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: VNML1

Calculation Name: 6RK0-B-Xray547

Preferred Name:

Target Type:

Ligand Name: flavin-adenine dinucleotide | protoporphyrin ix containing fe | sulfate ion

Ligand 3-letter code: FAD | HEM | SO4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6RK0

Chain ID: B

ChEMBL ID:

UniProt ID: C1DK98

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 214
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2297512.666921
FMO2-HF: Nuclear repulsion 2212939.709438
FMO2-HF: Total energy -84572.957482
FMO2-MP2: Total energy -84819.156844


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:10:PRO)


Summations of interaction energy for fragment #1(A:10:PRO)
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.
-52.36-45.6872.556-3.153-6.077-0.034
Interaction energy analysis for fragmet #1(A:10:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.807 / q_NPA : 0.887
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].
3A12ALA00.002-0.0142.703-10.436-6.8710.446-2.025-1.986-0.018
19A28TYR00.0650.0362.8136.4247.7340.211-0.378-1.143-0.002
20A29ASP-1-0.800-0.8502.440-58.055-55.4961.769-1.574-2.754-0.013
21A30GLN00.0700.0203.09510.0849.3230.1300.824-0.194-0.001
4A13PRO0-0.046-0.0035.0020.8000.8000.0000.0000.0000.000
5A14SER0-0.025-0.0466.4662.9992.9990.0000.0000.0000.000
6A15ASP-1-0.871-0.9319.834-23.094-23.0940.0000.0000.0000.000
7A16ARG10.6610.78312.19718.57618.5760.0000.0000.0000.000
8A17THR0-0.001-0.0169.038-0.373-0.3730.0000.0000.0000.000
9A18HIS0-0.043-0.0238.8450.8200.8200.0000.0000.0000.000
10A19VAL0-0.010-0.0119.8313.3253.3250.0000.0000.0000.000
11A20LYS10.9770.99011.81818.05818.0580.0000.0000.0000.000
12A21ARG10.9470.96314.67415.44415.4440.0000.0000.0000.000
13A22TYR00.0420.00315.385-0.501-0.5010.0000.0000.0000.000
14A23HIS00.0300.02610.894-1.802-1.8020.0000.0000.0000.000
15A24TRP00.0630.0279.933-2.865-2.8650.0000.0000.0000.000
16A25LEU0-0.045-0.01011.109-0.181-0.1810.0000.0000.0000.000
17A26ALA0-0.019-0.0048.2230.7540.7540.0000.0000.0000.000
18A27ARG10.8350.8875.59837.67137.6710.0000.0000.0000.000
22A31GLU-1-0.935-0.9486.211-25.596-25.5960.0000.0000.0000.000
23A32THR0-0.019-0.0406.8804.0094.0090.0000.0000.0000.000
24A33VAL0-0.003-0.0126.4582.8862.8860.0000.0000.0000.000
25A34LYS10.7850.8869.00826.63326.6330.0000.0000.0000.000
26A35ALA00.0410.02411.2301.7281.7280.0000.0000.0000.000
27A36ILE0-0.057-0.03111.1871.4091.4090.0000.0000.0000.000
28A37LEU0-0.049-0.02212.7681.3651.3650.0000.0000.0000.000
29A38ASP-1-0.753-0.84915.318-17.350-17.3500.0000.0000.0000.000
30A39ALA0-0.0270.01217.0690.8510.8510.0000.0000.0000.000
31A40THR0-0.015-0.03318.8391.1811.1810.0000.0000.0000.000
