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: MLMQZ

Calculation Name: 1NOX-A-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin mononucleotide

Ligand 3-letter code: FMN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1NOX

Chain ID: A

ChEMBL ID:

UniProt ID: Q60049

Base Structure: X-ray

Registration Date: 2025-10-05

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 200
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2087608.377158
FMO2-HF: Nuclear repulsion 2011578.621901
FMO2-HF: Total energy -76029.755257
FMO2-MP2: Total energy -76257.21899


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:6:PRO)


Summations of interaction energy for fragment #1(A:6: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.
20.22721.449-0.012-0.405-0.8050.001
Interaction energy analysis for fragmet #1(A:6:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.843 / q_NPA : 0.900
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].
3A8LEU0-0.0130.0023.8482.6833.905-0.012-0.405-0.8050.001
4A9ASP-1-0.774-0.8556.217-24.630-24.6300.0000.0000.0000.000
5A10ALA00.0560.0099.2310.6850.6850.0000.0000.0000.000
6A11LYS10.9600.98912.48319.04219.0420.0000.0000.0000.000
7A12THR0-0.041-0.0649.2221.8511.8510.0000.0000.0000.000
8A13ALA00.001-0.00210.3170.7250.7250.0000.0000.0000.000
9A14ALA0-0.012-0.02011.9371.2861.2860.0000.0000.0000.000
10A15LEU0-0.066-0.03115.1591.2091.2090.0000.0000.0000.000
11A16LYS10.8660.9449.67627.99327.9930.0000.0000.0000.000
12A17ARG10.8590.93914.38118.69418.6940.0000.0000.0000.000
13A18ARG10.8890.95515.21617.15317.1530.0000.0000.0000.000
14A19SER0-0.037-0.02516.796-0.857-0.8570.0000.0000.0000.000
15A20ILE0-0.051-0.01015.3100.5990.5990.0000.0000.0000.000
16A21ARG10.9200.96018.70013.09713.0970.0000.0000.0000.000
17A22ARG10.9590.99220.35813.17213.1720.0000.0000.0000.000
18A23TYR00.025-0.00116.716-0.600-0.6000.0000.0000.0000.000
19A24ARG10.8360.90511.41722.94622.9460.0000.0000.0000.000
20A25LYS10.9570.96517.85913.38713.3870.0000.0000.0000.000
21A26ASP-1-0.816-0.87514.635-18.672-18.6720.0000.0000.0000.000
22A27PRO00.0110.00316.159-0.282-0.2820.0000.0000.0000.000
23A28VAL00.0250.00512.173-1.155-1.1550.0000.0000.0000.000
24A29PRO0-0.011-0.00311.0511.2311.2310.0000.0000.0000.000
25A30GLU-1-0.800-0.88513.374-16.490-16.4900.0000.0000.0000.000
26A31GLY00.0190.01113.2170.0730.0730.0000.0000.0000.000
27A32LEU00.0200.0187.159-0.606-0.6060.0000.0000.0000.000
28A33LEU00.009-0.00510.436-0.504-0.5040.0000.0000.0000.000
29A34ARG10.8920.93613.26417.98617.9860.0000.0000.0000.000
30A35GLU-1-0.838-0.8826.918-38.088-38.0880.0000.0000.0000.000
31A36ILE0-0.005-0.0058.8900.5370.5370.0000.0000.0000.000
32A37LEU0-0.007-0.01511.4841.1831.1830.0000.0000.0000.000
33A38GLU-1-0.907-0.94014.129-18.069-18.0690.0000.0000.0000.000
34A39ALA00.0030.00411.7180.8320.8320.0000.0000.0000.000
35A40ALA0-0.009-0.01613.7850.9780.9780.0000.0000.0000.000
36A41LEU0-0.033-0.02515.9541.0371.0370.0000.0000.0000.000
37A42ARG10.9100.96516.84316.25416.2540.0000.0000.0000.000
38A43ALA00.0080.01319.0000.2430.2430.0000.0000.0000.000
39A44PRO0-0.0180.00420.8140.5570.5570.0000.0000.0000.000
40A45SER00.0350.00024.3320.1690.1690.0000.0000.0000.000
