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: QL3GY

Calculation Name: 5ZO3-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 1,2-ethanediol

Ligand 3-letter code: EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5ZO3

Chain ID: A

ChEMBL ID:

UniProt ID: A0A1S7

Base Structure: X-ray

Registration Date: 2025-10-06

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 207
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2408980.382561
FMO2-HF: Nuclear repulsion 2328500.171027
FMO2-HF: Total energy -80480.211534
FMO2-MP2: Total energy -80715.980167


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:2:ALA)


Summations of interaction energy for fragment #1(A:2: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.
-40.481-38.885-0.014-0.714-0.8670
Interaction energy analysis for fragmet #1(A:2:ALA)
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 : 0.916
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].
3A4THR00.0670.0343.863-4.247-2.949-0.012-0.616-0.6700.000
5A6ARG10.7570.8523.94142.77342.880-0.001-0.025-0.0800.000
18A19ARG10.8200.9094.15049.95550.146-0.001-0.073-0.1170.000
4A5ILE00.0160.0146.7123.2023.2020.0000.0000.0000.000
6A7TYR0-0.014-0.0317.5032.8432.8430.0000.0000.0000.000
7A8HIS10.8140.8928.68528.93328.9330.0000.0000.0000.000
8A9GLU-1-0.738-0.83712.794-16.361-16.3610.0000.0000.0000.000
9A10GLY00.0000.01116.411-0.166-0.1660.0000.0000.0000.000
10A11ASP-1-0.752-0.89316.764-16.933-16.9330.0000.0000.0000.000
11A12ILE0-0.037-0.00810.836-1.382-1.3820.0000.0000.0000.000
12A13SER0-0.025-0.0268.7901.7601.7600.0000.0000.0000.000
13A14ALA00.0670.01211.909-0.117-0.1170.0000.0000.0000.000
14A15GLU-1-0.930-0.9595.674-46.371-46.3710.0000.0000.0000.000
15A16ASP-1-0.793-0.8816.083-45.325-45.3250.0000.0000.0000.000
16A17ALA00.0490.0108.7180.8740.8740.0000.0000.0000.000
17A18ALA0-0.0080.01111.4531.4591.4590.0000.0000.0000.000
19A20TYR0-0.032-0.03710.2802.0182.0180.0000.0000.0000.000
20A21LYS10.8660.91511.96725.53325.5330.0000.0000.0000.000
21A22GLY00.0450.02016.0451.1181.1180.0000.0000.0000.000
22A23ALA0-0.043-0.01318.226-0.077-0.0770.0000.0000.0000.000
23A24ILE0-0.0020.00515.728-1.244-1.2440.0000.0000.0000.000
24A25ALA0-0.0230.01215.8961.1361.1360.0000.0000.0000.000
25A26ILE0-0.052-0.03816.344-1.156-1.1560.0000.0000.0000.000
26A27ASP-1-0.813-0.85218.631-13.362-13.3620.0000.0000.0000.000
27A28THR0-0.096-0.07219.566-0.648-0.6480.0000.0000.0000.000
28A29GLU-1-0.799-0.88020.812-13.791-13.7910.0000.0000.0000.000
29A30THR0-0.012-0.03723.271-0.172-0.1720.0000.0000.0000.000
30A31LEU00.000-0.00826.426-0.041-0.0410.0000.0000.0000.000
