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: RM1N8

Calculation Name: 2PLR-A-Xray547

Preferred Name:

Target Type:

Ligand Name: 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid | phosphate ion | pentaethylene glycol | tetraethylene glycol | 2,3-dihydroxy-1,4-dithiobutane | triethylene glycol | di(hydroxyethyl)ether | 1,2-ethanediol | chloride ion

Ligand 3-letter code: EPE | PO4 | 1PE | PG4 | DTT | PGE | PEG | EDO | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PLR

Chain ID: A

ChEMBL ID:

UniProt ID: Q970Q8

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 212
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2620936.590052
FMO2-HF: Nuclear repulsion 2537398.802475
FMO2-HF: Total energy -83537.787577
FMO2-MP2: Total energy -83789.124381


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:LYS)


Summations of interaction energy for fragment #1(A:2:LYS)
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.
-303.274-294.8866.507-6.257-8.635-0.066
Interaction energy analysis for fragmet #1(A:2:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.781 / q_NPA : 1.882
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].
3A4GLY00.0640.0483.321-12.872-11.0460.009-0.945-0.890-0.004
31A32ARG10.8300.9053.07091.70393.1070.272-0.680-0.996-0.008
85A86GLY0-0.0190.0013.653-5.552-5.4200.000-0.042-0.0890.000
86A87PHE0-0.005-0.0093.582-14.369-13.6990.002-0.392-0.279-0.003
211A212SER0-0.038-0.0045.059-4.809-4.699-0.001-0.017-0.0910.000
212A213PHE-1-0.879-0.9271.937-151.194-146.9486.225-4.181-6.290-0.051
4A5VAL0-0.034-0.0145.7320.3610.3610.0000.0000.0000.000
5A6LEU0-0.0110.0038.2121.9141.9140.0000.0000.0000.000
6A7ILE0-0.004-0.00710.8101.3081.3080.0000.0000.0000.000
7A8ALA00.0070.00713.9881.2051.2050.0000.0000.0000.000
8A9PHE00.0010.00116.6950.2620.2620.0000.0000.0000.000
9A10GLU-1-0.683-0.81620.719-23.885-23.8850.0000.0000.0000.000
10A11GLY00.0250.00624.217-0.018-0.0180.0000.0000.0000.000
11A12ILE0-0.0110.01727.681-0.088-0.0880.0000.0000.0000.000
12A13ASP-1-0.824-0.89630.083-20.028-20.0280.0000.0000.0000.000
13A14GLY00.008-0.01431.5710.4520.4520.0000.0000.0000.000
14A15SER0-0.039-0.04328.547-0.114-0.1140.0000.0000.0000.000
15A16GLY00.0040.00028.037-0.075-0.0750.0000.0000.0000.000
16A17LYS10.8050.88324.00822.56522.5650.0000.0000.0000.000
17A18SER00.042-0.00822.832-0.666-0.6660.0000.0000.0000.000
18A19SER0-0.0140.00222.706-0.612-0.6120.0000.0000.0000.000
19A20GLN0-0.025-0.00621.470-1.514-1.5140.0000.0000.0000.000
20A21ALA00.0400.02518.429-1.317-1.3170.0000.0000.0000.000
21A22THR0-0.026-0.01817.830-1.443-1.4430.0000.0000.0000.000
22A23LEU0-0.005-0.00318.690-1.015-1.0150.0000.0000.0000.000
