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: G8751

Calculation Name: 1E20-A-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin mononucleotide | beta-mercaptoethanol | nickel (ii) ion

Ligand 3-letter code: FMN | BME | NI

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1E20

Chain ID: A

ChEMBL ID:

UniProt ID: Q9SWE5

Base Structure: X-ray

Registration Date: 2025-09-02

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 184
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2012551.423174
FMO2-HF: Nuclear repulsion 1939836.81027
FMO2-HF: Total energy -72714.612904
FMO2-MP2: Total energy -72925.836194


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:18:ARG)


Summations of interaction energy for fragment #1(A:18:ARG)
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.
-397.005-391.30517.762-10.757-12.705-0.141
Interaction energy analysis for fragmet #1(A:18:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.722 / q_NPA : 1.836
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].
3A20PRO00.0100.0353.245-1.231-0.0940.027-0.357-0.807-0.001
4A21ARG10.8310.9024.60070.28870.363-0.001-0.012-0.0630.000
81A98ASP-1-0.838-0.9024.906-82.690-82.659-0.001-0.001-0.0280.000
179A197TRP0-0.021-0.0143.5882.0712.5790.003-0.099-0.4120.000
182A200GLN0-0.062-0.0342.7174.8775.5810.022-0.324-0.402-0.002
184A202HIS-1-0.833-0.8931.843-208.085-204.84017.712-9.964-10.993-0.138
5A22VAL00.0200.0097.5492.7722.7720.0000.0000.0000.000
6A23LEU0-0.003-0.00110.6642.3022.3020.0000.0000.0000.000
7A24LEU00.0260.01513.8860.9500.9500.0000.0000.0000.000
8A25ALA00.025-0.00216.6571.0551.0550.0000.0000.0000.000
9A26ALA00.0090.01520.1610.3560.3560.0000.0000.0000.000
10A27SER00.006-0.03123.6550.6990.6990.0000.0000.0000.000
11A28GLY0-0.011-0.01626.9520.2010.2010.0000.0000.0000.000
12A29SER0-0.045-0.05329.0390.5950.5950.0000.0000.0000.000
13A30VAL00.0180.01129.842-0.515-0.5150.0000.0000.0000.000
14A31ALA0-0.010-0.01127.425-0.080-0.0800.0000.0000.0000.000
15A32ALA00.0410.01925.920-0.734-0.7340.0000.0000.0000.000
16A33ILE00.0150.02526.355-0.564-0.5640.0000.0000.0000.000
17A34LYS10.9120.94824.70421.62721.6270.0000.0000.0000.000
18A35PHE00.0240.01819.539-0.819-0.8190.0000.0000.0000.000
19A36GLY00.0730.05021.000-1.298-1.2980.0000.0000.0000.000
20A37ASN0-0.017-0.01820.892-1.175-1.1750.0000.0000.0000.000
21A38LEU00.0250.01117.732-0.855-0.8550.0000.0000.0000.000
22A39CYS0-0.037-0.02116.697-1.960-1.9600.0000.0000.0000.000
23A40HIS0-0.004-0.00516.053-2.721-2.7210.0000.0000.0000.000
24A41CYS0-0.099-0.04016.371-0.234-0.2340.0000.0000.0000.000
25A42PHE00.0160.00010.960-1.716-1.7160.0000.0000.0000.000
26A43THR00.0250.01911.221-3.607-3.6070.0000.0000.0000.000
27A44GLU-1-0.915-0.95011.660-41.423-41.4230.0000.0000.0000.000
28A45TRP0-0.080-0.0396.899-3.116-3.1160.0000.0000.0000.000
29A46ALA00.011-0.0116.705-8.929-8.9290.0000.0000.0000.000
30A47GLU-1-0.821-0.8797.668-53.358-53.3580.0000.0000.0000.000
31A48VAL0-0.010-0.0079.469-0.215-0.2150.0000.0000.0000.000
