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: GR4G1

Calculation Name: 4XHF-B-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin mononucleotide

Ligand 3-letter code: FMN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4XHF

Chain ID: B

ChEMBL ID:

UniProt ID: Q8EID8

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 225
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2725434.832709
FMO2-HF: Nuclear repulsion 2638151.368841
FMO2-HF: Total energy -87283.463868
FMO2-MP2: Total energy -87538.876351


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:-3:ALA)


Summations of interaction energy for fragment #1(A:-3:ALA)
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.
109.666112.0570.001-0.933-1.457-0.001
Interaction energy analysis for fragmet #1(A:-3:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.935 / q_NPA : 0.951
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-1GLY00.0290.0273.4468.3949.893-0.005-0.647-0.847-0.001
4A0SER00.0600.0263.4229.39110.1400.007-0.271-0.4840.000
5A33LEU00.0190.0035.1397.1587.301-0.001-0.015-0.1260.000
6A34LYS10.9380.9647.05035.46435.4640.0000.0000.0000.000
7A35GLU-1-0.867-0.9357.239-35.762-35.7620.0000.0000.0000.000
8A36ARG10.9670.9817.11839.28839.2880.0000.0000.0000.000
9A37LYS10.8970.95510.50529.11929.1190.0000.0000.0000.000
10A38LEU0-0.015-0.00612.3331.5521.5520.0000.0000.0000.000
11A39ALA00.0220.00813.6061.3921.3920.0000.0000.0000.000
12A40LYS10.9831.00215.20920.15220.1520.0000.0000.0000.000
13A41LYS10.9890.99115.53220.28320.2830.0000.0000.0000.000
14A42ARG10.8700.91415.02719.31119.3110.0000.0000.0000.000
15A43ASP-1-0.814-0.88719.459-15.154-15.1540.0000.0000.0000.000
16A44GLU-1-0.960-0.98520.798-14.085-14.0850.0000.0000.0000.000
17A45LEU00.0010.01422.8110.6360.6360.0000.0000.0000.000
18A46GLN0-0.003-0.01823.4860.4150.4150.0000.0000.0000.000
19A47ARG10.9460.98622.46213.75113.7510.0000.0000.0000.000
20A48TYR00.004-0.01825.2190.6140.6140.0000.0000.0000.000
21A49VAL0-0.0130.00228.3720.4260.4260.0000.0000.0000.000
22A50LEU0-0.0050.00129.4310.3620.3620.0000.0000.0000.000
23A51MET0-0.013-0.00531.3450.1880.1880.0000.0000.0000.000
24A52ALA0-0.027-0.00432.9990.3150.3150.0000.0000.0000.000
25A53ALA00.007-0.00734.4240.2940.2940.0000.0000.0000.000
26A54ASP-1-0.890-0.92536.296-7.666-7.6660.0000.0000.0000.000
27A55VAL0-0.0020.00434.6160.1860.1860.0000.0000.0000.000
28A56ASN00.0290.00434.860-0.320-0.3200.0000.0000.0000.000
29A57LEU00.002-0.01029.421-0.222-0.2220.0000.0000.0000.000
30A58GLY00.0230.02030.843-0.299-0.2990.0000.0000.0000.000
31A59GLN0-0.023-0.02031.077-0.314-0.3140.0000.0000.0000.000
32A60GLY0-0.004-0.00927.614-0.176-0.1760.0000.0000.0000.000
