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: 1YMLZ

Calculation Name: 5KO7-A-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin mononucleotide

Ligand 3-letter code: FMN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5KO7

Chain ID: A

ChEMBL ID:

UniProt ID: F4KU78

Base Structure: X-ray

Registration Date: 2025-10-04

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 -2150417.211095
FMO2-HF: Nuclear repulsion 2070248.794941
FMO2-HF: Total energy -80168.416154
FMO2-MP2: Total energy -80402.691094


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:5:PRO)


Summations of interaction energy for fragment #1(A:5:PRO)
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.
-8.634-6.875-0.016-0.733-1.0090
Interaction energy analysis for fragmet #1(A:5:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.869 / q_NPA : 0.906
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].
3A7PHE00.0260.0093.663-0.7541.005-0.016-0.733-1.0090.000
4A8ILE00.0220.0106.8801.0371.0370.0000.0000.0000.000
5A9PRO0-0.0040.00910.3430.2280.2280.0000.0000.0000.000
6A10TYR00.0280.00513.7250.2330.2330.0000.0000.0000.000
7A11ALA00.0190.01515.1941.0211.0210.0000.0000.0000.000
8A12GLY0-0.003-0.00217.8800.2360.2360.0000.0000.0000.000
9A13ALA0-0.026-0.01520.1530.3230.3230.0000.0000.0000.000
10A14GLN0-0.0170.00023.892-0.238-0.2380.0000.0000.0000.000
11A15PHE00.006-0.01025.4870.1440.1440.0000.0000.0000.000
12A16GLU-1-0.855-0.92429.317-10.070-10.0700.0000.0000.0000.000
13A17PRO00.014-0.02531.9440.0850.0850.0000.0000.0000.000
14A18GLU-1-0.948-0.95733.381-7.973-7.9730.0000.0000.0000.000
15A19GLU-1-0.831-0.91732.404-9.580-9.5800.0000.0000.0000.000
16A20MET0-0.078-0.03528.485-0.110-0.1100.0000.0000.0000.000
17A21LEU00.0080.01232.1180.0020.0020.0000.0000.0000.000
18A22SER00.0360.02935.440-0.013-0.0130.0000.0000.0000.000
19A23LYS10.9170.95830.6279.7609.7600.0000.0000.0000.000
20A24SER0-0.075-0.03932.418-0.004-0.0040.0000.0000.0000.000
21A25ALA0-0.003-0.00733.4200.0620.0620.0000.0000.0000.000
22A26GLU-1-0.928-0.96935.852-8.330-8.3300.0000.0000.0000.000
23A27TYR00.0080.00229.627-0.013-0.0130.0000.0000.0000.000
24A28TYR0-0.032-0.01434.1110.0570.0570.0000.0000.0000.000
25A29GLN00.015-0.00435.8230.1970.1970.0000.0000.0000.000
26A30PHE0-0.020-0.00333.6610.1430.1430.0000.0000.0000.000
27A31MET0-0.022-0.00631.2000.0660.0660.0000.0000.0000.000
28A32ASP-1-0.897-0.92235.871-7.677-7.6770.0000.0000.0000.000
29A33HIS00.0450.02939.1210.1940.1940.0000.0000.0000.000
30A34ARG10.9160.98634.7888.7048.7040.0000.0000.0000.000
31A35ARG10.8500.91838.7727.1477.1470.0000.0000.0000.000
32A36THR0-0.038-0.02138.788-0.183-0.1830.0000.0000.0000.000
33A37VAL00.0270.01940.7730.1930.1930.0000.0000.0000.000
34A38ARG10.9590.96942.5377.0547.0540.0000.0000.0000.000
35A39GLU-1-0.821-0.90545.195-6.493-6.4930.0000.0000.0000.000
36A40PHE0-0.025-0.01539.882-0.057-0.0570.0000.0000.0000.000
37A41SER00.0220.00644.9820.1660.1660.0000.0000.0000.000
38A42ASN00.009-0.00144.399-0.149-0.1490.0000.0000.0000.000
39A43ARG10.9260.98044.0567.1347.1340.0000.0000.0000.000
40A44ALA00.0340.00741.708-0.161-0.1610.0000.0000.0000.000
41A45ILE00.0190.00836.1900.0580.0580.0000.0000.0000.000