41A46ALA0-0.004-0.00227.5930.1380.1380.0000.0000.0000.000
42A47TRP0-0.018-0.02931.2920.0190.0190.0000.0000.0000.000
43A48ASN0-0.035-0.01527.175-0.251-0.2510.0000.0000.0000.000
44A49LEU00.0130.00229.165-0.132-0.1320.0000.0000.0000.000
45A50GLN0-0.0200.00725.260-0.305-0.3050.0000.0000.0000.000
46A51PRO00.0080.00127.6970.0570.0570.0000.0000.0000.000
47A52TRP00.0120.01223.4570.3190.3190.0000.0000.0000.000
48A53ARG10.7930.88326.15110.72110.7210.0000.0000.0000.000
49A54ILE00.0250.00220.484-0.108-0.1080.0000.0000.0000.000
50A55VAL00.0090.02224.4290.1290.1290.0000.0000.0000.000
51A56VAL00.009-0.00619.648-0.347-0.3470.0000.0000.0000.000
52A57VAL0-0.0050.00822.4620.2370.2370.0000.0000.0000.000
53A58ARG10.8690.89519.44314.50714.5070.0000.0000.0000.000
54A59ASP-1-0.774-0.86123.611-10.560-10.5600.0000.0000.0000.000
55A60PRO00.014-0.00326.7620.0450.0450.0000.0000.0000.000
56A61ALA00.0170.02228.4000.1250.1250.0000.0000.0000.000
57A62THR00.004-0.02728.9780.2220.2220.0000.0000.0000.000
58A63LYS10.7970.89323.16913.05013.0500.0000.0000.0000.000
59A64ARG10.9590.98628.1059.1089.1080.0000.0000.0000.000
60A65ALA00.0160.01031.1130.2010.2010.0000.0000.0000.000
61A66LEU00.013-0.00727.6570.1260.1260.0000.0000.0000.000
62A67ARG10.8170.89829.39910.19610.1960.0000.0000.0000.000
63A68GLU-1-0.945-0.96130.758-8.214-8.2140.0000.0000.0000.000
64A69ALA00.0020.00632.6240.1810.1810.0000.0000.0000.000
65A70ALA0-0.038-0.01629.7080.0880.0880.0000.0000.0000.000
66A71PHE0-0.004-0.00331.730-0.117-0.1170.0000.0000.0000.000
67A72GLY00.0610.03633.1980.1230.1230.0000.0000.0000.000
68A73GLN0-0.058-0.03727.941-0.516-0.5160.0000.0000.0000.000
69A74ALA00.0450.02227.538-0.184-0.1840.0000.0000.0000.000
70A75HIS00.006-0.00122.759-0.211-0.2110.0000.0000.0000.000
71A76VAL0-0.026-0.01523.312-0.572-0.5720.0000.0000.0000.000
72A77GLU-1-0.834-0.91625.503-10.336-10.3360.0000.0000.0000.000
73A78GLU-1-0.966-0.99123.357-12.392-12.3920.0000.0000.0000.000
74A79ALA0-0.0230.01419.771-0.508-0.5080.0000.0000.0000.000
75A80PRO0-0.049-0.00516.6830.5560.5560.0000.0000.0000.000
76A81VAL0-0.009-0.01717.0170.2770.2770.0000.0000.0000.000
77A82VAL00.0060.00519.698-0.141-0.1410.0000.0000.0000.000
78A83LEU0-0.021-0.00117.2980.1760.1760.0000.0000.0000.000
79A84VAL00.007-0.00121.8440.2620.2620.0000.0000.0000.000
80A85LEU0-0.0160.00222.903-0.019-0.0190.0000.0000.0000.000
81A86TYR0-0.007-0.02325.1820.3430.3430.0000.0000.0000.000
82A87ALA00.0190.00227.884-0.334-0.3340.0000.0000.0000.000
83A88ASP-1-0.789-0.86830.421-8.732-8.7320.0000.0000.0000.000
84A89LEU00.0360.01633.179-0.112-0.1120.0000.0000.0000.000
85A90GLU-1-0.784-0.89234.992-8.200-8.2000.0000.0000.0000.000
86A91ASP-1-0.818-0.89732.473-9.474-9.4740.0000.0000.0000.000
87A92ALA00.0090.01332.184-0.010-0.0100.0000.0000.0000.000
88A93LEU0-0.042-0.02333.8330.0670.0670.0000.0000.0000.000
89A94ALA0-0.020-0.00537.4620.1900.1900.0000.0000.0000.000
90A95HIS10.8640.93333.9809.2239.2230.0000.0000.0000.000
91A96LEU00.0340.02434.510-0.193-0.1930.0000.0000.0000.000
92A97ASP-1-0.827-0.90735.014-8.308-8.3080.0000.0000.0000.000
93A98GLU-1-0.911-0.95030.732-10.021-10.0210.0000.0000.0000.000
94A99VAL0-0.048-0.00829.658-0.309-0.3090.0000.0000.0000.000
