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: 4N81N

Calculation Name: 1BVE-AB-NMR60-Model18

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 -2279004.066615
FMO2-HF: Nuclear repulsion 2202526.499796
FMO2-HF: Total energy -76477.566819
FMO2-MP2: Total energy -76703.297335


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.
-160.516-237.788302.019-102.629-122.1200.026


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.
-160.516-237.788302.019-102.629-122.12-0.026
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 : -0.027 / q_NPA : -0.074
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 10.8040.89317.7240.4230.4230.0000.0000.0000.000
2A2GLN 00.0640.05917.380-0.007-0.0070.0000.0000.0000.000
3A3VAL 00.0290.01713.2080.0580.0580.0000.0000.0000.000
4A4THR 0-0.004-0.00514.298-0.088-0.0880.0000.0000.0000.000
5A5LEU 00.0190.0159.135-0.002-0.0020.0000.0000.0000.000
6A6TRP 00.001-0.02012.5210.0120.0120.0000.0000.0000.000
7A7GLN 0-0.021-0.01214.6070.1060.1060.0000.0000.0000.000
8A8ARG 10.9540.9838.6290.8500.8500.0000.0000.0000.000
9A9PRO 00.0630.0438.7020.1260.1260.0000.0000.0000.000
10A10LEU 0-0.042-0.0309.1830.0630.0630.0000.0000.0000.000
11A11VAL 0-0.005-0.00212.187-0.016-0.0160.0000.0000.0000.000
12A12THR 00.0150.00214.0650.0760.0760.0000.0000.0000.000
13A13ILE 00.0080.01211.4310.0040.0040.0000.0000.0000.000
14A14LYS 10.9420.96315.462-0.183-0.1830.0000.0000.0000.000
15A15ILE 00.0130.01511.3420.0170.0170.0000.0000.0000.000
16A16GLY 00.028-0.00615.6120.0070.0070.0000.0000.0000.000
17A17GLY 0-0.043-0.01217.916-0.016-0.0160.0000.0000.0000.000
18A18GLN 00.0300.01717.411-0.038-0.0380.0000.0000.0000.000
19A19LEU 0-0.063-0.04217.748-0.021-0.0210.0000.0000.0000.000
20A20LYS 10.9030.97412.904-0.573-0.5730.0000.0000.0000.000
21A21GLU -1-0.869-0.92911.508-0.006-0.0060.0000.0000.0000.000
22A22ALA 0-0.022-0.0139.6780.1600.1600.0000.0000.0000.000
23A23LEU 0-0.016-0.0084.002-0.620-0.1840.001-0.035-0.4030.000
24A24LEU 0-0.030-0.0146.4890.0030.0030.0000.0000.0000.000
25A25ASH 00.036-0.0341.480-12.331-43.35059.878-23.388-5.4710.008
26A26THR 0-0.0520.0114.8210.3820.589-0.001-0.006-0.2000.000
27A27GLY 00.0510.0352.215-1.147-0.2041.765-1.521-1.186-0.008
28A28ALA 0-0.059-0.0092.103-1.208-1.78910.196-2.591-7.0240.000
29A29ASP -1-0.803-0.9292.386-2.269-0.3400.404-0.683-1.6490.004
30A30ASP -1-0.891-0.9672.6420.8913.0460.747-0.979-1.9220.010
31A31THR 0-0.095-0.0893.417-3.292-2.3460.039-0.438-0.547-0.003
32A32VAL 0-0.034-0.0012.993-1.0020.4470.196-0.303-1.3420.000
