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: 8J4MY

Calculation Name: 1BVE-AB-NMR60-Model12

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 -2282219.156107
FMO2-HF: Nuclear repulsion 2205741.492059
FMO2-HF: Total energy -76477.664047
FMO2-MP2: Total energy -76703.421221


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.
-154.604-209.650266.323-82.381-128.9010.016


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.
-154.604-209.65266.323-82.381-128.901-0.016
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 : -0.018 / q_NPA : -0.101
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 10.8220.89417.8331.2661.2660.0000.0000.0000.000
2A2GLN 00.0720.05618.074-0.114-0.1140.0000.0000.0000.000
3A3VAL 00.0060.00713.5730.0850.0850.0000.0000.0000.000
4A4THR 00.0520.02115.615-0.150-0.1500.0000.0000.0000.000
5A5LEU 0-0.040-0.01615.7720.1210.1210.0000.0000.0000.000
6A6TRP 00.026-0.00913.3420.0060.0060.0000.0000.0000.000
7A7GLN 00.0390.02710.9230.1750.1750.0000.0000.0000.000
8A8ARG 10.9060.9467.0320.8680.8680.0000.0000.0000.000
9A9PRO 00.0020.0308.7450.3890.3890.0000.0000.0000.000
10A10LEU 0-0.0060.0017.369-0.462-0.4620.0000.0000.0000.000
11A11VAL 0-0.025-0.02111.2870.3330.3330.0000.0000.0000.000
12A12THR 00.0010.00513.359-0.093-0.0930.0000.0000.0000.000
13A13ILE 0-0.0250.00311.6390.1090.1090.0000.0000.0000.000
14A14LYS 10.9540.97315.3460.7260.7260.0000.0000.0000.000
15A15ILE 00.0400.04111.5420.0160.0160.0000.0000.0000.000
16A16GLY 00.0350.01115.9440.0730.0730.0000.0000.0000.000
17A17GLY 0-0.059-0.03418.7250.0540.0540.0000.0000.0000.000
18A18GLN 0-0.018-0.01016.3420.0500.0500.0000.0000.0000.000
19A19LEU 0-0.026-0.01916.607-0.062-0.0620.0000.0000.0000.000
20A20LYS 10.9170.97210.8280.6890.6890.0000.0000.0000.000
21A21GLU -1-0.876-0.93410.037-1.244-1.2440.0000.0000.0000.000
22A22ALA 00.034-0.0138.988-0.116-0.1160.0000.0000.0000.000
23A23LEU 0-0.058-0.0183.232-0.8170.4650.110-0.281-1.1120.001
24A24LEU 0-0.065-0.0305.876-1.768-1.7680.0000.0000.0000.000
25A25ASP -1-0.648-0.7811.355-70.517-118.52294.879-38.053-8.821-0.141
26A26THR 0-0.106-0.0764.1980.6750.959-0.001-0.035-0.2480.000
27A27GLY 00.0540.0402.5431.6882.6710.428-0.538-0.8730.003
28A28ALA 0-0.081-0.0192.1215.5250.39916.854-4.287-7.440-0.002
29A29ASP -1-0.883-0.9552.195-3.752-1.6332.116-1.327-2.9090.020
30A30ASP -1-0.927-1.0032.679-1.5720.0140.249-0.586-1.2490.004
31A31THR 0-0.037-0.0053.317-4.508-3.4040.046-0.573-0.577-0.005
32A32VAL 0-0.067-0.0122.9720.2741.7400.126-0.308-1.2840.001
33A33LEU 00.008-0.0024.864-0.895-0.784-0.001-0.008-0.1030.000
34A34GLU -1-0.857-0.9597.116-0.475-0.4750.0000.0000.0000.000
35A35GLU -1-0.924-0.9748.0540.3100.3100.0000.0000.0000.000
36A36MET 00.002-0.00111.501-0.171-0.1710.0000.0000.0000.000
37A37SER 0-0.0150.00014.4100.0970.0970.0000.0000.0000.000
38A38LEU 00.000-0.00912.986-0.093-0.0930.0000.0000.0000.000
39A39PRO 00.0280.01117.1870.0640.0640.0000.0000.0000.000
40A40GLY 0-0.009-0.00318.0470.0110.0110.0000.0000.0000.000
41A41ARG 10.9560.95717.4070.0470.0470.0000.0000.0000.000
42A42TRP 00.0340.03812.7170.0010.0010.0000.0000.0000.000
