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: 2K8VR

Calculation Name: 1BVE-AB-NMR60-Model24

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 -2273608.088814
FMO2-HF: Nuclear repulsion 2197130.517699
FMO2-HF: Total energy -76477.571115
FMO2-MP2: Total energy -76703.222926


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.
-156.977-179.687195.725-60.461-112.5520.008


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.
-156.977-179.687195.725-60.461-112.552-0.008
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 : -0.009 / q_NPA : -0.081
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 10.8080.88617.3501.2471.2470.0000.0000.0000.000
2A2GLN 00.0140.03717.434-0.120-0.1200.0000.0000.0000.000
3A3VAL 00.0250.01613.2050.0980.0980.0000.0000.0000.000
4A4THR 00.0340.01114.616-0.197-0.1970.0000.0000.0000.000
5A5LEU 0-0.005-0.00412.435-0.162-0.1620.0000.0000.0000.000
6A6TRP 00.0240.00912.011-0.255-0.2550.0000.0000.0000.000
7A7GLN 0-0.027-0.0029.4030.0770.0770.0000.0000.0000.000
8A8ARG 10.9620.9673.7530.8021.0060.000-0.017-0.1870.000
9A9PRO 0-0.0120.0028.0230.5940.5940.0000.0000.0000.000
10A10LEU 0-0.009-0.0107.706-0.187-0.1870.0000.0000.0000.000
11A11VAL 0-0.036-0.01111.1120.1290.1290.0000.0000.0000.000
12A12THR 00.0490.01913.7900.0510.0510.0000.0000.0000.000
13A13ILE 0-0.022-0.00311.209-0.003-0.0030.0000.0000.0000.000
14A14LYS 10.9370.97015.3070.4470.4470.0000.0000.0000.000
15A15ILE 00.0450.02212.530-0.006-0.0060.0000.0000.0000.000
16A16GLY 0-0.033-0.01115.7520.0560.0560.0000.0000.0000.000
17A17GLY 0-0.054-0.02317.8870.0340.0340.0000.0000.0000.000
18A18GLN 00.0180.00417.5480.0530.0530.0000.0000.0000.000
19A19LEU 0-0.022-0.01317.605-0.069-0.0690.0000.0000.0000.000
20A20LYS 10.9040.97412.765-0.008-0.0080.0000.0000.0000.000
21A21GLU -1-0.870-0.93910.800-0.630-0.6300.0000.0000.0000.000
22A22ALA 0-0.033-0.0189.3810.0700.0700.0000.0000.0000.000
23A23LEU 0-0.039-0.0153.276-0.6780.3610.079-0.228-0.8900.001
24A24LEU 0-0.030-0.0216.177-1.165-1.1650.0000.0000.0000.000
25A25ASP -1-0.701-0.8852.435-33.410-28.0414.353-3.869-5.852-0.042
26A26THR 0-0.067-0.0474.5770.5380.707-0.001-0.005-0.1630.000
27A27GLY 00.0000.0052.5141.2442.1920.459-0.685-0.721-0.001
28A28ALA 0-0.0160.0172.0691.642-0.63412.999-3.768-6.9540.000
29A29ASP -1-0.928-0.9912.276-7.232-5.2112.269-1.413-2.8770.016
30A30ASP -1-0.899-0.9832.431-4.035-2.2681.054-0.996-1.8240.013
31A31THR 0-0.071-0.0303.425-3.518-2.6440.036-0.401-0.508-0.003
32A32VAL 0-0.015-0.0012.942-0.3601.0860.177-0.334-1.2900.001
