FMODB

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

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: N6LJQ

Calculation Name: 6V3A-I-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):

PDB ID: 6V3A

Chain ID: I

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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 142
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1228496.7622
FMO2-HF: Nuclear repulsion 1172961.46887
FMO2-HF: Total energy -55535.29333
FMO2-MP2: Total energy -55698.3152


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: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.
52.65455.497-0.02-1.242-1.581-0.003
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 : 0.872 / q_NPA : 0.923
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].
3A3THR00.0240.0213.7634.3356.897-0.019-1.226-1.317-0.003
4A4LEU00.0280.0244.627-3.359-3.078-0.001-0.016-0.2640.000
5A5SER0-0.014-0.0197.0022.3772.3770.0000.0000.0000.000
6A6ALA00.0390.0279.672-0.149-0.1490.0000.0000.0000.000
7A7LYS10.8790.93110.06322.53422.5340.0000.0000.0000.000
8A8PRO00.013-0.01314.0240.7610.7610.0000.0000.0000.000
9A9ALA0-0.0090.00217.1240.6820.6820.0000.0000.0000.000
10A10GLU-1-0.849-0.92014.187-19.652-19.6520.0000.0000.0000.000
11A11VAL0-0.067-0.02217.2850.0970.0970.0000.0000.0000.000
12A12GLN00.0560.04319.4950.1680.1680.0000.0000.0000.000
13A13HIS0-0.048-0.03722.2620.0610.0610.0000.0000.0000.000
14A14ASP-1-0.886-0.93225.536-11.066-11.0660.0000.0000.0000.000
15A15TRP0-0.005-0.02128.5400.1310.1310.0000.0000.0000.000
16A16PHE0-0.0110.00028.7380.0790.0790.0000.0000.0000.000
17A17VAL0-0.0010.00334.0220.0400.0400.0000.0000.0000.000
18A18VAL0-0.011-0.00535.225-0.045-0.0450.0000.0000.0000.000
19A19ASP-1-0.761-0.85638.360-6.968-6.9680.0000.0000.0000.000
20A20ALA0-0.018-0.03141.126-0.159-0.1590.0000.0000.0000.000
21A21THR0-0.008-0.03442.6180.1220.1220.0000.0000.0000.000
22A22GLY0-0.035-0.00945.663-0.023-0.0230.0000.0000.0000.000
23A23LYS10.8790.96439.7847.6837.6830.0000.0000.0000.000
24A24THR0-0.038-0.02741.2030.0920.0920.0000.0000.0000.000
25A25LEU00.0550.02939.779-0.230-0.2300.0000.0000.0000.000
26A26GLY0-0.013-0.01237.676-0.201-0.2010.0000.0000.0000.000
27A27ARG10.9500.96835.9627.9127.9120.0000.0000.0000.000
28A28LEU00.1000.06635.185-0.267-0.2670.0000.0000.0000.000
29A29ALA00.0140.00734.777-0.240-0.2400.0000.0000.0000.000
30A30THR0-0.024-0.03031.622-0.257-0.2570.0000.0000.0000.000
31A31GLU-1-0.828-0.89529.759-10.869-10.8690.0000.0000.0000.000
32A32ILE00.0560.02830.051-0.353-0.3530.0000.0000.0000.000
33A33ALA00.005-0.00928.835-0.338-0.3380.0000.0000.0000.000
34A34ARG10.8030.89425.03510.96110.9610.0000.0000.0000.000
35A35ARG10.9770.98825.1179.8839.8830.0000.0000.0000.000
36A36LEU00.0050.01425.977-0.344-0.3440.0000.0000.0000.000
37A37ARG10.9360.95218.92413.93413.9340.0000.0000.0000.000
38A38GLY00.0680.04721.492-0.606-0.6060.0000.0000.0000.000
39A39LYS10.8140.90719.31213.75413.7540.0000.0000.0000.000
40A40HIS0-0.033-0.01521.615-0.314-0.3140.0000.0000.0000.000
