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FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: Q8J2Y

Calculation Name: 1BVE-AB-NMR60-Model20

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
LigandCharge
Software MIZUHO/ABINIT-MP 4.0(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2281549.568568
FMO2-HF: Nuclear repulsion 2205072.190104
FMO2-HF: Total energy -76477.378464
FMO2-MP2: Total energy -76703.101418


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.
-176.741-213.009239.873-82.004-121.6080.043


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.
-176.741-213.009239.873-82.004-121.608-0.043
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 : -0.044 / q_NPA : -0.110
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 10.7860.87818.2461.4881.4880.0000.0000.0000.000
2A2GLN 00.0860.06617.957-0.184-0.1840.0000.0000.0000.000
3A3VAL 0-0.0120.00613.2380.1010.1010.0000.0000.0000.000
4A4THR 00.0650.03014.561-0.199-0.1990.0000.0000.0000.000
5A5LEU 0-0.029-0.02914.460-0.160-0.1600.0000.0000.0000.000
6A6TRP 00.0220.00113.637-0.031-0.0310.0000.0000.0000.000
7A7GLN 0-0.010-0.00710.4460.1690.1690.0000.0000.0000.000
8A8ARG 10.9320.9765.5691.9051.9050.0000.0000.0000.000
9A9PRO 00.0470.0378.1050.5930.5930.0000.0000.0000.000
10A10LEU 00.010-0.0088.249-0.295-0.2950.0000.0000.0000.000
11A11VAL 0-0.020-0.01411.3830.2900.2900.0000.0000.0000.000
12A12THR 0-0.015-0.01413.763-0.025-0.0250.0000.0000.0000.000
13A13ILE 00.0100.01911.1640.0480.0480.0000.0000.0000.000
14A14LYS 10.9230.95815.2180.7380.7380.0000.0000.0000.000
15A15ILE 00.0680.02810.9310.0180.0180.0000.0000.0000.000
16A16GLY 00.015-0.01115.3670.0920.0920.0000.0000.0000.000
17A17GLY 0-0.062-0.02217.6990.0510.0510.0000.0000.0000.000
18A18GLN 00.0230.01617.670-0.014-0.0140.0000.0000.0000.000
19A19LEU 0-0.024-0.02417.405-0.091-0.0910.0000.0000.0000.000
20A20LYS 10.9560.99112.7780.1470.1470.0000.0000.0000.000
21A21GLU -1-0.887-0.94011.600-0.962-0.9620.0000.0000.0000.000
22A22ALA 0-0.010-0.0229.4620.0700.0700.0000.0000.0000.000
23A23LEU 0-0.008-0.0083.408-0.1570.7350.024-0.146-0.7710.000
24A24LEU 0-0.022-0.0275.953-1.813-1.8130.0000.0000.0000.000
25A25ASP -1-0.669-0.7691.320-70.062-123.429103.894-42.687-7.840-0.139
26A26THR 0-0.065-0.0504.3440.2640.555-0.001-0.040-0.2500.000
27A27GLY 00.0470.0312.4641.3012.2980.702-0.677-1.0220.003
28A28ALA 0-0.079-0.0162.0762.4271.9699.802-2.680-6.6630.001
29A29ASP -1-0.914-0.9772.411-5.503-3.3040.246-0.696-1.7500.001
30A30ASP -1-0.891-0.9662.5611.2433.3970.742-0.974-1.9220.007