33A61ASN0-0.027-0.04122.520-0.457-0.4570.0000.0000.0000.000
34A62GLU-1-0.801-0.87725.855-10.083-10.0830.0000.0000.0000.000
35A63PHE0-0.0090.00622.714-0.051-0.0510.0000.0000.0000.000
36A64ARG10.8000.87320.09414.76214.7620.0000.0000.0000.000
37A65ASP-1-0.887-0.93625.694-11.768-11.7680.0000.0000.0000.000
38A66ILE0-0.010-0.00128.2540.2500.2500.0000.0000.0000.000
39A67PHE00.0170.00726.4760.1540.1540.0000.0000.0000.000
40A68ALA0-0.041-0.02826.4040.1730.1730.0000.0000.0000.000
41A69LYS10.9290.98128.3679.0419.0410.0000.0000.0000.000
42A70SER0-0.009-0.01632.0690.3840.3840.0000.0000.0000.000
43A71VAL0-0.026-0.00729.9230.2690.2690.0000.0000.0000.000
44A72LYS10.9520.98829.88010.15410.1540.0000.0000.0000.000
45A73PRO0-0.013-0.01526.5810.1690.1690.0000.0000.0000.000
46A74LEU0-0.059-0.03129.2250.1200.1200.0000.0000.0000.000
47A75LEU00.0300.02626.830-0.215-0.2150.0000.0000.0000.000
48A76ILE0-0.036-0.01629.7670.3230.3230.0000.0000.0000.000
49A77ASN00.0910.07132.8440.1810.1810.0000.0000.0000.000
50A78LEU0-0.052-0.03433.3240.3130.3130.0000.0000.0000.000
51A79ASP-1-0.846-0.90836.490-8.375-8.3750.0000.0000.0000.000
52A80THR0-0.040-0.03637.8050.2810.2810.0000.0000.0000.000
53A81GLY0-0.010-0.00538.6730.2230.2230.0000.0000.0000.000
54A82LYS10.8450.90937.5137.8337.8330.0000.0000.0000.000
55A83VAL0-0.028-0.02033.127-0.196-0.1960.0000.0000.0000.000
56A84ASP-1-0.831-0.91130.837-9.624-9.6240.0000.0000.0000.000
57A85SER0-0.085-0.05229.327-0.129-0.1290.0000.0000.0000.000
58A86ASP-1-0.844-0.93823.163-14.118-14.1180.0000.0000.0000.000
59A87ALA0-0.017-0.00521.3520.1660.1660.0000.0000.0000.000
60A88ASN0-0.083-0.06117.6130.4290.4290.0000.0000.0000.000
61A89VAL00.0890.04821.294-0.382-0.3820.0000.0000.0000.000
62A90LEU0-0.017-0.00221.3680.1270.1270.0000.0000.0000.000
63A91ASP-1-0.840-0.88516.807-18.864-18.8640.0000.0000.0000.000
64A92PHE00.0150.02218.569-0.751-0.7510.0000.0000.0000.000
65A93ASP-1-0.893-0.95618.479-16.545-16.5450.0000.0000.0000.000
66A94GLU-1-0.815-0.91720.984-12.115-12.1150.0000.0000.0000.000
67A95ARG10.7520.86021.39414.10614.1060.0000.0000.0000.000
68A96MET0-0.020-0.02518.7450.2800.2800.0000.0000.0000.000
69A97ALA00.0120.01922.2210.3870.3870.0000.0000.0000.000
70A98ALA00.0260.01425.0610.4780.4780.0000.0000.0000.000
71A99ILE0-0.045-0.01924.1160.4130.4130.0000.0000.0000.000
72A100ASN00.000-0.00723.9330.4830.4830.0000.0000.0000.000
73A101PRO00.0000.01325.8300.2650.2650.0000.0000.0000.000
74A102GLU-1-0.903-0.93125.880-11.893-11.8930.0000.0000.0000.000
75A103THR0-0.046-0.03525.8160.0290.0290.0000.0000.0000.000
76A104SER0-0.075-0.03728.7680.0840.0840.0000.0000.0000.000
77A105SER00.0350.01530.9180.3170.3170.0000.0000.0000.000