95A100ILE0-0.0200.00431.366-0.126-0.1260.0000.0000.0000.000
96A101HIS00.0560.02230.2390.1390.1390.0000.0000.0000.000
97A102PRO00.0540.02430.3760.3310.3310.0000.0000.0000.000
98A103GLY00.0130.01033.5280.2400.2400.0000.0000.0000.000
99A104VAL0-0.055-0.01235.5650.2760.2760.0000.0000.0000.000
100A105GLN0-0.001-0.00736.9510.1610.1610.0000.0000.0000.000
101A106GLY00.0330.00940.4550.1080.1080.0000.0000.0000.000
102A107GLU-1-0.848-0.93243.718-6.745-6.7450.0000.0000.0000.000
103A108ARG10.9150.95641.2167.4667.4660.0000.0000.0000.000
104A109ARG10.7610.86334.7428.6498.6490.0000.0000.0000.000
105A110GLU-1-0.813-0.89440.761-7.209-7.2090.0000.0000.0000.000
106A111ALA00.0080.00043.615-0.026-0.0260.0000.0000.0000.000
107A112GLN0-0.012-0.01437.367-0.160-0.1600.0000.0000.0000.000
108A113LYS10.8830.94138.9347.7537.7530.0000.0000.0000.000
109A114GLN0-0.006-0.01440.7870.0550.0550.0000.0000.0000.000
110A115ALA0-0.048-0.01441.3440.0880.0880.0000.0000.0000.000
111A116ILE00.0000.00236.4070.0130.0130.0000.0000.0000.000
112A117GLN00.023-0.00639.9550.0300.0300.0000.0000.0000.000
113A118ARG10.9040.94242.3246.9066.9060.0000.0000.0000.000
114A119ALA0-0.0150.00940.7150.0930.0930.0000.0000.0000.000
115A120PHE00.032-0.00836.2160.0030.0030.0000.0000.0000.000
116A121ALA0-0.020-0.00241.7410.0500.0500.0000.0000.0000.000
117A122ALA0-0.0150.00445.2450.1280.1280.0000.0000.0000.000
118A123MET0-0.055-0.00938.779-0.032-0.0320.0000.0000.0000.000
119A124GLY00.0670.03044.0220.0120.0120.0000.0000.0000.000
120A125GLN0-0.025-0.03839.761-0.072-0.0720.0000.0000.0000.000
121A126GLU-1-0.891-0.94740.076-7.590-7.5900.0000.0000.0000.000
122A127ALA00.0320.01639.110-0.243-0.2430.0000.0000.0000.000
123A128ARG10.8300.91538.0077.3707.3700.0000.0000.0000.000
124A129LYS10.8420.92035.6208.1198.1190.0000.0000.0000.000
125A130ALA00.0220.02734.293-0.370-0.3700.0000.0000.0000.000
126A131TRP00.0370.01332.815-0.421-0.4210.0000.0000.0000.000
127A132ALA00.014-0.00231.881-0.351-0.3510.0000.0000.0000.000
128A133SER0-0.006-0.01829.991-0.497-0.4970.0000.0000.0000.000
129A134GLY0-0.012-0.00428.863-0.414-0.4140.0000.0000.0000.000
130A135GLN00.0150.00428.195-0.599-0.5990.0000.0000.0000.000
131A136SER00.008-0.01125.593-0.562-0.5620.0000.0000.0000.000
132A137TYR0-0.038-0.03424.192-0.497-0.4970.0000.0000.0000.000
133A138ILE0-0.0200.01122.411-0.571-0.5710.0000.0000.0000.000
134A139LEU00.0070.01419.127-0.790-0.7900.0000.0000.0000.000
135A140LEU00.003-0.00319.287-0.919-0.9190.0000.0000.0000.000
136A141GLY00.0090.00519.153-0.726-0.7260.0000.0000.0000.000
137A142TYR00.001-0.00316.525-0.724-0.7240.0000.0000.0000.000
138A143LEU00.0150.01114.849-1.524-1.5240.0000.0000.0000.000
139A144LEU0-0.026-0.02614.499-1.293-1.2930.0000.0000.0000.000
140A145LEU0-0.0250.00013.390-0.818-0.8180.0000.0000.0000.000
141A146LEU00.0170.00110.280-2.246-2.2460.0000.0000.0000.000
142A147LEU0-0.016-0.0069.674-2.917-2.9170.0000.0000.0000.000
143A148GLU-1-0.838-0.9019.580-27.592-27.5920.0000.0000.0000.000
144A149ALA0-0.027-0.0127.839-2.813-2.8130.0000.0000.0000.000
145A150TYR0-0.052-0.0705.152-9.606-9.6060.0000.0000.0000.000
146A151GLY0-0.045-0.0075.994-1.502-1.5020.0000.0000.0000.000
147A152LEU0-0.064-0.0317.3232.5902.5900.0000.0000.0000.000
