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: 2G8MR

Calculation Name: 7OTC-l-Other547

Preferred Name:

Target Type:

Ligand Name: argyrin b | adenosine-5'-triphosphate | guanosine-5'-diphosphate | 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 | 5,6-dihydrouridine-5'-monophosphate | o2'-methylycytidine-5'-monophosphate | o2'-methyluridine 5'-monophosphate | (2s,3r)-2-azanyl-5-carbamimidamido-3-oxidanyl-pentanoic acid | (3r)-3-(methylsulfanyl)-l-aspartic acid | spermidine | 1,4-diaminobutane | magnesium ion | zinc ion

Ligand 3-letter code: 1I7 | ATP | GDP | G7M | 1MG | 2MG | MA6 | 2MA | 4OC | 6MZ | PSU | 3TD | 5MC | 5MU | OMG | UR3 | H2U | OMC | OMU | 4D4 | D2T | SPD | PUT | MG | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7OTC

Chain ID: l

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 123
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -903396.374104
FMO2-HF: Nuclear repulsion 855852.875793
FMO2-HF: Total energy -47543.498311
FMO2-MP2: Total energy -47682.167661


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.
254.226258.5131.298-2.026-3.559-0.017
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 : 0.822 / q_NPA : 0.906
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].
3A4VAL00.0930.0453.839-1.597-0.5120.004-0.437-0.6520.000
5A6GLN0-0.018-0.0032.520-11.279-9.2970.821-1.206-1.597-0.014
6A7LEU0-0.034-0.0192.6521.0661.9140.470-0.282-1.037-0.002
7A8VAL00.0250.0175.0803.1983.237-0.001-0.004-0.0340.000
11A12ARG10.9110.9403.74052.49552.8280.004-0.097-0.239-0.001
4A5ASN00.1020.0366.2432.1102.1100.0000.0000.0000.000
8A9ARG10.9490.9846.74331.42231.4220.0000.0000.0000.000
9A10LYS10.9350.9696.81526.35426.3540.0000.0000.0000.000
10A11PRO00.0670.0476.355-4.475-4.4750.0000.0000.0000.000
12A13ALA00.0450.0318.2202.5612.5610.0000.0000.0000.000
13A14ARG10.9590.98211.21516.59716.5970.0000.0000.0000.000
14A15LYS10.9720.98213.07922.24822.2480.0000.0000.0000.000
15A16VAL00.0510.03115.7530.4510.4510.0000.0000.0000.000
16A17ALA00.0030.00419.1870.0510.0510.0000.0000.0000.000
17A18LYS10.9830.98722.20313.08813.0880.0000.0000.0000.000
18A19SER00.0500.02624.8640.1930.1930.0000.0000.0000.000
19A20ASN0-0.002-0.01428.2690.0450.0450.0000.0000.0000.000
20A21VAL0-0.026-0.01130.5310.2280.2280.0000.0000.0000.000
21A22PRO00.0170.00331.1530.1170.1170.0000.0000.0000.000
22A23ALA00.0490.02732.9900.0400.0400.0000.0000.0000.000
23A24LEU00.0010.00135.9030.2170.2170.0000.0000.0000.000
24A25GLU-1-0.839-0.90734.112-8.432-8.4320.0000.0000.0000.000
25A26ALA0-0.0020.00232.9180.1210.1210.0000.0000.0000.000
26A27CYS00.0110.03834.6740.1780.1780.0000.0000.0000.000
27A28PRO00.013-0.00638.362-0.056-0.0560.0000.0000.0000.000
28A29GLN0-0.034-0.02639.3970.0230.0230.0000.0000.0000.000
