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: 9YK12

Calculation Name: 1BVE-AB-NMR60-Model27

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 -2280346.215563
FMO2-HF: Nuclear repulsion 2203869.049061
FMO2-HF: Total energy -76477.166502
FMO2-MP2: Total energy -76702.979295


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.
-172.005-250.545307.325-101.296-127.4940.146


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.
-172.005-250.545307.325-101.296-127.494-0.146
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 : -0.147 / q_NPA : -0.180
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 10.8080.89616.8001.5501.5500.0000.0000.0000.000
2A2GLN 00.0100.03217.225-0.154-0.1540.0000.0000.0000.000
3A3VAL 00.0160.01513.9240.1100.1100.0000.0000.0000.000
4A4THR 00.0390.00515.026-0.245-0.2450.0000.0000.0000.000
5A5LEU 00.011-0.0099.598-0.187-0.1870.0000.0000.0000.000
6A6TRP 0-0.0170.00411.951-0.057-0.0570.0000.0000.0000.000
7A7GLN 0-0.020-0.01610.5560.2640.2640.0000.0000.0000.000
8A8ARG 10.9770.9887.0641.2901.2900.0000.0000.0000.000
9A9PRO 0-0.0180.0077.7160.6510.6510.0000.0000.0000.000
10A10LEU 0-0.039-0.0167.854-0.453-0.4530.0000.0000.0000.000
11A11VAL 00.003-0.00510.8430.4160.4160.0000.0000.0000.000
12A12THR 0-0.017-0.02512.925-0.007-0.0070.0000.0000.0000.000
13A13ILE 00.0180.02011.5230.1010.1010.0000.0000.0000.000
14A14LYS 10.9610.96714.9710.7470.7470.0000.0000.0000.000
15A15ILE 00.0200.05611.1100.0460.0460.0000.0000.0000.000
16A16GLY 00.0210.00815.4000.0780.0780.0000.0000.0000.000
17A17GLY 0-0.056-0.03218.0140.0430.0430.0000.0000.0000.000
18A18GLN 0-0.011-0.01017.2960.0370.0370.0000.0000.0000.000
19A19LEU 0-0.007-0.01017.385-0.058-0.0580.0000.0000.0000.000
20A20LYS 10.8940.96412.2100.6130.6130.0000.0000.0000.000
21A21GLU -1-0.842-0.92010.315-1.777-1.7770.0000.0000.0000.000
22A22ALA 0-0.007-0.0308.9130.0080.0080.0000.0000.0000.000
23A23LEU 0-0.0240.0233.156-0.9520.7610.166-0.458-1.4210.001
24A24LEU 00.010-0.0175.488-2.223-2.2230.0000.0000.0000.000
25A25ASP -1-0.644-0.7271.344-72.525-159.389153.819-57.357-9.597-0.185
26A26THR 0-0.060-0.0554.1101.1331.5300.000-0.076-0.3210.000
27A27GLY 00.0560.0302.7541.6103.1730.465-0.842-1.1870.003
28A28ALA 0-0.053-0.0092.0841.592-2.24417.914-5.454-8.623-0.006
29A29ASP -1-0.871-0.9511.981-3.406-2.8394.739-1.519-3.7870.014
30A30ASP -1-0.795-0.9012.290-4.063-2.9821.975-0.922-2.1340.011
31A31THR 0-0.056-0.0103.216-4.858-3.7110.077-0.577-0.647-0.005
32A32VAL 0-0.028-0.0042.8650.0451.5450.224-0.319-1.4050.000
