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: N6L9Q

Calculation Name: 6V3A-g-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: g

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 141
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1203718.665248
FMO2-HF: Nuclear repulsion 1147893.054035
FMO2-HF: Total energy -55825.611213
FMO2-MP2: Total energy -55986.991918


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:2:PRO)


Summations of interaction energy for fragment #1(A:2:PRO)
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.
160.71167.7582.274-3.773-5.55-0.037
Interaction energy analysis for fragmet #1(A:2:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.858 / q_NPA : 0.910
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].
3A4ARG11.0121.0123.77030.20332.565-0.016-1.181-1.165-0.006
4A5ARG11.0031.0092.84049.05650.0240.100-0.247-0.8210.000
5A6VAL00.0400.0202.573-21.502-18.4631.331-2.004-2.366-0.026
6A7VAL0-0.032-0.0262.3750.4211.0900.860-0.335-1.196-0.005
7A8ALA00.0470.0314.7630.2130.223-0.001-0.006-0.0020.000
8A9ALA0-0.021-0.0188.162-1.221-1.2210.0000.0000.0000.000
9A10ARG10.9400.96810.16924.21724.2170.0000.0000.0000.000
10A11GLU-1-0.884-0.93412.348-15.110-15.1100.0000.0000.0000.000
11A12ILE0-0.070-0.04416.030-0.191-0.1910.0000.0000.0000.000
12A13LEU00.0740.03218.6870.2590.2590.0000.0000.0000.000
13A14PRO00.0000.00222.152-0.154-0.1540.0000.0000.0000.000
14A15ASP-1-0.777-0.89225.017-10.434-10.4340.0000.0000.0000.000
15A16PRO00.012-0.01127.4850.1900.1900.0000.0000.0000.000
16A17LYS10.8970.98330.5868.8538.8530.0000.0000.0000.000
17A18PHE00.031-0.00530.9210.2670.2670.0000.0000.0000.000
18A19SER00.0200.02928.992-0.008-0.0080.0000.0000.0000.000
19A20SER00.0290.01127.248-0.443-0.4430.0000.0000.0000.000
20A21GLN0-0.005-0.01519.520-0.650-0.6500.0000.0000.0000.000
21A22THR0-0.0020.00222.439-0.663-0.6630.0000.0000.0000.000
22A23ILE00.0550.03623.827-0.227-0.2270.0000.0000.0000.000
23A24ALA00.0180.01623.022-0.100-0.1000.0000.0000.0000.000
24A25LYS10.8820.94015.16317.59817.5980.0000.0000.0000.000
25A26PHE00.0330.00521.061-0.416-0.4160.0000.0000.0000.000
26A27MET00.0290.02023.6210.0950.0950.0000.0000.0000.000
27A28ASN0-0.026-0.01619.3560.5250.5250.0000.0000.0000.000
28A29HIS0-0.052-0.03417.765-1.314-1.3140.0000.0000.0000.000
29A30VAL00.0050.01521.3890.0560.0560.0000.0000.0000.000
30A31MET0-0.072-0.01521.2930.4150.4150.0000.0000.0000.000
31A32GLN00.0010.00823.034-0.427-0.4270.0000.0000.0000.000
32A33ASP-1-0.874-0.94323.725-11.677-11.6770.0000.0000.0000.000
33A34GLY00.0090.00223.3240.2220.2220.0000.0000.0000.000
34A35LYS10.9240.96924.23410.47610.4760.0000.0000.0000.000
35A36LYS10.9070.93623.57812.58812.5880.0000.0000.0000.000
36A37SER00.0600.03527.250-0.001-0.0010.0000.0000.0000.000
37A38ILE00.0150.01030.0200.2370.2370.0000.0000.0000.000
38A39ALA00.0170.02127.0140.1810.1810.0000.0000.0000.000
39A40GLU-1-0.871-0.96428.286-10.628-10.6280.0000.0000.0000.000
40A41SER0-0.056-0.03330.4470.2820.2820.0000.0000.0000.000
