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

tag_button

FMODB ID: R1V78

Calculation Name: 1BVE-AB-NMR60-Model21

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 -2273922.135818
FMO2-HF: Nuclear repulsion 2197444.197844
FMO2-HF: Total energy -76477.937974
FMO2-MP2: Total energy -76703.563661


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.
-158.407-204.111245.099-81.374-118.027-0.011


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.
-158.407-204.111245.099-81.374-118.0270.011
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 : 0.008 / q_NPA : -0.087
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 10.8100.89117.2341.1501.1500.0000.0000.0000.000
2A2GLN 00.0820.05617.759-0.123-0.1230.0000.0000.0000.000
3A3VAL 0-0.0060.00213.0760.0570.0570.0000.0000.0000.000
4A4THR 00.000-0.00615.072-0.183-0.1830.0000.0000.0000.000
5A5LEU 00.0650.06310.403-0.174-0.1740.0000.0000.0000.000
6A6TRP 0-0.021-0.00412.477-0.117-0.1170.0000.0000.0000.000
7A7GLN 0-0.023-0.00413.4180.1600.1600.0000.0000.0000.000
8A8ARG 10.9440.9637.5282.1382.1380.0000.0000.0000.000
9A9PRO 00.0510.0338.3330.4470.4470.0000.0000.0000.000
10A10LEU 0-0.035-0.0118.217-0.254-0.2540.0000.0000.0000.000
11A11VAL 0-0.011-0.01011.5390.3300.3300.0000.0000.0000.000
12A12THR 0-0.012-0.01013.531-0.033-0.0330.0000.0000.0000.000
13A13ILE 00.0110.01211.3320.0740.0740.0000.0000.0000.000
14A14LYS 10.9370.96215.4170.5200.5200.0000.0000.0000.000
15A15ILE 00.0470.02510.6850.0260.0260.0000.0000.0000.000
16A16GLY 00.009-0.01815.0920.0510.0510.0000.0000.0000.000
17A17GLY 0-0.009-0.00217.4030.0000.0000.0000.0000.0000.000
18A18GLN 0-0.037-0.01716.7900.0680.0680.0000.0000.0000.000
19A19LEU 00.0070.00117.452-0.035-0.0350.0000.0000.0000.000
20A20LYS 10.8600.93911.3790.5650.5650.0000.0000.0000.000
21A21GLU -1-0.881-0.94210.223-1.343-1.3430.0000.0000.0000.000
22A22ALA 00.023-0.0229.4820.1130.1130.0000.0000.0000.000
23A23LEU 0-0.033-0.0023.601-0.0030.8500.026-0.138-0.7410.000
24A24LEU 0-0.014-0.0185.813-1.443-1.4430.0000.0000.0000.000
25A25ASP -1-0.690-0.7931.343-55.488-111.893105.195-43.596-5.194-0.112
26A26THR 0-0.070-0.0574.2711.0311.382-0.001-0.090-0.2600.000
27A27GLY 00.0180.0282.1701.3381.8671.345-0.783-1.0920.004
28A28ALA 0-0.0180.0072.2194.4931.95513.279-2.741-8.0000.005
29A29ASP -1-0.886-0.9782.417-5.848-3.6071.905-0.936-3.2110.014
30A30ASP -1-0.890-0.9692.289-3.113-1.9042.249-1.131-2.3270.011
31A31THR 0-0.057-0.0303.487-3.828-3.0290.034-0.318-0.515-0.002
