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

tag_button

FMODB ID: Y7912

Calculation Name: 7S1K-p-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: p

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 127
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1026789.183823
FMO2-HF: Nuclear repulsion 976351.378363
FMO2-HF: Total energy -50437.80546
FMO2-MP2: Total energy -50586.206456


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:4:ASN)


Summations of interaction energy for fragment #1(A:4:ASN)
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.
124.049128.6673.195-2.346-5.466-0.01
Interaction energy analysis for fragmet #1(A:4:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.889 / q_NPA : 0.945
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].
3A6TYR00.0660.0502.582-3.3230.9983.196-2.279-5.238-0.010
4A7TYR0-0.001-0.0255.5932.2102.234-0.0010.000-0.0220.000
20A23PRO00.0510.0353.5934.0494.3220.000-0.067-0.2060.000
5A8GLY00.0520.0439.0600.3510.3510.0000.0000.0000.000
6A9THR0-0.061-0.02912.6400.7710.7710.0000.0000.0000.000
7A10GLY00.0320.02116.0050.1480.1480.0000.0000.0000.000
8A11ARG10.8950.93419.26513.44513.4450.0000.0000.0000.000
9A12ARG10.9531.00222.93910.52510.5250.0000.0000.0000.000
10A13LYS10.9270.96426.3389.4339.4330.0000.0000.0000.000
11A14SER00.0210.01128.634-0.131-0.1310.0000.0000.0000.000
12A15SER0-0.045-0.02125.4350.1530.1530.0000.0000.0000.000
13A16ALA0-0.027-0.03621.831-0.090-0.0900.0000.0000.0000.000
14A17ALA00.0020.00519.1190.1220.1220.0000.0000.0000.000
15A18ARG10.9420.97114.85017.51617.5160.0000.0000.0000.000
16A19VAL00.0230.00012.7170.5530.5530.0000.0000.0000.000
17A20PHE0-0.013-0.0048.357-0.181-0.1810.0000.0000.0000.000
18A21ILE00.0410.0197.5302.0362.0360.0000.0000.0000.000
19A22LYS10.9100.9464.94635.05535.0550.0000.0000.0000.000
21A24GLY00.0240.0056.552-1.768-1.7680.0000.0000.0000.000
22A25ASN00.0530.0249.2970.8710.8710.0000.0000.0000.000
23A26GLY00.0540.05013.003-0.653-0.6530.0000.0000.0000.000
24A27LYS10.7340.83912.40024.49624.4960.0000.0000.0000.000
25A28ILE0-0.005-0.01614.932-0.863-0.8630.0000.0000.0000.000
26A29VAL00.0040.00915.3770.9440.9440.0000.0000.0000.000
27A30ILE00.016-0.00316.845-0.740-0.7400.0000.0000.0000.000
28A31ASN0-0.064-0.04219.6760.0950.0950.0000.0000.0000.000
29A32GLN00.0330.02817.4070.2540.2540.0000.0000.0000.000
30A33ARG10.9260.98620.60912.16712.1670.0000.0000.0000.000
31A34SER00.0720.02720.516-0.684-0.6840.0000.0000.0000.000
32A35LEU0-0.015-0.01421.5320.3980.3980.0000.0000.0000.000
33A36GLU-1-0.861-0.95523.142-12.636-12.6360.0000.0000.0000.000
34A37GLN00.0500.04724.5550.0070.0070.0000.0000.0000.000
35A38TYR0-0.094-0.06824.5730.2090.2090.0000.0000.0000.000
