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: Z218N

Calculation Name: 1BVE-AB-NMR60-Model1

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 -2276709.513968
FMO2-HF: Nuclear repulsion 2200232.124992
FMO2-HF: Total energy -76477.388976
FMO2-MP2: Total energy -76703.068468


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.
-155.712-215.853263.415-78.141-125.1350.027


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.
-155.712-215.853263.415-78.141-125.135-0.027
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 : -0.024 / q_NPA : -0.111
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 10.8400.90217.8131.1841.1840.0000.0000.0000.000
2A2GLN 00.0400.05117.802-0.101-0.1010.0000.0000.0000.000
3A3VAL 0-0.016-0.00314.6640.0960.0960.0000.0000.0000.000
4A4THR 00.0530.01715.813-0.161-0.1610.0000.0000.0000.000
5A5LEU 0-0.028-0.00217.1200.0720.0720.0000.0000.0000.000
6A6TRP 00.019-0.01113.324-0.017-0.0170.0000.0000.0000.000
7A7GLN 00.0150.00011.4130.0570.0570.0000.0000.0000.000
8A8ARG 10.8950.9547.3351.0771.0770.0000.0000.0000.000
9A9PRO 00.0310.0388.8230.3550.3550.0000.0000.0000.000
10A10LEU 00.008-0.0067.334-0.326-0.3260.0000.0000.0000.000
11A11VAL 0-0.021-0.01711.1480.2470.2470.0000.0000.0000.000
12A12THR 0-0.024-0.01313.395-0.060-0.0600.0000.0000.0000.000
13A13ILE 00.0690.02912.5410.0240.0240.0000.0000.0000.000
14A14LYS 10.9200.95715.4620.5070.5070.0000.0000.0000.000
15A15ILE 00.0580.02511.5390.0170.0170.0000.0000.0000.000
16A16GLY 0-0.021-0.00615.7970.0650.0650.0000.0000.0000.000
17A17GLY 0-0.045-0.02018.1770.0350.0350.0000.0000.0000.000
18A18GLN 0-0.0030.00516.8880.0410.0410.0000.0000.0000.000
19A19LEU 0-0.012-0.02616.563-0.050-0.0500.0000.0000.0000.000
20A20LYS 10.9090.98011.1990.2050.2050.0000.0000.0000.000
21A21GLU -1-0.906-0.9489.697-0.734-0.7340.0000.0000.0000.000
22A22ALA 0-0.017-0.0079.2220.0030.0030.0000.0000.0000.000
23A23LEU 0-0.027-0.0043.232-0.8660.5260.188-0.343-1.2370.001
24A24LEU 0-0.014-0.0196.043-1.649-1.6490.0000.0000.0000.000
25A25ASP -1-0.708-0.8471.687-45.995-61.14136.102-11.295-9.660-0.099
26A26THR 0-0.055-0.0324.2011.3271.548-0.001-0.014-0.2060.000
27A27GLY 00.0870.0452.5681.6242.6300.566-0.770-0.8030.000
28A28ALA 0-0.091-0.0232.1961.6410.91210.172-2.955-6.4880.006
29A29ASP -1-0.861-0.9562.100-2.255-1.9053.546-1.246-2.6500.014
30A30ASP -1-0.901-0.9892.841-1.626-0.1190.207-0.581-1.1330.006
31A31THR 0-0.063-0.0203.702-3.087-2.5520.008-0.218-0.325-0.001
32A32VAL 0-0.037-0.0113.0930.0901.1810.065-0.200-0.9560.000