32A32VAL 0-0.039-0.0052.928-0.7030.9530.225-0.395-1.4870.001
33A33LEU 0-0.011-0.0274.505-0.636-0.5330.000-0.015-0.0880.000
34A34GLU -1-0.984-1.0017.7790.6080.6080.0000.0000.0000.000
35A35GLU -1-0.935-0.9848.7740.3100.3100.0000.0000.0000.000
36A36MET 0-0.0150.00712.302-0.185-0.1850.0000.0000.0000.000
37A37SER 00.0120.02115.0630.0800.0800.0000.0000.0000.000
38A38LEU 0-0.0070.00912.368-0.075-0.0750.0000.0000.0000.000
39A39PRO 00.0460.06916.0310.0800.0800.0000.0000.0000.000
40A40GLY 00.0630.02917.317-0.019-0.0190.0000.0000.0000.000
41A41ARG 10.8880.92917.407-0.233-0.2330.0000.0000.0000.000
42A42TRP 00.0630.04012.9550.0410.0410.0000.0000.0000.000
43A43LYS 10.9300.95312.215-0.451-0.4510.0000.0000.0000.000
44A44PRO 0-0.0020.01711.2740.0810.0810.0000.0000.0000.000
45A45LYS 10.9480.9895.849-1.424-1.4240.0000.0000.0000.000
46A46MET 0-0.007-0.0248.265-0.053-0.0530.0000.0000.0000.000
47A47ILE 0-0.0370.0142.396-3.862-0.9291.281-1.060-3.1550.011
48A48GLY 00.0330.0154.2330.4650.8370.000-0.061-0.3110.000
49A49GLY 0-0.014-0.0082.013-5.265-4.5889.272-5.202-4.7480.019
50A50ILE 0-0.0160.0031.991-4.613-21.78239.395-1.748-20.4780.035
51A51GLY 00.008-0.0013.863-0.0200.7970.011-0.156-0.6710.002
52A52GLY 00.0170.0126.063-2.094-2.0940.0000.0000.0000.000
53A53PHE 00.025-0.0195.8001.6651.6650.0000.0000.0000.000
54A54ILE 0-0.0070.0295.791-0.718-0.7180.0000.0000.0000.000
55A55LYS 10.9380.9568.324-2.036-2.0360.0000.0000.0000.000
56A56VAL 00.004-0.0035.2320.0080.0080.0000.0000.0000.000
57A57ARG 10.9360.9638.406-0.696-0.6960.0000.0000.0000.000
58A58GLN 0-0.013-0.0177.9320.1020.1020.0000.0000.0000.000
59A59TYR 0-0.045-0.0568.879-0.056-0.0560.0000.0000.0000.000
60A60ASP -1-0.850-0.92510.5450.6210.6210.0000.0000.0000.000
61A61GLN 0-0.052-0.04612.654-0.073-0.0730.0000.0000.0000.000
62A62ILE 00.0140.01512.224-0.020-0.0200.0000.0000.0000.000
63A63LEU 0-0.045-0.04313.683-0.062-0.0620.0000.0000.0000.000
64A64ILE 00.0210.01910.3850.0020.0020.0000.0000.0000.000
65A65GLU -1-0.969-0.99014.144-0.702-0.7020.0000.0000.0000.000
66A66ILE 00.0680.02612.477-0.082-0.0820.0000.0000.0000.000
67A67CYS 00.009-0.01516.2670.0970.0970.0000.0000.0000.000
68A68GLY 00.0350.05118.7760.0010.0010.0000.0000.0000.000
69A69HIS 10.8860.93217.9250.8700.8700.0000.0000.0000.000
70A70LYS 10.9630.99017.5940.3150.3150.0000.0000.0000.000
71A71ALA 00.0300.02414.1230.0140.0140.0000.0000.0000.000
72A72ILE 0-0.0250.00514.254-0.002-0.0020.0000.0000.0000.000
73A73GLY 00.039-0.00310.707-0.061-0.0610.0000.0000.0000.000