36A39PHE0-0.036-0.01623.4850.1810.1810.0000.0000.0000.000
37A40GLY00.0280.02627.9370.1100.1100.0000.0000.0000.000
38A41ARG10.9650.97929.4109.3109.3100.0000.0000.0000.000
39A42GLU-1-0.846-0.90731.112-9.914-9.9140.0000.0000.0000.000
40A43THR00.003-0.01832.229-0.156-0.1560.0000.0000.0000.000
41A44ALA0-0.023-0.02428.746-0.213-0.2130.0000.0000.0000.000
42A45ARG10.9730.98526.9059.5239.5230.0000.0000.0000.000
43A46MET00.0260.02025.576-0.586-0.5860.0000.0000.0000.000
44A47VAL0-0.015-0.00324.832-0.322-0.3220.0000.0000.0000.000
45A48VAL0-0.013-0.02920.076-0.279-0.2790.0000.0000.0000.000
46A49ARG10.9640.97420.14712.93012.9300.0000.0000.0000.000
47A50GLN00.0190.02321.025-0.316-0.3160.0000.0000.0000.000
48A51PRO0-0.057-0.03817.6620.1680.1680.0000.0000.0000.000
49A52LEU0-0.012-0.00614.539-0.736-0.7360.0000.0000.0000.000
50A53GLU-1-0.978-0.97618.295-12.658-12.6580.0000.0000.0000.000
51A54LEU00.0360.02019.4140.2350.2350.0000.0000.0000.000
52A55VAL0-0.013-0.01415.169-0.867-0.8670.0000.0000.0000.000
53A56ASP-1-0.729-0.85117.147-16.295-16.2950.0000.0000.0000.000
54A57MET0-0.058-0.02215.885-1.212-1.2120.0000.0000.0000.000
55A58VAL0-0.032-0.02315.261-1.268-1.2680.0000.0000.0000.000
56A59GLU-1-0.938-0.96213.965-19.264-19.2640.0000.0000.0000.000
57A60LYS10.8930.93511.41618.12618.1260.0000.0000.0000.000
58A61LEU0-0.020-0.0129.636-3.331-3.3310.0000.0000.0000.000
59A62ASP-1-0.831-0.8679.238-23.876-23.8760.0000.0000.0000.000
60A63LEU0-0.029-0.0259.666-2.365-2.3650.0000.0000.0000.000
61A64TYR0-0.066-0.03511.6961.4411.4410.0000.0000.0000.000
62A65ILE0-0.009-0.00413.307-0.318-0.3180.0000.0000.0000.000
63A66THR0-0.037-0.02316.0870.6690.6690.0000.0000.0000.000
64A67VAL0-0.036-0.00718.578-0.144-0.1440.0000.0000.0000.000
65A68LYS10.9951.00421.49212.98012.9800.0000.0000.0000.000
66A69GLY00.0810.04224.528-0.043-0.0430.0000.0000.0000.000
67A70GLY0-0.0010.00927.577-0.254-0.2540.0000.0000.0000.000
68A71GLY00.0780.03930.2360.0450.0450.0000.0000.0000.000
69A72ILE00.0780.03729.126-0.276-0.2760.0000.0000.0000.000
70A73SER00.0540.01928.422-0.277-0.2770.0000.0000.0000.000
71A74GLY0-0.082-0.03128.657-0.129-0.1290.0000.0000.0000.000
72A75GLN00.0770.03725.104-0.689-0.6890.0000.0000.0000.000
73A76ALA00.0560.03723.893-0.561-0.5610.0000.0000.0000.000
74A77GLY0-0.008-0.00623.816-0.414-0.4140.0000.0000.0000.000
75A78ALA0-0.060-0.04422.564-0.307-0.3070.0000.0000.0000.000
76A79ILE00.0520.00919.078-0.572-0.5720.0000.0000.0000.000
77A80ARG10.9310.99918.98811.99411.9940.0000.0000.0000.000
78A81HIS0-0.055-0.02219.470-0.566-0.5660.0000.0000.0000.000
79A82GLY00.0510.00916.745-0.429-0.4290.0000.0000.0000.000
80A83ILE00.0350.01714.397-0.985-0.9850.0000.0000.0000.000
81A84THR00.006-0.00314.567-0.635-0.6350.0000.0000.0000.000