42A46PRO00.0210.01035.308-0.039-0.0390.0000.0000.0000.000
43A47LEU00.0480.03131.373-0.077-0.0770.0000.0000.0000.000
44A48GLU-1-0.839-0.91830.035-10.476-10.4760.0000.0000.0000.000
45A49VAL0-0.058-0.02129.845-0.301-0.3010.0000.0000.0000.000
46A50ILE0-0.010-0.01030.739-0.206-0.2060.0000.0000.0000.000
47A51GLU-1-0.896-0.95426.805-11.279-11.2790.0000.0000.0000.000
48A52ASN00.0280.00926.010-0.877-0.8770.0000.0000.0000.000
49A53ILE0-0.0250.01025.994-0.399-0.3990.0000.0000.0000.000
50A54VAL00.005-0.01024.521-0.281-0.2810.0000.0000.0000.000
51A55MET0-0.032-0.01821.367-0.830-0.8300.0000.0000.0000.000
52A56THR0-0.004-0.01321.379-0.649-0.6490.0000.0000.0000.000
53A57ALA0-0.013-0.00222.350-0.398-0.3980.0000.0000.0000.000
54A58SER0-0.017-0.00918.205-0.222-0.2220.0000.0000.0000.000
55A59THR0-0.052-0.03717.672-0.941-0.9410.0000.0000.0000.000
56A60ALA0-0.0170.01317.895-0.366-0.3660.0000.0000.0000.000
57A61PRO00.0010.00415.635-1.025-1.0250.0000.0000.0000.000
58A62SER00.023-0.00614.9730.5810.5810.0000.0000.0000.000
59A63GLY00.0080.01014.363-1.239-1.2390.0000.0000.0000.000
60A64ALA0-0.052-0.04011.529-0.058-0.0580.0000.0000.0000.000
61A65HIS0-0.008-0.0019.220-0.926-0.9260.0000.0000.0000.000
62A66LYS10.7860.87111.91119.72919.7290.0000.0000.0000.000
63A67GLN00.0170.02713.3401.5401.5400.0000.0000.0000.000
64A68PRO0-0.0180.01516.7550.5850.5850.0000.0000.0000.000
65A69TRP00.004-0.03118.0021.0671.0670.0000.0000.0000.000
66A70THR0-0.053-0.04421.979-0.646-0.6460.0000.0000.0000.000
67A71PHE00.0230.00622.8490.5610.5610.0000.0000.0000.000
68A72VAL00.002-0.00126.977-0.033-0.0330.0000.0000.0000.000
69A73VAL00.0310.02529.3250.3150.3150.0000.0000.0000.000
70A74VAL0-0.024-0.01431.8150.0610.0610.0000.0000.0000.000
71A75SER00.0660.02635.4610.0870.0870.0000.0000.0000.000
72A76ASP-1-0.828-0.91238.057-7.447-7.4470.0000.0000.0000.000
73A77PRO00.0410.01040.2610.0080.0080.0000.0000.0000.000
74A78GLN00.0330.01843.4250.0510.0510.0000.0000.0000.000
75A79ILE0-0.037-0.02137.4080.0670.0670.0000.0000.0000.000
76A80LYS10.8360.93239.8137.7037.7030.0000.0000.0000.000
77A81ALA00.0520.03241.9010.0440.0440.0000.0000.0000.000
78A82LYS10.8480.92343.0667.3657.3650.0000.0000.0000.000
79A83ILE00.008-0.00537.7100.0260.0260.0000.0000.0000.000
80A84ARG10.7980.87941.9756.5496.5490.0000.0000.0000.000
81A85GLN00.007-0.00644.5900.0670.0670.0000.0000.0000.000
82A86ALA0-0.041-0.00943.0610.1090.1090.0000.0000.0000.000
83A87ALA00.0320.01342.2320.0480.0480.0000.0000.0000.000
84A88GLU-1-0.829-0.89344.065-6.441-6.4410.0000.0000.0000.000
85A89LYS10.9100.94947.7766.5716.5710.0000.0000.0000.000
86A90GLU-1-0.815-0.91642.423-7.484-7.4840.0000.0000.0000.000
87A91GLU-1-0.859-0.92145.568-6.898-6.8980.0000.0000.0000.000
88A92PHE0-0.062-0.03947.7640.1270.1270.0000.0000.0000.000
89A93GLU-1-1.019-0.99349.538-6.306-6.3060.0000.0000.0000.000
90A94SER-1-0.980-0.97650.009-6.092-6.0920.0000.0000.0000.000
91A113ASP0-0.121-0.05448.5820.3310.3310.0000.0000.0000.000
92A114TRP00.1280.05448.436-0.141-0.1410.0000.0000.0000.000
93A115HIS00.0060.01249.167-0.100-0.1000.0000.0000.0000.000
94A116LYS10.7900.87043.7867.0707.0700.0000.0000.0000.000
95A117PRO00.0460.01746.267-0.132-0.1320.0000.0000.0000.000
96A118PHE00.0310.00942.528-0.074-0.0740.0000.0000.0000.000