32A41PRO00.0870.06320.437-0.425-0.4250.0000.0000.0000.000
33A42LEU0-0.045-0.01122.6140.2700.2700.0000.0000.0000.000
34A43ALA00.001-0.00420.399-0.713-0.7130.0000.0000.0000.000
35A44HIS00.006-0.00821.0780.9360.9360.0000.0000.0000.000
36A45VAL00.0120.00521.290-0.694-0.6940.0000.0000.0000.000
37A46GLY0-0.0210.00722.0110.6440.6440.0000.0000.0000.000
38A47CYS0-0.001-0.01222.897-0.364-0.3640.0000.0000.0000.000
39A48MET0-0.0200.01325.6390.2930.2930.0000.0000.0000.000
40A49MET0-0.027-0.01228.4050.2590.2590.0000.0000.0000.000
41A50ASN0-0.024-0.02531.7750.1500.1500.0000.0000.0000.000
42A51GLY00.0350.02133.6940.1450.1450.0000.0000.0000.000
43A52VAL00.0150.01531.292-0.090-0.0900.0000.0000.0000.000
44A53PRO00.0500.00926.582-0.076-0.0760.0000.0000.0000.000
45A54PHE00.0140.00028.1610.0650.0650.0000.0000.0000.000
46A55VAL00.0410.02324.370-0.387-0.3870.0000.0000.0000.000
47A56THR0-0.053-0.02826.2270.5970.5970.0000.0000.0000.000
48A57PRO0-0.0010.01525.849-0.449-0.4490.0000.0000.0000.000
49A58THR0-0.038-0.02924.7200.4990.4990.0000.0000.0000.000
50A59PHE00.0510.02124.899-0.414-0.4140.0000.0000.0000.000
51A60PHE0-0.084-0.04917.6550.0510.0510.0000.0000.0000.000
52A61TRP00.0330.02421.1190.1780.1780.0000.0000.0000.000
53A62ARG10.7840.83213.87318.16518.1650.0000.0000.0000.000
54A63GLU-1-0.771-0.86918.267-12.176-12.1760.0000.0000.0000.000
55A64GLY0-0.003-0.00115.623-0.223-0.2230.0000.0000.0000.000
56A65ASP-1-0.806-0.90211.365-23.405-23.4050.0000.0000.0000.000
57A66ARG10.8850.94813.58214.42114.4210.0000.0000.0000.000
58A67VAL00.0180.01015.6820.1970.1970.0000.0000.0000.000
59A68TYR0-0.002-0.00818.1430.4820.4820.0000.0000.0000.000
60A69TRP00.0350.01520.432-0.139-0.1390.0000.0000.0000.000
61A70HIS00.0180.00824.7220.4390.4390.0000.0000.0000.000
62A71GLY00.0320.00828.538-0.083-0.0830.0000.0000.0000.000
63A72SER00.0070.01331.7650.1290.1290.0000.0000.0000.000
64A73SER00.0170.00034.006-0.149-0.1490.0000.0000.0000.000
65A74ALA0-0.011-0.00335.515-0.035-0.0350.0000.0000.0000.000
66A75GLY0-0.029-0.01233.8070.0770.0770.0000.0000.0000.000
67A76ARG10.8840.93232.7149.0969.0960.0000.0000.0000.000
68A77LEU00.0410.00226.173-0.043-0.0430.0000.0000.0000.000
69A78PHE00.0020.00127.520-0.265-0.2650.0000.0000.0000.000
70A79LYS10.8760.92929.6519.0089.0080.0000.0000.0000.000
71A80ALA0-0.023-0.01129.330-0.023-0.0230.0000.0000.0000.000
72A81LEU00.0090.00124.549-0.139-0.1390.0000.0000.0000.000
73A82GLU-1-0.828-0.87925.205-9.942-9.9420.0000.0000.0000.000
74A83HIS0-0.014-0.02426.500-0.430-0.4300.0000.0000.0000.000
75A84GLN0-0.070-0.03324.488-0.216-0.2160.0000.0000.0000.000
76A85ASP-1-0.777-0.87018.877-15.162-15.1620.0000.0000.0000.000
