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: LRVL9

Calculation Name: 6V3A-J-Other547

Preferred Name:

Target Type:

Ligand Name: 7n-methyl-8-hydroguanosine-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'-methyluridine 5'-monophosphate

Ligand 3-letter code: 7MG | 2MG | MA6 | 2MA | 4OC | 6MZ | PSU | 3TD | 5MC | 5MU | OMG | UR3 | 4SU | H2U | OMU

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6V3A

Chain ID: J

ChEMBL ID:

UniProt ID: B7I9B0

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 122
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -999596.473713
FMO2-HF: Nuclear repulsion 952152.025753
FMO2-HF: Total energy -47444.447959
FMO2-MP2: Total energy -47581.838212


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
83.00795.32510.255-7.482-15.093-0.07
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.804 / q_NPA : 0.903
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].
3A3GLN00.0670.0273.839-1.728-0.273-0.015-0.486-0.9550.002
32A32TYR0-0.026-0.0202.418-8.902-5.7894.634-2.036-5.712-0.020
33A33ALA0-0.0040.0143.7866.1416.4670.001-0.080-0.2480.000
34A34SER0-0.005-0.0212.714-33.985-30.4671.074-2.483-2.109-0.028
35A35VAL00.006-0.0103.8944.3094.366-0.001-0.006-0.0500.000
65A65THR0-0.013-0.0242.942-8.155-7.7220.037-0.147-0.322-0.001
67A67PHE0-0.063-0.0292.494-5.851-2.6494.527-2.228-5.501-0.023
68A68GLY00.0370.0204.5066.5136.647-0.001-0.014-0.1190.000
69A69ILE0-0.030-0.0165.014-7.283-7.203-0.001-0.002-0.0770.000
4A4THR00.022-0.0016.1751.5371.5370.0000.0000.0000.000
5A5GLU-1-0.857-0.9179.200-21.974-21.9740.0000.0000.0000.000
6A6THR0-0.049-0.0246.583-1.234-1.2340.0000.0000.0000.000
7A7MET0-0.025-0.0129.4511.3671.3670.0000.0000.0000.000
8A8LEU0-0.034-0.0197.464-3.099-3.0990.0000.0000.0000.000
9A9ASP-1-0.865-0.93411.349-20.104-20.1040.0000.0000.0000.000
10A10VAL0-0.057-0.03513.148-1.158-1.1580.0000.0000.0000.000
11A11ALA00.0240.01513.9320.8770.8770.0000.0000.0000.000
12A12ASP-1-0.753-0.85915.966-16.116-16.1160.0000.0000.0000.000
13A13ASN00.0360.00919.199-0.131-0.1310.0000.0000.0000.000
14A14SER0-0.052-0.04919.7480.8260.8260.0000.0000.0000.000
15A15GLY0-0.003-0.01022.1450.6410.6410.0000.0000.0000.000
16A16ALA00.0120.01119.2730.3000.3000.0000.0000.0000.000
17A17ARG10.9320.96719.20813.87213.8720.0000.0000.0000.000
18A18ARG10.9931.01514.62018.63818.6380.0000.0000.0000.000
19A19VAL00.004-0.00113.0291.1721.1720.0000.0000.0000.000
20A20GLN0-0.009-0.01713.109-0.040-0.0400.0000.0000.0000.000
21A21CYS0-0.049-0.0078.0402.0212.0210.0000.0000.0000.000
22A22ILE00.0300.00411.4930.1360.1360.0000.0000.0000.000
23A23LYS10.9140.94512.02021.45621.4560.0000.0000.0000.000
