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: N664Q

Calculation Name: 1LM6-A-Xray547

Preferred Name: Peptide deformylase

Target Type: SINGLE PROTEIN

Ligand Name: cysteinesulfonic acid | glycerol | fe (iii) ion

Ligand 3-letter code: OCS | GOL | FE

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1LM6

Chain ID: A

ChEMBL ID: CHEMBL2029196

UniProt ID: Q9F2F0

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 202
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2322708.096534
FMO2-HF: Nuclear repulsion 2242891.852879
FMO2-HF: Total energy -79816.243654
FMO2-MP2: Total energy -80046.726148


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.
-124.27-118.16412.261-6.072-12.295-0.067
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 : 0.829 / q_NPA : 0.925
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].
3A3ALA00.0800.0393.412-4.366-2.3860.031-0.989-1.022-0.002
5A5GLU-1-0.833-0.8882.362-78.405-76.0269.093-4.674-6.798-0.061
6A6ARG10.8550.9132.67736.77339.1052.206-1.666-2.872-0.004
7A7ILE00.0070.0083.7754.3493.0570.0621.576-0.346-0.001
9A9LYS10.8070.8962.27244.26444.9710.869-0.319-1.2570.001
4A4ILE00.0500.0255.7961.8331.8330.0000.0000.0000.000
8A8THR0-0.040-0.0397.1692.5332.5330.0000.0000.0000.000
10A10ALA00.0350.0087.2101.2961.2960.0000.0000.0000.000
11A11ALA0-0.011-0.0209.6830.8270.8270.0000.0000.0000.000
12A12HIS0-0.056-0.0167.534-0.532-0.5320.0000.0000.0000.000
13A13LEU00.0130.0079.6411.0231.0230.0000.0000.0000.000
14A14ILE0-0.0130.00011.595-0.841-0.8410.0000.0000.0000.000
15A15ASP-1-0.770-0.87812.678-18.363-18.3630.0000.0000.0000.000
16A16MET00.0320.01214.031-0.610-0.6100.0000.0000.0000.000
17A17ASN0-0.095-0.04412.0580.3200.3200.0000.0000.0000.000
18A18ASP-1-0.778-0.8638.660-28.704-28.7040.0000.0000.0000.000
19A19ILE0-0.0120.00410.973-0.704-0.7040.0000.0000.0000.000
20A20ILE0-0.0430.00712.1910.6310.6310.0000.0000.0000.000
21A21ARG10.8400.87714.82817.37317.3730.0000.0000.0000.000
22A22GLU-1-0.772-0.89018.493-12.696-12.6960.0000.0000.0000.000
23A23GLY0-0.025-0.00120.639-0.103-0.1030.0000.0000.0000.000
24A24ASN00.0010.00813.2140.1920.1920.0000.0000.0000.000
25A25PRO00.019-0.00815.9180.5190.5190.0000.0000.0000.000
26A26THR0-0.010-0.00913.5211.0771.0770.0000.0000.0000.000
27A27LEU00.0030.01116.6360.6580.6580.0000.0000.0000.000
28A28ARG10.7050.81819.23113.38713.3870.0000.0000.0000.000
29A29THR0-0.065-0.03117.5860.0770.0770.0000.0000.0000.000
30A30VAL0-0.038-0.01420.3020.1420.1420.0000.0000.0000.000
31A31ALA0-0.0160.00417.719-0.486-0.4860.0000.0000.0000.000
32A32GLU-1-0.885-0.94816.328-15.616-15.6160.0000.0000.0000.000
33A33GLU-1-1.015-1.01018.150-12.947-12.9470.0000.0000.0000.000
34A34VAL0-0.053-0.02116.323-0.752-0.7520.0000.0000.0000.000
35A35THR00.0310.01718.5730.6960.6960.0000.0000.0000.000
36A36PHE00.0110.01319.720-0.350-0.3500.0000.0000.0000.000
37A37PRO0-0.027-0.02721.2610.4420.4420.0000.0000.0000.000
38A38LEU0-0.0010.01717.151-0.495-0.4950.0000.0000.0000.000
39A39SER0-0.035-0.04213.197-0.472-0.4720.0000.0000.0000.000
40A40ASP-1-0.839-0.93413.542-17.603-17.6030.0000.0000.0000.000
41A41GLN0-0.040-0.0297.049-2.222-2.2220.0000.0000.0000.000
42A42GLU-1-0.764-0.85211.348-19.671-19.6710.0000.0000.0000.000