23A24LEU00.0070.02713.838-0.649-0.6490.0000.0000.0000.000
24A25LYS10.8680.92714.20129.43829.4380.0000.0000.0000.000
25A26ASP-1-0.867-0.94614.712-30.580-30.5800.0000.0000.0000.000
26A27TRP0-0.080-0.04912.8860.0750.0750.0000.0000.0000.000
27A28ILE00.0180.0009.037-1.407-1.4070.0000.0000.0000.000
28A29GLU-1-0.799-0.89610.765-37.416-37.4160.0000.0000.0000.000
29A30LEU0-0.076-0.02412.6930.5760.5760.0000.0000.0000.000
30A31LYS10.8900.9329.09247.50947.5090.0000.0000.0000.000
32A33ASP-1-0.869-0.9136.238-60.802-60.8020.0000.0000.0000.000
33A34VAL0-0.039-0.0217.257-4.489-4.4890.0000.0000.0000.000
34A35TYR00.0130.00310.0722.9602.9600.0000.0000.0000.000
35A36LEU0-0.011-0.00712.906-0.799-0.7990.0000.0000.0000.000
36A37THR00.0110.01016.1881.4641.4640.0000.0000.0000.000
37A38GLU-1-0.914-0.95118.932-23.983-23.9830.0000.0000.0000.000
38A39TRP0-0.023-0.01122.1260.0270.0270.0000.0000.0000.000
39A40ASN00.001-0.01623.8960.7330.7330.0000.0000.0000.000
40A41SER00.0010.02123.0520.4830.4830.0000.0000.0000.000
41A42SER0-0.018-0.00624.462-0.690-0.6900.0000.0000.0000.000
42A43ASP-1-0.806-0.91424.231-23.261-23.2610.0000.0000.0000.000
43A44TRP0-0.063-0.06126.0601.3501.3500.0000.0000.0000.000
44A45ILE0-0.0220.00027.9510.7840.7840.0000.0000.0000.000
45A46HIS0-0.007-0.02329.8630.8700.8700.0000.0000.0000.000
46A47ASP-1-0.868-0.91631.560-18.039-18.0390.0000.0000.0000.000
47A48ILE00.0010.00833.1610.6850.6850.0000.0000.0000.000
48A49ILE0-0.018-0.01633.4660.6310.6310.0000.0000.0000.000
49A50LYS10.7830.87533.45618.36718.3670.0000.0000.0000.000
50A51GLU-1-0.858-0.90837.694-14.482-14.4820.0000.0000.0000.000
51A52ALA0-0.037-0.02539.3170.4790.4790.0000.0000.0000.000
52A53LYS10.9390.97240.15314.95114.9510.0000.0000.0000.000
53A54LYS10.8540.93042.09214.19714.1970.0000.0000.0000.000
54A55LYS10.8910.94043.33212.77912.7790.0000.0000.0000.000
55A56ASP-1-0.904-0.93744.357-13.222-13.2220.0000.0000.0000.000
56A57LEU0-0.023-0.01844.497-0.262-0.2620.0000.0000.0000.000
57A58LEU0-0.013-0.00338.853-0.023-0.0230.0000.0000.0000.000
58A59THR00.0530.03141.649-0.122-0.1220.0000.0000.0000.000
59A60PRO00.0460.01438.555-0.355-0.3550.0000.0000.0000.000
60A61LEU00.0320.02436.851-0.456-0.4560.0000.0000.0000.000
61A62THR00.002-0.01036.480-0.360-0.3600.0000.0000.0000.000
62A63PHE0-0.016-0.01535.405-0.403-0.4030.0000.0000.0000.000
63A64SER0-0.031-0.02932.449-0.516-0.5160.0000.0000.0000.000
64A65LEU00.0270.00831.537-0.655-0.6550.0000.0000.0000.000
65A66ILE0-0.0090.01931.664-0.508-0.5080.0000.0000.0000.000
66A67HIS00.0080.00229.244-0.188-0.1880.0000.0000.0000.000
67A68ALA00.0300.02127.267-0.828-0.8280.0000.0000.0000.000
68A69THR0-0.012-0.01726.767-0.695-0.6950.0000.0000.0000.000
69A70ASP-1-0.781-0.89026.888-22.464-22.4640.0000.0000.0000.000