43A43LYS 10.9430.97112.111-0.308-0.3080.0000.0000.0000.000
44A44PRO 00.0310.02111.1710.0260.0260.0000.0000.0000.000
45A45LYS 10.9610.9845.030-2.875-2.8750.0000.0000.0000.000
46A46MET 00.006-0.0087.767-0.083-0.0830.0000.0000.0000.000
47A47ILE 0-0.0260.0112.323-3.572-1.2043.581-1.310-4.6390.015
48A48GLY 00.0680.0024.2580.2080.6110.001-0.069-0.3350.000
49A49GLY 0-0.022-0.0052.019-4.395-3.3987.275-4.193-4.0800.020
50A50ILE 0-0.027-0.0032.026-6.619-19.65834.031-1.902-19.0900.039
51A51GLY 00.018-0.0203.995-0.3350.3570.008-0.160-0.5410.001
52A52GLY 00.0110.0006.258-1.948-1.9480.0000.0000.0000.000
53A53PHE 00.0000.0146.1591.4171.4170.0000.0000.0000.000
54A54ILE 0-0.0080.0475.589-0.316-0.3160.0000.0000.0000.000
55A55LYS 10.9110.9448.265-1.775-1.7750.0000.0000.0000.000
56A56VAL 00.0140.0035.392-0.036-0.0360.0000.0000.0000.000
57A57ARG 10.9120.9528.452-0.540-0.5400.0000.0000.0000.000
58A58GLN 00.0020.0018.0280.1080.1080.0000.0000.0000.000
59A59TYR 00.001-0.0069.1170.0260.0260.0000.0000.0000.000
60A60ASP -1-0.846-0.90711.2050.0790.0790.0000.0000.0000.000
61A61GLN 0-0.081-0.05912.986-0.027-0.0270.0000.0000.0000.000
62A62ILE 00.0080.00212.4450.0380.0380.0000.0000.0000.000
63A63LEU 0-0.081-0.04514.443-0.091-0.0910.0000.0000.0000.000
64A64ILE 00.0380.01111.0870.0330.0330.0000.0000.0000.000
65A65GLU -1-0.925-0.96114.911-0.795-0.7950.0000.0000.0000.000
66A66ILE 00.0430.02612.588-0.054-0.0540.0000.0000.0000.000
67A67CYS 0-0.023-0.01516.5180.0420.0420.0000.0000.0000.000
68A68GLY 00.0190.00618.8220.0660.0660.0000.0000.0000.000
69A69HIS 10.8720.94218.5501.1561.1560.0000.0000.0000.000
70A70LYS 10.9691.00318.4060.5080.5080.0000.0000.0000.000
71A71ALA 00.0380.00215.1140.0080.0080.0000.0000.0000.000
72A72ILE 0-0.0290.00515.2050.0060.0060.0000.0000.0000.000
73A73GLY 00.0280.01211.361-0.084-0.0840.0000.0000.0000.000
74A74THR 0-0.008-0.0247.638-0.006-0.0060.0000.0000.0000.000
75A75VAL 00.0060.0047.456-0.167-0.1670.0000.0000.0000.000
76A76LEU 0-0.011-0.0183.3450.0450.5510.024-0.086-0.4440.000
77A77VAL 00.0310.0356.875-0.150-0.1500.0000.0000.0000.000
78A78GLY 00.006-0.0029.0770.2790.2790.0000.0000.0000.000
79A79PRO 0-0.0320.0068.798-0.287-0.2870.0000.0000.0000.000
80A80THR 0-0.0570.0233.6130.4111.0830.011-0.211-0.471-0.001
81A81PRO 00.0140.0051.980-1.176-1.2642.992-0.623-2.2810.002
82A82VAL 00.030-0.0042.362-2.715-0.9972.853-0.999-3.5730.005
83A83ASN 0-0.011-0.0324.306-0.318-0.1300.000-0.014-0.1740.000
84A84ILE 00.0150.0352.1352.696-5.59119.880-3.171-8.422-0.005
85A85ILE 00.0030.0045.4770.8100.8100.0000.0000.0000.000
86A86GLY 00.1040.0504.886-2.605-2.6050.0000.0000.0000.000
87A87ARG 10.8550.9205.7253.4143.4140.0000.0000.0000.000
88A88ASN 00.0300.0466.403-0.329-0.3290.0000.0000.0000.000
89A89LEU 00.001-0.0198.4390.2470.2470.0000.0000.0000.000
90A90LEU 0-0.0440.0027.9220.1910.1910.0000.0000.0000.000
91A91THR 0-0.027-0.01211.4500.2290.2290.0000.0000.0000.000
92A92GLN 0-0.037-0.01313.1540.2050.2050.0000.0000.0000.000
93A93ILE 0-0.070-0.02113.6250.1060.1060.0000.0000.0000.000
94A94GLY 00.0180.01716.3340.0490.0490.0000.0000.0000.000
95A95ALA 0-0.004-0.00813.0500.0180.0180.0000.0000.0000.000