43A43ILE00.0160.03013.8910.7080.7080.0000.0000.0000.000
44A44ILE00.0160.01111.7190.2060.2060.0000.0000.0000.000
45A45LEU0-0.023-0.01610.881-0.036-0.0360.0000.0000.0000.000
46A46GLY00.0610.02713.1710.4020.4020.0000.0000.0000.000
47A47GLU-1-0.861-0.93716.463-14.565-14.5650.0000.0000.0000.000
48A48LYS10.7570.87510.68721.46121.4610.0000.0000.0000.000
49A49MET0-0.036-0.01114.781-0.087-0.0870.0000.0000.0000.000
50A50MET00.0070.02316.8290.6170.6170.0000.0000.0000.000
51A51GLN0-0.037-0.02316.9790.8500.8500.0000.0000.0000.000
52A52PHE0-0.005-0.00716.2660.2740.2740.0000.0000.0000.000
53A53LEU00.0020.01118.2180.4840.4840.0000.0000.0000.000
54A54LYS10.8760.92621.71612.05412.0540.0000.0000.0000.000
55A55HIS10.8570.92718.00314.27114.2710.0000.0000.0000.000
56A56SER0-0.053-0.03121.2990.2600.2600.0000.0000.0000.000
57A57GLN00.019-0.01422.9450.4450.4450.0000.0000.0000.000
58A58ASP-1-0.850-0.89824.740-10.525-10.5250.0000.0000.0000.000
59A59PRO00.0520.01425.967-0.339-0.3390.0000.0000.0000.000
60A60VAL0-0.009-0.00526.661-0.234-0.2340.0000.0000.0000.000
61A61MET0-0.103-0.05720.609-0.421-0.4210.0000.0000.0000.000
62A62ALA00.0190.00022.390-0.585-0.5850.0000.0000.0000.000
63A63GLU-1-0.969-0.97723.348-10.860-10.8600.0000.0000.0000.000
64A64LYS10.9050.95522.48110.59210.5920.0000.0000.0000.000
65A65MET0-0.073-0.02816.132-0.390-0.3900.0000.0000.0000.000
66A66GLY0-0.0150.00719.197-0.614-0.6140.0000.0000.0000.000
67A67LEU0-0.083-0.04717.912-0.415-0.4150.0000.0000.0000.000
68A68ARG10.8430.91321.43113.02913.0290.0000.0000.0000.000
69A69GLY00.0930.05122.868-0.392-0.3920.0000.0000.0000.000
70A70GLY00.009-0.00724.173-0.120-0.1200.0000.0000.0000.000
71A71VAL00.0180.02425.147-0.032-0.0320.0000.0000.0000.000
72A72GLY0-0.014-0.01023.7260.2250.2250.0000.0000.0000.000
73A73LEU0-0.0050.01415.904-0.274-0.2740.0000.0000.0000.000
74A74ALA00.0330.01918.899-0.054-0.0540.0000.0000.0000.000
75A75ALA00.0160.00813.986-0.646-0.6460.0000.0000.0000.000
76A76PRO00.015-0.00113.875-1.418-1.4180.0000.0000.0000.000
77A77GLN00.047-0.00315.037-0.325-0.3250.0000.0000.0000.000
78A78LEU0-0.024-0.00710.953-0.220-0.2200.0000.0000.0000.000
79A79ASP-1-0.855-0.9239.557-30.205-30.2050.0000.0000.0000.000
80A80ILE0-0.077-0.0309.017-2.853-2.8530.0000.0000.0000.000
81A81SER00.0160.01111.5972.0552.0550.0000.0000.0000.000
82A82LYS10.8870.92511.92821.52421.5240.0000.0000.0000.000
83A83ARG10.8280.90115.81413.99013.9900.0000.0000.0000.000
84A84ILE0-0.008-0.00914.6470.5230.5230.0000.0000.0000.000
85A85ILE0-0.025-0.01018.398-0.434-0.4340.0000.0000.0000.000
86A86ALA00.0050.01319.9050.1840.1840.0000.0000.0000.000
87A87VAL0-0.015-0.02321.5870.0280.0280.0000.0000.0000.000
88A88LEU0-0.025-0.01724.2340.0510.0510.0000.0000.0000.000
89A89VAL00.0250.01226.813-0.065-0.0650.0000.0000.0000.000
90A90PRO00.0050.02129.4090.1780.1780.0000.0000.0000.000
91A91ASN0-0.091-0.05932.3880.2180.2180.0000.0000.0000.000
92A92ILE0-0.045-0.02634.8600.1820.1820.0000.0000.0000.000
93A93VAL0-0.010-0.02230.398-0.169-0.1690.0000.0000.0000.000
94A94GLU-1-0.903-0.96327.830-10.964-10.9640.0000.0000.0000.000
95A95GLU-1-0.870-0.91230.332-8.945-8.9450.0000.0000.0000.000
96A96GLY0-0.022-0.02427.5160.0910.0910.0000.0000.0000.000
97A97GLU-1-0.887-0.92828.305-9.883-9.8830.0000.0000.0000.000
