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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

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FMODB ID: JM7G9

Calculation Name: 1BVE-AB-NMR60-Model10

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 -2288313.497049
FMO2-HF: Nuclear repulsion 2211836.104048
FMO2-HF: Total energy -76477.393001
FMO2-MP2: Total energy -76703.238928


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.
-165.599-239.044304.016-101.582-128.992-0.007


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.
-165.599-239.044304.016-101.582-128.9920.007
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 : 0.004 / q_NPA : -0.046
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 10.8410.90417.8610.5520.5520.0000.0000.0000.000
2A2GLN 00.0560.05117.687-0.020-0.0200.0000.0000.0000.000
3A3VAL 0-0.006-0.00113.9980.0710.0710.0000.0000.0000.000
4A4THR 00.0030.00114.920-0.140-0.1400.0000.0000.0000.000
5A5LEU 00.0960.0229.262-0.245-0.2450.0000.0000.0000.000
6A6TRP 0-0.0090.00812.211-0.049-0.0490.0000.0000.0000.000
7A7GLN 0-0.043-0.03311.2510.1550.1550.0000.0000.0000.000
8A8ARG 10.9240.9604.3791.2451.443-0.001-0.009-0.1890.000
9A9PRO 00.0520.0467.9250.3250.3250.0000.0000.0000.000
10A10LEU 0-0.032-0.0208.3970.0060.0060.0000.0000.0000.000
11A11VAL 0-0.017-0.00211.4960.0390.0390.0000.0000.0000.000
12A12THR 00.002-0.01313.6810.0540.0540.0000.0000.0000.000
13A13ILE 00.0230.01311.430-0.012-0.0120.0000.0000.0000.000
14A14LYS 10.9200.95915.534-0.008-0.0080.0000.0000.0000.000
15A15ILE 00.0590.04311.0270.0030.0030.0000.0000.0000.000
16A16GLY 00.0400.00615.3540.0210.0210.0000.0000.0000.000
17A17GLY 0-0.069-0.02617.756-0.003-0.0030.0000.0000.0000.000
18A18GLN 0-0.029-0.01717.902-0.019-0.0190.0000.0000.0000.000
19A19LEU 0-0.010-0.01317.903-0.021-0.0210.0000.0000.0000.000
20A20LYS 10.9160.97112.858-0.283-0.2830.0000.0000.0000.000
21A21GLU -1-0.880-0.92410.6600.0220.0220.0000.0000.0000.000
22A22ALA 00.013-0.0079.4080.1380.1380.0000.0000.0000.000
23A23LEU 0-0.0480.0033.406-1.049-0.1000.028-0.211-0.7660.001
24A24LEU 0-0.001-0.0176.345-0.146-0.1460.0000.0000.0000.000
25A25ASH 00.005-0.0571.403-15.824-50.89167.429-27.859-4.5030.035
26A26THR 0-0.022-0.0544.8630.8361.034-0.001-0.004-0.1930.000
27A27GLY 00.007-0.0022.440-0.3050.5510.633-0.750-0.738-0.003
28A28ALA 0-0.042-0.0082.0502.320-4.50819.462-4.516-8.1180.001
29A29ASP -1-0.865-0.9632.091-12.453-10.8245.156-2.423-4.3630.014
30A30ASP -1-0.953-1.0002.376-2.485-1.0351.325-0.816-1.9580.009
