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FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: P4LGN

Calculation Name: 2PYQ-A-Xray32

Preferred Name:

Target Type:

Ligand Name: tetraethylene glycol

ligand 3-letter code: PG4

PDB ID: 2PYQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q28JX0

Base Structure: X-ray

Registration Date: 2018-09-07

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 175
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1059853.425047
FMO2-HF: Nuclear repulsion 1009555.901877
FMO2-HF: Total energy -50297.52317
FMO2-MP2: Total energy -50437.745016


3D Structure
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:0:GLY)


Summations of interaction energy for fragment #1(A:0:GLY)
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.
0.0641.8490-0.997-0.7890.003
Interaction energy analysis for fragmet #1(A:0:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.039 / q_NPA : 0.017
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].
3A2GLY00.0170.0273.445-0.0621.6760.001-0.994-0.7460.003
4A3LYS10.9790.9805.3560.6010.648-0.001-0.003-0.0430.000
5A4ARG10.9260.9357.9040.9300.9300.0000.0000.0000.000
6A5ASP-1-0.866-0.9397.695-1.500-1.5000.0000.0000.0000.000
7A6ASP-1-0.884-0.9305.235-0.741-0.7410.0000.0000.0000.000
8A7LEU0-0.103-0.0458.2670.2620.2620.0000.0000.0000.000
9A8ILE00.0230.01811.7820.1080.1080.0000.0000.0000.000
10A9ALA00.0220.01510.4610.0880.0880.0000.0000.0000.000
11A10GLN0-0.027-0.01412.1310.1270.1270.0000.0000.0000.000
12A11TYR0-0.022-0.01113.6870.0340.0340.0000.0000.0000.000
13A12ALA00.0240.00815.8020.0330.0330.0000.0000.0000.000
14A13ASP-1-0.852-0.89515.1120.0230.0230.0000.0000.0000.000
15A14ASP-1-0.720-0.84517.2080.0060.0060.0000.0000.0000.000
16A15LEU0-0.027-0.02019.6400.0140.0140.0000.0000.0000.000
17A16ARG10.8550.92020.3360.1240.1240.0000.0000.0000.000
18A17ASN0-0.013-0.02118.5950.0100.0100.0000.0000.0000.000
19A18LYS10.8070.93519.212-0.028-0.0280.0000.0000.0000.000
20A19CYS0-0.040-0.03423.7840.0060.0060.0000.0000.0000.000
21A20GLY00.0530.07025.294-0.001-0.0010.0000.0000.0000.000
22A21MET0-0.066-0.02625.324-0.002-0.0020.0000.0000.0000.000
23A22GLU-1-0.789-0.87624.108-0.108-0.1080.0000.0000.0000.000
24A23PRO0-0.0190.01720.007-0.004-0.0040.0000.0000.0000.000
25A24ASP-1-0.801-0.89322.562-0.225-0.2250.0000.0000.0000.000
26A25MET00.041-0.01216.0900.0090.0090.0000.0000.0000.000
27A26ALA0-0.0140.01120.164-0.037-0.0370.0000.0000.0000.000
28A27LEU00.0480.02822.541-0.012-0.0120.0000.0000.0000.000
29A28LEU00.005-0.00517.8080.0010.0010.0000.0000.0000.000
30A29GLU-1-0.825-0.90016.542-0.569-0.5690.0000.0000.0000.000
31A30LYS10.7880.87419.4180.2340.2340.0000.0000.0000.000
32A31VAL00.0000.00422.2750.0110.0110.0000.0000.0000.000
33A32THR00.008-0.00416.0000.0240.0240.0000.0000.0000.000