41A42ILE0-0.023-0.01631.1020.2310.2310.0000.0000.0000.000
42A43VAL00.006-0.00427.9340.1340.1340.0000.0000.0000.000
43A44TYR0-0.036-0.04630.5830.2120.2120.0000.0000.0000.000
44A45GLY00.0280.02134.2390.2250.2250.0000.0000.0000.000
45A46ALA0-0.044-0.02333.3000.1930.1930.0000.0000.0000.000
46A47LEU0-0.025-0.02231.2810.1140.1140.0000.0000.0000.000
47A48GLU-1-0.937-0.95535.474-7.365-7.3650.0000.0000.0000.000
48A49ARG11.0000.99138.9657.4077.4070.0000.0000.0000.000
49A50VAL0-0.062-0.02935.7770.1380.1380.0000.0000.0000.000
50A51GLN00.0160.01338.970-0.017-0.0170.0000.0000.0000.000
51A52GLU-1-0.882-0.94940.519-6.818-6.8180.0000.0000.0000.000
52A53LYS10.8600.95042.0987.5857.5850.0000.0000.0000.000
53A54ASN0-0.054-0.03940.0210.1440.1440.0000.0000.0000.000
54A55LYS10.9300.97341.8836.5956.5950.0000.0000.0000.000
55A56VAL0-0.0090.00638.1070.0730.0730.0000.0000.0000.000
56A57ASP-1-0.779-0.89835.320-8.822-8.8220.0000.0000.0000.000
57A58PRO00.0040.00234.648-0.190-0.1900.0000.0000.0000.000
58A59VAL0-0.043-0.03130.708-0.346-0.3460.0000.0000.0000.000
59A60GLU-1-0.911-0.94331.205-8.971-8.9710.0000.0000.0000.000
60A61PHE00.0190.01432.950-0.141-0.1410.0000.0000.0000.000
61A62PHE0-0.014-0.01326.100-0.226-0.2260.0000.0000.0000.000
62A63GLU-1-0.803-0.89525.916-12.383-12.3830.0000.0000.0000.000
63A64THR0-0.002-0.02528.852-0.169-0.1690.0000.0000.0000.000
64A65THR0-0.025-0.01531.1720.0770.0770.0000.0000.0000.000
65A66LEU0-0.066-0.02723.710-0.255-0.2550.0000.0000.0000.000
66A67GLU-1-0.988-1.00326.417-11.301-11.3010.0000.0000.0000.000
67A68LYS10.9781.00527.3968.8478.8470.0000.0000.0000.000
68A69VAL0-0.0200.00226.384-0.003-0.0030.0000.0000.0000.000
69A70ARG10.7330.85022.89112.06312.0630.0000.0000.0000.000
70A71PRO00.0270.03821.1480.2990.2990.0000.0000.0000.000
71A72MET00.029-0.00222.499-0.498-0.4980.0000.0000.0000.000
72A73VAL0-0.026-0.01620.582-0.693-0.6930.0000.0000.0000.000
73A74GLU-1-0.897-0.94718.031-14.815-14.8150.0000.0000.0000.000
74A75VAL00.0590.03019.754-0.493-0.4930.0000.0000.0000.000
75A76LYS10.8650.93212.93820.99720.9970.0000.0000.0000.000
76A77ALA00.010-0.00118.0910.8710.8710.0000.0000.0000.000
77A78ARG10.9080.94717.28713.13913.1390.0000.0000.0000.000
78A79ARG10.9020.95918.83314.47114.4710.0000.0000.0000.000
79A80VAL00.0170.01820.593-0.473-0.4730.0000.0000.0000.000
80A81GLY00.0530.02122.8380.0300.0300.0000.0000.0000.000
81A82GLY00.0030.01624.8470.4570.4570.0000.0000.0000.000
82A83ALA00.0300.02226.4280.0170.0170.0000.0000.0000.000
83A84THR0-0.003-0.03324.360-0.601-0.6010.0000.0000.0000.000
84A85TYR00.0270.00222.931-0.713-0.7130.0000.0000.0000.000
85A86GLN00.0080.02222.670-0.962-0.9620.0000.0000.0000.000
86A87VAL00.007-0.00420.1830.3710.3710.0000.0000.0000.000
87A88PRO00.0750.05721.214-0.757-0.7570.0000.0000.0000.000
88A89MET0-0.042-0.03316.668-0.604-0.6040.0000.0000.0000.000
89A90GLU-1-0.845-0.90517.874-15.598-15.5980.0000.0000.0000.000
90A91VAL0-0.037-0.03914.042-1.629-1.6290.0000.0000.0000.000
91A92ARG10.9980.9958.41028.37328.3730.0000.0000.0000.000