31A31THR 0-0.081-0.0392.859-6.022-4.2580.313-0.934-1.143-0.011
32A32VAL 0-0.013-0.0072.7780.4842.0360.231-0.346-1.4370.001
33A33LEU 0-0.033-0.0284.669-0.821-0.7270.000-0.012-0.0820.000
34A34GLU -1-0.890-0.9527.0650.8090.8090.0000.0000.0000.000
35A35GLU -1-0.955-0.9798.4731.2771.2770.0000.0000.0000.000
36A36MET 0-0.061-0.03311.741-0.188-0.1880.0000.0000.0000.000
37A37SER 0-0.0170.00014.7490.1020.1020.0000.0000.0000.000
38A38LEU 00.0600.02912.086-0.126-0.1260.0000.0000.0000.000
39A39PRO 0-0.0070.02615.9280.1030.1030.0000.0000.0000.000
40A40GLY 00.0380.00517.620-0.066-0.0660.0000.0000.0000.000
41A41ARG 10.9280.95317.321-0.129-0.1290.0000.0000.0000.000
42A42TRP 00.0100.02312.9800.0550.0550.0000.0000.0000.000
43A43LYS 10.9830.97212.374-0.702-0.7020.0000.0000.0000.000
44A44PRO 0-0.0160.00411.4590.1310.1310.0000.0000.0000.000
45A45LYS 10.9160.9764.899-3.848-3.8480.0000.0000.0000.000
46A46MET 0-0.013-0.0317.813-0.131-0.1310.0000.0000.0000.000
47A47ILE 00.0030.0202.240-4.790-1.5092.596-1.408-4.4690.015
48A48GLY 00.039-0.0124.210-0.0810.3270.000-0.065-0.3430.000
49A49GLY 0-0.0060.0072.064-4.708-3.0435.058-3.321-3.4020.018
50A50ILE 0-0.031-0.0032.007-9.551-20.64533.613-3.750-18.7690.043
51A51GLY 00.006-0.0063.9560.1180.8580.006-0.141-0.6060.001
52A52GLY 00.0000.0016.097-2.558-2.5580.0000.0000.0000.000
53A53PHE 00.0070.0146.0992.0072.0070.0000.0000.0000.000
54A54ILE 0-0.0490.0185.922-1.077-1.0770.0000.0000.0000.000
55A55LYS 10.9480.9658.148-3.410-3.4100.0000.0000.0000.000
56A56VAL 00.0200.0225.4010.0080.0080.0000.0000.0000.000
57A57ARG 10.9170.9578.699-1.181-1.1810.0000.0000.0000.000
58A58GLN 00.0350.0067.0890.3940.3940.0000.0000.0000.000
59A59TYR 0-0.042-0.0268.967-0.062-0.0620.0000.0000.0000.000
60A60ASP -1-0.869-0.94310.9750.5480.5480.0000.0000.0000.000
61A61GLN 0-0.077-0.07013.039-0.076-0.0760.0000.0000.0000.000
62A62ILE 00.0120.00212.3860.0420.0420.0000.0000.0000.000
63A63LEU 0-0.050-0.03314.076-0.137-0.1370.0000.0000.0000.000
64A64ILE 00.0380.02110.9130.0720.0720.0000.0000.0000.000
65A65GLU -1-0.988-0.99214.725-0.921-0.9210.0000.0000.0000.000
66A66ILE 00.1010.04512.431-0.046-0.0460.0000.0000.0000.000
67A67CYS 0-0.027-0.02016.4350.0660.0660.0000.0000.0000.000
68A68GLY 00.0300.03219.1230.0430.0430.0000.0000.0000.000
69A69HIS 10.8970.94318.3871.1641.1640.0000.0000.0000.000
70A70LYS 10.9560.97418.1510.4750.4750.0000.0000.0000.000
71A71ALA 00.0670.03814.486-0.011-0.0110.0000.0000.0000.000
72A72ILE 0-0.0180.02214.438-0.010-0.0100.0000.0000.0000.000
