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: N6ZKQ

Calculation Name: 7S1K-u-Other547

Preferred Name:

Target Type:

Ligand Name: radezolid | n7-methyl-guanosine-5'-monophosphate | 1n-methylguanosine-5'-monophosphate | 5'-o-(dihydroxyphosphanyl)-2,8-dimethyladenosine | 2n-methylguanosine-5'-monophosphate | n6-methyladenosine-5'-monophosphate | pseudouridine-5'-monophosphate | (1s)-1,4-anhydro-1-(3-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-o-phosphono-d-ribitol | 5-methylcytidine-5'-monophosphate | 5-methyluridine 5'-monophosphate | o2'-methylguanosine-5'-monophosphate | 5,6-dihydrouridine-5'-monophosphate | o2'-methylycytidine-5'-monophosphate | o2'-methyluridine 5'-monophosphate | (2s,3r)-2-azanyl-5-carbamimidamido-3-oxidanyl-pentanoic acid

Ligand 3-letter code: RD8 | G7M | 1MG | 8AH | 2MG | 6MZ | PSU | 3TD | 5MC | 5MU | OMG | H2U | OMC | OMU | 4D4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7S1K

Chain ID: u

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 115
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -775736.655261
FMO2-HF: Nuclear repulsion 731512.690855
FMO2-HF: Total energy -44223.964407
FMO2-MP2: Total energy -44353.709525


