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FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: PGQZ1

Calculation Name: 5C33-A-Xray13

Preferred Name:

Target Type:

Ligand Name: s,s-(2-hydroxyethyl)thiocysteine

ligand 3-letter code: CME

PDB ID: 5C33

Chain ID: A

ChEMBL ID:

UniProt ID: E9Q401

Base Structure: X-ray

Registration Date: 2018-03-01

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 No
Procedure Auto-FMO protocol ver. 1.20181228
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 194
LigandCharge CL-=-1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2113114.93577
FMO2-HF: Nuclear repulsion 2037720.963336
FMO2-HF: Total energy -75393.972434
FMO2-MP2: Total energy -75611.265908


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:651:ACE)


Summations of interaction energy for fragment #1(A:651:ACE)
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.
-0.2481.3722.983-2.623-1.978-0.02
Interaction energy analysis for fragmet #1(A:651:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.009
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].
3A653SER00.0400.0513.8720.5321.546-0.011-0.482-0.521-0.002
4A654SER0-0.032-0.0306.8400.0480.0480.0000.0000.0000.000
5A655MET0-0.042-0.01610.4950.1260.1260.0000.0000.0000.000
6A656ARG10.8800.92913.8250.1990.1990.0000.0000.0000.000
7A657PRO0-0.0290.00117.4010.0180.0180.0000.0000.0000.000
8A658ASN00.0190.00820.920-0.008-0.0080.0000.0000.0000.000
9A659ILE0-0.028-0.01723.4180.0140.0140.0000.0000.0000.000
10A660PHE0-0.005-0.00622.233-0.012-0.0120.0000.0000.0000.000
11A661LEU0-0.027-0.01226.0570.0100.0100.0000.0000.0000.000
12A662GLY00.0470.01128.010-0.006-0.0060.0000.0000.0000.000
13A663VAL0-0.0020.00930.4780.0040.0040.0000.0000.0000.000
14A664SER0-0.031-0.02133.7410.0010.0010.0000.0000.0000.000
15A665GLU-1-0.904-0.95336.457-0.047-0.0470.0000.0000.0000.000
16A666GLY0-0.0160.00839.2430.0030.0030.0000.0000.0000.000
17A667SER0-0.048-0.03040.649-0.001-0.0010.0000.0000.0000.000
18A668ALA00.0530.01337.410-0.003-0.0030.0000.0000.0000.000
19A669GLN0-0.054-0.01638.9970.0000.0000.0000.0000.0000.000
20A670TYR00.005-0.00235.0900.0010.0010.0000.0000.0000.000
21A671LYS10.9830.99134.2920.0620.0620.0000.0000.0000.000
22A672LYS10.9130.97632.0840.0740.0740.0000.0000.0000.000
23A673TRP00.0580.03428.5170.0020.0020.0000.0000.0000.000
24A674TYR0-0.015-0.06027.710-0.008-0.0080.0000.0000.0000.000
25A675TYR0-0.061-0.05519.6810.0000.0000.0000.0000.0000.000
26A676GLU-1-0.692-0.81223.701-0.134-0.1340.0000.0000.0000.000
27A677LEU0-0.011-0.00115.930-0.006-0.0060.0000.0000.0000.000
28A678MET0-0.0120.00420.4040.0140.0140.0000.0000.0000.000
29A679VAL00.0130.00315.816-0.029-0.0290.0000.0000.0000.000
30A680ASP-1-0.788-0.87517.438-0.167-0.1670.0000.0000.0000.000