31A31THR 0-0.053-0.0243.413-2.649-1.7390.036-0.430-0.516-0.003
32A32VAL 0-0.030-0.0022.864-1.2510.3480.247-0.366-1.4800.001
33A33LEU 00.000-0.0164.518-0.273-0.1620.000-0.016-0.0950.000
34A34GLU -1-0.909-0.9817.6800.8090.8090.0000.0000.0000.000
35A35GLU -1-0.984-1.0098.5920.7220.7220.0000.0000.0000.000
36A36MET 0-0.0010.01511.959-0.101-0.1010.0000.0000.0000.000
37A37SER 0-0.022-0.00714.9140.0190.0190.0000.0000.0000.000
38A38LEU 00.0550.02013.195-0.054-0.0540.0000.0000.0000.000
39A39PRO 0-0.0010.00617.1830.0000.0000.0000.0000.0000.000
40A40GLY 0-0.037-0.02918.590-0.013-0.0130.0000.0000.0000.000
41A41ARG 10.9430.96317.680-0.267-0.2670.0000.0000.0000.000
42A42TRP 00.0470.04313.1220.0390.0390.0000.0000.0000.000
43A43LYS 10.9750.96912.697-0.457-0.4570.0000.0000.0000.000
44A44PRO 0-0.0170.01211.4460.0880.0880.0000.0000.0000.000
45A45LYS 10.9180.9785.805-0.931-0.9310.0000.0000.0000.000
46A46MET 0-0.013-0.0317.8840.0710.0710.0000.0000.0000.000
47A47ILE 0-0.0330.0192.270-4.034-1.5502.801-1.324-3.9610.015
48A48GLY 00.0520.0053.7370.7941.3520.005-0.121-0.4410.000
49A49GLY 0-0.004-0.0122.007-6.557-4.9508.105-4.962-4.7490.012
50A50ILE 0-0.0080.0122.005-4.914-18.42834.065-1.588-18.9630.030
51A51GLY 0-0.003-0.0103.9590.1790.8940.009-0.151-0.5730.001
52A52GLY 00.0210.0096.053-1.898-1.8980.0000.0000.0000.000
53A53PHE 0-0.001-0.0015.7851.3571.3570.0000.0000.0000.000
54A54ILE 00.0120.0495.621-0.432-0.4320.0000.0000.0000.000
55A55LYS 10.9470.9677.782-1.688-1.6880.0000.0000.0000.000
56A56VAL 0-0.002-0.0155.3120.0990.0990.0000.0000.0000.000
57A57ARG 10.9140.9558.509-1.140-1.1400.0000.0000.0000.000
58A58GLN 0-0.078-0.0488.3380.0470.0470.0000.0000.0000.000
59A59TYR 00.0250.0119.243-0.099-0.0990.0000.0000.0000.000
60A60ASP -1-0.830-0.91011.4410.6410.6410.0000.0000.0000.000
61A61GLN 0-0.038-0.02912.759-0.051-0.0510.0000.0000.0000.000
62A62ILE 00.0370.00312.831-0.035-0.0350.0000.0000.0000.000
63A63LEU 0-0.069-0.04414.051-0.008-0.0080.0000.0000.0000.000
64A64ILE 00.0110.00410.3840.0040.0040.0000.0000.0000.000
65A65GLU -1-0.956-0.98714.215-0.118-0.1180.0000.0000.0000.000
66A66ILE 00.0800.03012.028-0.001-0.0010.0000.0000.0000.000
67A67CYS 0-0.021-0.00616.140-0.045-0.0450.0000.0000.0000.000
68A68GLY 00.0520.04619.1600.0040.0040.0000.0000.0000.000
69A69HIS 0-0.077-0.04318.187-0.004-0.0040.0000.0000.0000.000
70A70LYS 10.9110.93118.1500.0720.0720.0000.0000.0000.000
71A71ALA 00.0710.05214.373-0.013-0.0130.0000.0000.0000.000
72A72ILE 00.0070.03514.8270.0380.0380.0000.0000.0000.000
73A73GLY 00.0090.02010.974-0.027-0.0270.0000.0000.0000.000
