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: JK4N9

Calculation Name: 7M4X-J-Other547

Preferred Name:

Target Type:

Ligand Name: eravacycline | n7-methyl-guanosine-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 | 4-thiouridine-5'-monophosphate | 5,6-dihydrouridine-5'-monophosphate | o2'-methyluridine 5'-monophosphate | zinc ion

Ligand 3-letter code: YQM | G7M | 2MG | MA6 | 2MA | 4OC | 6MZ | PSU | 3TD | 5MC | 5MU | OMG | UR3 | 4SU | H2U | OMU | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7M4X

Chain ID: J

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 122
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1001423.012445
FMO2-HF: Nuclear repulsion 953978.551926
FMO2-HF: Total energy -47444.46052
FMO2-MP2: Total energy -47581.903373


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.
75.49888.18811.969-8.192-16.466-0.075
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 : 0.806 / q_NPA : 0.914
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].
3A3GLN00.0810.0353.8531.0762.510-0.018-0.470-0.9460.001
32A32TYR00.002-0.0102.293-4.940-2.2484.008-1.465-5.234-0.012
33A33ALA0-0.0020.0123.9535.6886.0250.000-0.080-0.2570.000
34A34SER0-0.008-0.0342.359-36.945-34.2653.222-3.111-2.792-0.033
35A35VAL00.0230.0103.7826.9467.0330.001-0.019-0.0690.000
62A62VAL0-0.0060.0024.3070.7750.822-0.001-0.007-0.0390.000
65A65THR0-0.039-0.0382.277-14.268-13.4130.689-0.565-0.979-0.004
66A66LYS10.9831.0075.02731.18831.300-0.001-0.005-0.1060.000
67A67PHE0-0.052-0.0282.240-5.267-1.2464.071-2.395-5.697-0.027
68A68GLY00.0190.0204.1206.9777.189-0.001-0.033-0.1780.000
69A69ILE0-0.047-0.0224.169-10.234-10.021-0.001-0.042-0.1690.000
4A4THR00.0430.0166.0191.4531.4530.0000.0000.0000.000
5A5GLU-1-0.888-0.9399.356-21.381-21.3810.0000.0000.0000.000
6A6THR0-0.048-0.0306.859-0.901-0.9010.0000.0000.0000.000
7A7MET0-0.016-0.0039.8071.2681.2680.0000.0000.0000.000
8A8LEU0-0.053-0.0266.558-3.213-3.2130.0000.0000.0000.000
9A9ASP-1-0.823-0.90610.706-19.465-19.4650.0000.0000.0000.000
10A10VAL0-0.054-0.03312.271-1.555-1.5550.0000.0000.0000.000
11A11ALA00.0070.01013.0750.9530.9530.0000.0000.0000.000
12A12ASP-1-0.741-0.85115.020-16.946-16.9460.0000.0000.0000.000
13A13ASN00.002-0.01218.276-0.129-0.1290.0000.0000.0000.000
14A14SER0-0.022-0.03218.9060.7910.7910.0000.0000.0000.000
15A15GLY0-0.011-0.01021.6150.5690.5690.0000.0000.0000.000
16A16ALA00.0050.00118.5220.3250.3250.0000.0000.0000.000
17A17ARG10.8980.94318.59814.59314.5930.0000.0000.0000.000
18A18ARG10.9320.96814.55419.22919.2290.0000.0000.0000.000
19A19VAL0-0.005-0.00412.1971.3401.3400.0000.0000.0000.000
20A20GLN00.003-0.01113.050-0.190-0.1900.0000.0000.0000.000
21A21CYS0-0.059-0.0118.2851.8281.8280.0000.0000.0000.000