33A33LEU 00.014-0.0104.582-0.670-0.5730.000-0.014-0.0830.000
34A34GLU -1-0.891-0.9377.266-0.327-0.3270.0000.0000.0000.000
35A35GLU -1-0.954-0.9958.1920.4860.4860.0000.0000.0000.000
36A36MET 00.0050.01611.541-0.089-0.0890.0000.0000.0000.000
37A37SER 0-0.0120.00114.5600.0970.0970.0000.0000.0000.000
38A38LEU 00.0330.00912.907-0.080-0.0800.0000.0000.0000.000
39A39PRO 0-0.0230.01016.5060.0810.0810.0000.0000.0000.000
40A40GLY 00.027-0.00117.934-0.052-0.0520.0000.0000.0000.000
41A41ARG 10.9430.95917.6000.0960.0960.0000.0000.0000.000
42A42TRP 00.0340.03212.6700.0370.0370.0000.0000.0000.000
43A43LYS 10.9700.96612.280-0.371-0.3710.0000.0000.0000.000
44A44PRO 0-0.0300.00911.1430.0890.0890.0000.0000.0000.000
45A45LYS 10.9500.9924.987-2.204-2.2040.0000.0000.0000.000
46A46MET 0-0.036-0.0348.119-0.072-0.0720.0000.0000.0000.000
47A47ILE 0-0.049-0.0012.624-3.588-0.7261.090-1.008-2.9450.011
48A48GLY 00.0690.0054.3440.3000.6430.000-0.058-0.2840.000
49A49GLY 0-0.0010.0072.151-4.618-2.9524.841-3.081-3.4260.016
50A50ILE 00.0070.0071.909-9.253-16.08524.790-2.316-15.6420.028
51A51GLY 0-0.004-0.0244.0340.6381.3380.006-0.132-0.5740.001
52A52GLY 0-0.018-0.0126.132-2.110-2.1100.0000.0000.0000.000
53A53PHE 00.0010.0136.1481.4201.4200.0000.0000.0000.000
54A54ILE 00.0190.0555.548-0.380-0.3800.0000.0000.0000.000
55A55LYS 10.9390.9657.878-1.388-1.3880.0000.0000.0000.000
56A56VAL 00.005-0.0095.226-0.038-0.0380.0000.0000.0000.000
57A57ARG 10.9090.9448.383-0.761-0.7610.0000.0000.0000.000
58A58GLN 0-0.052-0.0477.4970.0450.0450.0000.0000.0000.000
59A59TYR 0-0.019-0.0139.041-0.006-0.0060.0000.0000.0000.000
60A60ASP -1-0.826-0.88010.7850.3330.3330.0000.0000.0000.000
61A61GLN 0-0.019-0.00812.208-0.031-0.0310.0000.0000.0000.000
62A62ILE 0-0.007-0.02612.6620.0140.0140.0000.0000.0000.000
63A63LEU 0-0.044-0.04113.663-0.089-0.0890.0000.0000.0000.000
64A64ILE 00.027-0.01010.1230.0440.0440.0000.0000.0000.000
65A65GLU -1-1.008-1.01413.933-1.005-1.0050.0000.0000.0000.000
66A66ILE 00.0840.04611.608-0.080-0.0800.0000.0000.0000.000
67A67CYS 0-0.026-0.02115.8010.0460.0460.0000.0000.0000.000
68A68GLY 00.0360.02318.3780.1330.1330.0000.0000.0000.000
69A69HIS 0-0.015-0.00517.5640.0170.0170.0000.0000.0000.000
70A70LYS 10.9040.94917.4380.6490.6490.0000.0000.0000.000
71A71ALA 00.0830.04713.6800.0340.0340.0000.0000.0000.000
72A72ILE 0-0.0380.01514.4870.0250.0250.0000.0000.0000.000
73A73GLY 00.0380.03210.616-0.057-0.0570.0000.0000.0000.000
74A74THR 0-0.015-0.0287.666-0.023-0.0230.0000.0000.0000.000
