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: NLG9Q

Calculation Name: 3ZOH-D-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin mononucleotide | cyclohex-2-en-1-one

Ligand 3-letter code: FMN | A2Q

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3ZOH

Chain ID: D

ChEMBL ID:

UniProt ID: Q72HI0

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 178
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1784336.397993
FMO2-HF: Nuclear repulsion 1716656.550381
FMO2-HF: Total energy -67679.847613
FMO2-MP2: Total energy -67882.291069


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.
20.3222.9370.586-1.407-1.797-0.011
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 : 0.898 / q_NPA : 0.944
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].
3A3SER00.0540.0252.685-0.4142.2030.586-1.407-1.797-0.011
4A4TYR0-0.013-0.0165.4232.0112.0110.0000.0000.0000.000
5A5ARG10.9860.9939.01926.54926.5490.0000.0000.0000.000
6A6ALA00.0330.02312.0160.2060.2060.0000.0000.0000.000
7A7GLN0-0.023-0.02913.6650.9630.9630.0000.0000.0000.000
8A8GLY00.0540.04116.9420.8500.8500.0000.0000.0000.000
9A9PRO0-0.001-0.00716.316-0.752-0.7520.0000.0000.0000.000
10A10LEU0-0.0010.00810.154-0.567-0.5670.0000.0000.0000.000
11A11PRO0-0.012-0.00311.8820.6180.6180.0000.0000.0000.000
12A12GLY0-0.007-0.01512.5670.8520.8520.0000.0000.0000.000
13A13PHE0-0.047-0.01911.520-1.601-1.6010.0000.0000.0000.000
14A14TYR00.0730.01711.8620.7120.7120.0000.0000.0000.000
15A15HIS0-0.044-0.0247.135-1.169-1.1690.0000.0000.0000.000
16A16TYR00.0080.0188.610-0.745-0.7450.0000.0000.0000.000
17A17TYR0-0.0390.01511.2291.2381.2380.0000.0000.0000.000
18A18PRO0-0.005-0.01012.628-0.949-0.9490.0000.0000.0000.000
19A19GLY00.0310.02016.236-0.088-0.0880.0000.0000.0000.000
20A20VAL00.0460.01418.5870.1940.1940.0000.0000.0000.000
21A21PRO0-0.079-0.03622.278-0.003-0.0030.0000.0000.0000.000
22A22ALA00.0410.03424.4920.3200.3200.0000.0000.0000.000
23A23VAL0-0.032-0.02527.084-0.060-0.0600.0000.0000.0000.000
24A24VAL00.0130.01329.2380.2150.2150.0000.0000.0000.000
25A25GLY00.0200.01531.8660.0330.0330.0000.0000.0000.000
26A26VAL0-0.037-0.02835.6800.0230.0230.0000.0000.0000.000
27A27ARG10.8860.92037.9686.4326.4320.0000.0000.0000.000
28A28VAL0-0.055-0.01941.573-0.013-0.0130.0000.0000.0000.000
29A29GLU-1-0.931-0.96344.034-6.039-6.0390.0000.0000.0000.000
30A30GLU-1-0.872-0.93847.251-6.171-6.1710.0000.0000.0000.000
31A31ARG10.8070.91641.5746.7856.7850.0000.0000.0000.000
32A32VAL00.0040.00540.264-0.123-0.1230.0000.0000.0000.000
33A33ASN0-0.018-0.03035.2100.0050.0050.0000.0000.0000.000
34A34PHE00.0370.03334.278-0.088-0.0880.0000.0000.0000.000
35A35CYS0-0.073-0.05629.046-0.047-0.0470.0000.0000.0000.000
36A36PRO00.0190.04326.468-0.019-0.0190.0000.0000.0000.000
37A37ALA00.0020.00025.271-0.163-0.1630.0000.0000.0000.000