33A33LEU 00.004-0.0254.613-0.384-0.2920.000-0.015-0.0770.000
34A34GLU -1-0.941-0.9787.7071.2341.2340.0000.0000.0000.000
35A35GLU -1-0.957-0.9908.5491.1551.1550.0000.0000.0000.000
36A36MET 00.0170.01411.746-0.118-0.1180.0000.0000.0000.000
37A37SER 0-0.020-0.01014.8640.0430.0430.0000.0000.0000.000
38A38LEU 00.0020.01413.349-0.077-0.0770.0000.0000.0000.000
39A39PRO 00.0090.00517.162-0.012-0.0120.0000.0000.0000.000
40A40GLY 0-0.029-0.01518.833-0.018-0.0180.0000.0000.0000.000
41A41ARG 10.9530.96317.448-0.807-0.8070.0000.0000.0000.000
42A42TRP 00.0060.02912.7480.0770.0770.0000.0000.0000.000
43A43LYS 10.9660.98012.654-1.148-1.1480.0000.0000.0000.000
44A44PRO 00.0020.00411.6430.1510.1510.0000.0000.0000.000
45A45LYS 10.9901.0015.686-3.675-3.6750.0000.0000.0000.000
46A46MET 0-0.012-0.0188.077-0.059-0.0590.0000.0000.0000.000
47A47ILE 0-0.0390.0042.297-3.463-0.7781.592-0.971-3.3050.009
48A48GLY 00.0780.0004.110-0.0560.3590.001-0.071-0.3450.000
49A49GLY 0-0.036-0.0181.983-4.490-4.2489.077-5.021-4.2980.019
50A50ILE 0-0.0160.0041.986-4.759-20.46736.115-1.112-19.2950.037
51A51GLY 00.005-0.0053.8820.1870.9060.009-0.131-0.5980.001
52A52GLY 00.0140.0026.165-2.004-2.0040.0000.0000.0000.000
53A53PHE 00.0070.0245.9381.5571.5570.0000.0000.0000.000
54A54ILE 0-0.0200.0335.399-0.547-0.5470.0000.0000.0000.000
55A55LYS 10.9280.9577.605-2.004-2.0040.0000.0000.0000.000
56A56VAL 00.017-0.0065.2990.0650.0650.0000.0000.0000.000
57A57ARG 10.9010.9438.463-1.792-1.7920.0000.0000.0000.000
58A58GLN 0-0.023-0.0237.4210.3420.3420.0000.0000.0000.000
59A59TYR 00.0130.0089.174-0.255-0.2550.0000.0000.0000.000
60A60ASP -1-0.844-0.91511.5211.5751.5750.0000.0000.0000.000
61A61GLN 0-0.048-0.02912.882-0.126-0.1260.0000.0000.0000.000
62A62ILE 0-0.023-0.01312.485-0.076-0.0760.0000.0000.0000.000
63A63LEU 0-0.041-0.03314.191-0.010-0.0100.0000.0000.0000.000
64A64ILE 00.0270.00010.706-0.013-0.0130.0000.0000.0000.000
65A65GLU -1-0.862-0.91514.5510.0510.0510.0000.0000.0000.000
66A66ILE 00.0240.01912.2040.0140.0140.0000.0000.0000.000
67A67CYS 0-0.041-0.02816.244-0.061-0.0610.0000.0000.0000.000
68A68GLY 00.0330.01119.3990.0190.0190.0000.0000.0000.000
69A69HIS 0-0.065-0.01818.471-0.001-0.0010.0000.0000.0000.000
70A70LYS 10.9710.96618.029-0.125-0.1250.0000.0000.0000.000
71A71ALA 00.0200.01614.690-0.019-0.0190.0000.0000.0000.000
72A72ILE 0-0.0120.00015.0660.0400.0400.0000.0000.0000.000
73A73GLY 00.029-0.00111.185-0.040-0.0400.0000.0000.0000.000
74A74THR 0-0.007-0.0097.759-0.209-0.2090.0000.0000.0000.000
