FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2026-04-18

All entries: 88827

Number of unique PDB entries: 32070

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FMODB ID: 3MLQL

Calculation Name: 3PZJ-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: 3PZJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q7NX87

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 198
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2157196.857009
FMO2-HF: Nuclear repulsion 2080488.572006
FMO2-HF: Total energy -76708.285003
FMO2-MP2: Total energy -76932.861414


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:7:SER)


Summations of interaction energy for fragment #1(A:7:SER)
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.
-16.737-15.0860.023-0.785-0.889-0.002
Interaction energy analysis for fragmet #1(A:7:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.850 / q_NPA : 0.913
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].
3A9PRO00.0410.0123.389-5.540-4.0790.024-0.764-0.721-0.002
4A10ILE00.0000.0124.0300.8701.060-0.001-0.021-0.1680.000
5A11ALA00.0060.0087.4731.5681.5680.0000.0000.0000.000
6A12PRO00.0040.00711.0040.3160.3160.0000.0000.0000.000
7A13SER00.000-0.00613.8770.4660.4660.0000.0000.0000.000
8A14THR0-0.003-0.00717.1330.1930.1930.0000.0000.0000.000
9A15PRO0-0.0010.00419.6370.3160.3160.0000.0000.0000.000
10A16LEU00.0160.00122.896-0.250-0.2500.0000.0000.0000.000
11A17LEU00.0070.00722.8670.1930.1930.0000.0000.0000.000
12A18ALA00.003-0.00426.1060.3260.3260.0000.0000.0000.000
13A19GLY00.0070.00229.8130.0330.0330.0000.0000.0000.000
14A20TRP0-0.0220.00127.0190.0430.0430.0000.0000.0000.000
15A21ARG10.9420.96329.6659.1509.1500.0000.0000.0000.000
16A22SER0-0.011-0.00930.197-0.299-0.2990.0000.0000.0000.000
17A23ALA00.0270.03929.9030.2870.2870.0000.0000.0000.000
18A24GLY00.0130.00931.7980.1840.1840.0000.0000.0000.000
19A25LYS10.8450.91033.9317.8017.8010.0000.0000.0000.000
20A26ALA00.0350.01735.3470.0730.0730.0000.0000.0000.000
21A27PRO00.0120.00936.8470.1880.1880.0000.0000.0000.000
22A28GLU-1-0.794-0.86940.476-7.730-7.7300.0000.0000.0000.000
23A29ALA0-0.036-0.02243.5310.1970.1970.0000.0000.0000.000
24A30ALA0-0.030-0.01143.489-0.164-0.1640.0000.0000.0000.000
25A31ILE00.0350.02538.3650.0970.0970.0000.0000.0000.000
26A32ARG10.8770.93742.5636.7546.7540.0000.0000.0000.000
27A33GLY00.0420.03142.789-0.160-0.1600.0000.0000.0000.000
28A34GLU-1-0.920-0.96643.398-6.620-6.6200.0000.0000.0000.000
29A35ALA0-0.006-0.01144.8020.1800.1800.0000.0000.0000.000
30A36VAL0-0.035-0.00641.2510.1000.1000.0000.0000.0000.000
31A37SER0-0.031-0.01044.1860.0680.0680.0000.0000.0000.000
32A38LEU00.0150.01337.763-0.016-0.0160.0000.0000.0000.000
33A39GLN00.015-0.00442.2740.0480.0480.0000.0000.0000.000
34A40PRO00.0180.00442.395-0.141-0.1410.0000.0000.0000.000
35A41LEU0-0.046-0.01140.5770.1790.1790.0000.0000.0000.000
36A42ASP-1-0.808-0.90343.365-6.553-6.5530.0000.0000.0000.000
37A43ALA00.019-0.00243.6750.0910.0910.0000.0000.0000.000
38A44PRO00.011-0.00645.5640.0260.0260.0000.0000.0000.000
39A45ARG10.8690.95249.1806.4936.4930.0000.0000.0000.000
40A46HIS00.015-0.00546.1060.0170.0170.0000.0000.0000.000
