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: Y7J12

Calculation Name: 7OTC-M-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: M

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 136
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1152420.938373
FMO2-HF: Nuclear repulsion 1098977.915233
FMO2-HF: Total energy -53443.023139
FMO2-MP2: Total energy -53598.184767


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.
317.178322.8627.064-3.873-8.871-0.023
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 : 0.858 / q_NPA : 0.920
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].
3A3GLN00.0780.0273.1912.9735.7550.085-1.183-1.684-0.007
4A4PRO00.0110.0194.7710.0270.058-0.001-0.009-0.0200.000
42A42THR00.0010.0045.359-1.464-1.410-0.001-0.008-0.0450.000
43A43ALA00.0150.0012.756-1.488-1.6062.586-0.792-1.6750.001
44A44ARG10.9750.9692.24727.58529.7422.853-1.120-3.890-0.008
45A45GLN00.0670.0454.473-1.248-1.2140.0150.040-0.0890.000
47A47GLU-1-0.866-0.9072.379-58.643-58.0271.529-0.771-1.373-0.009
48A48ALA00.0340.0095.0392.6352.648-0.001-0.004-0.0070.000
50A50ARG10.9070.9533.88849.75449.869-0.001-0.026-0.0880.000
5A5LYS10.9670.9808.51330.12030.1200.0000.0000.0000.000
6A6ARG11.0221.01910.08118.09718.0970.0000.0000.0000.000
7A7THR0-0.033-0.02511.162-0.304-0.3040.0000.0000.0000.000
8A8LYS10.9851.00113.93314.12514.1250.0000.0000.0000.000
9A9PHE00.0610.02416.3400.5350.5350.0000.0000.0000.000
10A10ARG11.0121.01113.76814.39914.3990.0000.0000.0000.000
11A11LYS10.8690.93613.84214.73614.7360.0000.0000.0000.000
12A12MET00.0490.03514.9330.1920.1920.0000.0000.0000.000
13A13HIS00.0750.03917.032-0.425-0.4250.0000.0000.0000.000
14A14LYS10.9540.97418.23612.70012.7000.0000.0000.0000.000
15A15GLY00.0530.03218.668-0.573-0.5730.0000.0000.0000.000
16A16ARG10.9410.95020.98411.84711.8470.0000.0000.0000.000
17A17ASN0-0.016-0.00218.4730.2410.2410.0000.0000.0000.000
18A18ARG11.0091.00121.20710.50310.5030.0000.0000.0000.000
19A19GLY00.0780.04323.578-0.367-0.3670.0000.0000.0000.000
20A20LEU00.0610.02724.998-0.294-0.2940.0000.0000.0000.000
21A21ALA0-0.031-0.00721.235-0.187-0.1870.0000.0000.0000.000
22A22GLN00.0680.04421.5470.5750.5750.0000.0000.0000.000
23A23GLY0-0.007-0.01020.588-0.929-0.9290.0000.0000.0000.000
24A24THR00.004-0.00820.989-0.697-0.6970.0000.0000.0000.000
25A25ASP-1-0.845-0.90823.619-11.733-11.7330.0000.0000.0000.000
26A26VAL0-0.054-0.03221.312-0.740-0.7400.0000.0000.0000.000
27A27SER0-0.014-0.01321.3100.5990.5990.0000.0000.0000.000
28A28PHE0-0.092-0.04517.206-0.195-0.1950.0000.0000.0000.000
29A29GLY00.0160.02120.5240.1370.1370.0000.0000.0000.000
30A30SER00.026-0.01221.3760.4550.4550.0000.0000.0000.000
31A31PHE00.0110.01321.3760.4150.4150.0000.0000.0000.000
32A32GLY00.024-0.00218.860-0.812-0.8120.0000.0000.0000.000
33A33LEU0-0.061-0.00515.5550.4600.4600.0000.0000.0000.000
