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: 5981Z

Calculation Name: 1BVE-AB-NMR60-Model17

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 -2301328.031073
FMO2-HF: Nuclear repulsion 2224851.360719
FMO2-HF: Total energy -76476.670354
FMO2-MP2: Total energy -76702.601512


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.
-126.249-202.776288.191-69.927-141.7380.058


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.
-126.249-202.776288.191-69.927-141.738-0.058
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 : -0.059 / q_NPA : -0.094
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 10.8510.91416.9451.3951.3950.0000.0000.0000.000
2A2GLN 00.0500.05416.804-0.119-0.1190.0000.0000.0000.000
3A3VAL 00.0220.01511.3090.0520.0520.0000.0000.0000.000
4A4THR 00.011-0.02612.945-0.342-0.3420.0000.0000.0000.000
5A5LEU 00.028-0.00911.709-0.248-0.2480.0000.0000.0000.000
6A6TRP 0-0.033-0.01010.050-0.062-0.0620.0000.0000.0000.000
7A7GLN 0-0.031-0.0207.2670.4110.4110.0000.0000.0000.000
8A8ARG 10.9090.9484.9850.6530.6530.0000.0000.0000.000
9A9PRO 0-0.0250.0157.3760.6810.6810.0000.0000.0000.000
10A10LEU 0-0.001-0.0035.566-0.305-0.3050.0000.0000.0000.000
11A11VAL 0-0.039-0.0229.4940.2580.2580.0000.0000.0000.000
12A12THR 0-0.018-0.01011.9000.0030.0030.0000.0000.0000.000
13A13ILE 00.0060.00711.7900.0100.0100.0000.0000.0000.000
14A14LYS 10.9450.95614.9990.4380.4380.0000.0000.0000.000
15A15ILE 00.0460.03311.5080.0020.0020.0000.0000.0000.000
16A16GLY 00.0090.01115.8730.0640.0640.0000.0000.0000.000
17A17GLY 0-0.056-0.02718.4370.0300.0300.0000.0000.0000.000
18A18GLN 00.0080.00416.652-0.013-0.0130.0000.0000.0000.000
19A19LEU 0-0.009-0.00816.293-0.070-0.0700.0000.0000.0000.000
20A20LYS 10.9120.97711.171-0.012-0.0120.0000.0000.0000.000
21A21GLU -1-0.911-0.9537.397-0.625-0.6250.0000.0000.0000.000
22A22ALA 00.050-0.0269.0900.0810.0810.0000.0000.0000.000
23A23LEU 0-0.049-0.0072.574-1.2440.1082.753-0.743-3.3620.001
24A24LEU 0-0.007-0.0215.661-1.510-1.5100.0000.0000.0000.000
25A25ASP -1-0.680-0.8381.642-33.351-66.21858.644-14.904-10.872-0.120
26A26THR 0-0.050-0.0374.6080.9991.212-0.001-0.012-0.2000.000
27A27GLY 00.0680.0262.6481.5792.5310.369-0.539-0.7820.003
28A28ALA 0-0.064-0.0172.1372.1681.9858.947-2.859-5.9060.005
29A29ASP -1-0.902-0.9852.4961.1472.4300.447-0.165-1.5650.000
30A30ASP -1-0.787-0.9902.976-0.1681.2510.123-0.556-0.9860.005
31A31THR 0-0.043-0.0183.560-3.125-2.4400.016-0.304-0.396-0.002
32A32VAL 0-0.006-0.0042.968-0.1391.2190.190-0.282-1.2670.000
33A33LEU 00.004-0.0204.630-0.609-0.5100.000-0.014-0.0850.000
34A34GLU -1-0.952-0.9927.6481.0911.0910.0000.0000.0000.000
35A35GLU -1-0.969-0.9808.6760.8450.8450.0000.0000.0000.000
36A36MET 0-0.046-0.01512.184-0.129-0.1290.0000.0000.0000.000
37A37SER 0-0.016-0.00714.9430.0870.0870.0000.0000.0000.000
38A38LEU 00.031-0.01012.059-0.083-0.0830.0000.0000.0000.000
39A39PRO 00.0000.01915.7670.0220.0220.0000.0000.0000.000
40A40GLY 00.0750.01317.4130.0630.0630.0000.0000.0000.000
41A41ARG 10.8960.94017.166-0.288-0.2880.0000.0000.0000.000
42A42TRP 00.0300.03812.8430.0330.0330.0000.0000.0000.000