75A75VAL 00.0090.0107.4170.2890.2890.0000.0000.0000.000
76A76LEU 0-0.016-0.0163.662-0.3720.0040.007-0.055-0.3280.000
77A77VAL 00.0190.0306.605-0.066-0.0660.0000.0000.0000.000
78A78GLY 0-0.019-0.0228.9070.0910.0910.0000.0000.0000.000
79A79PRO 0-0.0140.0278.502-0.232-0.2320.0000.0000.0000.000
80A80THR 0-0.074-0.0214.0040.1650.5870.003-0.091-0.3340.000
81A81PRO 00.0690.0292.023-0.887-1.2823.656-0.720-2.542-0.003
82A82VAL 00.0890.0303.305-2.197-0.4710.229-0.399-1.5570.004
83A83ASN 0-0.045-0.0125.100-0.265-0.119-0.001-0.005-0.1400.000
84A84ILE 0-0.023-0.0202.259-3.314-0.6151.915-0.790-3.8240.001
85A85ILE 00.0340.0315.1380.0160.174-0.001-0.006-0.1510.000
86A86GLY 00.0840.0174.437-0.549-0.434-0.001-0.018-0.0960.000
87A87ARG 10.9110.9845.3350.9441.062-0.001-0.002-0.1140.000
88A88ASN 00.0420.0896.308-0.298-0.2980.0000.0000.0000.000
89A89LEU 00.0290.0107.992-0.174-0.1740.0000.0000.0000.000
90A90LEU 0-0.0130.0058.488-0.232-0.2320.0000.0000.0000.000
91A91THR 0-0.063-0.03811.157-0.109-0.1090.0000.0000.0000.000
92A92GLN 0-0.0340.00312.599-0.050-0.0500.0000.0000.0000.000
93A93ILE 0-0.053-0.02113.165-0.032-0.0320.0000.0000.0000.000
94A94GLY 00.0160.01715.623-0.052-0.0520.0000.0000.0000.000
95A95ALA 0-0.018-0.02613.066-0.069-0.0690.0000.0000.0000.000
96A96THR 0-0.088-0.04915.1030.0210.0210.0000.0000.0000.000
97A97LEU 00.0080.0069.530-0.049-0.0490.0000.0000.0000.000
98A98ASN 00.046-0.00413.983-0.029-0.0290.0000.0000.0000.000
99A99PHE -1-0.830-0.89013.193-1.188-1.1880.0000.0000.0000.000
100B1PRO 10.7980.88918.1621.0661.0660.0000.0000.0000.000
101B2GLN 00.0230.03618.065-0.071-0.0710.0000.0000.0000.000
102B3VAL 0-0.0010.00914.0780.0540.0540.0000.0000.0000.000
103B4THR 00.0550.02514.939-0.076-0.0760.0000.0000.0000.000
104B5LEU 0-0.010-0.01814.966-0.031-0.0310.0000.0000.0000.000
105B6TRP 00.0240.01114.3490.0350.0350.0000.0000.0000.000
106B7GLN 0-0.002-0.01710.8260.1510.1510.0000.0000.0000.000
107B8ARG 10.9020.9374.9530.6840.6840.0000.0000.0000.000
108B9PRO 00.0020.0198.6910.1640.1640.0000.0000.0000.000
109B10LEU 00.004-0.0047.994-0.457-0.4570.0000.0000.0000.000
110B11VAL 0-0.010-0.00611.2910.3420.3420.0000.0000.0000.000
111B12THR 00.006-0.01513.178-0.125-0.1250.0000.0000.0000.000
112B13ILE 0-0.005-0.00111.3740.0420.0420.0000.0000.0000.000
113B14LYS 10.9520.96114.6080.9960.9960.0000.0000.0000.000
114B15ILE 00.0560.05110.508-0.006-0.0060.0000.0000.0000.000
115B16GLY 00.017-0.00214.9270.0730.0730.0000.0000.0000.000
116B17GLY 0-0.067-0.03517.7160.0680.0680.0000.0000.0000.000
