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: 3N8RL

Calculation Name: 1BVE-AB-NMR60-Model9

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 -2277540.702271
FMO2-HF: Nuclear repulsion 2201063.176772
FMO2-HF: Total energy -76477.525499
FMO2-MP2: Total energy -76703.272403


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.
-157.903-161.512175.170-52.721-118.8370.009


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.
-157.903-161.512175.17-52.721-118.837-0.009
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 : -0.008 / q_NPA : -0.078
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 10.8380.91018.4961.5121.5120.0000.0000.0000.000
2A2GLN 00.0040.02718.310-0.177-0.1770.0000.0000.0000.000
3A3VAL 00.0000.00114.9510.1410.1410.0000.0000.0000.000
4A4THR 00.0060.00614.977-0.273-0.2730.0000.0000.0000.000
5A5LEU 00.0880.02611.386-0.209-0.2090.0000.0000.0000.000
6A6TRP 00.0040.00312.885-0.007-0.0070.0000.0000.0000.000
7A7GLN 0-0.053-0.02312.6350.2280.2280.0000.0000.0000.000
8A8ARG 10.9980.9849.2361.1601.1600.0000.0000.0000.000
9A9PRO 0-0.0120.0298.6510.5180.5180.0000.0000.0000.000
10A10LEU 00.021-0.0058.295-0.315-0.3150.0000.0000.0000.000
11A11VAL 0-0.020-0.01911.6810.2670.2670.0000.0000.0000.000
12A12THR 0-0.009-0.01213.793-0.055-0.0550.0000.0000.0000.000
13A13ILE 0-0.0100.01011.4540.0790.0790.0000.0000.0000.000
14A14LYS 10.9340.96115.4080.7040.7040.0000.0000.0000.000
15A15ILE 00.0340.02611.1070.0090.0090.0000.0000.0000.000
16A16GLY 00.0460.00815.4520.0670.0670.0000.0000.0000.000
17A17GLY 0-0.054-0.01717.6250.0390.0390.0000.0000.0000.000
18A18GLN 00.001-0.01516.9340.1080.1080.0000.0000.0000.000
19A19LEU 0-0.024-0.01717.380-0.083-0.0830.0000.0000.0000.000
20A20LYS 10.9140.98611.5710.6320.6320.0000.0000.0000.000
21A21GLU -1-0.903-0.95510.131-1.082-1.0820.0000.0000.0000.000
22A22ALA 0-0.014-0.0049.523-0.026-0.0260.0000.0000.0000.000
23A23LEU 00.001-0.0063.826-0.3740.3240.018-0.116-0.6000.000
24A24LEU 0-0.050-0.0236.201-1.487-1.4870.0000.0000.0000.000
25A25ASP -1-0.671-0.8511.956-53.919-55.02616.239-7.041-8.091-0.082
26A26THR 0-0.103-0.0684.346-0.712-0.501-0.001-0.030-0.1800.000
27A27GLY 00.0210.0402.5252.3513.3050.345-0.529-0.7700.003
28A28ALA 0-0.043-0.0022.1703.5102.12911.063-3.362-6.3190.002
29A29ASP -1-0.811-0.9232.368-2.063-0.6260.575-0.383-1.630-0.002
30A30ASP -1-0.871-0.9682.711-0.8591.1440.461-0.878-1.5860.009
31A31THR 0-0.063-0.0253.426-4.172-3.3220.035-0.396-0.488-0.003
32A32VAL 0-0.0090.0082.998-0.0911.3470.141-0.324-1.2550.001
33A33LEU 0-0.031-0.0384.613-0.573-0.4780.000-0.011-0.0840.000
34A34GLU -1-0.915-0.9777.1890.9240.9240.0000.0000.0000.000
35A35GLU -1-0.986-1.0098.2680.5110.5110.0000.0000.0000.000
36A36MET 0-0.0150.00211.733-0.161-0.1610.0000.0000.0000.000
37A37SER 0-0.0030.01114.6320.1020.1020.0000.0000.0000.000
38A38LEU 00.0150.00212.894-0.100-0.1000.0000.0000.0000.000
39A39PRO 00.0120.02316.3010.0400.0400.0000.0000.0000.000
40A40GLY 00.0440.01817.7870.0590.0590.0000.0000.0000.000
41A41ARG 10.9350.96517.484-0.067-0.0670.0000.0000.0000.000
42A42TRP 00.0350.03212.6040.0230.0230.0000.0000.0000.000
