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: VY3Q1

Calculation Name: 4PQX-A-Xray547

Preferred Name:

Target Type:

Ligand Name: glycerol | 1,2-ethanediol | isopropyl alcohol

Ligand 3-letter code: GOL | EDO | IPA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4PQX

Chain ID: A

ChEMBL ID:

UniProt ID: A5ZGW9

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 210
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2504480.321432
FMO2-HF: Nuclear repulsion 2418899.211028
FMO2-HF: Total energy -85581.110404
FMO2-MP2: Total energy -85833.694393


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:33:SER)


Summations of interaction energy for fragment #1(A:33: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.
-151.393-148.2910.053-1.57-1.585-0.006
Interaction energy analysis for fragmet #1(A:33:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.886 / q_NPA : 0.931
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].
3A35SER00.0180.0273.271-8.825-6.6650.048-1.064-1.144-0.005
53A85ASN0-0.055-0.0423.273-0.3550.5870.005-0.506-0.441-0.001
4A36LEU0-0.008-0.0045.9971.8071.8070.0000.0000.0000.000
5A37VAL0-0.0050.0079.4380.0040.0040.0000.0000.0000.000
6A38ILE00.0270.02612.7350.2670.2670.0000.0000.0000.000
7A39SER0-0.060-0.02516.513-0.270-0.2700.0000.0000.0000.000
8A40THR00.0370.02518.4460.4880.4880.0000.0000.0000.000
9A41ILE0-0.0130.00620.374-0.524-0.5240.0000.0000.0000.000
10A42ASN0-0.0010.01922.1660.2660.2660.0000.0000.0000.000
11A43GLN00.011-0.00323.888-0.035-0.0350.0000.0000.0000.000
12A44ILE0-0.023-0.02026.5050.3920.3920.0000.0000.0000.000
13A45SER0-0.015-0.01127.4040.2970.2970.0000.0000.0000.000
14A46GLU-1-0.919-0.97329.725-9.044-9.0440.0000.0000.0000.000
15A47ASP-1-0.867-0.92727.878-11.175-11.1750.0000.0000.0000.000
16A48SER0-0.049-0.03028.058-0.368-0.3680.0000.0000.0000.000
17A49LYS10.9060.94425.09010.81210.8120.0000.0000.0000.000
18A50GLU-1-0.904-0.91023.539-12.659-12.6590.0000.0000.0000.000
19A51PHE0-0.024-0.02518.1620.2270.2270.0000.0000.0000.000
20A52TYR0-0.020-0.01519.228-0.503-0.5030.0000.0000.0000.000
21A53PHE00.0300.00815.3110.1630.1630.0000.0000.0000.000
22A54THR00.020-0.01118.623-0.263-0.2630.0000.0000.0000.000
23A55LEU00.010-0.00413.868-0.153-0.1530.0000.0000.0000.000
24A56ASP-1-0.727-0.81918.175-14.253-14.2530.0000.0000.0000.000
25A57ASN00.0160.00115.7420.8680.8680.0000.0000.0000.000
26A58GLY0-0.028-0.03219.9970.4810.4810.0000.0000.0000.000
27A59LYS10.8440.93615.59618.30818.3080.0000.0000.0000.000
28A60THR00.0150.00018.098-0.130-0.1300.0000.0000.0000.000
29A61MET0-0.040-0.02012.963-1.595-1.5950.0000.0000.0000.000
30A62PHE00.0380.02415.2630.9120.9120.0000.0000.0000.000