33A33LEU 00.0290.0014.886-0.493-0.404-0.001-0.008-0.0800.000
34A34GLU -1-0.884-0.9526.3180.3880.3880.0000.0000.0000.000
35A35GLU -1-0.965-0.9898.1330.8890.8890.0000.0000.0000.000
36A36MET 0-0.032-0.01311.531-0.166-0.1660.0000.0000.0000.000
37A37SER 0-0.0150.00314.5660.0870.0870.0000.0000.0000.000
38A38LEU 00.010-0.00213.338-0.079-0.0790.0000.0000.0000.000
39A39PRO 00.0060.00916.1070.0250.0250.0000.0000.0000.000
40A40GLY 00.003-0.00217.7910.0420.0420.0000.0000.0000.000
41A41ARG 10.9430.95317.695-0.245-0.2450.0000.0000.0000.000
42A42TRP 00.0260.03913.0900.0250.0250.0000.0000.0000.000
43A43LYS 10.9880.98112.400-0.859-0.8590.0000.0000.0000.000
44A44PRO 0-0.0290.00411.0720.1200.1200.0000.0000.0000.000
45A45LYS 10.9450.9884.871-3.397-3.3970.0000.0000.0000.000
46A46MET 0-0.020-0.0278.135-0.039-0.0390.0000.0000.0000.000
47A47ILE 0-0.0220.0062.148-3.701-1.0721.853-1.171-3.3110.011
48A48GLY 00.072-0.0074.3990.1210.4600.000-0.049-0.2880.000
49A49GLY 0-0.026-0.0072.053-4.599-3.4816.731-3.948-3.9010.019
50A50ILE 0-0.0180.0012.014-7.307-19.63833.719-2.450-18.9370.041
51A51GLY 00.008-0.0054.026-0.0340.6590.009-0.165-0.5370.001
52A52GLY 00.0090.0046.249-2.104-2.1040.0000.0000.0000.000
53A53PHE 0-0.0090.0196.1781.6641.6640.0000.0000.0000.000
54A54ILE 00.0220.0575.678-0.605-0.6050.0000.0000.0000.000
55A55LYS 10.9110.9508.317-1.878-1.8780.0000.0000.0000.000
56A56VAL 00.0290.0085.320-0.073-0.0730.0000.0000.0000.000
57A57ARG 10.8970.9448.615-1.009-1.0090.0000.0000.0000.000
58A58GLN 0-0.006-0.0038.129-0.212-0.2120.0000.0000.0000.000
59A59TYR 00.0090.0099.211-0.036-0.0360.0000.0000.0000.000
60A60ASP -1-0.797-0.92011.1910.6280.6280.0000.0000.0000.000
61A61GLN 0-0.077-0.05413.368-0.061-0.0610.0000.0000.0000.000
62A62ILE 0-0.024-0.00911.9920.0110.0110.0000.0000.0000.000
63A63LEU 0-0.076-0.05114.709-0.074-0.0740.0000.0000.0000.000
64A64ILE 00.0140.00910.9950.0310.0310.0000.0000.0000.000
65A65GLU -1-0.950-0.97514.907-0.732-0.7320.0000.0000.0000.000
66A66ILE 00.0700.03112.388-0.083-0.0830.0000.0000.0000.000
67A67CYS 0-0.016-0.00516.3600.0170.0170.0000.0000.0000.000
68A68GLY 00.0510.03818.3570.0670.0670.0000.0000.0000.000
69A69HIS 0-0.077-0.04718.030-0.001-0.0010.0000.0000.0000.000
70A70LYS 10.9390.96018.4300.3070.3070.0000.0000.0000.000
71A71ALA 00.0750.04715.0680.0020.0020.0000.0000.0000.000
72A72ILE 0-0.0140.02515.4700.0470.0470.0000.0000.0000.000
73A73GLY 00.0340.00911.597-0.080-0.0800.0000.0000.0000.000
74A74THR 0-0.027-0.0208.213-0.085-0.0850.0000.0000.0000.000
