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: 5RK5Z

Calculation Name: 2FCR-A-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin mononucleotide

Ligand 3-letter code: FMN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2FCR

Chain ID: A

ChEMBL ID:

UniProt ID: P14070

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 173
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1781762.73403
FMO2-HF: Nuclear repulsion 1715244.70759
FMO2-HF: Total energy -66518.026441
FMO2-MP2: Total energy -66711.824307


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:LYS)


Summations of interaction energy for fragment #1(A:1:LYS)
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.
-1006.268-997.36341.965-25.409-25.461-0.294
Interaction energy analysis for fragmet #1(A:1:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.563 / q_NPA : 1.777
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].
3A3GLY00.0590.0273.075-11.029-8.6430.101-1.178-1.310-0.007
4A4ILE0-0.041-0.0285.3975.8895.933-0.001-0.002-0.0400.000
26A26ALA0-0.030-0.0313.786-6.164-5.8620.000-0.121-0.1810.000
27A27LYS10.7780.8771.96434.22434.9305.243-2.775-3.174-0.040
28A28ALA00.0340.0322.651-21.523-18.2111.019-2.030-2.301-0.022
29A29ASP-1-0.843-0.8961.812-199.980-198.12515.756-8.722-8.890-0.109
30A30ALA0-0.064-0.0423.31711.29511.5170.021-0.060-0.183-0.001
46A46TYR0-0.130-0.0932.362-21.519-18.0921.301-1.555-3.173-0.017
47A47ASP-1-0.882-0.9341.709-149.107-152.75718.527-8.929-5.947-0.098
48A48LEU0-0.019-0.0144.48911.67711.857-0.001-0.027-0.1520.000
173A173VAL-1-0.833-0.8864.349-72.626-72.505-0.001-0.010-0.1100.000
5A5PHE00.0320.0267.6400.0680.0680.0000.0000.0000.000
6A6PHE0-0.003-0.00811.5321.9231.9230.0000.0000.0000.000
7A7SER00.0400.00714.9450.7760.7760.0000.0000.0000.000
8A8THR0-0.026-0.02618.3980.8290.8290.0000.0000.0000.000
9A9SER00.0370.02921.1790.6960.6960.0000.0000.0000.000
10A10THR0-0.034-0.02724.7990.2200.2200.0000.0000.0000.000
11A11GLY00.0040.00821.3770.2470.2470.0000.0000.0000.000
12A12ASN00.0320.01020.399-0.900-0.9000.0000.0000.0000.000
13A13THR00.0250.00217.415-0.395-0.3950.0000.0000.0000.000
14A14THR0-0.0040.00515.512-1.301-1.3010.0000.0000.0000.000
15A15GLU-1-0.901-0.94715.463-29.367-29.3670.0000.0000.0000.000
16A16VAL00.0070.00016.314-1.413-1.4130.0000.0000.0000.000
17A17ALA00.0160.02012.505-2.263-2.2630.0000.0000.0000.000
18A18ASP-1-0.864-0.94711.438-46.116-46.1160.0000.0000.0000.000
19A19PHE0-0.066-0.02911.945-2.428-2.4280.0000.0000.0000.000
20A20ILE00.0370.0279.944-1.534-1.5340.0000.0000.0000.000
21A21GLY00.0800.0377.918-3.819-3.8190.0000.0000.0000.000
22A22LYS10.7670.8838.15548.65848.6580.0000.0000.0000.000
23A23THR0-0.047-0.03010.7630.1120.1120.0000.0000.0000.000
24A24LEU00.0330.0226.544-0.412-0.4120.0000.0000.0000.000
25A25GLY0-0.022-0.0076.506-5.031-5.0310.0000.0000.0000.000