78A106THR0-0.026-0.01134.332-0.073-0.0730.0000.0000.0000.000
79A107PRO0-0.0300.00135.7380.2160.2160.0000.0000.0000.000
80A108LYS10.8960.93138.6847.9617.9610.0000.0000.0000.000
81A109LYS10.9150.94942.1037.0037.0030.0000.0000.0000.000
82A110ASP-1-0.751-0.86336.789-8.980-8.9800.0000.0000.0000.000
83A111ILE0-0.047-0.03239.534-0.028-0.0280.0000.0000.0000.000
84A112ALA00.0210.01135.8620.0470.0470.0000.0000.0000.000
85A113LYS10.8680.93735.7527.8167.8160.0000.0000.0000.000
86A114ILE00.0500.02432.249-0.207-0.2070.0000.0000.0000.000
87A115LYS10.8680.94331.8608.6108.6100.0000.0000.0000.000
88A116THR0-0.052-0.04029.5140.3390.3390.0000.0000.0000.000
89A117ARG10.7940.87431.9938.8818.8810.0000.0000.0000.000
90A118ALA00.0480.03028.690-0.006-0.0060.0000.0000.0000.000
91A119ASN00.008-0.00230.5000.5050.5050.0000.0000.0000.000
92A120ASP-1-0.807-0.90029.237-10.189-10.1890.0000.0000.0000.000
93A121ALA0-0.047-0.03129.401-0.297-0.2970.0000.0000.0000.000
94A122ARG10.7700.89122.07813.68713.6870.0000.0000.0000.000
95A123VAL0-0.030-0.01328.8250.1580.1580.0000.0000.0000.000
96A124PHE00.012-0.01826.697-0.375-0.3750.0000.0000.0000.000
97A125LYS10.9390.99732.0558.7458.7450.0000.0000.0000.000
98A126VAL00.0160.01033.302-0.258-0.2580.0000.0000.0000.000
99A127PHE0-0.042-0.02635.4520.2940.2940.0000.0000.0000.000
100A128ASP-1-0.765-0.86137.475-7.690-7.6900.0000.0000.0000.000
101A129ASP-1-0.910-0.96039.458-8.200-8.2000.0000.0000.0000.000
102A130SER0-0.148-0.09340.4390.0820.0820.0000.0000.0000.000
103A131GLY0-0.005-0.00239.9090.0680.0680.0000.0000.0000.000
104A132LYS10.9280.97340.9886.8466.8460.0000.0000.0000.000
105A133LEU0-0.040-0.02538.882-0.166-0.1660.0000.0000.0000.000
106A134SER00.0170.00339.3180.2110.2110.0000.0000.0000.000
107A135SER0-0.029-0.02437.7970.0230.0230.0000.0000.0000.000
108A136VAL0-0.013-0.00936.240-0.161-0.1610.0000.0000.0000.000
109A137VAL0-0.0100.00432.5570.1050.1050.0000.0000.0000.000
110A138VAL00.0130.00633.127-0.216-0.2160.0000.0000.0000.000
111A139PRO00.0100.01129.3260.0930.0930.0000.0000.0000.000
112A140PHE0-0.051-0.02731.4490.3150.3150.0000.0000.0000.000
113A141TYR00.021-0.00130.052-0.301-0.3010.0000.0000.0000.000
114A142GLY00.0470.00832.0860.2720.2720.0000.0000.0000.000
115A143LYS10.8380.94132.8769.1739.1730.0000.0000.0000.000
116A144GLY00.0150.01133.4000.3310.3310.0000.0000.0000.000
117A145LEU0-0.082-0.04735.1720.1130.1130.0000.0000.0000.000
118A146TRP0-0.021-0.01931.6790.0080.0080.0000.0000.0000.000
119A147SER0-0.061-0.03428.660-0.244-0.2440.0000.0000.0000.000
120A148MET0-0.042-0.01027.8840.4540.4540.0000.0000.0000.000
121A149ILE0-0.007-0.00429.076-0.228-0.2280.0000.0000.0000.000
122A150TYR00.026-0.00726.3570.0630.0630.0000.0000.0000.000