75A75VAL 00.0280.0177.732-0.039-0.0390.0000.0000.0000.000
76A76LEU 0-0.022-0.0173.7710.1150.4080.003-0.037-0.2590.000
77A77VAL 00.0460.0327.414-0.169-0.1690.0000.0000.0000.000
78A78GLY 0-0.017-0.0289.2910.2060.2060.0000.0000.0000.000
79A79PRO 0-0.0110.0238.574-0.278-0.2780.0000.0000.0000.000
80A80THR 0-0.084-0.0043.6770.4631.0870.010-0.199-0.435-0.001
81A81PRO 00.0350.0131.981-0.948-1.6534.180-0.733-2.7420.000
82A82VAL 00.0730.0252.865-3.238-0.8291.130-0.762-2.7770.004
83A83ASN 0-0.021-0.0164.653-0.246-0.0790.000-0.012-0.1550.000
84A84ILE 0-0.022-0.0182.116-3.173-1.1564.212-1.197-5.0320.000
85A85ILE 0-0.0080.0265.3331.2061.351-0.001-0.005-0.1390.000
86A86GLY 00.0910.0204.860-1.144-1.1440.0000.0000.0000.000
87A87ARG 10.8700.9135.7143.8343.8340.0000.0000.0000.000
88A88ASN 00.0050.0536.695-0.366-0.3660.0000.0000.0000.000
89A89LEU 00.013-0.0158.6910.1030.1030.0000.0000.0000.000
90A90LEU 0-0.0240.0178.2920.0020.0020.0000.0000.0000.000
91A91THR 0-0.002-0.02511.4120.1660.1660.0000.0000.0000.000
92A92GLN 0-0.085-0.02013.2910.1030.1030.0000.0000.0000.000
93A93ILE 0-0.098-0.03613.2950.0630.0630.0000.0000.0000.000
94A94GLY 00.0440.02816.590-0.001-0.0010.0000.0000.0000.000
95A95ALA 00.001-0.03913.262-0.019-0.0190.0000.0000.0000.000
96A96THR 0-0.049-0.02515.2410.0960.0960.0000.0000.0000.000
97A97LEU 0-0.025-0.0159.490-0.094-0.0940.0000.0000.0000.000
98A98ASN 00.000-0.01614.0560.0640.0640.0000.0000.0000.000
99A99PHE -1-0.865-0.91712.160-1.379-1.3790.0000.0000.0000.000
100B1PRO 10.8370.90316.7181.2721.2720.0000.0000.0000.000
101B2GLN 00.0690.05217.425-0.114-0.1140.0000.0000.0000.000
102B3VAL 0-0.020-0.00312.3240.0880.0880.0000.0000.0000.000
103B4THR 00.0240.01115.134-0.126-0.1260.0000.0000.0000.000
104B5LEU 00.0650.01912.553-0.171-0.1710.0000.0000.0000.000
105B6TRP 0-0.041-0.00812.0880.0800.0800.0000.0000.0000.000
106B7GLN 00.0280.00812.2890.1770.1770.0000.0000.0000.000
107B8ARG 10.9110.9587.8950.2100.2100.0000.0000.0000.000
108B9PRO 00.0390.0318.7600.3060.3060.0000.0000.0000.000
109B10LEU 0-0.012-0.0167.988-0.314-0.3140.0000.0000.0000.000
110B11VAL 0-0.007-0.01511.5120.2160.2160.0000.0000.0000.000
111B12THR 00.0180.00713.503-0.055-0.0550.0000.0000.0000.000
112B13ILE 0-0.0200.00111.2980.0300.0300.0000.0000.0000.000
113B14LYS 10.9590.97415.3940.6850.6850.0000.0000.0000.000
114B15ILE 00.0390.03111.249-0.036-0.0360.0000.0000.0000.000
115B16GLY 00.012-0.00415.4630.0840.0840.0000.0000.0000.000
116B17GLY 0-0.085-0.04117.7970.0600.0600.0000.0000.0000.000