70A71PHE00.002-0.00519.798-0.971-0.9710.0000.0000.0000.000
71A72SER0-0.021-0.02722.357-1.114-1.1140.0000.0000.0000.000
72A73ASP-1-0.726-0.81722.370-24.610-24.6100.0000.0000.0000.000
73A74ARG10.8760.92620.99524.07924.0790.0000.0000.0000.000
74A75TYR0-0.017-0.00316.860-2.477-2.4770.0000.0000.0000.000
75A76GLU-1-0.880-0.95917.362-31.989-31.9890.0000.0000.0000.000
76A77ARG10.7510.86118.41923.64523.6450.0000.0000.0000.000
77A78TYR0-0.039-0.02016.139-0.833-0.8330.0000.0000.0000.000
78A79ILE0-0.0040.00214.226-2.615-2.6150.0000.0000.0000.000
79A80LEU00.0010.00412.735-3.791-3.7910.0000.0000.0000.000
80A81PRO00.0090.00312.263-3.795-3.7950.0000.0000.0000.000
81A82MET00.0080.02010.293-2.742-2.7420.0000.0000.0000.000
82A83LEU0-0.020-0.0028.255-6.117-6.1170.0000.0000.0000.000
83A84LYS10.9130.9537.47131.10831.1080.0000.0000.0000.000
84A85SER0-0.054-0.0267.753-2.140-2.1400.0000.0000.0000.000
87A88ILE0-0.044-0.0186.126-1.855-1.8550.0000.0000.0000.000
88A89VAL00.003-0.0048.1243.8613.8610.0000.0000.0000.000
89A90ILE0-0.016-0.00411.6330.4620.4620.0000.0000.0000.000
90A91SER00.016-0.01514.6961.2511.2510.0000.0000.0000.000
91A92ASP-1-0.769-0.85118.033-24.399-24.3990.0000.0000.0000.000
92A93ARG10.8000.89921.12422.57722.5770.0000.0000.0000.000
93A94TYR00.014-0.00918.436-0.798-0.7980.0000.0000.0000.000
94A95ILE00.0450.02021.7211.2501.2500.0000.0000.0000.000
95A96TYR0-0.032-0.02520.7660.7590.7590.0000.0000.0000.000
96A97THR0-0.009-0.02425.4291.3151.3150.0000.0000.0000.000
97A98ALA0-0.0320.00726.9020.8730.8730.0000.0000.0000.000
98A99TYR00.0520.00825.6270.6400.6400.0000.0000.0000.000
99A100ALA00.0100.02529.7190.8230.8230.0000.0000.0000.000
100A101ARG10.8370.90629.16220.86120.8610.0000.0000.0000.000
101A102ASP-1-0.787-0.87131.871-18.574-18.5740.0000.0000.0000.000
102A103SER0-0.028-0.02733.5620.6470.6470.0000.0000.0000.000
103A104VAL0-0.030-0.01435.4460.5500.5500.0000.0000.0000.000
104A105ARG10.7110.80435.81717.07817.0780.0000.0000.0000.000
105A106GLY00.0030.00339.1400.2790.2790.0000.0000.0000.000
106A107VAL0-0.072-0.02435.4410.2080.2080.0000.0000.0000.000
107A108ASP-1-0.816-0.91636.661-17.277-17.2770.0000.0000.0000.000
108A109ILE00.0320.00931.438-0.502-0.5020.0000.0000.0000.000
109A110ASP-1-0.877-0.93332.324-19.185-19.1850.0000.0000.0000.000
110A111TRP0-0.036-0.02832.418-0.676-0.6760.0000.0000.0000.000
111A112VAL00.000-0.00729.882-0.535-0.5350.0000.0000.0000.000
112A113LYS10.8970.95028.25119.93719.9370.0000.0000.0000.000
113A114LYS10.9110.96627.68820.12220.1220.0000.0000.0000.000
114A115LEU0-0.0160.01528.660-0.609-0.6090.0000.0000.0000.000
115A116TYR00.009-0.01224.577-0.537-0.5370.0000.0000.0000.000
116A117SER0-0.087-0.04823.839-1.109-1.1090.0000.0000.0000.000