96A96THR 0-0.054-0.05414.9840.0910.0910.0000.0000.0000.000
97A97LEU 0-0.0280.0019.484-0.036-0.0360.0000.0000.0000.000
98A98ASN 00.008-0.01613.9580.0580.0580.0000.0000.0000.000
99A99PHE -1-0.814-0.89112.283-1.127-1.1270.0000.0000.0000.000
100B1PRO 10.8200.89518.0551.0851.0850.0000.0000.0000.000
101B2GLN 00.0570.05017.724-0.119-0.1190.0000.0000.0000.000
102B3VAL 00.0190.01913.6430.0830.0830.0000.0000.0000.000
103B4THR 00.0330.00614.933-0.172-0.1720.0000.0000.0000.000
104B5LEU 00.0150.00915.099-0.114-0.1140.0000.0000.0000.000
105B6TRP 00.029-0.00313.457-0.015-0.0150.0000.0000.0000.000
106B7GLN 0-0.0090.01111.4320.1380.1380.0000.0000.0000.000
107B8ARG 10.9610.9736.9660.8800.8800.0000.0000.0000.000
108B9PRO 0-0.0050.0188.5550.4020.4020.0000.0000.0000.000
109B10LEU 00.0320.0077.840-0.307-0.3070.0000.0000.0000.000
110B11VAL 0-0.024-0.01311.4150.2110.2110.0000.0000.0000.000
111B12THR 00.004-0.00613.476-0.036-0.0360.0000.0000.0000.000
112B13ILE 00.0030.01611.8140.0460.0460.0000.0000.0000.000
113B14LYS 10.9560.96915.3070.3850.3850.0000.0000.0000.000
114B15ILE 00.0500.03011.1660.0090.0090.0000.0000.0000.000
115B16GLY 00.0160.01115.4010.0570.0570.0000.0000.0000.000
116B17GLY 0-0.033-0.01717.9600.0310.0310.0000.0000.0000.000
117B18GLN 0-0.036-0.02316.6400.0670.0670.0000.0000.0000.000
118B19LEU 0-0.010-0.02217.167-0.053-0.0530.0000.0000.0000.000
119B20LYS 10.8980.97410.5430.2630.2630.0000.0000.0000.000
120B21GLU -1-0.897-0.95110.152-0.752-0.7520.0000.0000.0000.000
121B22ALA 0-0.018-0.0029.2850.0120.0120.0000.0000.0000.000
122B23LEU 0-0.039-0.0123.421-0.7600.2740.073-0.221-0.8860.001
123B24LEU 0-0.032-0.0296.053-1.078-1.0780.0000.0000.0000.000
124B25ASP -1-0.673-0.8602.258-33.229-28.9747.693-4.807-7.141-0.052
125B26THR 0-0.065-0.0544.4260.6260.816-0.001-0.005-0.1840.000
126B27GLY 00.0440.0202.6680.8111.9650.376-0.781-0.749-0.001
127B28ALA 0-0.0280.0012.0543.614-3.08119.616-5.002-7.919-0.003
128B29ASP -1-0.941-0.9922.348-3.154-1.6431.397-0.530-2.3780.006
129B30ASP -1-0.863-0.9632.643-2.557-0.9780.457-0.670-1.3660.008
130B31THR 0-0.034-0.0173.655-2.991-2.3810.013-0.241-0.383-0.002
131B32VAL 0-0.0220.0022.975-0.3980.9930.130-0.302-1.2200.001
132B33LEU 0-0.029-0.0224.604-0.349-0.2510.000-0.011-0.0860.000
133B34GLU -1-0.955-0.9748.0100.8280.8280.0000.0000.0000.000
134B35GLU -1-0.956-0.9958.7500.7620.7620.0000.0000.0000.000
135B36MET 00.0310.02212.002-0.129-0.1290.0000.0000.0000.000
136B37SER 0-0.017-0.00515.1500.0630.0630.0000.0000.0000.000
137B38LEU 0-0.017-0.00312.620-0.071-0.0710.0000.0000.0000.000
138B39PRO 00.0190.00616.1590.0210.0210.0000.0000.0000.000
139B40GLY 00.019-0.00217.5660.0470.0470.0000.0000.0000.000
140B41ARG 10.9170.95016.958-0.127-0.1270.0000.0000.0000.000
141B42TRP 00.0500.03412.2230.0200.0200.0000.0000.0000.000
142B43LYS 10.9340.96011.736-0.423-0.4230.0000.0000.0000.000
143B44PRO 00.0160.02110.7140.1040.1040.0000.0000.0000.000
144B45LYS 10.9450.9824.926-1.641-1.6410.0000.0000.0000.000
145B46MET 00.018-0.0038.0650.0340.0340.0000.0000.0000.000
146B47ILE 0-0.034-0.0072.431-4.123-1.1691.760-1.149-3.5650.013
