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: QM3VY

Calculation Name: 7F76-B-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin mononucleotide | isopropyl alcohol

Ligand 3-letter code: FMN | IPA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7F76

Chain ID: B

ChEMBL ID:

UniProt ID:

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 173
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1809075.608056
FMO2-HF: Nuclear repulsion 1741778.651895
FMO2-HF: Total energy -67296.956162
FMO2-MP2: Total energy -67494.213987


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:0:HIS)


Summations of interaction energy for fragment #1(A:0:HIS)
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.
-30.708-27.0032.198-2.065-3.839-0.018
Interaction energy analysis for fragmet #1(A:0:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.849 / q_NPA : 0.904
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].
3A2GLN0-0.041-0.0183.8632.1953.429-0.004-0.418-0.8130.001
66A65ASP-1-0.785-0.8794.999-50.158-50.085-0.001-0.010-0.0620.000
168A167TYR00.021-0.0052.195-10.361-8.0752.204-1.620-2.870-0.019
172A171GLN0-0.093-0.0404.1911.1811.293-0.001-0.017-0.0940.000
4A3LEU0-0.0130.0066.0755.3025.3020.0000.0000.0000.000
5A4VAL00.0330.0238.8191.0651.0650.0000.0000.0000.000
6A5VAL0-0.023-0.01212.3790.3450.3450.0000.0000.0000.000
7A6ILE00.0460.02915.2960.6160.6160.0000.0000.0000.000
8A7ASN00.0180.01318.9000.3630.3630.0000.0000.0000.000
9A8GLY00.0440.02221.6760.4180.4180.0000.0000.0000.000
10A9SER0-0.068-0.02324.6070.8060.8060.0000.0000.0000.000
11A10PRO00.0750.03826.819-0.195-0.1950.0000.0000.0000.000
12A11ARG10.9210.95729.0929.7219.7210.0000.0000.0000.000
13A12LYS10.9670.96828.3209.7829.7820.0000.0000.0000.000
14A13SER00.0140.01728.459-0.275-0.2750.0000.0000.0000.000
15A14GLY0-0.045-0.02228.9280.2250.2250.0000.0000.0000.000
16A15ARG10.9450.97627.2409.6939.6930.0000.0000.0000.000
17A16THR00.0390.01423.081-0.120-0.1200.0000.0000.0000.000
18A17ARG10.8910.95222.41012.24712.2470.0000.0000.0000.000
19A18ILE0-0.0130.02621.924-0.523-0.5230.0000.0000.0000.000
20A19LEU00.0100.00418.908-0.511-0.5110.0000.0000.0000.000
21A20ALA0-0.006-0.00518.013-0.879-0.8790.0000.0000.0000.000
22A21THR00.0430.00116.881-0.905-0.9050.0000.0000.0000.000
23A22PHE0-0.074-0.02816.352-0.537-0.5370.0000.0000.0000.000
24A23ILE00.012-0.01112.783-0.958-0.9580.0000.0000.0000.000
25A24GLU-1-0.923-0.96712.353-19.763-19.7630.0000.0000.0000.000
26A25LYS10.9100.94712.18214.16514.1650.0000.0000.0000.000
27A26GLU-1-0.931-0.95012.828-20.287-20.2870.0000.0000.0000.000
28A27PHE0-0.063-0.0448.803-1.441-1.4410.0000.0000.0000.000
29A28ASN0-0.044-0.0076.184-2.037-2.0370.0000.0000.0000.000
30A29ALA0-0.0130.0067.925-3.033-3.0330.0000.0000.0000.000
31A30LYS10.9880.97810.29323.95823.9580.0000.0000.0000.000