73A73GLY 00.0680.04010.973-0.155-0.1550.0000.0000.0000.000
74A74THR 0-0.009-0.0027.716-0.064-0.0640.0000.0000.0000.000
75A75VAL 00.0070.0137.174-0.145-0.1450.0000.0000.0000.000
76A76LEU 00.004-0.0142.6640.1470.7610.197-0.136-0.6760.000
77A77VAL 00.0420.0256.540-0.088-0.0880.0000.0000.0000.000
78A78GLY 00.022-0.0119.0890.2570.2570.0000.0000.0000.000
79A79PRO 0-0.0060.0238.885-0.281-0.2810.0000.0000.0000.000
80A80THR 0-0.068-0.0153.5441.2271.7000.004-0.085-0.3930.000
81A81PRO 00.0530.0222.070-1.523-1.1991.942-0.436-1.829-0.001
82A82VAL 00.019-0.0013.127-2.885-0.6660.422-0.559-2.0820.005
83A83ASN 0-0.0220.0195.054-0.313-0.154-0.001-0.006-0.1530.000
84A84ILE 0-0.037-0.0152.350-2.976-0.6331.236-0.713-2.8660.000
85A85ILE 0-0.025-0.0045.9561.0271.0270.0000.0000.0000.000
86A86GLY 00.1010.0514.336-1.333-1.270-0.001-0.021-0.0420.000
87A87ARG 11.0000.9865.2063.2903.397-0.001-0.003-0.1030.000
88A88ASN 0-0.0650.0146.148-0.220-0.2200.0000.0000.0000.000
89A89LEU 0-0.002-0.0118.2220.4280.4280.0000.0000.0000.000
90A90LEU 0-0.0280.0157.8230.3390.3390.0000.0000.0000.000
91A91THR 0-0.028-0.02611.1830.2850.2850.0000.0000.0000.000
92A92GLN 0-0.130-0.06312.7750.2870.2870.0000.0000.0000.000
93A93ILE 0-0.066-0.03213.8420.1530.1530.0000.0000.0000.000
94A94GLY 00.0040.01116.0010.0510.0510.0000.0000.0000.000
95A95ALA 0-0.018-0.02013.0030.0370.0370.0000.0000.0000.000
96A96THR 0-0.031-0.00914.741-0.015-0.0150.0000.0000.0000.000
97A97LEU 00.003-0.0109.264-0.105-0.1050.0000.0000.0000.000
98A98ASN 0-0.019-0.03813.8710.0780.0780.0000.0000.0000.000
99A99PHE -1-0.850-0.90312.299-1.812-1.8120.0000.0000.0000.000
100B1PRO 10.8230.89817.7891.5791.5790.0000.0000.0000.000
101B2GLN 00.0420.04318.124-0.118-0.1180.0000.0000.0000.000
102B3VAL 00.0100.01613.6970.1110.1110.0000.0000.0000.000
103B4THR 00.0190.00615.772-0.165-0.1650.0000.0000.0000.000
104B5LEU 00.1360.03810.064-0.277-0.2770.0000.0000.0000.000
105B6TRP 0-0.055-0.01512.579-0.098-0.0980.0000.0000.0000.000
106B7GLN 0-0.023-0.01612.0170.1380.1380.0000.0000.0000.000
107B8ARG 10.9590.9777.6691.2271.2270.0000.0000.0000.000
108B9PRO 00.0400.0418.5180.5210.5210.0000.0000.0000.000
109B10LEU 0-0.006-0.0088.692-0.312-0.3120.0000.0000.0000.000
110B11VAL 0-0.025-0.01711.8330.1810.1810.0000.0000.0000.000
111B12THR 00.0020.00113.804-0.041-0.0410.0000.0000.0000.000
112B13ILE 00.0010.01711.1900.0190.0190.0000.0000.0000.000
113B14LYS 10.9390.97014.9300.8380.8380.0000.0000.0000.000
114B15ILE 00.0530.04010.911-0.038-0.0380.0000.0000.0000.000
115B16GLY 0-0.005-0.01315.3890.1220.1220.0000.0000.0000.000