38A38VAL00.0040.00119.399-0.016-0.0160.0000.0000.0000.000
39A39TRP0-0.046-0.01517.425-0.159-0.1590.0000.0000.0000.000
40A40ASN0-0.059-0.03821.2640.5670.5670.0000.0000.0000.000
41A41THR00.0350.00521.067-0.603-0.6030.0000.0000.0000.000
42A42GLY00.0170.02823.0530.4430.4430.0000.0000.0000.000
43A43LEU0-0.059-0.03423.911-0.405-0.4050.0000.0000.0000.000
44A44SER0-0.012-0.01726.149-0.062-0.0620.0000.0000.0000.000
45A45ALA00.0070.00928.7930.0250.0250.0000.0000.0000.000
46A46ASP-1-0.910-0.93230.609-7.452-7.4520.0000.0000.0000.000
47A47PRO00.014-0.00733.650-0.003-0.0030.0000.0000.0000.000
48A48PRO00.0200.02432.005-0.245-0.2450.0000.0000.0000.000
49A49LEU0-0.045-0.01629.8290.1600.1600.0000.0000.0000.000
50A50PHE00.0450.00225.806-0.309-0.3090.0000.0000.0000.000
51A51GLY00.0150.01326.4970.2690.2690.0000.0000.0000.000
52A52VAL0-0.015-0.01725.640-0.302-0.3020.0000.0000.0000.000
53A53SER0-0.0030.00322.7850.3200.3200.0000.0000.0000.000
54A54ILE0-0.025-0.01825.193-0.135-0.1350.0000.0000.0000.000
55A55SER00.0040.00626.5220.1740.1740.0000.0000.0000.000
56A56PRO00.0510.01528.1560.2030.2030.0000.0000.0000.000
57A57LYS10.9460.97728.3399.7629.7620.0000.0000.0000.000
58A58ARG10.8570.93525.20510.44510.4450.0000.0000.0000.000
59A59PHE00.0400.02732.0760.0610.0610.0000.0000.0000.000
60A60THR00.0500.00232.4600.2020.2020.0000.0000.0000.000
61A61HIS0-0.036-0.01131.1110.2940.2940.0000.0000.0000.000
62A62GLY00.0560.02234.1740.0920.0920.0000.0000.0000.000
63A63LEU0-0.003-0.00137.6770.1560.1560.0000.0000.0000.000
64A64LEU00.0080.01232.4740.1310.1310.0000.0000.0000.000
65A65LEU0-0.025-0.01035.0430.1310.1310.0000.0000.0000.000
66A66LYS10.9440.98638.0156.4936.4930.0000.0000.0000.000
67A67ALA00.0350.01539.7980.1460.1460.0000.0000.0000.000
68A68ARG10.8250.91337.9767.4287.4280.0000.0000.0000.000
69A69ARG10.9610.99138.6176.6756.6750.0000.0000.0000.000
70A70PHE0-0.011-0.02131.199-0.003-0.0030.0000.0000.0000.000
71A71SER00.010-0.00635.332-0.006-0.0060.0000.0000.0000.000
72A72ALA0-0.005-0.00529.772-0.196-0.1960.0000.0000.0000.000
73A73SER00.0410.02631.5990.1090.1090.0000.0000.0000.000
74A74PHE0-0.029-0.01226.708-0.312-0.3120.0000.0000.0000.000
75A75HIS10.8490.91328.9848.7348.7340.0000.0000.0000.000
76A76PRO00.0940.04828.665-0.375-0.3750.0000.0000.0000.000
77A77PHE0-0.004-0.01626.9270.0600.0600.0000.0000.0000.000
78A78GLY0-0.015-0.00128.486-0.028-0.0280.0000.0000.0000.000
79A79GLN00.0100.00331.4590.0110.0110.0000.0000.0000.000
80A80LYS10.8840.93527.3599.3999.3990.0000.0000.0000.000
81A81ASP-1-0.825-0.90229.114-9.177-9.1770.0000.0000.0000.000
82A82LEU00.0220.02031.5650.0290.0290.0000.0000.0000.000
83A83VAL00.022-0.00127.6920.0250.0250.0000.0000.0000.000
84A84HIS00.0560.04126.624-0.265-0.2650.0000.0000.0000.000
85A85TRP00.0150.01229.107-0.056-0.0560.0000.0000.0000.000
