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: MZ97Z

Calculation Name: 7S1K-N-Other547

Preferred Name:

Target Type:

Ligand Name: radezolid | n7-methyl-guanosine-5'-monophosphate | 1n-methylguanosine-5'-monophosphate | 5'-o-(dihydroxyphosphanyl)-2,8-dimethyladenosine | 2n-methylguanosine-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 | 5,6-dihydrouridine-5'-monophosphate | o2'-methylycytidine-5'-monophosphate | o2'-methyluridine 5'-monophosphate | (2s,3r)-2-azanyl-5-carbamimidamido-3-oxidanyl-pentanoic acid

Ligand 3-letter code: RD8 | G7M | 1MG | 8AH | 2MG | 6MZ | PSU | 3TD | 5MC | 5MU | OMG | H2U | OMC | OMU | 4D4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7S1K

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 177
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1801128.649522
FMO2-HF: Nuclear repulsion 1731059.225167
FMO2-HF: Total energy -70069.424355
FMO2-MP2: Total energy -70274.055391


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:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-167.488-166.03127.204-16.444-12.219-0.185
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.765 / q_NPA : 0.861
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].
3A4LEU00.0060.0063.4619.85511.997-0.007-0.983-1.151-0.001
4A5HIS0-0.0080.0024.34412.01612.290-0.001-0.067-0.2070.000
93A94GLU-1-0.808-0.9184.738-47.876-47.808-0.001-0.009-0.0570.000
96A97TRP00.0450.0143.4220.1850.4310.003-0.061-0.1890.000
97A98GLU-1-0.823-0.9021.716-125.303-126.20912.937-7.090-4.942-0.083
98A99PHE0-0.049-0.0263.7966.6736.7270.003-0.001-0.0570.000
100A101GLU-1-0.759-0.8831.846-123.490-123.96614.271-8.230-5.565-0.101
101A102ARG10.8230.9355.12742.48242.537-0.001-0.003-0.0510.000
5A6ASP-1-0.917-0.9535.442-38.114-38.1140.0000.0000.0000.000
6A7TYR00.0470.0107.4663.5663.5660.0000.0000.0000.000
7A8TYR0-0.047-0.0388.9133.7093.7090.0000.0000.0000.000
8A9LYS10.8660.9278.29933.72533.7250.0000.0000.0000.000
9A10ASP-1-0.877-0.91710.581-24.610-24.6100.0000.0000.0000.000
10A11GLU-1-0.951-1.00613.105-21.208-21.2080.0000.0000.0000.000
11A12VAL0-0.0410.00411.8171.5491.5490.0000.0000.0000.000
12A13VAL00.0100.00014.7081.4871.4870.0000.0000.0000.000
13A14LYS10.9150.94816.88318.95618.9560.0000.0000.0000.000
14A15LYS10.9340.96816.41218.22018.2200.0000.0000.0000.000
15A16LEU00.0310.01617.5190.5060.5060.0000.0000.0000.000
16A17MET0-0.066-0.01820.6520.5990.5990.0000.0000.0000.000
17A18THR0-0.038-0.02622.6920.5020.5020.0000.0000.0000.000
18A19GLU-1-0.999-0.99022.363-13.257-13.2570.0000.0000.0000.000
19A20PHE00.008-0.00521.7860.3260.3260.0000.0000.0000.000
20A21ASN0-0.073-0.02525.8980.2260.2260.0000.0000.0000.000
21A22TYR00.0500.02421.7710.1270.1270.0000.0000.0000.000
22A23ASN00.0060.00527.027-0.033-0.0330.0000.0000.0000.000
23A24SER0-0.020-0.01324.445-0.104-0.1040.0000.0000.0000.000
24A25VAL00.0710.01920.583-0.312-0.3120.0000.0000.0000.000