43A43LYS 10.9060.94412.241-0.593-0.5930.0000.0000.0000.000
44A44PRO 00.0240.02111.2470.1000.1000.0000.0000.0000.000
45A45LYS 10.9600.9846.095-1.998-1.9980.0000.0000.0000.000
46A46MET 00.015-0.0158.235-0.031-0.0310.0000.0000.0000.000
47A47ILE 0-0.0290.0062.689-3.601-0.8101.106-0.924-2.9740.011
48A48GLY 00.0620.0104.4960.1410.400-0.001-0.038-0.2200.000
49A49GLY 0-0.015-0.0012.200-4.237-2.5544.348-2.793-3.2380.016
50A50ILE 0-0.0160.0042.034-8.150-18.41032.218-3.535-18.4240.041
51A51GLY 0-0.009-0.0104.006-0.2740.4000.008-0.159-0.5230.001
52A52GLY 00.002-0.0056.215-2.176-2.1760.0000.0000.0000.000
53A53PHE 00.0100.0036.1461.5911.5910.0000.0000.0000.000
54A54ILE 0-0.0130.0385.733-0.434-0.4340.0000.0000.0000.000
55A55LYS 10.9210.9758.538-2.117-2.1170.0000.0000.0000.000
56A56VAL 00.0350.0125.447-0.108-0.1080.0000.0000.0000.000
57A57ARG 10.9170.9618.698-0.753-0.7530.0000.0000.0000.000
58A58GLN 0-0.082-0.0548.242-0.179-0.1790.0000.0000.0000.000
59A59TYR 00.008-0.0099.117-0.024-0.0240.0000.0000.0000.000
60A60ASP -1-0.774-0.88611.2120.0890.0890.0000.0000.0000.000
61A61GLN 0-0.077-0.04913.125-0.003-0.0030.0000.0000.0000.000
62A62ILE 0-0.0090.00312.1270.0390.0390.0000.0000.0000.000
63A63LEU 0-0.057-0.03014.338-0.113-0.1130.0000.0000.0000.000
64A64ILE 00.0760.02810.6870.0430.0430.0000.0000.0000.000
65A65GLU -1-0.963-1.00014.621-0.809-0.8090.0000.0000.0000.000
66A66ILE 00.0620.03611.848-0.048-0.0480.0000.0000.0000.000
67A67CYS 0-0.021-0.00916.1870.0430.0430.0000.0000.0000.000
68A68GLY 00.0340.02718.8260.0450.0450.0000.0000.0000.000
69A69HIS 0-0.012-0.00918.3410.0340.0340.0000.0000.0000.000
70A70LYS 10.9020.94618.0540.5730.5730.0000.0000.0000.000
71A71ALA 00.0560.03314.468-0.008-0.0080.0000.0000.0000.000
72A72ILE 0-0.0240.00614.642-0.004-0.0040.0000.0000.0000.000
73A73GLY 00.0250.00411.334-0.106-0.1060.0000.0000.0000.000
74A74THR 0-0.033-0.0348.1430.0230.0230.0000.0000.0000.000
75A75VAL 0-0.0030.0087.460-0.103-0.1030.0000.0000.0000.000
76A76LEU 0-0.033-0.0263.349-0.0160.4260.022-0.073-0.3910.000
77A77VAL 00.0140.0176.919-0.157-0.1570.0000.0000.0000.000
78A78GLY 00.012-0.0139.2360.2300.2300.0000.0000.0000.000
79A79PRO 0-0.0380.0118.608-0.311-0.3110.0000.0000.0000.000
80A80THR 0-0.091-0.0023.6920.1330.7730.012-0.206-0.445-0.001
81A81PRO 00.1030.0561.951-0.791-1.5774.198-0.730-2.682-0.003
82A82VAL 00.0710.0252.913-3.717-1.0741.376-0.896-3.1230.006
83A83ASN 0-0.088-0.0384.628-0.249-0.0370.000-0.014-0.1970.000
84A84ILE 00.0260.0072.055-2.944-0.8904.491-1.285-5.2590.001
85A85ILE 0-0.0090.0115.1160.9921.164-0.001-0.006-0.1650.000
86A86GLY 00.1260.0424.746-1.385-1.281-0.001-0.015-0.0880.000
87A87ARG 10.8850.9335.5924.6394.6390.0000.0000.0000.000
88A88ASN 00.0260.0746.371-0.204-0.2040.0000.0000.0000.000
89A89LEU 00.016-0.0098.3320.2930.2930.0000.0000.0000.000
90A90LEU 0-0.064-0.0107.9730.2030.2030.0000.0000.0000.000
91A91THR 0-0.021-0.04511.1820.2340.2340.0000.0000.0000.000
92A92GLN 0-0.074-0.02112.7130.3250.3250.0000.0000.0000.000
93A93ILE 0-0.050-0.01813.3660.0990.0990.0000.0000.0000.000
94A94GLY 00.0490.02816.0120.0470.0470.0000.0000.0000.000
95A95ALA 0-0.011-0.01612.518-0.015-0.0150.0000.0000.0000.000