117B18GLN 00.0250.02016.2170.0080.0080.0000.0000.0000.000
118B19LEU 0-0.001-0.00916.768-0.109-0.1090.0000.0000.0000.000
119B20LYS 10.9180.98212.1311.2251.2250.0000.0000.0000.000
120B21GLU -1-0.885-0.93710.783-1.268-1.2680.0000.0000.0000.000
121B22ALA 0-0.001-0.0299.097-0.188-0.1880.0000.0000.0000.000
122B23LEU 0-0.0270.0123.337-0.2330.7620.068-0.183-0.8810.000
123B24LEU 00.016-0.0045.725-1.954-1.9540.0000.0000.0000.000
124B25ASP -1-0.620-0.7201.317-73.998-124.255103.175-44.007-8.910-0.190
125B26THR 0-0.048-0.0764.3220.0640.338-0.001-0.050-0.2230.000
126B27GLY 00.024-0.0122.5370.9452.1580.980-0.940-1.2530.005
127B28ALA 0-0.043-0.0072.1422.506-0.47414.742-3.671-8.0920.000
128B29ASP -1-0.885-0.9662.073-5.312-6.0755.728-1.279-3.6860.017
129B30ASP -1-0.968-1.0072.121-16.946-15.2314.666-2.927-3.4550.010
130B31THR 0-0.044-0.0323.195-1.473-0.2990.095-0.564-0.705-0.005
131B32VAL 0-0.0290.0042.976-0.7200.8020.151-0.384-1.2890.001
132B33LEU 0-0.002-0.0224.460-0.103-0.0140.000-0.016-0.0730.000
133B34GLU -1-0.926-0.9887.807-0.324-0.3240.0000.0000.0000.000
134B35GLU -1-0.913-0.9598.798-0.524-0.5240.0000.0000.0000.000
135B36MET 0-0.051-0.00911.964-0.027-0.0270.0000.0000.0000.000
136B37SER 0-0.006-0.00514.9590.0550.0550.0000.0000.0000.000
137B38LEU 00.0810.01913.151-0.051-0.0510.0000.0000.0000.000
138B39PRO 0-0.022-0.00217.0460.0890.0890.0000.0000.0000.000
139B40GLY 0-0.018-0.01318.6310.0100.0100.0000.0000.0000.000
140B41ARG 10.9470.96416.6460.8950.8950.0000.0000.0000.000
141B42TRP 0-0.0080.03012.219-0.136-0.1360.0000.0000.0000.000
142B43LYS 10.9560.98112.1450.9270.9270.0000.0000.0000.000
143B44PRO 00.0200.00511.347-0.198-0.1980.0000.0000.0000.000
144B45LYS 10.9230.9805.8273.3423.3420.0000.0000.0000.000
145B46MET 0-0.002-0.0188.2100.0680.0680.0000.0000.0000.000
146B47ILE 0-0.0220.0142.687-3.810-1.4302.812-1.115-4.0770.015
147B48GLY 00.063-0.0024.3000.7731.0790.000-0.052-0.2540.000
148B49GLY 0-0.0120.0022.080-4.676-3.4927.056-4.016-4.2240.019
149B50ILE 0-0.007-0.0041.945-6.399-17.52830.598-1.513-17.9560.023
150B51GLY 00.010-0.0154.088-0.0290.6580.009-0.158-0.5380.001
151B52GLY 0-0.004-0.0056.214-1.997-1.9970.0000.0000.0000.000
152B53PHE 00.0030.0116.1131.6081.6080.0000.0000.0000.000
153B54ILE 00.0060.0405.690-0.517-0.5170.0000.0000.0000.000
154B55LYS 10.9290.9548.250-0.892-0.8920.0000.0000.0000.000
155B56VAL 00.009-0.0105.358-0.001-0.0010.0000.0000.0000.000
156B57ARG 10.8600.9288.6380.7660.7660.0000.0000.0000.000
