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: Q551Y

Calculation Name: 7ACR-5-Other547

Preferred Name:

Target Type:

Ligand Name: 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 | o2'-methylycytidine-5'-monophosphate | o2'-methyluridine 5'-monophosphate | (2s,3r)-2-azanyl-5-carbamimidamido-3-oxidanyl-pentanoic acid | (3s)-3-(methylsulfanyl)-l-aspartic acid

Ligand 3-letter code: G7M | 1MG | 2MG | MA6 | 2MA | 4OC | 6MZ | PSU | 3TD | 5MC | 5MU | OMG | UR3 | OMC | OMU | 4D4 | 0TD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7ACR

Chain ID: 5

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 150
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1313800.004907
FMO2-HF: Nuclear repulsion 1254049.414222
FMO2-HF: Total energy -59750.590685
FMO2-MP2: Total energy -59925.989429


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.
125.038129.2551.746-2.755-3.208-0.022
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 : 0.889 / q_NPA : 0.929
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].
3A13THR0-0.005-0.0092.326-7.996-3.9401.747-2.715-3.088-0.022
4A14ILE00.0110.0134.1330.0170.178-0.001-0.040-0.1200.000
5A15ALA00.0080.0037.390-0.670-0.6700.0000.0000.0000.000
6A16LEU00.005-0.0117.3840.3870.3870.0000.0000.0000.000
7A17ASN00.0020.00111.1840.8870.8870.0000.0000.0000.000
8A18LYS10.9960.98412.16523.61623.6160.0000.0000.0000.000
9A19ARG10.9590.98714.54014.54614.5460.0000.0000.0000.000
10A20ALA00.0480.03217.7160.8600.8600.0000.0000.0000.000
11A21ARG11.0061.00315.66017.28417.2840.0000.0000.0000.000
12A22HIS0-0.070-0.02618.2220.0930.0930.0000.0000.0000.000
13A23GLU-1-0.848-0.93920.867-11.785-11.7850.0000.0000.0000.000
14A24TYR0-0.031-0.00922.0560.7980.7980.0000.0000.0000.000
15A25PHE0-0.017-0.00822.331-0.528-0.5280.0000.0000.0000.000
16A26ILE0-0.038-0.03417.9950.0800.0800.0000.0000.0000.000
17A27GLU-1-0.946-0.96121.279-11.783-11.7830.0000.0000.0000.000
18A28GLU-1-0.861-0.93921.408-13.546-13.5460.0000.0000.0000.000
19A29GLU-1-0.895-0.92716.422-18.855-18.8550.0000.0000.0000.000
20A30PHE00.0230.00717.6550.2800.2800.0000.0000.0000.000
21A31GLU-1-0.815-0.89612.126-23.429-23.4290.0000.0000.0000.000
22A32ALA00.0240.01915.391-0.068-0.0680.0000.0000.0000.000
23A33GLY0-0.010-0.01115.843-1.334-1.3340.0000.0000.0000.000
24A34LEU0-0.008-0.00315.9440.7390.7390.0000.0000.0000.000
25A35ALA00.0030.00218.019-0.284-0.2840.0000.0000.0000.000
26A36LEU0-0.083-0.05617.3150.2290.2290.0000.0000.0000.000
27A37GLN00.0370.03221.4960.4460.4460.0000.0000.0000.000
28A38GLY00.0480.00821.746-0.739-0.7390.0000.0000.0000.000
29A39TRP00.0660.03621.782-0.298-0.2980.0000.0000.0000.000
30A40GLU-1-0.710-0.81719.353-15.152-15.1520.0000.0000.0000.000
31A41VAL00.0510.01316.146-1.205-1.2050.0000.0000.0000.000
32A42LYS10.9820.98315.51614.28414.2840.0000.0000.0000.000
33A43SER0-0.016-0.01715.438-1.050-1.0500.0000.0000.0000.000
34A44LEU0-0.016-0.00312.414-0.830-0.8300.0000.0000.0000.000
35A45ARG10.8130.93410.97622.14222.1420.0000.0000.0000.000
36A46ALA00.016-0.00610.929-1.939-1.9390.0000.0000.0000.000
37A47GLY00.002-0.02113.5161.4511.4510.0000.0000.0000.000
38A48LYS10.9370.97114.71319.69919.6990.0000.0000.0000.000
39A49ALA00.0710.05413.2651.1391.1390.0000.0000.0000.000
40A50ASN0-0.037-0.01214.002-0.763-0.7630.0000.0000.0000.000