74A74THR 0-0.023-0.0157.577-0.126-0.1260.0000.0000.0000.000
75A75VAL 00.0060.0107.0180.1140.1140.0000.0000.0000.000
76A76LEU 0-0.019-0.0213.135-0.3890.2360.066-0.117-0.5740.000
77A77VAL 00.0310.0246.490-0.125-0.1250.0000.0000.0000.000
78A78GLY 00.0330.0029.0260.1850.1850.0000.0000.0000.000
79A79PRO 0-0.0260.0159.009-0.270-0.2700.0000.0000.0000.000
80A80THR 0-0.0660.0044.1070.5890.9370.001-0.057-0.2930.000
81A81PRO 00.0720.0311.988-0.963-1.0502.518-0.490-1.941-0.001
82A82VAL 00.0510.0093.032-2.501-0.5840.425-0.512-1.8300.004
83A83ASN 0-0.039-0.0084.9080.1640.329-0.001-0.006-0.1580.000
84A84ILE 0-0.005-0.0052.181-3.391-0.7833.630-1.320-4.9170.003
85A85ILE 00.0230.0275.2000.9871.189-0.001-0.006-0.1960.000
86A86GLY 00.1030.0294.802-0.862-0.8620.0000.0000.0000.000
87A87ARG 10.8720.9615.7011.2311.2310.0000.0000.0000.000
88A88ASN 0-0.0110.0576.199-0.422-0.4220.0000.0000.0000.000
89A89LEU 00.0200.0028.308-0.038-0.0380.0000.0000.0000.000
90A90LEU 0-0.0130.0278.186-0.030-0.0300.0000.0000.0000.000
91A91THR 0-0.009-0.02011.2600.0990.0990.0000.0000.0000.000
92A92GLN 0-0.053-0.00412.6390.0830.0830.0000.0000.0000.000
93A93ILE 0-0.116-0.05713.4060.0620.0620.0000.0000.0000.000
94A94GLY 0-0.0010.01116.1850.0150.0150.0000.0000.0000.000
95A95ALA 0-0.016-0.01813.474-0.022-0.0220.0000.0000.0000.000
96A96THR 0-0.055-0.03915.5480.0960.0960.0000.0000.0000.000
97A97LEU 00.0010.0059.707-0.070-0.0700.0000.0000.0000.000
98A98ASN 0-0.025-0.02714.3190.1260.1260.0000.0000.0000.000
99A99PHE -1-0.810-0.89012.654-1.254-1.2540.0000.0000.0000.000
100B1PRO 10.8100.89718.3411.0891.0890.0000.0000.0000.000
101B2GLN 00.0350.04018.153-0.113-0.1130.0000.0000.0000.000
102B3VAL 00.0250.01814.1960.0850.0850.0000.0000.0000.000
103B4THR 00.0440.00715.782-0.100-0.1000.0000.0000.0000.000
104B5LEU 0-0.026-0.00813.6770.0990.0990.0000.0000.0000.000
105B6TRP 00.0160.03013.570-0.061-0.0610.0000.0000.0000.000
106B7GLN 0-0.046-0.02810.5890.0670.0670.0000.0000.0000.000
107B8ARG 10.9630.9636.7450.7130.7130.0000.0000.0000.000
108B9PRO 00.0370.0088.4160.2340.2340.0000.0000.0000.000
109B10LEU 00.032-0.0018.504-0.386-0.3860.0000.0000.0000.000
110B11VAL 0-0.007-0.00211.6570.1810.1810.0000.0000.0000.000
111B12THR 00.006-0.00813.849-0.030-0.0300.0000.0000.0000.000
112B13ILE 0-0.0100.01211.9400.0420.0420.0000.0000.0000.000
113B14LYS 10.9740.97415.5060.5410.5410.0000.0000.0000.000
114B15ILE 00.0560.04111.5330.0080.0080.0000.0000.0000.000
115B16GLY 0-0.003-0.00115.8760.0640.0640.0000.0000.0000.000
116B17GLY 0-0.050-0.02518.4490.0330.0330.0000.0000.0000.000