32A49ARG10.8840.97212.69039.14139.1410.0000.0000.0000.000
33A50ALA00.0260.01014.997-0.353-0.3530.0000.0000.0000.000
34A51VAL0-0.0030.00218.3030.7180.7180.0000.0000.0000.000
35A52VAL00.0130.00720.7740.1970.1970.0000.0000.0000.000
36A53THR00.0280.01724.5010.5040.5040.0000.0000.0000.000
37A54LYS11.0191.01627.50217.31617.3160.0000.0000.0000.000
38A55SER0-0.026-0.01830.8890.2570.2570.0000.0000.0000.000
39A56SER0-0.043-0.03127.4410.1290.1290.0000.0000.0000.000
40A57LEU00.015-0.00327.9750.0230.0230.0000.0000.0000.000
41A58HIS0-0.0150.00730.8420.3420.3420.0000.0000.0000.000
42A59PHE0-0.041-0.03130.4420.4620.4620.0000.0000.0000.000
43A60LEU0-0.0260.00324.415-0.208-0.2080.0000.0000.0000.000
44A61ASP-1-0.801-0.89428.829-19.370-19.3700.0000.0000.0000.000
45A62LYS10.9690.97826.38819.97319.9730.0000.0000.0000.000
46A63LEU0-0.016-0.00926.093-0.769-0.7690.0000.0000.0000.000
47A64SER0-0.056-0.03425.912-0.425-0.4250.0000.0000.0000.000
48A65LEU0-0.005-0.00921.495-0.695-0.6950.0000.0000.0000.000
49A66PRO00.0110.01317.7860.6650.6650.0000.0000.0000.000
50A67GLN0-0.020-0.01820.304-0.543-0.5430.0000.0000.0000.000
51A68GLU-1-0.896-0.94614.413-37.184-37.1840.0000.0000.0000.000
52A69VAL0-0.045-0.02316.089-1.023-1.0230.0000.0000.0000.000
53A70THR0-0.019-0.00117.1761.7011.7010.0000.0000.0000.000
54A71LEU0-0.040-0.02318.403-0.939-0.9390.0000.0000.0000.000
55A72TYR00.0270.01117.0380.1080.1080.0000.0000.0000.000
56A73THR0-0.068-0.07522.0860.3800.3800.0000.0000.0000.000
57A74ASP-1-0.795-0.91825.430-21.209-21.2090.0000.0000.0000.000
58A75GLU-1-0.880-0.92227.725-18.771-18.7710.0000.0000.0000.000
59A76ASP-1-0.796-0.87823.653-23.097-23.0970.0000.0000.0000.000
60A77GLU-1-0.821-0.90924.005-24.278-24.2780.0000.0000.0000.000
61A78TRP0-0.056-0.01925.9240.2680.2680.0000.0000.0000.000
62A79SER0-0.013-0.02427.1840.2580.2580.0000.0000.0000.000
63A80SER0-0.086-0.03623.468-0.088-0.0880.0000.0000.0000.000
64A81TRP0-0.089-0.03325.4560.3150.3150.0000.0000.0000.000
65A82ASN0-0.020-0.01528.0771.0251.0250.0000.0000.0000.000
66A83LYS10.8760.92530.61417.25917.2590.0000.0000.0000.000
67A84ILE00.0230.00729.969-0.589-0.5890.0000.0000.0000.000
68A85GLY0-0.011-0.01027.9040.3630.3630.0000.0000.0000.000
69A86ASP-1-0.796-0.87225.961-21.172-21.1720.0000.0000.0000.000
70A87PRO0-0.018-0.00721.304-0.190-0.1900.0000.0000.0000.000
71A88VAL00.0430.02622.9710.4640.4640.0000.0000.0000.000
72A89LEU00.0440.03019.321-1.343-1.3430.0000.0000.0000.000
73A90HIS0-0.025-0.05919.374-1.719-1.7190.0000.0000.0000.000
74A91ILE0-0.032-0.01218.984-1.510-1.5100.0000.0000.0000.000
75A92GLU-1-0.938-0.96816.123-32.438-32.4380.0000.0000.0000.000
76A93LEU0-0.002-0.00814.933-2.858-2.8580.0000.0000.0000.000
77A94ARG10.9040.96613.99431.49531.4950.0000.0000.0000.000
78A95ARG10.8820.94513.65828.73628.7360.0000.0000.0000.000
79A96TRP0-0.036-0.03110.209-2.818-2.8180.0000.0000.0000.000
80A97ALA00.0000.0059.164-4.617-4.6170.0000.0000.0000.000
82A99VAL0-0.035-0.0188.3052.2142.2140.0000.0000.0000.000