117A118PHE00.0080.00921.898-0.564-0.5640.0000.0000.0000.000
118A119ALA0-0.031-0.01419.707-1.301-1.3010.0000.0000.0000.000
119A120ILE0-0.0120.00513.6830.6360.6360.0000.0000.0000.000
120A121LYS10.8680.91017.90627.86327.8630.0000.0000.0000.000
121A122PRO0-0.031-0.02315.010-1.787-1.7870.0000.0000.0000.000
122A123ASP-1-0.839-0.89810.789-52.023-52.0230.0000.0000.0000.000
123A124ILE0-0.029-0.01513.4951.2391.2390.0000.0000.0000.000
124A125THR00.0400.01915.761-0.208-0.2080.0000.0000.0000.000
125A126PHE00.0030.00215.7471.1251.1250.0000.0000.0000.000
126A127TYR0-0.019-0.03620.7860.6210.6210.0000.0000.0000.000
127A128ILE0-0.026-0.02022.7060.3960.3960.0000.0000.0000.000
128A129ARG10.8410.90026.30019.45519.4550.0000.0000.0000.000
129A130VAL0-0.036-0.02429.7280.1170.1170.0000.0000.0000.000
130A131SER00.0300.01632.940-0.024-0.0240.0000.0000.0000.000
131A132PRO00.0710.02236.303-0.114-0.1140.0000.0000.0000.000
132A133ASP-1-0.807-0.90237.489-14.938-14.9380.0000.0000.0000.000
133A134ILE00.0180.00435.5200.0850.0850.0000.0000.0000.000
134A135ALA0-0.025-0.00434.271-0.131-0.1310.0000.0000.0000.000
135A136LEU00.0030.00635.7940.0560.0560.0000.0000.0000.000
136A137GLU-1-0.903-0.95439.264-14.728-14.7280.0000.0000.0000.000
137A138ARG10.8240.91431.28119.00919.0090.0000.0000.0000.000
138A139ILE0-0.0050.00935.5050.0250.0250.0000.0000.0000.000
139A140LYS10.9861.00837.99514.12914.1290.0000.0000.0000.000
140A141LYS10.8940.94939.50315.25915.2590.0000.0000.0000.000
141A142SER0-0.087-0.05536.784-0.031-0.0310.0000.0000.0000.000
142A143LYS10.8950.93938.77414.95414.9540.0000.0000.0000.000
143A144ARG10.7750.86834.36917.37017.3700.0000.0000.0000.000
144A145LYS10.9880.99040.64213.35613.3560.0000.0000.0000.000
145A146ILE00.0010.01038.836-0.457-0.4570.0000.0000.0000.000
146A147LYS10.9630.98033.31718.20618.2060.0000.0000.0000.000
147A148PRO00.0530.01139.190-0.126-0.1260.0000.0000.0000.000
148A149GLN00.0580.02435.6640.0200.0200.0000.0000.0000.000
149A150GLU-1-0.792-0.85134.450-17.592-17.5920.0000.0000.0000.000
150A151ALA00.0310.00636.670-0.066-0.0660.0000.0000.0000.000
151A152GLY00.0350.02938.8420.2480.2480.0000.0000.0000.000
152A153ALA0-0.019-0.01939.9480.2710.2710.0000.0000.0000.000
153A154ASP-1-0.830-0.88440.073-15.330-15.3300.0000.0000.0000.000
154A155ILE0-0.0110.00439.2090.1980.1980.0000.0000.0000.000
155A156PHE0-0.016-0.03041.2520.3230.3230.0000.0000.0000.000
156A157PRO00.0170.00945.6650.0620.0620.0000.0000.0000.000
157A158GLY0-0.0160.00047.7470.2120.2120.0000.0000.0000.000
158A159LEU0-0.038-0.00345.6730.1680.1680.0000.0000.0000.000
159A160SER00.014-0.00947.477-0.016-0.0160.0000.0000.0000.000
160A161PRO00.011-0.01543.311-0.224-0.2240.0000.0000.0000.000