31A32GLY0-0.0010.00629.3590.3610.3610.0000.0000.0000.000
32A33LEU00.0150.00930.142-0.228-0.2280.0000.0000.0000.000
33A34VAL00.0210.01432.4110.1750.1750.0000.0000.0000.000
34A35PRO00.0420.01331.1270.0180.0180.0000.0000.0000.000
35A36ARG10.8840.95132.4568.0658.0650.0000.0000.0000.000
36A37ARG10.8010.87134.3629.1479.1470.0000.0000.0000.000
37A38ASP-1-0.795-0.85331.018-9.612-9.6120.0000.0000.0000.000
38A39ARG10.8270.90424.29112.30512.3050.0000.0000.0000.000
39A40LEU00.0670.03422.477-0.146-0.1460.0000.0000.0000.000
40A41CYS0-0.132-0.04623.4450.2890.2890.0000.0000.0000.000
41A42VAL00.0180.00617.504-0.654-0.6540.0000.0000.0000.000
42A43VAL00.0250.01917.5320.8210.8210.0000.0000.0000.000
43A44GLN0-0.038-0.02415.012-1.646-1.6460.0000.0000.0000.000
44A45LEU00.018-0.00912.9901.1531.1530.0000.0000.0000.000
45A46SER00.003-0.02211.676-1.541-1.5410.0000.0000.0000.000
46A47SER0-0.013-0.0239.9412.0832.0830.0000.0000.0000.000
47A48GLY00.0270.02612.3931.2681.2680.0000.0000.0000.000
48A49ASP-1-0.878-0.9137.772-35.279-35.2790.0000.0000.0000.000
49A50GLY00.0250.0169.697-1.687-1.6870.0000.0000.0000.000
50A51THR0-0.083-0.0525.762-3.171-3.1710.0000.0000.0000.000
51A52ALA00.0420.0238.6362.9472.9470.0000.0000.0000.000
52A53ASP-1-0.819-0.8448.486-38.746-38.7460.0000.0000.0000.000
53A54VAL00.0290.00710.2852.4162.4160.0000.0000.0000.000
54A55ILE0-0.015-0.01113.078-1.000-1.0000.0000.0000.0000.000
55A56ARG10.8650.94715.30616.11416.1140.0000.0000.0000.000
56A57ILE0-0.017-0.00318.158-0.001-0.0010.0000.0000.0000.000
57A58ALA00.0480.02821.3600.4220.4220.0000.0000.0000.000
58A59ALA00.025-0.00223.8610.2950.2950.0000.0000.0000.000
59A60GLY0-0.010-0.01027.6230.0020.0020.0000.0000.0000.000
60A61GLN0-0.062-0.02920.8420.1500.1500.0000.0000.0000.000
61A62LYS10.9580.97126.58610.69210.6920.0000.0000.0000.000
62A63GLN0-0.013-0.00524.780-0.104-0.1040.0000.0000.0000.000
63A64ALA00.0550.03019.575-0.246-0.2460.0000.0000.0000.000
64A65PRO00.0210.01920.698-0.134-0.1340.0000.0000.0000.000
65A66ASN0-0.033-0.01515.7320.9640.9640.0000.0000.0000.000
66A67LEU00.0180.00317.024-0.056-0.0560.0000.0000.0000.000
67A68VAL0-0.011-0.01418.3070.4460.4460.0000.0000.0000.000
68A69HIS00.0050.00619.950-0.031-0.0310.0000.0000.0000.000
69A70MET0-0.0080.00013.9940.0010.0010.0000.0000.0000.000
70A71LEU00.000-0.00119.3660.3600.3600.0000.0000.0000.000
71A72ALA00.023-0.00622.1000.5150.5150.0000.0000.0000.000
72A73ASP-1-0.825-0.88921.230-13.818-13.8180.0000.0000.0000.000
73A74PRO00.008-0.00723.734-0.176-0.1760.0000.0000.0000.000
74A75ALA0-0.010-0.00623.3950.2500.2500.0000.0000.0000.000
75A76ARG10.7640.87716.19016.86216.8620.0000.0000.0000.000
76A77GLN00.0390.03221.734-0.395-0.3950.0000.0000.0000.000