31A31PRO0-0.016-0.0076.983-1.997-1.9970.0000.0000.0000.000
32A32ILE0-0.0160.0058.1732.3662.3660.0000.0000.0000.000
33A33ASP-1-0.776-0.87211.551-32.467-32.4670.0000.0000.0000.000
34A34VAL00.007-0.02115.125-0.742-0.7420.0000.0000.0000.000
35A35ASP-1-0.895-0.91516.446-27.049-27.0490.0000.0000.0000.000
36A36ASP-1-0.972-0.97515.220-34.247-34.2470.0000.0000.0000.000
37A37VAL0-0.080-0.03313.057-1.293-1.2930.0000.0000.0000.000
38A38THR0-0.061-0.03615.5411.4531.4530.0000.0000.0000.000
39A39ASP-1-0.880-0.94614.266-36.701-36.7010.0000.0000.0000.000
40A40PRO00.0250.02013.804-2.909-2.9090.0000.0000.0000.000
41A41GLN0-0.039-0.05113.114-3.387-3.3870.0000.0000.0000.000
42A42ALA00.0410.0279.411-2.502-2.5020.0000.0000.0000.000
43A43LEU0-0.021-0.0137.880-6.286-6.2860.0000.0000.0000.000
44A44LYS10.8920.9458.53038.48338.4830.0000.0000.0000.000
45A45ASP-1-0.976-0.9635.593-62.727-62.7270.0000.0000.0000.000
49A49LEU0-0.0330.0066.354-9.740-9.7400.0000.0000.0000.000
50A50PHE00.005-0.0078.5284.9624.9620.0000.0000.0000.000
51A51LEU0-0.014-0.01010.883-1.327-1.3270.0000.0000.0000.000
52A52GLY00.0450.01813.7891.8971.8970.0000.0000.0000.000
53A53ALA00.0290.00816.1650.1200.1200.0000.0000.0000.000
54A54PRO0-0.0540.00519.7860.2820.2820.0000.0000.0000.000
55A55THR00.005-0.01023.259-0.119-0.1190.0000.0000.0000.000
56A56TRP0-0.028-0.01226.0740.9020.9020.0000.0000.0000.000
57A57ASN0-0.065-0.02429.2561.2491.2490.0000.0000.0000.000
58A58THR00.005-0.00831.328-0.285-0.2850.0000.0000.0000.000
59A59GLY00.0110.01233.1990.5040.5040.0000.0000.0000.000
60A60ALA0-0.050-0.01131.3190.3340.3340.0000.0000.0000.000
61A61ASP-1-0.959-0.97631.733-19.454-19.4540.0000.0000.0000.000
62A62THR00.0150.01028.430-0.384-0.3840.0000.0000.0000.000
63A63GLU-1-0.982-0.98926.815-20.112-20.1120.0000.0000.0000.000
64A64ARG10.7690.85426.58722.45422.4540.0000.0000.0000.000
65A65SER0-0.034-0.03823.109-0.006-0.0060.0000.0000.0000.000
66A66GLY0-0.005-0.00625.1870.1740.1740.0000.0000.0000.000
67A67THR0-0.064-0.04922.018-0.639-0.6390.0000.0000.0000.000
68A68SER00.020-0.02520.5520.6870.6870.0000.0000.0000.000
69A69TRP0-0.052-0.04114.495-0.745-0.7450.0000.0000.0000.000
70A70ASP-1-0.781-0.86220.815-24.358-24.3580.0000.0000.0000.000
71A71GLU-1-0.843-0.89722.302-26.066-26.0660.0000.0000.0000.000
72A72PHE00.0430.01114.862-0.284-0.2840.0000.0000.0000.000
73A73LEU0-0.021-0.02518.945-0.847-0.8470.0000.0000.0000.000
74A74TYR0-0.103-0.08521.0990.3470.3470.0000.0000.0000.000
75A75ASP-1-0.909-0.95723.451-22.876-22.8760.0000.0000.0000.000
76A76LYS10.8020.89718.28629.57129.5710.0000.0000.0000.000
77A77LEU0-0.0200.00516.023-0.963-0.9630.0000.0000.0000.000
78A78PRO0-0.026-0.02318.397-0.654-0.6540.0000.0000.0000.000
79A79GLU-1-0.955-0.97218.681-28.325-28.3250.0000.0000.0000.000
80A80VAL0-0.074-0.01913.326-0.516-0.5160.0000.0000.0000.000