75A75VAL 00.0020.0037.0040.0060.0060.0000.0000.0000.000
76A76LEU 0-0.014-0.0213.291-0.0670.4660.034-0.095-0.4720.000
77A77VAL 00.0370.0336.489-0.226-0.2260.0000.0000.0000.000
78A78GLY 0-0.006-0.0118.8790.2770.2770.0000.0000.0000.000
79A79PRO 0-0.0290.0178.495-0.306-0.3060.0000.0000.0000.000
80A80THR 0-0.061-0.0243.9130.2390.7400.005-0.122-0.384-0.001
81A81PRO 00.0300.0071.980-0.973-1.5403.907-0.728-2.613-0.001
82A82VAL 00.0250.0062.926-3.455-0.7491.398-0.828-3.2760.006
83A83ASN 0-0.0290.0154.690-0.407-0.1750.000-0.015-0.2170.000
84A84ILE 0-0.036-0.0282.053-3.833-1.6314.022-1.327-4.897-0.005
85A85ILE 00.0130.0175.1181.4341.668-0.001-0.007-0.2260.000
86A86GLY 00.1090.0304.468-1.387-1.301-0.001-0.022-0.0640.000
87A87ARG 10.8370.8984.9223.7263.7260.0000.0000.0000.000
88A88ASN 0-0.089-0.0256.597-0.274-0.2740.0000.0000.0000.000
89A89LEU 00.0290.0108.1580.1180.1180.0000.0000.0000.000
90A90LEU 00.0070.0307.5640.0640.0640.0000.0000.0000.000
91A91THR 0-0.050-0.04211.2310.2330.2330.0000.0000.0000.000
92A92GLN 0-0.093-0.05511.6650.1040.1040.0000.0000.0000.000
93A93ILE 0-0.052-0.02412.5580.1010.1010.0000.0000.0000.000
94A94GLY 00.0320.02515.6670.0490.0490.0000.0000.0000.000
95A95ALA 00.012-0.03812.2910.0030.0030.0000.0000.0000.000
96A96THR 0-0.062-0.02914.2630.1140.1140.0000.0000.0000.000
97A97LEU 00.0170.0059.330-0.100-0.1000.0000.0000.0000.000
98A98ASN 0-0.042-0.04313.7790.1450.1450.0000.0000.0000.000
99A99PHE -1-0.854-0.88412.727-1.379-1.3790.0000.0000.0000.000
100B1PRO 10.8110.88918.2251.2901.2900.0000.0000.0000.000
101B2GLN 00.0610.04917.898-0.156-0.1560.0000.0000.0000.000
102B3VAL 0-0.012-0.00214.1540.1250.1250.0000.0000.0000.000
103B4THR 00.0280.00815.013-0.187-0.1870.0000.0000.0000.000
104B5LEU 00.0680.01912.647-0.194-0.1940.0000.0000.0000.000
105B6TRP 0-0.043-0.01312.934-0.046-0.0460.0000.0000.0000.000
106B7GLN 0-0.0070.00414.6840.0970.0970.0000.0000.0000.000
107B8ARG 10.9270.9586.0272.2052.2050.0000.0000.0000.000
108B9PRO 00.0540.0429.0500.3290.3290.0000.0000.0000.000
109B10LEU 0-0.026-0.0278.303-0.269-0.2690.0000.0000.0000.000
110B11VAL 0-0.013-0.01411.7170.2070.2070.0000.0000.0000.000
111B12THR 00.008-0.00113.8980.0290.0290.0000.0000.0000.000
112B13ILE 00.0280.01411.8460.0080.0080.0000.0000.0000.000
113B14LYS 10.9450.96015.0270.5160.5160.0000.0000.0000.000
114B15ILE 00.0430.03211.059-0.008-0.0080.0000.0000.0000.000
115B16GLY 0-0.013-0.01215.5710.0860.0860.0000.0000.0000.000
116B17GLY 00.001-0.00418.478-0.020-0.0200.0000.0000.0000.000