3D Structure Molmil
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:2:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
40.5749.1044.486-5.221-7.797-0.042
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.920 / q_NPA : 0.961
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].
3A4ILE00.0720.0412.7590.2991.9860.177-0.711-1.1540.000
7A8ASN0-0.031-0.0282.5251.5142.3770.205-0.330-0.737-0.001
8A9ILE00.0140.0351.8774.1365.0672.244-1.276-1.898-0.008
9A10PRO0-0.061-0.0432.626-22.678-20.2760.447-1.613-1.235-0.020
10A11ASP-1-0.803-0.8973.635-47.619-47.3670.000-0.036-0.2160.000
11A12HIS00.0410.0145.0085.9085.944-0.001-0.001-0.0330.000
44A45ILE0-0.018-0.0153.281-3.342-2.7840.052-0.185-0.425-0.001
49A50GLU-1-0.805-0.9094.183-51.891-51.5640.000-0.059-0.2680.000
52A53ILE0-0.023-0.0112.415-3.007-2.4261.195-0.577-1.199-0.007
56A57ARG10.6800.7992.64144.28045.1770.167-0.433-0.632-0.005
4A5ALA00.0460.0396.0764.5934.5930.0000.0000.0000.000
5A6GLY00.0050.0119.1062.2892.2890.0000.0000.0000.000
6A7ILE00.0220.0116.774-1.028-1.0280.0000.0000.0000.000
12A13LYS10.8910.9408.24831.83431.8340.0000.0000.0000.000
13A14HIS00.0930.0558.810-4.108-4.1080.0000.0000.0000.000
14A15ALA00.0900.0588.207-1.218-1.2180.0000.0000.0000.000
15A16VAL0-0.010-0.0019.174-0.695-0.6950.0000.0000.0000.000
16A17ILE0-0.064-0.02711.3941.3921.3920.0000.0000.0000.000
17A18ALA00.0190.0215.9330.5860.5860.0000.0000.0000.000
18A19LEU00.0660.0186.465-1.730-1.7300.0000.0000.0000.000
19A20THR0-0.116-0.0668.9302.0222.0220.0000.0000.0000.000
20A21SER0-0.039-0.0127.9971.4391.4390.0000.0000.0000.000
21A22ILE0-0.0130.0117.389-0.146-0.1460.0000.0000.0000.000
22A23TYR0-0.020-0.01710.8352.2202.2200.0000.0000.0000.000
23A24GLY00.0560.00914.5700.0650.0650.0000.0000.0000.000
24A25VAL0-0.0180.00811.5641.2141.2140.0000.0000.0000.000
25A26GLY00.0440.02914.547-0.459-0.4590.0000.0000.0000.000
26A27LYS10.9960.97816.13616.91816.9180.0000.0000.0000.000
27A28THR00.0260.00516.972-0.531-0.5310.0000.0000.0000.000
28A29ARG10.9140.96515.65016.74316.7430.0000.0000.0000.000
29A30SER0-0.008-0.00912.455-0.755-0.7550.0000.0000.0000.000
30A31LYS10.9650.97413.53915.16315.1630.0000.0000.0000.000
31A32ALA00.0000.00716.1590.1280.1280.0000.0000.0000.000
32A33ILE0-0.007-0.00310.5480.2390.2390.0000.0000.0000.000
33A34LEU0-0.009-0.00810.059-0.541-0.5410.0000.0000.0000.000
34A35ALA00.0360.01413.1300.3280.3280.0000.0000.0000.000
35A36ALA0-0.063-0.03115.6860.5720.5720.0000.0000.0000.000
36A37ALA0-0.0090.00311.7660.2680.2680.0000.0000.0000.000
37A38GLY0-0.0040.01913.7340.1710.1710.0000.0000.0000.000
38A39ILE0-0.075-0.0369.855-0.092-0.0920.0000.0000.0000.000
39A40ALA00.0490.02113.947-0.142-0.1420.0000.0000.0000.000
40A41GLU-1-0.924-0.99013.166-19.357-19.3570.0000.0000.0000.000
41A42ASP-1-0.992-1.01213.414-19.329-19.3290.0000.0000.0000.000
42A43VAL00.0470.05310.118-0.161-0.1610.0000.0000.0000.000
43A44LYS10.8710.9409.11723.53423.5340.0000.0000.0000.000
45A46SER00.004-0.0275.323-2.070-2.0700.0000.0000.0000.000
46A47GLU-1-0.896-0.9587.324-24.946-24.9460.0000.0000.0000.000
47A48LEU0-0.0400.0095.9231.9651.9650.0000.0000.0000.000
48A49SER00.0140.0106.885-1.917-1.9170.0000.0000.0000.000
50A51GLY00.0420.0256.794-0.804-0.8040.0000.0000.0000.000
51A52GLN00.0240.0158.7350.9100.9100.0000.0000.0000.000
53A54ASP-1-0.832-0.9165.899-30.641-30.6410.0000.0000.0000.000
54A55THR0-0.028-0.0137.9271.5671.5670.0000.0000.0000.000
55A56LEU00.0170.0086.3320.3180.3180.0000.0000.0000.000
