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: 1V6QZ

Calculation Name: 7OTC-N-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: N

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 120
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -994222.624146
FMO2-HF: Nuclear repulsion 946025.821197
FMO2-HF: Total energy -48196.80295
FMO2-MP2: Total energy -48336.585868


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.
209.776216.1221.195-3.223-4.317-0.022
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 : 0.920 / q_NPA : 0.954
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].
3A3HIS00.1300.0642.866-2.8333.4891.196-3.218-4.299-0.022
4A4ARG10.9910.9894.76223.04023.064-0.001-0.005-0.0180.000
5A5LYS10.9881.0205.75646.34846.3480.0000.0000.0000.000
6A6SER00.0260.0079.0310.0140.0140.0000.0000.0000.000
7A7GLY0-0.0070.01012.3190.4050.4050.0000.0000.0000.000
8A8ARG10.8710.94312.25017.18417.1840.0000.0000.0000.000
9A9GLN00.0470.0169.7652.7342.7340.0000.0000.0000.000
10A10LEU0-0.016-0.01913.1581.2941.2940.0000.0000.0000.000
11A11ASN00.0420.03514.1200.1760.1760.0000.0000.0000.000
12A12ARG10.9070.96415.30816.24616.2460.0000.0000.0000.000
13A13ASN00.1140.06015.501-1.384-1.3840.0000.0000.0000.000
14A14SER00.023-0.00717.5990.2460.2460.0000.0000.0000.000
15A15SER00.0790.04118.7250.0720.0720.0000.0000.0000.000
16A16HIS00.1020.05220.8290.6800.6800.0000.0000.0000.000
17A17ARG10.8290.90614.77820.14920.1490.0000.0000.0000.000
18A18GLN0-0.018-0.00420.4960.9160.9160.0000.0000.0000.000
19A19ALA00.0480.02823.1870.4300.4300.0000.0000.0000.000
20A20MET0-0.0010.00320.4220.3800.3800.0000.0000.0000.000
21A21PHE0-0.013-0.03318.5670.0410.0410.0000.0000.0000.000
22A22ARG10.9270.97524.64311.42411.4240.0000.0000.0000.000
23A23ASN00.0260.01427.9260.5120.5120.0000.0000.0000.000
24A24MET0-0.070-0.03523.1970.1660.1660.0000.0000.0000.000
25A25ALA00.0110.01027.8900.2260.2260.0000.0000.0000.000
26A26GLY00.0660.03829.5850.2760.2760.0000.0000.0000.000
27A27SER00.007-0.00131.7760.3950.3950.0000.0000.0000.000
28A28LEU0-0.040-0.02129.6650.1510.1510.0000.0000.0000.000
29A29VAL00.0140.01132.8930.1640.1640.0000.0000.0000.000
30A30ARG10.8090.88535.2778.6908.6900.0000.0000.0000.000
31A31HIS0-0.010-0.01535.4000.3730.3730.0000.0000.0000.000
32A32GLU-1-0.766-0.85235.817-7.990-7.9900.0000.0000.0000.000
33A33ILE0-0.010-0.01433.848-0.260-0.2600.0000.0000.0000.000
34A34ILE0-0.015-0.00128.899-0.009-0.0090.0000.0000.0000.000
35A35LYS10.9290.96230.4459.4519.4510.0000.0000.0000.000
36A36THR0-0.013-0.01325.315-0.228-0.2280.0000.0000.0000.000
37A37THR00.0400.01422.408-0.072-0.0720.0000.0000.0000.000
38A38LEU00.0430.01321.276-0.396-0.3960.0000.0000.0000.000
39A39PRO0-0.025-0.03517.283-0.275-0.2750.0000.0000.0000.000
40A40LYS10.9190.96319.24812.98812.9880.0000.0000.0000.000
41A41ALA00.0750.05121.3680.0200.0200.0000.0000.0000.000
42A42LYS10.9290.95318.69114.49214.4920.0000.0000.0000.000
43A43GLU-1-0.823-0.90416.790-19.007-19.0070.0000.0000.0000.000
44A44LEU00.0440.02220.067-0.026-0.0260.0000.0000.0000.000
45A45ARG10.9390.97820.68513.98313.9830.0000.0000.0000.000
46A46ARG10.8740.92216.85717.71017.7100.0000.0000.0000.000
47A47VAL0-0.045-0.01622.559-0.101-0.1010.0000.0000.0000.000
48A48VAL00.0600.01525.0380.3020.3020.0000.0000.0000.000
49A49GLU-1-0.783-0.86526.737-10.970-10.9700.0000.0000.0000.000
50A50PRO0-0.045-0.01625.0090.3610.3610.0000.0000.0000.000
51A51LEU0-0.028-0.00328.3030.2530.2530.0000.0000.0000.000
52A52ILE00.0460.02330.9840.2750.2750.0000.0000.0000.000
53A53THR0-0.033-0.02930.3670.2660.2660.0000.0000.0000.000
54A54LEU0-0.086-0.03831.9280.1540.1540.0000.0000.0000.000
55A55ALA00.0280.01033.6550.2200.2200.0000.0000.0000.000
56A56LYS10.8210.93434.7329.0919.0910.0000.0000.0000.000
57A57THR0-0.015-0.00537.4280.2510.2510.0000.0000.0000.000