43A43LYS 10.9020.95011.662-0.940-0.9400.0000.0000.0000.000
44A44PRO 00.0190.00610.9730.1000.1000.0000.0000.0000.000
45A45LYS 10.9861.0013.151-6.661-6.2450.009-0.116-0.3100.001
46A46MET 0-0.028-0.0167.247-0.074-0.0740.0000.0000.0000.000
47A47ILE 0-0.0300.0102.029-3.367-1.3763.618-1.343-4.2660.010
48A48GLY 00.0740.0024.320-0.0580.3320.000-0.062-0.3290.000
49A49GLY 0-0.029-0.0112.012-4.497-3.6287.746-4.427-4.1870.019
50A50ILE 0-0.027-0.0151.936-7.586-22.70037.800-2.829-19.8570.037
51A51GLY 00.022-0.0053.8680.5751.4230.007-0.152-0.7030.001
52A52GLY 00.0050.0056.080-2.235-2.2350.0000.0000.0000.000
53A53PHE 0-0.0170.0046.1441.7031.7030.0000.0000.0000.000
54A54ILE 00.0040.0365.858-0.646-0.6460.0000.0000.0000.000
55A55LYS 10.9270.9368.485-2.233-2.2330.0000.0000.0000.000
56A56VAL 00.0300.0144.465-0.169-0.037-0.001-0.006-0.1260.000
57A57ARG 10.9340.9757.825-1.157-1.1570.0000.0000.0000.000
58A58GLN 0-0.059-0.0387.5470.4590.4590.0000.0000.0000.000
59A59TYR 00.0100.0079.122-0.072-0.0720.0000.0000.0000.000
60A60ASP -1-0.813-0.90111.2350.8470.8470.0000.0000.0000.000
61A61GLN 0-0.074-0.04712.678-0.044-0.0440.0000.0000.0000.000
62A62ILE 00.0060.00512.3750.0200.0200.0000.0000.0000.000
63A63LEU 0-0.034-0.03214.530-0.099-0.0990.0000.0000.0000.000
64A64ILE 00.012-0.00410.9400.0360.0360.0000.0000.0000.000
65A65GLU -1-0.982-0.97714.856-0.660-0.6600.0000.0000.0000.000
66A66ILE 00.0560.01712.732-0.095-0.0950.0000.0000.0000.000
67A67CYS 00.0290.02315.5360.0500.0500.0000.0000.0000.000
68A68GLY 0-0.034-0.00617.1840.0830.0830.0000.0000.0000.000
69A69HIS 00.012-0.00418.8130.1740.1740.0000.0000.0000.000
70A70LYS 10.9320.94918.4950.3030.3030.0000.0000.0000.000
71A71ALA 00.0600.03914.907-0.019-0.0190.0000.0000.0000.000
72A72ILE 0-0.0510.00715.1780.0270.0270.0000.0000.0000.000
73A73GLY 00.0550.00711.705-0.115-0.1150.0000.0000.0000.000
74A74THR 0-0.044-0.0147.959-0.028-0.0280.0000.0000.0000.000
75A75VAL 00.0670.0337.606-0.068-0.0680.0000.0000.0000.000
76A76LEU 0-0.020-0.0323.4310.0740.5530.018-0.083-0.4130.000
77A77VAL 00.0180.0177.041-0.259-0.2590.0000.0000.0000.000
78A78GLY 00.012-0.0138.7360.2260.2260.0000.0000.0000.000
79A79PRO 0-0.0130.0229.209-0.276-0.2760.0000.0000.0000.000
80A80THR 0-0.082-0.0024.0520.4310.7810.001-0.059-0.2930.000
81A81PRO 00.0640.0322.175-1.267-0.5871.076-0.315-1.441-0.001
82A82VAL 00.0580.0132.425-2.387-0.9732.790-0.838-3.3660.003
83A83ASN 0-0.024-0.0014.584-0.1410.0230.000-0.010-0.1530.000
84A84ILE 0-0.010-0.0042.218-3.163-1.6934.892-1.163-5.1990.001
85A85ILE 00.0210.0345.3590.7940.958-0.001-0.005-0.1580.000
86A86GLY 00.1030.0305.208-1.352-1.3520.0000.0000.0000.000
87A87ARG 10.8380.9265.4114.2454.2450.0000.0000.0000.000
88A88ASN 0-0.1720.0146.615-0.560-0.5600.0000.0000.0000.000
89A89LEU 00.001-0.0528.9830.1390.1390.0000.0000.0000.000
90A90LEU 00.0220.0077.9690.0560.0560.0000.0000.0000.000
91A91THR 0-0.005-0.00412.0530.1160.1160.0000.0000.0000.000
92A92GLN 0-0.0940.05112.4000.1370.1370.0000.0000.0000.000
93A93ILE 0-0.063-0.01714.2630.0540.0540.0000.0000.0000.000
94A94GLY 00.0160.01417.3090.0060.0060.0000.0000.0000.000
95A95ALA 0-0.003-0.00513.209-0.048-0.0480.0000.0000.0000.000