83A100LEU0-0.0090.01711.2260.6540.6540.0000.0000.0000.000
84A101VAL0-0.003-0.00113.8500.4890.4890.0000.0000.0000.000
85A102ILE0-0.0090.00016.6350.9360.9360.0000.0000.0000.000
86A103ALA0-0.0120.01420.0490.7030.7030.0000.0000.0000.000
87A104PRO0-0.020-0.02121.902-0.102-0.1020.0000.0000.0000.000
88A105LEU00.0540.04324.0620.0660.0660.0000.0000.0000.000
89A106SER00.0130.00925.6680.4950.4950.0000.0000.0000.000
90A107ALA00.0680.01129.446-0.207-0.2070.0000.0000.0000.000
91A108ASN0-0.010-0.00432.0770.1360.1360.0000.0000.0000.000
92A109THR0-0.009-0.00625.9720.0790.0790.0000.0000.0000.000
93A110LEU00.0060.00627.812-0.257-0.2570.0000.0000.0000.000
94A111GLY00.0390.02029.004-0.078-0.0780.0000.0000.0000.000
95A112LYS10.7860.87429.69419.78319.7830.0000.0000.0000.000
96A113ILE00.0000.00924.294-0.049-0.0490.0000.0000.0000.000
97A114ALA00.0180.01327.660-0.109-0.1090.0000.0000.0000.000
98A115GLY0-0.035-0.00930.1650.3460.3460.0000.0000.0000.000
99A116GLY0-0.0010.00328.5820.3070.3070.0000.0000.0000.000
100A117LEU0-0.034-0.02829.6310.1470.1470.0000.0000.0000.000
101A118CYS0-0.022-0.02424.549-0.892-0.8920.0000.0000.0000.000
102A119ASP-1-0.830-0.87128.712-18.954-18.9540.0000.0000.0000.000
103A120ASN0-0.046-0.04226.8340.3190.3190.0000.0000.0000.000
104A121LEU00.0570.05121.256-0.563-0.5630.0000.0000.0000.000
105A122LEU0-0.029-0.02021.443-0.778-0.7780.0000.0000.0000.000
106A123THR00.012-0.02522.941-0.813-0.8130.0000.0000.0000.000
107A125ILE00.0010.00617.930-0.598-0.5980.0000.0000.0000.000
108A126ILE0-0.007-0.00919.917-0.921-0.9210.0000.0000.0000.000
109A127ARG10.8560.93921.49321.48821.4880.0000.0000.0000.000
110A128ALA00.0040.00820.8120.6830.6830.0000.0000.0000.000
111A129TRP0-0.066-0.03413.316-0.852-0.8520.0000.0000.0000.000
112A130ASP-1-0.847-0.91816.688-33.382-33.3820.0000.0000.0000.000
113A131TYR00.0300.00616.452-1.786-1.7860.0000.0000.0000.000
114A132THR0-0.047-0.02315.093-1.172-1.1720.0000.0000.0000.000
115A133LYS10.8100.90510.56142.67942.6790.0000.0000.0000.000
116A134PRO00.0100.01911.1252.9142.9140.0000.0000.0000.000
117A135LEU00.0310.00113.976-0.736-0.7360.0000.0000.0000.000
118A136PHE00.0430.01412.7181.3541.3540.0000.0000.0000.000
119A137VAL00.0100.00017.7430.6650.6650.0000.0000.0000.000
120A138ALA00.0370.02721.1660.2840.2840.0000.0000.0000.000
121A139PRO0-0.006-0.00822.9950.6000.6000.0000.0000.0000.000
122A140ALA0-0.019-0.00926.6320.1200.1200.0000.0000.0000.000
123A141MET0-0.0340.01529.0640.4660.4660.0000.0000.0000.000
124A142ASN00.0370.01832.7810.1910.1910.0000.0000.0000.000
125A143THR00.0330.00636.250-0.055-0.0550.0000.0000.0000.000
126A144LEU00.0040.00137.414-0.026-0.0260.0000.0000.0000.000
127A145MET0-0.024-0.01135.736-0.038-0.0380.0000.0000.0000.000
128A146TRP00.0350.01529.043-0.257-0.2570.0000.0000.0000.000
129A147ASN0-0.006-0.01235.068-0.494-0.4940.0000.0000.0000.000
130A148ASN00.0100.01737.6520.2660.2660.0000.0000.0000.000
131A149PRO00.0530.01537.162-0.435-0.4350.0000.0000.0000.000
132A150PHE0-0.028-0.02736.311-0.162-0.1620.0000.0000.0000.000
