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: 7J51K

Calculation Name: 1BVE-AB-NMR60-Model25

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:

Apendix: None


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 -2283480.824604
FMO2-HF: Nuclear repulsion 2207003.543806
FMO2-HF: Total energy -76477.280798
FMO2-MP2: Total energy -76703.056037


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.
-162.067-195.223227.603-67.470-126.9830.053


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.
-162.067-195.223227.603-67.47-126.983-0.053
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 : -0.052 / q_NPA : -0.106
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 10.7810.87217.7511.6911.6910.0000.0000.0000.000
2A2GLN 00.0600.06417.911-0.048-0.0480.0000.0000.0000.000
3A3VAL 0-0.019-0.00314.3490.1270.1270.0000.0000.0000.000
4A4THR 00.0730.01815.788-0.237-0.2370.0000.0000.0000.000
5A5LEU 0-0.009-0.00115.8800.1870.1870.0000.0000.0000.000
6A6TRP 00.0160.00413.850-0.050-0.0500.0000.0000.0000.000
7A7GLN 0-0.027-0.02311.0620.4050.4050.0000.0000.0000.000
8A8ARG 10.8540.9326.1151.4671.4670.0000.0000.0000.000
9A9PRO 00.0250.0299.2160.5440.5440.0000.0000.0000.000
10A10LEU 00.0230.0058.820-0.418-0.4180.0000.0000.0000.000
11A11VAL 0-0.024-0.01812.0650.2790.2790.0000.0000.0000.000
12A12THR 00.009-0.00513.866-0.005-0.0050.0000.0000.0000.000
13A13ILE 0-0.0030.00311.1770.0380.0380.0000.0000.0000.000
14A14LYS 10.8680.93915.2160.7650.7650.0000.0000.0000.000
15A15ILE 00.0530.03811.032-0.014-0.0140.0000.0000.0000.000
16A16GLY 00.0230.00915.4940.0890.0890.0000.0000.0000.000
17A17GLY 0-0.035-0.01218.0910.0510.0510.0000.0000.0000.000
18A18GLN 0-0.028-0.00917.8550.0270.0270.0000.0000.0000.000
19A19LEU 00.012-0.01317.600-0.084-0.0840.0000.0000.0000.000
20A20LYS 10.9440.98412.4030.2840.2840.0000.0000.0000.000
21A21GLU -1-0.909-0.94810.508-0.978-0.9780.0000.0000.0000.000
22A22ALA 0-0.037-0.0089.4290.0420.0420.0000.0000.0000.000
23A23LEU 0-0.0140.0063.9840.1500.5900.003-0.040-0.4030.000
24A24LEU 0-0.010-0.0266.484-1.372-1.3720.0000.0000.0000.000
25A25ASP -1-0.662-0.8461.911-54.551-53.17715.798-7.627-9.545-0.095
26A26THR 0-0.109-0.0754.376-0.0550.198-0.001-0.030-0.2230.000
27A27GLY 00.0590.0332.4181.6522.7480.818-0.893-1.0210.005
28A28ALA 0-0.085-0.0212.0926.0550.99417.402-4.438-7.9030.001
29A29ASP -1-0.851-0.9582.268-4.474-2.4570.728-0.658-2.087-0.001
30A30ASP -1-0.912-0.9752.360-0.0721.4562.640-1.427-2.7410.015
31A31THR 0-0.068-0.0463.191-5.545-4.3490.115-0.518-0.794-0.006