96A96THR 0-0.053-0.04715.1390.1280.1280.0000.0000.0000.000
97A97LEU 0-0.0020.0219.470-0.086-0.0860.0000.0000.0000.000
98A98ASN 0-0.033-0.03914.0050.2450.2450.0000.0000.0000.000
99A99PHE -1-0.838-0.91814.368-1.598-1.5980.0000.0000.0000.000
100B1PRO 10.8050.89117.6571.4271.4270.0000.0000.0000.000
101B2GLN 00.0950.08217.587-0.134-0.1340.0000.0000.0000.000
102B3VAL 0-0.031-0.01014.0780.1160.1160.0000.0000.0000.000
103B4THR 00.023-0.01015.522-0.151-0.1510.0000.0000.0000.000
104B5LEU 0-0.044-0.00816.1350.0820.0820.0000.0000.0000.000
105B6TRP 00.0410.00713.0040.0960.0960.0000.0000.0000.000
106B7GLN 00.0160.01111.2630.2300.2300.0000.0000.0000.000
107B8ARG 10.9450.9697.664-0.747-0.7470.0000.0000.0000.000
108B9PRO 0-0.0240.0088.9650.2420.2420.0000.0000.0000.000
109B10LEU 00.028-0.0016.872-0.412-0.4120.0000.0000.0000.000
110B11VAL 0-0.061-0.02810.4320.1810.1810.0000.0000.0000.000
111B12THR 00.028-0.00612.410-0.066-0.0660.0000.0000.0000.000
112B13ILE 0-0.0070.01111.204-0.025-0.0250.0000.0000.0000.000
113B14LYS 10.9510.96214.4860.6330.6330.0000.0000.0000.000
114B15ILE 00.0240.02511.414-0.074-0.0740.0000.0000.0000.000
115B16GLY 00.0230.01015.7290.1000.1000.0000.0000.0000.000
116B17GLY 0-0.051-0.02218.3080.0780.0780.0000.0000.0000.000
117B18GLN 00.0440.01513.7170.0230.0230.0000.0000.0000.000
118B19LEU 0-0.041-0.02915.147-0.097-0.0970.0000.0000.0000.000
119B20LYS 10.9440.9929.8130.1630.1630.0000.0000.0000.000
120B21GLU -1-0.889-0.9448.106-0.420-0.4200.0000.0000.0000.000
121B22ALA 00.003-0.0228.0690.0940.0940.0000.0000.0000.000
122B23LEU 0-0.046-0.0212.391-1.370-0.0021.496-0.545-2.3190.002
123B24LEU 0-0.015-0.0265.372-1.550-1.5500.0000.0000.0000.000
124B25ASP -1-0.694-0.8101.577-45.236-75.18755.129-16.282-8.897-0.088
125B26THR 0-0.080-0.0544.265-0.0830.2340.000-0.096-0.2200.000
126B27GLY 00.0490.0472.8001.3622.9030.189-0.795-0.9350.002
127B28ALA 0-0.0190.0032.1904.9662.93812.912-4.026-6.858-0.004
128B29ASP -1-0.769-0.8942.059-7.126-5.9033.234-1.608-2.8490.012
129B30ASP -1-0.974-1.0092.412-6.473-4.4940.317-0.922-1.373-0.003
130B31THR 0-0.083-0.0563.519-2.287-1.4950.021-0.364-0.449-0.003
131B32VAL 0-0.039-0.0063.104-0.1761.4620.110-0.433-1.3150.002
132B33LEU 00.007-0.0264.869-0.202-0.097-0.001-0.008-0.0960.000
133B34GLU -1-0.957-0.9676.8190.7960.7960.0000.0000.0000.000
134B35GLU -1-0.991-0.9947.5660.3980.3980.0000.0000.0000.000
135B36MET 0-0.0260.00011.047-0.072-0.0720.0000.0000.0000.000
136B37SER 0-0.039-0.01813.7820.0280.0280.0000.0000.0000.000
137B38LEU 00.0340.01413.537-0.098-0.0980.0000.0000.0000.000
138B39PRO 00.0150.01516.5440.0810.0810.0000.0000.0000.000
139B40GLY 0-0.031-0.02518.418-0.004-0.0040.0000.0000.0000.000
140B41ARG 10.9590.96117.3520.4050.4050.0000.0000.0000.000
141B42TRP 00.0260.03912.857-0.042-0.0420.0000.0000.0000.000
142B43LYS 10.9360.95412.0380.4460.4460.0000.0000.0000.000
143B44PRO 0-0.0030.01011.099-0.032-0.0320.0000.0000.0000.000
144B45LYS 10.9780.9924.3461.0561.190-0.001-0.006-0.1280.000
145B46MET 0-0.030-0.0217.6480.1050.1050.0000.0000.0000.000
146B47ILE 0-0.0140.0092.155-2.855-2.9688.394-1.808-6.4740.020