24A24VAL00.0500.0436.503-0.188-0.1880.0000.0000.0000.000
25A25LEU0-0.018-0.0059.5952.3782.3780.0000.0000.0000.000
26A26GLY00.0450.00711.192-1.594-1.5940.0000.0000.0000.000
27A27GLY00.0240.01113.3870.1790.1790.0000.0000.0000.000
28A28SER00.0070.00913.567-0.803-0.8030.0000.0000.0000.000
29A29HIS00.019-0.00112.326-1.451-1.4510.0000.0000.0000.000
30A30ARG10.8150.9237.39631.02031.0200.0000.0000.0000.000
31A31ARG10.9740.9845.62727.18327.1830.0000.0000.0000.000
36A36GLY00.0380.0216.4191.1041.1040.0000.0000.0000.000
37A37ASP-1-0.801-0.8796.845-35.821-35.8210.0000.0000.0000.000
38A38ILE0-0.028-0.0199.0070.0990.0990.0000.0000.0000.000
39A39ILE0-0.025-0.0217.947-0.914-0.9140.0000.0000.0000.000
40A40LYS10.8820.93411.22319.09819.0980.0000.0000.0000.000
41A41VAL00.0270.00012.393-1.458-1.4580.0000.0000.0000.000
42A42THR0-0.0150.00114.9021.5411.5410.0000.0000.0000.000
43A43VAL00.0260.01117.322-1.052-1.0520.0000.0000.0000.000
44A44LYS10.9000.95517.50118.23818.2380.0000.0000.0000.000
45A45GLU-1-0.912-0.96820.327-14.253-14.2530.0000.0000.0000.000
46A46ALA00.0270.00321.202-0.706-0.7060.0000.0000.0000.000
47A47ILE0-0.0180.00423.8190.3650.3650.0000.0000.0000.000
48A48PRO00.0150.00326.7880.0560.0560.0000.0000.0000.000
49A49ARG10.9540.96430.3349.6059.6050.0000.0000.0000.000
50A50ALA00.0040.03026.0410.0600.0600.0000.0000.0000.000
51A51ARG10.9200.94625.63612.03312.0330.0000.0000.0000.000
52A52VAL0-0.0200.00821.8460.0220.0220.0000.0000.0000.000
53A53LYS10.9040.93525.06011.55111.5510.0000.0000.0000.000
54A54LYS10.9640.97123.41212.34812.3480.0000.0000.0000.000
55A55GLY0-0.0040.00122.9630.5600.5600.0000.0000.0000.000
56A56ASP-1-0.814-0.88123.216-12.400-12.4000.0000.0000.0000.000
57A57VAL0-0.025-0.02818.819-0.899-0.8990.0000.0000.0000.000
58A58MET0-0.0140.00118.2200.7990.7990.0000.0000.0000.000
59A59ASN0-0.026-0.01015.965-1.300-1.3000.0000.0000.0000.000
60A60ALA00.0210.00912.6350.8600.8600.0000.0000.0000.000
61A61VAL00.0200.02711.000-0.901-0.9010.0000.0000.0000.000
62A62VAL0-0.0030.0085.0431.1151.1150.0000.0000.0000.000
63A63VAL0-0.008-0.0188.4290.3360.3360.0000.0000.0000.000
64A64ARG10.7850.8878.57823.80023.8000.0000.0000.0000.000
66A66LYS10.9520.9815.61130.58730.5870.0000.0000.0000.000
70A70ARG10.8610.9117.65026.58326.5830.0000.0000.0000.000
71A71ARG10.8760.94210.60820.96020.9600.0000.0000.0000.000
72A72PRO00.029-0.00514.215-0.053-0.0530.0000.0000.0000.000
73A73ASP-1-0.786-0.85817.064-16.870-16.8700.0000.0000.0000.000
74A74GLY00.0180.02415.6330.5320.5320.0000.0000.0000.000
75A75SER0-0.021-0.02615.011-0.933-0.9330.0000.0000.0000.000
76A76VAL0-0.070-0.0549.431-1.705-1.7050.0000.0000.0000.000
77A77ILE00.0090.02010.5291.5691.5690.0000.0000.0000.000