96A96THR 0-0.125-0.06514.396-0.047-0.0470.0000.0000.0000.000
97A97LEU 00.0380.0179.5790.0090.0090.0000.0000.0000.000
98A98ASN 00.029-0.02413.8460.0650.0650.0000.0000.0000.000
99A99PHE -1-0.868-0.91314.141-1.596-1.5960.0000.0000.0000.000
100B1PRO 10.8070.89718.3751.5751.5750.0000.0000.0000.000
101B2GLN 00.0420.04818.097-0.160-0.1600.0000.0000.0000.000
102B3VAL 00.0100.01712.8720.0860.0860.0000.0000.0000.000
103B4THR 00.0310.01214.258-0.312-0.3120.0000.0000.0000.000
104B5LEU 00.002-0.01714.225-0.192-0.1920.0000.0000.0000.000
105B6TRP 00.0170.00113.047-0.020-0.0200.0000.0000.0000.000
106B7GLN 0-0.0220.0019.9610.3970.3970.0000.0000.0000.000
107B8ARG 10.9280.9635.7022.1182.1180.0000.0000.0000.000
108B9PRO 0-0.0100.0108.6840.6500.6500.0000.0000.0000.000
109B10LEU 00.006-0.0097.830-0.424-0.4240.0000.0000.0000.000
110B11VAL 0-0.030-0.01911.3470.2850.2850.0000.0000.0000.000
111B12THR 00.0330.01113.652-0.002-0.0020.0000.0000.0000.000
112B13ILE 0-0.0190.00311.2280.0730.0730.0000.0000.0000.000
113B14LYS 10.9800.97115.0890.6820.6820.0000.0000.0000.000
114B15ILE 00.0520.03610.526-0.017-0.0170.0000.0000.0000.000
115B16GLY 00.0170.01314.8330.0940.0940.0000.0000.0000.000
116B17GLY 0-0.042-0.02017.4270.0570.0570.0000.0000.0000.000
117B18GLN 0-0.032-0.02116.5110.1020.1020.0000.0000.0000.000
118B19LEU 0-0.001-0.01417.095-0.082-0.0820.0000.0000.0000.000
119B20LYS 10.9080.96311.4630.3860.3860.0000.0000.0000.000
120B21GLU -1-0.875-0.93111.690-1.036-1.0360.0000.0000.0000.000
121B22ALA 00.0090.0029.249-0.042-0.0420.0000.0000.0000.000
122B23LEU 0-0.038-0.0073.435-0.1240.8100.063-0.166-0.8320.000
123B24LEU 0-0.029-0.0236.215-1.541-1.5410.0000.0000.0000.000
124B25ASP -1-0.732-0.8591.590-53.444-69.45036.474-12.006-8.462-0.098
125B26THR 0-0.056-0.0504.5760.6850.850-0.001-0.008-0.1560.000
126B27GLY 00.0710.0252.6701.7792.8140.373-0.565-0.8440.004
127B28ALA 0-0.069-0.0152.0864.6582.45412.993-3.664-7.1240.001
128B29ASP -1-0.846-0.9252.518-4.681-2.6610.369-0.538-1.8500.002
129B30ASP -1-0.917-0.9842.432-0.6491.2231.523-1.193-2.2010.014
130B31THR 0-0.031-0.0163.091-5.363-3.9460.146-0.717-0.846-0.007
131B32VAL 0-0.0080.0002.743-0.4431.3780.437-0.471-1.7870.001
132B33LEU 0-0.035-0.0424.337-0.768-0.6390.002-0.026-0.1050.000
133B34GLU -1-0.954-0.9887.5991.0511.0510.0000.0000.0000.000
134B35GLU -1-0.944-0.9738.9160.8970.8970.0000.0000.0000.000
135B36MET 0-0.014-0.00112.055-0.188-0.1880.0000.0000.0000.000
136B37SER 0-0.0170.00314.9040.1060.1060.0000.0000.0000.000
137B38LEU 0-0.022-0.01212.258-0.099-0.0990.0000.0000.0000.000
138B39PRO 00.0510.04015.1710.0240.0240.0000.0000.0000.000
139B40GLY 00.0690.04317.0890.0750.0750.0000.0000.0000.000
140B41ARG 10.9000.93517.495-0.208-0.2080.0000.0000.0000.000
141B42TRP 00.0550.05813.0670.0160.0160.0000.0000.0000.000
142B43LYS 10.9590.95612.568-0.577-0.5770.0000.0000.0000.000
143B44PRO 0-0.0330.00811.3140.1050.1050.0000.0000.0000.000
144B45LYS 10.9120.9685.926-2.182-2.1820.0000.0000.0000.000
145B46MET 00.015-0.0298.311-0.022-0.0220.0000.0000.0000.000
146B47ILE 0-0.0170.0082.758-3.310-0.8111.491-0.865-3.1250.011