81A81ASP-1-0.940-0.96016.226-33.198-33.1980.0000.0000.0000.000
82A82MET0-0.003-0.01511.187-2.078-2.0780.0000.0000.0000.000
83A83LYS10.9380.97613.50529.91329.9130.0000.0000.0000.000
84A84ASP-1-0.980-0.99213.088-35.931-35.9310.0000.0000.0000.000
85A85LEU0-0.0230.0097.805-0.811-0.8110.0000.0000.0000.000
86A86PRO0-0.032-0.0078.7923.0823.0820.0000.0000.0000.000
87A87VAL00.019-0.00410.160-4.613-4.6130.0000.0000.0000.000
88A88ALA00.0190.01612.5233.3963.3960.0000.0000.0000.000
89A89ILE00.0040.01014.032-1.545-1.5450.0000.0000.0000.000
90A90PHE0-0.022-0.00513.0931.0861.0860.0000.0000.0000.000
91A91GLY00.0300.00618.033-0.310-0.3100.0000.0000.0000.000
92A92LEU0-0.033-0.02419.8480.4340.4340.0000.0000.0000.000
93A93GLY00.005-0.01823.3410.3530.3530.0000.0000.0000.000
94A94ASP-1-0.838-0.91827.159-19.202-19.2020.0000.0000.0000.000
95A95ALA00.003-0.01330.5390.1790.1790.0000.0000.0000.000
96A96GLU-1-0.953-0.96232.593-16.523-16.5230.0000.0000.0000.000
97A97GLY0-0.058-0.03334.7730.5750.5750.0000.0000.0000.000
98A98TYR0-0.074-0.04832.3580.5320.5320.0000.0000.0000.000
99A99PRO00.0310.02533.588-0.555-0.5550.0000.0000.0000.000
100A100ASP-1-0.853-0.93235.406-16.545-16.5450.0000.0000.0000.000
101A101ASN0-0.092-0.06832.3080.3620.3620.0000.0000.0000.000
102A102PHE00.0420.03927.760-0.871-0.8710.0000.0000.0000.000
103A103CYS0-0.0370.00924.798-0.681-0.6810.0000.0000.0000.000
104A104ASP-1-0.716-0.84225.856-21.151-21.1510.0000.0000.0000.000
105A105ALA0-0.004-0.00323.697-0.030-0.0300.0000.0000.0000.000
106A106ILE0-0.040-0.00320.978-0.873-0.8730.0000.0000.0000.000
107A107GLU-1-0.757-0.86522.102-22.667-22.6670.0000.0000.0000.000
108A108GLU-1-0.736-0.82223.895-24.033-24.0330.0000.0000.0000.000
109A109ILE00.0400.02017.485-0.457-0.4570.0000.0000.0000.000
110A110HIS0-0.024-0.03519.390-1.467-1.4670.0000.0000.0000.000
111A111ASP-1-0.778-0.85020.396-24.795-24.7950.0000.0000.0000.000
112A112CYS0-0.047-0.01720.9370.3450.3450.0000.0000.0000.000
113A113PHE00.0430.00513.263-0.649-0.6490.0000.0000.0000.000
114A114ALA00.0120.01917.848-0.486-0.4860.0000.0000.0000.000
115A115LYS10.8030.90519.72326.13526.1350.0000.0000.0000.000
116A116GLN0-0.043-0.02417.4742.6052.6050.0000.0000.0000.000
117A117GLY0-0.025-0.01817.158-1.187-1.1870.0000.0000.0000.000
118A118ALA00.0340.03213.982-0.826-0.8260.0000.0000.0000.000
119A119LYS10.8810.94514.00037.74137.7410.0000.0000.0000.000
120A120PRO00.0110.00314.551-2.401-2.4010.0000.0000.0000.000
121A121VAL0-0.066-0.02912.4330.6640.6640.0000.0000.0000.000
122A122GLY00.0130.00115.896-0.458-0.4580.0000.0000.0000.000
123A123PHE0-0.0050.00317.4060.6470.6470.0000.0000.0000.000
124A124SER0-0.053-0.03821.0030.1530.1530.0000.0000.0000.000
125A125ASN00.003-0.01823.5110.9580.9580.0000.0000.0000.000
126A126PRO0-0.0170.00427.178-0.318-0.3180.0000.0000.0000.000