98A98THR0-0.049-0.04829.5810.2800.2800.0000.0000.0000.000
99A99PRO0-0.040-0.02332.443-0.035-0.0350.0000.0000.0000.000
100A100GLN0-0.091-0.05833.4370.0730.0730.0000.0000.0000.000
101A101GLU-1-0.754-0.84632.848-8.429-8.4290.0000.0000.0000.000
102A102ALA0-0.057-0.03432.977-0.116-0.1160.0000.0000.0000.000
103A103TYR00.006-0.01027.326-0.024-0.0240.0000.0000.0000.000
104A104ASP-1-0.896-0.92432.044-8.409-8.4090.0000.0000.0000.000
105A105LEU0-0.060-0.03729.0500.0370.0370.0000.0000.0000.000
106A106GLU-1-0.797-0.89225.302-11.522-11.5220.0000.0000.0000.000
107A107ALA0-0.060-0.03226.0160.2010.2010.0000.0000.0000.000
108A108ILE00.0150.02619.654-0.387-0.3870.0000.0000.0000.000
109A109MET0-0.093-0.04122.1690.5070.5070.0000.0000.0000.000
110A110TYR00.020-0.01316.978-0.327-0.3270.0000.0000.0000.000
111A111ASN00.011-0.00821.3270.1720.1720.0000.0000.0000.000
112A112PRO0-0.0150.00922.7010.6220.6220.0000.0000.0000.000
113A113LYS10.9660.96825.7899.9869.9860.0000.0000.0000.000
114A114ILE00.0240.02028.9060.2860.2860.0000.0000.0000.000
115A115VAL0-0.072-0.04232.1820.0430.0430.0000.0000.0000.000
116A116SER0-0.040-0.02134.9790.3100.3100.0000.0000.0000.000
117A117HIS0-0.0020.00036.845-0.282-0.2820.0000.0000.0000.000
118A118SER0-0.067-0.02538.7590.1640.1640.0000.0000.0000.000
119A119VAL00.0300.01141.222-0.118-0.1180.0000.0000.0000.000
120A120GLN00.0180.03443.878-0.031-0.0310.0000.0000.0000.000
121A121ASP-1-0.758-0.85740.210-7.954-7.9540.0000.0000.0000.000
122A122ALA0-0.044-0.04338.6390.2220.2220.0000.0000.0000.000
123A123ALA00.0250.02037.016-0.210-0.2100.0000.0000.0000.000
124A124LEU0-0.0060.01333.2900.1950.1950.0000.0000.0000.000
125A125GLY00.016-0.00437.369-0.009-0.0090.0000.0000.0000.000
126A126GLU-1-0.942-0.97834.827-8.542-8.5420.0000.0000.0000.000
127A127GLY0-0.0130.01135.201-0.127-0.1270.0000.0000.0000.000
128A128GLU-1-0.749-0.86129.709-10.409-10.4090.0000.0000.0000.000
129A129GLY00.0320.02028.3300.1050.1050.0000.0000.0000.000
130A130CYS-1-0.891-0.88923.044-13.422-13.4220.0000.0000.0000.000
131A131LEU00.0240.01319.6120.0320.0320.0000.0000.0000.000
132A132SER0-0.005-0.00317.951-0.446-0.4460.0000.0000.0000.000
133A133VAL0-0.043-0.02320.255-0.105-0.1050.0000.0000.0000.000
134A134ASP-1-0.849-0.88921.340-13.729-13.7290.0000.0000.0000.000
135A135ARG10.8420.91024.64611.50911.5090.0000.0000.0000.000
136A136ASN00.0300.01728.378-0.344-0.3440.0000.0000.0000.000
137A137VAL0-0.033-0.02230.021-0.001-0.0010.0000.0000.0000.000
138A138PRO00.0030.01132.595-0.033-0.0330.0000.0000.0000.000
139A139GLY00.0590.00635.7000.0770.0770.0000.0000.0000.000
140A140TYR0-0.042-0.01036.226-0.184-0.1840.0000.0000.0000.000
141A141VAL0-0.026-0.00431.734-0.001-0.0010.0000.0000.0000.000
142A142VAL0-0.026-0.01035.1060.0660.0660.0000.0000.0000.000
143A143ARG10.7650.84329.0549.9409.9400.0000.0000.0000.000
144A144HIS00.0490.02934.7550.4320.4320.0000.0000.0000.000
145A145ALA00.0180.00637.005-0.134-0.1340.0000.0000.0000.000
146A146ARG10.8350.88738.3167.2797.2790.0000.0000.0000.000
147A147VAL00.0360.02833.1290.0310.0310.0000.0000.0000.000
148A148THR0-0.061-0.03535.8540.1830.1830.0000.0000.0000.000
149A149VAL00.0070.00129.244-0.062-0.0620.0000.0000.0000.000