57A58ASP-1-0.785-0.8898.327-18.588-18.5880.0000.0000.0000.000
58A59GLU0-0.031-0.02211.8160.9160.9160.0000.0000.0000.000
59A60VAL0-0.031-0.0178.9711.1731.1730.0000.0000.0000.000
60A61ALA0-0.014-0.00112.0131.1341.1340.0000.0000.0000.000
61A62LYS10.8260.92414.20419.51719.5170.0000.0000.0000.000
62A63PHE0-0.052-0.02614.9201.2911.2910.0000.0000.0000.000
63A64VAL00.0410.03616.483-0.863-0.8630.0000.0000.0000.000
64A65VAL00.006-0.01612.986-0.046-0.0460.0000.0000.0000.000
65A66GLU-1-0.733-0.86611.995-22.796-22.7960.0000.0000.0000.000
66A67GLY0-0.024-0.01415.4141.3121.3120.0000.0000.0000.000
67A68ASP-1-0.832-0.89617.914-14.074-14.0740.0000.0000.0000.000
68A69LEU00.0300.02918.7220.8680.8680.0000.0000.0000.000
69A70ARG10.8310.88814.70320.34620.3460.0000.0000.0000.000
70A71ARG10.8820.95019.85815.77215.7720.0000.0000.0000.000
71A72GLU-1-0.901-0.94323.424-12.407-12.4070.0000.0000.0000.000
72A73ILE00.007-0.00523.3570.7040.7040.0000.0000.0000.000
73A74SER00.002-0.00524.6840.6510.6510.0000.0000.0000.000
74A75MET0-0.0050.01427.1600.7260.7260.0000.0000.0000.000
75A76SER0-0.052-0.04328.5290.5440.5440.0000.0000.0000.000
76A77ILE0-0.055-0.04029.0130.4950.4950.0000.0000.0000.000
77A78LYS10.8560.91431.3239.4639.4630.0000.0000.0000.000
78A79ARG11.0211.00833.2149.3159.3150.0000.0000.0000.000
79A80LEU0-0.052-0.03133.3380.3310.3310.0000.0000.0000.000
80A81MET0-0.024-0.01835.9760.3200.3200.0000.0000.0000.000
81A82ASP-1-0.770-0.87437.319-8.485-8.4850.0000.0000.0000.000
82A83LEU0-0.046-0.01538.7860.2000.2000.0000.0000.0000.000
83A84GLY00.0260.02841.4660.1900.1900.0000.0000.0000.000
84A85CYS0-0.0190.01839.9110.0700.0700.0000.0000.0000.000
85A86TYR00.0930.03941.616-0.145-0.1450.0000.0000.0000.000
86A87ARG10.9710.97533.7089.0329.0320.0000.0000.0000.000
87A88GLY00.0620.02137.364-0.247-0.2470.0000.0000.0000.000
88A89LEU0-0.016-0.00938.431-0.116-0.1160.0000.0000.0000.000
89A90ARG10.8820.93338.0407.6147.6140.0000.0000.0000.000
90A91HIS00.0210.01331.957-0.088-0.0880.0000.0000.0000.000
91A92ARG10.9800.99836.0847.6637.6630.0000.0000.0000.000
92A93ARG10.9200.95938.4027.4337.4330.0000.0000.0000.000
93A94GLY00.0580.05135.9840.0660.0660.0000.0000.0000.000
94A95LEU0-0.034-0.02637.0220.0600.0600.0000.0000.0000.000
95A96PRO0-0.014-0.00936.374-0.285-0.2850.0000.0000.0000.000
96A97VAL00.0160.00134.5800.1890.1890.0000.0000.0000.000
97A98ARG10.9180.96130.54010.10510.1050.0000.0000.0000.000
98A99GLY00.0880.05037.2500.0040.0040.0000.0000.0000.000
99A100GLN0-0.0130.00436.7150.0900.0900.0000.0000.0000.000
100A101ARG10.9680.98639.9437.2267.2260.0000.0000.0000.000
101A102THR00.059-0.01141.232-0.216-0.2160.0000.0000.0000.000
102A103LYS10.9440.99643.0666.2976.2970.0000.0000.0000.000
103A104THR00.0410.01643.8570.0560.0560.0000.0000.0000.000
104A105ASN00.010-0.00839.2880.0200.0200.0000.0000.0000.000
105A106ALA00.0680.03937.948-0.147-0.1470.0000.0000.0000.000
106A107ARG10.8600.92136.0418.1128.1120.0000.0000.0000.000
107A108THR00.0520.02630.4580.0460.0460.0000.0000.0000.000
108A109ARG10.7990.90231.9279.3709.3700.0000.0000.0000.000
109A110LYS10.9620.98034.5677.6737.6730.0000.0000.0000.000
110A111GLY00.0770.06534.1520.1240.1240.0000.0000.0000.000
111A112PRO00.0680.02534.1160.2080.2080.0000.0000.0000.000
112A113ARG10.8710.93436.9097.8707.8700.0000.0000.0000.000
113A114LYS10.9900.99340.6567.6027.6020.0000.0000.0000.000
114A115PRO00.0150.00842.8320.0160.0160.0000.0000.0000.000
115A116ILE-1-0.906-0.93746.628-6.549-6.5490.0000.0000.0000.000