29A30LYS10.8420.92139.0657.9887.9880.0000.0000.0000.000
30A31ARG10.9790.99443.1336.5026.5020.0000.0000.0000.000
31A32GLY00.0030.00545.985-0.135-0.1350.0000.0000.0000.000
32A33VAL00.0170.02347.5570.1000.1000.0000.0000.0000.000
33A34CYS0-0.080-0.04249.155-0.171-0.1710.0000.0000.0000.000
34A35THR0-0.012-0.02847.7750.0850.0850.0000.0000.0000.000
35A36ARG11.0211.01248.5326.3906.3900.0000.0000.0000.000
36A37VAL0-0.0240.00950.073-0.178-0.1780.0000.0000.0000.000
37A38TYR0-0.036-0.02345.3560.0380.0380.0000.0000.0000.000
38A39THR0-0.020-0.01650.549-0.045-0.0450.0000.0000.0000.000
39A40THR00.0220.00745.5820.0050.0050.0000.0000.0000.000
40A41THR00.0620.03546.6580.0440.0440.0000.0000.0000.000
41A42PRO0-0.109-0.04644.112-0.151-0.1510.0000.0000.0000.000
42A43LYS10.9080.97535.8528.7288.7280.0000.0000.0000.000
43A44LYS11.0351.01642.4966.8996.8990.0000.0000.0000.000
44A45PRO0-0.010-0.01840.193-0.232-0.2320.0000.0000.0000.000
45A46ASN0-0.046-0.03542.6270.1420.1420.0000.0000.0000.000
46A47SER00.0270.00545.002-0.002-0.0020.0000.0000.0000.000
47A48ALA00.004-0.00248.3600.0290.0290.0000.0000.0000.000
48A49LEU00.0830.04750.174-0.049-0.0490.0000.0000.0000.000
49A50ARG10.8360.89544.7047.0747.0740.0000.0000.0000.000
50A51LYS10.9620.97648.8586.1116.1110.0000.0000.0000.000
51A52VAL0-0.032-0.01945.358-0.159-0.1590.0000.0000.0000.000
52A53CYS0-0.0080.01246.9950.1360.1360.0000.0000.0000.000
53A54ARG10.8750.93441.3257.0977.0970.0000.0000.0000.000
54A55VAL00.0110.00244.9350.1570.1570.0000.0000.0000.000
55A56ARG11.0151.01744.4836.3596.3590.0000.0000.0000.000
56A57LEU0-0.008-0.01640.6700.1430.1430.0000.0000.0000.000
57A58THR0-0.041-0.03944.6460.1180.1180.0000.0000.0000.000
58A59ASN0-0.049-0.04438.6800.2400.2400.0000.0000.0000.000
59A60GLY00.0170.01341.528-0.110-0.1100.0000.0000.0000.000
60A61PHE0-0.0070.00635.109-0.045-0.0450.0000.0000.0000.000
61A62GLU-1-0.788-0.87240.888-6.828-6.8280.0000.0000.0000.000
62A63VAL0-0.058-0.02538.646-0.222-0.2220.0000.0000.0000.000
63A64THR0-0.011-0.00340.9400.1980.1980.0000.0000.0000.000
64A65SER0-0.004-0.02041.445-0.299-0.2990.0000.0000.0000.000
65A66TYR00.009-0.00243.6390.1860.1860.0000.0000.0000.000
66A67ILE00.0020.00545.355-0.034-0.0340.0000.0000.0000.000
67A68GLY00.0060.00947.8410.0540.0540.0000.0000.0000.000
68A69GLY0-0.025-0.02748.6290.0730.0730.0000.0000.0000.000
69A70GLU-1-0.910-0.94851.841-6.015-6.0150.0000.0000.0000.000
70A71GLY00.0530.03455.1960.1010.1010.0000.0000.0000.000
71A72HIS0-0.042-0.03553.829-0.070-0.0700.0000.0000.0000.000
72A73ASN00.0790.05056.220-0.024-0.0240.0000.0000.0000.000
73A74LEU00.0280.02551.7890.0220.0220.0000.0000.0000.000
74A75GLN00.0380.01455.832-0.024-0.0240.0000.0000.0000.000
75A76GLU-1-0.808-0.93553.543-6.111-6.1110.0000.0000.0000.000
76A77HIS00.0050.00354.1950.0310.0310.0000.0000.0000.000
