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: J41Q9

Calculation Name: 1YRE-A-Xray547

Preferred Name:

Target Type:

Ligand Name: coenzyme a

Ligand 3-letter code: COA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1YRE

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HYX1

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 183
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2008612.856466
FMO2-HF: Nuclear repulsion 1937011.80766
FMO2-HF: Total energy -71601.048806
FMO2-MP2: Total energy -71811.476869


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:11:LEU)


Summations of interaction energy for fragment #1(A:11:LEU)
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.
-19.859-17.7020.052-0.873-1.337-0.003
Interaction energy analysis for fragmet #1(A:11:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.858 / q_NPA : 0.920
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].
3A13ILE0-0.0010.0073.445-2.776-1.3250.026-0.659-0.818-0.001
59A69LEU0-0.044-0.0233.110-6.334-5.7190.027-0.205-0.438-0.002
117A127LEU0-0.066-0.0404.380-2.079-1.988-0.001-0.009-0.0810.000
4A14THR00.0190.0196.2062.9862.9860.0000.0000.0000.000
5A15LEU0-0.022-0.0049.557-0.048-0.0480.0000.0000.0000.000
6A16GLN00.020-0.00312.2451.1771.1770.0000.0000.0000.000
7A17ARG10.9370.95815.79914.25814.2580.0000.0000.0000.000
8A18GLY00.0200.01919.2560.5920.5920.0000.0000.0000.000
9A19ALA00.0260.00920.926-0.382-0.3820.0000.0000.0000.000
10A20LEU0-0.0210.00918.3810.0270.0270.0000.0000.0000.000
11A21ARG10.8540.90115.83016.17216.1720.0000.0000.0000.000
12A22LEU0-0.0140.00813.1000.7350.7350.0000.0000.0000.000
13A23GLU-1-0.767-0.87711.629-21.059-21.0590.0000.0000.0000.000
14A24PRO0-0.012-0.0167.8200.5690.5690.0000.0000.0000.000
15A25LEU0-0.0330.00710.0251.8991.8990.0000.0000.0000.000
16A26VAL00.020-0.00611.590-1.448-1.4480.0000.0000.0000.000
17A27GLU-1-0.852-0.95614.096-15.838-15.8380.0000.0000.0000.000
18A28ALA0-0.018-0.01017.2340.8230.8230.0000.0000.0000.000
19A29ASP-1-0.750-0.86015.644-18.468-18.4680.0000.0000.0000.000
20A30ILE0-0.053-0.01617.1990.6300.6300.0000.0000.0000.000
21A31PRO0-0.009-0.01020.4970.5110.5110.0000.0000.0000.000
22A32GLU-1-0.849-0.92122.799-12.764-12.7640.0000.0000.0000.000
23A33LEU0-0.010-0.00818.2510.3140.3140.0000.0000.0000.000
24A34VAL0-0.014-0.01422.7820.3410.3410.0000.0000.0000.000
25A35SER0-0.0180.00025.1980.5560.5560.0000.0000.0000.000
26A36LEU00.0050.00124.0940.3180.3180.0000.0000.0000.000
27A37ALA0-0.017-0.00824.8020.2060.2060.0000.0000.0000.000
28A38GLU-1-0.978-0.98326.845-9.272-9.2720.0000.0000.0000.000
29A39ALA00.0600.02730.3190.2160.2160.0000.0000.0000.000
30A40ASN0-0.045-0.03627.7130.2550.2550.0000.0000.0000.000
31A41ARG10.9540.98229.6999.0959.0950.0000.0000.0000.000
32A42GLU-1-0.931-0.96630.901-8.788-8.7880.0000.0000.0000.000
33A43ALA0-0.028-0.00929.1280.0280.0280.0000.0000.0000.000
34A44LEU0-0.028-0.01224.514-0.334-0.3340.0000.0000.0000.000
