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: Z97RN

Calculation Name: 7OSM-A-Xray547

Preferred Name:

Target Type:

Ligand Name: wybutosine | guanosine-5'-triphosphate | {3-[4-(2-amino-2-carboxy-ethyl)-1h-imidazol-2-yl]-1-carbamoyl-propyl}-trimethyl-ammonium | magnesium ion | zinc ion

Ligand 3-letter code: YG | GTP | DDE | MG | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7OSM

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

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 127
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -911658.890938
FMO2-HF: Nuclear repulsion 864780.966697
FMO2-HF: Total energy -46877.924242
FMO2-MP2: Total energy -47014.978762


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:11:SER)


Summations of interaction energy for fragment #1(A:11: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.
107.705109.198-0.023-0.677-0.7930
Interaction energy analysis for fragmet #1(A:11:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.863 / q_NPA : 0.921
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].
3A13VAL00.0710.0503.8540.9832.476-0.023-0.677-0.7930.000
4A14PHE0-0.020-0.0246.965-0.083-0.0830.0000.0000.0000.000
5A15GLY00.1290.07210.2760.5600.5600.0000.0000.0000.000
6A16VAL0-0.047-0.02913.978-0.318-0.3180.0000.0000.0000.000
7A17ALA00.0350.00717.2390.8100.8100.0000.0000.0000.000
8A18ARG10.8810.95119.66314.81714.8170.0000.0000.0000.000
9A19ILE00.0190.04522.9340.4670.4670.0000.0000.0000.000
10A20TYR0-0.009-0.01024.9030.3770.3770.0000.0000.0000.000
11A21ALA00.0190.02328.6660.1860.1860.0000.0000.0000.000
12A22SER0-0.028-0.02630.3490.2470.2470.0000.0000.0000.000
13A23PHE00.0530.00934.066-0.054-0.0540.0000.0000.0000.000
14A24ASN0-0.021-0.01437.125-0.014-0.0140.0000.0000.0000.000
15A25ASP-1-0.741-0.86033.518-9.622-9.6220.0000.0000.0000.000
16A26THR0-0.113-0.06329.626-0.030-0.0300.0000.0000.0000.000
17A27PHE00.0120.00228.111-0.152-0.1520.0000.0000.0000.000
18A28VAL00.0230.01322.354-0.179-0.1790.0000.0000.0000.000
19A29HIS0-0.005-0.00123.1640.1630.1630.0000.0000.0000.000
20A30VAL00.0230.01416.510-0.169-0.1690.0000.0000.0000.000
21A31THR0-0.054-0.03819.1960.3620.3620.0000.0000.0000.000
22A32ASP-1-0.718-0.86515.540-19.070-19.0700.0000.0000.0000.000
23A33LEU0-0.056-0.02014.1270.6750.6750.0000.0000.0000.000
24A34SER0-0.051-0.01516.7430.9730.9730.0000.0000.0000.000
25A35GLY0-0.051-0.03419.3620.6150.6150.0000.0000.0000.000
26A36LYS10.9250.96121.02512.08012.0800.0000.0000.0000.000
27A37GLU-1-0.914-0.93818.573-14.715-14.7150.0000.0000.0000.000
28A38THR0-0.029-0.05720.296-0.882-0.8820.0000.0000.0000.000
29A39ILE00.0230.01717.6830.4050.4050.0000.0000.0000.000
30A40ALA0-0.034-0.02421.108-0.035-0.0350.0000.0000.0000.000
31A41ARG10.8980.95523.31710.69310.6930.0000.0000.0000.000
32A42VAL00.0930.05624.709-0.201-0.2010.0000.0000.0000.000