127A127ASP-1-0.876-0.93029.453-18.791-18.7910.0000.0000.0000.000
128A128ASP-1-0.884-0.92126.324-23.554-23.5540.0000.0000.0000.000
129A129TYR0-0.036-0.03325.989-0.571-0.5710.0000.0000.0000.000
130A130ASP-1-0.930-0.95231.426-17.369-17.3690.0000.0000.0000.000
131A131TYR0-0.100-0.06930.867-0.375-0.3750.0000.0000.0000.000
132A132GLU-1-0.958-0.96035.175-15.894-15.8940.0000.0000.0000.000
133A133GLU-1-1.028-1.01634.790-16.925-16.9250.0000.0000.0000.000
134A134SER00.010-0.03029.167-0.475-0.4750.0000.0000.0000.000
135A135LYS10.8350.91929.81419.46719.4670.0000.0000.0000.000
136A136SER0-0.056-0.03325.595-0.503-0.5030.0000.0000.0000.000
137A137VAL00.0160.02426.670-0.922-0.9220.0000.0000.0000.000
138A138ARG10.7630.82925.82723.49223.4920.0000.0000.0000.000
139A139ASP-1-0.973-1.00127.975-21.904-21.9040.0000.0000.0000.000
140A140GLY0-0.025-0.01029.549-0.158-0.1580.0000.0000.0000.000
141A141LYS10.8630.95223.83323.90723.9070.0000.0000.0000.000
142A142PHE00.0790.03724.4050.2320.2320.0000.0000.0000.000
143A143LEU0-0.067-0.04722.911-1.032-1.0320.0000.0000.0000.000
144A144GLY00.0420.01219.718-1.396-1.3960.0000.0000.0000.000
145A145LEU0-0.0290.00118.8051.3841.3840.0000.0000.0000.000
146A146PRO00.0180.02820.865-0.746-0.7460.0000.0000.0000.000
147A147LEU0-0.012-0.03019.513-0.264-0.2640.0000.0000.0000.000
148A148ASP-1-0.724-0.83323.957-20.689-20.6890.0000.0000.0000.000
149A149MET0-0.028-0.01921.949-0.523-0.5230.0000.0000.0000.000
150A150VAL0-0.041-0.00826.3730.1660.1660.0000.0000.0000.000
151A151ASN0-0.072-0.07529.9961.0821.0820.0000.0000.0000.000
152A152ASP-1-0.965-0.96427.727-21.670-21.6700.0000.0000.0000.000
153A153GLN0-0.012-0.02529.625-0.453-0.4530.0000.0000.0000.000
154A154ILE0-0.056-0.03026.0070.0600.0600.0000.0000.0000.000
155A155PRO0-0.049-0.01125.092-0.527-0.5270.0000.0000.0000.000
156A156MET00.0750.04618.462-1.289-1.2890.0000.0000.0000.000
157A157GLU-1-0.861-0.94719.036-28.678-28.6780.0000.0000.0000.000
158A158LYS10.8840.92719.23823.32523.3250.0000.0000.0000.000
159A159ARG10.7950.89321.55825.39225.3920.0000.0000.0000.000
160A160VAL00.0270.01615.651-0.712-0.7120.0000.0000.0000.000
161A161ALA00.0050.00215.832-1.848-1.8480.0000.0000.0000.000
162A162GLY00.0290.01916.525-1.429-1.4290.0000.0000.0000.000
163A163TRP0-0.031-0.02314.737-0.994-0.9940.0000.0000.0000.000
164A164VAL00.0100.00211.590-1.325-1.3250.0000.0000.0000.000
165A165GLU-1-0.956-0.98213.194-36.561-36.5610.0000.0000.0000.000
166A166ALA0-0.0220.00415.246-0.312-0.3120.0000.0000.0000.000
167A167VAL00.0550.03011.2500.1170.1170.0000.0000.0000.000
168A168VAL0-0.0310.0009.405-1.904-1.9040.0000.0000.0000.000
169A169SER0-0.089-0.05711.5360.2230.2230.0000.0000.0000.000
170A170GLU-1-0.924-0.96814.445-33.811-33.8110.0000.0000.0000.000
171A171THR0-0.044-0.0479.446-0.895-0.8950.0000.0000.0000.000
172A172GLY0-0.052-0.01610.231-0.580-0.5800.0000.0000.0000.000