31A681HIS0-0.070-0.04113.8460.0580.0580.0000.0000.0000.000
32A682THR00.0300.02513.287-0.055-0.0550.0000.0000.0000.000
33A683GLU-1-0.833-0.92811.060-0.290-0.2900.0000.0000.0000.000
34A684PRO0-0.083-0.03814.094-0.011-0.0110.0000.0000.0000.000
35A685PHE00.0210.01812.1360.0160.0160.0000.0000.0000.000
36A686VAL00.0220.01114.107-0.011-0.0110.0000.0000.0000.000
37A687THR0-0.109-0.06014.5250.0250.0250.0000.0000.0000.000
38A688ALA00.005-0.01113.148-0.023-0.0230.0000.0000.0000.000
39A689GLU-1-0.918-0.9519.8420.1080.1080.0000.0000.0000.000
40A690ALA0-0.028-0.0128.483-0.067-0.0670.0000.0000.0000.000
41A691THR0-0.014-0.0017.043-0.061-0.0610.0000.0000.0000.000
42A692HIS0-0.033-0.0306.6840.0280.0280.0000.0000.0000.000
43A693LEU00.0160.0008.603-0.148-0.1480.0000.0000.0000.000
44A694ARG10.8030.90811.3200.6540.6540.0000.0000.0000.000
45A695VAL00.011-0.00313.470-0.043-0.0430.0000.0000.0000.000
46A696GLY00.0210.00316.2260.0300.0300.0000.0000.0000.000
47A697TRP00.0080.01119.0200.0050.0050.0000.0000.0000.000
48A698ALA00.0330.00617.437-0.015-0.0150.0000.0000.0000.000
49A699SER00.0200.01919.5690.0130.0130.0000.0000.0000.000
50A700THR00.008-0.01220.820-0.009-0.0090.0000.0000.0000.000
51A701GLU-1-0.949-0.97822.655-0.082-0.0820.0000.0000.0000.000
52A702GLY0-0.048-0.02119.3500.0060.0060.0000.0000.0000.000
53A703TYR0-0.046-0.01818.399-0.026-0.0260.0000.0000.0000.000
54A704SER0-0.019-0.00516.7740.0090.0090.0000.0000.0000.000
55A705PRO00.0720.05019.1530.0040.0040.0000.0000.0000.000
56A706TYR0-0.049-0.03417.8690.0090.0090.0000.0000.0000.000
57A707PRO0-0.022-0.03323.5540.0000.0000.0000.0000.0000.000
58A708GLY0-0.037-0.02426.937-0.002-0.0020.0000.0000.0000.000
59A709GLY0-0.0040.00928.318-0.001-0.0010.0000.0000.0000.000
60A710GLY0-0.0230.00625.267-0.005-0.0050.0000.0000.0000.000
61A711GLU-1-0.864-0.94622.641-0.073-0.0730.0000.0000.0000.000
62A712GLU-1-0.975-0.98218.359-0.090-0.0900.0000.0000.0000.000
63A713TRP0-0.034-0.01813.764-0.010-0.0100.0000.0000.0000.000
64A714GLY00.0420.01413.9260.0100.0100.0000.0000.0000.000
65A715GLY0-0.066-0.02911.390-0.010-0.0100.0000.0000.0000.000
66A716ASN00.0210.0139.036-0.163-0.1630.0000.0000.0000.000
67A717GLY00.0340.0179.209-0.062-0.0620.0000.0000.0000.000
68A718VAL0-0.016-0.0259.8660.1430.1430.0000.0000.0000.000
69A719GLY00.009-0.00713.404-0.015-0.0150.0000.0000.0000.000
70A720ASP-1-0.880-0.92810.052-0.515-0.5150.0000.0000.0000.000
71A721ASP-1-0.772-0.88813.579-0.230-0.2300.0000.0000.0000.000
72A722LEU0-0.044-0.03216.630-0.007-0.0070.0000.0000.0000.000
73A723PHE00.0100.03118.9000.0160.0160.0000.0000.0000.000
74A724SER0-0.024-0.02016.142-0.024-0.0240.0000.0000.0000.000
75A725TYR00.0350.02318.4220.0080.0080.0000.0000.0000.000
76A726GLY0-0.007-0.00316.297-0.010-0.0100.0000.0000.0000.000
77A727PHE0-0.011-0.00917.3600.0290.0290.0000.0000.0000.000
