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: 9R1M2

Calculation Name: 4PY3-G-Xray547

Preferred Name:

Target Type:

Ligand Name: 1,2-ethanediol

Ligand 3-letter code: EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4PY3

Chain ID: G

ChEMBL ID:

UniProt ID: E6YV77

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 217
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2726791.536116
FMO2-HF: Nuclear repulsion 2637577.049718
FMO2-HF: Total energy -89214.486398
FMO2-MP2: Total energy -89470.660726


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:8:HIS)


Summations of interaction energy for fragment #1(A:8: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.
31.19933.949-0.001-0.964-1.784-0.001
Interaction energy analysis for fragmet #1(A:8:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.875 / q_NPA : 0.922
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].
3A10ALA00.0310.0383.8005.3597.157-0.003-0.742-1.053-0.002
4A11ARG10.8220.9024.08237.49138.000-0.001-0.133-0.3750.000
5A12ASN0-0.013-0.0153.7174.9315.3740.003-0.089-0.3560.001
6A13TYR00.0600.0267.5222.1492.1490.0000.0000.0000.000
7A14ALA0-0.048-0.0049.9292.6882.6880.0000.0000.0000.000
8A15TYR00.0220.00210.297-1.272-1.2720.0000.0000.0000.000
9A16PRO00.0330.0108.758-0.751-0.7510.0000.0000.0000.000
10A17HIS00.0310.0239.846-1.879-1.8790.0000.0000.0000.000
11A18MET0-0.044-0.01612.8940.1720.1720.0000.0000.0000.000
12A19ASN00.0510.01312.408-1.228-1.2280.0000.0000.0000.000
13A20THR0-0.060-0.03913.495-0.437-0.4370.0000.0000.0000.000
14A21LEU00.0110.00812.812-0.830-0.8300.0000.0000.0000.000
15A22LYS10.8420.9248.86526.89126.8910.0000.0000.0000.000
16A23ASN0-0.065-0.05915.2840.8950.8950.0000.0000.0000.000
17A24LYS10.9440.96718.86513.98313.9830.0000.0000.0000.000
18A25HIS0-0.020-0.00321.3080.5850.5850.0000.0000.0000.000
19A26ASN0-0.0010.00420.0040.2960.2960.0000.0000.0000.000
20A27ILE0-0.064-0.02621.0830.2380.2380.0000.0000.0000.000
21A28MET00.0830.04617.104-0.891-0.8910.0000.0000.0000.000
22A29SER0-0.0130.01119.969-0.518-0.5180.0000.0000.0000.000
23A30THR00.0800.01718.4490.1370.1370.0000.0000.0000.000
24A31LYS10.9730.99720.74210.77210.7720.0000.0000.0000.000
25A32LYS10.9720.98324.39711.28411.2840.0000.0000.0000.000
26A33LEU00.0230.01819.0100.3560.3560.0000.0000.0000.000
27A34ALA00.0340.01422.9820.1990.1990.0000.0000.0000.000
28A35HIS0-0.028-0.02324.1720.4450.4450.0000.0000.0000.000
29A36VAL00.0050.00526.1780.3510.3510.0000.0000.0000.000
30A37CYS0-0.069-0.01922.1370.1610.1610.0000.0000.0000.000
31A38GLU-1-0.833-0.92325.520-10.336-10.3360.0000.0000.0000.000
32A39HIS0-0.050-0.02328.2000.6610.6610.0000.0000.0000.000
