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: LR9G9

Calculation Name: 6OSK-q-Other547

Preferred Name:

Target Type:

Ligand Name: n7-methyl-guanosine-5'-monophosphate | 1n-methylguanosine-5'-monophosphate | 2n-methylguanosine-5'-monophosphate | 6n-dimethyladenosine-5'-monophoshate | 2-methyladenosine-5'-monophosphate | 4n,o2'-methylcytidine-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 | 3-methyluridine-5'-monophoshate | 4-thiouridine-5'-monophosphate | 5,6-dihydrouridine-5'-monophosphate | o2'-methylycytidine-5'-monophosphate | o2'-methyluridine 5'-monophosphate | (3s)-3-(methylsulfanyl)-l-aspartic acid | n-formylmethionine

Ligand 3-letter code: G7M | 1MG | 2MG | MA6 | 2MA | 4OC | 6MZ | PSU | 3TD | 5MC | 5MU | OMG | UR3 | 4SU | H2U | OMC | OMU | 0TD | FME

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6OSK

Chain ID: q

ChEMBL ID:

UniProt ID: P0ADY7

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 123
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -901292.22156
FMO2-HF: Nuclear repulsion 853749.021699
FMO2-HF: Total energy -47543.19986
FMO2-MP2: Total energy -47681.860631