34A34LYS10.9240.96018.10111.94011.9400.0000.0000.0000.000
35A35ALA00.003-0.00617.9280.1520.1520.0000.0000.0000.000
36A36VAL0-0.0050.00019.7990.5550.5550.0000.0000.0000.000
37A37GLY00.0160.01021.4100.4620.4620.0000.0000.0000.000
38A38ARG10.8340.90819.97511.97511.9750.0000.0000.0000.000
39A39GLY00.008-0.01117.0670.2550.2550.0000.0000.0000.000
40A40ARG10.9120.95612.17717.68817.6880.0000.0000.0000.000
41A41LEU00.0580.03310.2990.1080.1080.0000.0000.0000.000
46A46ILE00.0470.0275.9810.5010.5010.0000.0000.0000.000
49A49ALA00.0210.0158.2412.5062.5060.0000.0000.0000.000
51A51ARG10.8330.8985.30543.16643.1660.0000.0000.0000.000
52A52ALA0-0.012-0.0049.4042.0042.0040.0000.0000.0000.000
53A53MET00.0330.02911.5651.4481.4480.0000.0000.0000.000
54A54THR0-0.017-0.02810.3690.9290.9290.0000.0000.0000.000
55A55ARG10.9460.97513.28420.77520.7750.0000.0000.0000.000
56A56ALA00.0010.01314.9971.0771.0770.0000.0000.0000.000
57A57VAL00.0400.01916.2200.7770.7770.0000.0000.0000.000
58A58LYS10.9680.98518.45914.17014.1700.0000.0000.0000.000
59A59ARG10.8690.94412.60420.81320.8130.0000.0000.0000.000
60A60GLN00.0280.02017.1120.4760.4760.0000.0000.0000.000
61A61GLY00.0320.03018.275-0.724-0.7240.0000.0000.0000.000
62A62LYS10.8810.94815.66517.75417.7540.0000.0000.0000.000
63A63ILE00.007-0.00511.863-0.032-0.0320.0000.0000.0000.000
64A64TRP00.0220.00713.221-1.123-1.1230.0000.0000.0000.000
65A65ILE0-0.068-0.0468.157-0.450-0.4500.0000.0000.0000.000
66A66ARG10.8660.93711.51616.04216.0420.0000.0000.0000.000
67A67VAL0-0.043-0.01810.3461.0511.0510.0000.0000.0000.000
68A68PHE00.041-0.0047.667-3.375-3.3750.0000.0000.0000.000
69A69PRO0-0.072-0.0315.2362.1232.1230.0000.0000.0000.000
70A70ASP-1-0.857-0.9287.568-23.321-23.3210.0000.0000.0000.000
71A71LYS10.8930.94610.33818.18518.1850.0000.0000.0000.000
72A72PRO0-0.0220.0069.504-1.264-1.2640.0000.0000.0000.000
73A73ILE0-0.075-0.05010.1652.2962.2960.0000.0000.0000.000
74A74THR0-0.054-0.03911.499-0.396-0.3960.0000.0000.0000.000
75A75GLU-1-0.803-0.88212.295-16.839-16.8390.0000.0000.0000.000
76A76LYS10.8480.92114.80312.50112.5010.0000.0000.0000.000
77A77PRO00.0370.02016.222-0.117-0.1170.0000.0000.0000.000
78A78LEU00.0680.02617.4620.5030.5030.0000.0000.0000.000
79A79ALA00.0270.01719.5780.1770.1770.0000.0000.0000.000
80A80VAL0-0.0130.01820.7960.3970.3970.0000.0000.0000.000
81A81ARG10.9830.98423.3549.2219.2210.0000.0000.0000.000
82A82MET00.017-0.00122.968-0.397-0.3970.0000.0000.0000.000
83A83GLY00.0230.01625.9620.3100.3100.0000.0000.0000.000
84A84LYS10.9580.96224.7059.2939.2930.0000.0000.0000.000
85A85GLY00.0830.06123.316-0.326-0.3260.0000.0000.0000.000
86A86LYS10.8600.92417.39815.01815.0180.0000.0000.0000.000
87A87GLY00.0590.03417.123-0.055-0.0550.0000.0000.0000.000
88A88ASN00.0220.00513.5880.3550.3550.0000.0000.0000.000
89A89VAL0-0.013-0.0158.8260.3080.3080.0000.0000.0000.000
