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: KQG23

Calculation Name: 1VY5-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 3'-deoxy-3'-[(l-methionyl-l-phenylalanyl)amino]adenosine 5'-(dihydrogen phosphate) | 2-methylthio-n6-isopentenyl-adenosine-5'-monophosphate | 7n-methyl-8-hydroguanosine-5'-monophosphate | pseudouridine-5'-monophosphate | 5-methylcytidine-5'-monophosphate | 5-methyluridine 5'-monophosphate | 4-thiouridine-5'-monophosphate | iron/sulfur cluster | magnesium ion | zinc ion | potassium ion

Ligand 3-letter code: 31M | MIA | 7MG | PSU | 5MC | 5MU | 4SU | SF4 | MG | ZN | K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VY5

Chain ID: A

ChEMBL ID:

UniProt ID: P60488

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 174
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1551077.919713
FMO2-HF: Nuclear repulsion 1486332.160359
FMO2-HF: Total energy -64745.759354
FMO2-MP2: Total energy -64939.928798


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.
163.509165.482-0.022-1.052-0.899-0.004
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 : 0.912 / q_NPA : 0.944
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].
3A4ILE00.0880.0523.8761.0553.028-0.022-1.052-0.899-0.004
4A5GLY00.021-0.0016.7202.3272.3270.0000.0000.0000.000
5A6ARG10.9570.9735.97839.18939.1890.0000.0000.0000.000
6A7LEU0-0.0050.0246.7680.2210.2210.0000.0000.0000.000
7A8PRO00.0520.0288.4541.5121.5120.0000.0000.0000.000
8A9ILE0-0.046-0.02312.257-1.174-1.1740.0000.0000.0000.000
9A10PRO00.0440.03014.1560.7900.7900.0000.0000.0000.000
10A11VAL0-0.003-0.01117.1230.0280.0280.0000.0000.0000.000
11A12PRO00.0000.00620.5340.4510.4510.0000.0000.0000.000
12A13LYS10.9861.00223.23411.61311.6130.0000.0000.0000.000
13A14GLY00.001-0.00126.7240.0910.0910.0000.0000.0000.000
14A15VAL0-0.017-0.02523.7060.2230.2230.0000.0000.0000.000
15A16SER0-0.019-0.00326.005-0.070-0.0700.0000.0000.0000.000
16A17VAL0-0.024-0.02821.679-0.124-0.1240.0000.0000.0000.000
17A18GLU-1-0.906-0.94024.947-10.350-10.3500.0000.0000.0000.000
18A19VAL0-0.016-0.02322.978-0.411-0.4110.0000.0000.0000.000
19A20ALA00.0400.02625.6660.4940.4940.0000.0000.0000.000
20A21PRO00.019-0.00126.473-0.500-0.5000.0000.0000.0000.000
21A22GLY00.0110.00825.3230.2600.2600.0000.0000.0000.000
22A23ARG10.8710.92825.10910.62910.6290.0000.0000.0000.000
23A24VAL00.0000.00621.655-0.232-0.2320.0000.0000.0000.000
24A25LYS10.8840.95824.75710.13510.1350.0000.0000.0000.000
25A26VAL0-0.015-0.00722.456-0.315-0.3150.0000.0000.0000.000
26A27LYS10.9090.93425.7669.9399.9390.0000.0000.0000.000
27A28GLY00.0420.01127.880-0.280-0.2800.0000.0000.0000.000
28A29PRO00.0110.00528.4250.2540.2540.0000.0000.0000.000
29A30LYS10.9130.96728.59910.86310.8630.0000.0000.0000.000
30A31GLY00.0210.02031.0180.1590.1590.0000.0000.0000.000
31A32GLU-1-0.870-0.93829.121-10.035-10.0350.0000.0000.0000.000