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.
229.22229.3689.316-4.764-4.7-0.06
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 : 0.793 / q_NPA : 0.883
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].
3A4VAL00.1000.0473.871-0.915-0.043-0.003-0.328-0.5410.001
5A6GLN0-0.005-0.0061.799-35.018-36.7348.854-4.073-3.065-0.061
6A7LEU0-0.041-0.0162.9870.9671.4890.082-0.138-0.4650.000
11A12ARG10.9040.9462.61347.86948.3390.383-0.225-0.6290.000
4A5ASN00.0880.0306.2263.2383.2380.0000.0000.0000.000
7A8VAL00.0390.0245.9793.2683.2680.0000.0000.0000.000
8A9ARG10.9761.0008.02733.21433.2140.0000.0000.0000.000
9A10LYS10.9370.9707.62132.41832.4180.0000.0000.0000.000
10A11PRO00.0710.0447.195-4.386-4.3860.0000.0000.0000.000
12A13ALA00.0230.0178.6192.5932.5930.0000.0000.0000.000
13A14ARG10.9660.98111.43219.73519.7350.0000.0000.0000.000
14A15LYS10.9740.98014.01619.33819.3380.0000.0000.0000.000
15A16VAL00.0630.03416.2910.5230.5230.0000.0000.0000.000
16A17ALA00.0060.00819.8810.2940.2940.0000.0000.0000.000
17A18LYS10.9440.98222.19211.82411.8240.0000.0000.0000.000
18A19SER00.0540.02725.3340.1100.1100.0000.0000.0000.000
19A20ASN0-0.019-0.02428.6920.0670.0670.0000.0000.0000.000
20A21VAL00.006-0.00230.4610.2880.2880.0000.0000.0000.000
21A22PRO0-0.017-0.01731.6650.0630.0630.0000.0000.0000.000
22A23ALA00.0430.02433.3320.0230.0230.0000.0000.0000.000
23A24LEU00.0360.01636.3430.2050.2050.0000.0000.0000.000
24A25GLU-1-0.838-0.90334.666-8.139-8.1390.0000.0000.0000.000
25A26ALA0-0.009-0.00533.0150.0580.0580.0000.0000.0000.000
26A27CYS00.0140.04234.8820.1590.1590.0000.0000.0000.000
27A28PRO00.0150.00538.369-0.078-0.0780.0000.0000.0000.000
28A29GLN0-0.021-0.03239.3810.1390.1390.0000.0000.0000.000
29A30LYS10.8010.89539.4347.9097.9090.0000.0000.0000.000
30A31ARG10.9931.01143.4396.3726.3720.0000.0000.0000.000
31A32GLY0-0.0100.00446.379-0.143-0.1430.0000.0000.0000.000
32A33VAL00.0180.02247.9310.1140.1140.0000.0000.0000.000
33A34CYS0-0.071-0.02749.778-0.168-0.1680.0000.0000.0000.000
34A35THR0-0.019-0.02848.7440.1530.1530.0000.0000.0000.000
35A36ARG10.9440.98049.4166.3656.3650.0000.0000.0000.000
36A37VAL0-0.0030.00550.783-0.195-0.1950.0000.0000.0000.000
37A38TYR0-0.021-0.01646.0200.0530.0530.0000.0000.0000.000
38A39THR00.008-0.00250.373-0.031-0.0310.0000.0000.0000.000
39A40THR0-0.048-0.03145.082-0.082-0.0820.0000.0000.0000.000
40A41THR00.0790.05046.5550.0430.0430.0000.0000.0000.000
41A42PRO0-0.068-0.02143.750-0.152-0.1520.0000.0000.0000.000
42A43LYS10.9060.93935.8698.4908.4900.0000.0000.0000.000
43A44LYS11.0361.00440.3707.6027.6020.0000.0000.0000.000
44A45PRO0-0.078-0.04139.2700.0770.0770.0000.0000.0000.000
45A46ASN0-0.0060.00242.4530.1080.1080.0000.0000.0000.000
46A47SER00.0510.02545.212-0.008-0.0080.0000.0000.0000.000
47A48ALA00.008-0.00448.0350.0410.0410.0000.0000.0000.000
48A49LEU00.0830.04849.699-0.061-0.0610.0000.0000.0000.000
49A50ARG10.8280.88944.3416.9946.9940.0000.0000.0000.000
50A51LYS10.9660.98148.5486.0236.0230.0000.0000.0000.000
51A52VAL0-0.035-0.01744.780-0.149-0.1490.0000.0000.0000.000
52A53CYS00.0080.02547.2990.0710.0710.0000.0000.0000.000
53A54ARG10.8670.93242.3787.0297.0290.0000.0000.0000.000
54A55VAL0-0.011-0.02045.1460.1420.1420.0000.0000.0000.000
55A56ARG10.9480.98045.2726.5076.5070.0000.0000.0000.000
56A57LEU0-0.014-0.02441.2520.0930.0930.0000.0000.0000.000
57A58THR0-0.033-0.04545.2420.0960.0960.0000.0000.0000.000
58A59ASN0-0.040-0.03739.5700.2050.2050.0000.0000.0000.000
59A60GLY00.0290.02342.237-0.120-0.1200.0000.0000.0000.000
60A61PHE0-0.029-0.00536.446-0.025-0.0250.0000.0000.0000.000
61A62GLU-1-0.741-0.83241.804-6.670-6.6700.0000.0000.0000.000
