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

tag_button

FMODB ID: 1991Z

Calculation Name: 2R6V-A-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin mononucleotide | nicotinamide | 1,2-ethanediol

Ligand 3-letter code: FMN | NCA | EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2R6V

Chain ID: A

ChEMBL ID:

UniProt ID: O58586

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 182
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1951828.025664
FMO2-HF: Nuclear repulsion 1880293.680854
FMO2-HF: Total energy -71534.34481
FMO2-MP2: Total energy -71745.188645


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:-9:HIS)


Summations of interaction energy for fragment #1(A:-9: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.
13.68222.99812.199-5.936-15.58-0.054
Interaction energy analysis for fragmet #1(A:-9:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.769 / q_NPA : 1.889
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].
3A-7HIS0-0.038-0.0332.496-22.283-19.9104.192-2.661-3.905-0.028
4A-6GLU-1-0.841-0.9044.337-53.190-53.065-0.001-0.013-0.1110.000
12A2GLU-1-0.791-0.8894.629-92.519-92.552-0.001-0.0170.0510.000
168A158TRP0-0.021-0.0332.598-19.046-12.4388.010-3.211-11.407-0.026
169A159SER00.0310.0074.5032.5392.782-0.001-0.034-0.2080.000
5A-5ASN0-0.020-0.0235.7585.6345.6340.0000.0000.0000.000
6A-4LEU0-0.0090.0197.0423.4273.4270.0000.0000.0000.000
7A-3TYR0-0.008-0.0169.250-1.795-1.7950.0000.0000.0000.000
8A-2PHE00.0180.02112.1111.9641.9640.0000.0000.0000.000
9A-1GLN00.0020.0036.363-0.294-0.2940.0000.0000.0000.000
10A0GLY00.0560.0227.6045.0485.0480.0000.0000.0000.000
11A1MET0-0.033-0.0117.052-10.592-10.5920.0000.0000.0000.000
13A3GLY00.0500.0219.1902.0682.0680.0000.0000.0000.000
14A4TYR00.0450.0116.267-0.143-0.1430.0000.0000.0000.000
15A5ARG10.8170.9015.29874.35174.3510.0000.0000.0000.000
16A6LEU00.009-0.00111.1501.0251.0250.0000.0000.0000.000
17A7LEU00.0060.01314.1732.2752.2750.0000.0000.0000.000
18A8TYR0-0.113-0.06510.234-0.555-0.5550.0000.0000.0000.000
19A9PRO00.011-0.01013.5710.3490.3490.0000.0000.0000.000
20A10MET00.0000.03013.5291.6391.6390.0000.0000.0000.000
21A11ARG10.8830.94115.28528.78428.7840.0000.0000.0000.000
22A12THR0-0.026-0.03213.436-1.348-1.3480.0000.0000.0000.000
23A13TYR0-0.024-0.02016.0282.4712.4710.0000.0000.0000.000
24A14LEU00.006-0.00516.239-2.424-2.4240.0000.0000.0000.000
25A15ILE0-0.022-0.00917.4351.3241.3240.0000.0000.0000.000
26A16VAL00.0270.02018.997-1.177-1.1770.0000.0000.0000.000
27A17SER0-0.004-0.01920.8560.1630.1630.0000.0000.0000.000
28A18GLY00.0440.02122.915-0.297-0.2970.0000.0000.0000.000
29A19HIS00.0550.00725.719-0.194-0.1940.0000.0000.0000.000
30A20GLY00.0240.02528.3680.2150.2150.0000.0000.0000.000
31A21GLU-1-0.884-0.93427.629-19.795-19.7950.0000.0000.0000.000
32A22GLU-1-0.824-0.88325.301-22.016-22.0160.0000.0000.0000.000
33A23THR0-0.042-0.02823.902-0.530-0.5300.0000.0000.0000.000
