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: 15RGZ

Calculation Name: 2B67-A-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin mononucleotide | acetic acid

Ligand 3-letter code: FMN | ACY

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2B67

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

Base Structure: X-ray

Registration Date: 2025-10-03

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 201
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2179801.147015
FMO2-HF: Nuclear repulsion 2101376.108756
FMO2-HF: Total energy -78425.038259
FMO2-MP2: Total energy -78657.627489


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.
10.45113.6030.001-1.16-1.994-0.003
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 : 0.917 / q_NPA : 0.936
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].
3A3PHE00.1070.0573.7572.8015.018-0.004-0.918-1.296-0.002
4A4LEU0-0.0010.0093.3445.4826.2180.006-0.222-0.520-0.001
5A5GLU-1-0.885-0.9354.957-29.298-29.099-0.001-0.020-0.1780.000
6A6LEU00.0200.0046.9843.7563.7560.0000.0000.0000.000
7A7ASN0-0.023-0.0268.1895.6585.6580.0000.0000.0000.000
8A8LYS10.9160.9627.40036.86136.8610.0000.0000.0000.000
9A9LYS10.8930.94810.38728.94028.9400.0000.0000.0000.000
10A10ARG10.9751.01412.87821.38721.3870.0000.0000.0000.000
11A11HIS0-0.018-0.01614.8300.6910.6910.0000.0000.0000.000
12A12ALA0-0.042-0.02417.9030.3310.3310.0000.0000.0000.000
13A13THR0-0.026-0.00921.1280.3560.3560.0000.0000.0000.000
14A14LYS10.9060.95923.36012.26912.2690.0000.0000.0000.000
15A15HIS00.004-0.00426.9340.7140.7140.0000.0000.0000.000
16A16PHE0-0.037-0.02325.050-0.553-0.5530.0000.0000.0000.000
17A17THR00.0060.00627.4570.3560.3560.0000.0000.0000.000
18A18ASP-1-0.886-0.94429.848-9.451-9.4510.0000.0000.0000.000
19A19LYS10.8130.93524.44512.74712.7470.0000.0000.0000.000
20A20LEU00.0410.00829.341-0.259-0.2590.0000.0000.0000.000
21A21VAL00.0350.02225.459-0.331-0.3310.0000.0000.0000.000
22A22ASP-1-0.768-0.87426.483-10.517-10.5170.0000.0000.0000.000
23A23PRO0-0.023-0.03127.011-0.346-0.3460.0000.0000.0000.000
24A24LYS10.9050.95326.30810.15510.1550.0000.0000.0000.000
25A25ASP-1-0.815-0.88622.735-13.480-13.4800.0000.0000.0000.000
26A26VAL0-0.004-0.00622.569-0.540-0.5400.0000.0000.0000.000
27A27ARG10.8330.90924.28811.18811.1880.0000.0000.0000.000
28A28THR00.009-0.00719.582-0.136-0.1360.0000.0000.0000.000
29A29ALA00.0070.00219.530-0.596-0.5960.0000.0000.0000.000
30A30ILE00.001-0.00520.267-0.411-0.4110.0000.0000.0000.000
31A31GLU-1-0.889-0.92322.010-12.334-12.3340.0000.0000.0000.000
32A32ILE00.0260.01215.594-0.294-0.2940.0000.0000.0000.000
33A33ALA0-0.014-0.00518.055-0.427-0.4270.0000.0000.0000.000
34A34THR0-0.067-0.05819.671-0.077-0.0770.0000.0000.0000.000
35A35LEU0-0.0030.01316.6820.3720.3720.0000.0000.0000.000
36A36ALA0-0.030-0.00217.472-0.601-0.6010.0000.0000.0000.000
37A37PRO0-0.0070.00516.7390.8400.8400.0000.0000.0000.000
38A38SER00.0570.01619.6690.3210.3210.0000.0000.0000.000
39A39ALA00.0190.01923.3330.0920.0920.0000.0000.0000.000
40A40HIS10.8260.89425.89810.34810.3480.0000.0000.0000.000
41A41ASN00.0270.02024.2330.0350.0350.0000.0000.0000.000
42A42SER0-0.009-0.01025.7130.2670.2670.0000.0000.0000.000