35A45GLN00.0000.00027.544-0.058-0.0580.0000.0000.0000.000
36A46TYR0-0.008-0.01727.4970.0390.0390.0000.0000.0000.000
37A47MET0-0.066-0.03420.795-0.300-0.3000.0000.0000.0000.000
38A48ASP-1-0.820-0.89925.076-11.643-11.6430.0000.0000.0000.000
39A49GLY00.0350.00523.113-0.628-0.6280.0000.0000.0000.000
40A50PRO0-0.034-0.01421.701-0.042-0.0420.0000.0000.0000.000
41A51THR00.0290.02123.124-0.205-0.2050.0000.0000.0000.000
42A52ARG10.8420.92324.57012.44912.4490.0000.0000.0000.000
43A53PRO00.0560.01322.407-0.616-0.6160.0000.0000.0000.000
44A54ASP-1-0.843-0.92320.668-13.820-13.8200.0000.0000.0000.000
45A55TRP00.0570.03218.172-1.197-1.1970.0000.0000.0000.000
46A56TYR00.010-0.01116.851-1.353-1.3530.0000.0000.0000.000
47A57ARG10.9070.96115.74813.76013.7600.0000.0000.0000.000
48A58GLN0-0.029-0.01915.719-0.311-0.3110.0000.0000.0000.000
49A59SER0-0.038-0.03112.687-1.483-1.4830.0000.0000.0000.000
50A60LEU00.003-0.00311.235-2.620-2.6200.0000.0000.0000.000
51A61ALA0-0.055-0.02611.729-1.104-1.1040.0000.0000.0000.000
52A62GLU-1-0.838-0.92410.510-23.281-23.2810.0000.0000.0000.000
53A63GLN0-0.050-0.0176.603-5.449-5.4490.0000.0000.0000.000
54A64ARG10.8770.9387.02418.22418.2240.0000.0000.0000.000
55A65GLU-1-0.925-0.9479.164-23.082-23.0820.0000.0000.0000.000
56A66GLY0-0.041-0.0165.471-0.349-0.3490.0000.0000.0000.000
57A67ARG10.9210.9565.89920.30420.3040.0000.0000.0000.000
58A68ALA0-0.006-0.0067.5521.9291.9290.0000.0000.0000.000
60A70PRO00.0050.0107.0782.7922.7920.0000.0000.0000.000
61A71LEU0-0.017-0.0109.347-1.385-1.3850.0000.0000.0000.000
62A72ALA00.0390.02812.4421.9431.9430.0000.0000.0000.000
63A73VAL0-0.021-0.01415.584-0.699-0.6990.0000.0000.0000.000
64A74ARG10.8540.90516.55418.40018.4000.0000.0000.0000.000
65A75LEU00.0030.00219.969-0.402-0.4020.0000.0000.0000.000
66A76GLY00.0050.00222.8350.6280.6280.0000.0000.0000.000
67A77VAL0-0.014-0.01522.443-0.654-0.6540.0000.0000.0000.000
68A78GLN0-0.033-0.00223.315-0.036-0.0360.0000.0000.0000.000
69A79LEU0-0.0060.00819.045-0.689-0.6890.0000.0000.0000.000
70A80VAL00.006-0.00821.7530.6560.6560.0000.0000.0000.000
71A81GLY00.0390.01421.0580.4440.4440.0000.0000.0000.000
72A82THR0-0.060-0.02515.647-0.830-0.8300.0000.0000.0000.000
73A83THR00.026-0.01613.5841.3171.3170.0000.0000.0000.000
74A84ARG10.9040.97011.28119.86319.8630.0000.0000.0000.000
75A85PHE00.0290.0267.8271.0761.0760.0000.0000.0000.000
76A86ALA00.0300.0049.148-2.026-2.0260.0000.0000.0000.000
77A87GLU-1-0.902-0.94910.550-20.973-20.9730.0000.0000.0000.000
78A88PHE0-0.032-0.0045.867-0.789-0.7890.0000.0000.0000.000
79A89LEU00.0170.01010.0501.3031.3030.0000.0000.0000.000
80A90PRO00.006-0.0289.0820.4200.4200.0000.0000.0000.000
81A91ALA0-0.022-0.01010.901-0.028-0.0280.0000.0000.0000.000
82A92LEU0-0.0450.01313.6891.3291.3290.0000.0000.0000.000
83A93PRO00.0220.02810.1340.7380.7380.0000.0000.0000.000
84A94ALA00.038-0.01311.9891.2471.2470.0000.0000.0000.000
85A95CYS0-0.031-0.0069.728-2.425-2.4250.0000.0000.0000.000
