FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 3MMML

Calculation Name: 2PK5-A-Xray547

Preferred Name: Gag-Pol polyprotein

Target Type: SINGLE PROTEIN

Ligand Name: (4r)-n-[(1s,2r)-2-hydroxy-2,3-dihydro-1h-inden-1-yl]-3-[(2s,3s)-2-hydroxy-3-({n-[(isoquinolin-5-yloxy)acetyl]-3-(methyl sulfonyl)-l-alanyl}amino)-4-phenylbutanoyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide

Ligand 3-letter code: 075

Ligand of Interest (LOI):

PDB ID: 2PK5

Chain ID: A

ChEMBL ID: CHEMBL3638326

UniProt ID: P03367

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 99
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -685678.790266
FMO2-HF: Nuclear repulsion 647949.939573
FMO2-HF: Total energy -37728.850693
FMO2-MP2: Total energy -37838.436028


3D Structure
Snapshot
 
Ligand structure

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.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:1:PRO)


Summations of interaction energy for fragment #1(A:1:PRO)
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.
-6.738-3.9210.067-1.137-1.747-0.004
Interaction energy analysis for fragmet #1(A:1:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.877 / q_NPA : 0.914
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].
3A3ILE00.001-0.0033.278-0.4921.7880.053-0.935-1.398-0.003
4A4THR00.0030.0025.1623.5673.581-0.001-0.003-0.0090.000
67A67CYS0-0.006-0.0054.042-2.092-1.9260.000-0.020-0.1460.000
69A69HIS0-0.043-0.0143.322-1.698-1.3410.015-0.179-0.194-0.001
5A5LEU00.0370.0058.7950.0250.0250.0000.0000.0000.000
6A6TRP00.0070.01311.7971.8031.8030.0000.0000.0000.000
7A7LYS10.9520.98210.69324.48724.4870.0000.0000.0000.000
8A8ARG11.0020.99712.50014.86214.8620.0000.0000.0000.000
9A9PRO00.0340.0288.937-0.493-0.4930.0000.0000.0000.000
10A10LEU0-0.037-0.0169.984-0.205-0.2050.0000.0000.0000.000
11A11VAL0-0.010-0.0125.995-2.735-2.7350.0000.0000.0000.000
12A12THR00.0030.0028.9732.0562.0560.0000.0000.0000.000
13A13ILE0-0.006-0.0069.567-2.282-2.2820.0000.0000.0000.000
14A14LYS10.9410.97112.20018.23218.2320.0000.0000.0000.000
15A15ILE00.0700.02715.005-0.339-0.3390.0000.0000.0000.000
16A16GLY00.0350.01918.0710.5270.5270.0000.0000.0000.000
17A17GLY0-0.047-0.02020.3500.5570.5570.0000.0000.0000.000
18A18GLN0-0.004-0.00420.047-0.305-0.3050.0000.0000.0000.000
19A19LEU0-0.001-0.00614.120-0.774-0.7740.0000.0000.0000.000
20A20LYS10.8290.90415.34915.29215.2920.0000.0000.0000.000
21A21GLU-1-0.898-0.94213.107-20.328-20.3280.0000.0000.0000.000
22A22ALA0-0.006-0.01512.5331.3341.3340.0000.0000.0000.000
23A23LEU0-0.003-0.00111.579-1.711-1.7110.0000.0000.0000.000
24A24LEU0-0.026-0.0145.9910.0030.0030.0000.0000.0000.000
25A25ASP-1-0.844-0.93010.664-17.759-17.7590.0000.0000.0000.000
26A26THR00.001-0.01912.2350.3750.3750.0000.0000.0000.000
27A27GLY0-0.0080.00314.8650.7290.7290.0000.0000.0000.000
28A28ALA0-0.0180.00617.3130.9530.9530.0000.0000.0000.000
29A29ASP-1-0.825-0.89517.663-15.382-15.3820.0000.0000.0000.000
30A30ASP-1-0.847-0.93118.896-13.990-13.9900.0000.0000.0000.000
31A31THR0-0.010-0.01116.126-0.778-0.7780.0000.0000.0000.000
32A32VAL0-0.034-0.01618.0040.9290.9290.0000.0000.0000.000
33A33ILE0-0.030-0.01116.579-0.753-0.7530.0000.0000.0000.000
34A34GLU-1-0.733-0.85120.364-13.523-13.5230.0000.0000.0000.000
35A35GLU-1-0.825-0.90322.976-10.847-10.8470.0000.0000.0000.000
36A36MET0-0.0190.00221.395-0.277-0.2770.0000.0000.0000.000
37A37SER0-0.012-0.00825.8350.3530.3530.0000.0000.0000.000
38A38LEU00.002-0.00222.008-0.475-0.4750.0000.0000.0000.000