22A22ILE00.0340.01511.6930.3710.3710.0000.0000.0000.000
23A23LYS10.9050.94112.38820.77020.7700.0000.0000.0000.000
24A24VAL00.0410.0416.938-0.697-0.6970.0000.0000.0000.000
25A25LEU0-0.025-0.0129.7442.4422.4420.0000.0000.0000.000
26A26GLY00.0390.01211.149-1.377-1.3770.0000.0000.0000.000
27A27GLY00.014-0.00412.963-0.099-0.0990.0000.0000.0000.000
28A28SER00.0060.01013.338-0.731-0.7310.0000.0000.0000.000
29A29HIS00.0270.00712.834-1.091-1.0910.0000.0000.0000.000
30A30ARG10.8270.9387.10130.45530.4550.0000.0000.0000.000
31A31ARG10.9630.9826.11423.45223.4520.0000.0000.0000.000
36A36GLY00.0220.0126.3602.2462.2460.0000.0000.0000.000
37A37ASP-1-0.817-0.8906.393-36.500-36.5000.0000.0000.0000.000
38A38ILE0-0.044-0.0328.8450.3200.3200.0000.0000.0000.000
39A39ILE0-0.005-0.0127.855-1.059-1.0590.0000.0000.0000.000
40A40LYS10.8730.93810.91818.82918.8290.0000.0000.0000.000
41A41VAL00.026-0.00112.078-1.355-1.3550.0000.0000.0000.000
42A42THR0-0.012-0.00414.6631.6051.6050.0000.0000.0000.000
43A43VAL00.0140.01216.766-1.109-1.1090.0000.0000.0000.000
44A44LYS10.9040.96817.60117.91417.9140.0000.0000.0000.000
45A45GLU-1-0.839-0.93419.216-15.358-15.3580.0000.0000.0000.000
46A46ALA00.0290.00220.213-0.708-0.7080.0000.0000.0000.000
47A47ILE0-0.030-0.00322.8780.3820.3820.0000.0000.0000.000
48A48PRO00.022-0.00325.8990.1230.1230.0000.0000.0000.000
49A49ARG10.9170.95429.5649.8109.8100.0000.0000.0000.000
50A50ALA00.0270.04325.1990.0410.0410.0000.0000.0000.000
51A51ARG10.9580.97423.65812.80212.8020.0000.0000.0000.000
52A52VAL0-0.0190.00521.4070.0010.0010.0000.0000.0000.000
53A53LYS10.9110.94824.31811.31211.3120.0000.0000.0000.000
54A54LYS10.9710.97822.70211.93811.9380.0000.0000.0000.000
55A55GLY00.0100.00522.2150.5840.5840.0000.0000.0000.000
56A56ASP-1-0.811-0.88622.124-12.836-12.8360.0000.0000.0000.000
57A57VAL0-0.023-0.02318.846-0.953-0.9530.0000.0000.0000.000
58A58MET0-0.048-0.02117.9600.6830.6830.0000.0000.0000.000
59A59ASN0-0.019-0.00815.527-1.123-1.1230.0000.0000.0000.000
60A60ALA00.0250.01012.0580.8640.8640.0000.0000.0000.000
61A61VAL00.0210.02810.334-0.996-0.9960.0000.0000.0000.000
63A63VAL0-0.005-0.0177.6780.1090.1090.0000.0000.0000.000
64A64ARG10.7870.8767.76325.40625.4060.0000.0000.0000.000
70A70ARG10.8410.9016.87326.81726.8170.0000.0000.0000.000
71A71ARG10.7690.86310.29622.00922.0090.0000.0000.0000.000
72A72PRO00.020-0.01113.6230.1460.1460.0000.0000.0000.000
73A73ASP-1-0.793-0.85716.707-17.388-17.3880.0000.0000.0000.000
74A74GLY00.0100.02015.5100.5560.5560.0000.0000.0000.000
75A75SER0-0.039-0.02615.044-1.308-1.3080.0000.0000.0000.000
76A76VAL0-0.035-0.0489.289-1.648-1.6480.0000.0000.0000.000
77A77ILE00.0160.0259.9051.5631.5630.0000.0000.0000.000