34A33LYS10.8220.90719.2550.4530.4530.0000.0000.0000.000
35A34GLY0-0.060-0.01820.5420.0130.0130.0000.0000.0000.000
36A35CYS0-0.046-0.02120.2500.0310.0310.0000.0000.0000.000
37A36GLY00.0290.03420.3960.0300.0300.0000.0000.0000.000
38A37PRO0-0.053-0.03016.608-0.049-0.0490.0000.0000.0000.000
39A38ALA00.0190.01811.8630.0390.0390.0000.0000.0000.000
40A39ILE00.0270.02013.9580.0270.0270.0000.0000.0000.000
41A40TYR00.020-0.0058.890-0.023-0.0230.0000.0000.0000.000
42A41ASN00.0040.00613.1100.1000.1000.0000.0000.0000.000
43A42ARG10.8880.91115.443-0.127-0.1270.0000.0000.0000.000
44A43ASP-1-0.816-0.89516.7490.0580.0580.0000.0000.0000.000
45A44ALA0-0.007-0.00119.467-0.010-0.0100.0000.0000.0000.000
46A45SER0-0.090-0.03617.256-0.024-0.0240.0000.0000.0000.000
47A46THR0-0.040-0.01919.222-0.010-0.0100.0000.0000.0000.000
48A47VAL00.0070.01721.618-0.003-0.0030.0000.0000.0000.000
49A48ALA00.0210.00725.3370.0120.0120.0000.0000.0000.000
50A49GLY00.004-0.02127.927-0.005-0.0050.0000.0000.0000.000
51A50SER0-0.013-0.00629.813-0.001-0.0010.0000.0000.0000.000
52A51ASP-1-0.842-0.91331.671-0.007-0.0070.0000.0000.0000.000
53A52THR00.0320.00733.430-0.006-0.0060.0000.0000.0000.000
54A53ALA00.0250.00935.204-0.005-0.0050.0000.0000.0000.000
55A54GLU-1-0.833-0.91127.941-0.048-0.0480.0000.0000.0000.000
56A55LEU00.0100.00731.208-0.011-0.0110.0000.0000.0000.000
57A56GLU-1-0.873-0.93833.426-0.040-0.0400.0000.0000.0000.000
58A57THR0-0.028-0.02331.432-0.005-0.0050.0000.0000.0000.000
59A58ILE0-0.0240.00628.680-0.009-0.0090.0000.0000.0000.000
60A59LYS10.9000.95831.9070.0350.0350.0000.0000.0000.000
61A60LYS10.9120.96335.3840.0450.0450.0000.0000.0000.000
62A61ASN0-0.016-0.03932.115-0.001-0.0010.0000.0000.0000.000
63A62PHE0-0.036-0.00827.949-0.009-0.0090.0000.0000.0000.000
64A63LEU00.0070.00731.734-0.005-0.0050.0000.0000.0000.000
65A64MET0-0.0430.00134.380-0.001-0.0010.0000.0000.0000.000
66A65LYS10.8970.95434.6470.0790.0790.0000.0000.0000.000
67A66LYS10.8890.96426.5010.1710.1710.0000.0000.0000.000
68A67LEU0-0.028-0.02330.291-0.005-0.0050.0000.0000.0000.000
69A68GLY00.0030.01734.1020.0010.0010.0000.0000.0000.000
70A69LEU0-0.060-0.02035.7080.0040.0040.0000.0000.0000.000
71A70ALA00.0460.01439.0930.0010.0010.0000.0000.0000.000
72A71ASP-1-0.763-0.87741.640-0.043-0.0430.0000.0000.0000.000
73A72SER00.0120.01442.3630.0020.0020.0000.0000.0000.000
74A73GLU-1-0.846-0.90742.084-0.030-0.0300.0000.0000.0000.000
75A74SER0-0.019-0.00540.784-0.001-0.0010.0000.0000.0000.000
76A75LEU0-0.0110.01237.581-0.002-0.0020.0000.0000.0000.000
77A76MET00.0370.01736.681-0.002-0.0020.0000.0000.0000.000
78A77GLY00.0500.03537.1260.0020.0020.0000.0000.0000.000
79A78GLY00.014-0.00635.7670.0010.0010.0000.0000.0000.000
80A79ILE0-0.030-0.01631.921-0.002-0.0020.0000.0000.0000.000
81A80GLN00.001-0.01132.5730.0000.0000.0000.0000.0000.000