32A32VAL 0-0.031-0.0052.839-0.4221.6170.373-0.529-1.8830.002
33A33LEU 0-0.020-0.0224.369-0.713-0.5740.001-0.023-0.1170.000
34A34GLU -1-0.931-1.0106.8160.7410.7410.0000.0000.0000.000
35A35GLU -1-0.972-0.9957.8560.8750.8750.0000.0000.0000.000
36A36MET 00.0160.03711.169-0.115-0.1150.0000.0000.0000.000
37A37SER 0-0.033-0.02214.0640.0980.0980.0000.0000.0000.000
38A38LEU 00.004-0.01912.499-0.101-0.1010.0000.0000.0000.000
39A39PRO 00.0480.03916.7180.0600.0600.0000.0000.0000.000
40A40GLY 00.0650.05717.2900.0460.0460.0000.0000.0000.000
41A41ARG 10.9640.97818.000-0.318-0.3180.0000.0000.0000.000
42A42TRP 0-0.0030.04813.0530.0160.0160.0000.0000.0000.000
43A43LYS 10.9690.97012.806-0.783-0.7830.0000.0000.0000.000
44A44PRO 00.0090.01511.5950.1020.1020.0000.0000.0000.000
45A45LYS 10.9410.9805.070-3.135-3.1350.0000.0000.0000.000
46A46MET 0-0.009-0.0108.695-0.105-0.1050.0000.0000.0000.000
47A47ILE 0-0.041-0.0013.140-2.960-0.6500.514-0.741-2.0830.008
48A48GLY 00.066-0.0134.5870.2590.498-0.001-0.034-0.2040.000
49A49GLY 0-0.023-0.0022.195-4.489-2.7544.281-2.787-3.2300.016
50A50ILE 0-0.0140.0011.957-7.110-21.00838.314-4.692-19.7250.034
51A51GLY 0-0.005-0.0153.8660.6661.4570.007-0.132-0.6660.001
52A52GLY 00.0290.0156.127-2.299-2.2990.0000.0000.0000.000
53A53PHE 0-0.0120.0236.2751.6201.6200.0000.0000.0000.000
54A54ILE 00.0000.0415.727-0.710-0.7100.0000.0000.0000.000
55A55LYS 10.9250.9498.458-2.345-2.3450.0000.0000.0000.000
56A56VAL 00.0220.0095.9000.0200.0200.0000.0000.0000.000
57A57ARG 10.9160.9509.033-0.974-0.9740.0000.0000.0000.000
58A58GLN 0-0.011-0.0138.267-0.193-0.1930.0000.0000.0000.000
59A59TYR 0-0.077-0.0969.244-0.046-0.0460.0000.0000.0000.000
60A60ASP -1-0.844-0.90310.5380.3370.3370.0000.0000.0000.000
61A61GLN 0-0.039-0.02512.2140.0060.0060.0000.0000.0000.000
62A62ILE 00.0370.00712.4710.0220.0220.0000.0000.0000.000
63A63LEU 0-0.078-0.04913.750-0.126-0.1260.0000.0000.0000.000
64A64ILE 00.0470.02010.3130.0540.0540.0000.0000.0000.000
65A65GLU -1-0.962-0.99114.158-0.848-0.8480.0000.0000.0000.000
66A66ILE 00.0890.05011.189-0.014-0.0140.0000.0000.0000.000
67A67CYS 0-0.031-0.01815.3110.0210.0210.0000.0000.0000.000
68A68GLY 00.0360.02318.4340.0580.0580.0000.0000.0000.000
69A69HIS 10.8780.94117.7111.3031.3030.0000.0000.0000.000
70A70LYS 10.9630.97817.3570.5280.5280.0000.0000.0000.000
71A71ALA 00.0470.02813.897-0.033-0.0330.0000.0000.0000.000
72A72ILE 0-0.0090.02413.884-0.006-0.0060.0000.0000.0000.000
73A73GLY 00.025-0.00110.612-0.125-0.1250.0000.0000.0000.000