25A26MET0-0.041-0.01019.412-0.434-0.4340.0000.0000.0000.000
26A27GLN00.000-0.01319.788-0.371-0.3710.0000.0000.0000.000
27A28VAL00.0280.03517.4790.2060.2060.0000.0000.0000.000
28A29PRO0-0.008-0.00518.230-0.708-0.7080.0000.0000.0000.000
29A30ARG10.9360.98013.41117.53817.5380.0000.0000.0000.000
30A31VAL00.0450.02310.2101.3541.3540.0000.0000.0000.000
31A32GLU-1-0.834-0.90913.136-17.307-17.3070.0000.0000.0000.000
32A33LYS10.8080.87213.23716.00316.0030.0000.0000.0000.000
33A34ILE00.0370.0409.4900.5120.5120.0000.0000.0000.000
34A35THR0-0.108-0.05813.3430.2170.2170.0000.0000.0000.000
35A36LEU00.0610.04513.7550.4110.4110.0000.0000.0000.000
36A37ASN0-0.061-0.06617.4790.7610.7610.0000.0000.0000.000
37A38MET00.0860.06921.083-0.116-0.1160.0000.0000.0000.000
38A39GLY0-0.014-0.00123.8380.2500.2500.0000.0000.0000.000
39A40VAL00.0140.00727.4120.3160.3160.0000.0000.0000.000
40A41GLY00.0150.01428.9340.3070.3070.0000.0000.0000.000
41A42GLU-1-0.884-0.96831.733-9.652-9.6520.0000.0000.0000.000
42A43ALA00.0160.00831.3830.2210.2210.0000.0000.0000.000
43A44ILE0-0.064-0.03033.4900.1140.1140.0000.0000.0000.000
44A45ALA0-0.030-0.01336.9330.2330.2330.0000.0000.0000.000
45A46ASP-1-0.781-0.89835.694-8.912-8.9120.0000.0000.0000.000
46A47LYS10.9210.96832.1409.4399.4390.0000.0000.0000.000
47A48LYS10.8960.95631.5619.4429.4420.0000.0000.0000.000
48A49LEU0-0.008-0.00130.325-0.427-0.4270.0000.0000.0000.000
49A50LEU0-0.022-0.01327.683-0.426-0.4260.0000.0000.0000.000
50A51ASP-1-0.917-0.97627.141-11.362-11.3620.0000.0000.0000.000
51A52ASN0-0.019-0.01826.068-0.889-0.8890.0000.0000.0000.000
52A53ALA00.0190.00824.472-0.530-0.5300.0000.0000.0000.000
53A54ALA0-0.035-0.04922.823-0.713-0.7130.0000.0000.0000.000
54A55ALA0-0.009-0.00421.453-0.767-0.7670.0000.0000.0000.000
55A56ASP-1-0.722-0.83120.144-14.630-14.6300.0000.0000.0000.000
56A57LEU0-0.049-0.03217.735-1.051-1.0510.0000.0000.0000.000
57A58ALA0-0.036-0.01716.283-1.247-1.2470.0000.0000.0000.000
58A59ALA00.0130.02715.877-0.624-0.6240.0000.0000.0000.000
59A60ILE0-0.013-0.00613.914-1.440-1.4400.0000.0000.0000.000
60A61SER0-0.041-0.03511.679-2.554-2.5540.0000.0000.0000.000
61A62GLY00.0950.06511.5731.5131.5130.0000.0000.0000.000
62A63GLN0-0.062-0.05913.236-1.920-1.9200.0000.0000.0000.000
63A64LYS10.9791.00915.50214.00714.0070.0000.0000.0000.000
64A65PRO00.0050.02019.2910.1160.1160.0000.0000.0000.000
65A66LEU0-0.054-0.03420.6660.7180.7180.0000.0000.0000.000
66A67ILE00.0450.01723.6150.0110.0110.0000.0000.0000.000
67A68THR0-0.083-0.05225.1660.4510.4510.0000.0000.0000.000
68A69LYS10.9730.97627.92810.37810.3780.0000.0000.0000.000
69A70ALA00.0050.01631.665-0.119-0.1190.0000.0000.0000.000
70A71ARG10.9920.99232.4109.4249.4240.0000.0000.0000.000
71A72LYS10.9530.97934.7198.3068.3060.0000.0000.0000.000
72A73SER00.0300.03037.946-0.123-0.1230.0000.0000.0000.000
73A74VAL0-0.053-0.03338.7430.0830.0830.0000.0000.0000.000
74A75ALA00.0640.03341.254-0.082-0.0820.0000.0000.0000.000