32A33LEU0-0.013-0.01324.8300.1090.1090.0000.0000.0000.000
33A34GLU-1-0.812-0.88226.848-10.784-10.7840.0000.0000.0000.000
34A35VAL0-0.040-0.02120.431-0.196-0.1960.0000.0000.0000.000
35A36PRO00.0120.01423.2890.0200.0200.0000.0000.0000.000
36A37VAL0-0.032-0.03419.954-0.959-0.9590.0000.0000.0000.000
37A38SER00.0240.00919.9060.8340.8340.0000.0000.0000.000
38A39PRO00.0540.00521.654-0.457-0.4570.0000.0000.0000.000
39A40GLU-1-0.804-0.85820.466-14.881-14.8810.0000.0000.0000.000
40A41MET0-0.109-0.05214.999-0.699-0.6990.0000.0000.0000.000
41A42ARG10.9400.98218.63016.38116.3810.0000.0000.0000.000
42A43VAL0-0.019-0.01418.049-1.287-1.2870.0000.0000.0000.000
43A44VAL00.0090.00318.3500.8290.8290.0000.0000.0000.000
44A45VAL00.0180.00919.211-0.749-0.7490.0000.0000.0000.000
45A46GLU-1-0.804-0.90017.523-17.602-17.6020.0000.0000.0000.000
46A47GLU-1-0.908-0.95421.247-12.211-12.2110.0000.0000.0000.000
47A48GLY0-0.0020.01021.098-0.382-0.3820.0000.0000.0000.000
48A49VAL0-0.028-0.01816.070-0.834-0.8340.0000.0000.0000.000
49A50VAL00.0110.01517.1500.6380.6380.0000.0000.0000.000
50A51ARG10.7550.84813.45617.87317.8730.0000.0000.0000.000
51A52VAL00.0090.00013.6631.0771.0770.0000.0000.0000.000
52A53GLU-1-0.820-0.88313.377-20.540-20.5400.0000.0000.0000.000
53A54ARG10.7580.8338.44129.95029.9500.0000.0000.0000.000
54A55PRO00.0220.02615.520-0.284-0.2840.0000.0000.0000.000
55A56SER00.0540.00916.5030.1630.1630.0000.0000.0000.000
56A57ASP-1-0.773-0.87110.564-29.298-29.2980.0000.0000.0000.000
57A58GLU-1-0.815-0.87212.875-17.393-17.3930.0000.0000.0000.000
58A59ARG10.9550.96212.84119.45019.4500.0000.0000.0000.000
59A60ARG10.9040.93913.94613.97013.9700.0000.0000.0000.000
60A61HIS00.0470.00914.931-1.416-1.4160.0000.0000.0000.000
61A62LYS10.8670.9258.30125.73925.7390.0000.0000.0000.000
62A63SER0-0.036-0.02810.652-2.576-2.5760.0000.0000.0000.000
63A64LEU00.0550.02112.538-0.648-0.6480.0000.0000.0000.000
64A65HIS00.0170.0269.973-2.284-2.2840.0000.0000.0000.000
65A66GLY0-0.059-0.0309.958-1.556-1.5560.0000.0000.0000.000
66A67LEU00.0210.03110.6220.2860.2860.0000.0000.0000.000
67A68THR00.0330.00514.0820.9460.9460.0000.0000.0000.000
68A69ARG10.8940.95310.41526.50926.5090.0000.0000.0000.000
69A70THR0-0.043-0.03811.7210.0560.0560.0000.0000.0000.000
70A71LEU0-0.014-0.01513.8470.8540.8540.0000.0000.0000.000
71A72ILE00.0570.03617.1500.7390.7390.0000.0000.0000.000
72A73ALA00.0040.00014.6060.6170.6170.0000.0000.0000.000
73A74ASN0-0.030-0.02016.2400.4460.4460.0000.0000.0000.000
74A75ALA00.0600.03418.6310.7110.7110.0000.0000.0000.000
75A76VAL00.0030.00519.2320.6630.6630.0000.0000.0000.000
76A77LYS10.8710.94218.74315.19815.1980.0000.0000.0000.000
77A78GLY00.000-0.00121.2840.5650.5650.0000.0000.0000.000
78A79VAL0-0.003-0.00124.0880.5250.5250.0000.0000.0000.000
79A80SER0-0.021-0.01523.4100.3560.3560.0000.0000.0000.000