33A43THR0-0.054-0.03327.221-0.123-0.1230.0000.0000.0000.000
34A44GLY00.0630.03130.088-0.166-0.1660.0000.0000.0000.000
35A45GLY00.0470.02132.1850.0700.0700.0000.0000.0000.000
36A46MET0-0.118-0.05029.5070.2150.2150.0000.0000.0000.000
37A47LYS00.0000.00228.4200.2070.2070.0000.0000.0000.000
38A48VAL0-0.044-0.00632.4350.0990.0990.0000.0000.0000.000
39A49LYS10.9540.96935.8658.6798.6790.0000.0000.0000.000
40A50ALA00.0270.00339.2420.1290.1290.0000.0000.0000.000
41A51ASP-1-0.850-0.89940.978-7.379-7.3790.0000.0000.0000.000
42A52ARG10.8080.88441.6297.2667.2660.0000.0000.0000.000
43A53ASP-1-0.839-0.91439.015-7.972-7.9720.0000.0000.0000.000
44A54GLU-1-0.916-0.94736.493-8.657-8.6570.0000.0000.0000.000
45A55SER0-0.053-0.02734.149-0.262-0.2620.0000.0000.0000.000
46A56SER00.002-0.01234.317-0.145-0.1450.0000.0000.0000.000
47A57PRO0-0.019-0.03231.800-0.249-0.2490.0000.0000.0000.000
48A58TYR00.0100.01230.894-0.434-0.4340.0000.0000.0000.000
49A59ALA00.0930.04631.419-0.264-0.2640.0000.0000.0000.000
50A60ALA0-0.0140.00728.699-0.292-0.2920.0000.0000.0000.000
51A61MET0-0.047-0.03626.466-0.452-0.4520.0000.0000.0000.000
52A62LEU00.0150.02026.500-0.485-0.4850.0000.0000.0000.000
53A63ALA00.0380.01827.561-0.228-0.2280.0000.0000.0000.000
54A64ALA0-0.044-0.03822.812-0.454-0.4540.0000.0000.0000.000
55A65GLN0-0.011-0.00922.343-0.577-0.5770.0000.0000.0000.000
56A66ASP-1-0.915-0.94822.992-12.753-12.7530.0000.0000.0000.000
57A67VAL00.0100.00120.156-0.490-0.4900.0000.0000.0000.000
58A68ALA0-0.038-0.02318.522-0.879-0.8790.0000.0000.0000.000
59A69ALA0-0.0080.00018.266-0.958-0.9580.0000.0000.0000.000
60A70LYS10.8370.91619.35813.27913.2790.0000.0000.0000.000
61A71CYS0-0.060-0.01713.627-0.697-0.6970.0000.0000.0000.000
62A72LYS10.9010.93812.25820.91620.9160.0000.0000.0000.000
63A73GLU-1-0.796-0.88715.680-13.559-13.5590.0000.0000.0000.000
64A74VAL00.0300.00414.4080.3460.3460.0000.0000.0000.000
65A75GLY0-0.059-0.01112.398-0.777-0.7770.0000.0000.0000.000
66A76ILE00.0240.01610.390-2.658-2.6580.0000.0000.0000.000
67A77THR0-0.008-0.0077.1230.7720.7720.0000.0000.0000.000
68A78ALA00.0210.0199.1510.8610.8610.0000.0000.0000.000
69A79VAL0-0.031-0.01210.9820.7320.7320.0000.0000.0000.000
70A80HIS0-0.017-0.00211.4770.5080.5080.0000.0000.0000.000
71A81VAL00.0070.00015.2570.8650.8650.0000.0000.0000.000
72A82LYS10.8460.90518.92315.14015.1400.0000.0000.0000.000
73A83ILE00.0190.01722.2320.1980.1980.0000.0000.0000.000
74A84ARG10.9010.96825.31410.53510.5350.0000.0000.0000.000
75A85ALA00.0680.03528.8220.0520.0520.0000.0000.0000.000
76A86THR0-0.013-0.02132.310-0.058-0.0580.0000.0000.0000.000
77A87GLY0-0.0160.00034.936-0.003-0.0030.0000.0000.0000.000
78A88GLY00.0400.00835.8220.2710.2710.0000.0000.0000.000
79A89THR00.024-0.01037.8540.0670.0670.0000.0000.0000.000
80A90ARG10.8800.94939.6507.8967.8960.0000.0000.0000.000
