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: 2RN3R

Calculation Name: 3K2C-B-Xray547

Preferred Name:

Target Type:

Ligand Name: 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane | 1,2-ethanediol

Ligand 3-letter code: PG5 | EDO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3K2C

Chain ID: B

ChEMBL ID:

UniProt ID: Q8SRE1

Base Structure: X-ray

Registration Date: 2025-10-04

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 175
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1832234.927352
FMO2-HF: Nuclear repulsion 1763626.112308
FMO2-HF: Total energy -68608.815044
FMO2-MP2: Total energy -68806.414233


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:-5:THR)


Summations of interaction energy for fragment #1(A:-5:THR)
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.
-31.226-28.3860.241-1.529-1.552-0.014
Interaction energy analysis for fragmet #1(A:-5:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.851 / q_NPA : 0.910
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].
3A-3GLY00.0500.0202.878-2.858-0.0170.242-1.528-1.556-0.014
4A-2PRO0-0.0070.0145.277-0.982-0.983-0.001-0.0010.0040.000
5A-1GLY00.0240.0127.914-1.631-1.6310.0000.0000.0000.000
6A0SER0-0.026-0.0109.5930.8780.8780.0000.0000.0000.000
7A1MET00.0020.00212.6020.0210.0210.0000.0000.0000.000
8A2ALA00.0020.00515.464-0.661-0.6610.0000.0000.0000.000
9A3LYS10.9740.98017.35512.83512.8350.0000.0000.0000.000
10A4GLU-1-0.874-0.94618.983-15.686-15.6860.0000.0000.0000.000
11A5ALA00.0220.02218.4120.4090.4090.0000.0000.0000.000
12A6SER0-0.025-0.00520.4010.4280.4280.0000.0000.0000.000
13A7GLY0-0.004-0.00522.2110.3500.3500.0000.0000.0000.000
14A8ASN0-0.014-0.00722.8451.1521.1520.0000.0000.0000.000
15A9VAL00.011-0.00526.048-0.029-0.0290.0000.0000.0000.000
16A10TYR0-0.041-0.02624.634-0.243-0.2430.0000.0000.0000.000
17A11PHE0-0.024-0.02526.8520.5070.5070.0000.0000.0000.000
18A12ASP-1-0.764-0.84325.255-13.138-13.1380.0000.0000.0000.000
19A13VAL0-0.029-0.02928.1250.4670.4670.0000.0000.0000.000
20A14TYR00.003-0.00327.295-0.333-0.3330.0000.0000.0000.000
21A15ALA00.001-0.00132.8900.3390.3390.0000.0000.0000.000
22A16ASN0-0.056-0.05335.9500.0570.0570.0000.0000.0000.000
23A17GLU-1-0.788-0.86134.303-9.223-9.2230.0000.0000.0000.000
24A18GLU-1-0.911-0.93730.544-10.799-10.7990.0000.0000.0000.000
25A19SER0-0.032-0.01327.682-0.023-0.0230.0000.0000.0000.000
26A20LEU0-0.019-0.01129.061-0.088-0.0880.0000.0000.0000.000
27A21GLY00.0370.01425.915-0.316-0.3160.0000.0000.0000.000
28A22ARG10.8400.89121.40114.21914.2190.0000.0000.0000.000
29A23ILE0-0.034-0.01225.269-0.108-0.1080.0000.0000.0000.000
30A24VAL00.0460.01522.2370.1330.1330.0000.0000.0000.000
31A25MET0-0.050-0.02425.6290.3310.3310.0000.0000.0000.000
32A26LYS10.8990.94626.53210.75610.7560.0000.0000.0000.000
