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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: Z214N

Calculation Name: 1BVE-AB-NMR60-Model22

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 -2294038.345468
FMO2-HF: Nuclear repulsion 2217560.923859
FMO2-HF: Total energy -76477.421609
FMO2-MP2: Total energy -76703.247193


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.
-151.913-219.941284.514-84.323-132.1670.076


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.
-151.913-219.941284.514-84.323-132.167-0.076
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 : -0.077 / q_NPA : -0.128
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 10.8010.88617.3111.3491.3490.0000.0000.0000.000
2A2GLN 00.1020.08917.502-0.177-0.1770.0000.0000.0000.000
3A3VAL 00.0020.01312.6460.0330.0330.0000.0000.0000.000
4A4THR 00.0610.00615.403-0.123-0.1230.0000.0000.0000.000
5A5LEU 0-0.018-0.02113.0660.0890.0890.0000.0000.0000.000
6A6TRP 00.0160.02312.463-0.280-0.2800.0000.0000.0000.000
7A7GLN 0-0.0230.00110.0060.0150.0150.0000.0000.0000.000
8A8ARG 10.9230.9333.2242.8713.2890.012-0.054-0.3760.000
9A9PRO 0-0.045-0.0018.2610.6280.6280.0000.0000.0000.000
10A10LEU 0-0.0030.0027.530-0.400-0.4000.0000.0000.0000.000
11A11VAL 0-0.013-0.00711.0250.3870.3870.0000.0000.0000.000
12A12THR 0-0.011-0.01713.128-0.064-0.0640.0000.0000.0000.000
13A13ILE 00.0060.00211.8150.0980.0980.0000.0000.0000.000
14A14LYS 10.9340.95815.5450.6510.6510.0000.0000.0000.000
15A15ILE 00.0580.03811.5980.0210.0210.0000.0000.0000.000
16A16GLY 00.0520.01415.3890.0660.0660.0000.0000.0000.000
17A17GLY 0-0.068-0.02617.7050.0510.0510.0000.0000.0000.000
18A18GLN 0-0.033-0.00817.1060.0380.0380.0000.0000.0000.000
19A19LEU 0-0.009-0.01817.152-0.073-0.0730.0000.0000.0000.000
20A20LYS 10.9270.97711.8370.5420.5420.0000.0000.0000.000
21A21GLU -1-0.875-0.9389.561-1.227-1.2270.0000.0000.0000.000
22A22ALA 0-0.008-0.0349.0740.0070.0070.0000.0000.0000.000
23A23LEU 0-0.0090.0153.173-0.0240.9200.067-0.167-0.8430.001
24A24LEU 0-0.017-0.0285.588-1.992-1.9920.0000.0000.0000.000
25A25ASP -1-0.660-0.7561.334-72.004-122.00696.852-38.253-8.597-0.145
26A26THR 0-0.096-0.0574.3181.3081.564-0.001-0.039-0.2160.000
27A27GLY 00.0490.0242.6801.8992.8330.245-0.422-0.7570.002
28A28ALA 0-0.054-0.0202.0855.157-0.82217.770-4.508-7.2830.004
29A29ASP -1-0.856-0.9512.038-1.177-2.9265.981-1.279-2.9530.016
30A30ASP -1-0.887-0.9762.707-3.041-1.4480.369-0.609-1.3530.007
31A31THR 0-0.051-0.0463.751-3.068-2.5640.008-0.188-0.324-0.001