86A96GLU-1-0.791-0.86011.766-15.356-15.3560.0000.0000.0000.000
87A97ILE0-0.028-0.01512.300-1.888-1.8880.0000.0000.0000.000
88A98GLY00.0600.00814.1801.6821.6820.0000.0000.0000.000
89A99TRP0-0.060-0.03713.975-0.963-0.9630.0000.0000.0000.000
90A100THR0-0.045-0.02317.0930.0460.0460.0000.0000.0000.000
91A101TRP0-0.031-0.01218.7390.8700.8700.0000.0000.0000.000
92A102LEU00.004-0.00920.628-0.584-0.5840.0000.0000.0000.000
93A103ASP-1-0.735-0.86723.543-10.737-10.7370.0000.0000.0000.000
94A104GLN0-0.020-0.02126.7720.1220.1220.0000.0000.0000.000
95A105ALA00.0400.03329.8680.1980.1980.0000.0000.0000.000
96A106GLN0-0.013-0.00925.412-0.127-0.1270.0000.0000.0000.000
97A107HIS0-0.108-0.04526.6390.0230.0230.0000.0000.0000.000
98A108GLY0-0.025-0.01728.4490.3940.3940.0000.0000.0000.000
99A109SER0-0.013-0.02027.135-0.063-0.0630.0000.0000.0000.000
100A110GLY00.0130.00926.6110.0120.0120.0000.0000.0000.000
101A111LEU00.0310.02921.404-0.553-0.5530.0000.0000.0000.000
102A112ASN00.0730.02221.073-1.256-1.2560.0000.0000.0000.000
103A113ARG10.8840.94520.63911.34411.3440.0000.0000.0000.000
104A114MET00.0360.04019.828-0.762-0.7620.0000.0000.0000.000
105A115ILE00.0010.00016.127-0.862-0.8620.0000.0000.0000.000
106A116LYS10.8990.94415.91815.37715.3770.0000.0000.0000.000
107A117TYR0-0.016-0.02916.375-1.170-1.1700.0000.0000.0000.000
108A118LEU0-0.029-0.01514.344-0.680-0.6800.0000.0000.0000.000
109A119MET0-0.041-0.00611.482-0.808-0.8080.0000.0000.0000.000
110A120LEU00.0240.01311.722-1.827-1.8270.0000.0000.0000.000
111A121LYS10.9090.95913.69716.98016.9800.0000.0000.0000.000
112A122HIS00.0130.0085.3213.9423.9420.0000.0000.0000.000
113A123ALA00.0270.0109.394-2.373-2.3730.0000.0000.0000.000
114A124PHE00.0390.02110.419-0.711-0.7110.0000.0000.0000.000
115A125ASP-1-0.844-0.88313.317-18.052-18.0520.0000.0000.0000.000
116A126ASN0-0.062-0.0378.5301.6081.6080.0000.0000.0000.000
118A128ARG10.8460.9108.21221.84221.8420.0000.0000.0000.000
119A129MET0-0.0560.0087.6661.3771.3770.0000.0000.0000.000
120A130VAL00.0410.02012.1871.2951.2950.0000.0000.0000.000
121A131ARG10.7800.83714.82717.30217.3020.0000.0000.0000.000
122A132VAL0-0.024-0.01212.855-1.840-1.8400.0000.0000.0000.000
123A133GLN0-0.005-0.00315.3211.6801.6800.0000.0000.0000.000
124A134LEU0-0.003-0.01016.454-0.929-0.9290.0000.0000.0000.000
125A135SER0-0.002-0.02418.9581.1301.1300.0000.0000.0000.000
126A136THR0-0.072-0.03621.301-0.249-0.2490.0000.0000.0000.000
127A137ALA00.0170.00624.0710.2250.2250.0000.0000.0000.000
128A138ALA00.0140.01627.3550.0620.0620.0000.0000.0000.000
129A139SER0-0.001-0.03230.6020.3480.3480.0000.0000.0000.000
130A140ASN0-0.042-0.01226.2250.3970.3970.0000.0000.0000.000
131A141LEU00.0780.03129.028-0.312-0.3120.0000.0000.0000.000
132A142ARG10.9470.98128.91610.40210.4020.0000.0000.0000.000
133A143ALA0-0.018-0.01924.682-0.228-0.2280.0000.0000.0000.000
134A144GLN0-0.031-0.01525.723-0.152-0.1520.0000.0000.0000.000
135A145GLY00.0970.06127.459-0.196-0.1960.0000.0000.0000.000
