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: MMJYZ

Calculation Name: 1BVE-AB-NMR60-Model6

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 -2278202.277553
FMO2-HF: Nuclear repulsion 2201724.970425
FMO2-HF: Total energy -76477.307128
FMO2-MP2: Total energy -76703.030138


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.
-169.598-219.650256.196-84.486-121.6610.050


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.
-169.598-219.65256.196-84.486-121.661-0.05
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 : -0.153
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 10.8280.89917.0271.5091.5090.0000.0000.0000.000
2A2GLN 00.0540.05317.131-0.114-0.1140.0000.0000.0000.000
3A3VAL 00.0090.00213.8570.0660.0660.0000.0000.0000.000
4A4THR 00.013-0.01415.445-0.171-0.1710.0000.0000.0000.000
5A5LEU 00.0410.03111.110-0.109-0.1090.0000.0000.0000.000
6A6TRP 0-0.0100.00011.719-0.056-0.0560.0000.0000.0000.000
7A7GLN 0-0.016-0.03611.2040.0780.0780.0000.0000.0000.000
8A8ARG 10.9300.9666.5660.9000.9000.0000.0000.0000.000
9A9PRO 00.0300.0298.5830.3880.3880.0000.0000.0000.000
10A10LEU 00.015-0.0048.563-0.388-0.3880.0000.0000.0000.000
11A11VAL 0-0.040-0.02011.3680.2470.2470.0000.0000.0000.000
12A12THR 00.0150.00213.795-0.018-0.0180.0000.0000.0000.000
13A13ILE 0-0.0250.00511.5020.0700.0700.0000.0000.0000.000
14A14LYS 10.9530.96415.0820.6590.6590.0000.0000.0000.000
15A15ILE 00.0670.03211.0960.0130.0130.0000.0000.0000.000
16A16GLY 0-0.006-0.03115.1880.0820.0820.0000.0000.0000.000
17A17GLY 0-0.0230.00417.2280.0460.0460.0000.0000.0000.000
18A18GLN 0-0.069-0.03616.7570.1020.1020.0000.0000.0000.000
19A19LEU 0-0.011-0.01917.146-0.069-0.0690.0000.0000.0000.000
20A20LYS 10.9670.99112.4840.2800.2800.0000.0000.0000.000
21A21GLU -1-0.862-0.93111.651-1.106-1.1060.0000.0000.0000.000
22A22ALA 0-0.012-0.0259.358-0.029-0.0290.0000.0000.0000.000
23A23LEU 0-0.0120.0023.5440.2010.9350.015-0.092-0.6570.000
24A24LEU 0-0.023-0.0145.701-2.154-2.1540.0000.0000.0000.000
25A25ASP -1-0.701-0.7591.348-71.499-133.652115.211-44.499-8.560-0.157
26A26THR 0-0.066-0.0564.3930.5860.871-0.001-0.045-0.2390.000
27A27GLY 00.0770.0322.8801.4882.4380.187-0.422-0.7140.002
28A28ALA 0-0.091-0.0172.083-0.1031.9066.121-2.569-5.5610.000
29A29ASP -1-0.924-0.9852.375-3.716-1.5410.310-0.788-1.6980.004
30A30ASP -1-0.911-0.9622.7910.4702.6410.530-0.951-1.7500.009
31A31THR 0-0.108-0.0913.269-4.835-3.6990.071-0.574-0.632-0.005
32A32VAL 0-0.042-0.0022.721-0.1101.6510.517-0.436-1.8420.000
33A33LEU 00.022-0.0104.229-0.678-0.5440.002-0.037-0.1000.000
34A34GLU -1-0.898-0.9567.7020.5220.5220.0000.0000.0000.000
35A35GLU -1-0.905-0.9668.8870.8130.8130.0000.0000.0000.000
36A36MET 0-0.081-0.02911.845-0.135-0.1350.0000.0000.0000.000
37A37SER 00.0010.00814.4380.1230.1230.0000.0000.0000.000
38A38LEU 00.0480.03012.063-0.123-0.1230.0000.0000.0000.000
39A39PRO 00.0170.02715.4630.0310.0310.0000.0000.0000.000
40A40GLY 00.0480.02617.3180.0690.0690.0000.0000.0000.000
41A41ARG 10.8760.92617.553-0.296-0.2960.0000.0000.0000.000
42A42TRP 00.0340.03312.6630.0190.0190.0000.0000.0000.000