32A31ILE00.0100.01412.5530.3210.3210.0000.0000.0000.000
33A32ILE00.0060.00516.0590.1730.1730.0000.0000.0000.000
34A33ASP-1-0.701-0.82318.898-12.763-12.7630.0000.0000.0000.000
35A34LEU00.0180.01521.9370.4810.4810.0000.0000.0000.000
36A35SER0-0.126-0.07725.0190.6730.6730.0000.0000.0000.000
37A36GLU-1-0.957-0.99323.304-12.859-12.8590.0000.0000.0000.000
38A37GLU-1-0.939-0.95427.112-9.426-9.4260.0000.0000.0000.000
39A38THR00.0110.01324.7550.2790.2790.0000.0000.0000.000
40A39LEU0-0.042-0.01223.672-0.067-0.0670.0000.0000.0000.000
41A40PRO00.0190.01827.9910.2270.2270.0000.0000.0000.000
42A41LEU00.017-0.00130.719-0.263-0.2630.0000.0000.0000.000
43A42TYR00.0140.01130.6750.0900.0900.0000.0000.0000.000
44A43ASN00.001-0.00832.6220.0030.0030.0000.0000.0000.000
45A44GLY0-0.0070.00033.1890.2030.2030.0000.0000.0000.000
46A45GLU-1-0.933-0.96334.232-8.266-8.2660.0000.0000.0000.000
47A46GLU-1-0.910-0.96333.423-9.164-9.1640.0000.0000.0000.000
48A47TYR00.0180.00932.672-0.323-0.3230.0000.0000.0000.000
49A48GLN0-0.024-0.03630.919-0.450-0.4500.0000.0000.0000.000
50A49GLY0-0.067-0.03728.377-0.435-0.4350.0000.0000.0000.000
51A50GLU-1-0.877-0.94327.695-11.119-11.1190.0000.0000.0000.000
52A51LEU0-0.052-0.00928.778-0.142-0.1420.0000.0000.0000.000
53A52GLU-1-0.797-0.88625.230-12.391-12.3910.0000.0000.0000.000
54A53HIS00.0320.01423.761-0.991-0.9910.0000.0000.0000.000
55A54VAL00.0040.00823.373-0.581-0.5810.0000.0000.0000.000
56A55ARG10.8330.90823.10611.93111.9310.0000.0000.0000.000
57A56ALA00.0300.01819.843-0.793-0.7930.0000.0000.0000.000
58A57LEU0-0.0200.00418.672-1.241-1.2410.0000.0000.0000.000
59A58ARG10.9050.93918.93111.57011.5700.0000.0000.0000.000
60A59ASP-1-0.874-0.94217.343-17.263-17.2630.0000.0000.0000.000
61A60THR0-0.088-0.05813.838-1.814-1.8140.0000.0000.0000.000
62A61VAL00.000-0.01113.817-1.763-1.7630.0000.0000.0000.000
63A62LYS10.8230.89914.56115.32315.3230.0000.0000.0000.000
64A63LYS10.8440.91511.55418.68718.6870.0000.0000.0000.000
65A64ALA0-0.0170.0249.873-2.748-2.7480.0000.0000.0000.000
67A66ALA0-0.023-0.0238.2821.9941.9940.0000.0000.0000.000
68A67VAL00.008-0.00110.183-0.354-0.3540.0000.0000.0000.000
69A68ILE0-0.0130.00513.3180.7220.7220.0000.0000.0000.000
70A69LEU00.0170.01115.5810.4320.4320.0000.0000.0000.000
71A70THR0-0.020-0.03918.6720.5510.5510.0000.0000.0000.000
72A71SER00.041-0.01421.1650.2720.2720.0000.0000.0000.000
73A72PRO0-0.068-0.00924.9840.0200.0200.0000.0000.0000.000
74A73GLU-1-0.787-0.87628.149-10.011-10.0110.0000.0000.0000.000
75A74TYR0-0.058-0.03730.6270.2190.2190.0000.0000.0000.000
76A75HIS00.0320.00633.485-0.102-0.1020.0000.0000.0000.000
77A76SER00.0000.00734.1380.1010.1010.0000.0000.0000.000
78A77GLY00.0550.03431.5980.0110.0110.0000.0000.0000.000
79A78MET0-0.013-0.00326.196-0.221-0.2210.0000.0000.0000.000