90A90GLU-1-0.853-0.9098.584-21.866-21.8660.0000.0000.0000.000
91A91TYR0-0.117-0.0795.996-3.664-3.6640.0000.0000.0000.000
92A92TRP00.0270.0064.8132.8622.8620.0000.0000.0000.000
93A93VAL0-0.028-0.0356.568-1.610-1.6100.0000.0000.0000.000
94A94ALA00.0480.0439.1190.5430.5430.0000.0000.0000.000
95A95LEU0-0.051-0.03911.3240.7510.7510.0000.0000.0000.000
96A96ILE00.0290.01713.380-0.099-0.0990.0000.0000.0000.000
97A97GLN00.0240.02217.0830.2590.2590.0000.0000.0000.000
98A98PRO00.001-0.00220.625-0.422-0.4220.0000.0000.0000.000
99A99GLY00.0690.02622.9040.2840.2840.0000.0000.0000.000
100A100LYS10.8780.95015.93217.29717.2970.0000.0000.0000.000
101A101VAL00.0460.03417.675-0.331-0.3310.0000.0000.0000.000
102A102LEU0-0.078-0.03813.844-0.813-0.8130.0000.0000.0000.000
103A103TYR00.004-0.02610.070-2.951-2.9510.0000.0000.0000.000
104A104GLU-1-0.693-0.83914.632-14.374-14.3740.0000.0000.0000.000
105A105MET0-0.042-0.00615.917-1.110-1.1100.0000.0000.0000.000
106A106ASP-1-0.811-0.88718.348-12.409-12.4090.0000.0000.0000.000
107A107GLY00.007-0.00420.564-0.670-0.6700.0000.0000.0000.000
108A108VAL0-0.040-0.02420.686-0.077-0.0770.0000.0000.0000.000
109A109PRO00.0760.03523.5850.0410.0410.0000.0000.0000.000
110A110GLU-1-0.803-0.87224.539-11.810-11.8100.0000.0000.0000.000
111A111GLU-1-0.815-0.92425.134-11.446-11.4460.0000.0000.0000.000
112A112LEU0-0.0040.00321.809-0.377-0.3770.0000.0000.0000.000
113A113ALA00.018-0.00820.622-0.799-0.7990.0000.0000.0000.000
114A114ARG10.7920.87820.51910.59610.5960.0000.0000.0000.000
115A115GLU-1-0.853-0.93122.047-13.470-13.4700.0000.0000.0000.000
116A116ALA0-0.023-0.02517.448-0.707-0.7070.0000.0000.0000.000
117A117PHE0-0.010-0.03215.952-1.552-1.5520.0000.0000.0000.000
118A118LYS10.9420.99617.98911.94911.9490.0000.0000.0000.000
119A119LEU00.006-0.00116.855-0.592-0.5920.0000.0000.0000.000
120A120ALA0-0.054-0.02613.529-1.049-1.0490.0000.0000.0000.000
121A121ALA00.0270.00214.383-1.028-1.0280.0000.0000.0000.000
122A122ALA0-0.0020.01016.618-0.116-0.1160.0000.0000.0000.000
123A123LYS10.8690.94511.55819.76719.7670.0000.0000.0000.000
124A124LEU0-0.076-0.03411.564-1.744-1.7440.0000.0000.0000.000
125A125PRO0-0.0110.00312.9070.7840.7840.0000.0000.0000.000
126A126ILE0-0.028-0.00415.8480.9010.9010.0000.0000.0000.000
127A127LYS11.0151.01118.23311.78711.7870.0000.0000.0000.000
128A128THR00.016-0.00617.3140.0170.0170.0000.0000.0000.000
129A129THR0-0.010-0.01420.7240.7290.7290.0000.0000.0000.000
130A130PHE00.0310.02821.809-0.774-0.7740.0000.0000.0000.000
131A131VAL0-0.023-0.01222.1270.5170.5170.0000.0000.0000.000
132A132THR00.0240.00023.544-0.559-0.5590.0000.0000.0000.000
133A133LYS10.9350.98125.19311.46811.4680.0000.0000.0000.000
134A134THR0-0.039-0.02926.4810.2950.2950.0000.0000.0000.000
135A135VAL0-0.0090.00329.847-0.274-0.2740.0000.0000.0000.000
136A136MET-1-0.894-0.93629.585-8.879-8.8790.0000.0000.0000.000