81A91THR00.017-0.00138.2640.2080.2080.0000.0000.0000.000
82A92LYS10.9230.96335.8347.9567.9560.0000.0000.0000.000
83A93THR00.0730.05834.773-0.063-0.0630.0000.0000.0000.000
84A94PRO00.002-0.01530.4390.0810.0810.0000.0000.0000.000
85A95GLY00.0290.03832.5530.2350.2350.0000.0000.0000.000
86A96PRO00.005-0.00431.999-0.331-0.3310.0000.0000.0000.000
87A97GLY00.0420.01530.937-0.201-0.2010.0000.0000.0000.000
88A98GLY00.036-0.00427.819-0.424-0.4240.0000.0000.0000.000
89A99GLN0-0.025-0.02226.212-0.324-0.3240.0000.0000.0000.000
90A100ALA0-0.030-0.00226.452-0.242-0.2420.0000.0000.0000.000
91A101ALA00.0710.02624.995-0.365-0.3650.0000.0000.0000.000
92A102LEU00.0090.00720.642-0.565-0.5650.0000.0000.0000.000
93A103ARG10.9510.96421.05111.11411.1140.0000.0000.0000.000
94A104ALA0-0.0080.01722.344-0.287-0.2870.0000.0000.0000.000
95A105LEU00.0390.01317.642-0.380-0.3800.0000.0000.0000.000
96A106ALA0-0.019-0.00117.319-0.870-0.8700.0000.0000.0000.000
97A107ARG10.9250.95917.89011.98211.9820.0000.0000.0000.000
98A108SER0-0.020-0.00319.2340.3200.3200.0000.0000.0000.000
99A109GLY00.0250.02015.890-0.424-0.4240.0000.0000.0000.000
100A110LEU0-0.0120.01913.409-2.233-2.2330.0000.0000.0000.000
101A111ARG10.8250.9038.48030.99130.9910.0000.0000.0000.000
102A112ILE00.019-0.00412.057-0.677-0.6770.0000.0000.0000.000
103A113GLY00.014-0.00613.064-0.863-0.8630.0000.0000.0000.000
104A114ARG10.9110.95214.26019.54119.5410.0000.0000.0000.000
105A115ILE00.0390.02616.7120.1210.1210.0000.0000.0000.000
106A116GLU-1-0.844-0.91619.985-13.498-13.4980.0000.0000.0000.000
107A117ASP-1-0.838-0.89222.968-10.833-10.8330.0000.0000.0000.000
108A118VAL00.010-0.00324.4630.0500.0500.0000.0000.0000.000
109A119THR0-0.054-0.06227.6500.3340.3340.0000.0000.0000.000
110A120PRO0-0.054-0.00331.1740.1220.1220.0000.0000.0000.000
111A121VAL00.0480.00833.2700.2580.2580.0000.0000.0000.000
112A122PRO0-0.047-0.01436.078-0.041-0.0410.0000.0000.0000.000
113A123SER00.0340.01039.076-0.024-0.0240.0000.0000.0000.000
114A124ASP-1-0.897-0.94041.048-7.118-7.1180.0000.0000.0000.000
115A125SER0-0.027-0.02242.6250.1150.1150.0000.0000.0000.000
116A126THR0-0.022-0.00942.530-0.027-0.0270.0000.0000.0000.000
117A127ARG11.0071.00745.3265.9955.9950.0000.0000.0000.000
118A128LYS10.9110.96343.8137.2357.2350.0000.0000.0000.000
119A129LYS10.9750.98746.6536.5126.5120.0000.0000.0000.000
120A130GLY00.018-0.00948.216-0.092-0.0920.0000.0000.0000.000
121A131GLY00.0150.01750.9280.1190.1190.0000.0000.0000.000
122A132ARG10.9670.96753.6605.4345.4340.0000.0000.0000.000
123A133ARG11.0041.00156.0045.3065.3060.0000.0000.0000.000
124A134GLY00.0480.04252.527-0.003-0.0030.0000.0000.0000.000
125A135ARG10.9180.94848.4396.6826.6820.0000.0000.0000.000
126A136ARG10.8830.94552.6805.6625.6620.0000.0000.0000.000
127A137LEU-1-0.864-0.91550.778-5.804-5.8040.0000.0000.0000.000