32A32VAL 0-0.0100.0062.974-0.2451.2800.140-0.351-1.3140.001
33A33LEU 00.001-0.0224.673-0.929-0.828-0.001-0.009-0.0910.000
34A34GLU -1-0.925-0.9867.6470.5380.5380.0000.0000.0000.000
35A35GLU -1-0.932-0.9798.4860.2090.2090.0000.0000.0000.000
36A36MET 0-0.065-0.04211.890-0.159-0.1590.0000.0000.0000.000
37A37SER 00.0050.01114.8360.0830.0830.0000.0000.0000.000
38A38LEU 00.0080.00112.935-0.087-0.0870.0000.0000.0000.000
39A39PRO 0-0.0030.00616.8950.0600.0600.0000.0000.0000.000
40A40GLY 00.051-0.01117.4090.0220.0220.0000.0000.0000.000
41A41ARG 10.9580.98317.4490.0000.0000.0000.0000.0000.000
42A42TRP 00.0310.02613.1590.0070.0070.0000.0000.0000.000
43A43LYS 10.9410.95811.402-0.370-0.3700.0000.0000.0000.000
44A44PRO 0-0.0040.01110.6100.0840.0840.0000.0000.0000.000
45A45LYS 10.9240.9755.575-1.549-1.5490.0000.0000.0000.000
46A46MET 00.001-0.0147.9440.0740.0740.0000.0000.0000.000
47A47ILE 0-0.0470.0132.261-3.480-1.0682.438-1.217-3.6330.013
48A48GLY 00.073-0.0033.7700.2070.7970.005-0.131-0.4640.000
49A49GLY 0-0.021-0.0231.988-7.906-5.4508.197-5.331-5.3210.002
50A50ILE 0-0.036-0.0041.895-6.196-19.09633.477-2.141-18.4350.031
51A51GLY 00.0350.0034.0110.5081.2800.007-0.172-0.6080.001
52A52GLY 00.0140.0116.078-1.930-1.9300.0000.0000.0000.000
53A53PHE 0-0.0070.0245.8221.3461.3460.0000.0000.0000.000
54A54ILE 00.0040.0255.672-0.389-0.3890.0000.0000.0000.000
55A55LYS 10.9620.9628.105-1.567-1.5670.0000.0000.0000.000
56A56VAL 00.0160.0235.260-0.068-0.0680.0000.0000.0000.000
57A57ARG 10.9080.9588.646-0.573-0.5730.0000.0000.0000.000
58A58GLN 00.0360.0097.778-0.035-0.0350.0000.0000.0000.000
59A59TYR 0-0.0310.0129.7600.0250.0250.0000.0000.0000.000
60A60ASP -1-0.816-0.92211.7440.1290.1290.0000.0000.0000.000
61A61GLN 0-0.080-0.03613.501-0.015-0.0150.0000.0000.0000.000
62A62ILE 00.005-0.00112.9510.0140.0140.0000.0000.0000.000
63A63LEU 0-0.054-0.05714.687-0.101-0.1010.0000.0000.0000.000
64A64ILE 00.0250.01111.2960.0140.0140.0000.0000.0000.000
65A65GLU -1-0.933-0.97915.222-0.754-0.7540.0000.0000.0000.000
66A66ILE 00.0420.02212.895-0.105-0.1050.0000.0000.0000.000
67A67CYS 0-0.046-0.03417.0180.0580.0580.0000.0000.0000.000
68A68GLY 00.0150.01918.8610.0650.0650.0000.0000.0000.000
69A69HIS 10.9000.94719.2421.0041.0040.0000.0000.0000.000
70A70LYS 11.0181.01619.2220.4160.4160.0000.0000.0000.000
71A71ALA 00.0240.01915.4230.0100.0100.0000.0000.0000.000
72A72ILE 0-0.0160.03115.219-0.038-0.0380.0000.0000.0000.000
73A73GLY 00.044-0.00212.088-0.050-0.0500.0000.0000.0000.000