41A41LYS10.8200.91519.66313.22913.2290.0000.0000.0000.000
42A42THR00.001-0.01416.829-0.428-0.4280.0000.0000.0000.000
43A43SER00.0040.00714.470-1.035-1.0350.0000.0000.0000.000
44A44TYR00.0080.01014.943-0.218-0.2180.0000.0000.0000.000
45A45THR00.010-0.00511.666-1.021-1.0210.0000.0000.0000.000
46A46PRO0-0.043-0.02112.5501.0911.0910.0000.0000.0000.000
47A47HIS00.002-0.01010.3541.5951.5950.0000.0000.0000.000
48A48VAL00.0050.00814.0620.3260.3260.0000.0000.0000.000
49A49ASP-1-0.823-0.90216.797-12.644-12.6440.0000.0000.0000.000
50A50THR00.0240.00916.9460.1000.1000.0000.0000.0000.000
51A51GLY0-0.017-0.00120.2910.1410.1410.0000.0000.0000.000
52A52ASP-1-0.749-0.86023.848-12.098-12.0980.0000.0000.0000.000
53A53TYR0-0.006-0.01527.1040.1690.1690.0000.0000.0000.000
54A54ILE0-0.036-0.01630.1690.0790.0790.0000.0000.0000.000
55A55ILE0-0.0050.00033.1970.0740.0740.0000.0000.0000.000
56A56VAL00.000-0.00336.8420.0420.0420.0000.0000.0000.000
57A57ILE00.0010.00739.1650.1060.1060.0000.0000.0000.000
58A58ASN00.0190.00342.8450.0420.0420.0000.0000.0000.000
59A59ALA00.0070.01243.318-0.017-0.0170.0000.0000.0000.000
60A60GLU-1-0.868-0.96244.626-6.663-6.6630.0000.0000.0000.000
61A61GLN0-0.0150.00547.3430.0050.0050.0000.0000.0000.000
62A62VAL00.0070.03141.907-0.061-0.0610.0000.0000.0000.000
63A63GLN00.0190.00444.9540.1460.1460.0000.0000.0000.000
64A64VAL0-0.056-0.03944.264-0.233-0.2330.0000.0000.0000.000
65A65THR00.0260.00945.6620.0980.0980.0000.0000.0000.000
66A66GLY00.0320.00647.983-0.036-0.0360.0000.0000.0000.000
67A67ASN00.025-0.00251.1200.0560.0560.0000.0000.0000.000
68A68LYS10.8980.94744.1136.9966.9960.0000.0000.0000.000
69A69ALA00.0120.01948.970-0.083-0.0830.0000.0000.0000.000
70A70LEU00.0700.03651.120-0.016-0.0160.0000.0000.0000.000
71A71ASP-1-0.851-0.91850.332-5.946-5.9460.0000.0000.0000.000
72A72LYS10.8300.92441.2357.2207.2200.0000.0000.0000.000
73A73LYS10.8840.94846.8516.0686.0680.0000.0000.0000.000
74A74TYR0-0.009-0.02041.350-0.297-0.2970.0000.0000.0000.000
75A75TYR00.0660.04243.4310.0370.0370.0000.0000.0000.000
76A76ARG10.9410.95942.7596.3456.3450.0000.0000.0000.000
77A77HIS00.0590.03542.9370.1420.1420.0000.0000.0000.000
78A78THR0-0.087-0.03543.462-0.083-0.0830.0000.0000.0000.000
79A79GLU-1-0.840-0.94741.022-7.016-7.0160.0000.0000.0000.000
80A80PHE0-0.0210.01045.3710.0660.0660.0000.0000.0000.000
81A81PRO00.0350.00249.037-0.040-0.0400.0000.0000.0000.000
82A82GLY00.0380.02550.678-0.016-0.0160.0000.0000.0000.000
83A83GLY0-0.062-0.02249.0480.0480.0480.0000.0000.0000.000
84A84LEU00.0320.02446.220-0.134-0.1340.0000.0000.0000.000
85A85LYS10.8560.92347.5576.1946.1940.0000.0000.0000.000
86A86GLU-1-0.824-0.92847.525-6.401-6.4010.0000.0000.0000.000
87A87THR0-0.046-0.02747.2060.1430.1430.0000.0000.0000.000
88A88ASN00.0230.01348.549-0.142-0.1420.0000.0000.0000.000
89A89PHE00.0270.01044.797-0.052-0.0520.0000.0000.0000.000
90A90GLU-1-0.890-0.94448.437-5.816-5.8160.0000.0000.0000.000
91A91LYS10.9520.97451.6025.6985.6980.0000.0000.0000.000
92A92LEU0-0.0260.00244.1130.0280.0280.0000.0000.0000.000