33A40TYR0-0.009-0.02227.4430.4060.4060.0000.0000.0000.000
34A41ALA00.0820.05727.0910.2060.2060.0000.0000.0000.000
35A42LYS10.9570.97628.9759.3699.3690.0000.0000.0000.000
36A43LYS10.8840.94532.4339.0399.0390.0000.0000.0000.000
37A44ALA00.0290.02730.2850.2670.2670.0000.0000.0000.000
38A45ILE00.0270.01130.7070.2280.2280.0000.0000.0000.000
39A46ILE0-0.041-0.01633.7640.2460.2460.0000.0000.0000.000
40A47ASN0-0.027-0.02135.2080.5110.5110.0000.0000.0000.000
41A48LEU00.0700.04331.1550.1340.1340.0000.0000.0000.000
42A49ASN0-0.023-0.02035.0760.0090.0090.0000.0000.0000.000
43A50LYS10.8540.93138.1278.1818.1810.0000.0000.0000.000
44A51GLU-1-0.864-0.89134.304-9.247-9.2470.0000.0000.0000.000
45A52PRO0-0.019-0.01538.4780.0260.0260.0000.0000.0000.000
46A53LEU00.0130.01937.655-0.254-0.2540.0000.0000.0000.000
47A54PRO0-0.033-0.00333.7830.1760.1760.0000.0000.0000.000
48A55GLN00.001-0.01336.7000.1670.1670.0000.0000.0000.000
49A56LYS10.9030.96433.0659.3139.3130.0000.0000.0000.000
50A57PHE00.0330.02632.399-0.204-0.2040.0000.0000.0000.000
51A58ASP-1-0.838-0.92528.973-10.582-10.5820.0000.0000.0000.000
52A59SER0-0.006-0.05623.557-0.262-0.2620.0000.0000.0000.000
53A60SER0-0.051-0.02024.673-0.660-0.6600.0000.0000.0000.000
54A61TYR00.0410.02426.776-0.156-0.1560.0000.0000.0000.000
55A62LEU0-0.016-0.00723.215-0.095-0.0950.0000.0000.0000.000
56A63LYS10.9210.96520.68513.74213.7420.0000.0000.0000.000
57A64TYR0-0.012-0.02623.893-0.334-0.3340.0000.0000.0000.000
58A65ILE00.0070.00927.0370.0330.0330.0000.0000.0000.000
59A66HIS0-0.021-0.00119.1380.1650.1650.0000.0000.0000.000
60A67GLN00.016-0.00223.768-0.249-0.2490.0000.0000.0000.000
61A68ARG10.8370.89824.64110.35110.3510.0000.0000.0000.000
62A69LEU0-0.066-0.02425.3450.2030.2030.0000.0000.0000.000
63A70PHE00.000-0.01321.798-0.073-0.0730.0000.0000.0000.000
64A71GLU-1-0.795-0.87923.116-11.822-11.8220.0000.0000.0000.000
65A72SER0-0.031-0.01324.4050.0270.0270.0000.0000.0000.000
66A73THR0-0.025-0.01921.2360.2220.2220.0000.0000.0000.000
67A74PHE00.009-0.00718.117-0.528-0.5280.0000.0000.0000.000
68A75GLU-1-0.856-0.93716.026-17.134-17.1340.0000.0000.0000.000
69A76TRP0-0.0250.00315.1670.2500.2500.0000.0000.0000.000
70A77ALA0-0.046-0.01217.352-0.119-0.1190.0000.0000.0000.000
71A78GLY00.0420.01620.5860.3290.3290.0000.0000.0000.000
72A79TYR0-0.059-0.02616.3810.0870.0870.0000.0000.0000.000
73A80THR0-0.041-0.04916.3890.0480.0480.0000.0000.0000.000
74A81ARG10.7380.84711.34321.32721.3270.0000.0000.0000.000
75A82ASP-1-0.764-0.85510.629-21.938-21.9380.0000.0000.0000.000
76A83PHE0-0.028-0.00412.472-0.139-0.1390.0000.0000.0000.000
77A84SER0-0.022-0.0358.611-0.934-0.9340.0000.0000.0000.000