31A63PRO0-0.0090.00214.230-1.735-1.7350.0000.0000.0000.000
32A64SER00.0360.00313.4281.7191.7190.0000.0000.0000.000
33A65ASN0-0.062-0.03112.6580.5910.5910.0000.0000.0000.000
34A66SER00.0320.01215.8020.5810.5810.0000.0000.0000.000
35A67GLN00.0080.00118.3500.3090.3090.0000.0000.0000.000
36A68ALA0-0.042-0.01017.5350.6730.6730.0000.0000.0000.000
37A69TRP00.0230.00114.338-0.117-0.1170.0000.0000.0000.000
38A70GLY00.0160.00921.1420.5080.5080.0000.0000.0000.000
39A71GLY0-0.044-0.02724.2980.6210.6210.0000.0000.0000.000
40A72GLU-1-0.913-0.94022.669-12.635-12.6350.0000.0000.0000.000
41A73LYS10.8170.90524.61910.79310.7930.0000.0000.0000.000
42A74PHE00.0390.01520.6110.2750.2750.0000.0000.0000.000
43A75GLU-1-0.904-0.94625.828-10.093-10.0930.0000.0000.0000.000
44A76ASN00.0180.00726.845-0.902-0.9020.0000.0000.0000.000
45A77GLY00.0390.00926.3430.4370.4370.0000.0000.0000.000
46A78GLN0-0.024-0.00523.6000.5480.5480.0000.0000.0000.000
47A79ARG10.7820.84121.14613.49013.4900.0000.0000.0000.000
48A80ALA00.0250.00818.9170.3340.3340.0000.0000.0000.000
49A81PHE00.0310.02514.926-0.629-0.6290.0000.0000.0000.000
50A82VAL0-0.0070.00412.5810.1290.1290.0000.0000.0000.000
51A83ILE0-0.0040.0018.565-2.590-2.5900.0000.0000.0000.000
52A84PHE00.022-0.0068.2480.8720.8720.0000.0000.0000.000
54A86GLU-1-0.860-0.9324.988-28.844-28.8440.0000.0000.0000.000
55A87LEU0-0.098-0.0445.923-5.337-5.3370.0000.0000.0000.000
56A88GLU-1-0.934-0.9618.631-25.089-25.0890.0000.0000.0000.000
57A89GLN0-0.0140.00410.1261.9381.9380.0000.0000.0000.000
58A90PRO00.0240.00413.587-0.280-0.2800.0000.0000.0000.000
59A91VAL00.0170.00815.3930.6490.6490.0000.0000.0000.000
60A92ASN0-0.031-0.03017.963-0.270-0.2700.0000.0000.0000.000
61A93GLY00.0170.00521.2180.1520.1520.0000.0000.0000.000
62A94TYR00.0040.01017.2670.2250.2250.0000.0000.0000.000
63A95ASP-1-0.846-0.89415.965-16.908-16.9080.0000.0000.0000.000
64A96TYR0-0.009-0.00110.756-0.068-0.0680.0000.0000.0000.000
65A97ASN00.0250.02712.1091.5151.5150.0000.0000.0000.000
66A98ILE00.001-0.0129.681-3.222-3.2220.0000.0000.0000.000
67A99GLN00.0150.0138.1733.1433.1430.0000.0000.0000.000
68A100VAL00.011-0.0068.968-3.775-3.7750.0000.0000.0000.000
69A101ARG10.7950.8836.88835.17435.1740.0000.0000.0000.000
70A102ASP-1-0.841-0.91311.554-18.517-18.5170.0000.0000.0000.000
71A103ILE0-0.0150.00114.158-1.082-1.0820.0000.0000.0000.000
72A104THR00.0120.00816.8821.2911.2910.0000.0000.0000.000
73A105LYS10.8400.90918.66612.49812.4980.0000.0000.0000.000
74A106VAL00.0060.00620.1130.1410.1410.0000.0000.0000.000
75A107LEU00.0190.01422.7570.3260.3260.0000.0000.0000.000
76A108THR00.0040.00025.673-0.137-0.1370.0000.0000.0000.000
77A109LYS10.8280.91127.8769.5429.5420.0000.0000.0000.000