77A86ILE0-0.039-0.01819.9020.5050.5050.0000.0000.0000.000
78A87CYS0-0.025-0.00917.884-1.079-1.0790.0000.0000.0000.000
79A88LEU0-0.0010.01417.2140.9170.9170.0000.0000.0000.000
80A89THR00.000-0.01016.516-1.292-1.2920.0000.0000.0000.000
81A90VAL00.0160.01116.1800.9560.9560.0000.0000.0000.000
82A91SER0-0.049-0.03516.632-0.785-0.7850.0000.0000.0000.000
83A92LEU0-0.0150.00518.2200.7180.7180.0000.0000.0000.000
84A93LEU0-0.0040.00519.772-0.604-0.6040.0000.0000.0000.000
85A94ASP-1-0.753-0.86618.937-15.464-15.4640.0000.0000.0000.000
86A95GLY00.004-0.01122.5320.3440.3440.0000.0000.0000.000
87A96LEU0-0.0180.01024.620-0.398-0.3980.0000.0000.0000.000
88A97VAL0-0.046-0.02122.7510.1840.1840.0000.0000.0000.000
89A98ILE0-0.0040.00026.2270.0980.0980.0000.0000.0000.000
90A99ALA00.0240.00427.571-0.098-0.0980.0000.0000.0000.000
91A100ARG10.8620.91429.39010.62810.6280.0000.0000.0000.000
92A101SER00.0400.02430.3250.2270.2270.0000.0000.0000.000
93A102ALA0-0.030-0.03730.263-0.290-0.2900.0000.0000.0000.000
94A103TYR0-0.047-0.02025.448-0.136-0.1360.0000.0000.0000.000
95A104ASN00.001-0.00225.210-0.858-0.8580.0000.0000.0000.000
96A105PHE0-0.0300.00425.668-0.245-0.2450.0000.0000.0000.000
97A106ASN0-0.054-0.04421.019-1.123-1.1230.0000.0000.0000.000
98A107CYS0-0.0220.00322.1340.3900.3900.0000.0000.0000.000
99A108ASN00.0170.00720.047-1.116-1.1160.0000.0000.0000.000
100A109PHE0-0.040-0.02415.4950.4980.4980.0000.0000.0000.000
101A110ARG10.8150.86814.56415.15415.1540.0000.0000.0000.000
102A111SER0-0.031-0.02514.0021.2541.2540.0000.0000.0000.000
103A112VAL00.0310.00310.654-2.016-2.0160.0000.0000.0000.000
104A113MET0-0.024-0.00312.3511.8191.8190.0000.0000.0000.000
105A114LEU00.0010.01011.708-2.208-2.2080.0000.0000.0000.000
106A115LEU00.007-0.00213.2041.6651.6650.0000.0000.0000.000
107A116GLY00.0580.03114.832-0.525-0.5250.0000.0000.0000.000
108A117ARG10.7980.89916.93713.47313.4730.0000.0000.0000.000
109A118ALA00.0050.00719.502-0.444-0.4440.0000.0000.0000.000
110A119GLU-1-0.930-0.97021.611-13.064-13.0640.0000.0000.0000.000
111A120LEU0-0.029-0.03024.451-0.130-0.1300.0000.0000.0000.000
112A121ILE0-0.017-0.00525.1310.0000.0000.0000.0000.0000.000
113A122SER0-0.016-0.01428.4650.1860.1860.0000.0000.0000.000
114A123ASP-1-0.841-0.90130.640-9.036-9.0360.0000.0000.0000.000
115A124GLU-1-0.736-0.89531.827-8.916-8.9160.0000.0000.0000.000
116A125ALA0-0.0200.00333.8370.0030.0030.0000.0000.0000.000
117A126VAL00.016-0.00527.129-0.163-0.1630.0000.0000.0000.000
118A127LYS10.7780.89228.9148.7208.7200.0000.0000.0000.000
119A128ALA00.005-0.00930.365-0.134-0.1340.0000.0000.0000.000
120A129GLU-1-0.940-0.95827.140-10.850-10.8500.0000.0000.0000.000
121A130LYS10.8180.89323.78811.92811.9280.0000.0000.0000.000