74A74THR 0-0.074-0.0308.678-0.041-0.0410.0000.0000.0000.000
75A75VAL 00.0360.0237.935-0.097-0.0970.0000.0000.0000.000
76A76LEU 0-0.011-0.0214.1670.3080.4990.000-0.016-0.1760.000
77A77VAL 0-0.0030.0117.817-0.259-0.2590.0000.0000.0000.000
78A78GLY 0-0.019-0.0439.4140.2190.2190.0000.0000.0000.000
79A79PRO 0-0.0090.0258.625-0.248-0.2480.0000.0000.0000.000
80A80THR 0-0.0640.0123.9790.2640.6880.003-0.090-0.3360.000
81A81PRO 00.0550.0222.001-0.957-1.0662.871-0.560-2.203-0.002
82A82VAL 00.0280.0053.037-3.065-0.5130.853-0.733-2.6730.007
83A83ASN 0-0.0420.0104.843-0.227-0.034-0.001-0.011-0.1820.000
84A84ILE 00.013-0.0052.124-3.258-1.1064.276-1.440-4.987-0.001
85A85ILE 0-0.015-0.0015.3471.1031.290-0.001-0.005-0.1820.000
86A86GLY 00.1070.0524.973-1.135-1.1350.0000.0000.0000.000
87A87ARG 10.8280.9075.9052.7282.7280.0000.0000.0000.000
88A88ASN 00.0480.0686.643-0.286-0.2860.0000.0000.0000.000
89A89LEU 0-0.0170.0008.6250.0470.0470.0000.0000.0000.000
90A90LEU 0-0.0570.0028.0140.1720.1720.0000.0000.0000.000
91A91THR 0-0.039-0.02411.6220.1090.1090.0000.0000.0000.000
92A92GLN 0-0.055-0.01213.5180.1560.1560.0000.0000.0000.000
93A93ILE 0-0.083-0.03013.7730.0780.0780.0000.0000.0000.000
94A94GLY 00.0350.02616.5160.0210.0210.0000.0000.0000.000
95A95ALA 0-0.006-0.01712.583-0.027-0.0270.0000.0000.0000.000
96A96THR 0-0.037-0.04614.3020.0910.0910.0000.0000.0000.000
97A97LEU 0-0.0230.0018.855-0.017-0.0170.0000.0000.0000.000
98A98ASN 0-0.001-0.01813.3290.0580.0580.0000.0000.0000.000
99A99PHE -1-0.818-0.88712.250-1.352-1.3520.0000.0000.0000.000
100B1PRO 10.8240.89717.7071.2171.2170.0000.0000.0000.000
101B2GLN 00.0280.03517.366-0.153-0.1530.0000.0000.0000.000
102B3VAL 00.0070.01912.0750.0830.0830.0000.0000.0000.000
103B4THR 00.0280.01013.760-0.197-0.1970.0000.0000.0000.000
104B5LEU 0-0.032-0.02712.330-0.085-0.0850.0000.0000.0000.000
105B6TRP 00.0220.00312.4620.0260.0260.0000.0000.0000.000
106B7GLN 00.0200.0089.0450.1400.1400.0000.0000.0000.000
107B8ARG 10.9800.9984.3810.7391.002-0.001-0.012-0.2500.000
108B9PRO 00.0040.0187.4840.5310.5310.0000.0000.0000.000
109B10LEU 0-0.037-0.0167.808-0.283-0.2830.0000.0000.0000.000
110B11VAL 0-0.012-0.00211.0710.2370.2370.0000.0000.0000.000
111B12THR 0-0.010-0.01013.203-0.009-0.0090.0000.0000.0000.000
112B13ILE 00.0250.00611.617-0.008-0.0080.0000.0000.0000.000
113B14LYS 10.9400.95515.3900.5550.5550.0000.0000.0000.000
114B15ILE 00.0570.03611.1250.0120.0120.0000.0000.0000.000
115B16GLY 00.0350.00915.3870.0680.0680.0000.0000.0000.000