117B18GLN 0-0.015-0.00817.7790.0810.0810.0000.0000.0000.000
118B19LEU 0-0.041-0.02917.955-0.056-0.0560.0000.0000.0000.000
119B20LYS 10.8800.95211.7280.3690.3690.0000.0000.0000.000
120B21GLU -1-0.927-0.95512.491-0.978-0.9780.0000.0000.0000.000
121B22ALA 00.006-0.0099.275-0.018-0.0180.0000.0000.0000.000
122B23LEU 0-0.013-0.0093.614-0.2310.4850.012-0.132-0.5960.000
123B24LEU 0-0.023-0.0236.328-1.428-1.4280.0000.0000.0000.000
124B25ASP -1-0.737-0.8722.143-37.920-34.6577.301-4.212-6.352-0.051
125B26THR 0-0.027-0.0384.7390.5440.695-0.001-0.005-0.1450.000
126B27GLY 00.0020.0063.0041.5642.0180.071-0.245-0.280-0.001
127B28ALA 0-0.0430.0022.021-2.503-2.4448.003-2.668-5.3930.001
128B29ASP -1-0.943-0.9912.078-7.171-4.5641.794-1.632-2.7690.006
129B30ASP -1-0.926-0.9822.6420.7242.4310.509-0.669-1.5470.005
130B31THR 0-0.016-0.0493.437-3.828-2.9460.032-0.427-0.486-0.003
131B32VAL 0-0.036-0.0052.858-0.0321.4370.254-0.304-1.4190.001
132B33LEU 00.013-0.0024.806-0.798-0.694-0.001-0.010-0.0940.000
133B34GLU -1-0.897-0.9697.0680.2610.2610.0000.0000.0000.000
134B35GLU -1-0.980-1.0108.3740.3390.3390.0000.0000.0000.000
135B36MET 00.0070.00111.702-0.146-0.1460.0000.0000.0000.000
136B37SER 0-0.0080.01314.5790.0910.0910.0000.0000.0000.000
137B38LEU 00.006-0.00612.892-0.070-0.0700.0000.0000.0000.000
138B39PRO 00.0790.05316.7160.0500.0500.0000.0000.0000.000
139B40GLY 00.0570.04617.4970.0480.0480.0000.0000.0000.000
140B41ARG 10.9130.94217.841-0.148-0.1480.0000.0000.0000.000
141B42TRP 00.0490.05913.2810.0030.0030.0000.0000.0000.000
142B43LYS 10.9320.95212.530-0.278-0.2780.0000.0000.0000.000
143B44PRO 0-0.0040.01411.3480.0700.0700.0000.0000.0000.000
144B45LYS 10.9500.9975.659-1.810-1.8100.0000.0000.0000.000
145B46MET 0-0.020-0.0318.061-0.097-0.0970.0000.0000.0000.000
146B47ILE 0-0.0060.0202.473-4.115-1.0852.363-1.252-4.1400.016
147B48GLY 00.076-0.0234.0200.2750.7000.001-0.077-0.3500.000
148B49GLY 0-0.017-0.0072.047-6.135-4.4887.298-4.533-4.4120.015
149B50ILE 0-0.0080.0021.936-7.357-17.88729.270-1.477-17.2640.032
150B51GLY 0-0.026-0.0104.0450.3080.9530.008-0.144-0.5080.001
151B52GLY 00.0170.0095.980-2.196-2.1960.0000.0000.0000.000
152B53PHE 0-0.0100.0365.8051.7591.7590.0000.0000.0000.000
153B54ILE 00.0060.0315.586-0.604-0.6040.0000.0000.0000.000
154B55LYS 10.9180.9468.079-1.680-1.6800.0000.0000.0000.000
155B56VAL 00.0200.0155.301-0.018-0.0180.0000.0000.0000.000
156B57ARG 10.9310.9598.506-0.549-0.5490.0000.0000.0000.000
157B58GLN 0-0.042-0.0318.5310.0470.0470.0000.0000.0000.000