74A74THR 0-0.030-0.0387.054-0.029-0.0290.0000.0000.0000.000
75A75VAL 00.0060.0086.911-0.051-0.0510.0000.0000.0000.000
76A76LEU 0-0.017-0.0182.821-0.0680.4830.120-0.094-0.5760.000
77A77VAL 00.0140.0226.567-0.105-0.1050.0000.0000.0000.000
78A78GLY 00.037-0.0049.0440.1810.1810.0000.0000.0000.000
79A79PRO 0-0.0350.0118.393-0.307-0.3070.0000.0000.0000.000
80A80THR 0-0.0700.0093.5670.4581.3030.020-0.297-0.567-0.002
81A81PRO 00.0580.0301.952-0.653-2.2495.562-0.933-3.033-0.002
82A82VAL 00.0650.0132.988-2.639-0.5680.603-0.550-2.1240.005
83A83ASN 0-0.049-0.0304.705-0.415-0.244-0.001-0.008-0.1620.000
84A84ILE 00.0120.0032.019-2.280-0.7435.131-1.443-5.225-0.006
85A85ILE 00.0060.0205.0650.9171.108-0.001-0.007-0.1840.000
86A86GLY 00.1330.0334.432-1.728-1.616-0.001-0.015-0.0960.000
87A87ARG 10.9230.9585.3555.4505.562-0.001-0.003-0.1090.000
88A88ASN 00.0640.0925.991-0.241-0.2410.0000.0000.0000.000
89A89LEU 00.003-0.0097.7640.2360.2360.0000.0000.0000.000
90A90LEU 0-0.095-0.0207.5340.2410.2410.0000.0000.0000.000
91A91THR 0-0.007-0.02310.6820.2160.2160.0000.0000.0000.000
92A92GLN 0-0.072-0.02112.4460.2070.2070.0000.0000.0000.000
93A93ILE 0-0.087-0.03312.4530.1200.1200.0000.0000.0000.000
94A94GLY 00.0650.03815.5750.0100.0100.0000.0000.0000.000
95A95ALA 0-0.008-0.02312.179-0.027-0.0270.0000.0000.0000.000
96A96THR 0-0.086-0.03914.1440.0410.0410.0000.0000.0000.000
97A97LEU 00.0040.0009.569-0.152-0.1520.0000.0000.0000.000
98A98ASN 00.008-0.01013.7350.2140.2140.0000.0000.0000.000
99A99PHE -1-0.795-0.88712.366-1.870-1.8700.0000.0000.0000.000
100B1PRO 10.7890.88217.8991.7501.7500.0000.0000.0000.000
101B2GLN 00.0620.05217.500-0.183-0.1830.0000.0000.0000.000
102B3VAL 00.0030.01812.9320.0730.0730.0000.0000.0000.000
103B4THR 00.024-0.00114.298-0.209-0.2090.0000.0000.0000.000
104B5LEU 0-0.014-0.01514.155-0.150-0.1500.0000.0000.0000.000
105B6TRP 0-0.002-0.00713.294-0.059-0.0590.0000.0000.0000.000
106B7GLN 0-0.008-0.0069.8880.2890.2890.0000.0000.0000.000
107B8ARG 10.9280.9765.9832.0042.0040.0000.0000.0000.000
108B9PRO 0-0.0020.0107.7850.7120.7120.0000.0000.0000.000
109B10LEU 00.025-0.0047.991-0.491-0.4910.0000.0000.0000.000
110B11VAL 0-0.015-0.00511.1810.3290.3290.0000.0000.0000.000
111B12THR 0-0.001-0.00613.324-0.024-0.0240.0000.0000.0000.000
112B13ILE 0-0.0010.01510.7450.0550.0550.0000.0000.0000.000
113B14LYS 10.9630.98014.6030.8600.8600.0000.0000.0000.000
114B15ILE 00.0600.03210.6820.0090.0090.0000.0000.0000.000
115B16GLY 0-0.004-0.00615.0390.1060.1060.0000.0000.0000.000
