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: LR729

Calculation Name: 7OTC-P-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: P

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 114
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -877989.61674
FMO2-HF: Nuclear repulsion 833346.877858
FMO2-HF: Total energy -44642.738882
FMO2-MP2: Total energy -44775.917351


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:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
146.498150.5540.68-1.69-3.0460
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.894 / q_NPA : 0.930
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].
3A4ILE00.0790.0553.4492.3794.293-0.007-0.809-1.098-0.003
4A5ILE00.0340.0252.6770.4842.1430.687-0.731-1.6160.003
5A6LYS10.9190.9593.88146.77047.2530.000-0.150-0.3320.000
6A7GLN0-0.081-0.0505.5473.4103.4100.0000.0000.0000.000
7A8LEU00.0680.0448.1142.6222.6220.0000.0000.0000.000
8A9GLU-1-0.880-0.9396.845-36.759-36.7590.0000.0000.0000.000
9A10GLN0-0.010-0.0219.172-0.402-0.4020.0000.0000.0000.000
10A11GLU-1-0.891-0.93811.487-22.214-22.2140.0000.0000.0000.000
11A12GLN0-0.023-0.01313.1681.3591.3590.0000.0000.0000.000
12A13MET0-0.115-0.03712.5760.2890.2890.0000.0000.0000.000
13A14LYS10.8670.95915.24514.80214.8020.0000.0000.0000.000
14A15GLN0-0.002-0.01718.648-0.938-0.9380.0000.0000.0000.000
15A16ASP-1-0.871-0.93620.165-13.096-13.0960.0000.0000.0000.000
16A17VAL0-0.047-0.01819.3940.4730.4730.0000.0000.0000.000
17A18PRO00.000-0.00222.6530.0480.0480.0000.0000.0000.000
18A19SER0-0.016-0.00223.747-0.513-0.5130.0000.0000.0000.000
19A20PHE0-0.004-0.00322.9800.6320.6320.0000.0000.0000.000
20A21ARG10.9260.95324.40010.84710.8470.0000.0000.0000.000
21A22PRO0-0.011-0.00524.4680.2230.2230.0000.0000.0000.000
22A23GLY00.001-0.02227.3190.1830.1830.0000.0000.0000.000
23A24ASP-1-0.771-0.87029.177-10.211-10.2110.0000.0000.0000.000
24A25THR0-0.034-0.02031.028-0.028-0.0280.0000.0000.0000.000
25A26VAL00.000-0.00628.103-0.002-0.0020.0000.0000.0000.000
26A27GLU-1-0.820-0.92631.417-8.939-8.9390.0000.0000.0000.000
27A28VAL0-0.029-0.01527.294-0.306-0.3060.0000.0000.0000.000
28A29LYS10.8970.95830.1189.3289.3280.0000.0000.0000.000
29A30VAL00.006-0.00627.812-0.435-0.4350.0000.0000.0000.000
30A31TRP00.005-0.00728.1220.6950.6950.0000.0000.0000.000
31A32VAL0-0.042-0.02030.384-0.155-0.1550.0000.0000.0000.000
32A33VAL0-0.015-0.03030.2690.2060.2060.0000.0000.0000.000
33A34GLU-1-0.850-0.91133.402-8.209-8.2090.0000.0000.0000.000
34A35GLY00.0560.03335.2340.2430.2430.0000.0000.0000.000
35A36SER00.0160.00035.574-0.168-0.1680.0000.0000.0000.000
36A37LYS10.8400.93637.5438.3718.3710.0000.0000.0000.000
37A38LYS10.9290.96032.0319.4589.4580.0000.0000.0000.000
38A39ARG10.9690.98135.2938.2138.2130.0000.0000.0000.000
39A40LEU00.0670.04731.689-0.197-0.1970.0000.0000.0000.000
40A41GLN0-0.034-0.01633.5850.0950.0950.0000.0000.0000.000
41A42ALA0-0.007-0.00833.530-0.227-0.2270.0000.0000.0000.000
42A43PHE0-0.033-0.02831.1080.1380.1380.0000.0000.0000.000
43A44GLU-1-0.894-0.93332.264-8.651-8.6510.0000.0000.0000.000
44A45GLY00.0260.01033.3750.1680.1680.0000.0000.0000.000
45A46VAL0-0.0160.00131.808-0.174-0.1740.0000.0000.0000.000
46A47VAL00.0180.01825.749-0.179-0.1790.0000.0000.0000.000
47A48ILE00.0060.00227.7290.0650.0650.0000.0000.0000.000
48A49ALA0-0.017-0.02123.542-0.126-0.1260.0000.0000.0000.000
49A50ILE00.0440.03919.563-0.007-0.0070.0000.0000.0000.000
50A51ARG10.8650.93513.58420.44420.4440.0000.0000.0000.000
51A52ASN00.0770.03215.082-0.262-0.2620.0000.0000.0000.000
52A53ARG10.8580.90911.01722.13222.1320.0000.0000.0000.000