123A151GLY00.0250.00229.576-0.035-0.0350.0000.0000.0000.000
124A152TYR0-0.013-0.00326.043-0.221-0.2210.0000.0000.0000.000
125A153VAL00.0170.00432.5610.1910.1910.0000.0000.0000.000
126A154ALA0-0.0040.01136.065-0.134-0.1340.0000.0000.0000.000
127A155VAL0-0.022-0.00737.5600.2010.2010.0000.0000.0000.000
128A156GLU-1-0.852-0.94140.649-7.308-7.3080.0000.0000.0000.000
129A157PRO0-0.016-0.02543.2960.0030.0030.0000.0000.0000.000
130A158ASP-1-0.754-0.82844.738-6.832-6.8320.0000.0000.0000.000
131A159PHE0-0.067-0.04741.4100.0190.0190.0000.0000.0000.000
132A160ASN0-0.002-0.01344.753-0.098-0.0980.0000.0000.0000.000
133A161THR00.006-0.02345.659-0.018-0.0180.0000.0000.0000.000
134A162ILE0-0.040-0.01340.696-0.193-0.1930.0000.0000.0000.000
135A163LYS10.8870.95539.7998.0598.0590.0000.0000.0000.000
136A164GLY00.0630.02138.6910.0670.0670.0000.0000.0000.000
137A165VAL0-0.038-0.01536.445-0.092-0.0920.0000.0000.0000.000
138A166VAL0-0.0010.00231.0310.0210.0210.0000.0000.0000.000
139A167VAL0-0.016-0.01031.583-0.217-0.2170.0000.0000.0000.000
140A168TYR0-0.005-0.00124.715-0.089-0.0890.0000.0000.0000.000
141A169GLU-1-0.818-0.86823.396-14.127-14.1270.0000.0000.0000.000
142A170HIS00.0090.00626.9970.4310.4310.0000.0000.0000.000
143A171GLY00.0230.00627.291-0.426-0.4260.0000.0000.0000.000
144A172GLU-1-0.753-0.84628.414-9.169-9.1690.0000.0000.0000.000
145A173THR0-0.010-0.01131.538-0.133-0.1330.0000.0000.0000.000
146A174PRO00.0330.00430.7220.2220.2220.0000.0000.0000.000
147A175GLY00.0190.01233.5260.1690.1690.0000.0000.0000.000
148A176ILE0-0.064-0.02536.4880.2920.2920.0000.0000.0000.000
149A177GLY00.016-0.00435.7200.1310.1310.0000.0000.0000.000
150A178ASP-1-0.819-0.91732.623-9.317-9.3170.0000.0000.0000.000
151A179PHE00.0060.00834.034-0.075-0.0750.0000.0000.0000.000
152A180VAL0-0.034-0.01333.2780.0710.0710.0000.0000.0000.000
153A181THR0-0.035-0.03330.391-0.112-0.1120.0000.0000.0000.000
154A182ASP-1-0.794-0.87833.496-8.382-8.3820.0000.0000.0000.000
155A183PRO00.0290.00734.9630.1910.1910.0000.0000.0000.000
156A184HIS10.8320.90937.5268.1608.1600.0000.0000.0000.000
157A185TRP00.0210.00637.6980.0940.0940.0000.0000.0000.000
158A186LEU0-0.017-0.01034.4150.1140.1140.0000.0000.0000.000
159A187SER0-0.015-0.02439.0290.0600.0600.0000.0000.0000.000
160A188LEU0-0.060-0.02041.7160.1530.1530.0000.0000.0000.000
161A189TRP00.005-0.02240.6620.1960.1960.0000.0000.0000.000
162A190LYS10.8070.91141.5327.6527.6520.0000.0000.0000.000
163A191GLY00.0110.00943.9160.1580.1580.0000.0000.0000.000
164A192LYS10.7930.91845.5756.8106.8100.0000.0000.0000.000
165A193GLN0-0.010-0.01246.287-0.031-0.0310.0000.0000.0000.000
166A194LEU0-0.0030.00241.6890.0460.0460.0000.0000.0000.000