86A86LEU00.006-0.00131.9630.0720.0720.0000.0000.0000.000
87A87GLY0-0.010-0.01428.4460.0300.0300.0000.0000.0000.000
88A88SER0-0.087-0.03929.137-0.242-0.2420.0000.0000.0000.000
89A89HIS0-0.0170.00130.6950.1520.1520.0000.0000.0000.000
90A90SER0-0.070-0.05233.778-0.072-0.0720.0000.0000.0000.000
91A91GLY00.0720.02535.4300.1310.1310.0000.0000.0000.000
92A92ARG10.8220.91633.8238.3348.3340.0000.0000.0000.000
93A93GLU-1-0.800-0.88637.204-7.709-7.7090.0000.0000.0000.000
94A94VAL00.0100.00338.1170.1230.1230.0000.0000.0000.000
95A95ASP-1-0.788-0.89140.279-6.866-6.8660.0000.0000.0000.000
96A96LYS10.7530.87433.4818.4378.4370.0000.0000.0000.000
97A97GLY00.0260.02339.444-0.085-0.0850.0000.0000.0000.000
98A98GLN0-0.044-0.03642.0970.1360.1360.0000.0000.0000.000
99A99ALA0-0.044-0.00738.269-0.007-0.0070.0000.0000.0000.000
100A100PRO00.0090.00940.0640.0230.0230.0000.0000.0000.000
101A101HIS0-0.020-0.02140.008-0.163-0.1630.0000.0000.0000.000
102A102PHE00.0610.05239.6800.1640.1640.0000.0000.0000.000
103A103LEU0-0.028-0.02842.099-0.140-0.1400.0000.0000.0000.000
104A104GLY00.0300.01941.8340.0510.0510.0000.0000.0000.000
105A105HIS00.0210.00142.5610.2260.2260.0000.0000.0000.000
106A106THR0-0.112-0.08241.5480.0850.0850.0000.0000.0000.000
107A107GLY00.0060.00344.0820.0080.0080.0000.0000.0000.000
108A108VAL0-0.035-0.00238.8330.0040.0040.0000.0000.0000.000
109A109PRO00.0190.02338.8120.0600.0600.0000.0000.0000.000
110A110ILE00.0030.00936.586-0.281-0.2810.0000.0000.0000.000
111A111LEU0-0.038-0.01134.1520.0980.0980.0000.0000.0000.000
112A112GLU-1-0.850-0.94436.846-6.953-6.9530.0000.0000.0000.000
113A113GLY00.0050.00036.694-0.193-0.1930.0000.0000.0000.000
114A114ALA0-0.081-0.03933.494-0.225-0.2250.0000.0000.0000.000
115A115TYR00.0630.02427.0640.0340.0340.0000.0000.0000.000
116A116ALA00.0420.02331.5320.0740.0740.0000.0000.0000.000
117A117ALA0-0.040-0.03032.828-0.178-0.1780.0000.0000.0000.000
118A118TYR0-0.0060.01628.7910.1580.1580.0000.0000.0000.000
119A119GLU-1-0.724-0.82534.455-6.899-6.8990.0000.0000.0000.000
120A120LEU0-0.041-0.02031.873-0.054-0.0540.0000.0000.0000.000
121A121GLU-1-0.887-0.94935.943-6.883-6.8830.0000.0000.0000.000
122A122LEU0-0.084-0.04233.518-0.193-0.1930.0000.0000.0000.000
123A123LEU00.0040.01933.9980.1760.1760.0000.0000.0000.000
124A124GLU-1-0.864-0.91932.327-8.463-8.4630.0000.0000.0000.000
125A125VAL0-0.023-0.01931.302-0.127-0.1270.0000.0000.0000.000
126A126HIS10.8160.89127.9709.1649.1640.0000.0000.0000.000
127A127THR00.0070.00127.464-0.155-0.1550.0000.0000.0000.000
128A128PHE0-0.032-0.02222.543-0.081-0.0810.0000.0000.0000.000
129A129GLY00.0030.01122.976-0.392-0.3920.0000.0000.0000.000
130A130ASP-1-0.877-0.92722.881-11.490-11.4900.0000.0000.0000.000
131A131HIS0-0.050-0.05923.3800.4340.4340.0000.0000.0000.000
132A132ASP-1-0.745-0.83725.678-9.419-9.4190.0000.0000.0000.000