82A85ARG10.8680.92914.98115.15415.1540.0000.0000.0000.000
83A86ALA00.0080.00110.792-0.505-0.5050.0000.0000.0000.000
84A87LEU00.0070.01110.177-1.932-1.9320.0000.0000.0000.000
85A88MET0-0.104-0.04612.2200.7490.7490.0000.0000.0000.000
86A89GLU-1-0.865-0.9236.754-38.223-38.2230.0000.0000.0000.000
87A90TYR0-0.064-0.0368.6920.0630.0630.0000.0000.0000.000
88A91ASP-1-0.775-0.84711.497-18.537-18.5370.0000.0000.0000.000
89A92GLU-1-0.952-1.01214.009-16.281-16.2810.0000.0000.0000.000
90A93SER0-0.041-0.02315.9870.7950.7950.0000.0000.0000.000
91A94LEU00.0720.04114.3250.6760.6760.0000.0000.0000.000
92A95ARG10.9330.96415.77117.40817.4080.0000.0000.0000.000
93A96SER0-0.063-0.04718.3651.0071.0070.0000.0000.0000.000
94A97GLU-1-0.897-0.95020.445-13.971-13.9710.0000.0000.0000.000
95A98LEU00.0570.03017.2540.6540.6540.0000.0000.0000.000
96A99ARG10.8790.92821.05812.34812.3480.0000.0000.0000.000
97A100LYS10.9060.95423.30712.21612.2160.0000.0000.0000.000
98A101ALA00.0460.04223.5020.4430.4430.0000.0000.0000.000
99A102GLY0-0.0100.00325.5370.2030.2030.0000.0000.0000.000
100A103PHE0-0.014-0.02621.2960.1280.1280.0000.0000.0000.000
101A104VAL00.0590.03119.729-0.257-0.2570.0000.0000.0000.000
102A105THR0-0.064-0.01721.868-0.075-0.0750.0000.0000.0000.000
103A106ARG10.8640.92623.74111.11211.1120.0000.0000.0000.000
104A107ASP-1-0.771-0.87525.269-9.510-9.5100.0000.0000.0000.000
105A108ALA00.0410.02428.654-0.084-0.0840.0000.0000.0000.000
106A109ARG10.8340.89830.4909.5439.5430.0000.0000.0000.000
107A110GLN0-0.011-0.00832.755-0.057-0.0570.0000.0000.0000.000
108A111VAL0-0.026-0.01833.8250.1430.1430.0000.0000.0000.000
109A112GLU-1-0.779-0.85637.150-7.252-7.2520.0000.0000.0000.000
110A113ARG10.9710.97239.6077.0057.0050.0000.0000.0000.000
111A114LYS10.9210.95941.6346.4096.4090.0000.0000.0000.000
112A115LYS10.8510.91944.1506.8966.8960.0000.0000.0000.000
113A116VAL00.0940.04147.9730.0110.0110.0000.0000.0000.000
114A117GLY00.0610.03651.3910.0060.0060.0000.0000.0000.000
115A118LEU0-0.066-0.01749.0340.0600.0600.0000.0000.0000.000
116A119ARG10.9830.98251.1555.6115.6110.0000.0000.0000.000
117A120LYS10.9850.98145.4446.5956.5950.0000.0000.0000.000
118A121ALA00.0190.01243.5580.1020.1020.0000.0000.0000.000
119A122ARG10.9490.95142.6597.1207.1200.0000.0000.0000.000
120A123ARG10.8900.95948.1975.9715.9710.0000.0000.0000.000
121A124ARG11.0741.03650.7425.7865.7860.0000.0000.0000.000
122A125PRO0-0.0010.00054.088-0.058-0.0580.0000.0000.0000.000
123A126GLN0-0.005-0.00556.884-0.101-0.1010.0000.0000.0000.000
124A127PHE00.012-0.00159.4070.0230.0230.0000.0000.0000.000
125A128SER0-0.004-0.03062.1210.0020.0020.0000.0000.0000.000
126A129LYS10.9170.95765.8914.5864.5860.0000.0000.0000.000
127A130ARG00.1440.12268.731-0.127-0.1270.0000.0000.0000.000