150A150ASP-1-0.751-0.83630.554-9.103-9.1030.0000.0000.0000.000
151A151TYR00.030-0.00425.815-0.260-0.2600.0000.0000.0000.000
152A152PHE0-0.0030.01424.1580.5150.5150.0000.0000.0000.000
153A153ASP-1-0.712-0.84723.777-11.726-11.7260.0000.0000.0000.000
154A154LYS10.8850.92420.43113.39013.3900.0000.0000.0000.000
155A155ASP-1-0.887-0.93821.581-12.439-12.4390.0000.0000.0000.000
156A156GLY0-0.038-0.02124.3850.1670.1670.0000.0000.0000.000
157A157GLU-1-0.959-0.97025.418-9.597-9.5970.0000.0000.0000.000
158A158LYS10.8190.90227.9409.4269.4260.0000.0000.0000.000
159A159HIS10.8340.91028.05910.60910.6090.0000.0000.0000.000
160A160ARG10.8400.87331.1118.5688.5680.0000.0000.0000.000
161A161ILE00.0170.02130.7310.2330.2330.0000.0000.0000.000
162A162LYS10.8930.93834.5527.6527.6520.0000.0000.0000.000
163A163LEU00.0370.03131.6000.0480.0480.0000.0000.0000.000
164A164LYS10.9600.95636.2627.6107.6100.0000.0000.0000.000
165A165GLY00.0340.02737.196-0.092-0.0920.0000.0000.0000.000
166A166TYR00.1240.05430.763-0.119-0.1190.0000.0000.0000.000
167A167ASN00.0670.01532.208-0.373-0.3730.0000.0000.0000.000
168A168SER0-0.068-0.02331.912-0.353-0.3530.0000.0000.0000.000
169A169ILE00.0210.01131.636-0.211-0.2110.0000.0000.0000.000
170A170VAL00.0300.02227.397-0.318-0.3180.0000.0000.0000.000
171A171VAL00.023-0.00127.568-0.427-0.4270.0000.0000.0000.000
172A172GLN0-0.075-0.05527.647-0.294-0.2940.0000.0000.0000.000
173A173HIS10.8080.87124.27511.58811.5880.0000.0000.0000.000
174A174GLU-1-0.811-0.92322.115-13.729-13.7290.0000.0000.0000.000
175A175ILE0-0.031-0.02923.291-0.460-0.4600.0000.0000.0000.000
176A176ASP-1-0.763-0.83525.256-10.953-10.9530.0000.0000.0000.000
177A177HIS10.8700.91820.55313.48413.4840.0000.0000.0000.000
178A178ILE0-0.0080.01619.484-0.729-0.7290.0000.0000.0000.000
179A179ASN0-0.056-0.03321.503-0.177-0.1770.0000.0000.0000.000
180A180GLY00.0520.05822.3240.3420.3420.0000.0000.0000.000
181A181ILE0-0.048-0.02123.3130.3350.3350.0000.0000.0000.000
182A182MET0-0.010-0.00822.410-0.657-0.6570.0000.0000.0000.000
183A183PHE00.0450.01126.3130.3100.3100.0000.0000.0000.000
184A184TYR0-0.012-0.04025.8500.3570.3570.0000.0000.0000.000
185A185ASP-1-0.768-0.83628.291-11.077-11.0770.0000.0000.0000.000
186A186ARG10.7790.86530.46410.24510.2450.0000.0000.0000.000
187A187ILE00.0200.03633.4060.2420.2420.0000.0000.0000.000
188A188ASN0-0.056-0.03236.167-0.024-0.0240.0000.0000.0000.000
189A189GLU-1-0.908-0.96236.800-8.516-8.5160.0000.0000.0000.000
190A190LYS10.8220.91739.1577.5047.5040.0000.0000.0000.000
191A191ASP-1-0.826-0.92642.421-6.982-6.9820.0000.0000.0000.000
192A192PRO00.0220.02038.617-0.003-0.0030.0000.0000.0000.000
193A193PHE00.007-0.00439.182-0.153-0.1530.0000.0000.0000.000
194A194ALA00.0000.01542.7730.1680.1680.0000.0000.0000.000
195A195VAL0-0.015-0.01043.644-0.151-0.1510.0000.0000.0000.000
196A196LYS10.7830.88642.3057.4617.4610.0000.0000.0000.000
197A197ASP-1-0.838-0.93346.156-6.359-6.3590.0000.0000.0000.000
198A198GLY0-0.030-0.01446.557-0.157-0.1570.0000.0000.0000.000
199A199LEU0-0.049-0.01240.419-0.140-0.1400.0000.0000.0000.000
200A200LEU0-0.069-0.03742.5750.1640.1640.0000.0000.0000.000
201A201ILE0-0.007-0.00741.576-0.188-0.1880.0000.0000.0000.000
202A202LEU-1-0.889-0.93037.989-7.587-7.5870.0000.0000.0000.000