116B17GLY 0-0.025-0.01217.9780.0180.0180.0000.0000.0000.000
117B18GLN 0-0.025-0.01617.5100.0410.0410.0000.0000.0000.000
118B19LEU 0-0.029-0.02217.490-0.090-0.0900.0000.0000.0000.000
119B20LYS 10.9220.98112.7480.3720.3720.0000.0000.0000.000
120B21GLU -1-0.883-0.94911.693-1.166-1.1660.0000.0000.0000.000
121B22ALA 00.002-0.0119.5290.0510.0510.0000.0000.0000.000
122B23LEU 0-0.026-0.0173.765-0.0560.4490.007-0.059-0.4530.000
123B24LEU 0-0.019-0.0226.477-1.137-1.1370.0000.0000.0000.000
124B25ASP -1-0.716-0.8752.333-35.267-30.1085.059-4.085-6.133-0.048
125B26THR 0-0.040-0.0504.7700.7870.946-0.001-0.004-0.1550.000
126B27GLY 0-0.021-0.0062.5820.7081.7930.466-0.823-0.727-0.002
127B28ALA 0-0.0010.0262.090-0.408-0.44310.036-3.081-6.920-0.004
128B29ASP -1-0.897-0.9802.395-3.660-1.2642.050-1.164-3.2820.008
129B30ASP -1-0.870-0.9842.158-10.216-8.2922.820-1.901-2.8430.001
130B31THR 0-0.030-0.0203.372-1.053-0.1800.049-0.356-0.567-0.004
131B32VAL 0-0.045-0.0022.984-0.3071.1880.203-0.354-1.3440.001
132B33LEU 00.007-0.0204.596-0.186-0.0900.000-0.016-0.0810.000
133B34GLU -1-0.923-0.9797.5980.5870.5870.0000.0000.0000.000
134B35GLU -1-0.937-0.9828.6880.1740.1740.0000.0000.0000.000
135B36MET 0-0.0310.00211.936-0.102-0.1020.0000.0000.0000.000
136B37SER 0-0.0180.00014.8300.0420.0420.0000.0000.0000.000
137B38LEU 00.0670.00613.198-0.110-0.1100.0000.0000.0000.000
138B39PRO 00.0110.01416.4160.0930.0930.0000.0000.0000.000
139B40GLY 0-0.039-0.03118.1370.0030.0030.0000.0000.0000.000
140B41ARG 10.9350.95717.2990.1690.1690.0000.0000.0000.000
141B42TRP 00.0560.05712.954-0.034-0.0340.0000.0000.0000.000
142B43LYS 10.9210.95112.5560.1380.1380.0000.0000.0000.000
143B44PRO 00.0150.01011.491-0.065-0.0650.0000.0000.0000.000
144B45LYS 10.9260.9766.6680.2430.2430.0000.0000.0000.000
145B46MET 00.001-0.0287.910-0.003-0.0030.0000.0000.0000.000
146B47ILE 0-0.0050.0262.161-4.588-1.6182.711-1.601-4.0800.016
147B48GLY 00.058-0.0393.5470.1390.7620.008-0.147-0.4830.000
148B49GLY 0-0.006-0.0111.965-6.558-6.45013.694-7.194-6.6080.008
149B50ILE 0-0.0060.0172.018-4.131-20.60234.6581.263-19.4510.037
150B51GLY 0-0.012-0.0213.965-0.2130.5040.011-0.163-0.5650.001
151B52GLY 00.000-0.0046.006-2.572-2.5720.0000.0000.0000.000
152B53PHE 00.0030.0515.7102.2352.2350.0000.0000.0000.000
153B54ILE 0-0.0050.0315.346-0.941-0.9410.0000.0000.0000.000
154B55LYS 10.9360.9647.962-2.790-2.7900.0000.0000.0000.000
155B56VAL 0-0.006-0.0265.5550.1660.1660.0000.0000.0000.000
156B57ARG 10.9010.9438.676-0.801-0.8010.0000.0000.0000.000