41A47GLY00.0360.02145.857-0.040-0.0400.0000.0000.0000.000
42A48ALA00.0680.02546.868-0.051-0.0510.0000.0000.0000.000
43A49ALA0-0.060-0.02649.0050.0420.0420.0000.0000.0000.000
44A50LEU0-0.012-0.02242.724-0.050-0.0500.0000.0000.0000.000
45A51PHE00.0120.02644.806-0.119-0.1190.0000.0000.0000.000
46A52ARG10.8970.93846.2586.0816.0810.0000.0000.0000.000
47A53LEU0-0.090-0.02343.724-0.004-0.0040.0000.0000.0000.000
48A54PHE0-0.041-0.03840.494-0.135-0.1350.0000.0000.0000.000
49A55ALA0-0.0030.00744.057-0.051-0.0510.0000.0000.0000.000
50A56GLY0-0.0180.00946.5950.0970.0970.0000.0000.0000.000
51A57ASP-1-0.882-0.92342.412-7.593-7.5930.0000.0000.0000.000
52A58ASP-1-0.849-0.93841.409-7.521-7.5210.0000.0000.0000.000
53A59SER0-0.095-0.07238.700-0.318-0.3180.0000.0000.0000.000
54A60HIS0-0.009-0.00536.974-0.397-0.3970.0000.0000.0000.000
55A61TRP00.0190.01235.875-0.371-0.3710.0000.0000.0000.000
56A62GLU-1-0.910-0.94533.289-9.699-9.6990.0000.0000.0000.000
57A63HIS0-0.086-0.05429.275-0.588-0.5880.0000.0000.0000.000
58A64LEU00.0020.00729.518-0.480-0.4800.0000.0000.0000.000
59A65PRO0-0.058-0.02929.6370.1070.1070.0000.0000.0000.000
60A66TYR00.0050.00831.5680.1190.1190.0000.0000.0000.000
61A67GLY00.0610.04935.381-0.107-0.1070.0000.0000.0000.000
62A68PRO0-0.012-0.02337.691-0.272-0.2720.0000.0000.0000.000
63A69PHE0-0.043-0.03438.735-0.123-0.1230.0000.0000.0000.000
64A70GLU-1-0.924-0.95643.681-6.711-6.7110.0000.0000.0000.000
65A71ASP-1-0.856-0.92747.074-6.308-6.3080.0000.0000.0000.000
66A72GLU-1-0.839-0.93747.362-6.317-6.3170.0000.0000.0000.000
67A73ASP-1-0.851-0.91448.065-6.289-6.2890.0000.0000.0000.000
68A74ALA0-0.0110.00745.070-0.152-0.1520.0000.0000.0000.000
69A75PHE0-0.056-0.03340.861-0.229-0.2290.0000.0000.0000.000
70A76ILE00.0100.00143.438-0.179-0.1790.0000.0000.0000.000
71A77THR0-0.025-0.02343.685-0.074-0.0740.0000.0000.0000.000
72A78TRP0-0.018-0.01035.646-0.114-0.1140.0000.0000.0000.000
73A79LEU00.0010.01239.808-0.205-0.2050.0000.0000.0000.000
74A80ALA0-0.008-0.00540.843-0.122-0.1220.0000.0000.0000.000
75A81LEU0-0.033-0.02139.402-0.076-0.0760.0000.0000.0000.000
76A82THR0-0.045-0.03135.164-0.270-0.2700.0000.0000.0000.000
77A83VAL0-0.038-0.03536.814-0.201-0.2010.0000.0000.0000.000
78A84ALA0-0.0170.00839.3440.0260.0260.0000.0000.0000.000
79A85GLN0-0.071-0.02131.8250.0190.0190.0000.0000.0000.000
80A86SER00.0410.00734.240-0.017-0.0170.0000.0000.0000.000
81A87ASP-1-0.907-0.94029.964-10.265-10.2650.0000.0000.0000.000
82A88THR0-0.047-0.04531.645-0.430-0.4300.0000.0000.0000.000
83A89ALA0-0.0110.00533.9120.2690.2690.0000.0000.0000.000
84A90LEU0-0.0070.00335.556-0.212-0.2120.0000.0000.0000.000
85A91TYR0-0.012-0.03536.8740.1170.1170.0000.0000.0000.000
86A92VAL00.006-0.00639.700-0.135-0.1350.0000.0000.0000.000
87A93VAL0-0.030-0.01439.3300.0430.0430.0000.0000.0000.000
88A94CYS0-0.0060.01142.3520.1280.1280.0000.0000.0000.000
89A95ALA00.0450.01245.435-0.122-0.1220.0000.0000.0000.000
90A96LYS10.7910.89547.6406.7446.7440.0000.0000.0000.000
91A97ASP-1-0.902-0.96548.740-6.277-6.2770.0000.0000.0000.000
92A98SER0-0.0370.00150.2430.1260.1260.0000.0000.0000.000
93A99ASP-1-0.905-0.96449.938-6.137-6.1370.0000.0000.0000.000