43A43LYS 10.9520.97512.486-0.729-0.7290.0000.0000.0000.000
44A44PRO 00.0310.02311.5430.1260.1260.0000.0000.0000.000
45A45LYS 10.9530.9806.826-2.331-2.3310.0000.0000.0000.000
46A46MET 0-0.001-0.0297.832-0.185-0.1850.0000.0000.0000.000
47A47ILE 0-0.0150.0242.300-4.298-1.3943.100-1.443-4.5610.017
48A48GLY 00.067-0.0154.001-0.0060.4740.002-0.093-0.3890.000
49A49GLY 00.007-0.0101.998-4.938-4.2279.528-5.322-4.9160.019
50A50ILE 0-0.0100.0071.984-4.567-20.06534.3490.033-18.8840.035
51A51GLY 00.011-0.0144.049-0.0960.5660.007-0.156-0.5130.001
52A52GLY 00.0180.0136.340-1.941-1.9410.0000.0000.0000.000
53A53PHE 0-0.0010.0295.8321.8481.8480.0000.0000.0000.000
54A54ILE 0-0.0530.0215.752-0.744-0.7440.0000.0000.0000.000
55A55LYS 10.9290.9608.096-2.925-2.9250.0000.0000.0000.000
56A56VAL 00.016-0.0075.1400.0190.0190.0000.0000.0000.000
57A57ARG 10.8580.9288.175-1.089-1.0890.0000.0000.0000.000
58A58GLN 00.006-0.0038.051-0.118-0.1180.0000.0000.0000.000
59A59TYR 0-0.010-0.0159.001-0.133-0.1330.0000.0000.0000.000
60A60ASP -1-0.860-0.94310.7090.4810.4810.0000.0000.0000.000
61A61GLN 0-0.052-0.03112.9320.0130.0130.0000.0000.0000.000
62A62ILE 0-0.0020.00312.2660.0340.0340.0000.0000.0000.000
63A63LEU 0-0.040-0.04414.126-0.114-0.1140.0000.0000.0000.000
64A64ILE 00.0210.01410.5280.0360.0360.0000.0000.0000.000
65A65GLU -1-0.931-0.96214.341-0.789-0.7890.0000.0000.0000.000
66A66ILE 00.0490.02811.700-0.048-0.0480.0000.0000.0000.000
67A67CYS 0-0.021-0.01115.8790.0160.0160.0000.0000.0000.000
68A68GLY 0-0.0020.01618.3250.0670.0670.0000.0000.0000.000
69A69HIS 0-0.020-0.00518.6100.1210.1210.0000.0000.0000.000
70A70LYS 10.9340.94817.9710.4410.4410.0000.0000.0000.000
71A71ALA 00.0490.02114.606-0.006-0.0060.0000.0000.0000.000
72A72ILE 0-0.0020.01614.7970.0190.0190.0000.0000.0000.000
73A73GLY 00.015-0.00411.322-0.120-0.1200.0000.0000.0000.000
74A74THR 0-0.029-0.0247.999-0.029-0.0290.0000.0000.0000.000
75A75VAL 00.0120.0157.446-0.108-0.1080.0000.0000.0000.000
76A76LEU 0-0.022-0.0183.022-0.2700.3860.064-0.120-0.6000.000
77A77VAL 00.0260.0266.155-0.348-0.3480.0000.0000.0000.000
78A78GLY 00.018-0.0038.5690.3020.3020.0000.0000.0000.000
79A79PRO 0-0.0310.0069.215-0.321-0.3210.0000.0000.0000.000
80A80THR 0-0.0530.0093.9460.9441.2970.001-0.053-0.3010.000
81A81PRO 00.0350.0131.942-1.012-1.2782.609-0.571-1.771-0.001
82A82VAL 00.0420.0133.172-2.666-0.4070.458-0.580-2.1380.006
83A83ASN 0-0.041-0.0025.064-0.318-0.120-0.001-0.007-0.1900.000
84A84ILE 0-0.038-0.0262.086-3.800-1.0563.173-1.287-4.629-0.002
85A85ILE 00.0040.0194.8931.3481.577-0.001-0.009-0.2200.000
86A86GLY 00.1760.0484.426-1.420-1.334-0.001-0.014-0.0710.000
87A87ARG 10.9540.9645.3353.8203.943-0.001-0.003-0.1200.000
88A88ASN 00.0130.0776.207-0.233-0.2330.0000.0000.0000.000
89A89LEU 00.001-0.0087.9760.3260.3260.0000.0000.0000.000
90A90LEU 0-0.0340.0197.8820.1600.1600.0000.0000.0000.000
91A91THR 0-0.040-0.02011.2400.2720.2720.0000.0000.0000.000
92A92GLN 0-0.060-0.01812.8320.2640.2640.0000.0000.0000.000
93A93ILE 0-0.059-0.01012.1760.0970.0970.0000.0000.0000.000
94A94GLY 00.0220.01815.5960.0490.0490.0000.0000.0000.000
95A95ALA 00.0050.00612.3190.0220.0220.0000.0000.0000.000