80A81GLU-1-0.845-0.90821.225-14.342-14.3420.0000.0000.0000.000
81A82GLY0-0.037-0.00724.9920.5560.5560.0000.0000.0000.000
82A83TYR0-0.040-0.04518.977-1.039-1.0390.0000.0000.0000.000
83A84SER00.0490.01625.0820.5610.5610.0000.0000.0000.000
84A85LYS10.8630.94322.68912.39712.3970.0000.0000.0000.000
85A86GLU-1-0.790-0.86927.176-9.662-9.6620.0000.0000.0000.000
86A87LEU0-0.034-0.01729.022-0.384-0.3840.0000.0000.0000.000
87A88LEU00.0220.01031.1770.2350.2350.0000.0000.0000.000
88A89ILE0-0.014-0.00133.947-0.050-0.0500.0000.0000.0000.000
89A90LYS10.8600.91433.5749.0419.0410.0000.0000.0000.000
90A91GLY00.0630.02338.6330.0290.0290.0000.0000.0000.000
91A92ILE00.0210.00642.016-0.002-0.0020.0000.0000.0000.000
92A93GLY00.0250.01745.5580.0510.0510.0000.0000.0000.000
93A94TYR0-0.071-0.03140.5130.1590.1590.0000.0000.0000.000
94A95ARG10.9050.95342.1106.7946.7940.0000.0000.0000.000
95A96ALA00.002-0.00240.0090.0110.0110.0000.0000.0000.000
96A97ARG10.8280.87942.0526.6656.6650.0000.0000.0000.000
97A98LEU00.0070.00839.980-0.124-0.1240.0000.0000.0000.000
98A99VAL0-0.015-0.00843.3310.1810.1810.0000.0000.0000.000
99A100GLY00.0420.02145.6940.0010.0010.0000.0000.0000.000
100A101ARG10.9220.94638.6617.7657.7650.0000.0000.0000.000
101A102ALA00.0420.03640.821-0.232-0.2320.0000.0000.0000.000
102A103LEU0-0.014-0.00236.9600.0470.0470.0000.0000.0000.000
103A104GLU-1-0.809-0.86441.009-6.643-6.6430.0000.0000.0000.000
104A105LEU0-0.012-0.01338.423-0.057-0.0570.0000.0000.0000.000
105A106THR00.0250.01542.4320.2010.2010.0000.0000.0000.000
106A107VAL00.015-0.01040.020-0.072-0.0720.0000.0000.0000.000
107A108GLY00.0470.01643.280-0.070-0.0700.0000.0000.0000.000
108A109PHE0-0.0200.00541.8170.0260.0260.0000.0000.0000.000
109A110SER0-0.004-0.00747.2810.0190.0190.0000.0000.0000.000
110A111HIS0-0.010-0.00845.6520.1310.1310.0000.0000.0000.000
111A112PRO00.0200.02046.542-0.130-0.1300.0000.0000.0000.000
112A113VAL0-0.007-0.00741.2600.0280.0280.0000.0000.0000.000
113A114VAL00.0340.01942.932-0.108-0.1080.0000.0000.0000.000
114A115VAL0-0.028-0.01736.849-0.081-0.0810.0000.0000.0000.000
115A116GLU-1-0.841-0.92440.228-7.321-7.3210.0000.0000.0000.000
116A117PRO0-0.072-0.02136.671-0.232-0.2320.0000.0000.0000.000
117A118PRO00.0090.00633.8000.1570.1570.0000.0000.0000.000
118A119GLU-1-0.860-0.93835.809-8.751-8.7510.0000.0000.0000.000
119A120GLY0-0.014-0.01132.487-0.323-0.3230.0000.0000.0000.000
120A121ILE0-0.091-0.04529.862-0.429-0.4290.0000.0000.0000.000
121A122THR00.0010.00533.4370.3950.3950.0000.0000.0000.000
122A123PHE0-0.026-0.02333.939-0.366-0.3660.0000.0000.0000.000
123A124GLU-1-0.807-0.88633.931-9.147-9.1470.0000.0000.0000.000
124A125VAL0-0.021-0.02236.678-0.173-0.1730.0000.0000.0000.000
125A126PRO0-0.0220.00235.7810.1840.1840.0000.0000.0000.000
126A127GLU-1-0.786-0.86637.671-8.143-8.1430.0000.0000.0000.000
127A128PRO00.0360.00840.062-0.108-0.1080.0000.0000.0000.000