94A100GLN0-0.052-0.02049.804-0.115-0.1150.0000.0000.0000.000
95A101ALA00.009-0.00545.664-0.122-0.1220.0000.0000.0000.000
96A102LEU00.0120.00844.1230.0290.0290.0000.0000.0000.000
97A103GLY00.0340.00140.922-0.128-0.1280.0000.0000.0000.000
98A104PHE0-0.011-0.00137.3050.1440.1440.0000.0000.0000.000
99A105LEU0-0.017-0.00133.616-0.185-0.1850.0000.0000.0000.000
100A106GLY00.0160.00333.7660.2910.2910.0000.0000.0000.000
101A107TYR0-0.011-0.02130.806-0.197-0.1970.0000.0000.0000.000
102A108ARG10.8370.91026.19011.55111.5510.0000.0000.0000.000
103A109GLN00.0170.01125.230-0.097-0.0970.0000.0000.0000.000
104A110MET0-0.0150.00926.918-0.275-0.2750.0000.0000.0000.000
105A111VAL0-0.024-0.01424.8420.1700.1700.0000.0000.0000.000
106A112GLN00.006-0.01427.189-0.176-0.1760.0000.0000.0000.000
107A113ALA0-0.015-0.01127.685-0.065-0.0650.0000.0000.0000.000
108A114HIS0-0.020-0.01722.475-0.348-0.3480.0000.0000.0000.000
109A115GLY00.0170.03124.204-0.351-0.3510.0000.0000.0000.000
110A116ALA0-0.0110.00422.805-0.242-0.2420.0000.0000.0000.000
111A117ILE00.0200.01324.7560.4910.4910.0000.0000.0000.000
112A118GLU-1-0.844-0.90424.822-12.752-12.7520.0000.0000.0000.000
113A119ILE00.0070.00626.5170.5220.5220.0000.0000.0000.000
114A120GLY00.012-0.01527.886-0.409-0.4090.0000.0000.0000.000
115A121HIS00.0200.01029.9630.2720.2720.0000.0000.0000.000
116A122VAL0-0.0150.01531.1720.3060.3060.0000.0000.0000.000
117A123ASN0-0.024-0.00833.790-0.016-0.0160.0000.0000.0000.000
118A124PHE00.014-0.01135.7660.1970.1970.0000.0000.0000.000
119A125SER00.0770.02738.817-0.035-0.0350.0000.0000.0000.000
120A126PRO00.018-0.01341.418-0.116-0.1160.0000.0000.0000.000
121A127ALA00.0120.01442.675-0.029-0.0290.0000.0000.0000.000
122A128LEU00.0060.03039.9070.0140.0140.0000.0000.0000.000
123A129ARG10.9390.97133.6728.7868.7860.0000.0000.0000.000
124A130ARG0-0.030-0.02831.7530.0900.0900.0000.0000.0000.000
125A131THR00.0350.02438.0200.0850.0850.0000.0000.0000.000
126A132ARG10.8460.88939.0397.6027.6020.0000.0000.0000.000
127A133LEU00.0390.02340.663-0.050-0.0500.0000.0000.0000.000
128A134ALA00.0330.01536.831-0.113-0.1130.0000.0000.0000.000
129A135THR0-0.035-0.03235.008-0.275-0.2750.0000.0000.0000.000
130A136GLU-1-0.752-0.85135.859-7.799-7.7990.0000.0000.0000.000
131A137ALA00.0310.01237.534-0.063-0.0630.0000.0000.0000.000
132A138VAL00.003-0.00130.952-0.112-0.1120.0000.0000.0000.000
133A139PHE00.0120.01033.097-0.146-0.1460.0000.0000.0000.000
134A140LEU00.0180.00534.487-0.055-0.0550.0000.0000.0000.000
135A141LEU00.0010.02433.0450.0270.0270.0000.0000.0000.000
136A142LEU00.0140.01927.955-0.157-0.1570.0000.0000.0000.000
137A143LYS10.9430.99131.5438.1978.1970.0000.0000.0000.000
138A144THR0-0.041-0.03334.3680.1090.1090.0000.0000.0000.000
139A145ALA00.0080.00830.2550.0510.0510.0000.0000.0000.000
140A146PHE00.0230.00726.532-0.058-0.0580.0000.0000.0000.000
141A147GLU-1-0.895-0.95531.551-8.446-8.4460.0000.0000.0000.000
142A148LEU0-0.081-0.03334.0650.2150.2150.0000.0000.0000.000
143A149GLY0-0.010-0.00231.5760.0080.0080.0000.0000.0000.000
144A150TYR0-0.100-0.07827.740-0.366-0.3660.0000.0000.0000.000
145A151ARG10.8990.95221.00913.76813.7680.0000.0000.0000.000
146A152ARG10.7000.80417.61516.22316.2230.0000.0000.0000.000