96A96THR 0-0.085-0.06714.1100.0070.0070.0000.0000.0000.000
97A97LEU 00.0510.0209.3860.0100.0100.0000.0000.0000.000
98A98ASN 00.022-0.01413.9700.0640.0640.0000.0000.0000.000
99A99PHE -1-0.834-0.87714.010-1.312-1.3120.0000.0000.0000.000
100B1PRO 10.7850.88318.7861.2491.2490.0000.0000.0000.000
101B2GLN 00.0360.04818.236-0.058-0.0580.0000.0000.0000.000
102B3VAL 00.0090.01813.4680.0890.0890.0000.0000.0000.000
103B4THR 0-0.029-0.02014.768-0.155-0.1550.0000.0000.0000.000
104B5LEU 00.0790.03510.416-0.055-0.0550.0000.0000.0000.000
105B6TRP 0-0.028-0.01312.696-0.036-0.0360.0000.0000.0000.000
106B7GLN 0-0.081-0.03912.9440.2030.2030.0000.0000.0000.000
107B8ARG 10.9710.9788.0041.1521.1520.0000.0000.0000.000
108B9PRO 00.0610.0419.0090.4190.4190.0000.0000.0000.000
109B10LEU 00.007-0.0068.221-0.248-0.2480.0000.0000.0000.000
110B11VAL 0-0.032-0.01911.6780.2180.2180.0000.0000.0000.000
111B12THR 0-0.007-0.01713.998-0.025-0.0250.0000.0000.0000.000
112B13ILE 00.0070.01712.1060.0170.0170.0000.0000.0000.000
113B14LYS 10.9540.97115.6110.7000.7000.0000.0000.0000.000
114B15ILE 00.0420.03111.497-0.018-0.0180.0000.0000.0000.000
115B16GLY 00.039-0.00315.8970.0850.0850.0000.0000.0000.000
116B17GLY 0-0.043-0.01118.5710.0580.0580.0000.0000.0000.000
117B18GLN 0-0.050-0.02517.5990.0900.0900.0000.0000.0000.000
118B19LEU 0-0.012-0.02217.479-0.071-0.0710.0000.0000.0000.000
119B20LYS 10.8990.97612.2400.6190.6190.0000.0000.0000.000
120B21GLU -1-0.885-0.94310.729-0.840-0.8400.0000.0000.0000.000
121B22ALA 0-0.035-0.0059.5440.0670.0670.0000.0000.0000.000
122B23LEU 0-0.0030.0043.365-0.2380.4230.036-0.115-0.5830.000
123B24LEU 0-0.034-0.0246.298-0.852-0.8520.0000.0000.0000.000
124B25ASP -1-0.676-0.8552.309-32.991-28.5698.229-5.310-7.341-0.069
125B26THR 0-0.098-0.0624.7780.8030.965-0.001-0.006-0.1550.000
126B27GLY 00.0240.0282.3900.6551.7560.719-0.977-0.842-0.004
127B28ALA 0-0.0140.0132.1363.7550.80813.426-3.319-7.1590.001
128B29ASP -1-0.854-0.9432.095-6.231-6.5564.692-1.420-2.9470.016
129B30ASP -1-0.921-0.9992.289-9.844-7.4661.615-1.617-2.3770.008
130B31THR 0-0.066-0.0253.501-0.755-0.0020.027-0.318-0.463-0.002
131B32VAL 00.0270.0043.039-0.5900.7090.093-0.288-1.1050.001
132B33LEU 0-0.003-0.0334.692-0.135-0.047-0.001-0.008-0.0790.000
133B34GLU -1-0.873-0.9317.2600.9600.9600.0000.0000.0000.000
134B35GLU -1-0.970-1.0058.5690.4930.4930.0000.0000.0000.000
135B36MET 0-0.044-0.02011.924-0.134-0.1340.0000.0000.0000.000
136B37SER 00.0180.01414.9690.0650.0650.0000.0000.0000.000
137B38LEU 00.0570.01913.885-0.091-0.0910.0000.0000.0000.000
138B39PRO 0-0.0080.01217.4570.0620.0620.0000.0000.0000.000
139B40GLY 0-0.037-0.02519.0930.0040.0040.0000.0000.0000.000
140B41ARG 10.9450.95717.9500.0720.0720.0000.0000.0000.000
141B42TRP 00.0620.04113.518-0.015-0.0150.0000.0000.0000.000
142B43LYS 10.9410.96711.6990.3830.3830.0000.0000.0000.000
143B44PRO 0-0.0130.00511.046-0.054-0.0540.0000.0000.0000.000
144B45LYS 10.9100.9716.4750.3360.3360.0000.0000.0000.000
145B46MET 0-0.010-0.0198.353-0.028-0.0280.0000.0000.0000.000
146B47ILE 0-0.0010.0272.839-3.914-1.1260.584-0.938-2.4350.010