133A133LEU0-0.025-0.00924.256-0.043-0.0430.0000.0000.0000.000
134A134PHE00.017-0.00626.9900.2990.2990.0000.0000.0000.000
135A135VAL00.010-0.00428.478-0.242-0.2420.0000.0000.0000.000
136A136GLY00.0420.01230.6240.2830.2830.0000.0000.0000.000
137A137ARG10.9760.98432.1827.1777.1770.0000.0000.0000.000
138A138VAL0-0.013-0.00832.5480.1090.1090.0000.0000.0000.000
139A139VAL0-0.057-0.03835.2670.1080.1080.0000.0000.0000.000
140A140ALA00.0010.00738.1960.1880.1880.0000.0000.0000.000
141A141VAL0-0.016-0.01234.971-0.226-0.2260.0000.0000.0000.000
142A142TRP0-0.046-0.02736.7110.2160.2160.0000.0000.0000.000
143A143GLU-1-0.922-0.98035.313-8.043-8.0430.0000.0000.0000.000
144A144GLU-1-0.911-0.94336.289-7.049-7.0490.0000.0000.0000.000
145A145GLU-1-0.859-0.93937.093-7.049-7.0490.0000.0000.0000.000
146A146GLY0-0.049-0.02037.9780.0270.0270.0000.0000.0000.000
147A147LEU0-0.044-0.02733.970-0.229-0.2290.0000.0000.0000.000
148A148LEU0-0.0100.00631.645-0.378-0.3780.0000.0000.0000.000
149A149ASP-1-0.864-0.93230.157-8.923-8.9230.0000.0000.0000.000
150A150GLU-1-0.909-0.96633.481-8.017-8.0170.0000.0000.0000.000
151A151LYS10.8800.94130.5938.8428.8420.0000.0000.0000.000
152A152GLY00.0750.04931.325-0.142-0.1420.0000.0000.0000.000
153A153ARG10.8190.90426.6409.5259.5250.0000.0000.0000.000
154A154PRO00.0060.00426.8840.2300.2300.0000.0000.0000.000
155A155LYS10.9180.96328.3938.3888.3880.0000.0000.0000.000
156A156PRO00.0360.01626.340-0.198-0.1980.0000.0000.0000.000
157A157GLY0-0.0030.02025.6900.2640.2640.0000.0000.0000.000
158A158LEU0-0.002-0.00826.784-0.036-0.0360.0000.0000.0000.000
159A159ALA00.0210.00524.6640.1120.1120.0000.0000.0000.000
160A160LEU0-0.0140.00125.103-0.254-0.2540.0000.0000.0000.000
161A161LEU0-0.023-0.00919.104-0.199-0.1990.0000.0000.0000.000
162A162TYR0-0.002-0.00620.6050.0750.0750.0000.0000.0000.000
163A163TYR00.0590.00414.920-0.214-0.2140.0000.0000.0000.000
164A164GLY0-0.0090.00516.134-0.760-0.7600.0000.0000.0000.000
165A165LYS10.8790.92117.07015.30715.3070.0000.0000.0000.000
166A166GLY00.0510.02720.6510.0500.0500.0000.0000.0000.000
167A167LEU00.0050.02317.5040.3610.3610.0000.0000.0000.000
168A168TYR0-0.014-0.03720.572-0.329-0.3290.0000.0000.0000.000
169A169GLY0-0.012-0.00821.563-0.149-0.1490.0000.0000.0000.000
170A170ARG10.8580.94822.35910.42610.4260.0000.0000.0000.000
171A171PRO0-0.023-0.00221.311-0.482-0.4820.0000.0000.0000.000
172A172ALA00.0170.01021.5620.2670.2670.0000.0000.0000.000
173A173GLU-1-0.828-0.93923.277-9.608-9.6080.0000.0000.0000.000
174A174GLU-1-0.920-0.96123.890-10.691-10.6910.0000.0000.0000.000
175A175THR0-0.089-0.04723.350-0.235-0.2350.0000.0000.0000.000
176A176PHE00.0050.00421.1150.1340.1340.0000.0000.0000.000
177A177ALA0-0.042-0.02522.821-0.201-0.2010.0000.0000.0000.000
178A178PRO-1-0.939-0.94920.803-10.705-10.7050.0000.0000.0000.000