78A110GLU0-0.051-0.07131.558-0.243-0.2430.0000.0000.0000.000
79A111ILE00.0450.03634.3830.0010.0010.0000.0000.0000.000
80A112VAL0-0.033-0.00736.4240.1120.1120.0000.0000.0000.000
81A113THR00.017-0.01939.636-0.021-0.0210.0000.0000.0000.000
82A114MET0-0.0040.01142.4520.1100.1100.0000.0000.0000.000
83A115ASP-1-0.815-0.91745.873-6.835-6.8350.0000.0000.0000.000
84A116ASP-1-0.898-0.95642.407-7.380-7.3800.0000.0000.0000.000
85A117GLU-1-0.931-0.96245.854-6.302-6.3020.0000.0000.0000.000
86A118GLU-1-0.872-0.92542.536-7.127-7.1270.0000.0000.0000.000
87A119ASN0-0.072-0.04443.723-0.053-0.0530.0000.0000.0000.000
88A120THR0-0.008-0.01244.6270.2250.2250.0000.0000.0000.000
89A121GLU-1-0.831-0.93145.030-7.077-7.0770.0000.0000.0000.000
90A122GLU-1-0.980-0.98044.660-6.891-6.8910.0000.0000.0000.000
91A123LYS10.7790.88443.1446.8546.8540.0000.0000.0000.000
92A124ILE0-0.053-0.02939.911-0.270-0.2700.0000.0000.0000.000
93A125GLY00.0220.01939.647-0.235-0.2350.0000.0000.0000.000
94A126ASP-1-0.710-0.83340.385-7.724-7.7240.0000.0000.0000.000
95A127ASP-1-0.817-0.87138.480-7.655-7.6550.0000.0000.0000.000
96A128LYS10.8300.91537.2187.6367.6360.0000.0000.0000.000
97A129ILE0-0.023-0.01130.914-0.181-0.1810.0000.0000.0000.000
98A130ASN00.0420.01930.2560.4440.4440.0000.0000.0000.000
99A131ALA00.0200.00728.831-0.246-0.2460.0000.0000.0000.000
100A132THR0-0.065-0.02424.4320.4200.4200.0000.0000.0000.000
101A133TYR00.0250.01321.0170.0400.0400.0000.0000.0000.000
102A134MET0-0.021-0.01024.8660.1040.1040.0000.0000.0000.000
103A135TRP0-0.066-0.03720.247-0.072-0.0720.0000.0000.0000.000
104A136ILE00.0300.01525.1720.0530.0530.0000.0000.0000.000
105A137SER0-0.050-0.03923.579-0.256-0.2560.0000.0000.0000.000
106A138LYS10.9660.97322.70913.58313.5830.0000.0000.0000.000
107A139ASP-1-0.891-0.93125.287-11.802-11.8020.0000.0000.0000.000
108A140LYS10.8970.95927.40010.35510.3550.0000.0000.0000.000
109A141LYS10.9580.99327.65910.84210.8420.0000.0000.0000.000
110A142TYR0-0.019-0.02725.5410.1840.1840.0000.0000.0000.000
111A143LEU00.0310.03926.881-0.210-0.2100.0000.0000.0000.000
112A144THR0-0.046-0.02122.245-0.134-0.1340.0000.0000.0000.000
113A145ILE00.0080.00125.3670.0590.0590.0000.0000.0000.000
114A146GLU-1-0.832-0.87920.572-14.342-14.3420.0000.0000.0000.000
115A147PHE00.002-0.01724.0690.4760.4760.0000.0000.0000.000
116A148GLN0-0.039-0.03224.0850.1030.1030.0000.0000.0000.000
117A149TYR00.0270.00128.2870.4190.4190.0000.0000.0000.000
118A150TYR00.0110.02430.727-0.236-0.2360.0000.0000.0000.000
119A151SER0-0.055-0.02231.3680.0510.0510.0000.0000.0000.000
120A152THR00.014-0.02833.663-0.131-0.1310.0000.0000.0000.000
121A153HIS0-0.066-0.02527.546-0.118-0.1180.0000.0000.0000.000