34A24ASN0-0.015-0.02817.191-1.231-1.2310.0000.0000.0000.000
35A25VAL00.0600.03517.7010.4620.4620.0000.0000.0000.000
36A26MET0-0.073-0.01813.545-1.682-1.6820.0000.0000.0000.000
37A27ALA00.0440.02911.7871.6611.6610.0000.0000.0000.000
38A28ALA0-0.029-0.02312.809-1.457-1.4570.0000.0000.0000.000
39A29ASP-1-0.718-0.80810.717-49.194-49.1940.0000.0000.0000.000
40A30TRP0-0.059-0.02910.1562.6712.6710.0000.0000.0000.000
41A31VAL0-0.005-0.01415.7791.1241.1240.0000.0000.0000.000
42A32THR0-0.020-0.01219.199-0.371-0.3710.0000.0000.0000.000
43A33VAL00.0090.00422.6080.3410.3410.0000.0000.0000.000
44A34VAL0-0.054-0.03625.616-0.545-0.5450.0000.0000.0000.000
45A35SER0-0.007-0.00428.1780.5750.5750.0000.0000.0000.000
46A36PHE00.002-0.00131.612-0.414-0.4140.0000.0000.0000.000
47A37ASP-1-0.894-0.93733.949-15.828-15.8280.0000.0000.0000.000
48A38PRO00.0580.02135.3830.1790.1790.0000.0000.0000.000
49A39PHE0-0.0120.00328.856-0.608-0.6080.0000.0000.0000.000
50A40ILE0-0.025-0.00828.714-0.102-0.1020.0000.0000.0000.000
51A41VAL00.0090.00624.813-0.446-0.4460.0000.0000.0000.000
52A42GLY00.0450.01323.3760.5960.5960.0000.0000.0000.000
53A43VAL0-0.028-0.00917.411-0.998-0.9980.0000.0000.0000.000
54A44ALA0-0.0010.02215.7680.8090.8090.0000.0000.0000.000
55A45VAL0-0.022-0.02414.925-2.120-2.1200.0000.0000.0000.000
56A46ALA00.0370.02812.4741.3061.3060.0000.0000.0000.000
57A47PRO00.0600.02414.4810.0970.0970.0000.0000.0000.000
58A48LYS10.8750.9259.81647.87147.8710.0000.0000.0000.000
59A49ARG10.8900.9578.63848.66548.6650.0000.0000.0000.000
60A50THR00.0340.00114.5060.9280.9280.0000.0000.0000.000
61A51THR00.0610.01116.3451.2731.2730.0000.0000.0000.000
62A52HIS0-0.0100.01117.6011.6611.6610.0000.0000.0000.000
63A53LYS10.8730.92817.39131.41231.4120.0000.0000.0000.000
64A54LEU00.0040.00920.8740.9440.9440.0000.0000.0000.000
65A55ILE00.0310.01720.5700.9000.9000.0000.0000.0000.000
66A56LYS10.8740.93723.39223.90423.9040.0000.0000.0000.000
67A57LYS10.8030.90925.51721.14121.1410.0000.0000.0000.000
68A58TYR0-0.014-0.04026.8801.0281.0280.0000.0000.0000.000
69A59GLY00.0330.02427.9710.6310.6310.0000.0000.0000.000
70A60GLU-1-0.795-0.89627.640-18.380-18.3800.0000.0000.0000.000
71A61PHE0-0.017-0.02622.996-0.824-0.8240.0000.0000.0000.000
72A62VAL00.0050.02023.9810.7830.7830.0000.0000.0000.000
73A63ILE00.0000.00221.048-1.435-1.4350.0000.0000.0000.000
74A64SER00.018-0.00821.8170.9550.9550.0000.0000.0000.000
75A65VAL0-0.036-0.02621.129-1.721-1.7210.0000.0000.0000.000
76A66PRO00.0000.01418.0490.9950.9950.0000.0000.0000.000
77A67SER00.0670.02621.161-0.429-0.4290.0000.0000.0000.000
78A68LEU0-0.009-0.02016.337-1.229-1.2290.0000.0000.0000.000
79A69ASP-1-0.840-0.90318.952-26.920-26.9200.0000.0000.0000.000
80A70VAL0-0.0040.00320.248-0.214-0.2140.0000.0000.0000.000
81A71LEU00.0200.01212.908-1.031-1.0310.0000.0000.0000.000
82A72ARG10.9540.96915.05828.63328.6330.0000.0000.0000.000
83A73ASP-1-0.763-0.87715.114-31.652-31.6520.0000.0000.0000.000