80A79SER0-0.069-0.04827.7980.4150.4150.0000.0000.0000.000
81A80GLY00.0570.01529.465-0.196-0.1960.0000.0000.0000.000
82A81ALA00.0170.01328.325-0.022-0.0220.0000.0000.0000.000
83A82LEU00.0360.00722.409-0.274-0.2740.0000.0000.0000.000
84A83LYS10.8100.87425.86810.36310.3630.0000.0000.0000.000
85A84ASN00.0080.00628.1680.1720.1720.0000.0000.0000.000
86A85ALA00.0090.00223.678-0.085-0.0850.0000.0000.0000.000
87A86LEU0-0.032-0.03721.657-0.412-0.4120.0000.0000.0000.000
88A87ASP-1-0.797-0.86424.861-10.853-10.8530.0000.0000.0000.000
89A88PHE0-0.0060.01125.4060.1620.1620.0000.0000.0000.000
90A89LEU0-0.077-0.02120.192-0.410-0.4100.0000.0000.0000.000
91A90SER00.0400.00722.3670.5770.5770.0000.0000.0000.000
92A91ASN00.0480.01321.050-0.668-0.6680.0000.0000.0000.000
93A92GLU-1-0.839-0.89220.172-15.082-15.0820.0000.0000.0000.000
94A93GLN0-0.005-0.00118.094-0.435-0.4350.0000.0000.0000.000
95A94PHE00.026-0.01816.516-1.455-1.4550.0000.0000.0000.000
96A95ALA00.0010.00516.893-0.434-0.4340.0000.0000.0000.000
97A96HIS0-0.044-0.02915.563-1.131-1.1310.0000.0000.0000.000
98A97LYS10.8390.95511.88622.27722.2770.0000.0000.0000.000
99A98PRO00.0000.0029.7921.3001.3000.0000.0000.0000.000
100A99VAL00.004-0.00212.649-0.892-0.8920.0000.0000.0000.000
101A100GLY00.0360.02315.0550.7400.7400.0000.0000.0000.000
102A101LEU0-0.024-0.01116.3170.1930.1930.0000.0000.0000.000
103A102ILE00.002-0.01117.2050.1860.1860.0000.0000.0000.000
104A103ALA00.0090.01921.3580.1240.1240.0000.0000.0000.000
105A104VAL0-0.044-0.02324.375-0.063-0.0630.0000.0000.0000.000
106A105ALA00.0250.01126.8590.2800.2800.0000.0000.0000.000
107A106GLY0-0.030-0.02830.465-0.027-0.0270.0000.0000.0000.000
108A107GLY00.0390.02433.0020.2740.2740.0000.0000.0000.000
109A108GLY0-0.014-0.00934.5930.0660.0660.0000.0000.0000.000
110A109LYS10.9360.95334.2888.7298.7290.0000.0000.0000.000
111A110GLY00.0330.04033.158-0.029-0.0290.0000.0000.0000.000
112A111GLY0-0.002-0.02229.104-0.233-0.2330.0000.0000.0000.000
113A112ILE00.0300.01228.585-0.400-0.4000.0000.0000.0000.000
114A113ASN00.0070.02229.772-0.204-0.2040.0000.0000.0000.000
115A114ALA0-0.005-0.00627.953-0.139-0.1390.0000.0000.0000.000
116A115LEU0-0.001-0.00523.448-0.321-0.3210.0000.0000.0000.000
117A116THR00.005-0.00325.618-0.347-0.3470.0000.0000.0000.000
118A117ASN00.0060.01127.841-0.191-0.1910.0000.0000.0000.000
119A118MET0-0.012-0.01622.4390.0610.0610.0000.0000.0000.000
120A119ARG10.8280.91120.63313.49613.4960.0000.0000.0000.000
121A120THR0-0.048-0.02924.051-0.095-0.0950.0000.0000.0000.000
122A121VAL0-0.010-0.01324.9270.0290.0290.0000.0000.0000.000
123A122GLY00.0320.02021.680-0.166-0.1660.0000.0000.0000.000
124A123ARG10.9800.99221.75711.45311.4530.0000.0000.0000.000
125A124GLY0-0.058-0.02723.5210.1630.1630.0000.0000.0000.000