117B18GLN 0-0.046-0.01617.6360.0120.0120.0000.0000.0000.000
118B19LEU 00.0210.00217.504-0.056-0.0560.0000.0000.0000.000
119B20LYS 10.9120.97012.7780.1480.1480.0000.0000.0000.000
120B21GLU -1-0.835-0.92111.162-1.121-1.1210.0000.0000.0000.000
121B22ALA 0-0.0270.0019.6190.0650.0650.0000.0000.0000.000
122B23LEU 0-0.012-0.0073.713-0.2260.3650.018-0.097-0.5120.000
123B24LEU 0-0.053-0.0216.248-1.096-1.0960.0000.0000.0000.000
124B25ASP -1-0.663-0.8562.103-35.804-35.80817.953-7.898-10.052-0.106
125B26THR 0-0.089-0.0574.6830.1140.339-0.001-0.009-0.2150.000
126B27GLY 00.0460.0252.046-0.5600.6194.002-3.170-2.010-0.010
127B28ALA 0-0.0370.0032.0602.673-1.79013.950-1.645-7.8430.000
128B29ASP -1-0.824-0.9342.567-3.409-1.8850.206-0.398-1.331-0.003
129B30ASP -1-0.896-0.9842.8370.9532.7720.257-0.773-1.3030.006
130B31THR 0-0.060-0.0363.488-3.978-3.1530.029-0.374-0.479-0.003
131B32VAL 0-0.030-0.0022.642-0.3181.4140.458-0.446-1.7460.001
132B33LEU 0-0.022-0.0304.382-0.531-0.4070.001-0.023-0.1020.000
133B34GLU -1-0.933-0.9567.8930.9810.9810.0000.0000.0000.000
134B35GLU -1-0.969-0.9779.1770.8620.8620.0000.0000.0000.000
135B36MET 0-0.0010.01012.351-0.127-0.1270.0000.0000.0000.000
136B37SER 0-0.052-0.03214.9560.0920.0920.0000.0000.0000.000
137B38LEU 00.0180.00012.408-0.085-0.0850.0000.0000.0000.000
138B39PRO 00.0220.00816.7510.0500.0500.0000.0000.0000.000
139B40GLY 0-0.023-0.01618.150-0.003-0.0030.0000.0000.0000.000
140B41ARG 10.9360.95917.183-0.298-0.2980.0000.0000.0000.000
141B42TRP 00.0400.04112.6630.0190.0190.0000.0000.0000.000
142B43LYS 10.9380.95711.793-0.603-0.6030.0000.0000.0000.000
143B44PRO 0-0.0120.00911.0910.1330.1330.0000.0000.0000.000
144B45LYS 10.9510.9865.417-3.269-3.2690.0000.0000.0000.000
145B46MET 00.013-0.0128.144-0.110-0.1100.0000.0000.0000.000
146B47ILE 0-0.0380.0022.517-4.171-1.1342.165-1.195-4.0070.016
147B48GLY 00.052-0.0044.208-0.1460.2250.000-0.062-0.3090.000
148B49GLY 0-0.005-0.0032.059-4.383-3.7729.050-4.902-4.7600.021
149B50ILE 0-0.0120.0012.043-5.066-20.41135.712-0.810-19.5570.039
150B51GLY 00.019-0.0174.087-0.3660.3000.011-0.176-0.5010.001
151B52GLY 00.0070.0056.340-1.925-1.9250.0000.0000.0000.000
152B53PHE 0-0.0180.0016.1321.5811.5810.0000.0000.0000.000
153B54ILE 00.0010.0505.621-0.712-0.7120.0000.0000.0000.000
154B55LYS 10.9520.9628.123-1.710-1.7100.0000.0000.0000.000
155B56VAL 00.0290.0105.243-0.023-0.0230.0000.0000.0000.000
156B57ARG 10.9220.9638.261-0.930-0.9300.0000.0000.0000.000
157B58GLN 00.0310.0077.3050.1300.1300.0000.0000.0000.000