43A43GLN00.0090.00025.4790.3830.3830.0000.0000.0000.000
44A44PRO00.0000.01726.7940.2650.2650.0000.0000.0000.000
45A45TRP00.0640.02622.5630.3060.3060.0000.0000.0000.000
46A46LYS10.8830.94429.2479.2559.2550.0000.0000.0000.000
47A47PHE00.0410.02324.280-0.029-0.0290.0000.0000.0000.000
48A48VAL0-0.0020.00229.6960.2100.2100.0000.0000.0000.000
49A49VAL0-0.008-0.00828.707-0.171-0.1710.0000.0000.0000.000
50A50VAL0-0.032-0.00731.3390.2700.2700.0000.0000.0000.000
51A51ARG10.8980.93529.4369.9839.9830.0000.0000.0000.000
52A52GLU-1-0.852-0.92335.305-8.302-8.3020.0000.0000.0000.000
53A53LYS10.8430.91638.4177.7377.7370.0000.0000.0000.000
54A54ASN00.0130.01233.6970.1900.1900.0000.0000.0000.000
55A55ALA00.0630.02336.997-0.037-0.0370.0000.0000.0000.000
56A56GLU-1-0.970-0.98939.956-7.252-7.2520.0000.0000.0000.000
57A57LEU00.008-0.00333.6360.0080.0080.0000.0000.0000.000
58A58ALA00.0330.01336.329-0.086-0.0860.0000.0000.0000.000
59A59LYS10.9100.95937.3357.2807.2800.0000.0000.0000.000
60A60LEU0-0.0150.01237.6740.1420.1420.0000.0000.0000.000
61A61ALA0-0.030-0.00834.069-0.129-0.1290.0000.0000.0000.000
62A62TYR00.007-0.00835.1010.2090.2090.0000.0000.0000.000
63A63GLY00.0280.01234.725-0.264-0.2640.0000.0000.0000.000
64A64SER00.0590.03032.332-0.007-0.0070.0000.0000.0000.000
65A65ASN0-0.045-0.02130.620-0.564-0.5640.0000.0000.0000.000
66A66PHE00.0050.02032.758-0.098-0.0980.0000.0000.0000.000
67A67GLU-1-0.802-0.91134.275-8.685-8.6850.0000.0000.0000.000
68A68GLN0-0.055-0.01928.070-0.582-0.5820.0000.0000.0000.000
69A69VAL0-0.017-0.02031.349-0.188-0.1880.0000.0000.0000.000
70A70SER0-0.068-0.04232.9540.1490.1490.0000.0000.0000.000
71A71SER0-0.035-0.02332.2230.1930.1930.0000.0000.0000.000
72A72ALA0-0.045-0.00529.241-0.142-0.1420.0000.0000.0000.000
73A73PRO0-0.009-0.00629.2430.1930.1930.0000.0000.0000.000
74A74VAL0-0.044-0.01828.4480.2010.2010.0000.0000.0000.000
75A75THR00.0300.01629.263-0.323-0.3230.0000.0000.0000.000
76A76ILE0-0.030-0.01625.2510.2740.2740.0000.0000.0000.000
77A77ALA00.0350.02628.741-0.208-0.2080.0000.0000.0000.000
78A78LEU0-0.044-0.01625.458-0.001-0.0010.0000.0000.0000.000
79A79PHE00.0440.00229.4790.1040.1040.0000.0000.0000.000
80A80THR0-0.047-0.05529.683-0.184-0.1840.0000.0000.0000.000
81A81ASP-1-0.794-0.86232.202-8.554-8.5540.0000.0000.0000.000
82A82THR00.009-0.01934.614-0.024-0.0240.0000.0000.0000.000
83A83ASP-1-0.823-0.90237.135-7.679-7.6790.0000.0000.0000.000
84A84LEU00.0370.00432.498-0.088-0.0880.0000.0000.0000.000
85A85ALA00.0140.01835.721-0.101-0.1010.0000.0000.0000.000
86A86LYS10.8770.92438.1497.3817.3810.0000.0000.0000.000
87A87ARG10.6860.85530.0959.9529.9520.0000.0000.0000.000
88A88ALA00.0420.02133.390-0.149-0.1490.0000.0000.0000.000
89A89ARG10.9420.94734.4487.4517.4510.0000.0000.0000.000
90A90LYS10.8660.94433.1039.1909.1900.0000.0000.0000.000
91A91ILE00.0170.02729.6460.0350.0350.0000.0000.0000.000
92A92ALA00.0190.01232.554-0.016-0.0160.0000.0000.0000.000
93A93ARG10.9090.95235.0697.9177.9170.0000.0000.0000.000
94A94VAL0-0.045-0.02032.1430.1390.1390.0000.0000.0000.000
95A95GLY00.0230.02831.797-0.084-0.0840.0000.0000.0000.000
96A96GLY00.0370.01632.4730.0500.0500.0000.0000.0000.000
97A97ALA00.041-0.00134.142-0.205-0.2050.0000.0000.0000.000