161A162GLU-1-0.873-0.94342.648-14.003-14.0030.0000.0000.0000.000
162A163GLU-1-0.871-0.92943.217-13.473-13.4730.0000.0000.0000.000
163A164GLY00.0090.00743.433-0.140-0.1400.0000.0000.0000.000
164A165PHE0-0.057-0.02835.659-0.382-0.3820.0000.0000.0000.000
165A166LEU0-0.004-0.00639.124-0.471-0.4710.0000.0000.0000.000
166A167LYS10.9370.98640.33213.69313.6930.0000.0000.0000.000
167A168TYR00.0120.01934.764-0.261-0.2610.0000.0000.0000.000
168A169GLN0-0.014-0.03233.665-0.890-0.8900.0000.0000.0000.000
169A170GLY00.0420.03835.357-0.488-0.4880.0000.0000.0000.000
170A171LEU00.0080.00736.788-0.258-0.2580.0000.0000.0000.000
171A172ILE0-0.030-0.01431.457-0.401-0.4010.0000.0000.0000.000
172A173THR0-0.056-0.04732.338-0.686-0.6860.0000.0000.0000.000
173A174GLU-1-0.914-0.95732.938-16.343-16.3430.0000.0000.0000.000
174A175VAL0-0.052-0.01930.901-0.164-0.1640.0000.0000.0000.000
175A176TYR0-0.019-0.02226.774-0.238-0.2380.0000.0000.0000.000
176A177ASP-1-0.761-0.84129.372-19.559-19.5590.0000.0000.0000.000
177A178LYS10.8860.94331.72417.09817.0980.0000.0000.0000.000
178A179LEU00.0040.01327.201-0.102-0.1020.0000.0000.0000.000
179A180VAL0-0.035-0.01326.666-0.727-0.7270.0000.0000.0000.000
180A181LYS10.9350.95726.14118.71418.7140.0000.0000.0000.000
181A182ASP-1-0.857-0.92226.791-21.510-21.5100.0000.0000.0000.000
182A183GLU-1-0.827-0.88823.339-26.679-26.6790.0000.0000.0000.000
183A184ASN0-0.043-0.00919.506-0.230-0.2300.0000.0000.0000.000
184A185PHE0-0.030-0.00821.365-0.871-0.8710.0000.0000.0000.000
185A186ILE00.0360.01919.0720.8880.8880.0000.0000.0000.000
186A187VAL0-0.034-0.02322.2600.1120.1120.0000.0000.0000.000
187A188ILE0-0.058-0.02322.000-0.004-0.0040.0000.0000.0000.000
188A189ASP-1-0.783-0.87525.852-18.956-18.9560.0000.0000.0000.000
189A190GLY00.0430.00928.847-0.312-0.3120.0000.0000.0000.000
190A191THR0-0.091-0.07429.7230.4870.4870.0000.0000.0000.000
191A192LYS10.8440.93128.84520.89720.8970.0000.0000.0000.000
192A193THR00.0370.01829.760-0.238-0.2380.0000.0000.0000.000
193A194PRO00.032-0.00527.069-0.660-0.6600.0000.0000.0000.000
194A195LYS10.9920.99925.22622.16922.1690.0000.0000.0000.000
195A196GLU-1-0.848-0.90424.712-21.723-21.7230.0000.0000.0000.000
196A197ILE00.0160.01523.603-0.949-0.9490.0000.0000.0000.000
197A198GLN00.0340.01918.620-2.457-2.4570.0000.0000.0000.000
198A199ILE0-0.031-0.01320.026-1.448-1.4480.0000.0000.0000.000
199A200GLN0-0.012-0.01420.441-0.447-0.4470.0000.0000.0000.000
200A201ILE00.0030.01716.960-1.013-1.0130.0000.0000.0000.000
201A202ARG10.8540.90615.82229.94929.9490.0000.0000.0000.000
202A203LYS10.9240.97715.58927.42727.4270.0000.0000.0000.000
203A204PHE00.0340.01416.316-0.804-0.8040.0000.0000.0000.000
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