33A27LEU0-0.037-0.02128.1170.4290.4290.0000.0000.0000.000
34A28GLU-1-0.832-0.90430.784-10.523-10.5230.0000.0000.0000.000
35A29ASP-1-0.786-0.87331.959-9.456-9.4560.0000.0000.0000.000
36A30ASP-1-0.926-0.96332.303-9.483-9.4830.0000.0000.0000.000
37A31ILE0-0.024-0.00235.3620.2140.2140.0000.0000.0000.000
38A32VAL0-0.052-0.02237.1590.3040.3040.0000.0000.0000.000
39A33PRO00.0520.04236.968-0.106-0.1060.0000.0000.0000.000
40A34LYS10.8680.92337.9397.4367.4360.0000.0000.0000.000
41A35THR00.019-0.01839.0900.0600.0600.0000.0000.0000.000
42A36ALA00.0170.02534.055-0.070-0.0700.0000.0000.0000.000
43A37LYS10.9880.99535.0337.9677.9670.0000.0000.0000.000
44A38ASN0-0.017-0.00536.5120.0330.0330.0000.0000.0000.000
45A39PHE00.0530.01632.020-0.003-0.0030.0000.0000.0000.000
46A40ARG10.8130.86829.43410.20110.2010.0000.0000.0000.000
47A41THR0-0.007-0.01832.985-0.073-0.0730.0000.0000.0000.000
48A42LEU0-0.064-0.03135.3330.0740.0740.0000.0000.0000.000
49A43CYS0-0.054-0.01930.6880.0020.0020.0000.0000.0000.000
50A44GLU-1-0.895-0.95030.163-10.194-10.1940.0000.0000.0000.000
51A45ARG10.9090.97632.1848.0558.0550.0000.0000.0000.000
52A46PRO00.0120.01234.751-0.197-0.1970.0000.0000.0000.000
53A47LYS10.8910.93634.7078.9958.9950.0000.0000.0000.000
54A48GLY0-0.018-0.00137.7900.1510.1510.0000.0000.0000.000
55A49GLU-1-0.957-0.98139.347-7.506-7.5060.0000.0000.0000.000
56A50GLY00.024-0.00637.038-0.031-0.0310.0000.0000.0000.000
57A51TYR0-0.078-0.05334.5650.1560.1560.0000.0000.0000.000
58A52LYS10.9560.99530.05610.26710.2670.0000.0000.0000.000
59A53GLY0-0.058-0.04034.8580.2570.2570.0000.0000.0000.000
60A54SER0-0.077-0.04937.1400.2840.2840.0000.0000.0000.000
61A55THR0-0.006-0.02537.616-0.142-0.1420.0000.0000.0000.000
62A56PHE00.0300.01134.1340.0540.0540.0000.0000.0000.000
63A57HIS00.0030.01539.479-0.051-0.0510.0000.0000.0000.000
64A58ARG10.8920.94442.5617.1767.1760.0000.0000.0000.000
65A59ILE0-0.0020.01739.051-0.142-0.1420.0000.0000.0000.000
66A60ILE0-0.0060.00941.8950.1610.1610.0000.0000.0000.000
67A61PRO00.0320.00840.311-0.151-0.1510.0000.0000.0000.000
68A62GLY0-0.0040.00439.7950.1730.1730.0000.0000.0000.000
69A63PHE0-0.020-0.00741.0100.0830.0830.0000.0000.0000.000
70A64MET0-0.044-0.01039.107-0.173-0.1730.0000.0000.0000.000
71A65VAL00.0160.01135.8000.1300.1300.0000.0000.0000.000
72A66GLN00.0400.00838.674-0.070-0.0700.0000.0000.0000.000
73A67GLY00.0290.01239.3950.0090.0090.0000.0000.0000.000
74A68GLY00.0450.02339.4000.0940.0940.0000.0000.0000.000
75A69ASP-1-0.739-0.86440.182-6.881-6.8810.0000.0000.0000.000
76A70TYR00.003-0.02140.4150.0280.0280.0000.0000.0000.000
77A71THR0-0.0170.00042.3450.0150.0150.0000.0000.0000.000
78A72ALA0-0.051-0.03046.0100.1110.1110.0000.0000.0000.000
79A73HIS0-0.071-0.02141.979-0.051-0.0510.0000.0000.0000.000
80A74ASN00.0260.02345.398-0.035-0.0350.0000.0000.0000.000
81A75GLY0-0.0070.00047.0650.0460.0460.0000.0000.0000.000