98A98ASN0-0.030-0.00432.9600.0780.0780.0000.0000.0000.000
99A99ASN0-0.080-0.04128.708-0.546-0.5460.0000.0000.0000.000
100A100PHE0-0.072-0.02428.558-0.289-0.2890.0000.0000.0000.000
101A101SER00.0720.01832.2850.2940.2940.0000.0000.0000.000
102A102GLU-1-0.868-0.94734.590-7.512-7.5120.0000.0000.0000.000
103A103GLU-1-0.938-0.96535.178-8.337-8.3370.0000.0000.0000.000
104A104GLN00.0380.02928.8810.1310.1310.0000.0000.0000.000
105A105LEU00.0110.01433.871-0.059-0.0590.0000.0000.0000.000
106A106GLN00.0130.00236.4540.1240.1240.0000.0000.0000.000
107A107TYR0-0.001-0.00531.197-0.019-0.0190.0000.0000.0000.000
108A108PHE00.0190.00128.9800.0470.0470.0000.0000.0000.000
109A109MET0-0.013-0.00735.2230.0670.0670.0000.0000.0000.000
110A110LYS10.8920.94938.9087.2417.2410.0000.0000.0000.000
111A111ASN00.0190.01637.0380.0910.0910.0000.0000.0000.000
112A112LEU00.0510.02431.3940.0080.0080.0000.0000.0000.000
113A113PRO0-0.052-0.02535.9640.0040.0040.0000.0000.0000.000
114A114ALA00.0490.03438.8590.0860.0860.0000.0000.0000.000
115A115GLU-1-0.912-0.93833.950-9.007-9.0070.0000.0000.0000.000
116A116PHE0-0.007-0.01432.025-0.008-0.0080.0000.0000.0000.000
117A117ALA0-0.029-0.01037.6420.0400.0400.0000.0000.0000.000
118A118ARG10.8690.92140.0937.8957.8950.0000.0000.0000.000
119A119TYR0-0.0160.00432.983-0.234-0.2340.0000.0000.0000.000
120A120SER00.0420.02138.7470.1010.1010.0000.0000.0000.000
121A121GLU-1-0.864-0.94738.238-7.732-7.7320.0000.0000.0000.000
122A122GLN0-0.061-0.02834.1640.0580.0580.0000.0000.0000.000
123A123GLN00.0380.02534.207-0.174-0.1740.0000.0000.0000.000
124A124VAL00.016-0.00233.391-0.361-0.3610.0000.0000.0000.000
125A125SER00.0160.02133.446-0.272-0.2720.0000.0000.0000.000
126A126ASP-1-0.817-0.90630.554-10.043-10.0430.0000.0000.0000.000
127A127TYR0-0.020-0.01429.124-0.525-0.5250.0000.0000.0000.000
128A128LEU0-0.028-0.00928.580-0.472-0.4720.0000.0000.0000.000
129A129ALA00.0610.03428.481-0.363-0.3630.0000.0000.0000.000
130A130LEU00.0000.00823.468-0.499-0.4990.0000.0000.0000.000
131A131ASN0-0.028-0.04623.792-0.919-0.9190.0000.0000.0000.000
132A132ALA00.0240.01624.233-0.380-0.3800.0000.0000.0000.000
133A133GLY00.0180.01022.849-0.363-0.3630.0000.0000.0000.000
134A134LEU0-0.049-0.02318.962-0.774-0.7740.0000.0000.0000.000
135A135VAL0-0.0070.00119.189-0.826-0.8260.0000.0000.0000.000
136A136ALA00.0290.01320.874-0.301-0.3010.0000.0000.0000.000
137A137MET0-0.023-0.00714.181-0.301-0.3010.0000.0000.0000.000
138A138ASN0-0.034-0.02615.396-2.060-2.0600.0000.0000.0000.000
139A139LEU00.0180.01416.946-0.411-0.4110.0000.0000.0000.000
140A140VAL00.0170.00216.846-0.216-0.2160.0000.0000.0000.000
141A141LEU0-0.060-0.00811.680-0.749-0.7490.0000.0000.0000.000
142A142ALA00.0290.01514.780-0.649-0.6490.0000.0000.0000.000
143A143LEU0-0.010-0.00216.3530.4760.4760.0000.0000.0000.000
144A144THR0-0.029-0.02313.8580.0920.0920.0000.0000.0000.000
145A145ASP-1-0.999-0.99911.475-25.168-25.1680.0000.0000.0000.000
146A146GLN0-0.055-0.02314.1420.6080.6080.0000.0000.0000.000
147A147GLY0-0.022-0.01016.7680.8790.8790.0000.0000.0000.000
148A148ILE0-0.087-0.04218.2610.8820.8820.0000.0000.0000.000
149A149GLY00.0440.03119.899-0.685-0.6850.0000.0000.0000.000
