8690.0610.0610.0000.0000.0000.000
122B23LEU 0-0.0540.0013.154-1.2480.3780.261-0.395-1.4930.002
123B24LEU 0-0.024-0.0345.623-1.528-1.5280.0000.0000.0000.000
124B25ASP -1-0.668-0.8181.557-57.374-77.89948.179-17.026-10.628-0.111
125B26THR 0-0.108-0.0604.0700.3840.8540.000-0.177-0.294-0.001
126B27GLY 00.0740.0382.4881.7233.3320.788-1.104-1.2930.003
127B28ALA 0-0.0390.0032.0216.9540.54819.766-5.234-8.125-0.004
128B29ASP -1-0.892-0.9762.136-9.514-8.0384.679-2.148-4.0070.003
129B30ASP -1-0.952-0.9922.687-3.702-1.9940.329-0.720-1.3160.009
130B31THR 0-0.047-0.0253.734-2.894-2.3710.008-0.193-0.339-0.001
131B32VAL 0-0.0370.0013.015-0.3101.2060.158-0.329-1.3450.001
132B33LEU 0-0.012-0.0224.587-0.477-0.3740.000-0.013-0.0890.000
133B34GLU -1-0.923-0.9707.2581.1091.1090.0000.0000.0000.000
134B35GLU -1-0.971-0.9758.0920.4460.4460.0000.0000.0000.000
135B36MET 0-0.029-0.01511.329-0.114-0.1140.0000.0000.0000.000
136B37SER 0-0.020-0.00514.4490.0670.0670.0000.0000.0000.000
137B38LEU 00.0350.00312.541-0.070-0.0700.0000.0000.0000.000
138B39PRO 00.0030.00316.6910.0490.0490.0000.0000.0000.000
139B40GLY 0-0.040-0.02818.275-0.002-0.0020.0000.0000.0000.000
140B41ARG 10.9420.96217.426-0.039-0.0390.0000.0000.0000.000
141B42TRP 00.0390.04012.6800.0070.0070.0000.0000.0000.000
142B43LYS 10.9460.97112.202-0.094-0.0940.0000.0000.0000.000
143B44PRO 00.0090.00811.1020.0470.0470.0000.0000.0000.000
144B45LYS 10.9550.9843.732-1.436-1.1640.004-0.047-0.2300.000
145B46MET 0-0.062-0.0137.3010.0850.0850.0000.0000.0000.000
146B47ILE 0-0.0290.0032.307-4.546-2.3343.717-1.299-4.6290.017
147B48GLY 00.0630.0114.2090.4080.8100.001-0.070-0.3330.000
148B49GLY 0-0.0030.0072.073-4.528-3.0935.907-3.654-3.6890.020
149B50ILE 0-0.011-0.0071.953-8.481-18.74830.648-2.792-17.5890.034
150B51GLY 00.012-0.0103.9580.3601.0650.008-0.137-0.5760.001
151B52GLY 00.0020.0006.015-2.224-2.2240.0000.0000.0000.000
152B53PHE 0-0.009-0.0095.9981.5421.5420.0000.0000.0000.000
153B54ILE 0-0.0060.0315.585-0.413-0.4130.0000.0000.0000.000
154B55LYS 10.9240.9477.363-1.341-1.3410.0000.0000.0000.000
155B56VAL 00.0410.0364.999-0.010-0.0100.0000.0000.0000.000
156B57ARG 10.9110.9538.266-0.633-0.6330.0000.0000.0000.000
157B58GLN 00.0420.0077.0530.1130.1130.0000.0000.0000.000
158B59TYR 00.0250.0139.0230.0220.0220.0000.0000.0000.000
159B60ASP -1-0.872-0.94311.382-0.127-0.1270.0000.0000.0000.000
160B61GLN 0-0.045-0.02713.171-0.025-0.0250.0000.0000.0000.000
161B62ILE 0-0.019-0.00912.4820.0490.0490.0000.0000.0000.000
162B63LEU 0-0.053-0.04914.456-0.097-0.0970.0000.0000.0000.000
163B64ILE 00.0470.02111.1310.0620.0620.0000.0000.0000.000
164B65GLU -1-0.963-0.97814.983-0.776-0.7760.0000.0000.0000.000
165B66ILE 00.0710.02812.700-0.046-0.0460.0000.0000.0000.000
166B67CYS 0-0.049-0.02316.5290.0240.0240.0000.0000.0000.000
167B68GLY 00.0450.02618.4970.0410.0410.0000.0000.0000.000
168B69HIS 00.0020.00019.7800.0710.0710.0000.0000.0000.000
169B70LYS 10.8760.92918.9790.5350.5350.0000.0000.0000.000
170B71ALA 00.0590.03614.847-0.027-0.0270.0000.0000.0000.000
171B72ILE 0-0.0150.01514.9730.0010.0010.0000.0000.0000.000
172B73GLY 00.0110.00311.630-0.101-0.1010.0000.0000.0000.000
173B74THR 0-0.007-0.0178.2470.0220.0220.0000.0000.0000.000
174B75VAL 00.0090.0187.667-0.119-0.1190.0000.0000.0000.000
175B76LEU 0-0.004-0.0143.6750.0150.3800.008-0.060-0.3130.000
176B77VAL 00.0090.0147.166-0.134-0.1340.0000.0000.0000.000
177B78GLY 00.028-0.0188.6880.1730.1730.0000.0000.0000.000
178B79PRO 0-0.0340.0148.484-0.244-0.2440.0000.0000.0000.000
179B80THR 0-0.067-0.0193.552-0.1920.7370.026-0.349-0.605-0.002
180B81PRO 00.0900.0422.068-1.164-1.2733.263-0.661-2.494-0.001
181B82VAL 00.0440.0022.616-2.710-0.6001.509-0.744-2.8750.005
182B83ASN 0-0.0370.0014.542-0.352-0.1730.000-0.010-0.1690.000
183B84ILE 00.0240.0071.999-0.610-3.49011.892-1.932-7.080-0.002
184B85ILE 00.0150.0305.3850.5340.710-0.001-0.007-0.1680.000
185B86GLY 00.1120.0264.927-1.449-1.4490.0000.0000.0000.000
186B87ARG 10.8300.8845.7813.7933.7930.0000.0000.0000.000
187B88ASN 00.0280.0536.614-0.190-0.1900.0000.0000.0000.000
188B89LEU 0-0.001-0.0188.3930.2020.2020.0000.0000.0000.000
189B90LEU 0-0.056-0.0147.5210.0650.0650.0000.0000.0000.000
190B91THR 00.008-0.00211.5420.1050.1050.0000.0000.0000.000
191B92GLN 0-0.0300.00211.4500.1660.1660.0000.0000.0000.000
192B93ILE 0-0.061-0.01113.5950.1100.1100.0000.0000.0000.000
193B94GLY 00.0310.01916.6610.0430.0430.0000.0000.0000.000
194B95ALA 0-0.002-0.00812.6640.0040.0040.0000.0000.0000.000
195B96THR 0-0.091-0.05714.4110.0400.0400.0000.0000.0000.000
196B97LEU 0-0.025-0.0059.2550.0100.0100.0000.0000.0000.000
197B98ASN 0-0.018-0.02413.7020.0570.0570.0000.0000.0000.000
198B99PHE -1-0.806-0.90012.540-1.445-1.4450.0000.0000.0000.000