78A78ARG10.9510.9687.85523.04823.0480.0000.0000.0000.000
79A79PHE00.0410.0238.0752.6892.6890.0000.0000.0000.000
80A80ASP-1-0.833-0.9148.976-25.434-25.4340.0000.0000.0000.000
81A81ASP-1-0.880-0.9379.995-26.541-26.5410.0000.0000.0000.000
82A82ASN00.002-0.0075.361-8.840-8.8400.0000.0000.0000.000
83A83ALA00.0240.0197.6563.2563.2560.0000.0000.0000.000
84A84ALA00.001-0.0038.548-2.986-2.9860.0000.0000.0000.000
85A85VAL0-0.0060.01410.6702.0372.0370.0000.0000.0000.000
86A86ILE00.011-0.00413.861-0.754-0.7540.0000.0000.0000.000
87A87LEU0-0.044-0.01514.2000.7670.7670.0000.0000.0000.000
88A88ASN00.0470.01517.9190.1100.1100.0000.0000.0000.000
89A89ASN00.0310.00320.011-1.152-1.1520.0000.0000.0000.000
90A90ASN0-0.001-0.00721.467-0.409-0.4090.0000.0000.0000.000
91A91LYS10.9120.96416.71816.23916.2390.0000.0000.0000.000
92A92ALA00.0920.06218.014-0.666-0.6660.0000.0000.0000.000
93A93PRO00.0280.00117.2750.0800.0800.0000.0000.0000.000
94A94ILE0-0.085-0.03719.3071.0471.0470.0000.0000.0000.000
95A95ALA00.0210.02020.104-0.001-0.0010.0000.0000.0000.000
96A96THR00.001-0.01222.0430.1510.1510.0000.0000.0000.000
97A97ARG10.9600.98122.54512.75012.7500.0000.0000.0000.000
98A98ILE00.0300.01716.278-0.456-0.4560.0000.0000.0000.000
99A99PHE0-0.062-0.03017.3571.0191.0190.0000.0000.0000.000
100A100GLY00.0500.02815.916-1.304-1.3040.0000.0000.0000.000
101A101PRO00.0440.03414.2750.2230.2230.0000.0000.0000.000
102A102VAL0-0.007-0.00812.753-1.739-1.7390.0000.0000.0000.000
103A103THR00.0140.00710.3940.8040.8040.0000.0000.0000.000
104A104ARG10.9080.94012.73417.41717.4170.0000.0000.0000.000
105A105GLU-1-0.776-0.88910.411-24.304-24.3040.0000.0000.0000.000
106A106LEU0-0.025-0.00710.8810.2170.2170.0000.0000.0000.000
107A107ARG10.9070.96314.09915.61215.6120.0000.0000.0000.000
108A108THR00.0150.00416.0770.3400.3400.0000.0000.0000.000
109A109GLU-1-0.824-0.92018.862-14.566-14.5660.0000.0000.0000.000
110A110GLN0-0.053-0.01616.1200.7450.7450.0000.0000.0000.000
111A111PHE0-0.012-0.03613.312-0.247-0.2470.0000.0000.0000.000
112A112MET00.0700.05117.448-0.496-0.4960.0000.0000.0000.000
113A113LYS10.8800.95220.25113.84513.8450.0000.0000.0000.000
114A114ILE0-0.013-0.01814.4320.2780.2780.0000.0000.0000.000
115A115ILE0-0.031-0.02015.9890.1110.1110.0000.0000.0000.000
116A116SER0-0.032-0.02218.8100.5770.5770.0000.0000.0000.000
117A117LEU0-0.037-0.01720.9040.5690.5690.0000.0000.0000.000
118A118ALA0-0.036-0.00417.540-0.008-0.0080.0000.0000.0000.000
119A119PRO0-0.046-0.02018.9050.5050.5050.0000.0000.0000.000
120A120GLU-1-0.896-0.93818.842-14.843-14.8430.0000.0000.0000.000
121A121VAL0-0.038-0.03116.353-1.080-1.0800.0000.0000.0000.000
122A122LEU-1-0.745-0.84012.956-19.891-19.8910.0000.0000.0000.000