82A81SER00.0400.03733.8690.0050.0050.0000.0000.0000.000
83A82VAL00.0270.00729.0760.0020.0020.0000.0000.0000.000
84A83ILE0-0.031-0.01328.2610.0020.0020.0000.0000.0000.000
85A84GLU-1-0.797-0.85029.6700.0080.0080.0000.0000.0000.000
86A85THR00.0000.01328.2710.0060.0060.0000.0000.0000.000
87A86TYR0-0.035-0.03720.124-0.002-0.0020.0000.0000.0000.000
88A87GLY00.0440.03726.0970.0100.0100.0000.0000.0000.000
89A88ARG10.8370.87528.070-0.006-0.0060.0000.0000.0000.000
90A89SER0-0.012-0.02027.8000.0030.0030.0000.0000.0000.000
91A90GLU-1-0.780-0.85221.4850.0760.0760.0000.0000.0000.000
92A91ARG10.9250.94823.543-0.110-0.1100.0000.0000.0000.000
93A92ASN0-0.0170.01618.706-0.007-0.0070.0000.0000.0000.000
94A93LYS10.9000.96320.461-0.018-0.0180.0000.0000.0000.000
95A94TYR00.0080.00215.152-0.005-0.0050.0000.0000.0000.000
96A95ARG10.9470.95820.3760.0830.0830.0000.0000.0000.000
97A96ALA00.003-0.01219.0610.0010.0010.0000.0000.0000.000
98A97VAL00.0180.02019.386-0.007-0.0070.0000.0000.0000.000
99A98VAL00.0210.01022.0090.0050.0050.0000.0000.0000.000
100A99TYR00.016-0.01424.4600.0090.0090.0000.0000.0000.000
101A100TYR00.0150.00723.151-0.004-0.0040.0000.0000.0000.000
102A101MET00.0290.02325.2330.0060.0060.0000.0000.0000.000
103A102LEU00.0080.01027.5820.0060.0060.0000.0000.0000.000
104A103THR0-0.019-0.01928.1640.0020.0020.0000.0000.0000.000
105A104LYS10.8640.93627.7810.1360.1360.0000.0000.0000.000
106A105HIS0-0.0120.02430.6490.0090.0090.0000.0000.0000.000
107A106PHE0-0.020-0.01333.2820.0050.0050.0000.0000.0000.000
108A107GLY00.0500.04734.0770.0020.0020.0000.0000.0000.000
109A108LYS10.8750.92932.9460.0930.0930.0000.0000.0000.000
110A109GLU-1-0.723-0.86629.699-0.130-0.1300.0000.0000.0000.000
111A110SER0-0.002-0.01430.298-0.012-0.0120.0000.0000.0000.000
112A111VAL0-0.0260.00331.112-0.004-0.0040.0000.0000.0000.000
113A112TYR0-0.044-0.02525.710-0.009-0.0090.0000.0000.0000.000
114A113GLY-1-0.816-0.85428.218-0.226-0.2260.0000.0000.0000.000
115A114HOH0-0.022-0.01118.1130.0030.0030.0000.0000.0000.000
116A115HOH0-0.023-0.01738.523-0.001-0.0010.0000.0000.0000.000
117A116HOH0-0.050-0.03338.094-0.001-0.0010.0000.0000.0000.000
118A117HOH00.019-0.00241.052-0.001-0.0010.0000.0000.0000.000
119A118HOH0-0.015-0.02523.9070.0040.0040.0000.0000.0000.000
120A119HOH0-0.066-0.05518.8840.0130.0130.0000.0000.0000.000
121A120HOH0-0.014-0.00727.2590.0050.0050.0000.0000.0000.000
122A121HOH00.0070.00125.970-0.003-0.0030.0000.0000.0000.000
123A122HOH0-0.031-0.02524.182-0.004-0.0040.0000.0000.0000.000
124A123HOH0-0.035-0.02930.5100.0010.0010.0000.0000.0000.000
125A124HOH00.0130.01234.696-0.003-0.0030.0000.0000.0000.000
126A125HOH0-0.037-0.02234.0840.0010.0010.0000.0000.0000.000
127A126HOH0-0.045-0.04628.884-0.002-0.0020.0000.0000.0000.000
128A127HOH0-0.016-0.01522.5460.0000.0000.0000.0000.0000.000