133A151THR0-0.030-0.01631.805-0.564-0.5640.0000.0000.0000.000
134A152GLU-1-0.880-0.93632.112-19.369-19.3690.0000.0000.0000.000
135A153ARG10.9160.96532.66215.48815.4880.0000.0000.0000.000
136A154HIS00.0270.01730.880-0.471-0.4710.0000.0000.0000.000
137A155LEU00.001-0.01226.799-0.713-0.7130.0000.0000.0000.000
138A156LEU00.0410.03427.873-0.713-0.7130.0000.0000.0000.000
139A157SER00.004-0.01729.021-0.267-0.2670.0000.0000.0000.000
140A158LEU0-0.076-0.04324.659-0.521-0.5210.0000.0000.0000.000
141A159ASP-1-0.935-0.96324.340-25.437-25.4370.0000.0000.0000.000
142A160GLU-1-0.977-0.98124.821-21.150-21.1500.0000.0000.0000.000
143A161LEU0-0.080-0.03723.506-0.264-0.2640.0000.0000.0000.000
144A162GLY00.0080.01421.235-1.122-1.1220.0000.0000.0000.000
145A163ILE0-0.091-0.04519.664-1.805-1.8050.0000.0000.0000.000
146A164THR00.0040.00117.9450.3160.3160.0000.0000.0000.000
147A165LEU00.004-0.00519.958-0.126-0.1260.0000.0000.0000.000
148A166ILE00.000-0.00317.662-0.158-0.1580.0000.0000.0000.000
149A167PRO00.007-0.00422.2200.7670.7670.0000.0000.0000.000
150A168PRO0-0.0260.00025.957-0.228-0.2280.0000.0000.0000.000
151A169ILE00.008-0.00627.6570.4030.4030.0000.0000.0000.000
152A170LYS10.8590.94230.09018.22018.2200.0000.0000.0000.000
153A171LYS10.8990.91933.06817.41717.4170.0000.0000.0000.000
154A172ARG10.9500.99131.45919.41219.4120.0000.0000.0000.000
155A173LEU0-0.013-0.00835.1350.1320.1320.0000.0000.0000.000
156A174ALA00.0400.02238.2140.3580.3580.0000.0000.0000.000
157A175CYS0-0.072-0.03538.4400.3430.3430.0000.0000.0000.000
158A176GLY00.0360.03439.263-0.193-0.1930.0000.0000.0000.000
159A177ASP-1-0.815-0.90338.279-16.317-16.3170.0000.0000.0000.000
160A178TYR00.0310.00238.508-0.268-0.2680.0000.0000.0000.000
161A179GLY00.044-0.00834.329-0.192-0.1920.0000.0000.0000.000
162A180ASN0-0.025-0.01033.362-0.161-0.1610.0000.0000.0000.000
163A181GLY00.0680.04231.6850.3230.3230.0000.0000.0000.000
164A182ALA0-0.035-0.01031.032-0.314-0.3140.0000.0000.0000.000
165A183MET00.0110.01223.382-0.095-0.0950.0000.0000.0000.000
166A184ALA00.0290.02023.3180.3660.3660.0000.0000.0000.000
167A185GLU-1-0.945-0.97723.973-22.626-22.6260.0000.0000.0000.000
168A186PRO00.013-0.00520.309-0.866-0.8660.0000.0000.0000.000
169A187SER00.0590.03918.768-1.603-1.6030.0000.0000.0000.000
170A188LEU00.0310.03718.684-1.375-1.3750.0000.0000.0000.000
171A189ILE0-0.0010.01016.929-1.237-1.2370.0000.0000.0000.000
172A190TYR00.0430.02611.253-2.667-2.6670.0000.0000.0000.000
173A191SER0-0.024-0.02613.709-2.374-2.3740.0000.0000.0000.000
174A192THR0-0.023-0.02514.555-1.361-1.3610.0000.0000.0000.000
175A193VAL0-0.017-0.00610.743-1.603-1.6030.0000.0000.0000.000
176A194ARG10.8210.8959.16949.62949.6290.0000.0000.0000.000
177A195LEU00.0160.0009.724-3.826-3.8260.0000.0000.0000.000
178A196PHE00.0140.02710.911-1.028-1.0280.0000.0000.0000.000
180A198GLU-1-0.856-0.9386.442-68.103-68.1030.0000.0000.0000.000
181A199SER0-0.069-0.0417.7101.2341.2340.0000.0000.0000.000
183A201ALA0-0.0230.0006.0396.6756.6750.0000.0000.0000.000