74A74THR 0-0.009-0.0097.839-0.101-0.1010.0000.0000.0000.000
75A75VAL 00.0190.0177.2360.2130.2130.0000.0000.0000.000
76A76LEU 0-0.008-0.0173.594-0.444-0.0200.013-0.074-0.3630.000
77A77VAL 00.0350.0326.8210.0170.0170.0000.0000.0000.000
78A78GLY 0-0.019-0.0249.144-0.028-0.0280.0000.0000.0000.000
79A79PRO 0-0.0350.0148.733-0.159-0.1590.0000.0000.0000.000
80A80THR 0-0.0750.0104.1240.2900.6110.000-0.047-0.2750.000
81A81PRO 00.0480.0221.956-0.758-1.1423.144-0.639-2.121-0.002
82A82VAL 00.0500.0093.318-1.901-0.1620.244-0.423-1.5610.004
83A83ASN 00.005-0.0095.126-0.0290.103-0.001-0.004-0.1280.000
84A84ILE 0-0.010-0.0082.082-2.853-1.4434.567-1.020-4.9570.002
85A85ILE 00.0250.0275.2370.0060.161-0.001-0.005-0.1500.000
86A86GLY 00.0870.0154.537-0.596-0.469-0.001-0.019-0.1070.000
87A87ARG 10.9330.9895.427-0.071-0.0710.0000.0000.0000.000
88A88ASN 0-0.0110.0716.300-0.272-0.2720.0000.0000.0000.000
89A89LEU 00.026-0.0038.074-0.175-0.1750.0000.0000.0000.000
90A90LEU 0-0.0120.0328.538-0.222-0.2220.0000.0000.0000.000
91A91THR 0-0.011-0.03310.964-0.058-0.0580.0000.0000.0000.000
92A92GLN 0-0.089-0.06111.606-0.016-0.0160.0000.0000.0000.000
93A93ILE 0-0.060-0.02213.231-0.007-0.0070.0000.0000.0000.000
94A94GLY 00.0390.02515.958-0.025-0.0250.0000.0000.0000.000
95A95ALA 00.007-0.01613.060-0.043-0.0430.0000.0000.0000.000
96A96THR 0-0.103-0.04215.020-0.018-0.0180.0000.0000.0000.000
97A97LEU 00.0400.0159.018-0.046-0.0460.0000.0000.0000.000
98A98ASN 00.032-0.01813.572-0.068-0.0680.0000.0000.0000.000
99A99PHE -1-0.828-0.87513.377-1.177-1.1770.0000.0000.0000.000
100B1PRO 10.7590.87317.6101.1081.1080.0000.0000.0000.000
101B2GLN 00.0530.05117.881-0.048-0.0480.0000.0000.0000.000
102B3VAL 00.0020.00912.9230.0220.0220.0000.0000.0000.000
103B4THR 0-0.004-0.00414.254-0.122-0.1220.0000.0000.0000.000
104B5LEU 0-0.0170.00612.7340.0100.0100.0000.0000.0000.000
105B6TRP 00.0650.03412.987-0.051-0.0510.0000.0000.0000.000
106B7GLN 0-0.058-0.04410.4430.1080.1080.0000.0000.0000.000
107B8ARG 10.9740.9724.9072.6832.6830.0000.0000.0000.000
108B9PRO 00.0700.0267.6700.3320.3320.0000.0000.0000.000
109B10LEU 0-0.026-0.0098.582-0.533-0.5330.0000.0000.0000.000
110B11VAL 0-0.0030.00111.3090.3630.3630.0000.0000.0000.000
111B12THR 00.002-0.01813.665-0.124-0.1240.0000.0000.0000.000
112B13ILE 00.0140.02511.9290.0790.0790.0000.0000.0000.000
113B14LYS 10.9480.95215.2330.7710.7710.0000.0000.0000.000
114B15ILE 00.0220.02711.1590.0090.0090.0000.0000.0000.000
115B16GLY 00.0370.00515.4780.0500.0500.0000.0000.0000.000