75A76GLY00.0190.01542.4660.0440.0440.0000.0000.0000.000
76A77PHE00.014-0.01737.1980.0360.0360.0000.0000.0000.000
77A78LYS10.9280.98139.5617.3217.3210.0000.0000.0000.000
78A79ILE00.0450.04535.988-0.009-0.0090.0000.0000.0000.000
79A80ARG10.9970.97539.2377.3747.3740.0000.0000.0000.000
80A81GLN00.020-0.01237.898-0.130-0.1300.0000.0000.0000.000
81A82GLY0-0.0010.01035.9490.1320.1320.0000.0000.0000.000
82A83TYR00.0100.00735.233-0.147-0.1470.0000.0000.0000.000
83A84PRO0-0.028-0.02331.048-0.189-0.1890.0000.0000.0000.000
84A85ILE0-0.004-0.00130.0810.2170.2170.0000.0000.0000.000
85A86GLY00.0640.02927.087-0.009-0.0090.0000.0000.0000.000
86A87CYS0-0.0380.03722.7120.1830.1830.0000.0000.0000.000
87A88LYS10.9730.98920.29513.76713.7670.0000.0000.0000.000
88A89VAL00.0600.04315.0450.4390.4390.0000.0000.0000.000
89A90THR0-0.062-0.02516.0030.5360.5360.0000.0000.0000.000
90A91LEU00.0110.02710.268-0.011-0.0110.0000.0000.0000.000
91A92ARG10.9290.93011.47519.43219.4320.0000.0000.0000.000
92A93GLY00.0430.0268.912-0.732-0.7320.0000.0000.0000.000
94A95ARG10.8770.9365.35921.79521.7950.0000.0000.0000.000
95A96MET0-0.0530.0077.5781.1831.1830.0000.0000.0000.000
99A100PHE00.019-0.0016.1052.6882.6880.0000.0000.0000.000
102A103LEU0-0.037-0.0097.8274.3954.3950.0000.0000.0000.000
103A104ILE00.0330.0098.9473.0963.0960.0000.0000.0000.000
104A105THR0-0.047-0.0577.0342.5652.5650.0000.0000.0000.000
105A106ILE0-0.031-0.0179.8292.3232.3230.0000.0000.0000.000
106A107ALA0-0.018-0.00511.8071.9941.9940.0000.0000.0000.000
107A108VAL00.000-0.00913.5581.8361.8360.0000.0000.0000.000
108A109PRO0-0.006-0.00213.6881.5761.5760.0000.0000.0000.000
109A110ARG10.8540.94115.81918.85018.8500.0000.0000.0000.000
110A111ILE0-0.082-0.02618.2260.9560.9560.0000.0000.0000.000
111A112ARG10.8710.92520.39312.36112.3610.0000.0000.0000.000
112A113ASP-1-0.916-0.97524.047-11.807-11.8070.0000.0000.0000.000
113A114PHE00.0270.02718.7450.2770.2770.0000.0000.0000.000
114A115ARG10.9370.96723.05011.46111.4610.0000.0000.0000.000
115A116GLY00.0890.05920.9120.3610.3610.0000.0000.0000.000
116A117LEU0-0.040-0.02316.7600.6640.6640.0000.0000.0000.000
117A118SER00.0190.00621.2530.4740.4740.0000.0000.0000.000
118A119ALA00.0770.03322.483-0.398-0.3980.0000.0000.0000.000
119A120LYS10.9110.93423.52311.30011.3000.0000.0000.0000.000
120A121SER0-0.0220.00721.8490.4450.4450.0000.0000.0000.000
121A122PHE0-0.022-0.00719.676-0.821-0.8210.0000.0000.0000.000
122A123ASP-1-0.791-0.89423.755-12.767-12.7670.0000.0000.0000.000
123A124GLY00.0090.01725.7760.4250.4250.0000.0000.0000.000
124A125ARG10.8380.91624.43611.84711.8470.0000.0000.0000.000
125A126GLY00.0360.04121.939-0.183-0.1830.0000.0000.0000.000
126A127ASN0-0.065-0.04319.289-1.633-1.6330.0000.0000.0000.000
127A128TYR00.0070.01117.0650.3110.3110.0000.0000.0000.000
128A129SER0-0.009-0.01218.372-0.634-0.6340.0000.0000.0000.000
129A130MET0-0.020-0.00417.0850.2530.2530.0000.0000.0000.000
130A131GLY00.0660.03620.395-0.247-0.2470.0000.0000.0000.000