116B17GLY 0-0.037-0.01717.5720.0340.0340.0000.0000.0000.000
117B18GLN 0-0.032-0.01017.0980.0630.0630.0000.0000.0000.000
118B19LEU 0-0.006-0.01516.962-0.060-0.0600.0000.0000.0000.000
119B20LYS 10.9140.97411.8050.4440.4440.0000.0000.0000.000
120B21GLU -1-0.886-0.93810.031-0.691-0.6910.0000.0000.0000.000
121B22ALA 00.041-0.0249.2900.0190.0190.0000.0000.0000.000
122B23LEU 0-0.0640.0173.438-1.0890.2010.062-0.335-1.0170.002
123B24LEU 0-0.013-0.0325.994-1.305-1.3050.0000.0000.0000.000
124B25ASP -1-0.689-0.8722.112-33.083-41.03923.544-6.557-9.031-0.072
125B26THR 0-0.102-0.0674.4630.5620.746-0.001-0.007-0.1770.000
126B27GLY 00.0510.0252.4270.8381.9780.662-0.967-0.835-0.004
127B28ALA 0-0.0430.0022.1511.7051.1239.994-2.678-6.7340.000
128B29ASP -1-0.801-0.9042.417-3.814-1.9540.352-0.639-1.5730.000
129B30ASP -1-0.891-0.9692.7121.0273.0801.116-0.996-2.1740.007
130B31THR 0-0.108-0.0463.260-4.891-3.7040.075-0.584-0.679-0.005
131B32VAL 0-0.036-0.0103.116-0.0871.5310.132-0.403-1.3470.001
132B33LEU 00.011-0.0174.793-0.551-0.442-0.001-0.010-0.0980.000
133B34GLU -1-0.920-0.9926.8110.7130.7130.0000.0000.0000.000
134B35GLU -1-0.988-0.9987.8530.5170.5170.0000.0000.0000.000
135B36MET 0-0.0200.00211.334-0.109-0.1090.0000.0000.0000.000
136B37SER 0-0.014-0.00914.1530.1000.1000.0000.0000.0000.000
137B38LEU 0-0.007-0.00312.488-0.061-0.0610.0000.0000.0000.000
138B39PRO 00.0120.01816.3700.0560.0560.0000.0000.0000.000
139B40GLY 00.0560.00616.9950.0510.0510.0000.0000.0000.000
140B41ARG 10.9570.96016.836-0.132-0.1320.0000.0000.0000.000
141B42TRP 00.0390.04612.6080.0240.0240.0000.0000.0000.000
142B43LYS 10.9410.95612.175-0.512-0.5120.0000.0000.0000.000
143B44PRO 00.0050.01811.2250.1040.1040.0000.0000.0000.000
144B45LYS 10.9320.9696.786-1.869-1.8690.0000.0000.0000.000
145B46MET 0-0.005-0.0178.301-0.223-0.2230.0000.0000.0000.000
146B47ILE 0-0.0050.0332.420-3.989-0.9651.236-1.018-3.2420.011
147B48GLY 00.054-0.0224.099-0.1030.3040.001-0.066-0.3420.000
148B49GLY 0-0.014-0.0071.993-4.397-3.7358.882-5.052-4.4920.017
149B50ILE 00.0000.0081.967-6.880-22.05137.279-2.134-19.9750.038
150B51GLY 0-0.010-0.0153.8350.0210.7090.009-0.096-0.6020.001
151B52GLY 00.0000.0046.105-1.924-1.9240.0000.0000.0000.000
152B53PHE 0-0.0160.0155.9611.7861.7860.0000.0000.0000.000
153B54ILE 00.0220.0535.548-0.649-0.6490.0000.0000.0000.000
154B55LYS 10.9390.9578.202-1.499-1.4990.0000.0000.0000.000
155B56VAL 00.018-0.0035.490-0.059-0.0590.0000.0000.0000.000
156B57ARG 10.9080.9578.618-0.657-0.6570.0000.0000.0000.000
157B58GLN 0-0.053-0.0206.6290.1340.1340.0000.0000.0000.000