33A33LEU 00.013-0.0164.534-0.453-0.3620.000-0.014-0.0770.000
34A34GLU -1-0.950-0.9778.0140.8880.8880.0000.0000.0000.000
35A35GLU -1-0.927-0.9838.9441.0271.0270.0000.0000.0000.000
36A36MET 00.0280.02312.214-0.105-0.1050.0000.0000.0000.000
37A37SER 0-0.038-0.02415.2430.0580.0580.0000.0000.0000.000
38A38LEU 00.0160.00812.384-0.071-0.0710.0000.0000.0000.000
39A39PRO 00.0280.01316.6350.0350.0350.0000.0000.0000.000
40A40GLY 0-0.023-0.02518.040-0.007-0.0070.0000.0000.0000.000
41A41ARG 10.9680.97117.099-0.122-0.1220.0000.0000.0000.000
42A42TRP 00.0050.02612.6290.0120.0120.0000.0000.0000.000
43A43LYS 10.9330.95912.283-0.325-0.3250.0000.0000.0000.000
44A44PRO 00.0210.01411.0950.0730.0730.0000.0000.0000.000
45A45LYS 10.9170.9706.013-1.043-1.0430.0000.0000.0000.000
46A46MET 0-0.046-0.0298.148-0.005-0.0050.0000.0000.0000.000
47A47ILE 0-0.0050.0212.757-3.609-0.8620.799-0.920-2.6260.011
48A48GLY 00.066-0.0074.3560.6991.0230.000-0.054-0.2710.000
49A49GLY 0-0.019-0.0042.072-4.812-3.6606.696-3.858-3.9890.019
50A50ILE 0-0.0140.0012.019-5.116-20.46438.112-2.816-19.9480.031
51A51GLY 00.006-0.0043.9330.2431.0120.009-0.158-0.6200.001
52A52GLY 00.000-0.0056.145-2.132-2.1320.0000.0000.0000.000
53A53PHE 00.0030.0226.1511.4021.4020.0000.0000.0000.000
54A54ILE 00.0030.0445.811-0.515-0.5150.0000.0000.0000.000
55A55LYS 10.9500.9678.122-1.748-1.7480.0000.0000.0000.000
56A56VAL 00.0400.0165.2560.0010.0010.0000.0000.0000.000
57A57ARG 10.9220.9668.540-0.898-0.8980.0000.0000.0000.000
58A58GLN 0-0.055-0.0307.9230.1290.1290.0000.0000.0000.000
59A59TYR 00.0180.0149.504-0.028-0.0280.0000.0000.0000.000
60A60ASP -1-0.806-0.90311.2550.3020.3020.0000.0000.0000.000
61A61GLN 0-0.039-0.03112.807-0.002-0.0020.0000.0000.0000.000
62A62ILE 0-0.0010.00412.4480.0150.0150.0000.0000.0000.000
63A63LEU 0-0.042-0.03314.013-0.075-0.0750.0000.0000.0000.000
64A64ILE 00.0520.00510.7140.0380.0380.0000.0000.0000.000
65A65GLU -1-0.946-0.98014.487-0.584-0.5840.0000.0000.0000.000
66A66ILE 00.0640.02811.869-0.020-0.0200.0000.0000.0000.000
67A67CYS 0-0.051-0.01615.765-0.044-0.0440.0000.0000.0000.000
68A68GLY 00.0260.01918.6130.0350.0350.0000.0000.0000.000
69A69HIS 0-0.007-0.00218.4900.0680.0680.0000.0000.0000.000
70A70LYS 10.9100.95118.1900.3990.3990.0000.0000.0000.000
71A71ALA 00.0640.04114.518-0.021-0.0210.0000.0000.0000.000
72A72ILE 0-0.0130.00614.8230.0740.0740.0000.0000.0000.000
73A73GLY 00.023-0.00410.856-0.092-0.0920.0000.0000.0000.000
74A74THR 0-0.031-0.0178.063-0.060-0.0600.0000.0000.0000.000