117B18GLN 00.0270.02116.5050.0700.0700.0000.0000.0000.000
118B19LEU 0-0.019-0.01916.931-0.082-0.0820.0000.0000.0000.000
119B20LYS 10.8780.94910.3540.4430.4430.0000.0000.0000.000
120B21GLU -1-0.896-0.94110.222-0.878-0.8780.0000.0000.0000.000
121B22ALA 0-0.031-0.0249.287-0.023-0.0230.0000.0000.0000.000
122B23LEU 00.0170.0033.477-0.2780.4670.026-0.116-0.6550.000
123B24LEU 0-0.041-0.0185.915-1.390-1.3900.0000.0000.0000.000
124B25ASP -1-0.683-0.8081.414-46.384-95.14687.405-30.365-8.278-0.120
125B26THR 0-0.075-0.0584.2820.6800.916-0.001-0.039-0.1970.000
126B27GLY 00.0140.0202.4250.8931.9290.768-0.747-1.0580.003
127B28ALA 0-0.0070.0122.1424.6300.71415.207-3.704-7.5870.003
128B29ASP -1-0.829-0.9282.102-6.319-6.5074.427-1.249-2.9910.015
129B30ASP -1-0.946-1.0052.486-9.231-6.7600.759-1.263-1.9670.007
130B31THR 0-0.026-0.0293.900-0.552-0.1550.005-0.110-0.293-0.001
131B32VAL 0-0.0360.0073.060-0.4760.8490.109-0.274-1.1600.001
132B33LEU 0-0.005-0.0224.735-0.282-0.196-0.001-0.009-0.0770.000
133B34GLU -1-0.905-0.9646.9890.4670.4670.0000.0000.0000.000
134B35GLU -1-0.900-0.9618.0410.5380.5380.0000.0000.0000.000
135B36MET 0-0.027-0.01111.333-0.101-0.1010.0000.0000.0000.000
136B37SER 0-0.023-0.00814.4020.0280.0280.0000.0000.0000.000
137B38LEU 00.0110.00912.988-0.069-0.0690.0000.0000.0000.000
138B39PRO 00.0030.01916.8180.0270.0270.0000.0000.0000.000
139B40GLY 00.0610.01517.789-0.065-0.0650.0000.0000.0000.000
140B41ARG 10.9350.95616.9630.4610.4610.0000.0000.0000.000
141B42TRP 00.0360.02612.730-0.045-0.0450.0000.0000.0000.000
142B43LYS 10.9400.96811.6070.5390.5390.0000.0000.0000.000
143B44PRO 00.0200.02310.879-0.072-0.0720.0000.0000.0000.000
144B45LYS 10.9130.9715.5110.7160.7160.0000.0000.0000.000
145B46MET 00.015-0.0358.2880.0390.0390.0000.0000.0000.000
146B47ILE 0-0.0520.0092.484-4.009-1.1400.986-1.068-2.7870.010
147B48GLY 00.0600.0054.3410.4090.7200.000-0.053-0.2580.000
148B49GLY 0-0.0020.0082.098-4.572-2.7954.933-3.300-3.4110.019
149B50ILE 0-0.0010.0061.959-7.296-19.65333.776-3.511-17.9070.032
150B51GLY 0-0.010-0.0284.0360.3831.0440.008-0.145-0.5230.001
151B52GLY 00.0050.0015.990-2.248-2.2480.0000.0000.0000.000
152B53PHE 00.012-0.0025.8671.7371.7370.0000.0000.0000.000
153B54ILE 00.0000.0435.750-0.736-0.7360.0000.0000.0000.000
154B55LYS 10.9330.9748.503-1.395-1.3950.0000.0000.0000.000
155B56VAL 0-0.013-0.0185.2730.0310.0310.0000.0000.0000.000
156B57ARG 10.8970.9388.495-0.220-0.2200.0000.0000.0000.000
157B58GLN 0-0.019-0.0188.141-0.397-0.3970.0000.0000.0000.000