122A131LEU0-0.022-0.00927.180-0.184-0.1840.0000.0000.0000.000
123A132ARG10.9540.98929.4539.8229.8220.0000.0000.0000.000
124A133ASN0-0.066-0.04724.8860.2760.2760.0000.0000.0000.000
125A134PHE0-0.032-0.00725.715-0.272-0.2720.0000.0000.0000.000
126A135VAL00.0060.00426.912-0.045-0.0450.0000.0000.0000.000
127A136ASP-1-0.783-0.87229.023-9.567-9.5670.0000.0000.0000.000
128A137GLY0-0.025-0.00725.199-0.123-0.1230.0000.0000.0000.000
129A138LEU0-0.073-0.02625.525-0.311-0.3110.0000.0000.0000.000
130A139ILE00.001-0.01027.8390.0720.0720.0000.0000.0000.000
131A140PRO0-0.0110.00028.5580.1410.1410.0000.0000.0000.000
132A141GLY00.0200.01130.7790.3010.3010.0000.0000.0000.000
133A142GLU-1-0.801-0.89432.956-8.145-8.1450.0000.0000.0000.000
134A143TRP0-0.006-0.01232.9960.2470.2470.0000.0000.0000.000
135A144GLU0-0.141-0.12332.9520.2040.2040.0000.0000.0000.000
136A145ARG10.7720.87234.8618.8168.8160.0000.0000.0000.000
137A146LEU0-0.0100.01736.0110.2020.2020.0000.0000.0000.000
138A147ARG10.7540.83540.0857.4237.4230.0000.0000.0000.000
139A148PRO00.007-0.00641.050-0.124-0.1240.0000.0000.0000.000
140A149VAL00.0170.03236.9490.1460.1460.0000.0000.0000.000
141A150HIS0-0.016-0.01440.1410.0840.0840.0000.0000.0000.000
142A151ALA00.0180.00540.037-0.130-0.1300.0000.0000.0000.000
143A152LYS11.0160.99739.7656.7736.7730.0000.0000.0000.000
144A153GLU-1-0.773-0.84038.893-7.555-7.5550.0000.0000.0000.000
145A154ILE0-0.0200.01234.302-0.225-0.2250.0000.0000.0000.000
146A155GLU-1-0.899-0.95935.640-7.687-7.6870.0000.0000.0000.000
147A156ALA0-0.032-0.01237.289-0.104-0.1040.0000.0000.0000.000
148A157THR0-0.038-0.01232.101-0.107-0.1070.0000.0000.0000.000
149A158ALA0-0.011-0.00330.7520.0060.0060.0000.0000.0000.000
150A159VAL00.027-0.00425.989-0.090-0.0900.0000.0000.0000.000
151A160ALA0-0.0230.00224.7600.1150.1150.0000.0000.0000.000
152A161SER00.0200.01620.668-0.403-0.4030.0000.0000.0000.000
153A162LEU00.0200.00616.3110.3680.3680.0000.0000.0000.000
154A163SER00.0030.01113.778-0.666-0.6660.0000.0000.0000.000
155A164ILE0-0.009-0.01310.140-0.114-0.1140.0000.0000.0000.000
156A165ALA00.0000.0009.237-2.209-2.2090.0000.0000.0000.000
157A166GLU-1-0.752-0.8078.262-23.798-23.7980.0000.0000.0000.000
158A167ALA00.0180.0067.8781.9611.9610.0000.0000.0000.000
159A168SER0-0.038-0.0187.506-3.173-3.1730.0000.0000.0000.000
160A169CYS0-0.0080.0107.7343.4103.4100.0000.0000.0000.000
161A170LYS10.8710.9409.60318.98218.9820.0000.0000.0000.000
162A171VAL00.0170.00911.3271.3491.3490.0000.0000.0000.000
163A172ARG10.8170.91613.71514.63614.6360.0000.0000.0000.000
164A173THR00.0160.00216.2740.6590.6590.0000.0000.0000.000
165A174GLY00.0400.02118.337-0.072-0.0720.0000.0000.0000.000