116B17GLY 0-0.046-0.01218.0190.0610.0610.0000.0000.0000.000
117B18GLN 00.0220.01217.431-0.030-0.0300.0000.0000.0000.000
118B19LEU 00.007-0.02817.469-0.049-0.0490.0000.0000.0000.000
119B20LYS 10.8450.95112.5211.1721.1720.0000.0000.0000.000
120B21GLU -1-0.855-0.91911.262-1.612-1.6120.0000.0000.0000.000
121B22ALA 00.000-0.0259.279-0.051-0.0510.0000.0000.0000.000
122B23LEU 0-0.0430.0163.274-0.6640.4550.056-0.246-0.9300.000
123B24LEU 00.000-0.0125.819-2.159-2.1590.0000.0000.0000.000
124B25ASP -1-0.622-0.7301.349-73.571-108.21576.006-32.695-8.668-0.170
125B26THR 0-0.032-0.0164.5060.0310.220-0.001-0.023-0.1650.000
126B27GLY 00.041-0.0112.8101.8122.6930.207-0.415-0.6740.002
127B28ALA 0-0.077-0.0142.0831.299-0.21212.113-3.642-6.960-0.001
128B29ASP -1-0.903-0.9762.091-5.960-2.9222.138-1.771-3.4050.003
129B30ASP -1-0.852-0.9602.116-2.653-2.7074.690-1.708-2.9280.013
130B31THR 0-0.085-0.0282.939-6.121-4.4600.247-0.865-1.043-0.010
131B32VAL 0-0.0290.0043.065-0.0291.5890.174-0.373-1.4190.001
132B33LEU 0-0.013-0.0334.667-0.621-0.5140.000-0.013-0.0930.000
133B34GLU -1-0.911-0.9907.175-0.172-0.1720.0000.0000.0000.000
134B35GLU -1-0.933-0.9658.1080.0020.0020.0000.0000.0000.000
135B36MET 0-0.0020.01411.429-0.097-0.0970.0000.0000.0000.000
136B37SER 0-0.037-0.01814.4440.1150.1150.0000.0000.0000.000
137B38LEU 00.0690.01412.962-0.057-0.0570.0000.0000.0000.000
138B39PRO 0-0.045-0.00716.6270.0730.0730.0000.0000.0000.000
139B40GLY 00.0490.01218.962-0.027-0.0270.0000.0000.0000.000
140B41ARG 10.9080.95018.238-0.025-0.0250.0000.0000.0000.000
141B42TRP 00.0460.02613.213-0.008-0.0080.0000.0000.0000.000
142B43LYS 10.9460.97812.687-0.125-0.1250.0000.0000.0000.000
143B44PRO 00.0090.01611.4070.0410.0410.0000.0000.0000.000
144B45LYS 10.9680.9946.806-1.093-1.0930.0000.0000.0000.000
145B46MET 0-0.013-0.0258.385-0.116-0.1160.0000.0000.0000.000
146B47ILE 0-0.0350.0142.832-3.157-0.5570.578-0.800-2.3780.008
147B48GLY 00.062-0.0104.1870.3610.7190.000-0.054-0.3040.000
148B49GLY 0-0.024-0.0152.028-5.020-3.7217.071-4.247-4.1230.015
149B50ILE 0-0.023-0.0031.916-6.159-21.43739.729-3.614-20.8360.034
150B51GLY 00.019-0.0073.845-0.1700.6100.011-0.129-0.6620.001
151B52GLY 0-0.003-0.0085.964-2.096-2.0960.0000.0000.0000.000
152B53PHE 0-0.0020.0285.9431.4141.4140.0000.0000.0000.000
153B54ILE 00.0100.0385.684-0.481-0.4810.0000.0000.0000.000
154B55LYS 10.9290.9508.309-1.241-1.2410.0000.0000.0000.000
155B56VAL 0-0.007-0.0215.758-0.031-0.0310.0000.0000.0000.000
156B57ARG 10.8990.9458.869-0.040-0.0400.0000.0000.0000.000