147B48GLY 00.077-0.0123.852-0.1270.3920.004-0.110-0.4120.000
148B49GLY 0-0.019-0.0131.995-4.693-4.69212.203-6.392-5.8120.017
149B50ILE 00.0130.0121.957-4.252-18.68629.8732.092-17.5310.022
150B51GLY 0-0.023-0.0244.1150.1840.7890.012-0.160-0.4570.001
151B52GLY 00.0100.0086.167-1.970-1.9700.0000.0000.0000.000
152B53PHE 0-0.0040.0305.8371.9101.9100.0000.0000.0000.000
153B54ILE 00.0190.0455.288-0.373-0.3730.0000.0000.0000.000
154B55LYS 10.9340.9587.649-1.376-1.3760.0000.0000.0000.000
155B56VAL 00.007-0.0025.5710.0250.0250.0000.0000.0000.000
156B57ARG 10.9210.9538.574-0.335-0.3350.0000.0000.0000.000
157B58GLN 0-0.004-0.0157.069-0.409-0.4090.0000.0000.0000.000
158B59TYR 00.0310.0279.1510.2370.2370.0000.0000.0000.000
159B60ASP -1-0.829-0.92211.202-1.613-1.6130.0000.0000.0000.000
160B61GLN 0-0.090-0.06613.2940.1120.1120.0000.0000.0000.000
161B62ILE 0-0.011-0.00411.7980.1630.1630.0000.0000.0000.000
162B63LEU 0-0.074-0.04414.787-0.123-0.1230.0000.0000.0000.000
163B64ILE 00.0440.02211.4140.1050.1050.0000.0000.0000.000
164B65GLU -1-0.947-0.97315.303-0.823-0.8230.0000.0000.0000.000
165B66ILE 00.0550.03212.4250.0240.0240.0000.0000.0000.000
166B67CYS 0-0.038-0.01615.9920.0420.0420.0000.0000.0000.000
167B68GLY 00.0940.04317.8470.0530.0530.0000.0000.0000.000
168B69HIS 10.7840.89118.3801.1941.1940.0000.0000.0000.000
169B70LYS 10.9570.97518.7320.5810.5810.0000.0000.0000.000
170B71ALA 00.0630.04315.825-0.001-0.0010.0000.0000.0000.000
171B72ILE 00.0010.02715.5420.0680.0680.0000.0000.0000.000
172B73GLY 00.0420.01711.793-0.123-0.1230.0000.0000.0000.000
173B74THR 0-0.006-0.0038.0830.2300.2300.0000.0000.0000.000
174B75VAL 00.0060.0057.749-0.630-0.6300.0000.0000.0000.000
175B76LEU 0-0.015-0.0173.4530.2110.6610.016-0.079-0.3870.000
176B77VAL 00.0350.0267.1230.0980.0980.0000.0000.0000.000
177B78GLY 00.0340.0038.9530.1400.1400.0000.0000.0000.000
178B79PRO 0-0.0040.0218.333-0.243-0.2430.0000.0000.0000.000
179B80THR 0-0.056-0.0133.3350.3161.4440.031-0.395-0.764-0.002
180B81PRO 00.0520.0422.026-1.402-2.2715.060-0.933-3.2570.003
181B82VAL 00.019-0.0042.444-3.572-1.6364.274-1.577-4.6330.004
182B83ASN 00.0190.0024.123-0.513-0.2830.001-0.013-0.2180.000
183B84ILE 00.0290.0321.9674.427-7.49825.476-3.658-9.893-0.006
184B85ILE 00.0100.0165.189-0.273-0.083-0.001-0.009-0.1810.000
185B86GLY 00.1280.0454.785-1.134-1.061-0.001-0.014-0.0580.000
186B87ARG 10.9140.9045.7624.9364.9360.0000.0000.0000.000
187B88ASN 00.0620.0866.392-0.030-0.0300.0000.0000.0000.000
188B89LEU 0-0.024-0.0318.1630.6800.6800.0000.0000.0000.000
189B90LEU 0-0.0830.0258.1220.3580.3580.0000.0000.0000.000
190B91THR 0-0.025-0.00310.6550.3360.3360.0000.0000.0000.000
191B92GLN 0-0.063-0.01913.0590.4140.4140.0000.0000.0000.000
192B93ILE 0-0.073-0.02713.0830.1980.1980.0000.0000.0000.000
193B94GLY 00.0570.03315.7510.1050.1050.0000.0000.0000.000
194B95ALA 0-0.0350.00112.0950.0390.0390.0000.0000.0000.000
195B96THR 0-0.063-0.04413.234-0.207-0.2070.0000.0000.0000.000
196B97LEU 00.0000.0028.6930.0140.0140.0000.0000.0000.000
197B98ASN 00.033-0.00613.069-0.016-0.0160.0000.0000.0000.000
198B99PHE -1-0.839-0.90411.758-1.325-1.3250.0000.0000.0000.000