82A76THR0-0.078-0.05147.9870.0770.0770.0000.0000.0000.000
83A77GLY0-0.0030.00648.1720.0950.0950.0000.0000.0000.000
84A78GLY00.0270.01944.775-0.092-0.0920.0000.0000.0000.000
85A79ARG10.8360.90644.3736.7656.7650.0000.0000.0000.000
86A80SER00.0320.02143.203-0.211-0.2110.0000.0000.0000.000
87A81ILE0-0.015-0.01338.9970.1090.1090.0000.0000.0000.000
88A82TYR0-0.083-0.05840.8050.0090.0090.0000.0000.0000.000
89A83GLY0-0.0180.01245.7840.1560.1560.0000.0000.0000.000
90A84GLU-1-0.895-0.95648.119-5.996-5.9960.0000.0000.0000.000
91A85LYS10.8800.96248.2035.8755.8750.0000.0000.0000.000
92A86PHE0-0.020-0.01342.1320.0780.0780.0000.0000.0000.000
93A87PRO00.038-0.01047.865-0.006-0.0060.0000.0000.0000.000
94A88ASP-1-0.802-0.89346.164-6.929-6.9290.0000.0000.0000.000
95A89GLU-1-0.807-0.87441.202-7.730-7.7300.0000.0000.0000.000
96A90ASN00.0220.00241.4210.0000.0000.0000.0000.0000.000
97A91PHE00.0150.00343.946-0.068-0.0680.0000.0000.0000.000
98A92GLU-1-0.914-0.94539.833-7.843-7.8430.0000.0000.0000.000
99A93LEU0-0.0020.00736.188-0.050-0.0500.0000.0000.0000.000
100A94LYS10.8830.93339.4947.4707.4700.0000.0000.0000.000
101A95HIS0-0.017-0.01738.816-0.304-0.3040.0000.0000.0000.000
102A96THR0-0.025-0.03536.5640.0450.0450.0000.0000.0000.000
103A97LYS10.8290.90630.62610.22310.2230.0000.0000.0000.000
104A98GLU-1-0.832-0.90131.055-9.913-9.9130.0000.0000.0000.000
105A99GLY00.0650.01331.584-0.221-0.2210.0000.0000.0000.000
106A100ILE0-0.062-0.01832.457-0.166-0.1660.0000.0000.0000.000
107A101LEU0-0.0030.00332.7600.1730.1730.0000.0000.0000.000
108A102SER00.008-0.02335.6350.1070.1070.0000.0000.0000.000
109A103MET00.0090.01939.246-0.104-0.1040.0000.0000.0000.000
110A104ALA0-0.043-0.01941.8910.1560.1560.0000.0000.0000.000
111A105ASN0-0.041-0.03044.4160.0690.0690.0000.0000.0000.000
112A106CYS0-0.023-0.02447.8690.0210.0210.0000.0000.0000.000
113A107GLY00.0390.02250.9770.1690.1690.0000.0000.0000.000
114A108ALA00.0170.02450.983-0.119-0.1190.0000.0000.0000.000
115A109HIS0-0.012-0.00449.8960.0270.0270.0000.0000.0000.000
116A110THR0-0.065-0.05049.9820.0530.0530.0000.0000.0000.000
117A111ASN0-0.018-0.00744.595-0.091-0.0910.0000.0000.0000.000
118A112GLY00.0540.01645.2840.1000.1000.0000.0000.0000.000
119A113SER00.0160.00040.946-0.048-0.0480.0000.0000.0000.000
120A114GLN0-0.042-0.02040.673-0.280-0.2800.0000.0000.0000.000
121A115PHE00.0220.02435.8470.0440.0440.0000.0000.0000.000
122A116PHE0-0.045-0.03439.1250.0870.0870.0000.0000.0000.000
123A117ILE00.0430.03132.579-0.111-0.1110.0000.0000.0000.000
124A118THR0-0.041-0.01736.4320.0950.0950.0000.0000.0000.000
125A119LEU0-0.031-0.01435.290-0.296-0.2960.0000.0000.0000.000
126A120GLY00.0500.01436.856-0.006-0.0060.0000.0000.0000.000
127A121LYS10.9140.97937.9387.6667.6660.0000.0000.0000.000
128A122THR00.004-0.01139.7540.1030.1030.0000.0000.0000.000