39A39PRO00.0030.00324.6280.4910.4910.0000.0000.0000.000
40A40GLY00.0360.01827.281-0.216-0.2160.0000.0000.0000.000
41A41ARG10.9320.95729.7009.5789.5780.0000.0000.0000.000
42A42TRP00.0200.01429.229-0.346-0.3460.0000.0000.0000.000
43A43LYS10.8890.95629.06911.10111.1010.0000.0000.0000.000
44A44PRO0-0.019-0.00930.504-0.329-0.3290.0000.0000.0000.000
45A45LYS10.8630.93625.26512.18912.1890.0000.0000.0000.000
46A46MET0-0.0140.00330.2920.0480.0480.0000.0000.0000.000
47A47ILE00.0120.00023.794-0.174-0.1740.0000.0000.0000.000
48A48GLY00.0410.00526.8000.3450.3450.0000.0000.0000.000
49A49GLY00.0150.01625.761-0.473-0.4730.0000.0000.0000.000
50A50ILE00.0030.00224.5190.4970.4970.0000.0000.0000.000
51A51GLY00.0030.00727.552-0.151-0.1510.0000.0000.0000.000
52A52GLY0-0.0150.01029.9950.3450.3450.0000.0000.0000.000
53A53PHE00.005-0.01629.447-0.383-0.3830.0000.0000.0000.000
54A54ILE00.0020.01325.5350.2650.2650.0000.0000.0000.000
55A55LYS10.9750.97529.5778.7908.7900.0000.0000.0000.000
56A56VAL0-0.018-0.00825.578-0.106-0.1060.0000.0000.0000.000
57A57ARG10.8010.86827.96411.04511.0450.0000.0000.0000.000
58A58GLN0-0.011-0.03525.707-0.216-0.2160.0000.0000.0000.000
59A59TYR00.0420.02624.4620.5460.5460.0000.0000.0000.000
60A60ASP-1-0.798-0.88524.155-12.345-12.3450.0000.0000.0000.000
61A61GLN0-0.032-0.02322.1560.3310.3310.0000.0000.0000.000
62A62ILE00.0320.03019.5170.0890.0890.0000.0000.0000.000
63A63ILE0-0.008-0.00616.301-0.584-0.5840.0000.0000.0000.000
64A64ILE0-0.024-0.01213.1800.6170.6170.0000.0000.0000.000
65A65GLU-1-0.960-0.97510.910-23.023-23.0230.0000.0000.0000.000
66A66ILE00.0540.0147.2570.9960.9960.0000.0000.0000.000
68A68GLY00.0140.0195.588-4.417-4.4170.0000.0000.0000.000
70A70LYS10.9220.9617.92820.67020.6700.0000.0000.0000.000
71A71ALA00.0520.03411.695-0.247-0.2470.0000.0000.0000.000
72A72ILE0-0.017-0.02013.4220.8990.8990.0000.0000.0000.000
73A73GLY00.0290.01017.207-0.218-0.2180.0000.0000.0000.000
74A74THR0-0.071-0.04319.4520.3330.3330.0000.0000.0000.000
75A75VAL0-0.014-0.00118.537-0.826-0.8260.0000.0000.0000.000
76A76LEU0-0.035-0.00821.1260.8850.8850.0000.0000.0000.000
77A77VAL0-0.020-0.00322.245-0.488-0.4880.0000.0000.0000.000
78A78GLY00.0290.01724.6770.5450.5450.0000.0000.0000.000
79A79PRO0-0.0140.00525.555-0.363-0.3630.0000.0000.0000.000
80A80THR0-0.005-0.01721.0690.2820.2820.0000.0000.0000.000
81A81PRO0-0.022-0.00922.9740.0310.0310.0000.0000.0000.000
82A82VAL0-0.004-0.01117.164-0.236-0.2360.0000.0000.0000.000
83A83ASN0-0.0400.00216.5940.6820.6820.0000.0000.0000.000
84A84ILE00.013-0.00115.286-1.092-1.0920.0000.0000.0000.000
85A85ILE0-0.001-0.00410.8900.6130.6130.0000.0000.0000.000
86A86GLY00.0990.04913.322-0.828-0.8280.0000.0000.0000.000
87A87ARG10.8790.90314.48215.16915.1690.0000.0000.0000.000
88A88ASN0-0.028-0.01315.093-1.345-1.3450.0000.0000.0000.000
89A89LEU0-0.009-0.00313.3220.1580.1580.0000.0000.0000.000
90A90LEU0-0.011-0.0069.355-2.027-2.0270.0000.0000.0000.000
91A91THR0-0.010-0.00710.004-2.201-2.2010.0000.0000.0000.000
92A92GLN0-0.059-0.01811.804-0.448-0.4480.0000.0000.0000.000
93A93ILE0-0.042-0.0176.541-0.042-0.0420.0000.0000.0000.000
94A94GLY0-0.0010.0096.681-5.110-5.1100.0000.0000.0000.000
95A95CYS0-0.087-0.0356.254-4.491-4.4910.0000.0000.0000.000
96A96THR0-0.009-0.0167.0473.7463.7460.0000.0000.0000.000
97A97LEU0-0.041-0.0178.402-1.989-1.9890.0000.0000.0000.000
98A98ASN0-0.035-0.0258.988-1.633-1.6330.0000.0000.0000.000
99A99PHE-1-0.898-0.92711.544-20.523-20.5230.0000.0000.0000.000