131A132VAL0-0.053-0.02017.8390.2850.2850.0000.0000.0000.000
132A133ARG10.9150.95121.24412.26712.2670.0000.0000.0000.000
133A134GLU-1-0.806-0.90922.415-11.738-11.7380.0000.0000.0000.000
134A135GLN00.0410.01020.149-0.257-0.2570.0000.0000.0000.000
135A136ILE00.0460.01219.258-0.806-0.8060.0000.0000.0000.000
136A137ILE0-0.0200.00716.739-0.227-0.2270.0000.0000.0000.000
137A138PHE00.017-0.00112.806-1.058-1.0580.0000.0000.0000.000
138A139PRO0-0.024-0.01713.1411.2061.2060.0000.0000.0000.000
139A140GLU-1-0.821-0.89210.973-26.862-26.8620.0000.0000.0000.000
140A141ILE0-0.052-0.02715.3890.7620.7620.0000.0000.0000.000
141A142ASP-1-0.787-0.87519.241-13.985-13.9850.0000.0000.0000.000
142A143TYR0-0.026-0.02922.2550.3550.3550.0000.0000.0000.000
143A144ASP-1-0.893-0.95424.645-11.582-11.5820.0000.0000.0000.000
144A145LYS10.7990.89124.76212.63512.6350.0000.0000.0000.000
145A146VAL0-0.0380.00323.821-0.055-0.0550.0000.0000.0000.000
146A147ASP-1-0.867-0.91926.464-10.493-10.4930.0000.0000.0000.000
147A148ARG10.8540.90928.49510.36510.3650.0000.0000.0000.000
148A149VAL00.0070.01225.931-0.379-0.3790.0000.0000.0000.000
149A150ARG10.7930.88323.87513.04813.0480.0000.0000.0000.000
150A151GLY00.0340.02823.292-0.528-0.5280.0000.0000.0000.000
151A152LEU0-0.033-0.03617.4710.1260.1260.0000.0000.0000.000
152A153ASP-1-0.894-0.93920.699-13.527-13.5270.0000.0000.0000.000
153A154ILE0-0.027-0.03114.194-0.808-0.8080.0000.0000.0000.000
154A155THR0-0.043-0.02516.9580.7050.7050.0000.0000.0000.000
155A156ILE00.0300.00712.966-1.212-1.2120.0000.0000.0000.000
156A157THR0-0.061-0.03215.5301.3881.3880.0000.0000.0000.000
157A158THR00.030-0.00915.850-1.800-1.8000.0000.0000.0000.000
158A159THR0-0.031-0.01317.5000.4680.4680.0000.0000.0000.000
159A160ALA0-0.0050.01119.7440.4340.4340.0000.0000.0000.000
160A161LYS10.9000.95821.60011.51711.5170.0000.0000.0000.000
161A162SER0-0.008-0.02424.4680.7790.7790.0000.0000.0000.000
162A163ASP-1-0.803-0.92723.837-12.713-12.7130.0000.0000.0000.000
163A164GLU-1-0.974-0.99623.514-12.849-12.8490.0000.0000.0000.000
164A165GLU-1-0.726-0.86822.049-13.269-13.2690.0000.0000.0000.000
165A166GLY0-0.009-0.00219.373-0.807-0.8070.0000.0000.0000.000
166A167ARG10.8910.95418.61211.80711.8070.0000.0000.0000.000
167A168ALA00.0250.03019.276-0.670-0.6700.0000.0000.0000.000
168A169LEU0-0.0010.00114.115-0.819-0.8190.0000.0000.0000.000
169A170LEU0-0.019-0.01513.564-1.391-1.3910.0000.0000.0000.000
170A171ALA00.0190.00414.964-0.951-0.9510.0000.0000.0000.000
171A172ALA0-0.055-0.01715.644-0.081-0.0810.0000.0000.0000.000
172A173PHE0-0.055-0.0358.328-1.343-1.3430.0000.0000.0000.000
173A174ASP-1-0.905-0.94811.725-27.508-27.5080.0000.0000.0000.000
174A175PHE00.0190.01612.6550.5060.5060.0000.0000.0000.000
175A176PRO00.0260.02514.6681.4091.4090.0000.0000.0000.000
176A177PHE0-0.046-0.04217.6360.5890.5890.0000.0000.0000.000
177A178ARG0-0.077-0.02720.6940.0500.0500.0000.0000.0000.000