116B17GLY 0-0.002-0.00117.705-0.003-0.0030.0000.0000.0000.000
117B18GLN 0-0.088-0.04416.9220.0980.0980.0000.0000.0000.000
118B19LEU 0-0.013-0.01216.802-0.061-0.0610.0000.0000.0000.000
119B20LYS 10.9200.98012.7810.6760.6760.0000.0000.0000.000
120B21GLU -1-0.902-0.93911.669-1.360-1.3600.0000.0000.0000.000
121B22ALA 0-0.013-0.0099.010-0.055-0.0550.0000.0000.0000.000
122B23LEU 0-0.041-0.0123.275-0.7140.5490.069-0.325-1.0070.001
123B24LEU 0-0.019-0.0156.095-2.063-2.0630.0000.0000.0000.000
124B25ASP -1-0.694-0.8201.452-53.824-95.46772.750-22.957-8.151-0.107
125B26THR 0-0.099-0.0604.3520.4510.667-0.001-0.037-0.1780.000
126B27GLY 00.0310.0312.9721.4642.6230.231-0.521-0.8690.003
127B28ALA 0-0.0280.0022.1171.4253.2326.788-2.493-6.102-0.002
128B29ASP -1-0.813-0.9472.288-2.549-0.4210.494-0.736-1.886-0.003
129B30ASP -1-0.877-0.9972.5650.0101.8670.647-0.906-1.5990.008
130B31THR 0-0.0140.0063.224-5.170-3.9170.085-0.634-0.704-0.006
131B32VAL 0-0.0180.0032.375-0.2381.6781.275-0.676-2.5150.000
132B33LEU 0-0.001-0.0174.018-0.709-0.5240.007-0.050-0.1430.000
133B34GLU -1-0.893-0.9697.6580.2720.2720.0000.0000.0000.000
134B35GLU -1-0.968-0.9979.0800.7430.7430.0000.0000.0000.000
135B36MET 00.0280.01712.327-0.130-0.1300.0000.0000.0000.000
136B37SER 0-0.047-0.01514.6150.1150.1150.0000.0000.0000.000
137B38LEU 00.0710.01411.369-0.104-0.1040.0000.0000.0000.000
138B39PRO 0-0.058-0.02115.6030.0960.0960.0000.0000.0000.000
139B40GLY 00.0610.01317.366-0.062-0.0620.0000.0000.0000.000
140B41ARG 10.9060.95716.993-0.351-0.3510.0000.0000.0000.000
141B42TRP 00.0340.03112.6950.0310.0310.0000.0000.0000.000
142B43LYS 10.9510.97012.626-0.771-0.7710.0000.0000.0000.000
143B44PRO 00.0000.00311.6770.0730.0730.0000.0000.0000.000
144B45LYS 10.9390.9765.712-3.443-3.4430.0000.0000.0000.000
145B46MET 00.008-0.0027.958-0.078-0.0780.0000.0000.0000.000
146B47ILE 0-0.0360.0012.517-3.956-1.1382.626-1.181-4.2640.015
147B48GLY 00.068-0.0094.092-0.3250.0940.001-0.071-0.3480.000
148B49GLY 0-0.018-0.0072.020-4.371-3.4968.552-4.799-4.6270.020
149B50ILE 0-0.0190.0002.019-6.089-21.18436.794-1.722-19.9760.041
150B51GLY 00.015-0.0133.967-0.0640.6530.009-0.146-0.5800.001
151B52GLY 0-0.0060.0046.497-1.913-1.9130.0000.0000.0000.000
152B53PHE 00.0050.0106.0561.8731.8730.0000.0000.0000.000
153B54ILE 00.0010.0435.544-0.690-0.6900.0000.0000.0000.000
154B55LYS 10.9270.9528.105-2.193-2.1930.0000.0000.0000.000
155B56VAL 00.0010.0205.052-0.102-0.1020.0000.0000.0000.000
156B57ARG 10.9130.9638.288-0.667-0.6670.0000.0000.0000.000