147B48GLY 00.0420.0084.4830.3360.599-0.001-0.041-0.2210.000
148B49GLY 0-0.0110.0062.170-3.920-2.3094.792-2.997-3.4060.017
149B50ILE 0-0.0170.0001.983-7.335-20.85537.308-4.186-19.6010.037
150B51GLY 00.020-0.0123.9080.2621.0010.008-0.135-0.6110.001
151B52GLY 0-0.005-0.0016.102-2.386-2.3860.0000.0000.0000.000
152B53PHE 0-0.010-0.0216.0961.6581.6580.0000.0000.0000.000
153B54ILE 0-0.0110.0475.945-0.812-0.8120.0000.0000.0000.000
154B55LYS 10.9340.9538.472-1.577-1.5770.0000.0000.0000.000
155B56VAL 00.0300.0095.3610.0060.0060.0000.0000.0000.000
156B57ARG 10.8850.9378.715-0.720-0.7200.0000.0000.0000.000
157B58GLN 00.0510.0157.7950.1020.1020.0000.0000.0000.000
158B59TYR 00.012-0.0019.7980.1670.1670.0000.0000.0000.000
159B60ASP -1-0.797-0.85310.521-1.180-1.1800.0000.0000.0000.000
160B61GLN 0-0.033-0.02412.6240.1250.1250.0000.0000.0000.000
161B62ILE 00.022-0.00212.8270.1290.1290.0000.0000.0000.000
162B63LEU 0-0.077-0.04114.406-0.096-0.0960.0000.0000.0000.000
163B64ILE 00.0230.00811.0400.0800.0800.0000.0000.0000.000
164B65GLU -1-0.947-0.98314.921-0.790-0.7900.0000.0000.0000.000
165B66ILE 00.0510.03412.266-0.015-0.0150.0000.0000.0000.000
166B67CYS 0-0.060-0.01616.361-0.003-0.0030.0000.0000.0000.000
167B68GLY 00.0090.01419.2290.0650.0650.0000.0000.0000.000
168B69HIS 00.0220.01518.9390.0860.0860.0000.0000.0000.000
169B70LYS 10.9480.95318.3990.5490.5490.0000.0000.0000.000
170B71ALA 00.0510.02814.719-0.012-0.0120.0000.0000.0000.000
171B72ILE 0-0.0250.00614.692-0.017-0.0170.0000.0000.0000.000
172B73GLY 00.0300.01011.283-0.069-0.0690.0000.0000.0000.000
173B74THR 0-0.098-0.0927.3430.2520.2520.0000.0000.0000.000
174B75VAL 00.0040.0137.440-0.418-0.4180.0000.0000.0000.000
175B76LEU 0-0.048-0.0224.060-0.0110.2220.001-0.025-0.2080.000
176B77VAL 0-0.0250.0207.5190.0500.0500.0000.0000.0000.000
177B78GLY 00.001-0.0179.5000.0880.0880.0000.0000.0000.000
178B79PRO 0-0.0210.0188.733-0.238-0.2380.0000.0000.0000.000
179B80THR 0-0.098-0.0343.9340.6181.0360.003-0.096-0.3250.000
180B81PRO 00.0710.0442.022-1.163-1.1202.708-0.554-2.197-0.002
181B82VAL 00.0320.0092.970-3.414-0.9571.003-0.750-2.7110.006
182B83ASN 0-0.040-0.0284.7460.1540.3140.000-0.011-0.1500.000
183B84ILE 0-0.012-0.0082.083-3.109-1.0624.707-1.315-5.4390.002
184B85ILE 0-0.0020.0105.1480.2090.362-0.001-0.006-0.1460.000
185B86GLY 00.1190.0394.623-0.675-0.554-0.001-0.016-0.1040.000
186B87ARG 10.9050.9635.5031.9781.9780.0000.0000.0000.000
187B88ASN 0-0.0350.0326.322-0.058-0.0580.0000.0000.0000.000
188B89LEU 00.005-0.0067.9940.2890.2890.0000.0000.0000.000
189B90LEU 0-0.0300.0008.4560.2080.2080.0000.0000.0000.000
190B91THR 00.018-0.00410.8650.1900.1900.0000.0000.0000.000
191B92GLN 0-0.087-0.03312.7330.2350.2350.0000.0000.0000.000
192B93ILE 0-0.054-0.02313.8920.1200.1200.0000.0000.0000.000
193B94GLY 00.0360.02416.0980.0640.0640.0000.0000.0000.000
194B95ALA 0-0.027-0.03113.5900.0190.0190.0000.0000.0000.000
195B96THR 0-0.060-0.04815.5090.0540.0540.0000.0000.0000.000
196B97LEU 00.006-0.01210.074-0.202-0.2020.0000.0000.0000.000
197B98ASN 0-0.029-0.02314.4540.0490.0490.0000.0000.0000.000
198B99PHE -1-0.823-0.90013.700-1.641-1.6410.0000.0000.0000.000