158B59TYR 0-0.008-0.0108.694-0.084-0.0840.0000.0000.0000.000
159B60ASP -1-0.798-0.85311.0150.3510.3510.0000.0000.0000.000
160B61GLN 0-0.090-0.05112.366-0.085-0.0850.0000.0000.0000.000
161B62ILE 00.0190.00512.1980.0340.0340.0000.0000.0000.000
162B63LEU 0-0.062-0.03313.932-0.100-0.1000.0000.0000.0000.000
163B64ILE 00.0300.01210.4340.0500.0500.0000.0000.0000.000
164B65GLU -1-0.971-0.99014.315-0.711-0.7110.0000.0000.0000.000
165B66ILE 00.0650.03011.965-0.026-0.0260.0000.0000.0000.000
166B67CYS 0-0.038-0.02316.0190.0040.0040.0000.0000.0000.000
167B68GLY 00.0510.04519.1470.0500.0500.0000.0000.0000.000
168B69HIS 0-0.027-0.01017.8270.0830.0830.0000.0000.0000.000
169B70LYS 10.9130.94917.5970.4100.4100.0000.0000.0000.000
170B71ALA 00.0700.04214.4650.0010.0010.0000.0000.0000.000
171B72ILE 0-0.047-0.00514.6790.0320.0320.0000.0000.0000.000
172B73GLY 00.0360.00310.863-0.113-0.1130.0000.0000.0000.000
173B74THR 0-0.056-0.0857.5030.0200.0200.0000.0000.0000.000
174B75VAL 00.0090.0076.997-0.002-0.0020.0000.0000.0000.000
175B76LEU 0-0.017-0.0163.165-0.3350.3620.086-0.134-0.6500.000
176B77VAL 0-0.0090.0056.295-0.127-0.1270.0000.0000.0000.000
177B78GLY 00.015-0.0038.6060.2130.2130.0000.0000.0000.000
178B79PRO 0-0.0150.0239.295-0.250-0.2500.0000.0000.0000.000
179B80THR 0-0.080-0.0284.3780.6910.9430.000-0.019-0.2340.000
180B81PRO 00.0600.0222.123-1.297-0.8521.439-0.392-1.492-0.001
181B82VAL 00.018-0.0013.357-2.373-0.5750.219-0.474-1.5420.005
182B83ASN 0-0.012-0.0045.3050.1610.284-0.001-0.004-0.1180.000
183B84ILE 0-0.021-0.0182.232-3.449-0.4802.303-0.997-4.2750.000
184B85ILE 0-0.0040.0134.9930.6680.818-0.001-0.007-0.1430.000
185B86GLY 00.1240.0414.782-0.859-0.756-0.001-0.014-0.0880.000
186B87ARG 10.8890.9375.6144.1374.1370.0000.0000.0000.000
187B88ASN 00.0150.0786.379-0.241-0.2410.0000.0000.0000.000
188B89LEU 0-0.004-0.0078.4050.3350.3350.0000.0000.0000.000
189B90LEU 0-0.032-0.0118.4330.2370.2370.0000.0000.0000.000
190B91THR 00.000-0.03711.2630.1640.1640.0000.0000.0000.000
191B92GLN 0-0.089-0.02313.1450.1900.1900.0000.0000.0000.000
192B93ILE 0-0.064-0.02013.6430.0960.0960.0000.0000.0000.000
193B94GLY 00.0410.02216.1790.0460.0460.0000.0000.0000.000
194B95ALA 00.004-0.01313.305-0.022-0.0220.0000.0000.0000.000
195B96THR 0-0.092-0.04815.2440.0320.0320.0000.0000.0000.000
196B97LEU 00.0310.0209.100-0.006-0.0060.0000.0000.0000.000
197B98ASN 00.006-0.02613.6000.0000.0000.0000.0000.0000.000
198B99PHE -1-0.847-0.87512.747-1.596-1.5960.0000.0000.0000.000