78A85PHE0-0.0100.00110.8601.6521.6520.0000.0000.0000.000
79A86THR0-0.022-0.01411.185-2.198-2.1980.0000.0000.0000.000
80A87PHE0-0.039-0.03010.8631.1941.1940.0000.0000.0000.000
81A88ASP-1-0.889-0.94313.220-15.313-15.3130.0000.0000.0000.000
82A89ASP-1-0.816-0.86310.610-23.234-23.2340.0000.0000.0000.000
83A90GLY00.0220.01411.279-0.607-0.6070.0000.0000.0000.000
84A91THR0-0.142-0.0986.570-2.289-2.2890.0000.0000.0000.000
85A92VAL00.0480.0206.9781.1661.1660.0000.0000.0000.000
86A93ALA0-0.048-0.0246.450-4.836-4.8360.0000.0000.0000.000
87A94GLU-1-0.825-0.9006.593-31.046-31.0460.0000.0000.0000.000
88A95MET0-0.098-0.0646.017-6.867-6.8670.0000.0000.0000.000
89A96PRO00.0560.0295.9863.6693.6690.0000.0000.0000.000
90A97MET00.0230.0237.8223.1703.1700.0000.0000.0000.000
91A98MET0-0.020-0.0158.921-2.642-2.6420.0000.0000.0000.000
92A99LYS10.8340.90911.60819.94419.9440.0000.0000.0000.000
93A100VAL00.0630.03114.1150.0050.0050.0000.0000.0000.000
94A101PRO0-0.007-0.01817.555-0.121-0.1210.0000.0000.0000.000
95A102ASN0-0.078-0.05318.4660.8470.8470.0000.0000.0000.000
96A103LEU00.0370.03819.1080.4660.4660.0000.0000.0000.000
97A104ASP-1-0.867-0.90917.422-18.023-18.0230.0000.0000.0000.000
98A105ILE00.0080.00918.3590.1910.1910.0000.0000.0000.000
99A106PHE0-0.045-0.03311.093-0.997-0.9970.0000.0000.0000.000
100A107TYR00.0280.02315.1820.8530.8530.0000.0000.0000.000
101A108VAL0-0.027-0.00615.335-0.924-0.9240.0000.0000.0000.000
102A109GLN00.0210.01612.462-1.830-1.8300.0000.0000.0000.000
103A110GLY0-0.022-0.02311.4720.8820.8820.0000.0000.0000.000
104A111ASN0-0.048-0.02812.4420.5870.5870.0000.0000.0000.000
105A112ASP-1-0.792-0.89314.201-16.956-16.9560.0000.0000.0000.000
106A113ILE0-0.0410.00014.0791.2681.2680.0000.0000.0000.000
107A114GLN0-0.020-0.03817.5241.8411.8410.0000.0000.0000.000
108A115GLU-1-0.986-0.98119.794-12.512-12.5120.0000.0000.0000.000
109A116ASN0-0.020-0.03520.0421.2491.2490.0000.0000.0000.000
110A117LEU00.0100.00319.8130.5990.5990.0000.0000.0000.000
111A118LYS10.9731.00023.24113.13113.1310.0000.0000.0000.000
112A119LYS10.9730.98625.22711.69111.6910.0000.0000.0000.000
113A120PHE0-0.009-0.00225.8840.4650.4650.0000.0000.0000.000
114A121ASP-1-0.740-0.86126.850-11.244-11.2440.0000.0000.0000.000
115A122GLN0-0.030-0.01829.2790.3010.3010.0000.0000.0000.000
116A123LEU0-0.045-0.00529.4000.4080.4080.0000.0000.0000.000
117A124LEU00.0330.01830.3370.3400.3400.0000.0000.0000.000
118A125ALA0-0.018-0.00433.3300.3070.3070.0000.0000.0000.000
119A126SER0-0.069-0.04734.8520.3140.3140.0000.0000.0000.000
120A127LYS10.8450.91534.9698.8478.8470.0000.0000.0000.000
121A128ASN00.0150.01438.1480.0280.0280.0000.0000.0000.000