92A93PRO00.0830.02115.863-0.409-0.4090.0000.0000.0000.000
93A94SER00.0080.00513.7390.0790.0790.0000.0000.0000.000
94A95ARG10.9140.97113.12620.13420.1340.0000.0000.0000.000
95A96ARG10.9130.96115.09214.84114.8410.0000.0000.0000.000
96A97THR00.0790.03918.4310.8060.8060.0000.0000.0000.000
97A98ALA0-0.037-0.01116.2310.4000.4000.0000.0000.0000.000
98A99LEU0-0.015-0.01816.8630.1690.1690.0000.0000.0000.000
99A100ALA00.0570.04619.8450.4780.4780.0000.0000.0000.000
100A101MET0-0.0170.01320.9750.2400.2400.0000.0000.0000.000
101A102ARG10.8290.91519.18014.40114.4010.0000.0000.0000.000
102A103TRP00.0910.02621.6200.3530.3530.0000.0000.0000.000
103A104LEU00.0530.03725.3430.4040.4040.0000.0000.0000.000
104A105VAL0-0.022-0.01124.9960.3710.3710.0000.0000.0000.000
105A106ASP-1-0.852-0.93425.449-11.384-11.3840.0000.0000.0000.000
106A107ALA0-0.0210.00627.5790.3500.3500.0000.0000.0000.000
107A108ALA00.0300.01430.3530.3430.3430.0000.0000.0000.000
108A109ALA0-0.047-0.03629.6630.3140.3140.0000.0000.0000.000
109A110LYS10.8270.89829.14010.71810.7180.0000.0000.0000.000
110A111ARG10.8210.92133.5048.6068.6060.0000.0000.0000.000
111A112SER0-0.006-0.00536.641-0.053-0.0530.0000.0000.0000.000
112A113GLU-1-0.852-0.94138.727-7.382-7.3820.0000.0000.0000.000
113A114LYS10.9230.97140.2356.8876.8870.0000.0000.0000.000
114A115THR00.0410.01338.162-0.092-0.0920.0000.0000.0000.000
115A116MET00.0280.01829.8750.0590.0590.0000.0000.0000.000
116A117ALA00.0470.02134.481-0.120-0.1200.0000.0000.0000.000
117A118LEU00.0160.00635.710-0.022-0.0220.0000.0000.0000.000
118A119ARG10.8620.94534.3468.6748.6740.0000.0000.0000.000
119A120LEU0-0.0060.00829.950-0.144-0.1440.0000.0000.0000.000
120A121ALA00.0160.01133.723-0.100-0.1000.0000.0000.0000.000
121A122GLY00.0000.00136.3980.0590.0590.0000.0000.0000.000
122A123GLU-1-0.785-0.90232.166-9.139-9.1390.0000.0000.0000.000
123A124LEU0-0.037-0.02230.609-0.134-0.1340.0000.0000.0000.000
124A125LEU0-0.018-0.00234.0070.0330.0330.0000.0000.0000.000
125A126ASP-1-0.757-0.86137.003-7.976-7.9760.0000.0000.0000.000
126A127ALA0-0.056-0.03432.4720.0240.0240.0000.0000.0000.000
127A128ALA0-0.058-0.01734.493-0.116-0.1160.0000.0000.0000.000
128A129GLU-1-0.956-0.98336.002-7.501-7.5010.0000.0000.0000.000
129A130GLY00.0080.01437.1580.1310.1310.0000.0000.0000.000
130A131LYS10.8860.92738.1907.6807.6800.0000.0000.0000.000
131A132GLY00.0130.00835.4030.0320.0320.0000.0000.0000.000
132A133ALA0-0.001-0.00533.474-0.065-0.0650.0000.0000.0000.000
133A134ALA0-0.014-0.02629.299-0.252-0.2520.0000.0000.0000.000
134A135ILE0-0.019-0.01729.457-0.371-0.3710.0000.0000.0000.000
135A136LYS10.8470.92731.4589.0349.0340.0000.0000.0000.000
136A137LYS10.9040.96423.77012.47812.4780.0000.0000.0000.000
137A138ARG10.8300.91426.42410.44010.4400.0000.0000.0000.000
138A139GLU-1-0.806-0.87528.099-9.275-9.2750.0000.0000.0000.000
139A140ASP-1-0.981-1.00427.310-10.779-10.7790.0000.0000.0000.000
140A141VAL0-0.042-0.02228.270-0.176-0.1760.0000.0000.0000.000
141A142HIS-1-0.977-0.96926.785-11.746-11.7460.0000.0000.0000.000