75A75VAL 00.0140.0147.2910.0660.0660.0000.0000.0000.000
76A76LEU 0-0.029-0.0283.402-0.2140.2340.022-0.078-0.3910.000
77A77VAL 0-0.0160.0136.811-0.158-0.1580.0000.0000.0000.000
78A78GLY 0-0.020-0.0349.3130.0710.0710.0000.0000.0000.000
79A79PRO 00.0330.0519.120-0.148-0.1480.0000.0000.0000.000
80A80THR 0-0.082-0.0184.4050.6790.9220.000-0.018-0.2250.000
81A81PRO 00.0320.0092.137-1.311-0.7931.262-0.357-1.4230.000
82A82VAL 00.0540.0113.247-2.265-0.3500.279-0.500-1.6950.005
83A83ASN 0-0.049-0.0155.189-0.437-0.281-0.001-0.006-0.1500.000
84A84ILE 00.006-0.0062.244-2.897-0.2132.459-0.958-4.185-0.002
85A85ILE 00.0170.0265.0680.6180.773-0.001-0.005-0.1490.000
86A86GLY 00.1260.0454.562-1.118-0.987-0.001-0.018-0.1130.000
87A87ARG 10.9150.9505.4322.7092.7090.0000.0000.0000.000
88A88ASN 0-0.0120.0446.315-0.337-0.3370.0000.0000.0000.000
89A89LEU 00.0150.0028.1730.1070.1070.0000.0000.0000.000
90A90LEU 0-0.0310.0068.3080.0250.0250.0000.0000.0000.000
91A91THR 0-0.053-0.02811.3480.1200.1200.0000.0000.0000.000
92A92GLN 0-0.052-0.01812.6940.1930.1930.0000.0000.0000.000
93A93ILE 0-0.045-0.01513.4710.0740.0740.0000.0000.0000.000
94A94GLY 00.0150.01915.8120.0340.0340.0000.0000.0000.000
95A95ALA 0-0.005-0.02713.3670.0100.0100.0000.0000.0000.000
96A96THR 0-0.090-0.06915.3570.0650.0650.0000.0000.0000.000
97A97LEU 00.0040.0269.8550.0270.0270.0000.0000.0000.000
98A98ASN 0-0.004-0.02514.3670.0640.0640.0000.0000.0000.000
99A99PHE -1-0.849-0.89414.672-1.534-1.5340.0000.0000.0000.000
100B1PRO 10.8250.90718.5431.5041.5040.0000.0000.0000.000
101B2GLN 00.0440.04418.173-0.128-0.1280.0000.0000.0000.000
102B3VAL 0-0.0070.00314.1290.0650.0650.0000.0000.0000.000
103B4THR 00.0500.02015.096-0.200-0.2000.0000.0000.0000.000
104B5LEU 0-0.018-0.01715.341-0.115-0.1150.0000.0000.0000.000
105B6TRP 00.0200.00514.416-0.002-0.0020.0000.0000.0000.000
106B7GLN 00.0060.00712.0990.1640.1640.0000.0000.0000.000
107B8ARG 10.9370.9618.0921.9751.9750.0000.0000.0000.000
108B9PRO 00.0120.0298.9700.4120.4120.0000.0000.0000.000
109B10LEU 0-0.003-0.0028.225-0.469-0.4690.0000.0000.0000.000
110B11VAL 0-0.020-0.00111.5230.3910.3910.0000.0000.0000.000
111B12THR 00.0240.01113.733-0.066-0.0660.0000.0000.0000.000
112B13ILE 0-0.0140.00411.2970.1430.1430.0000.0000.0000.000
113B14LYS 10.9700.96815.3460.8400.8400.0000.0000.0000.000
114B15ILE 00.0370.03511.8190.0480.0480.0000.0000.0000.000
115B16GLY 0-0.009-0.00715.1840.1060.1060.0000.0000.0000.000
116B17GLY 0-0.057-0.02417.7190.0750.0750.0000.0000.0000.000