129A128HOH0-0.041-0.04643.0830.0000.0000.0000.0000.0000.000
130A129HOH0-0.005-0.01321.2410.0050.0050.0000.0000.0000.000
131A130HOH00.0230.02435.6860.0010.0010.0000.0000.0000.000
132A131HOH0-0.027-0.0266.392-0.041-0.0410.0000.0000.0000.000
133A132HOH0-0.032-0.02133.1800.0030.0030.0000.0000.0000.000
134A133HOH0-0.054-0.04917.8730.0130.0130.0000.0000.0000.000
135A134HOH0-0.001-0.00523.9960.0010.0010.0000.0000.0000.000
136A135HOH0-0.038-0.03434.3400.0030.0030.0000.0000.0000.000
137A136HOH0-0.027-0.02230.116-0.002-0.0020.0000.0000.0000.000
138A137HOH0-0.045-0.04131.983-0.003-0.0030.0000.0000.0000.000
139A138HOH00.0260.01822.142-0.012-0.0120.0000.0000.0000.000
140A139HOH0-0.039-0.04340.726-0.001-0.0010.0000.0000.0000.000
141A140HOH00.001-0.00826.935-0.009-0.0090.0000.0000.0000.000
142A141HOH0-0.021-0.01027.304-0.002-0.0020.0000.0000.0000.000
143A143HOH00.0150.01822.016-0.001-0.0010.0000.0000.0000.000
144A144HOH00.0300.02221.981-0.014-0.0140.0000.0000.0000.000
145A146HOH0-0.037-0.0279.3690.0210.0210.0000.0000.0000.000
146A147HOH0-0.044-0.03324.8550.0040.0040.0000.0000.0000.000
147A148HOH00.0190.01641.2400.0000.0000.0000.0000.0000.000
148A149HOH0-0.0030.0047.4920.2170.2170.0000.0000.0000.000
149A150HOH00.0060.0079.2130.0260.0260.0000.0000.0000.000
150A151HOH0-0.038-0.03129.3780.0030.0030.0000.0000.0000.000
151A154HOH0-0.025-0.02314.0360.0230.0230.0000.0000.0000.000
152A157HOH0-0.0060.00041.474-0.001-0.0010.0000.0000.0000.000
153A158HOH00.0130.00426.089-0.003-0.0030.0000.0000.0000.000
154A159HOH0-0.014-0.00516.722-0.019-0.0190.0000.0000.0000.000
155A160HOH00.0440.03440.502-0.003-0.0030.0000.0000.0000.000
156A162HOH0-0.038-0.03029.6890.0020.0020.0000.0000.0000.000
157A164HOH0-0.069-0.05132.8930.0030.0030.0000.0000.0000.000
158A165HOH0-0.030-0.01721.951-0.008-0.0080.0000.0000.0000.000
159A166HOH0-0.036-0.02235.9900.0020.0020.0000.0000.0000.000
160A168HOH0-0.012-0.00135.906-0.001-0.0010.0000.0000.0000.000
161A169HOH0-0.039-0.02525.4740.0060.0060.0000.0000.0000.000
162A170HOH00.0360.01811.402-0.055-0.0550.0000.0000.0000.000
163A171HOH0-0.033-0.02638.0710.0000.0000.0000.0000.0000.000
164A172HOH0-0.035-0.02343.1740.0000.0000.0000.0000.0000.000
165A177HOH0-0.036-0.03219.9950.0100.0100.0000.0000.0000.000
166A178HOH00.010-0.00537.5760.0000.0000.0000.0000.0000.000
167A179HOH0-0.053-0.02823.4520.0060.0060.0000.0000.0000.000
168A180HOH00.0150.00633.512-0.003-0.0030.0000.0000.0000.000
169A181HOH0-0.039-0.02931.6580.0030.0030.0000.0000.0000.000
170A182HOH00.010-0.01415.933-0.025-0.0250.0000.0000.0000.000
171A184HOH00.0310.01829.6080.0020.0020.0000.0000.0000.000
172A185HOH00.0200.00916.762-0.005-0.0050.0000.0000.0000.000
173A188HOH00.0150.02727.525-0.003-0.0030.0000.0000.0000.000
174A190HOH0-0.004-0.00535.742-0.001-0.0010.0000.0000.0000.000
175C132HOH0-0.020-0.01624.9320.0050.0050.0000.0000.0000.000