122A154SER0-0.004-0.01030.953-0.107-0.1070.0000.0000.0000.000
123A155GLU-1-0.837-0.91029.648-10.499-10.4990.0000.0000.0000.000
124A156ASP-1-0.934-0.96632.337-8.630-8.6300.0000.0000.0000.000
125A157LYS10.7890.90635.3628.0968.0960.0000.0000.0000.000
126A158LYS10.8400.90331.8269.5189.5180.0000.0000.0000.000
127A159HIS10.7810.87632.7609.4119.4110.0000.0000.0000.000
128A160PHE00.0120.01333.502-0.354-0.3540.0000.0000.0000.000
129A161LEU00.0210.01829.7520.0980.0980.0000.0000.0000.000
130A162ASN0-0.035-0.02333.822-0.166-0.1660.0000.0000.0000.000
131A163LEU00.0280.03332.417-0.056-0.0560.0000.0000.0000.000
132A164VAL00.0050.00435.5510.0290.0290.0000.0000.0000.000
133A165ILE00.0480.02839.312-0.053-0.0530.0000.0000.0000.000
134A166ASN0-0.006-0.01242.0940.2370.2370.0000.0000.0000.000
135A167ASN0-0.028-0.03145.1620.0280.0280.0000.0000.0000.000
136A168LYS10.8430.93748.2686.7716.7710.0000.0000.0000.000
137A169GLU0-0.043-0.04144.4720.0570.0570.0000.0000.0000.000
138A170ALA0-0.029-0.01349.6370.0810.0810.0000.0000.0000.000
139A171ASP-1-0.922-0.93152.239-5.590-5.5900.0000.0000.0000.000
140A172SER0-0.050-0.04753.843-0.006-0.0060.0000.0000.0000.000
141A173ALA0-0.0210.00150.272-0.061-0.0610.0000.0000.0000.000
142A174ALA0-0.049-0.03151.2370.1360.1360.0000.0000.0000.000
143A175GLU-1-0.870-0.93148.048-6.588-6.5880.0000.0000.0000.000
144A176ASN0-0.105-0.06150.0330.2320.2320.0000.0000.0000.000
145A177GLU-1-0.944-0.96347.379-6.488-6.4880.0000.0000.0000.000
146A178ASP-1-0.895-0.94549.568-6.259-6.2590.0000.0000.0000.000
147A179ASN0-0.092-0.05345.611-0.281-0.2810.0000.0000.0000.000
148A180THR0-0.008-0.01741.420-0.077-0.0770.0000.0000.0000.000
149A181ASP-1-0.897-0.95041.950-7.085-7.0850.0000.0000.0000.000
150A182ASP-1-0.909-0.95342.987-7.117-7.1170.0000.0000.0000.000
151A183GLU-1-0.833-0.89239.718-7.845-7.8450.0000.0000.0000.000
152A184TYR0-0.081-0.08534.646-0.260-0.2600.0000.0000.0000.000
153A185ILE00.0200.01136.8350.1830.1830.0000.0000.0000.000
154A186ASN00.0220.01137.945-0.366-0.3660.0000.0000.0000.000
155A187LEU0-0.024-0.00735.1910.0210.0210.0000.0000.0000.000
156A188GLU-1-0.829-0.90138.303-7.507-7.5070.0000.0000.0000.000
157A189PHE0-0.023-0.02030.197-0.161-0.1610.0000.0000.0000.000
158A190ARG0-0.066-0.01835.3790.1560.1560.0000.0000.0000.000
159A191HIS00.0370.00834.791-0.387-0.3870.0000.0000.0000.000
160A192ASN00.0570.05836.5820.1920.1920.0000.0000.0000.000
161A193SER0-0.040-0.05736.725-0.223-0.2230.0000.0000.0000.000
162A194GLU-1-0.852-0.92737.805-7.779-7.7790.0000.0000.0000.000
163A195ARG10.8360.90740.2927.4127.4120.0000.0000.0000.000
164A196ASP-1-0.743-0.81435.501-8.687-8.6870.0000.0000.0000.000
165A197SER0-0.035-0.03238.8580.1710.1710.0000.0000.0000.000