122A129ASN0-0.014-0.02535.932-0.142-0.1420.0000.0000.0000.000
123A130LEU0-0.023-0.01335.159-0.029-0.0290.0000.0000.0000.000
124A131GLN00.0220.01138.9410.0070.0070.0000.0000.0000.000
125A132GLY0-0.024-0.01242.1810.0360.0360.0000.0000.0000.000
126A133LEU0-0.0170.01740.4780.1020.1020.0000.0000.0000.000
127A134SER0-0.030-0.05644.5990.0260.0260.0000.0000.0000.000
128A135ARG10.7970.84943.8816.9876.9870.0000.0000.0000.000
129A136GLU-1-0.752-0.86842.694-7.638-7.6380.0000.0000.0000.000
130A137GLU-1-0.826-0.87241.904-7.110-7.1100.0000.0000.0000.000
131A138PHE00.0000.00036.951-0.219-0.2190.0000.0000.0000.000
132A139VAL00.0240.01338.223-0.307-0.3070.0000.0000.0000.000
133A140ASP-1-0.821-0.89837.325-8.384-8.3840.0000.0000.0000.000
134A141GLU-1-0.797-0.89636.205-8.810-8.8100.0000.0000.0000.000
135A142ALA00.0140.00734.085-0.355-0.3550.0000.0000.0000.000
136A143ALA00.0020.00232.683-0.371-0.3710.0000.0000.0000.000
137A144LYS10.7920.88131.6868.1118.1110.0000.0000.0000.000
138A145LEU0-0.002-0.00529.854-0.439-0.4390.0000.0000.0000.000
139A146PHE00.0060.00127.638-0.524-0.5240.0000.0000.0000.000
140A147VAL00.0000.00326.996-0.489-0.4890.0000.0000.0000.000
141A148PHE0-0.0280.00224.001-0.502-0.5020.0000.0000.0000.000
142A149LEU00.0130.01622.966-0.665-0.6650.0000.0000.0000.000
143A150ASN0-0.052-0.04322.448-0.724-0.7240.0000.0000.0000.000
144A151SER0-0.003-0.01921.132-0.767-0.7670.0000.0000.0000.000
145A152ILE0-0.009-0.00618.551-0.922-0.9220.0000.0000.0000.000
146A153ALA00.0110.01717.208-1.150-1.1500.0000.0000.0000.000
147A154PRO00.0280.02516.447-1.258-1.2580.0000.0000.0000.000
148A155PHE00.0500.02416.157-0.865-0.8650.0000.0000.0000.000
149A156ARG10.9290.97610.03724.87724.8770.0000.0000.0000.000
150A157ALA0-0.011-0.01413.920-0.425-0.4250.0000.0000.0000.000
151A158GLY00.0720.04116.9380.2570.2570.0000.0000.0000.000
152A159ASN00.0320.02117.1170.6670.6670.0000.0000.0000.000
153A160GLU-1-0.842-0.92620.891-13.947-13.9470.0000.0000.0000.000
154A161PRO0-0.001-0.00423.5810.4510.4510.0000.0000.0000.000
155A162THR00.013-0.01223.2650.4400.4400.0000.0000.0000.000
156A163GLN00.0070.00723.928-0.048-0.0480.0000.0000.0000.000
157A164ARG10.8130.88226.85111.27311.2730.0000.0000.0000.000
158A165VAL00.0650.03229.5670.3030.3030.0000.0000.0000.000
159A166PHE0-0.013-0.01128.6130.2820.2820.0000.0000.0000.000
160A167PHE00.006-0.01528.6590.2570.2570.0000.0000.0000.000
161A168GLU-1-0.852-0.92232.702-8.869-8.8690.0000.0000.0000.000
162A169LYS10.8440.92833.9318.8288.8280.0000.0000.0000.000
163A170LEU00.0000.00833.0470.1910.1910.0000.0000.0000.000
164A171ALA0-0.025-0.01835.8770.2250.2250.0000.0000.0000.000