157B58GLN 00.023-0.0086.544-0.978-0.9780.0000.0000.0000.000
158B59TYR 00.0250.0158.7810.4210.4210.0000.0000.0000.000
159B60ASP -1-0.849-0.92910.416-2.275-2.2750.0000.0000.0000.000
160B61GLN 0-0.047-0.04112.2750.1910.1910.0000.0000.0000.000
161B62ILE 0-0.0010.00012.0260.1850.1850.0000.0000.0000.000
162B63LEU 0-0.034-0.03713.641-0.104-0.1040.0000.0000.0000.000
163B64ILE 00.0360.00210.0300.0710.0710.0000.0000.0000.000
164B65GLU -1-0.950-0.97413.933-1.030-1.0300.0000.0000.0000.000
165B66ILE 00.0580.02511.871-0.074-0.0740.0000.0000.0000.000
166B67CYS 0-0.060-0.04015.9520.1230.1230.0000.0000.0000.000
167B68GLY 00.0250.01618.8160.0920.0920.0000.0000.0000.000
168B69HIS 00.0110.01518.5950.0770.0770.0000.0000.0000.000
169B70LYS 10.9350.96617.9970.7240.7240.0000.0000.0000.000
170B71ALA 00.0420.03014.2280.0270.0270.0000.0000.0000.000
171B72ILE 0-0.0150.02614.373-0.087-0.0870.0000.0000.0000.000
172B73GLY 00.0290.00310.718-0.043-0.0430.0000.0000.0000.000
173B74THR 0-0.012-0.0147.0930.2260.2260.0000.0000.0000.000
174B75VAL 00.0220.0077.000-0.594-0.5940.0000.0000.0000.000
175B76LEU 0-0.030-0.0203.082-0.0640.6240.097-0.138-0.6480.000
176B77VAL 00.0140.0226.4550.0040.0040.0000.0000.0000.000
177B78GLY 00.002-0.0189.2860.1860.1860.0000.0000.0000.000
178B79PRO 0-0.0160.0208.932-0.204-0.2040.0000.0000.0000.000
179B80THR 0-0.0710.0124.1300.5230.8570.001-0.050-0.2860.000
180B81PRO 00.0620.0301.985-0.881-0.9902.677-0.591-1.977-0.003
181B82VAL 00.0590.0143.266-2.104-0.2260.322-0.461-1.7390.004
182B83ASN 0-0.0440.0065.148-0.410-0.236-0.001-0.006-0.1660.000
183B84ILE 0-0.023-0.0252.177-3.640-1.0953.022-1.127-4.440-0.002
184B85ILE 00.0100.0235.0700.6190.837-0.001-0.007-0.2100.000
185B86GLY 00.0950.0254.545-0.705-0.600-0.001-0.020-0.0850.000
186B87ARG 10.8680.9385.3451.9182.128-0.001-0.003-0.2050.000
187B88ASN 0-0.0290.0396.149-0.048-0.0480.0000.0000.0000.000
188B89LEU 00.028-0.0017.9990.3150.3150.0000.0000.0000.000
189B90LEU 0-0.0060.0167.7400.3410.3410.0000.0000.0000.000
190B91THR 00.0200.00611.5140.2290.2290.0000.0000.0000.000
191B92GLN 0-0.119-0.04312.6410.2820.2820.0000.0000.0000.000
192B93ILE 0-0.041-0.02413.4350.1470.1470.0000.0000.0000.000
193B94GLY 00.0320.02615.8360.1140.1140.0000.0000.0000.000
194B95ALA 0-0.044-0.03012.4860.0630.0630.0000.0000.0000.000
195B96THR 0-0.077-0.03514.0170.0140.0140.0000.0000.0000.000
196B97LEU 0-0.013-0.0239.083-0.024-0.0240.0000.0000.0000.000
197B98ASN 00.009-0.01213.5810.0800.0800.0000.0000.0000.000
198B99PHE -1-0.836-0.90711.931-0.411-0.4110.0000.0000.0000.000