77A78LYS10.7930.90120.28213.10613.1060.0000.0000.0000.000
78A79ILE0-0.051-0.02419.5730.8570.8570.0000.0000.0000.000
79A80PHE00.0790.03920.947-0.628-0.6280.0000.0000.0000.000
80A81HIS0-0.0100.00723.5010.0610.0610.0000.0000.0000.000
81A82TYR00.009-0.05325.6940.2200.2200.0000.0000.0000.000
82A83GLY00.0670.02526.6280.0580.0580.0000.0000.0000.000
83A84ARG10.7710.85727.3938.8288.8280.0000.0000.0000.000
84A85PHE0-0.0040.01026.8330.3250.3250.0000.0000.0000.000
85A86ASP-1-0.761-0.87024.364-12.609-12.6090.0000.0000.0000.000
86A87ILE0-0.008-0.00926.464-0.135-0.1350.0000.0000.0000.000
87A88ALA00.0290.02527.9450.1470.1470.0000.0000.0000.000
88A89VAL00.0140.00326.1590.1410.1410.0000.0000.0000.000
89A90LEU0-0.0030.00222.268-0.082-0.0820.0000.0000.0000.000
90A91PHE0-0.0100.00026.2830.1050.1050.0000.0000.0000.000
91A92HIS0-0.025-0.01129.5370.4320.4320.0000.0000.0000.000
92A93THR0-0.106-0.05625.6440.1920.1920.0000.0000.0000.000
93A94PHE0-0.011-0.03022.262-0.072-0.0720.0000.0000.0000.000
94A95GLY00.0200.03127.4250.0250.0250.0000.0000.0000.000
95A96VAL0-0.042-0.01524.5090.2250.2250.0000.0000.0000.000
96A97THR00.000-0.00327.7360.2740.2740.0000.0000.0000.000
97A98THR0-0.009-0.00423.657-0.060-0.0600.0000.0000.0000.000
98A99THR0-0.0040.02225.8050.4070.4070.0000.0000.0000.000
99A100PRO00.0600.05425.159-0.306-0.3060.0000.0000.0000.000
100A101VAL0-0.010-0.02425.117-0.592-0.5920.0000.0000.0000.000
101A102PHE00.0150.00324.8910.2990.2990.0000.0000.0000.000
102A103CYS-1-0.866-0.78725.480-11.470-11.4700.0000.0000.0000.000
103A104THR00.048-0.03024.1750.2360.2360.0000.0000.0000.000
104A105LYS10.8890.92427.23210.35610.3560.0000.0000.0000.000
105A106ILE00.061-0.02730.0910.3900.3900.0000.0000.0000.000
106A107ALA00.0220.01529.4110.2880.2880.0000.0000.0000.000
107A108SER00.017-0.00730.3850.1820.1820.0000.0000.0000.000
108A109ARG10.9060.94632.1178.7868.7860.0000.0000.0000.000
109A110LEU00.0290.03734.8250.2970.2970.0000.0000.0000.000
110A111CYS0-0.065-0.02933.1590.1080.1080.0000.0000.0000.000
111A112ARG10.7980.87731.29710.11310.1130.0000.0000.0000.000
112A113THR0-0.016-0.01435.8180.0060.0060.0000.0000.0000.000
113A114TYR0-0.023-0.01034.4260.2340.2340.0000.0000.0000.000
114A115THR00.0130.00535.6620.0380.0380.0000.0000.0000.000
115A116ASP-1-0.834-0.89538.325-7.956-7.9560.0000.0000.0000.000
116A117ARG10.7990.89133.2569.1179.1170.0000.0000.0000.000
117A118HIS00.0510.05132.422-0.582-0.5820.0000.0000.0000.000
118A119GLY00.0060.00030.281-0.205-0.2050.0000.0000.0000.000
119A120LEU00.0420.03422.0120.1590.1590.0000.0000.0000.000
120A121LYS10.9270.96025.90911.73111.7310.0000.0000.0000.000