158B59TYR 0-0.039-0.0188.7060.0100.0100.0000.0000.0000.000
159B60ASP -1-0.856-0.92011.1600.2670.2670.0000.0000.0000.000
160B61GLN 0-0.068-0.05412.806-0.027-0.0270.0000.0000.0000.000
161B62ILE 00.014-0.00312.4290.0390.0390.0000.0000.0000.000
162B63LEU 0-0.058-0.05214.075-0.101-0.1010.0000.0000.0000.000
163B64ILE 00.0200.01510.8290.0420.0420.0000.0000.0000.000
164B65GLU -1-1.004-0.99614.700-0.667-0.6670.0000.0000.0000.000
165B66ILE 00.0650.03212.434-0.047-0.0470.0000.0000.0000.000
166B67CYS 0-0.051-0.03516.4040.0630.0630.0000.0000.0000.000
167B68GLY 00.0280.03018.8060.1000.1000.0000.0000.0000.000
168B69HIS 00.002-0.00518.6770.0050.0050.0000.0000.0000.000
169B70LYS 10.9640.97518.7230.4430.4430.0000.0000.0000.000
170B71ALA 00.0140.02014.333-0.010-0.0100.0000.0000.0000.000
171B72ILE 0-0.0200.03014.384-0.014-0.0140.0000.0000.0000.000
172B73GLY 00.0230.01011.280-0.059-0.0590.0000.0000.0000.000
173B74THR 0-0.024-0.0197.666-0.027-0.0270.0000.0000.0000.000
174B75VAL 00.0280.0237.293-0.128-0.1280.0000.0000.0000.000
175B76LEU 0-0.039-0.0193.3880.0420.4240.011-0.053-0.3390.000
176B77VAL 00.0390.0216.646-0.254-0.2540.0000.0000.0000.000
177B78GLY 0-0.032-0.0359.4170.2420.2420.0000.0000.0000.000
178B79PRO 00.0160.0368.443-0.277-0.2770.0000.0000.0000.000
179B80THR 0-0.0710.0043.733-0.1320.5410.009-0.217-0.464-0.001
180B81PRO 00.0880.0631.996-0.855-1.5184.074-0.677-2.734-0.001
181B82VAL 00.014-0.0172.298-1.318-1.5496.530-1.362-4.9360.002
182B83ASN 0-0.039-0.0064.443-0.390-0.2150.000-0.017-0.1580.000
183B84ILE 00.0220.0092.0721.372-5.46916.984-2.701-7.442-0.008
184B85ILE 0-0.0080.0095.3390.2760.2760.0000.0000.0000.000
185B86GLY 00.1480.0414.436-1.217-1.087-0.001-0.015-0.1140.000
186B87ARG 10.9360.8995.3864.4004.506-0.001-0.001-0.1050.000
187B88ASN 00.0410.0856.083-0.173-0.1730.0000.0000.0000.000
188B89LEU 00.045-0.0138.0330.3080.3080.0000.0000.0000.000
189B90LEU 0-0.0340.0268.3450.1850.1850.0000.0000.0000.000
190B91THR 0-0.070-0.03011.4900.2300.2300.0000.0000.0000.000
191B92GLN 0-0.052-0.01011.1840.2100.2100.0000.0000.0000.000
192B93ILE 0-0.066-0.01813.2870.0980.0980.0000.0000.0000.000
193B94GLY 00.0380.02616.0170.0380.0380.0000.0000.0000.000
194B95ALA 0-0.012-0.01613.0930.0080.0080.0000.0000.0000.000
195B96THR 0-0.075-0.04215.0400.0330.0330.0000.0000.0000.000
196B97LEU 0-0.018-0.0119.3420.0050.0050.0000.0000.0000.000
197B98ASN 00.005-0.02413.7490.0570.0570.0000.0000.0000.000
198B99PHE -1-0.850-0.90512.742-1.399-1.3990.0000.0000.0000.000