78A78ARG10.9350.9677.97723.42223.4220.0000.0000.0000.000
79A79PHE00.0330.0128.7642.5262.5260.0000.0000.0000.000
80A80ASP-1-0.799-0.8959.595-23.358-23.3580.0000.0000.0000.000
81A81ASP-1-0.862-0.92110.567-25.165-25.1650.0000.0000.0000.000
82A82ASN0-0.004-0.0095.620-7.246-7.2460.0000.0000.0000.000
83A83ALA00.0230.0238.1932.8622.8620.0000.0000.0000.000
84A84ALA0-0.006-0.0089.322-2.647-2.6470.0000.0000.0000.000
85A85VAL00.0040.01911.5661.9041.9040.0000.0000.0000.000
86A86ILE0-0.005-0.00914.575-0.778-0.7780.0000.0000.0000.000
87A87LEU0-0.032-0.01114.9770.7600.7600.0000.0000.0000.000
88A88ASN00.0630.02618.450-0.132-0.1320.0000.0000.0000.000
89A89ASN00.020-0.00720.440-1.139-1.1390.0000.0000.0000.000
90A90ASN0-0.018-0.01022.067-0.403-0.4030.0000.0000.0000.000
91A91LYS10.9180.97117.35715.96715.9670.0000.0000.0000.000
92A92ALA00.0920.05518.836-0.445-0.4450.0000.0000.0000.000
93A93PRO00.022-0.00718.0720.0290.0290.0000.0000.0000.000
94A94ILE0-0.027-0.01420.1480.7990.7990.0000.0000.0000.000
95A95ALA0-0.0290.01320.7030.5500.5500.0000.0000.0000.000
96A96THR0-0.002-0.01422.6220.1630.1630.0000.0000.0000.000
97A97ARG10.9530.97723.61212.13612.1360.0000.0000.0000.000
98A98ILE00.0340.01417.375-0.403-0.4030.0000.0000.0000.000
99A99PHE0-0.041-0.01918.4600.9160.9160.0000.0000.0000.000
100A100GLY00.0380.02316.971-1.135-1.1350.0000.0000.0000.000
101A101PRO00.0310.02915.0710.1440.1440.0000.0000.0000.000
102A102VAL0-0.004-0.00713.311-1.525-1.5250.0000.0000.0000.000
103A103THR00.0410.01710.4671.2411.2410.0000.0000.0000.000
104A104ARG10.8480.89713.34716.52516.5250.0000.0000.0000.000
105A105GLU-1-0.915-0.9429.692-25.697-25.6970.0000.0000.0000.000
106A106LEU0-0.013-0.02011.8710.6330.6330.0000.0000.0000.000
107A107ARG10.8840.95114.95615.65115.6510.0000.0000.0000.000
108A108THR00.0410.03416.0300.4780.4780.0000.0000.0000.000
109A109GLU-1-0.870-0.94718.560-15.008-15.0080.0000.0000.0000.000
110A110GLN0-0.023-0.01317.109-0.012-0.0120.0000.0000.0000.000
111A111PHE0-0.019-0.03113.695-0.111-0.1110.0000.0000.0000.000
112A112MET00.0450.04718.011-0.122-0.1220.0000.0000.0000.000
113A113LYS10.9120.94320.70713.32813.3280.0000.0000.0000.000
114A114ILE0-0.021-0.02115.3050.2770.2770.0000.0000.0000.000
115A115ILE0-0.048-0.02416.6320.1140.1140.0000.0000.0000.000
116A116SER0-0.027-0.00819.6990.4350.4350.0000.0000.0000.000
117A117LEU0-0.019-0.00821.5480.4620.4620.0000.0000.0000.000
118A118ALA0-0.039-0.00618.2830.0640.0640.0000.0000.0000.000
119A119PRO0-0.028-0.00219.8030.4220.4220.0000.0000.0000.000
120A120GLU-1-0.883-0.94919.517-15.107-15.1070.0000.0000.0000.000
121A121VAL0-0.021-0.02117.360-0.999-0.9990.0000.0000.0000.000
122A122LEU-1-0.774-0.87115.322-18.695-18.6950.0000.0000.0000.000