77A78SER0-0.071-0.01554.797-0.034-0.0340.0000.0000.0000.000
78A79VAL00.005-0.00451.680-0.179-0.1790.0000.0000.0000.000
79A80ILE00.012-0.00748.2010.0290.0290.0000.0000.0000.000
80A81LEU00.0340.00646.530-0.109-0.1090.0000.0000.0000.000
81A82ILE0-0.0200.00641.1560.0260.0260.0000.0000.0000.000
82A83ARG10.9430.96740.9457.5257.5250.0000.0000.0000.000
83A84GLY00.0630.03437.294-0.043-0.0430.0000.0000.0000.000
84A85GLY0-0.004-0.00636.8280.1420.1420.0000.0000.0000.000
85A86ARG10.9570.98033.3289.4299.4290.0000.0000.0000.000
86A87VAL00.0550.03537.5970.0740.0740.0000.0000.0000.000
87A88LYS10.9390.96934.3498.7818.7810.0000.0000.0000.000
88A89ASP-1-0.804-0.88637.544-7.619-7.6190.0000.0000.0000.000
89A90LEU00.0750.04139.8810.1480.1480.0000.0000.0000.000
90A91PRO00.003-0.00137.060-0.211-0.2110.0000.0000.0000.000
91A92GLY00.0290.02036.4350.1620.1620.0000.0000.0000.000
92A93VAL0-0.0130.00137.514-0.028-0.0280.0000.0000.0000.000
93A94ARG10.8450.91132.2559.2259.2250.0000.0000.0000.000
94A95TYR00.0800.04436.115-0.260-0.2600.0000.0000.0000.000
95A96HIS0-0.046-0.01840.1290.2540.2540.0000.0000.0000.000
96A97THR00.0750.02843.279-0.115-0.1150.0000.0000.0000.000
97A98VAL0-0.071-0.03045.5550.0060.0060.0000.0000.0000.000
98A99ARG10.7940.87247.9106.2016.2010.0000.0000.0000.000
99A100GLY0-0.032-0.01851.308-0.049-0.0490.0000.0000.0000.000
100A101ALA0-0.039-0.00750.3080.0340.0340.0000.0000.0000.000
101A102LEU0-0.014-0.01451.131-0.052-0.0520.0000.0000.0000.000
102A103ASP-1-0.713-0.83354.291-5.626-5.6260.0000.0000.0000.000
103A104CYS0-0.095-0.02652.4330.0400.0400.0000.0000.0000.000
104A105SER00.003-0.00454.421-0.011-0.0110.0000.0000.0000.000
105A106GLY00.0280.01054.867-0.114-0.1140.0000.0000.0000.000
106A107VAL0-0.082-0.03553.8620.0870.0870.0000.0000.0000.000
107A108LYS10.9670.97556.2945.3975.3970.0000.0000.0000.000
108A109ASP-1-0.783-0.90259.028-5.237-5.2370.0000.0000.0000.000
109A110ARG10.8980.97150.3286.1896.1890.0000.0000.0000.000
110A111LYS10.9390.95857.6195.2515.2510.0000.0000.0000.000
111A112GLN00.0610.03153.392-0.102-0.1020.0000.0000.0000.000
112A113ALA00.002-0.01549.227-0.036-0.0360.0000.0000.0000.000
113A114ARG10.9230.97250.7275.6435.6430.0000.0000.0000.000
114A115SER00.0420.02749.4250.0160.0160.0000.0000.0000.000
115A116LYS10.9450.96943.5227.2427.2420.0000.0000.0000.000
116A117TYR0-0.036-0.02048.175-0.091-0.0910.0000.0000.0000.000
117A118GLY00.0830.04951.1830.1090.1090.0000.0000.0000.000
118A119VAL0-0.066-0.03053.2340.1190.1190.0000.0000.0000.000
119A120LYS10.9990.98856.2415.5745.5740.0000.0000.0000.000
120A121ARG10.9120.96458.7725.2645.2640.0000.0000.0000.000
121A122PRO0-0.009-0.00660.3860.0410.0410.0000.0000.0000.000
122A123LYS10.9310.95663.5984.9494.9490.0000.0000.0000.000
123A124ALA-1-0.802-0.88665.149-4.925-4.9250.0000.0000.0000.000