58A58ASP-1-0.798-0.88339.289-7.705-7.7050.0000.0000.0000.000
59A59SER00.0860.03539.7150.0700.0700.0000.0000.0000.000
60A60VAL00.0400.01240.938-0.183-0.1830.0000.0000.0000.000
61A61ALA00.0060.00638.242-0.130-0.1300.0000.0000.0000.000
62A62ASN00.0150.00136.269-0.363-0.3630.0000.0000.0000.000
63A63ARG10.8860.94636.3067.3167.3160.0000.0000.0000.000
64A64ARG10.9770.99237.7427.5617.5610.0000.0000.0000.000
65A65LEU0-0.0020.01130.850-0.279-0.2790.0000.0000.0000.000
66A66ALA00.0210.00532.651-0.404-0.4040.0000.0000.0000.000
67A67PHE00.0330.02633.338-0.287-0.2870.0000.0000.0000.000
68A68ALA0-0.015-0.01231.915-0.152-0.1520.0000.0000.0000.000
69A69ARG10.9020.95227.58410.86010.8600.0000.0000.0000.000
70A70THR0-0.036-0.02029.385-0.435-0.4350.0000.0000.0000.000
71A71ARG10.8560.92132.0019.1359.1350.0000.0000.0000.000
72A72ASP-1-0.784-0.88234.456-8.355-8.3550.0000.0000.0000.000
73A73ASN00.038-0.00536.871-0.120-0.1200.0000.0000.0000.000
74A74GLU-1-0.806-0.86140.059-7.925-7.9250.0000.0000.0000.000
75A75ILE0-0.0020.01234.624-0.048-0.0480.0000.0000.0000.000
76A76VAL0-0.027-0.02236.245-0.067-0.0670.0000.0000.0000.000
77A77ALA0-0.009-0.00438.3780.0480.0480.0000.0000.0000.000
78A78LYS10.8880.94239.2328.0848.0840.0000.0000.0000.000
79A79LEU0-0.063-0.03834.167-0.036-0.0360.0000.0000.0000.000
80A80PHE0-0.022-0.03136.716-0.132-0.1320.0000.0000.0000.000
81A81ASN00.0040.00140.4970.0510.0510.0000.0000.0000.000
82A82GLU-1-0.859-0.92441.850-7.323-7.3230.0000.0000.0000.000
83A83LEU0-0.056-0.03235.819-0.088-0.0880.0000.0000.0000.000
84A84GLY00.0190.00938.175-0.095-0.0950.0000.0000.0000.000
85A85PRO0-0.019-0.01839.140-0.030-0.0300.0000.0000.0000.000
86A86ARG10.7920.88839.2177.9587.9580.0000.0000.0000.000
87A87PHE00.006-0.01735.891-0.166-0.1660.0000.0000.0000.000
88A88ALA00.0460.02937.458-0.201-0.2010.0000.0000.0000.000
89A89SER0-0.005-0.01338.863-0.169-0.1690.0000.0000.0000.000
90A90ARG10.9240.98434.0778.7378.7370.0000.0000.0000.000
91A91ALA00.002-0.00232.824-0.096-0.0960.0000.0000.0000.000
92A92GLY00.0000.00829.591-0.291-0.2910.0000.0000.0000.000
93A93GLY0-0.007-0.00828.8640.2270.2270.0000.0000.0000.000
94A94TYR0-0.008-0.01929.7980.3290.3290.0000.0000.0000.000
95A95THR0-0.075-0.05027.9250.0420.0420.0000.0000.0000.000
96A96ARG10.8540.92729.7608.8998.8990.0000.0000.0000.000
97A97ILE0-0.075-0.04524.242-0.191-0.1910.0000.0000.0000.000
98A98LEU00.0470.02628.183-0.117-0.1170.0000.0000.0000.000
99A99LYS10.9050.94424.23511.75511.7550.0000.0000.0000.000
100A100CYS0-0.0420.01128.1960.2040.2040.0000.0000.0000.000
101A101GLY00.0730.04929.8220.1420.1420.0000.0000.0000.000
102A102PHE00.006-0.00624.580-0.545-0.5450.0000.0000.0000.000
103A103ARG10.8090.86624.99712.13912.1390.0000.0000.0000.000
104A104ALA00.0630.01928.971-0.246-0.2460.0000.0000.0000.000
105A105GLY00.0310.03030.3540.0900.0900.0000.0000.0000.000
106A106ASP-1-0.863-0.90224.805-12.154-12.1540.0000.0000.0000.000
107A107ASN00.0340.02125.054-0.109-0.1090.0000.0000.0000.000
108A108ALA00.0200.01023.136-0.465-0.4650.0000.0000.0000.000
109A109PRO00.008-0.00421.4390.4740.4740.0000.0000.0000.000
110A110MET0-0.0390.00124.040-0.558-0.5580.0000.0000.0000.000
111A111ALA0-0.031-0.04425.969-0.055-0.0550.0000.0000.0000.000
112A112TYR00.1090.04727.776-0.056-0.0560.0000.0000.0000.000
113A113ILE0-0.092-0.05326.284-0.398-0.3980.0000.0000.0000.000
114A114GLU-1-0.770-0.86929.832-8.751-8.7510.0000.0000.0000.000
115A115LEU00.0450.02231.978-0.412-0.4120.0000.0000.0000.000
116A116VAL0-0.084-0.05332.5330.1620.1620.0000.0000.0000.000
117A117ASP-1-0.827-0.92035.095-8.213-8.2130.0000.0000.0000.000
118A118ARG10.8740.96337.1498.3978.3970.0000.0000.0000.000
119A119SER0-0.073-0.03439.703-0.040-0.0400.0000.0000.0000.000
120A120GLU-2-1.756-1.86342.456-14.512-14.5120.0000.0000.0000.000