53A54GLY00.0950.0659.908-1.531-1.5310.0000.0000.0000.000
54A55LEU00.1360.08710.2342.2182.2180.0000.0000.0000.000
55A56HIS0-0.043-0.0308.4504.8274.8270.0000.0000.0000.000
56A57SER0-0.046-0.04013.0220.7960.7960.0000.0000.0000.000
57A58ALA00.0010.02115.4240.7740.7740.0000.0000.0000.000
58A59PHE00.0020.00018.921-0.043-0.0430.0000.0000.0000.000
59A60THR0-0.021-0.01122.3750.1080.1080.0000.0000.0000.000
60A61VAL0-0.0040.01025.4710.1220.1220.0000.0000.0000.000
61A62ARG10.8860.93028.9769.1759.1750.0000.0000.0000.000
62A63LYS10.8800.94132.2988.8528.8520.0000.0000.0000.000
63A64ILE0-0.0070.00035.793-0.029-0.0290.0000.0000.0000.000
64A65SER0-0.018-0.02038.4670.0020.0020.0000.0000.0000.000
65A66ASN00.000-0.00140.457-0.152-0.1520.0000.0000.0000.000
66A67GLY00.0450.03743.4820.1360.1360.0000.0000.0000.000
67A68GLU-1-0.905-0.93640.129-7.705-7.7050.0000.0000.0000.000
68A69GLY0-0.040-0.03537.801-0.085-0.0850.0000.0000.0000.000
69A70VAL00.0060.01033.475-0.158-0.1580.0000.0000.0000.000
70A71GLU-1-0.762-0.85629.654-10.424-10.4240.0000.0000.0000.000
71A72ARG10.9570.98727.54710.86610.8660.0000.0000.0000.000
72A73VAL0-0.010-0.00121.977-0.134-0.1340.0000.0000.0000.000
73A74PHE00.0010.00123.3980.1190.1190.0000.0000.0000.000
74A75GLN00.0410.00617.544-1.084-1.0840.0000.0000.0000.000
75A76THR0-0.026-0.04618.3050.6240.6240.0000.0000.0000.000
76A77HIS00.0750.03415.2801.0371.0370.0000.0000.0000.000
77A78SER00.0110.02518.2450.1050.1050.0000.0000.0000.000
78A79PRO00.0690.02320.2830.4600.4600.0000.0000.0000.000
79A80VAL0-0.018-0.00123.3540.5680.5680.0000.0000.0000.000
80A81VAL0-0.047-0.03323.3740.5920.5920.0000.0000.0000.000
81A82ASP-1-0.849-0.89924.803-10.973-10.9730.0000.0000.0000.000
82A83SER00.0360.00626.803-0.214-0.2140.0000.0000.0000.000
83A84ILE0-0.045-0.02323.5700.1460.1460.0000.0000.0000.000
84A85SER00.0130.00227.9710.1540.1540.0000.0000.0000.000
85A86VAL00.014-0.00129.4270.1660.1660.0000.0000.0000.000
86A87LYS10.9010.95731.9139.3309.3300.0000.0000.0000.000
87A88ARG10.8960.95534.4598.4128.4120.0000.0000.0000.000
88A89ARG10.8400.92432.5048.5068.5060.0000.0000.0000.000
89A90GLY00.0450.02532.6900.2890.2890.0000.0000.0000.000
90A91ALA0-0.057-0.02832.752-0.300-0.3000.0000.0000.0000.000
91A92VAL00.002-0.00230.1430.2150.2150.0000.0000.0000.000
92A93ARG10.9620.98131.3939.0979.0970.0000.0000.0000.000
93A94LYS10.9650.97428.61210.19410.1940.0000.0000.0000.000
94A95ALA00.0410.02523.4930.0550.0550.0000.0000.0000.000
95A96LYS10.8570.93720.80514.01414.0140.0000.0000.0000.000
96A97LEU0-0.016-0.01326.9120.3340.3340.0000.0000.0000.000
97A98TYR00.0490.00724.2130.1110.1110.0000.0000.0000.000
98A99TYR00.0550.03830.7490.2230.2230.0000.0000.0000.000
99A100LEU0-0.046-0.02733.1490.3210.3210.0000.0000.0000.000
100A101ARG10.8050.87328.09910.65710.6570.0000.0000.0000.000
101A102GLU-1-0.849-0.92035.510-8.891-8.8910.0000.0000.0000.000
102A103ARG10.8620.93737.8338.3978.3970.0000.0000.0000.000
103A104THR00.0800.03539.876-0.119-0.1190.0000.0000.0000.000
104A105GLY00.0600.02442.3840.1040.1040.0000.0000.0000.000
105A106LYS10.9480.96243.2446.4456.4450.0000.0000.0000.000
106A107ALA00.0660.03042.844-0.041-0.0410.0000.0000.0000.000
107A108ALA00.0120.00938.670-0.179-0.1790.0000.0000.0000.000
108A109ARG10.8760.95638.4077.0857.0850.0000.0000.0000.000
109A110ILE00.0100.01834.7190.0040.0040.0000.0000.0000.000
110A111LYS10.9530.97138.0018.2508.2500.0000.0000.0000.000
111A112GLU-1-0.774-0.88837.264-8.627-8.6270.0000.0000.0000.000
112A113ARG10.7600.86530.62610.08210.0820.0000.0000.0000.000
113A114LEU00.006-0.00636.541-0.074-0.0740.0000.0000.0000.000
114A115ASN-1-0.785-0.86633.703-8.590-8.5900.0000.0000.0000.000