148A153GLY00.0240.01310.6500.6510.6510.0000.0000.0000.000
149A154SER00.0410.00313.9530.7710.7710.0000.0000.0000.000
150A155VAL0-0.023-0.01416.8450.2490.2490.0000.0000.0000.000
151A156PRO00.0110.01720.1370.1740.1740.0000.0000.0000.000
152A157MET0-0.065-0.02622.6120.4740.4740.0000.0000.0000.000
153A158LEU00.0770.02126.356-0.019-0.0190.0000.0000.0000.000
154A159GLY0-0.0280.00929.6750.3530.3530.0000.0000.0000.000
155A160PHE0-0.033-0.03629.224-0.100-0.1000.0000.0000.0000.000
156A161ASP-1-0.746-0.84232.764-8.168-8.1680.0000.0000.0000.000
157A162PRO00.011-0.02534.407-0.121-0.1210.0000.0000.0000.000
158A163GLU-1-0.957-0.97135.431-7.624-7.6240.0000.0000.0000.000
159A164ARG10.8870.92436.3778.2528.2520.0000.0000.0000.000
160A165VAL00.0060.00130.708-0.099-0.0990.0000.0000.0000.000
161A166ARG10.8830.95233.6298.1858.1850.0000.0000.0000.000
162A167ALA0-0.007-0.00235.666-0.008-0.0080.0000.0000.0000.000
163A168ILE0-0.037-0.02132.5590.0190.0190.0000.0000.0000.000
164A169LEU0-0.030-0.01829.240-0.184-0.1840.0000.0000.0000.000
165A170GLY00.0150.03233.141-0.086-0.0860.0000.0000.0000.000
166A171LEU0-0.037-0.01130.8930.0160.0160.0000.0000.0000.000
167A172PRO00.0220.00234.6230.2730.2730.0000.0000.0000.000
168A173SER00.0110.00237.080-0.169-0.1690.0000.0000.0000.000
169A174ARG10.8460.89035.9408.5288.5280.0000.0000.0000.000
170A175ALA00.0140.02133.393-0.065-0.0650.0000.0000.0000.000
171A176ALA0-0.0060.01232.6950.2250.2250.0000.0000.0000.000
172A177ILE00.031-0.01029.297-0.206-0.2060.0000.0000.0000.000
173A178PRO0-0.0070.01627.0950.0230.0230.0000.0000.0000.000
174A179ALA00.0200.01124.533-0.113-0.1130.0000.0000.0000.000
175A180LEU00.0260.04125.349-0.136-0.1360.0000.0000.0000.000
176A181VAL0-0.011-0.02918.893-0.150-0.1500.0000.0000.0000.000
177A182ALA00.0100.03420.836-0.184-0.1840.0000.0000.0000.000
178A183LEU0-0.004-0.02114.411-0.526-0.5260.0000.0000.0000.000
179A184GLY00.0640.01514.8860.6580.6580.0000.0000.0000.000
180A185TYR00.0370.0208.726-0.080-0.0800.0000.0000.0000.000
181A186PRO00.0000.00611.6761.7061.7060.0000.0000.0000.000
182A187ALA0-0.016-0.01714.799-0.400-0.4000.0000.0000.0000.000
183A188GLU-1-0.863-0.93317.331-13.139-13.1390.0000.0000.0000.000
184A189GLU-1-0.890-0.95016.785-16.507-16.5070.0000.0000.0000.000
185A190GLY00.0220.01417.636-0.474-0.4740.0000.0000.0000.000
186A191TYR0-0.010-0.01119.9330.0240.0240.0000.0000.0000.000
187A192PRO00.0050.01522.130-0.433-0.4330.0000.0000.0000.000
188A193SER00.002-0.00422.9490.4740.4740.0000.0000.0000.000
189A194HIS00.0540.03524.326-0.681-0.6810.0000.0000.0000.000
190A195ARG10.8780.92321.89213.15113.1510.0000.0000.0000.000
191A196LEU00.0150.01027.6350.2350.2350.0000.0000.0000.000
192A197PRO00.0380.02429.124-0.350-0.3500.0000.0000.0000.000
193A198LEU00.0490.03526.8810.0800.0800.0000.0000.0000.000
194A199GLU-1-0.835-0.93230.139-9.592-9.5920.0000.0000.0000.000
195A200ARG10.8580.93133.2388.9918.9910.0000.0000.0000.000
196A201VAL0-0.058-0.03230.1880.1590.1590.0000.0000.0000.000
197A202VAL0-0.011-0.00429.6220.0490.0490.0000.0000.0000.000
198A203LEU0-0.034-0.00733.0380.1490.1490.0000.0000.0000.000
199A204TRP00.003-0.00429.243-0.122-0.1220.0000.0000.0000.000
200A205ARG00.0290.02036.203-0.260-0.2600.0000.0000.0000.000