121A122ASP-1-0.827-0.91926.880-10.171-10.1710.0000.0000.0000.000
122A123ASN0-0.034-0.03027.1430.1940.1940.0000.0000.0000.000
123A124LEU00.0090.00321.6780.0480.0480.0000.0000.0000.000
124A125LYS10.8810.93525.21111.47711.4770.0000.0000.0000.000
125A126GLU-1-0.771-0.84027.450-9.522-9.5220.0000.0000.0000.000
126A127MET0-0.048-0.02826.6990.1710.1710.0000.0000.0000.000
127A128LEU0-0.084-0.05721.159-0.166-0.1660.0000.0000.0000.000
128A129GLU-1-0.928-0.93823.735-11.605-11.6050.0000.0000.0000.000
129A130VAL0-0.031-0.00520.346-0.261-0.2610.0000.0000.0000.000
130A131ASP-1-0.868-0.92022.743-11.576-11.5760.0000.0000.0000.000
131A132ILE00.0350.01920.430-0.565-0.5650.0000.0000.0000.000
132A133SER00.016-0.00122.3701.0501.0500.0000.0000.0000.000
133A134LYS10.9360.95623.47112.74512.7450.0000.0000.0000.000
134A135ALA0-0.0070.00725.8000.1490.1490.0000.0000.0000.000
135A136GLN00.0490.01422.2880.4100.4100.0000.0000.0000.000
136A137GLN00.0060.02724.777-0.039-0.0390.0000.0000.0000.000
137A138SER0-0.041-0.01925.9780.3120.3120.0000.0000.0000.000
138A139SER0-0.011-0.00824.7920.0890.0890.0000.0000.0000.000
139A140ASP-1-0.832-0.92927.068-11.677-11.6770.0000.0000.0000.000
140A141TRP00.0120.00219.523-0.975-0.9750.0000.0000.0000.000
141A142ALA0-0.030-0.02223.157-0.469-0.4690.0000.0000.0000.000
142A143ALA00.0400.02423.275-0.051-0.0510.0000.0000.0000.000
143A144GLU-1-0.963-0.97622.528-13.218-13.2180.0000.0000.0000.000
144A145THR0-0.046-0.02618.519-0.679-0.6790.0000.0000.0000.000
145A146LEU0-0.0020.01816.9520.4260.4260.0000.0000.0000.000
146A147SER00.022-0.00618.057-0.741-0.7410.0000.0000.0000.000
147A148PRO00.033-0.00916.410-0.484-0.4840.0000.0000.0000.000
148A149ALA00.0130.01317.171-0.636-0.6360.0000.0000.0000.000
149A150GLN00.0190.02219.699-0.346-0.3460.0000.0000.0000.000
150A151LEU00.000-0.00113.421-0.439-0.4390.0000.0000.0000.000
151A152GLU-1-0.900-0.92914.897-18.121-18.1210.0000.0000.0000.000
152A153TYR00.0010.00716.3100.0090.0090.0000.0000.0000.000
153A154ALA00.0220.00516.1500.1010.1010.0000.0000.0000.000
154A155ALA00.0020.00112.491-0.483-0.4830.0000.0000.0000.000
155A156SER0-0.040-0.05914.216-0.257-0.2570.0000.0000.0000.000
156A157ASP0-0.154-0.12616.7831.0101.0100.0000.0000.0000.000
157A158VAL00.011-0.00314.4320.7120.7120.0000.0000.0000.000
158A159LEU0-0.045-0.01711.3210.0540.0540.0000.0000.0000.000
159A160TYR00.0040.00615.009-0.157-0.1570.0000.0000.0000.000
160A161LEU00.0010.00218.1650.8950.8950.0000.0000.0000.000
161A162HIS00.0060.00615.8571.1171.1170.0000.0000.0000.000
162A163ALA00.0510.02919.4130.7770.7770.0000.0000.0000.000
163A164LEU00.0020.00021.1830.7830.7830.0000.0000.0000.000