117B18GLN 00.007-0.00516.897-0.052-0.0520.0000.0000.0000.000
118B19LEU 0-0.025-0.02617.062-0.052-0.0520.0000.0000.0000.000
119B20LYS 10.8800.96811.8050.9060.9060.0000.0000.0000.000
120B21GLU -1-0.874-0.93410.961-1.688-1.6880.0000.0000.0000.000
121B22ALA 00.010-0.0139.351-0.271-0.2710.0000.0000.0000.000
122B23LEU 0-0.038-0.0223.669-0.2840.4480.013-0.103-0.6430.000
123B24LEU 0-0.005-0.0146.205-1.847-1.8470.0000.0000.0000.000
124B25ASP -1-0.710-0.8021.388-67.370-97.53263.578-25.794-7.622-0.123
125B26THR 0-0.071-0.0574.5290.8661.042-0.001-0.019-0.1570.000
126B27GLY 00.0310.0282.5441.2092.0900.417-0.468-0.8290.003
127B28ALA 0-0.062-0.0122.0402.8731.8939.389-2.634-5.7750.002
128B29ASP -1-0.793-0.9152.632-4.454-2.5010.153-0.672-1.433-0.004
129B30ASP -1-0.886-0.9802.8401.0082.5880.153-0.608-1.1250.003
130B31THR 0-0.070-0.0303.484-4.150-3.3230.027-0.399-0.455-0.003
131B32VAL 0-0.0170.0002.9860.4781.7560.146-0.260-1.1650.000
132B33LEU 0-0.017-0.0424.755-0.688-0.6030.000-0.009-0.0760.000
133B34GLU -1-0.948-0.9837.7300.2380.2380.0000.0000.0000.000
134B35GLU -1-0.922-0.9578.9710.8130.8130.0000.0000.0000.000
135B36MET 0-0.048-0.00912.075-0.147-0.1470.0000.0000.0000.000
136B37SER 0-0.039-0.02115.1610.1390.1390.0000.0000.0000.000
137B38LEU 00.010-0.00411.903-0.070-0.0700.0000.0000.0000.000
138B39PRO 00.0440.03515.7110.0620.0620.0000.0000.0000.000
139B40GLY 00.0760.04017.0560.0770.0770.0000.0000.0000.000
140B41ARG 10.9090.94217.085-0.106-0.1060.0000.0000.0000.000
141B42TRP 00.0230.04912.9150.0160.0160.0000.0000.0000.000
142B43LYS 10.9590.95812.393-0.582-0.5820.0000.0000.0000.000
143B44PRO 0-0.0240.01111.4080.1210.1210.0000.0000.0000.000
144B45LYS 10.9270.9845.325-4.284-4.2840.0000.0000.0000.000
145B46MET 00.002-0.0307.974-0.336-0.3360.0000.0000.0000.000
146B47ILE 0-0.0300.0172.416-3.833-0.8221.459-1.126-3.3440.012
147B48GLY 00.0420.0063.964-0.561-0.0400.003-0.099-0.4240.000
148B49GLY 0-0.006-0.0111.988-3.539-3.55710.604-5.543-5.0430.017
149B50ILE 0-0.0040.0101.995-4.108-20.28934.9020.658-19.3800.031
150B51GLY 00.009-0.0204.012-0.2990.3690.011-0.164-0.5150.001
151B52GLY 0-0.0010.0016.155-2.059-2.0590.0000.0000.0000.000
152B53PHE 00.008-0.0115.9031.7771.7770.0000.0000.0000.000
153B54ILE 0-0.0020.0395.879-0.873-0.8730.0000.0000.0000.000
154B55LYS 10.9250.9588.429-1.849-1.8490.0000.0000.0000.000
155B56VAL 00.029-0.0015.331-0.098-0.0980.0000.0000.0000.000
156B57ARG 10.9280.9608.415-0.694-0.6940.0000.0000.0000.000
157B58GLN 00.0420.0126.8810.3730.3730.0000.0000.0000.000