147B48GLY 00.0450.0114.4580.3250.6260.000-0.047-0.2540.000
148B49GLY 0-0.0100.0082.192-4.613-2.9765.166-3.198-3.6040.018
149B50ILE 0-0.0050.0021.976-6.356-18.77233.979-2.981-18.5820.038
150B51GLY 00.014-0.0104.0970.0280.6550.009-0.162-0.4740.001
151B52GLY 00.0050.0006.383-2.031-2.0310.0000.0000.0000.000
152B53PHE 00.020-0.0096.2361.5251.5250.0000.0000.0000.000
153B54ILE 0-0.0250.0265.820-0.659-0.6590.0000.0000.0000.000
154B55LYS 10.9180.9708.612-2.202-2.2020.0000.0000.0000.000
155B56VAL 00.0130.0195.5820.0060.0060.0000.0000.0000.000
156B57ARG 10.9380.9598.630-1.124-1.1240.0000.0000.0000.000
157B58GLN 00.0180.0126.977-0.025-0.0250.0000.0000.0000.000
158B59TYR 0-0.020-0.0478.999-0.078-0.0780.0000.0000.0000.000
159B60ASP -1-0.838-0.94010.5660.3460.3460.0000.0000.0000.000
160B61GLN 0-0.070-0.05612.759-0.072-0.0720.0000.0000.0000.000
161B62ILE 0-0.010-0.00511.1400.0320.0320.0000.0000.0000.000
162B63LEU 0-0.049-0.04813.884-0.115-0.1150.0000.0000.0000.000
163B64ILE 00.0370.01110.3080.0490.0490.0000.0000.0000.000
164B65GLU -1-0.983-0.98414.155-0.866-0.8660.0000.0000.0000.000
165B66ILE 00.0590.03111.605-0.039-0.0390.0000.0000.0000.000
166B67CYS 0-0.057-0.01915.7470.0570.0570.0000.0000.0000.000
167B68GLY 00.0340.03218.6090.0730.0730.0000.0000.0000.000
168B69HIS 10.8820.93018.1281.2421.2420.0000.0000.0000.000
169B70LYS 11.0021.00417.7120.5510.5510.0000.0000.0000.000
170B71ALA 00.0500.02613.965-0.020-0.0200.0000.0000.0000.000
171B72ILE 0-0.0340.03114.2700.0060.0060.0000.0000.0000.000
172B73GLY 00.0290.00210.883-0.153-0.1530.0000.0000.0000.000
173B74THR 00.0070.0027.8870.0390.0390.0000.0000.0000.000
174B75VAL 00.0060.0047.106-0.020-0.0200.0000.0000.0000.000
175B76LEU 0-0.030-0.0113.007-0.2630.3200.077-0.101-0.5580.000
176B77VAL 00.0200.0176.446-0.098-0.0980.0000.0000.0000.000
177B78GLY 00.026-0.0148.7910.1760.1760.0000.0000.0000.000
178B79PRO 0-0.0260.0129.202-0.234-0.2340.0000.0000.0000.000
179B80THR 0-0.069-0.0034.0590.8171.1600.001-0.054-0.2910.000
180B81PRO 00.0800.0332.015-1.208-1.0942.002-0.455-1.661-0.001
181B82VAL 00.0500.0163.125-2.978-0.7230.437-0.623-2.0700.006
182B83ASN 0-0.062-0.0335.030-0.265-0.098-0.001-0.009-0.1570.000
183B84ILE 00.0020.0012.188-3.567-0.7492.981-1.101-4.6980.001
184B85ILE 00.0010.0134.8911.0431.229-0.001-0.008-0.1770.000
185B86GLY 00.1260.0404.481-1.319-1.208-0.001-0.017-0.0930.000
186B87ARG 10.8400.9005.2925.4255.582-0.001-0.002-0.1540.000
187B88ASN 00.0150.0526.0700.1820.1820.0000.0000.0000.000
188B89LEU 0-0.043-0.0128.0410.2870.2870.0000.0000.0000.000
189B90LEU 00.0010.0238.0260.1870.1870.0000.0000.0000.000
190B91THR 0-0.007-0.01111.3550.2560.2560.0000.0000.0000.000
191B92GLN 0-0.104-0.04313.0580.1940.1940.0000.0000.0000.000
192B93ILE 0-0.069-0.03113.4250.1350.1350.0000.0000.0000.000
193B94GLY 00.0250.02215.6140.0870.0870.0000.0000.0000.000
194B95ALA 0-0.010-0.01712.8720.0320.0320.0000.0000.0000.000
195B96THR 0-0.053-0.03614.8270.0620.0620.0000.0000.0000.000
196B97LEU 00.0210.0109.585-0.083-0.0830.0000.0000.0000.000
197B98ASN 0-0.008-0.03114.1010.0720.0720.0000.0000.0000.000
198B99PHE -1-0.855-0.89714.292-1.632-1.6320.0000.0000.0000.000