147A153CYS00.0060.02523.6960.4670.4670.0000.0000.0000.000
148A154GLU-1-0.773-0.87620.115-15.760-15.7600.0000.0000.0000.000
149A155TRP00.0150.01022.7990.8090.8090.0000.0000.0000.000
150A156ARG10.8390.89319.46614.07114.0710.0000.0000.0000.000
151A157CYS0-0.087-0.03323.1470.5750.5750.0000.0000.0000.000
152A158ASP-1-0.781-0.89123.222-12.497-12.4970.0000.0000.0000.000
153A159SER00.004-0.00721.1330.1270.1270.0000.0000.0000.000
154A160ARG10.8590.92522.82910.88510.8850.0000.0000.0000.000
155A161ASN00.0220.02026.1160.5670.5670.0000.0000.0000.000
156A162ALA00.0310.00626.584-0.197-0.1970.0000.0000.0000.000
157A163ALA00.0060.00427.628-0.071-0.0710.0000.0000.0000.000
158A164SER00.0440.02727.4680.0590.0590.0000.0000.0000.000
159A165ALA00.0400.01323.593-0.195-0.1950.0000.0000.0000.000
160A166ALA0-0.031-0.02225.060-0.259-0.2590.0000.0000.0000.000
161A167ALA0-0.037-0.01327.5160.1610.1610.0000.0000.0000.000
162A168ALA00.0100.01824.1280.0780.0780.0000.0000.0000.000
163A169ARG10.9920.98918.48315.42115.4210.0000.0000.0000.000
164A170ARG10.8690.94825.18110.25710.2570.0000.0000.0000.000
165A171PHE0-0.039-0.03328.5910.3930.3930.0000.0000.0000.000
166A172GLY00.0660.04626.0470.1220.1220.0000.0000.0000.000
167A173PHE0-0.032-0.00422.977-0.304-0.3040.0000.0000.0000.000
168A174GLN00.0210.01518.621-0.575-0.5750.0000.0000.0000.000
169A175PHE0-0.079-0.05414.998-0.064-0.0640.0000.0000.0000.000
170A176GLU-1-0.756-0.81714.320-19.180-19.1800.0000.0000.0000.000
171A177GLY0-0.010-0.00612.707-2.320-2.3200.0000.0000.0000.000
172A178THR0-0.025-0.03013.8731.2741.2740.0000.0000.0000.000
173A179LEU0-0.013-0.00314.515-1.078-1.0780.0000.0000.0000.000
174A180ARG10.9570.96612.32022.69622.6960.0000.0000.0000.000
175A181GLN0-0.029-0.02917.2680.0040.0040.0000.0000.0000.000
176A182ALA0-0.0290.01019.5780.1780.1780.0000.0000.0000.000
177A183MET0-0.007-0.00820.9400.4000.4000.0000.0000.0000.000
178A184VAL00.0060.01624.757-0.107-0.1070.0000.0000.0000.000
179A185VAL00.0250.00627.6800.2120.2120.0000.0000.0000.000
180A186LYS10.8130.89630.0239.0729.0720.0000.0000.0000.000
181A187ARG10.9390.96932.6528.6448.6440.0000.0000.0000.000
182A188ARG10.9660.99628.12810.55810.5580.0000.0000.0000.000
183A189ASN00.030-0.00621.928-0.053-0.0530.0000.0000.0000.000
184A190ARG10.8890.94923.80912.45912.4590.0000.0000.0000.000
185A191ASP-1-0.791-0.87319.341-15.806-15.8060.0000.0000.0000.000
186A192THR0-0.048-0.02719.6960.9910.9910.0000.0000.0000.000
187A193HIS0-0.0090.02218.660-1.544-1.5440.0000.0000.0000.000
188A194VAL0-0.008-0.01117.0010.8970.8970.0000.0000.0000.000
189A195PHE0-0.006-0.01317.901-0.870-0.8700.0000.0000.0000.000
190A196SER0-0.065-0.05318.6390.6610.6610.0000.0000.0000.000
191A197MET00.0520.04521.1570.0990.0990.0000.0000.0000.000
192A198LEU0-0.018-0.02118.7830.1620.1620.0000.0000.0000.000
193A199ASP-1-0.788-0.91023.366-12.617-12.6170.0000.0000.0000.000
194A200GLY0-0.026-0.01724.8050.3340.3340.0000.0000.0000.000
195A201GLU-1-0.931-0.97121.075-15.248-15.2480.0000.0000.0000.000
196A202TRP0-0.013-0.01325.4420.3390.3390.0000.0000.0000.000
197A203ASP-1-0.973-0.98328.819-10.292-10.2920.0000.0000.0000.000
198A204ALA-1-1.023-0.98827.595-10.463-10.4630.0000.0000.0000.000