157B58GLN 0-0.025-0.0197.4860.2410.2410.0000.0000.0000.000
158B59TYR 00.0300.0198.954-0.056-0.0560.0000.0000.0000.000
159B60ASP -1-0.851-0.93510.9500.4600.4600.0000.0000.0000.000
160B61GLN 0-0.045-0.03412.207-0.052-0.0520.0000.0000.0000.000
161B62ILE 00.0090.00412.0360.0340.0340.0000.0000.0000.000
162B63LEU 0-0.059-0.04913.593-0.127-0.1270.0000.0000.0000.000
163B64ILE 00.007-0.00210.1020.0540.0540.0000.0000.0000.000
164B65GLU -1-0.957-0.97313.846-1.214-1.2140.0000.0000.0000.000
165B66ILE 00.0820.02311.433-0.115-0.1150.0000.0000.0000.000
166B67CYS 0-0.071-0.03015.656-0.011-0.0110.0000.0000.0000.000
167B68GLY 00.0750.05218.7570.0920.0920.0000.0000.0000.000
168B69HIS 0-0.032-0.01817.4410.0190.0190.0000.0000.0000.000
169B70LYS 10.9640.96617.3370.5850.5850.0000.0000.0000.000
170B71ALA 00.0530.03113.9030.0290.0290.0000.0000.0000.000
171B72ILE 0-0.0320.01414.3540.0100.0100.0000.0000.0000.000
172B73GLY 00.0710.05110.559-0.053-0.0530.0000.0000.0000.000
173B74THR 0-0.037-0.0207.4140.0060.0060.0000.0000.0000.000
174B75VAL 00.0130.0106.926-0.066-0.0660.0000.0000.0000.000
175B76LEU 0-0.022-0.0192.679-0.1990.5320.255-0.157-0.8290.000
176B77VAL 0-0.0040.0166.085-0.328-0.3280.0000.0000.0000.000
177B78GLY 00.004-0.0298.5920.2990.2990.0000.0000.0000.000
178B79PRO 0-0.0050.0199.251-0.339-0.3390.0000.0000.0000.000
179B80THR 0-0.0700.0074.1400.8481.1530.000-0.037-0.2690.000
180B81PRO 00.0370.0152.040-1.193-1.0251.947-0.500-1.6150.000
181B82VAL 00.0710.0253.444-1.964-0.3200.166-0.394-1.4150.003
182B83ASN 0-0.076-0.0365.298-0.172-0.010-0.001-0.006-0.1550.000
183B84ILE 0-0.005-0.0102.233-4.238-0.9102.488-1.175-4.642-0.002
184B85ILE 00.0060.0264.7171.0441.272-0.001-0.011-0.2160.000
185B86GLY 00.1040.0344.683-1.517-1.424-0.001-0.016-0.0760.000
186B87ARG 10.9000.9625.3443.3153.433-0.001-0.001-0.1160.000
187B88ASN 0-0.0450.0146.212-0.332-0.3320.0000.0000.0000.000
188B89LEU 00.0280.0138.2410.3800.3800.0000.0000.0000.000
189B90LEU 0-0.0100.0167.7840.3420.3420.0000.0000.0000.000
190B91THR 0-0.032-0.02411.5650.4150.4150.0000.0000.0000.000
191B92GLN 0-0.036-0.03412.1840.1670.1670.0000.0000.0000.000
192B93ILE 0-0.080-0.02713.4690.1790.1790.0000.0000.0000.000
193B94GLY 00.0050.01716.1670.0790.0790.0000.0000.0000.000
194B95ALA 0-0.006-0.01413.3530.0150.0150.0000.0000.0000.000
195B96THR 0-0.032-0.04715.3200.1210.1210.0000.0000.0000.000
196B97LEU 0-0.072-0.0149.550-0.094-0.0940.0000.0000.0000.000
197B98ASN 00.0290.00514.0160.1910.1910.0000.0000.0000.000
198B99PHE -1-0.850-0.90613.052-1.803-1.8030.0000.0000.0000.000