136A146ALA0-0.109-0.06724.988-0.061-0.0610.0000.0000.0000.000
137A147ILE0-0.012-0.00321.996-0.513-0.5130.0000.0000.0000.000
138A148ASP-1-0.805-0.91024.295-11.201-11.2010.0000.0000.0000.000
139A149LYS10.8570.92126.89911.26711.2670.0000.0000.0000.000
140A150LEU0-0.074-0.02919.993-0.142-0.1420.0000.0000.0000.000
141A151GLY00.0160.01123.254-0.308-0.3080.0000.0000.0000.000
142A152ALA0-0.025-0.00421.730-0.072-0.0720.0000.0000.0000.000
143A153GLN00.0300.02523.4510.8960.8960.0000.0000.0000.000
144A154ARG10.8780.94124.71610.01910.0190.0000.0000.0000.000
145A155GLU-1-0.782-0.83422.691-13.859-13.8590.0000.0000.0000.000
146A156GLY0-0.010-0.01026.8100.3650.3650.0000.0000.0000.000
147A157VAL0-0.036-0.01927.807-0.222-0.2220.0000.0000.0000.000
148A158LEU0-0.0120.00723.7830.2710.2710.0000.0000.0000.000
149A159ARG10.9710.97028.1479.1899.1890.0000.0000.0000.000
150A160ASN0-0.040-0.02930.214-0.067-0.0670.0000.0000.0000.000
151A161HIS00.0560.05422.0520.1220.1220.0000.0000.0000.000
152A162ARG10.9060.95422.54712.45612.4560.0000.0000.0000.000
153A163ARG10.9180.94426.30110.70710.7070.0000.0000.0000.000
154A164LEU0-0.042-0.00726.864-0.432-0.4320.0000.0000.0000.000
155A165ALA00.0180.01128.7120.1070.1070.0000.0000.0000.000
156A166GLY0-0.0090.00129.5730.1090.1090.0000.0000.0000.000
157A167GLY00.0180.01231.1140.2850.2850.0000.0000.0000.000
158A168ARG10.9160.96532.1079.0309.0300.0000.0000.0000.000
159A169LEU0-0.024-0.00430.325-0.318-0.3180.0000.0000.0000.000
160A170ASP-1-0.787-0.89929.881-9.736-9.7360.0000.0000.0000.000
161A171ASP-1-0.809-0.89729.491-10.100-10.1000.0000.0000.0000.000
162A172THR0-0.068-0.03723.362-0.170-0.1700.0000.0000.0000.000
163A173PHE0-0.0080.00926.7230.2690.2690.0000.0000.0000.000
164A174VAL00.0290.00621.463-0.449-0.4490.0000.0000.0000.000
165A175TYR0-0.012-0.01622.2080.6730.6730.0000.0000.0000.000
166A176SER0-0.068-0.05719.373-0.939-0.9390.0000.0000.0000.000
167A177ILE00.0070.02218.4080.6460.6460.0000.0000.0000.000
168A178THR00.002-0.02518.376-0.977-0.9770.0000.0000.0000.000
169A179ASP-1-0.852-0.94217.330-15.924-15.9240.0000.0000.0000.000
170A180HIS0-0.024-0.01918.7990.4470.4470.0000.0000.0000.000
171A181GLU-1-0.807-0.88122.080-12.930-12.9300.0000.0000.0000.000
172A182TRP0-0.011-0.00816.9620.2300.2300.0000.0000.0000.000
173A183PRO0-0.027-0.01920.1690.1300.1300.0000.0000.0000.000
174A184GLN00.000-0.00122.3530.2950.2950.0000.0000.0000.000
175A185VAL00.0160.01620.6640.2560.2560.0000.0000.0000.000
176A186LYS10.8200.90018.01516.59516.5950.0000.0000.0000.000
177A187ALA00.0260.01221.6370.1980.1980.0000.0000.0000.000
178A188ALA0-0.006-0.00225.2660.3770.3770.0000.0000.0000.000
179A189LEU0-0.042-0.02220.3120.1240.1240.0000.0000.0000.000
180A190GLU-1-0.829-0.88421.263-14.418-14.4180.0000.0000.0000.000
181A191ALA0-0.0080.00624.8010.2910.2910.0000.0000.0000.000
182A192SER0-0.084-0.04825.9220.3790.3790.0000.0000.0000.000
183A193PHE-1-0.954-0.98022.115-11.236-11.2360.0000.0000.0000.000