158B59TYR 0-0.034-0.0509.103-0.045-0.0450.0000.0000.0000.000
159B60ASP -1-0.856-0.95611.4180.3350.3350.0000.0000.0000.000
160B61GLN 0-0.068-0.04212.707-0.090-0.0900.0000.0000.0000.000
161B62ILE 0-0.015-0.00712.4770.0420.0420.0000.0000.0000.000
162B63LEU 0-0.042-0.02714.089-0.122-0.1220.0000.0000.0000.000
163B64ILE 00.0370.00410.4920.0480.0480.0000.0000.0000.000
164B65GLU -1-0.921-0.94814.406-1.159-1.1590.0000.0000.0000.000
165B66ILE 00.0700.04012.364-0.087-0.0870.0000.0000.0000.000
166B67CYS 0-0.024-0.02416.5980.0180.0180.0000.0000.0000.000
167B68GLY 00.0640.03319.7670.1010.1010.0000.0000.0000.000
168B69HIS 0-0.092-0.05818.2820.0670.0670.0000.0000.0000.000
169B70LYS 10.9380.94618.1150.6310.6310.0000.0000.0000.000
170B71ALA 00.0570.04914.4250.0530.0530.0000.0000.0000.000
171B72ILE 0-0.0190.02614.625-0.030-0.0300.0000.0000.0000.000
172B73GLY 00.0730.04511.195-0.012-0.0120.0000.0000.0000.000
173B74THR 0-0.079-0.0387.8460.0380.0380.0000.0000.0000.000
174B75VAL 00.0180.0237.361-0.098-0.0980.0000.0000.0000.000
175B76LEU 0-0.023-0.0093.4600.3630.8420.019-0.082-0.4150.000
176B77VAL 0-0.0050.0016.580-0.275-0.2750.0000.0000.0000.000
177B78GLY 00.013-0.0028.7010.3400.3400.0000.0000.0000.000
178B79PRO 00.0100.0359.079-0.328-0.3280.0000.0000.0000.000
179B80THR 0-0.092-0.0223.9470.7571.1090.001-0.054-0.2990.000
180B81PRO 00.0640.0372.049-1.165-0.9371.941-0.474-1.695-0.001
181B82VAL 00.0530.0133.411-2.175-0.5610.148-0.392-1.3700.003
182B83ASN 0-0.052-0.0325.3010.0410.179-0.001-0.006-0.1300.000
183B84ILE 00.0140.0112.494-2.718-0.2271.704-0.723-3.4730.001
184B85ILE 0-0.0050.0035.5621.0851.0850.0000.0000.0000.000
185B86GLY 00.1170.0344.700-1.221-1.150-0.001-0.014-0.0560.000
186B87ARG 10.8840.9245.5094.1724.1720.0000.0000.0000.000
187B88ASN 0-0.0310.0496.414-0.270-0.2700.0000.0000.0000.000
188B89LEU 00.003-0.0088.4270.4630.4630.0000.0000.0000.000
189B90LEU 0-0.0280.0038.3040.3630.3630.0000.0000.0000.000
190B91THR 0-0.001-0.01211.7230.2930.2930.0000.0000.0000.000
191B92GLN 0-0.101-0.06112.9190.1800.1800.0000.0000.0000.000
192B93ILE 0-0.044-0.01613.5510.1380.1380.0000.0000.0000.000
193B94GLY 00.0500.02616.1560.0650.0650.0000.0000.0000.000
194B95ALA 00.015-0.00312.9390.0210.0210.0000.0000.0000.000
195B96THR 0-0.108-0.05514.658-0.018-0.0180.0000.0000.0000.000
196B97LEU 0-0.005-0.0119.272-0.034-0.0340.0000.0000.0000.000
197B98ASN 00.0460.00313.7260.0940.0940.0000.0000.0000.000
198B99PHE -1-0.827-0.87713.074-1.344-1.3440.0000.0000.0000.000