41A51ILE00.0240.01513.1690.5820.5820.0000.0000.0000.000
42A52SER0-0.042-0.03516.2690.2290.2290.0000.0000.0000.000
43A53ASP-1-0.875-0.95218.930-12.459-12.4590.0000.0000.0000.000
44A54SER0-0.0250.00217.2840.5400.5400.0000.0000.0000.000
45A55TYR0-0.008-0.00220.260-0.218-0.2180.0000.0000.0000.000
46A56VAL0-0.002-0.00522.272-0.129-0.1290.0000.0000.0000.000
47A57LEU0-0.027-0.01924.3310.3790.3790.0000.0000.0000.000
48A58LEU0-0.001-0.00426.8780.0330.0330.0000.0000.0000.000
49A59ARG10.9160.97229.5939.9719.9710.0000.0000.0000.000
50A60ASP-1-0.847-0.91432.813-8.698-8.6980.0000.0000.0000.000
51A61GLY00.033-0.00231.404-0.067-0.0670.0000.0000.0000.000
52A62GLU-1-0.911-0.96128.691-10.634-10.6340.0000.0000.0000.000
53A63ALA00.0180.01125.1760.0060.0060.0000.0000.0000.000
54A64PHE0-0.039-0.03324.021-0.720-0.7200.0000.0000.0000.000
55A65LEU0-0.0120.00217.913-0.017-0.0170.0000.0000.0000.000
56A66PHE00.001-0.00122.1160.0990.0990.0000.0000.0000.000
57A67GLY00.0450.02922.1490.0180.0180.0000.0000.0000.000
58A68ALA0-0.019-0.03218.381-1.031-1.0310.0000.0000.0000.000
59A69ASN00.0050.02018.9781.2251.2250.0000.0000.0000.000
60A70ILE0-0.064-0.04516.859-1.155-1.1550.0000.0000.0000.000
61A71THR00.0130.00218.5501.0241.0240.0000.0000.0000.000
62A72PRO00.0300.01920.070-0.623-0.6230.0000.0000.0000.000
63A73MET0-0.048-0.01018.4700.1810.1810.0000.0000.0000.000
64A74ALA0-0.042-0.02621.8600.1860.1860.0000.0000.0000.000
65A75VAL00.0740.03725.181-0.082-0.0820.0000.0000.0000.000
66A76ALA00.0120.01728.4220.3430.3430.0000.0000.0000.000
67A77SER0-0.0050.00728.7800.1410.1410.0000.0000.0000.000
68A78THR0-0.024-0.02630.842-0.050-0.0500.0000.0000.0000.000
69A79HIS00.0140.01033.0560.2990.2990.0000.0000.0000.000
70A80VAL0-0.041-0.01429.1700.1090.1090.0000.0000.0000.000
71A81VAL00.0360.01631.229-0.134-0.1340.0000.0000.0000.000
72A82CYS0-0.066-0.03026.531-0.264-0.2640.0000.0000.0000.000
73A83ASP-1-0.784-0.89127.198-11.095-11.0950.0000.0000.0000.000
74A84PRO0-0.037-0.02822.885-0.452-0.4520.0000.0000.0000.000
75A85THR0-0.004-0.02022.553-0.776-0.7760.0000.0000.0000.000
76A86ARG10.8530.93022.38613.43313.4330.0000.0000.0000.000
77A87THR00.0110.00123.750-0.460-0.4600.0000.0000.0000.000
78A88ARG10.7500.87819.56314.71214.7120.0000.0000.0000.000
79A89LYS10.9160.97222.53410.96410.9640.0000.0000.0000.000
80A90LEU00.0120.00320.076-0.776-0.7760.0000.0000.0000.000
81A91LEU0-0.023-0.00720.3600.6040.6040.0000.0000.0000.000
82A92LEU00.0250.00120.405-0.962-0.9620.0000.0000.0000.000
83A93ASN00.0030.00222.2320.0800.0800.0000.0000.0000.000
84A94GLN00.1030.04024.817-0.310-0.3100.0000.0000.0000.000
85A95ARG10.9090.94127.15910.97110.9710.0000.0000.0000.000
86A96GLU-1-0.864-0.92323.102-12.302-12.3020.0000.0000.0000.000
87A97LEU0-0.052-0.02325.544-0.185-0.1850.0000.0000.0000.000
88A98ASP-1-0.832-0.90926.791-9.950-9.9500.0000.0000.0000.000
89A99SER0-0.043-0.03225.9720.2550.2550.0000.0000.0000.000
90A100LEU0-0.085-0.03823.2450.0080.0080.0000.0000.0000.000
91A101TYR00.0030.00927.5600.1630.1630.0000.0000.0000.000
92A102GLY00.0240.02730.9260.3160.3160.0000.0000.0000.000
93A103ARG10.8350.92125.99211.59711.5970.0000.0000.0000.000
94A104VAL00.0100.00328.543-0.371-0.3710.0000.0000.0000.000
95A105ASN00.0250.00930.203-0.067-0.0670.0000.0000.0000.000
96A106ARG10.9420.97533.1649.6679.6670.0000.0000.0000.000