97A119LEU0-0.026-0.01240.583-0.182-0.1820.0000.0000.0000.000
98A120GLU-1-0.874-0.93742.489-6.816-6.8160.0000.0000.0000.000
99A121ILE0-0.029-0.02044.296-0.071-0.0710.0000.0000.0000.000
100A122ALA00.0050.02040.296-0.005-0.0050.0000.0000.0000.000
101A123PRO0-0.038-0.01639.532-0.068-0.0680.0000.0000.0000.000
102A124TYR0-0.002-0.01535.258-0.083-0.0830.0000.0000.0000.000
103A125LEU0-0.0220.00236.4200.0720.0720.0000.0000.0000.000
104A126ILE00.0110.00729.757-0.214-0.2140.0000.0000.0000.000
105A127VAL0-0.003-0.00432.3020.1220.1220.0000.0000.0000.000
106A128VAL00.0090.00826.737-0.322-0.3220.0000.0000.0000.000
107A129PHE00.002-0.01127.4820.3700.3700.0000.0000.0000.000
108A130ARG10.9370.97624.56410.32910.3290.0000.0000.0000.000
109A131LYS10.8980.95018.96516.11116.1110.0000.0000.0000.000
110A132ALA00.0150.00721.984-0.545-0.5450.0000.0000.0000.000
111A133TYR00.002-0.01820.077-0.388-0.3880.0000.0000.0000.000
112A134ASP-1-0.789-0.86116.080-17.563-17.5630.0000.0000.0000.000
113A135VAL0-0.015-0.02618.9470.1200.1200.0000.0000.0000.000
114A136LEU0-0.0090.00814.444-0.708-0.7080.0000.0000.0000.000
115A137PRO00.0120.00117.4440.7300.7300.0000.0000.0000.000
116A138ASP-1-0.836-0.89918.116-15.634-15.6340.0000.0000.0000.000
117A139GLY00.0160.01021.1860.4930.4930.0000.0000.0000.000
118A140THR0-0.096-0.06618.3560.0000.0000.0000.0000.0000.000
119A141GLN00.0170.00219.587-0.464-0.4640.0000.0000.0000.000
120A142ARG10.9430.97911.24021.95921.9590.0000.0000.0000.000
121A143LYS10.9750.97317.17412.72112.7210.0000.0000.0000.000
122A144ASN0-0.0120.01517.119-1.893-1.8930.0000.0000.0000.000
123A145TYR00.019-0.00314.5120.4290.4290.0000.0000.0000.000
124A146TYR00.0240.01418.548-0.540-0.5400.0000.0000.0000.000
125A147VAL00.0530.04720.696-0.120-0.1200.0000.0000.0000.000
126A148GLN0-0.003-0.01022.2320.2960.2960.0000.0000.0000.000
127A149GLU-1-0.849-0.92822.378-12.327-12.3270.0000.0000.0000.000
128A150SER0-0.007-0.02019.198-0.345-0.3450.0000.0000.0000.000
129A151VAL00.0000.00021.0870.0260.0260.0000.0000.0000.000
130A152GLY00.0280.01923.7710.3780.3780.0000.0000.0000.000
131A153ILE0-0.018-0.00821.3920.3110.3110.0000.0000.0000.000
132A154ALA00.0410.02921.7260.2220.2220.0000.0000.0000.000
133A155CYS0-0.048-0.02623.4460.4020.4020.0000.0000.0000.000
134A156GLY00.0040.00826.7730.4130.4130.0000.0000.0000.000
135A157PHE00.003-0.00220.5660.3300.3300.0000.0000.0000.000
136A158LEU0-0.0160.00325.8000.2060.2060.0000.0000.0000.000
137A159LEU0-0.036-0.02827.9110.3560.3560.0000.0000.0000.000
138A160ALA00.0030.00728.1100.3360.3360.0000.0000.0000.000
139A161ALA00.0180.01027.3300.2110.2110.0000.0000.0000.000
140A162ILE0-0.030-0.02629.4280.2330.2330.0000.0000.0000.000
141A163HIS0-0.017-0.01732.8130.2180.2180.0000.0000.0000.000
142A164GLN0-0.022-0.01929.7830.1930.1930.0000.0000.0000.000
143A165ALA0-0.032-0.00432.7330.0760.0760.0000.0000.0000.000
144A166GLY0-0.0150.00134.3110.2150.2150.0000.0000.0000.000
145A167LEU0-0.084-0.02834.8450.2490.2490.0000.0000.0000.000
146A168VAL00.0150.00337.447-0.050-0.0500.0000.0000.0000.000
147A169ALA00.027-0.00935.940-0.083-0.0830.0000.0000.0000.000
148A170LEU0-0.047-0.01537.8840.1290.1290.0000.0000.0000.000
149A171THR0-0.010-0.01334.135-0.071-0.0710.0000.0000.0000.000