93A93VAL00.0270.00146.160-0.069-0.0690.0000.0000.0000.000
94A94ALA00.0180.02047.949-0.014-0.0140.0000.0000.0000.000
95A95HIS0-0.072-0.04849.1590.0030.0030.0000.0000.0000.000
96A96LYS10.8660.92944.6256.7456.7450.0000.0000.0000.000
97A97PRO00.0660.03944.712-0.142-0.1420.0000.0000.0000.000
98A98GLU-1-0.924-0.95639.154-7.895-7.8950.0000.0000.0000.000
99A99GLU-1-0.712-0.84339.939-7.278-7.2780.0000.0000.0000.000
100A100ILE0-0.072-0.03940.080-0.142-0.1420.0000.0000.0000.000
101A101PHE00.0200.00137.694-0.206-0.2060.0000.0000.0000.000
102A102GLU-1-0.923-0.94635.488-8.531-8.5310.0000.0000.0000.000
103A103ARG10.7580.85835.0737.1317.1310.0000.0000.0000.000
104A104ALA0-0.0340.00035.580-0.166-0.1660.0000.0000.0000.000
105A105VAL00.0380.01031.055-0.279-0.2790.0000.0000.0000.000
106A106LYS10.9310.95730.7608.8548.8540.0000.0000.0000.000
107A107GLY0-0.0180.00130.942-0.126-0.1260.0000.0000.0000.000
108A108MET0-0.067-0.02730.020-0.247-0.2470.0000.0000.0000.000
109A109LEU00.0240.03725.752-0.472-0.4720.0000.0000.0000.000
110A110PRO0-0.039-0.03122.1290.1460.1460.0000.0000.0000.000
111A111LYS10.8620.92824.24910.76210.7620.0000.0000.0000.000
112A112GLY00.0640.03923.390-0.348-0.3480.0000.0000.0000.000
113A113PRO00.019-0.01221.8190.0550.0550.0000.0000.0000.000
114A114LEU00.0350.02617.8800.2700.2700.0000.0000.0000.000
115A115GLY00.0270.02121.8210.1010.1010.0000.0000.0000.000
116A116TYR00.007-0.01024.7960.3510.3510.0000.0000.0000.000
117A117ALA0-0.0060.00823.7680.4120.4120.0000.0000.0000.000
118A118MET0-0.0210.00320.5590.3410.3410.0000.0000.0000.000
119A119ILE00.0370.00625.9780.2020.2020.0000.0000.0000.000
120A120LYS10.9010.95528.62610.25710.2570.0000.0000.0000.000
121A121LYS10.7540.87825.02012.13912.1390.0000.0000.0000.000
122A122MET0-0.0170.00830.4850.0610.0610.0000.0000.0000.000
123A123LYS10.8750.94333.3109.1229.1220.0000.0000.0000.000
124A124VAL0-0.001-0.00336.913-0.028-0.0280.0000.0000.0000.000
125A125TYR0-0.017-0.02639.8680.1260.1260.0000.0000.0000.000
126A126ALA00.0140.01743.531-0.023-0.0230.0000.0000.0000.000
127A127GLY00.0280.00746.8810.0330.0330.0000.0000.0000.000
128A128SER00.015-0.00646.530-0.109-0.1090.0000.0000.0000.000
129A129GLU-1-0.968-0.99146.298-6.797-6.7970.0000.0000.0000.000
130A130HIS00.0360.01140.194-0.170-0.1700.0000.0000.0000.000
131A131PRO00.0430.03441.509-0.014-0.0140.0000.0000.0000.000
132A132HIS0-0.0220.00537.553-0.051-0.0510.0000.0000.0000.000
133A133ALA00.0590.02238.893-0.175-0.1750.0000.0000.0000.000
134A134ALA00.001-0.01039.576-0.071-0.0710.0000.0000.0000.000
135A135GLN0-0.056-0.03534.4630.0000.0000.0000.0000.0000.000
136A136GLN0-0.040-0.00534.849-0.365-0.3650.0000.0000.0000.000
137A137PRO0-0.033-0.01035.197-0.194-0.1940.0000.0000.0000.000
138A138GLN00.0140.01332.7980.4120.4120.0000.0000.0000.000
139A139VAL00.0130.00135.6480.0280.0280.0000.0000.0000.000
140A140LEU0-0.068-0.03832.602-0.224-0.2240.0000.0000.0000.000
141A141ASP-1-0.925-0.95236.454-7.791-7.7910.0000.0000.0000.000
142A142ILE-1-0.959-0.98934.204-8.924-8.9240.0000.0000.0000.000