157B58GLN 00.0020.0008.580-0.121-0.1210.0000.0000.0000.000
158B59TYR 0-0.0060.0129.5050.0500.0500.0000.0000.0000.000
159B60ASP -1-0.833-0.93011.0290.0110.0110.0000.0000.0000.000
160B61GLN 0-0.082-0.05513.1830.0320.0320.0000.0000.0000.000
161B62ILE 00.0240.01112.8550.0230.0230.0000.0000.0000.000
162B63LEU 0-0.062-0.04514.092-0.074-0.0740.0000.0000.0000.000
163B64ILE 00.0390.00710.3490.0100.0100.0000.0000.0000.000
164B65GLU -1-1.020-1.00214.322-0.945-0.9450.0000.0000.0000.000
165B66ILE 00.0760.03611.749-0.093-0.0930.0000.0000.0000.000
166B67CYS 0-0.068-0.01916.0120.0680.0680.0000.0000.0000.000
167B68GLY 00.0630.03018.5590.0920.0920.0000.0000.0000.000
168B69HIS 00.0030.00818.5530.0880.0880.0000.0000.0000.000
169B70LYS 10.9230.95318.0220.4810.4810.0000.0000.0000.000
170B71ALA 00.0670.03813.8780.0280.0280.0000.0000.0000.000
171B72ILE 00.0030.01514.052-0.067-0.0670.0000.0000.0000.000
172B73GLY 00.0210.01011.107-0.035-0.0350.0000.0000.0000.000
173B74THR 0-0.017-0.0157.566-0.017-0.0170.0000.0000.0000.000
174B75VAL 00.0120.0097.403-0.153-0.1530.0000.0000.0000.000
175B76LEU 0-0.049-0.0273.5010.0080.3680.009-0.052-0.3170.000
176B77VAL 00.0120.0156.700-0.337-0.3370.0000.0000.0000.000
177B78GLY 0-0.014-0.0119.2550.3010.3010.0000.0000.0000.000
178B79PRO 0-0.0070.0258.592-0.251-0.2510.0000.0000.0000.000
179B80THR 0-0.0650.0153.5680.3070.9590.011-0.200-0.463-0.001
180B81PRO 00.0450.0222.052-1.076-1.0322.793-0.570-2.266-0.003
181B82VAL 00.031-0.0023.028-2.533-0.4590.638-0.582-2.1300.005
182B83ASN 0-0.0230.0014.839-0.369-0.206-0.001-0.007-0.1560.000
183B84ILE 00.0250.0142.311-1.422-2.63710.285-1.755-7.315-0.007
184B85ILE 0-0.035-0.0095.0280.5950.860-0.001-0.009-0.2550.000
185B86GLY 00.1350.0433.998-2.076-1.9380.000-0.031-0.1070.000
186B87ARG 10.9630.9844.8731.8671.999-0.001-0.004-0.1270.000
187B88ASN 0-0.0250.0445.907-0.292-0.2920.0000.0000.0000.000
188B89LEU 00.006-0.0097.6850.1550.1550.0000.0000.0000.000
189B90LEU 0-0.0100.0008.1220.3080.3080.0000.0000.0000.000
190B91THR 00.007-0.01010.8240.3040.3040.0000.0000.0000.000
191B92GLN 0-0.101-0.03212.5070.2040.2040.0000.0000.0000.000
192B93ILE 0-0.045-0.01912.7870.1090.1090.0000.0000.0000.000
193B94GLY 00.0380.02515.2560.0670.0670.0000.0000.0000.000
194B95ALA 0-0.018-0.03612.3010.0390.0390.0000.0000.0000.000
195B96THR 0-0.093-0.05514.3570.1040.1040.0000.0000.0000.000
196B97LEU 00.007-0.0029.160-0.067-0.0670.0000.0000.0000.000
197B98ASN 0-0.045-0.03713.6050.1460.1460.0000.0000.0000.000
198B99PHE -1-0.876-0.91212.388-0.578-0.5780.0000.0000.0000.000