164A165ARG10.8600.89921.15814.74714.7470.0000.0000.0000.000
165A166ASP-1-0.834-0.87422.056-13.492-13.4920.0000.0000.0000.000
166A167LYS10.8930.95124.58612.84412.8440.0000.0000.0000.000
167A168LEU0-0.011-0.01627.2710.5300.5300.0000.0000.0000.000
168A169THR00.007-0.01227.3950.4690.4690.0000.0000.0000.000
169A170ALA0-0.0040.00129.3900.3830.3830.0000.0000.0000.000
170A171ARG10.8210.88931.25910.04610.0460.0000.0000.0000.000
171A172LEU00.004-0.00131.1680.3140.3140.0000.0000.0000.000
172A173ILE0-0.0040.00331.9160.2810.2810.0000.0000.0000.000
173A174ARG10.7770.85735.3948.9188.9180.0000.0000.0000.000
174A175ASP-1-0.839-0.88937.228-8.274-8.2740.0000.0000.0000.000
175A176GLY0-0.0020.00538.8620.1730.1730.0000.0000.0000.000
176A177ARG10.8660.91637.8118.1958.1950.0000.0000.0000.000
177A178ILE00.0090.00731.506-0.132-0.1320.0000.0000.0000.000
178A179GLU-1-0.874-0.93135.029-8.100-8.1000.0000.0000.0000.000
179A180HIS00.0340.01137.403-0.164-0.1640.0000.0000.0000.000
180A181ALA00.0040.00632.700-0.033-0.0330.0000.0000.0000.000
181A182ASP-1-0.876-0.94132.089-9.958-9.9580.0000.0000.0000.000
182A183ALA0-0.013-0.00833.727-0.077-0.0770.0000.0000.0000.000
183A184CYS0-0.064-0.03834.6800.0970.0970.0000.0000.0000.000
184A185PHE0-0.027-0.02730.032-0.153-0.1530.0000.0000.0000.000
185A186ALA00.0040.00131.700-0.171-0.1710.0000.0000.0000.000
186A187PHE00.0430.01733.7670.0350.0350.0000.0000.0000.000
187A188LEU0-0.0100.01229.1520.0590.0590.0000.0000.0000.000
188A189PRO00.013-0.01329.9220.0180.0180.0000.0000.0000.000
189A190THR0-0.037-0.00732.1960.1160.1160.0000.0000.0000.000
190A191ARG10.7730.85834.9838.3428.3420.0000.0000.0000.000
191A192ALA00.0490.02731.7900.1250.1250.0000.0000.0000.000
192A193LYS10.8740.92632.7599.5489.5480.0000.0000.0000.000
193A194LEU00.0110.01135.8730.1560.1560.0000.0000.0000.000
194A195ASP-1-0.755-0.83335.430-8.655-8.6550.0000.0000.0000.000
195A196LEU0-0.093-0.04332.6480.0860.0860.0000.0000.0000.000
196A197LEU0-0.058-0.02836.9290.1150.1150.0000.0000.0000.000
197A198GLY0-0.0090.01540.3320.1910.1910.0000.0000.0000.000
198A199TRP0-0.005-0.00741.4000.1340.1340.0000.0000.0000.000
199A200ASP-1-0.893-0.94338.430-8.063-8.0630.0000.0000.0000.000
200A201GLU-1-0.976-0.98839.847-8.049-8.0490.0000.0000.0000.000
201A202THR0-0.036-0.01742.4740.1410.1410.0000.0000.0000.000
202A203ASP-1-0.872-0.94242.505-7.747-7.7470.0000.0000.0000.000
203A204ILE0-0.026-0.01042.3910.1360.1360.0000.0000.0000.000
204A205PHE0-0.057-0.03240.7900.0970.0970.0000.0000.0000.000
205A206ALA0-0.0250.00646.1650.1150.1150.0000.0000.0000.000
206A207HIS0-0.040-0.03448.5300.0480.0480.0000.0000.0000.000
207A208SER-1-0.907-0.92849.163-6.470-6.4700.0000.0000.0000.000