158B59TYR 0-0.067-0.0859.453-0.007-0.0070.0000.0000.0000.000
159B60ASP -1-0.784-0.84211.723-0.078-0.0780.0000.0000.0000.000
160B61GLN 0-0.052-0.03012.995-0.027-0.0270.0000.0000.0000.000
161B62ILE 0-0.004-0.00712.7850.0390.0390.0000.0000.0000.000
162B63LEU 0-0.051-0.05314.329-0.092-0.0920.0000.0000.0000.000
163B64ILE 00.0290.01110.9590.0430.0430.0000.0000.0000.000
164B65GLU -1-0.959-0.99414.779-0.652-0.6520.0000.0000.0000.000
165B66ILE 00.0350.02212.158-0.033-0.0330.0000.0000.0000.000
166B67CYS 0-0.042-0.02716.2470.0080.0080.0000.0000.0000.000
167B68GLY 00.0460.03919.2380.0340.0340.0000.0000.0000.000
168B69HIS 00.0000.00018.2270.0280.0280.0000.0000.0000.000
169B70LYS 10.9280.95518.1020.4110.4110.0000.0000.0000.000
170B71ALA 00.0460.03414.3920.0010.0010.0000.0000.0000.000
171B72ILE 0-0.0130.02614.495-0.018-0.0180.0000.0000.0000.000
172B73GLY 00.0120.00311.392-0.078-0.0780.0000.0000.0000.000
173B74THR 0-0.037-0.0798.4450.0630.0630.0000.0000.0000.000
174B75VAL 00.0090.0077.656-0.061-0.0610.0000.0000.0000.000
175B76LEU 0-0.012-0.0203.4070.0150.4030.013-0.063-0.3390.000
176B77VAL 00.0170.0246.844-0.125-0.1250.0000.0000.0000.000
177B78GLY 00.028-0.0048.6190.2050.2050.0000.0000.0000.000
178B79PRO 0-0.062-0.0078.600-0.290-0.2900.0000.0000.0000.000
179B80THR 0-0.0540.0123.6170.2520.9600.014-0.230-0.492-0.001
180B81PRO 00.0470.0211.963-0.778-1.5074.059-0.795-2.535-0.003
181B82VAL 00.0720.0253.125-2.767-0.4360.582-0.584-2.3300.005
182B83ASN 0-0.089-0.0144.940-0.412-0.238-0.001-0.009-0.1640.000
183B84ILE 0-0.006-0.0132.059-3.036-0.6962.666-1.015-3.991-0.006
184B85ILE 0-0.0010.0205.0780.2920.451-0.001-0.007-0.1510.000
185B86GLY 00.1600.0594.780-0.967-0.877-0.001-0.006-0.0830.000
186B87ARG 10.9040.9395.7876.0856.0850.0000.0000.0000.000
187B88ASN 00.0780.0886.354-0.177-0.1770.0000.0000.0000.000
188B89LEU 0-0.011-0.0158.0520.2220.2220.0000.0000.0000.000
189B90LEU 0-0.0530.0048.2250.1090.1090.0000.0000.0000.000
190B91THR 0-0.013-0.05211.2040.2140.2140.0000.0000.0000.000
191B92GLN 0-0.075-0.03811.7300.1170.1170.0000.0000.0000.000
192B93ILE 0-0.049-0.00912.9310.0810.0810.0000.0000.0000.000
193B94GLY 00.0240.02115.3800.0600.0600.0000.0000.0000.000
194B95ALA 0-0.015-0.02413.1790.0380.0380.0000.0000.0000.000
195B96THR 0-0.047-0.01415.208-0.004-0.0040.0000.0000.0000.000
196B97LEU 0-0.017-0.0169.713-0.012-0.0120.0000.0000.0000.000
197B98ASN 0-0.034-0.03014.2310.0730.0730.0000.0000.0000.000
198B99PHE -1-0.839-0.91212.234-1.099-1.0990.0000.0000.0000.000