150A172HIS0-0.004-0.01236.5430.3900.3900.0000.0000.0000.000
151A173THR00.0570.02136.267-0.279-0.2790.0000.0000.0000.000
152A174PRO0-0.0270.00233.9270.1190.1190.0000.0000.0000.000
153A175SER0-0.0060.00836.387-0.114-0.1140.0000.0000.0000.000
154A176PRO00.0390.02440.0150.0090.0090.0000.0000.0000.000
155A177MET00.005-0.01433.282-0.072-0.0720.0000.0000.0000.000
156A178ASN00.034-0.00236.405-0.364-0.3640.0000.0000.0000.000
157A179PHE0-0.018-0.00138.2220.0010.0010.0000.0000.0000.000
158A180LEU00.0210.01035.273-0.087-0.0870.0000.0000.0000.000
159A181GLN0-0.023-0.04230.391-0.065-0.0650.0000.0000.0000.000
160A182LYS10.9580.98134.4527.6617.6610.0000.0000.0000.000
161A183ILE0-0.029-0.00137.007-0.034-0.0340.0000.0000.0000.000
162A184LEU0-0.012-0.00832.897-0.005-0.0050.0000.0000.0000.000
163A185GLN0-0.055-0.01932.511-0.456-0.4560.0000.0000.0000.000
164A186ARG10.8230.89626.06411.04111.0410.0000.0000.0000.000
165A187PRO00.0350.03026.0280.2940.2940.0000.0000.0000.000
166A188GLU-1-0.885-0.95228.060-10.590-10.5900.0000.0000.0000.000
167A189ASN0-0.023-0.00622.3510.4960.4960.0000.0000.0000.000
168A190GLU-1-0.787-0.84325.182-12.523-12.5230.0000.0000.0000.000
169A191ARG10.8500.91227.05910.69910.6990.0000.0000.0000.000
170A192PRO0-0.0270.01129.120-0.321-0.3210.0000.0000.0000.000
171A193PHE0-0.053-0.03727.9550.0180.0180.0000.0000.0000.000
172A194LEU00.0330.00430.3500.2270.2270.0000.0000.0000.000
173A195LEU0-0.0220.01032.423-0.204-0.2040.0000.0000.0000.000
174A196VAL00.0190.00432.1980.1370.1370.0000.0000.0000.000
175A197PRO0-0.0100.01135.055-0.124-0.1240.0000.0000.0000.000
176A198VAL00.019-0.00233.695-0.020-0.0200.0000.0000.0000.000
177A199GLY00.008-0.01337.1850.0830.0830.0000.0000.0000.000
178A200TYR00.0450.03239.902-0.073-0.0730.0000.0000.0000.000
179A201PRO00.0250.01742.4960.0210.0210.0000.0000.0000.000
180A202ALA0-0.023-0.02144.8920.0570.0570.0000.0000.0000.000
181A203GLU-1-0.935-0.97748.494-6.109-6.1090.0000.0000.0000.000
182A204GLY0-0.0050.00250.9990.0520.0520.0000.0000.0000.000
183A205ALA0-0.070-0.02147.5510.0380.0380.0000.0000.0000.000
184A206MET0-0.022-0.01049.6390.0550.0550.0000.0000.0000.000
185A207VAL0-0.027-0.02044.653-0.147-0.1470.0000.0000.0000.000
186A208PRO0-0.0060.00546.7970.0960.0960.0000.0000.0000.000
187A209ASP-1-0.824-0.90747.915-6.423-6.4230.0000.0000.0000.000
188A210LEU0-0.085-0.03944.6130.0180.0180.0000.0000.0000.000
189A211GLN00.0100.00446.223-0.159-0.1590.0000.0000.0000.000
190A212ARG10.7710.85739.0807.8257.8250.0000.0000.0000.000
191A213LYS10.9210.96440.0917.8047.8040.0000.0000.0000.000
192A214ASP-1-0.760-0.87841.858-7.221-7.2210.0000.0000.0000.000
193A215LYS10.9790.97639.4477.7037.7030.0000.0000.0000.000
194A216ALA00.0130.00740.415-0.166-0.1660.0000.0000.0000.000
195A217ALA0-0.026-0.00842.472-0.045-0.0450.0000.0000.0000.000
196A218VAL0-0.084-0.05737.016-0.084-0.0840.0000.0000.0000.000
197A219MET0-0.059-0.01634.477-0.198-0.1980.0000.0000.0000.000
198A220VAL00.0220.01636.8060.1840.1840.0000.0000.0000.000
199A221VAL0-0.043-0.02735.771-0.273-0.2730.0000.0000.0000.000
200A222TYR0-0.010-0.00235.3010.2630.2630.0000.0000.0000.000
201A223HIS0-0.030-0.02035.902-0.169-0.1690.0000.0000.0000.000
202A224HIS-1-0.921-0.94635.488-8.082-8.0820.0000.0000.0000.000