150A150SER00.025-0.02020.2540.4270.4270.0000.0000.0000.000
151A151ASN0-0.018-0.00621.648-0.916-0.9160.0000.0000.0000.000
152A152ILE0-0.0140.00320.4940.2740.2740.0000.0000.0000.000
153A153ILE0-0.020-0.00424.4170.1340.1340.0000.0000.0000.000
154A154LEU00.0370.00628.0530.1240.1240.0000.0000.0000.000
155A155GLY0-0.024-0.00529.7390.3100.3100.0000.0000.0000.000
156A156PHE00.014-0.00130.9700.0130.0130.0000.0000.0000.000
157A157ASP-1-0.767-0.84635.209-7.736-7.7360.0000.0000.0000.000
158A158LYS10.8450.91831.4729.8639.8630.0000.0000.0000.000
159A159SER0-0.088-0.05937.5610.0730.0730.0000.0000.0000.000
160A160LYS10.9770.97940.6897.4117.4110.0000.0000.0000.000
161A161VAL0-0.024-0.01135.346-0.001-0.0010.0000.0000.0000.000
162A162ASN0-0.040-0.03838.790-0.185-0.1850.0000.0000.0000.000
163A163GLU-1-0.910-0.94340.552-6.917-6.9170.0000.0000.0000.000
164A164VAL00.0150.00239.7730.0080.0080.0000.0000.0000.000
165A165LEU0-0.065-0.04535.527-0.101-0.1010.0000.0000.0000.000
166A166GLU-1-0.851-0.90339.723-7.492-7.4920.0000.0000.0000.000
167A167ILE0-0.107-0.04837.001-0.126-0.1260.0000.0000.0000.000
168A168GLU-1-0.890-0.95240.210-7.277-7.2770.0000.0000.0000.000
169A169ASP-1-0.826-0.92040.161-7.683-7.6830.0000.0000.0000.000
170A170ARG10.7880.87636.6798.2778.2770.0000.0000.0000.000
171A171PHE0-0.075-0.03934.596-0.264-0.2640.0000.0000.0000.000
172A172ARG10.9100.94431.9099.7509.7500.0000.0000.0000.000
173A173PRO00.0170.02333.551-0.373-0.3730.0000.0000.0000.000
174A174GLU-1-0.831-0.89529.039-10.225-10.2250.0000.0000.0000.000
175A175LEU0-0.022-0.03524.808-0.068-0.0680.0000.0000.0000.000
176A176LEU00.0290.02828.9440.1340.1340.0000.0000.0000.000
177A177ILE0-0.011-0.00623.477-0.382-0.3820.0000.0000.0000.000
178A178THR00.0250.02526.3740.1300.1300.0000.0000.0000.000
179A179VAL0-0.017-0.02624.040-0.663-0.6630.0000.0000.0000.000
180A180GLY00.0520.01724.8250.5820.5820.0000.0000.0000.000
181A181TYR00.009-0.00122.214-0.338-0.3380.0000.0000.0000.000
182A182THR00.0240.00022.1800.4340.4340.0000.0000.0000.000
183A183ASP-1-0.914-0.95324.404-10.858-10.8580.0000.0000.0000.000
184A184GLU-1-0.910-0.95124.720-11.583-11.5830.0000.0000.0000.000
185A185LYS10.8990.95821.53411.59011.5900.0000.0000.0000.000
186A186LEU00.001-0.00620.6140.6250.6250.0000.0000.0000.000
187A187GLU-1-0.870-0.92718.640-16.829-16.8290.0000.0000.0000.000
188A188PRO0-0.063-0.02614.686-0.004-0.0040.0000.0000.0000.000
189A189SER00.0150.00916.8120.4240.4240.0000.0000.0000.000
190A190TYR00.0400.01017.479-0.857-0.8570.0000.0000.0000.000
191A191ARG10.8440.90814.87117.51617.5160.0000.0000.0000.000
192A192LEU00.0540.04017.8070.0290.0290.0000.0000.0000.000
193A193PRO00.0150.01316.774-1.194-1.1940.0000.0000.0000.000
194A194VAL00.027-0.00412.8750.3310.3310.0000.0000.0000.000
195A195ASP-1-0.935-0.98215.795-17.334-17.3340.0000.0000.0000.000
196A196GLU-1-0.968-0.97018.675-12.308-12.3080.0000.0000.0000.000
197A197ILE0-0.060-0.03415.8200.3980.3980.0000.0000.0000.000
198A198ILE0-0.091-0.03014.561-0.413-0.4130.0000.0000.0000.000
199A199GLU-1-0.791-0.87119.189-11.699-11.6990.0000.0000.0000.000
200A200LYS10.8840.93118.84915.23115.2310.0000.0000.0000.000
201A201ARG0-0.074-0.03923.178-0.390-0.3900.0000.0000.0000.000