126A125VAL0-0.027-0.00720.8870.1960.1960.0000.0000.0000.000
127A126TYR0-0.043-0.03420.616-0.569-0.5690.0000.0000.0000.000
128A127ALA00.0460.03417.411-0.604-0.6040.0000.0000.0000.000
129A128ASN0-0.059-0.03314.9871.6701.6700.0000.0000.0000.000
130A129VAL0-0.038-0.02315.959-0.956-0.9560.0000.0000.0000.000
131A130ILE00.0230.02213.8110.5850.5850.0000.0000.0000.000
132A131PRO00.0050.00617.2320.7660.7660.0000.0000.0000.000
133A132LYS10.8770.96517.21716.41616.4160.0000.0000.0000.000
134A133GLN00.0270.01718.981-0.685-0.6850.0000.0000.0000.000
135A134LEU0-0.016-0.00620.3830.3120.3120.0000.0000.0000.000
136A135VAL00.0140.00422.850-0.021-0.0210.0000.0000.0000.000
137A136LEU0-0.011-0.00221.740-0.001-0.0010.0000.0000.0000.000
138A137ASP-1-0.769-0.90625.921-9.780-9.7800.0000.0000.0000.000
139A138PRO0-0.078-0.06128.953-0.235-0.2350.0000.0000.0000.000
140A139HIS00.0610.03229.9490.1390.1390.0000.0000.0000.000
141A140CYS0-0.054-0.00825.412-0.124-0.1240.0000.0000.0000.000
142A141PHE0-0.045-0.04024.065-0.546-0.5460.0000.0000.0000.000
143A142ASP-1-0.741-0.83427.134-9.820-9.8200.0000.0000.0000.000
144A143ARG10.8350.87928.0699.5009.5000.0000.0000.0000.000
145A144GLU-1-0.957-0.95330.181-8.763-8.7630.0000.0000.0000.000
146A145ASN0-0.047-0.04828.3960.0450.0450.0000.0000.0000.000
147A146TYR0-0.040-0.01323.837-0.584-0.5840.0000.0000.0000.000
148A147THR00.011-0.01223.196-0.903-0.9030.0000.0000.0000.000
149A148LEU0-0.037-0.00819.7710.4030.4030.0000.0000.0000.000
150A149THR00.0760.04423.458-0.200-0.2000.0000.0000.0000.000
151A150ASP-1-0.800-0.90722.504-13.169-13.1690.0000.0000.0000.000
152A151ASP-1-0.875-0.93621.952-12.148-12.1480.0000.0000.0000.000
153A152SER0-0.042-0.03722.493-0.373-0.3730.0000.0000.0000.000
154A153LYS10.8540.93218.39213.26613.2660.0000.0000.0000.000
155A154LEU00.0040.01817.621-1.184-1.1840.0000.0000.0000.000
156A155LEU0-0.007-0.01318.366-0.663-0.6630.0000.0000.0000.000
157A156VAL0-0.001-0.00815.768-0.521-0.5210.0000.0000.0000.000
158A157LYS10.8850.92711.79421.48021.4800.0000.0000.0000.000
159A158GLY00.0290.01813.834-1.283-1.2830.0000.0000.0000.000
160A159VAL0-0.045-0.03415.686-0.107-0.1070.0000.0000.0000.000
161A160ILE00.0030.0059.394-1.183-1.1830.0000.0000.0000.000
162A161ASP-1-0.848-0.91010.548-26.538-26.5380.0000.0000.0000.000
163A162GLU-1-0.832-0.92611.085-18.147-18.1470.0000.0000.0000.000
164A163LEU0-0.0110.00210.114-0.692-0.6920.0000.0000.0000.000
165A164LYS10.9690.9655.40938.43238.4320.0000.0000.0000.000
166A165LEU0-0.061-0.0097.286-2.532-2.5320.0000.0000.0000.000
167A166TYR00.0860.0189.956-0.044-0.0440.0000.0000.0000.000
169A168LYS10.8470.9035.81831.83931.8390.0000.0000.0000.000
170A169MET0-0.029-0.0067.3850.7620.7620.0000.0000.0000.000
171A170HIS00.0260.0249.6441.9771.9770.0000.0000.0000.000
173A172TYR-1-0.952-0.9437.402-21.449-21.4490.0000.0000.0000.000