97A107GLU-1-0.828-0.92434.299-9.114-9.1140.0000.0000.0000.000
98A108GLY0-0.016-0.01732.2400.0760.0760.0000.0000.0000.000
99A109TYR0-0.075-0.01427.734-0.137-0.1370.0000.0000.0000.000
100A110THR00.0240.01324.3140.0640.0640.0000.0000.0000.000
101A111VAL00.0080.00621.210-0.193-0.1930.0000.0000.0000.000
102A112VAL00.0110.01519.1410.0790.0790.0000.0000.0000.000
103A113ALA00.0250.01215.893-0.557-0.5570.0000.0000.0000.000
104A114LEU00.0270.02113.462-0.338-0.3380.0000.0000.0000.000
105A115SER0-0.061-0.0578.813-2.230-2.2300.0000.0000.0000.000
106A116LEU00.0300.0389.7511.6991.6990.0000.0000.0000.000
107A117TYR0-0.081-0.0616.056-5.281-5.2810.0000.0000.0000.000
108A118TRP00.0010.0046.9435.7005.7000.0000.0000.0000.000
109A119LYS10.9830.9917.23217.90117.9010.0000.0000.0000.000
110A120ASN0-0.002-0.0169.3430.5620.5620.0000.0000.0000.000
111A121ALA0-0.009-0.00710.4531.6491.6490.0000.0000.0000.000
112A122TRP00.0640.04412.2460.7590.7590.0000.0000.0000.000
113A123CYS0-0.036-0.01111.876-1.805-1.8050.0000.0000.0000.000
114A124LYS10.8270.91111.07122.17022.1700.0000.0000.0000.000
115A125VAL00.0270.00611.175-2.233-2.2330.0000.0000.0000.000
116A126LYS10.8400.91911.59622.05322.0530.0000.0000.0000.000
117A127ILE0-0.006-0.00313.4260.1290.1290.0000.0000.0000.000
118A128GLY00.0350.01317.100-0.305-0.3050.0000.0000.0000.000
119A129VAL00.0150.00418.9630.3410.3410.0000.0000.0000.000
120A130ALA00.0150.00121.757-0.296-0.2960.0000.0000.0000.000
121A131LYS10.9130.95823.88110.22010.2200.0000.0000.0000.000
122A132GLY00.0260.01926.255-0.309-0.3090.0000.0000.0000.000
123A133LYS10.7870.90023.39413.29313.2930.0000.0000.0000.000
124A134LYS10.9480.97329.1829.5059.5050.0000.0000.0000.000
125A135GLN0-0.021-0.00230.6110.1470.1470.0000.0000.0000.000
126A136HIS00.013-0.00331.7330.0890.0890.0000.0000.0000.000
127A137ASP-1-0.787-0.89929.553-10.011-10.0110.0000.0000.0000.000
128A138LYS10.8300.90325.80711.51411.5140.0000.0000.0000.000
129A139ARG10.9770.98328.5878.7698.7690.0000.0000.0000.000
130A140SER00.0390.02931.0520.2000.2000.0000.0000.0000.000
131A141ASP-1-0.836-0.91925.608-12.164-12.1640.0000.0000.0000.000
132A142ILE0-0.094-0.04826.405-0.391-0.3910.0000.0000.0000.000
133A143LYS11.0251.02028.0188.8058.8050.0000.0000.0000.000
134A144GLU-1-0.885-0.94628.995-9.720-9.7200.0000.0000.0000.000
135A145ARG10.8740.93822.90113.21513.2150.0000.0000.0000.000
136A146GLU-1-0.946-0.96026.783-10.065-10.0650.0000.0000.0000.000
137A147TRP00.0560.01729.3350.0470.0470.0000.0000.0000.000
138A148GLN0-0.017-0.01628.2320.2280.2280.0000.0000.0000.000
139A149VAL0-0.033-0.00725.8520.0040.0040.0000.0000.0000.000
140A150ASP-1-0.808-0.89428.896-9.799-9.7990.0000.0000.0000.000
141A151LYS10.9520.98532.4469.4889.4880.0000.0000.0000.000
142A152ALA0-0.026-0.01930.0550.2180.2180.0000.0000.0000.000
143A153ARG10.8510.90829.23010.38310.3830.0000.0000.0000.000
144A154ILE00.013-0.00333.0280.1980.1980.0000.0000.0000.000
145A155MET0-0.0370.00834.2950.2760.2760.0000.0000.0000.000
146A156LYS10.9820.97931.7099.6559.6550.0000.0000.0000.000
147A157ASN0-0.073-0.03535.5130.2430.2430.0000.0000.0000.000
148A158ALA00.0230.02238.0420.1820.1820.0000.0000.0000.000
149A159HIS0-0.046-0.05038.1640.2370.2370.0000.0000.0000.000
150A160ARG0-0.0260.01937.373-0.983-0.9830.0000.0000.0000.000