167A195PHE0-0.043-0.02743.741-0.016-0.0160.0000.0000.0000.000
168A196ASP-1-0.860-0.94148.831-6.064-6.0640.0000.0000.0000.000
169A197ASP-1-0.861-0.93652.217-5.905-5.9050.0000.0000.0000.000
170A198LYS10.8540.93354.2225.8415.8410.0000.0000.0000.000
171A199GLY00.0250.02550.096-0.032-0.0320.0000.0000.0000.000
172A200LYS10.8350.91848.9106.4366.4360.0000.0000.0000.000
173A201PHE00.0230.00642.9760.0600.0600.0000.0000.0000.000
174A202ALA0-0.020-0.01747.4050.0960.0960.0000.0000.0000.000
175A203MET00.0040.05144.3880.1100.1100.0000.0000.0000.000
176A204ARG10.8280.90846.4216.7526.7520.0000.0000.0000.000
177A205LEU00.0090.01742.078-0.013-0.0130.0000.0000.0000.000
178A206VAL0-0.014-0.00246.6480.0880.0880.0000.0000.0000.000
179A207LYS10.9270.95149.4106.2276.2270.0000.0000.0000.000
180A208GLY00.011-0.00151.4770.0930.0930.0000.0000.0000.000
181A209GLY00.0030.02651.5410.0920.0920.0000.0000.0000.000
182A210VAL0-0.054-0.01648.9760.1020.1020.0000.0000.0000.000
183A211LYS10.9240.95252.0255.7455.7450.0000.0000.0000.000
184A212GLU-1-0.890-0.95352.136-6.136-6.1360.0000.0000.0000.000
185A213GLY00.0120.00252.649-0.068-0.0680.0000.0000.0000.000
186A214ASP-1-0.877-0.91252.789-6.178-6.1780.0000.0000.0000.000
187A215ILE00.0680.03051.017-0.138-0.1380.0000.0000.0000.000
188A216HIS10.8400.89949.1966.3116.3110.0000.0000.0000.000
189A217GLY00.0470.02548.639-0.131-0.1310.0000.0000.0000.000
190A218VAL00.0150.00444.008-0.013-0.0130.0000.0000.0000.000
191A219ASP-1-0.796-0.89746.160-6.633-6.6330.0000.0000.0000.000
192A220ALA0-0.039-0.02044.897-0.221-0.2210.0000.0000.0000.000
193A221VAL00.0370.02641.9310.1330.1330.0000.0000.0000.000
194A222SER0-0.002-0.01944.481-0.020-0.0200.0000.0000.0000.000
195A223GLY00.0070.00944.409-0.086-0.0860.0000.0000.0000.000
196A224ALA00.0550.03439.913-0.122-0.1220.0000.0000.0000.000
197A225THR0-0.050-0.03241.157-0.043-0.0430.0000.0000.0000.000
198A226MET0-0.036-0.02140.3510.0090.0090.0000.0000.0000.000
199A227THR00.024-0.00335.7320.0290.0290.0000.0000.0000.000
200A228GLY00.0520.02438.217-0.120-0.1200.0000.0000.0000.000
201A229ARG10.8850.93240.6017.0297.0290.0000.0000.0000.000
202A230GLY00.0450.03337.5500.0530.0530.0000.0000.0000.000
203A231VAL00.0450.02235.878-0.077-0.0770.0000.0000.0000.000
204A232GLN0-0.016-0.01137.9540.1340.1340.0000.0000.0000.000
205A233ARG10.9530.97040.0837.5827.5820.0000.0000.0000.000
206A234ALA00.0230.02035.348-0.012-0.0120.0000.0000.0000.000
207A235MET0-0.020-0.00137.333-0.056-0.0560.0000.0000.0000.000
208A236GLU-1-0.940-0.97639.400-7.090-7.0900.0000.0000.0000.000
209A237PHE0-0.044-0.02435.9140.1210.1210.0000.0000.0000.000
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