166A175PRO00.0370.02120.8920.2550.2550.0000.0000.0000.000
167A176PRO00.0290.01922.583-0.693-0.6930.0000.0000.0000.000
168A177LEU0-0.066-0.04219.550-0.132-0.1320.0000.0000.0000.000
169A178ASP-1-0.776-0.86724.010-10.936-10.9360.0000.0000.0000.000
170A179ASP-1-0.804-0.89326.081-11.890-11.8900.0000.0000.0000.000
171A180GLU-1-0.980-0.99927.446-11.044-11.0440.0000.0000.0000.000
172A181GLU-1-0.909-0.96429.006-10.030-10.0300.0000.0000.0000.000
173A182ASP-1-0.852-0.92730.715-9.649-9.6490.0000.0000.0000.000
174A183TYR0-0.094-0.04726.3200.1070.1070.0000.0000.0000.000
175A184ALA0-0.038-0.00632.3990.1540.1540.0000.0000.0000.000
176A185PHE0-0.013-0.00735.2810.3460.3460.0000.0000.0000.000
177A186PRO0-0.040-0.01436.245-0.172-0.1720.0000.0000.0000.000
178A187SER0-0.012-0.01035.0740.2430.2430.0000.0000.0000.000
179A188TRP0-0.031-0.01432.126-0.194-0.1940.0000.0000.0000.000
180A189ALA00.0140.00729.950-0.101-0.1010.0000.0000.0000.000
181A190GLY0-0.019-0.01428.8140.0750.0750.0000.0000.0000.000
182A191VAL0-0.037-0.02324.507-0.314-0.3140.0000.0000.0000.000
183A192ILE00.0000.01727.7720.3090.3090.0000.0000.0000.000
184A193PRO0-0.015-0.01626.476-0.321-0.3210.0000.0000.0000.000
185A194ILE0-0.041-0.01225.8640.4930.4930.0000.0000.0000.000
186A195ARG10.9760.98625.11410.35810.3580.0000.0000.0000.000
187A196TYR00.0260.02023.7490.5650.5650.0000.0000.0000.000
188A197GLN0-0.041-0.02727.504-0.112-0.1120.0000.0000.0000.000
189A198VAL00.0090.01529.3980.0500.0500.0000.0000.0000.000
190A199LEU0-0.018-0.01132.0890.0830.0830.0000.0000.0000.000
191A200PRO0-0.001-0.01435.918-0.101-0.1010.0000.0000.0000.000
192A201PRO00.0200.01136.7160.0540.0540.0000.0000.0000.000
193A202GLU-1-0.931-0.95338.898-7.399-7.3990.0000.0000.0000.000
194A203PRO0-0.052-0.02041.594-0.069-0.0690.0000.0000.0000.000
195A204ASP-1-0.806-0.90943.956-6.702-6.7020.0000.0000.0000.000
196A205PRO0-0.033-0.02345.4940.0940.0940.0000.0000.0000.000
197A206ARG10.8670.92548.4816.4756.4750.0000.0000.0000.000
198A207ASN0-0.026-0.00344.465-0.009-0.0090.0000.0000.0000.000
199A208LEU0-0.0020.00648.5390.1370.1370.0000.0000.0000.000
200A209PRO0-0.020-0.02949.936-0.082-0.0820.0000.0000.0000.000
201A210ASP-1-0.920-0.95251.665-6.059-6.0590.0000.0000.0000.000
202A211VAL0-0.028-0.00845.377-0.056-0.0560.0000.0000.0000.000
203A212PRO0-0.035-0.00544.772-0.036-0.0360.0000.0000.0000.000
204A213MET00.0170.00239.026-0.097-0.0970.0000.0000.0000.000
205A214PRO00.005-0.00337.5650.0140.0140.0000.0000.0000.000
206A215GLU-1-0.872-0.94937.313-8.192-8.1920.0000.0000.0000.000
207A216ASP-1-0.868-0.93533.111-9.344-9.3440.0000.0000.0000.000
208A217ILE00.0150.00832.789-0.323-0.3230.0000.0000.0000.000
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