157B58GLN 00.008-0.0037.827-0.269-0.2690.0000.0000.0000.000
158B59TYR 0-0.0020.0139.2090.2320.2320.0000.0000.0000.000
159B60ASP -1-0.799-0.92210.579-1.474-1.4740.0000.0000.0000.000
160B61GLN 0-0.052-0.04112.5280.0790.0790.0000.0000.0000.000
161B62ILE 0-0.017-0.01011.7440.1590.1590.0000.0000.0000.000
162B63LEU 0-0.062-0.03713.987-0.141-0.1410.0000.0000.0000.000
163B64ILE 00.0320.01010.4350.1120.1120.0000.0000.0000.000
164B65GLU -1-0.985-1.00114.275-1.275-1.2750.0000.0000.0000.000
165B66ILE 00.0980.04711.611-0.050-0.0500.0000.0000.0000.000
166B67CYS 0-0.059-0.02415.833-0.006-0.0060.0000.0000.0000.000
167B68GLY 00.0840.04318.9420.1320.1320.0000.0000.0000.000
168B69HIS 0-0.069-0.02818.2000.0760.0760.0000.0000.0000.000
169B70LYS 10.9060.95017.7250.8800.8800.0000.0000.0000.000
170B71ALA 00.0520.03413.788-0.001-0.0010.0000.0000.0000.000
171B72ILE 0-0.0190.02413.921-0.042-0.0420.0000.0000.0000.000
172B73GLY 00.0660.02510.658-0.075-0.0750.0000.0000.0000.000
173B74THR 0-0.039-0.0197.2000.2800.2800.0000.0000.0000.000
174B75VAL 00.0140.0087.156-0.633-0.6330.0000.0000.0000.000
175B76LEU 0-0.033-0.0233.4440.3110.7600.015-0.087-0.3770.000
176B77VAL 00.0320.0286.5900.1070.1070.0000.0000.0000.000
177B78GLY 0-0.003-0.0028.8980.2000.2000.0000.0000.0000.000
178B79PRO 0-0.0430.0048.715-0.275-0.2750.0000.0000.0000.000
179B80THR 0-0.0460.0143.9131.0011.4450.004-0.100-0.3470.000
180B81PRO 00.0370.0161.933-1.016-1.8684.023-0.787-2.384-0.001
181B82VAL 00.0710.0233.268-2.408-0.5430.273-0.458-1.6800.005
182B83ASN 0-0.047-0.0035.123-0.378-0.228-0.001-0.007-0.1430.000
183B84ILE 0-0.003-0.0102.050-2.764-0.3902.766-1.025-4.115-0.005
184B85ILE 0-0.0070.0174.9850.1700.321-0.001-0.008-0.1420.000
185B86GLY 00.1660.0564.522-0.820-0.693-0.001-0.011-0.1150.000
186B87ARG 10.8680.9265.4653.0813.0810.0000.0000.0000.000
187B88ASN 00.0180.0575.9780.0010.0010.0000.0000.0000.000
188B89LEU 00.019-0.0037.6960.4640.4640.0000.0000.0000.000
189B90LEU 0-0.0530.0147.9520.3380.3380.0000.0000.0000.000
190B91THR 0-0.063-0.02111.0280.3360.3360.0000.0000.0000.000
191B92GLN 0-0.050-0.03111.3320.3180.3180.0000.0000.0000.000
192B93ILE 0-0.069-0.01812.4320.1470.1470.0000.0000.0000.000
193B94GLY 00.0430.03015.2690.0860.0860.0000.0000.0000.000
194B95ALA 0-0.004-0.01912.5850.0590.0590.0000.0000.0000.000
195B96THR 0-0.076-0.04814.6000.0580.0580.0000.0000.0000.000
196B97LEU 00.0030.0109.488-0.004-0.0040.0000.0000.0000.000
197B98ASN 0-0.046-0.03014.0250.1510.1510.0000.0000.0000.000
198B99PHE -1-0.840-0.91412.802-1.473-1.4730.0000.0000.0000.000