166A198PRO0-0.029-0.02436.480-0.255-0.2550.0000.0000.0000.000
167A199ASP-1-0.886-0.92135.607-8.220-8.2200.0000.0000.0000.000
168A200HIS0-0.017-0.01630.883-0.182-0.1820.0000.0000.0000.000
169A201LEU0-0.040-0.01128.2400.0240.0240.0000.0000.0000.000
170A202GLY00.0110.00026.698-0.252-0.2520.0000.0000.0000.000
171A203GLU-1-0.885-0.94120.855-13.724-13.7240.0000.0000.0000.000
172A204GLY0-0.0010.00023.179-0.158-0.1580.0000.0000.0000.000
173A205TYR0-0.045-0.04619.077-0.245-0.2450.0000.0000.0000.000
174A206VAL0-0.036-0.01423.4940.1260.1260.0000.0000.0000.000
175A207SER0-0.027-0.02024.448-0.211-0.2110.0000.0000.0000.000
176A208PHE00.0160.00326.5560.1420.1420.0000.0000.0000.000
177A209LYS10.8940.95429.32810.50810.5080.0000.0000.0000.000
178A210LEU0-0.010-0.01830.4800.3010.3010.0000.0000.0000.000
179A211ASP-1-0.804-0.86733.228-8.993-8.9930.0000.0000.0000.000
180A212LYS10.8560.92135.3568.5428.5420.0000.0000.0000.000
181A213ILE00.0150.01835.1140.1930.1930.0000.0000.0000.000
182A214GLU-1-0.949-0.97135.260-9.132-9.1320.0000.0000.0000.000
183A215GLU-1-0.951-0.98537.209-7.360-7.3600.0000.0000.0000.000
184A216GLN0-0.047-0.02739.8750.0580.0580.0000.0000.0000.000
185A217ILE0-0.021-0.00533.3530.0160.0160.0000.0000.0000.000
186A218GLU-1-0.925-0.95937.146-8.296-8.2960.0000.0000.0000.000
187A219GLY0-0.025-0.01238.9020.1810.1810.0000.0000.0000.000
188A220LYS10.8160.93437.1237.7807.7800.0000.0000.0000.000
189A221LYS10.8090.88335.2597.7327.7320.0000.0000.0000.000
190A222GLY00.002-0.02033.341-0.373-0.3730.0000.0000.0000.000
191A223LEU0-0.0080.01431.8790.2320.2320.0000.0000.0000.000
192A224ASN0-0.016-0.01234.473-0.189-0.1890.0000.0000.0000.000
193A225ILE00.002-0.00532.3010.1330.1330.0000.0000.0000.000
194A226ARG10.8670.90735.6867.5897.5890.0000.0000.0000.000
195A227VAL0-0.004-0.01533.556-0.141-0.1410.0000.0000.0000.000
196A228ARG10.8930.94836.8477.6157.6150.0000.0000.0000.000
197A229THR0-0.016-0.02335.148-0.144-0.1440.0000.0000.0000.000
198A230LEU0-0.037-0.02031.7960.2520.2520.0000.0000.0000.000
199A231TYR0-0.026-0.04232.6270.1800.1800.0000.0000.0000.000
200A232ASP-1-0.900-0.93936.020-8.284-8.2840.0000.0000.0000.000
201A233GLY0-0.0120.00039.1580.1410.1410.0000.0000.0000.000
202A234ILE00.0150.01739.552-0.226-0.2260.0000.0000.0000.000
203A235LYS10.8840.95136.7448.0088.0080.0000.0000.0000.000
204A236ASN00.0600.02537.879-0.075-0.0750.0000.0000.0000.000
205A237TYR00.0030.00832.4270.0430.0430.0000.0000.0000.000
206A238LYS10.9120.96334.2578.0068.0060.0000.0000.0000.000
207A239VAL0-0.0150.00428.321-0.218-0.2180.0000.0000.0000.000
208A240GLN00.0330.02729.4920.3850.3850.0000.0000.0000.000
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