158B59TYR 00.0180.0189.2550.1910.1910.0000.0000.0000.000
159B60ASP -1-0.877-0.94711.114-1.186-1.1860.0000.0000.0000.000
160B61GLN 0-0.065-0.04012.7350.1300.1300.0000.0000.0000.000
161B62ILE 00.0050.00712.7450.1320.1320.0000.0000.0000.000
162B63LEU 0-0.051-0.04114.337-0.101-0.1010.0000.0000.0000.000
163B64ILE 00.0530.01410.9720.0700.0700.0000.0000.0000.000
164B65GLU -1-0.954-0.96814.842-0.806-0.8060.0000.0000.0000.000
165B66ILE 00.0480.02012.264-0.023-0.0230.0000.0000.0000.000
166B67CYS 0-0.030-0.02516.2590.0120.0120.0000.0000.0000.000
167B68GLY 00.0330.03118.3790.0750.0750.0000.0000.0000.000
168B69HIS 0-0.045-0.01818.9050.0740.0740.0000.0000.0000.000
169B70LYS 10.9450.96618.3240.6330.6330.0000.0000.0000.000
170B71ALA 00.0610.02614.714-0.008-0.0080.0000.0000.0000.000
171B72ILE 0-0.034-0.00314.714-0.031-0.0310.0000.0000.0000.000
172B73GLY 00.0400.00911.333-0.077-0.0770.0000.0000.0000.000
173B74THR 0-0.046-0.0227.9410.2060.2060.0000.0000.0000.000
174B75VAL 00.0400.0157.508-0.425-0.4250.0000.0000.0000.000
175B76LEU 0-0.013-0.0133.5200.1400.5490.014-0.071-0.3520.000
176B77VAL 0-0.0050.0136.9140.1090.1090.0000.0000.0000.000
177B78GLY 00.0140.0018.8620.1350.1350.0000.0000.0000.000
178B79PRO 00.0090.0258.484-0.229-0.2290.0000.0000.0000.000
179B80THR 0-0.063-0.0093.424-0.0421.0030.039-0.397-0.687-0.003
180B81PRO 00.0440.0191.983-0.900-1.7534.462-0.814-2.795-0.002
181B82VAL 00.0450.0122.795-3.802-1.0642.527-1.094-4.1720.006
182B83ASN 0-0.023-0.0034.454-0.351-0.1040.000-0.014-0.2330.000
183B84ILE 0-0.015-0.0142.009-2.842-1.1705.269-1.433-5.5080.000
184B85ILE 0-0.0080.0065.2070.2930.489-0.001-0.007-0.1880.000
185B86GLY 00.1110.0464.992-0.538-0.5380.0000.0000.0000.000
186B87ARG 10.9320.9495.9342.2762.2760.0000.0000.0000.000
187B88ASN 0-0.0320.0326.410-0.039-0.0390.0000.0000.0000.000
188B89LEU 0-0.018-0.0208.1510.3320.3320.0000.0000.0000.000
189B90LEU 0-0.0230.0078.2160.2780.2780.0000.0000.0000.000
190B91THR 0-0.055-0.02710.9950.2380.2380.0000.0000.0000.000
191B92GLN 0-0.060-0.01512.7890.2730.2730.0000.0000.0000.000
192B93ILE 0-0.054-0.02013.4270.1240.1240.0000.0000.0000.000
193B94GLY 00.0010.01316.0980.0750.0750.0000.0000.0000.000
194B95ALA 00.009-0.00913.4930.0430.0430.0000.0000.0000.000
195B96THR 0-0.053-0.04515.5330.1000.1000.0000.0000.0000.000
196B97LEU 0-0.0240.0119.867-0.035-0.0350.0000.0000.0000.000
197B98ASN 00.017-0.01714.1770.0210.0210.0000.0000.0000.000
198B99PHE -1-0.876-0.89313.202-1.186-1.1860.0000.0000.0000.000