147B48GLY 00.0320.0084.2290.3320.6880.000-0.064-0.2920.000
148B49GLY 0-0.0110.0042.086-4.964-3.4046.080-3.758-3.8820.020
149B50ILE 00.0010.0071.988-6.899-19.54435.118-3.282-19.1900.036
150B51GLY 00.000-0.0223.9680.5141.2210.008-0.152-0.5630.001
151B52GLY 0-0.002-0.0035.962-2.137-2.1370.0000.0000.0000.000
152B53PHE 00.025-0.0075.8121.7131.7130.0000.0000.0000.000
153B54ILE 0-0.0380.0425.620-0.698-0.6980.0000.0000.0000.000
154B55LYS 10.9160.9497.707-2.206-2.2060.0000.0000.0000.000
155B56VAL 00.012-0.0045.2160.0890.0890.0000.0000.0000.000
156B57ARG 10.9260.9648.380-0.821-0.8210.0000.0000.0000.000
157B58GLN 0-0.0290.0016.9490.1920.1920.0000.0000.0000.000
158B59TYR 00.0440.0098.587-0.046-0.0460.0000.0000.0000.000
159B60ASP -1-0.852-0.92411.3130.4000.4000.0000.0000.0000.000
160B61GLN 0-0.063-0.03512.685-0.070-0.0700.0000.0000.0000.000
161B62ILE 0-0.010-0.01612.5360.0180.0180.0000.0000.0000.000
162B63LEU 0-0.081-0.04414.155-0.066-0.0660.0000.0000.0000.000
163B64ILE 00.0130.00910.8250.0240.0240.0000.0000.0000.000
164B65GLU -1-0.964-0.98814.587-0.506-0.5060.0000.0000.0000.000
165B66ILE 00.0340.02212.321-0.045-0.0450.0000.0000.0000.000
166B67CYS 0-0.053-0.03216.5840.0070.0070.0000.0000.0000.000
167B68GLY 00.0210.02219.4600.0290.0290.0000.0000.0000.000
168B69HIS 00.0240.02018.5970.0810.0810.0000.0000.0000.000
169B70LYS 10.9390.95318.3940.2940.2940.0000.0000.0000.000
170B71ALA 00.0560.03114.579-0.007-0.0070.0000.0000.0000.000
171B72ILE 0-0.0070.02414.8550.0230.0230.0000.0000.0000.000
172B73GLY 00.0250.03011.413-0.052-0.0520.0000.0000.0000.000
173B74THR 0-0.023-0.0098.096-0.048-0.0480.0000.0000.0000.000
174B75VAL 0-0.0030.0047.3380.0330.0330.0000.0000.0000.000
175B76LEU 0-0.023-0.0183.160-0.4350.2010.083-0.118-0.6010.000
176B77VAL 00.0150.0196.668-0.212-0.2120.0000.0000.0000.000
177B78GLY 0-0.015-0.0179.1610.1610.1610.0000.0000.0000.000
178B79PRO 00.0130.0308.717-0.214-0.2140.0000.0000.0000.000
179B80THR 0-0.065-0.0193.9590.4080.8520.004-0.102-0.3450.000
180B81PRO 00.0660.0291.941-0.807-1.4763.845-0.755-2.422-0.003
181B82VAL 00.0700.0193.167-2.838-0.6030.498-0.578-2.1560.005
182B83ASN 0-0.064-0.0525.051-0.263-0.111-0.001-0.010-0.1420.000
183B84ILE 00.0300.0182.193-2.639-0.6063.713-1.103-4.642-0.003
184B85ILE 00.0230.0345.3280.6890.819-0.001-0.006-0.1230.000
185B86GLY 00.1160.0345.001-0.887-0.8870.0000.0000.0000.000
186B87ARG 10.8800.9295.8713.8313.8310.0000.0000.0000.000
187B88ASN 0-0.0010.0696.541-0.293-0.2930.0000.0000.0000.000
188B89LEU 0-0.002-0.0228.5280.0720.0720.0000.0000.0000.000
189B90LEU 0-0.0380.0008.0970.0900.0900.0000.0000.0000.000
190B91THR 0-0.034-0.03811.2770.1060.1060.0000.0000.0000.000
191B92GLN 0-0.024-0.04612.0680.0870.0870.0000.0000.0000.000
192B93ILE 0-0.067-0.01213.9640.0590.0590.0000.0000.0000.000
193B94GLY 00.0210.01416.6270.0140.0140.0000.0000.0000.000
194B95ALA 0-0.006-0.00513.477-0.013-0.0130.0000.0000.0000.000
195B96THR 0-0.070-0.03515.4160.0460.0460.0000.0000.0000.000
196B97LEU 0-0.021-0.0079.759-0.063-0.0630.0000.0000.0000.000
197B98ASN 00.012-0.01414.2610.0110.0110.0000.0000.0000.000
198B99PHE -1-0.870-0.92612.660-1.343-1.3430.0000.0000.0000.000