128A129THR00.0370.01138.9400.0220.0220.0000.0000.0000.000
129A130ARG10.7720.87132.8248.8228.8220.0000.0000.0000.000
130A131VAL00.0270.02034.5560.1660.1660.0000.0000.0000.000
131A132ARG10.8320.90928.7539.9469.9460.0000.0000.0000.000
132A133VAL0-0.0150.00630.0780.2710.2710.0000.0000.0000.000
133A134SER00.011-0.03929.551-0.627-0.6270.0000.0000.0000.000
134A135GLY00.0340.00928.9040.3600.3600.0000.0000.0000.000
135A136ILE00.0090.01427.039-0.355-0.3550.0000.0000.0000.000
136A137ASP-1-0.839-0.91525.362-12.661-12.6610.0000.0000.0000.000
137A138LYS10.8770.93016.94717.34917.3490.0000.0000.0000.000
138A139GLN0-0.019-0.00422.366-0.125-0.1250.0000.0000.0000.000
139A140LYS10.9150.96823.81310.42010.4200.0000.0000.0000.000
140A141VAL00.0130.01325.7730.3000.3000.0000.0000.0000.000
141A142GLY0-0.043-0.02524.3290.1800.1800.0000.0000.0000.000
142A143GLN0-0.019-0.01425.305-0.033-0.0330.0000.0000.0000.000
143A144VAL00.0280.01127.7660.3480.3480.0000.0000.0000.000
144A145ALA00.0130.00527.7300.2880.2880.0000.0000.0000.000
145A146ALA0-0.050-0.02327.1780.1620.1620.0000.0000.0000.000
146A147ASN00.0190.00229.2200.0580.0580.0000.0000.0000.000
147A148ILE00.0300.01432.6740.2510.2510.0000.0000.0000.000
148A149ARG10.8200.89828.41510.86210.8620.0000.0000.0000.000
149A150ALA0-0.074-0.03832.8330.0870.0870.0000.0000.0000.000
150A151ILE00.0120.02434.1840.1790.1790.0000.0000.0000.000
151A152ARG10.8550.91836.8427.7017.7010.0000.0000.0000.000
152A153LYS10.9911.00331.1099.6759.6750.0000.0000.0000.000
153A154PRO0-0.040-0.01531.6750.2470.2470.0000.0000.0000.000
154A155SER0-0.0020.01034.935-0.019-0.0190.0000.0000.0000.000
155A156ALA00.0200.00935.588-0.157-0.1570.0000.0000.0000.000
156A157TYR00.0100.00136.612-0.083-0.0830.0000.0000.0000.000
157A158HIS00.006-0.00338.9490.0630.0630.0000.0000.0000.000
158A159GLU-1-0.786-0.87035.755-8.869-8.8690.0000.0000.0000.000
159A160LYS10.9050.94937.8227.4487.4480.0000.0000.0000.000
160A161GLY00.0190.00736.980-0.073-0.0730.0000.0000.0000.000
161A162ILE0-0.034-0.00333.2680.0210.0210.0000.0000.0000.000
162A163TYR00.0340.00430.811-0.132-0.1320.0000.0000.0000.000
163A164TYR0-0.016-0.03026.000-0.082-0.0820.0000.0000.0000.000
164A165ALA00.0260.01427.5740.1090.1090.0000.0000.0000.000
165A166GLY00.0150.00825.056-0.463-0.4630.0000.0000.0000.000
166A167GLU-1-0.850-0.90724.970-11.225-11.2250.0000.0000.0000.000
167A168PRO0-0.037-0.02124.8840.3770.3770.0000.0000.0000.000
168A169VAL00.0070.00327.941-0.034-0.0340.0000.0000.0000.000
169A170ARG10.9170.96324.23511.81411.8140.0000.0000.0000.000
170A171LEU0-0.0220.00031.7970.0780.0780.0000.0000.0000.000
171A172LYS10.9340.97735.4508.3268.3260.0000.0000.0000.000
172A173PRO00.0460.01437.3100.1150.1150.0000.0000.0000.000
173A174GLY0-0.024-0.03740.931-0.101-0.1010.0000.0000.0000.000
174A175LYS00.0450.05243.714-0.352-0.3520.0000.0000.0000.000