84A74VAL00.0040.00513.452-0.852-0.8520.0000.0000.0000.000
85A75TRP00.0140.0096.027-3.203-3.2030.0000.0000.0000.000
86A76ILE00.0020.01810.926-3.387-3.3870.0000.0000.0000.000
87A77ALA00.0150.00513.104-0.369-0.3690.0000.0000.0000.000
88A78GLY0-0.025-0.01510.2300.3770.3770.0000.0000.0000.000
89A79THR0-0.076-0.0446.875-3.288-3.2880.0000.0000.0000.000
90A80LYS10.9710.9939.19437.02637.0260.0000.0000.0000.000
91A81LYS10.8580.9078.72249.87149.8710.0000.0000.0000.000
92A82GLY00.0350.01514.5251.2481.2480.0000.0000.0000.000
93A83PRO00.0820.03418.231-1.071-1.0710.0000.0000.0000.000
94A84SER0-0.0340.00318.3490.0310.0310.0000.0000.0000.000
95A85LYS10.8140.90314.15236.65936.6590.0000.0000.0000.000
96A86LEU00.0240.00918.219-0.464-0.4640.0000.0000.0000.000
97A87LYS10.8690.94121.03726.60526.6050.0000.0000.0000.000
98A88GLU-1-0.959-0.96917.220-29.179-29.1790.0000.0000.0000.000
99A89MET0-0.072-0.02817.901-1.530-1.5300.0000.0000.0000.000
100A90SER0-0.0070.00020.3741.4651.4650.0000.0000.0000.000
101A91VAL0-0.079-0.04721.693-0.161-0.1610.0000.0000.0000.000
102A92THR00.032-0.00424.3980.4360.4360.0000.0000.0000.000
103A93LEU0-0.060-0.03324.791-0.122-0.1220.0000.0000.0000.000
104A94ILE00.0200.01628.5930.7490.7490.0000.0000.0000.000
105A95PRO0-0.022-0.01330.932-0.432-0.4320.0000.0000.0000.000
106A96SER0-0.026-0.01729.784-0.043-0.0430.0000.0000.0000.000
107A97LYS10.8970.93732.57417.74417.7440.0000.0000.0000.000
108A98LYS10.8440.91034.19216.96316.9630.0000.0000.0000.000
109A99VAL0-0.078-0.01229.2840.2250.2250.0000.0000.0000.000
110A100LYS10.8910.94231.38018.55718.5570.0000.0000.0000.000
111A101VAL0-0.0400.00325.309-0.065-0.0650.0000.0000.0000.000
112A102PRO0-0.0010.01926.6440.2920.2920.0000.0000.0000.000
113A103SER00.012-0.01026.711-0.950-0.9500.0000.0000.0000.000
114A104ILE0-0.020-0.01522.124-0.002-0.0020.0000.0000.0000.000
115A105GLU-1-0.883-0.93726.377-18.962-18.9620.0000.0000.0000.000
116A106GLU-1-0.775-0.86825.158-22.395-22.3950.0000.0000.0000.000
117A107ALA0-0.083-0.02824.338-0.370-0.3700.0000.0000.0000.000
118A108LEU0-0.009-0.00524.4921.0491.0490.0000.0000.0000.000
119A109ALA00.024-0.00626.1260.9800.9800.0000.0000.0000.000
120A110ASN0-0.0070.02025.803-1.894-1.8940.0000.0000.0000.000
121A111ILE00.0410.01725.6580.9430.9430.0000.0000.0000.000
122A112GLU-1-0.752-0.87026.762-19.263-19.2630.0000.0000.0000.000
123A113CYS0-0.045-0.01126.2180.4050.4050.0000.0000.0000.000
124A114ARG10.9320.94828.29217.25217.2520.0000.0000.0000.000
125A115VAL0-0.071-0.04125.767-0.237-0.2370.0000.0000.0000.000
126A116ILE00.0280.02228.4480.4980.4980.0000.0000.0000.000
127A117ASP-1-0.783-0.85628.440-20.190-20.1900.0000.0000.0000.000
128A118ALA0-0.072-0.04524.365-0.847-0.8470.0000.0000.0000.000
129A119ARG10.8310.90324.06720.87620.8760.0000.0000.0000.000
130A120SER0-0.027-0.02121.050-1.146-1.1460.0000.0000.0000.000
131A121TYR00.0360.01419.7781.1271.1270.0000.0000.0000.000
132A122GLY00.0260.01817.597-1.581-1.5810.0000.0000.0000.000