129A123GLN00.0670.02342.742-0.070-0.0700.0000.0000.0000.000
130A124TRP0-0.0040.01044.3380.0990.0990.0000.0000.0000.000
131A125LEU0-0.022-0.01243.2480.1780.1780.0000.0000.0000.000
132A126ASP-1-0.750-0.85543.334-7.540-7.5400.0000.0000.0000.000
133A127GLU-1-0.949-0.98445.807-6.393-6.3930.0000.0000.0000.000
134A128LYS10.8020.90747.6226.6796.6790.0000.0000.0000.000
135A129HIS10.8280.92043.7817.0697.0690.0000.0000.0000.000
136A130VAL00.0290.03540.723-0.032-0.0320.0000.0000.0000.000
137A131VAL00.0090.01337.209-0.117-0.1170.0000.0000.0000.000
138A132PHE0-0.008-0.02534.9860.0960.0960.0000.0000.0000.000
139A133GLY00.0510.02932.831-0.197-0.1970.0000.0000.0000.000
140A134GLU-1-0.879-0.91929.193-10.304-10.3040.0000.0000.0000.000
141A135VAL0-0.027-0.01627.492-0.248-0.2480.0000.0000.0000.000
142A136VAL0-0.027-0.00923.8770.0260.0260.0000.0000.0000.000
143A137GLU-1-0.913-0.95519.854-16.563-16.5630.0000.0000.0000.000
144A138GLY00.0580.03023.6240.4810.4810.0000.0000.0000.000
145A139MET0-0.0070.00425.3800.4670.4670.0000.0000.0000.000
146A140ASP-1-0.829-0.93325.533-12.120-12.1200.0000.0000.0000.000
147A141VAL0-0.041-0.01026.3600.4040.4040.0000.0000.0000.000
148A142VAL00.0150.01129.1470.4220.4220.0000.0000.0000.000
149A143HIS0-0.029-0.03530.9070.5600.5600.0000.0000.0000.000
150A144LYS10.7960.90126.43612.20412.2040.0000.0000.0000.000
151A145ILE0-0.0050.00132.8500.3280.3280.0000.0000.0000.000
152A146ALA00.0230.00335.2400.3260.3260.0000.0000.0000.000
153A147LYS10.8990.95235.3689.0969.0960.0000.0000.0000.000
154A148TYR0-0.041-0.01935.1000.1710.1710.0000.0000.0000.000
155A149GLY00.0410.01640.0850.1480.1480.0000.0000.0000.000
156A150SER0-0.050-0.02842.4350.1330.1330.0000.0000.0000.000
157A151GLU-1-0.844-0.93245.669-6.892-6.8920.0000.0000.0000.000
158A152SER0-0.054-0.03147.7610.0610.0610.0000.0000.0000.000
159A153GLY00.001-0.00945.5150.0630.0630.0000.0000.0000.000
160A154GLN0-0.0200.00045.507-0.159-0.1590.0000.0000.0000.000
161A155VAL00.0630.04941.896-0.053-0.0530.0000.0000.0000.000
162A156LYS10.9380.96941.6707.7387.7380.0000.0000.0000.000
163A157LYS10.8810.92144.3286.6356.6350.0000.0000.0000.000
164A158GLY00.0340.01645.112-0.051-0.0510.0000.0000.0000.000
165A159TYR0-0.0130.00338.460-0.188-0.1880.0000.0000.0000.000
166A160ARG10.9400.99139.0138.0008.0000.0000.0000.0000.000
167A161ILE00.0010.00135.901-0.174-0.1740.0000.0000.0000.000
168A162GLU-1-0.800-0.89535.388-8.756-8.7560.0000.0000.0000.000
169A163ILE00.0160.02331.994-0.324-0.3240.0000.0000.0000.000
170A164ARG10.7150.82030.8879.5329.5320.0000.0000.0000.000
171A165ASP-1-0.824-0.91926.943-11.075-11.0750.0000.0000.0000.000
172A166CYS0-0.068-0.02828.6610.1330.1330.0000.0000.0000.000
173A167GLY00.0490.04827.4570.1440.1440.0000.0000.0000.000
174A168VAL0-0.029-0.01524.8230.0030.0030.0000.0000.0000.000
175A169LEU-1-0.893-0.94520.304-14.745-14.7450.0000.0000.0000.000