165A172GLU-1-0.872-0.93938.617-7.796-7.7960.0000.0000.0000.000
166A173ALA0-0.004-0.00438.5690.2150.2150.0000.0000.0000.000
167A174ALA0-0.042-0.01639.7090.1840.1840.0000.0000.0000.000
168A175GLY0-0.0140.01141.5580.1550.1550.0000.0000.0000.000
169A176HIS10.7360.86141.5917.4107.4100.0000.0000.0000.000
170A177GLN00.0620.02540.6410.1070.1070.0000.0000.0000.000
171A178LEU0-0.021-0.01634.965-0.022-0.0220.0000.0000.0000.000
172A179ASP-1-0.769-0.85337.043-8.244-8.2440.0000.0000.0000.000
173A180PHE0-0.026-0.04331.621-0.018-0.0180.0000.0000.0000.000
174A181SER0-0.115-0.07134.669-0.056-0.0560.0000.0000.0000.000
175A182VAL00.0110.01636.3130.1180.1180.0000.0000.0000.000
176A183ALA0-0.031-0.01435.2140.1330.1330.0000.0000.0000.000
177A184THR0-0.053-0.02634.692-0.142-0.1420.0000.0000.0000.000
178A185GLU-1-0.689-0.81927.826-10.861-10.8610.0000.0000.0000.000
179A186LYS10.9230.95429.9818.5938.5930.0000.0000.0000.000
180A187ARG10.7420.85331.4198.2328.2320.0000.0000.0000.000
181A188ILE00.0590.04128.520-0.102-0.1020.0000.0000.0000.000
182A189MET00.0270.01722.280-0.197-0.1970.0000.0000.0000.000
183A190ARG10.9380.96727.1988.9778.9770.0000.0000.0000.000
184A191ALA00.0750.03829.282-0.124-0.1240.0000.0000.0000.000
185A192CYS0-0.057-0.02024.832-0.070-0.0700.0000.0000.0000.000
186A193ILE0-0.005-0.00323.124-0.329-0.3290.0000.0000.0000.000
187A194ASP-1-0.874-0.94125.923-10.111-10.1110.0000.0000.0000.000
188A195GLY0-0.010-0.01527.8720.0530.0530.0000.0000.0000.000
189A196MET0-0.064-0.02921.419-0.476-0.4760.0000.0000.0000.000
190A197THR0-0.044-0.02624.381-0.455-0.4550.0000.0000.0000.000
191A198LEU0-0.031-0.00826.5060.2500.2500.0000.0000.0000.000
192A199LYS10.9750.97829.6738.7568.7560.0000.0000.0000.000
193A200ASP-1-0.836-0.92930.924-8.863-8.8630.0000.0000.0000.000
194A201ASN00.0130.00832.5270.0010.0010.0000.0000.0000.000
195A202MET0-0.038-0.01434.1000.1920.1920.0000.0000.0000.000
196A203ALA00.0190.03329.6480.0680.0680.0000.0000.0000.000
197A204TYR00.0410.01130.299-0.171-0.1710.0000.0000.0000.000
198A205LYS10.8300.92133.3788.3738.3730.0000.0000.0000.000
199A206GLU-1-0.855-0.94433.138-8.366-8.3660.0000.0000.0000.000
200A207MET0-0.0460.00328.9480.0850.0850.0000.0000.0000.000
201A208LYS10.8040.86433.7097.9717.9710.0000.0000.0000.000
202A209SER0-0.0050.02337.1770.2420.2420.0000.0000.0000.000
203A210LEU0-0.041-0.02632.7280.1420.1420.0000.0000.0000.000
204A211PHE00.028-0.00232.0110.0550.0550.0000.0000.0000.000
205A212GLU-1-0.785-0.85937.600-7.001-7.0010.0000.0000.0000.000
206A213ASP-1-0.785-0.87239.712-7.456-7.4560.0000.0000.0000.000
207A214ILE0-0.068-0.03635.1180.1390.1390.0000.0000.0000.000
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