133A123ASP-1-0.866-0.91512.289-40.635-40.6350.0000.0000.0000.000
134A124HIS0-0.070-0.07611.019-2.375-2.3750.0000.0000.0000.000
135A125THR0-0.027-0.00616.2381.4191.4190.0000.0000.0000.000
136A126PHE00.0240.01818.957-1.066-1.0660.0000.0000.0000.000
137A127PHE0-0.012-0.01719.7281.2901.2900.0000.0000.0000.000
138A128VAL00.0250.00923.066-0.677-0.6770.0000.0000.0000.000
139A129GLY00.003-0.01126.0620.4620.4620.0000.0000.0000.000
140A130GLU-1-0.886-0.94127.470-17.391-17.3910.0000.0000.0000.000
141A131VAL0-0.021-0.01328.861-0.255-0.2550.0000.0000.0000.000
142A132VAL00.0160.01531.3240.6240.6240.0000.0000.0000.000
143A133GLY0-0.019-0.01632.6910.7190.7190.0000.0000.0000.000
144A134TYR00.0310.01230.872-0.743-0.7430.0000.0000.0000.000
145A135THR0-0.035-0.00930.9740.5850.5850.0000.0000.0000.000
146A136TYR00.0200.00230.413-0.852-0.8520.0000.0000.0000.000
147A137LYS10.8770.95128.94021.26921.2690.0000.0000.0000.000
148A138ASP-1-0.853-0.92832.489-17.373-17.3730.0000.0000.0000.000
149A139TYR00.025-0.00628.718-0.183-0.1830.0000.0000.0000.000
150A140ALA00.0220.00828.933-0.207-0.2070.0000.0000.0000.000
151A141PHE0-0.026-0.02227.722-0.758-0.7580.0000.0000.0000.000
152A142GLU-1-0.836-0.89432.958-16.911-16.9110.0000.0000.0000.000
153A143LYS10.8530.91835.74117.25317.2530.0000.0000.0000.000
154A144GLY00.0370.02836.7740.3000.3000.0000.0000.0000.000
155A145LYS10.9020.94432.65216.85916.8590.0000.0000.0000.000
156A146PRO0-0.024-0.01027.9580.1740.1740.0000.0000.0000.000
157A147ASN0-0.011-0.00230.076-0.174-0.1740.0000.0000.0000.000
158A148LEU00.0240.00425.816-0.604-0.6040.0000.0000.0000.000
159A149LYS10.9881.00026.20118.02518.0250.0000.0000.0000.000
160A150ALA0-0.035-0.01027.050-0.089-0.0890.0000.0000.0000.000
161A151LYS10.8280.91122.12124.18224.1820.0000.0000.0000.000
162A152PHE00.0200.00821.592-1.577-1.5770.0000.0000.0000.000
163A153LEU0-0.0070.02915.286-0.700-0.7000.0000.0000.0000.000
164A154ALA00.0330.02416.1300.6030.6030.0000.0000.0000.000
165A155HIS10.7860.8747.90458.11658.1160.0000.0000.0000.000
166A156VAL00.0510.02610.4131.1551.1550.0000.0000.0000.000
167A157SER0-0.014-0.0455.674-5.471-5.4710.0000.0000.0000.000
170A160GLU-1-0.859-0.8706.629-56.330-56.3300.0000.0000.0000.000
171A161PHE0-0.014-0.0289.148-0.788-0.7880.0000.0000.0000.000
172A162VAL00.0150.01112.5450.9830.9830.0000.0000.0000.000
173A163THR00.000-0.02715.9880.6610.6610.0000.0000.0000.000
174A164PHE0-0.008-0.00719.531-0.531-0.5310.0000.0000.0000.000
175A165SER00.0360.02122.3690.4830.4830.0000.0000.0000.000
176A166GLU-1-0.904-0.97024.839-20.964-20.9640.0000.0000.0000.000
177A167LYS10.7690.89427.99020.67820.6780.0000.0000.0000.000
178A168VAL00.0290.01228.566-0.660-0.6600.0000.0000.0000.000
179A169HIS-1-0.886-0.94128.671-20.282-20.2820.0000.0000.0000.000
180A170LYS0-0.048-0.03332.008-0.282-0.2820.0000.0000.0000.000
181A171ALA0-0.033-0.02734.037-0.039-0.0390.0000.0000.0000.000
182A172GLU-2-1.889-1.91635.931-31.408-31.4080.0000.0000.0000.000