62A63VAL0-0.0150.00039.564-0.131-0.1310.0000.0000.0000.000
63A64THR0-0.002-0.00241.0030.2260.2260.0000.0000.0000.000
64A65SER0-0.048-0.04641.656-0.190-0.1900.0000.0000.0000.000
65A66TYR00.0100.00043.3740.1510.1510.0000.0000.0000.000
66A67ILE00.0440.03445.100-0.028-0.0280.0000.0000.0000.000
67A68GLY00.0010.00547.5210.0260.0260.0000.0000.0000.000
68A69GLY0-0.002-0.01248.2130.1040.1040.0000.0000.0000.000
69A70GLU-1-0.952-0.96751.135-5.799-5.7990.0000.0000.0000.000
70A71GLY00.0340.01854.6050.0870.0870.0000.0000.0000.000
71A72HIS0-0.028-0.02953.270-0.061-0.0610.0000.0000.0000.000
72A73ASN00.0370.01655.9680.0020.0020.0000.0000.0000.000
73A74LEU00.0110.01452.2970.0210.0210.0000.0000.0000.000
74A75GLN00.0060.00255.7800.1260.1260.0000.0000.0000.000
75A76GLU-1-0.808-0.92855.109-5.871-5.8710.0000.0000.0000.000
76A77HIS0-0.021-0.01954.9160.0400.0400.0000.0000.0000.000
77A78SER0-0.043-0.01354.6390.0090.0090.0000.0000.0000.000
78A79VAL00.006-0.01252.315-0.184-0.1840.0000.0000.0000.000
79A80ILE00.0160.00747.668-0.001-0.0010.0000.0000.0000.000
80A81LEU00.0290.00246.129-0.095-0.0950.0000.0000.0000.000
81A82ILE0-0.0060.00241.029-0.021-0.0210.0000.0000.0000.000
82A83ARG10.9590.96940.7507.2897.2890.0000.0000.0000.000
83A84GLY00.0180.02137.775-0.178-0.1780.0000.0000.0000.000
84A85GLY00.000-0.00436.3160.1580.1580.0000.0000.0000.000
85A86ARG10.9380.96931.2799.5569.5560.0000.0000.0000.000
86A87VAL00.0290.02236.9020.0220.0220.0000.0000.0000.000
87A88LYS10.9300.95534.0988.6038.6030.0000.0000.0000.000
88A89ASP-1-0.807-0.86837.275-7.482-7.4820.0000.0000.0000.000
89A90LEU00.0820.04239.5400.1660.1660.0000.0000.0000.000
90A91PRO0-0.0060.00537.449-0.230-0.2300.0000.0000.0000.000
91A92GLY00.0280.00636.8530.1550.1550.0000.0000.0000.000
92A93VAL0-0.0100.00737.926-0.041-0.0410.0000.0000.0000.000
93A94ARG10.9260.94932.5549.2129.2120.0000.0000.0000.000
94A95TYR00.0680.02936.564-0.247-0.2470.0000.0000.0000.000
95A96HIS0-0.0360.01740.0030.2820.2820.0000.0000.0000.000
96A97THR00.0530.00943.008-0.033-0.0330.0000.0000.0000.000
97A98VAL0-0.074-0.04345.681-0.045-0.0450.0000.0000.0000.000
98A99ARG10.7290.81347.7276.1286.1280.0000.0000.0000.000
99A100GLY0-0.0030.00150.926-0.026-0.0260.0000.0000.0000.000
100A101ALA0-0.034-0.02950.441-0.018-0.0180.0000.0000.0000.000
101A102LEU0-0.023-0.02151.188-0.056-0.0560.0000.0000.0000.000
102A103ASP-1-0.728-0.81654.286-5.554-5.5540.0000.0000.0000.000
103A104CYS-1-0.844-0.85252.691-5.934-5.9340.0000.0000.0000.000
104A105SER0-0.014-0.01754.7130.0410.0410.0000.0000.0000.000
105A106GLY00.015-0.00454.745-0.112-0.1120.0000.0000.0000.000
106A107VAL0-0.070-0.03052.5650.0310.0310.0000.0000.0000.000
107A108LYS10.9980.99055.6845.2015.2010.0000.0000.0000.000
108A109ASP-1-0.856-0.91859.008-5.088-5.0880.0000.0000.0000.000
109A110ARG10.9150.97551.1356.0156.0150.0000.0000.0000.000
110A111LYS10.9980.97957.1805.0065.0060.0000.0000.0000.000
111A112GLN00.0470.02653.400-0.104-0.1040.0000.0000.0000.000
112A113ALA0-0.006-0.02148.931-0.050-0.0500.0000.0000.0000.000
113A114ARG10.9270.97650.4035.5375.5370.0000.0000.0000.000
114A115SER00.0430.01549.5880.0240.0240.0000.0000.0000.000
115A116LYS10.8980.95343.2457.0337.0330.0000.0000.0000.000
116A117TYR0-0.034-0.02547.837-0.111-0.1110.0000.0000.0000.000
117A118GLY00.0940.06251.1040.0910.0910.0000.0000.0000.000
118A119VAL0-0.0150.00253.1040.0990.0990.0000.0000.0000.000
119A120LYS10.9900.98556.2775.4935.4930.0000.0000.0000.000
120A121ARG10.9350.96358.7045.2375.2370.0000.0000.0000.000
121A122PRO0-0.0140.00259.9660.0430.0430.0000.0000.0000.000
122A123LYS10.9390.95263.0624.7414.7410.0000.0000.0000.000
123A124ALA-1-0.848-0.90366.006-4.585-4.5850.0000.0000.0000.000