78A728ASP-1-0.668-0.81314.623-0.339-0.3390.0000.0000.0000.000
79A729GLY00.0210.01216.443-0.002-0.0020.0000.0000.0000.000
80A730LEU0-0.049-0.02818.1130.0330.0330.0000.0000.0000.000
81A731HIS10.8220.88016.7150.2480.2480.0000.0000.0000.000
82A732LEU0-0.057-0.00818.989-0.024-0.0240.0000.0000.0000.000
83A733TRP0-0.030-0.02714.4780.0100.0100.0000.0000.0000.000
84A734SER00.003-0.01317.790-0.002-0.0020.0000.0000.0000.000
85A735GLY00.0110.01818.2840.0170.0170.0000.0000.0000.000
86A736CYS0-0.058-0.01814.6360.0120.0120.0000.0000.0000.000
87A737ILE0-0.031-0.00615.7630.0180.0180.0000.0000.0000.000
88A738ALA0-0.001-0.00217.253-0.016-0.0160.0000.0000.0000.000
89A739ARG10.8640.91519.0880.1500.1500.0000.0000.0000.000
90A740THR0-0.014-0.02521.964-0.020-0.0200.0000.0000.0000.000
91A741VAL0-0.0100.01822.7050.0090.0090.0000.0000.0000.000
92A742SER00.0030.01224.938-0.002-0.0020.0000.0000.0000.000
93A743SER00.0310.00925.786-0.007-0.0070.0000.0000.0000.000
94A744PRO00.0320.01227.8240.0040.0040.0000.0000.0000.000
95A745ASN0-0.022-0.00327.421-0.004-0.0040.0000.0000.0000.000
96A746GLN0-0.0140.00122.9720.0040.0040.0000.0000.0000.000
97A747HIS10.7720.84920.2280.1730.1730.0000.0000.0000.000
98A748LEU00.0270.01814.834-0.001-0.0010.0000.0000.0000.000
99A749LEU0-0.034-0.01415.5180.0230.0230.0000.0000.0000.000
100A750ARG10.9450.97015.8790.1300.1300.0000.0000.0000.000
101A751THR0-0.022-0.02117.660-0.004-0.0040.0000.0000.0000.000
102A752ASP-1-0.891-0.95619.248-0.121-0.1210.0000.0000.0000.000
103A753ASP-1-0.833-0.87219.887-0.182-0.1820.0000.0000.0000.000
104A754VAL0-0.018-0.02821.213-0.014-0.0140.0000.0000.0000.000
105A755ILE0-0.016-0.00418.7540.0110.0110.0000.0000.0000.000
106A756SER0-0.030-0.01322.3360.0020.0020.0000.0000.0000.000
107A757CYS0-0.020-0.00120.717-0.006-0.0060.0000.0000.0000.000
108A758CME0-0.044-0.01324.1880.0110.0110.0000.0000.0000.000
109A759LEU00.0230.02125.859-0.006-0.0060.0000.0000.0000.000
110A760ASP-1-0.815-0.89727.780-0.080-0.0800.0000.0000.0000.000
111A761LEU00.0380.00228.7880.0010.0010.0000.0000.0000.000
112A762SER0-0.166-0.10332.0210.0060.0060.0000.0000.0000.000
113A763ALA0-0.0340.02033.0430.0040.0040.0000.0000.0000.000
114A764PRO00.0110.01230.0350.0050.0050.0000.0000.0000.000
115A765SER00.018-0.01829.235-0.001-0.0010.0000.0000.0000.000
116A766ILE00.0030.01022.917-0.004-0.0040.0000.0000.0000.000
117A767SER0-0.017-0.00826.1890.0010.0010.0000.0000.0000.000
118A768PHE00.0850.02420.650-0.005-0.0050.0000.0000.0000.000
119A769ARG10.8200.89025.2510.1280.1280.0000.0000.0000.000
120A770ILE00.0110.00821.842-0.016-0.0160.0000.0000.0000.000
121A771ASN0-0.001-0.00824.0990.0090.0090.0000.0000.0000.000
122A772GLY00.0210.01126.9120.0110.0110.0000.0000.0000.000
123A773GLN0-0.053-0.02628.7680.0100.0100.0000.0000.0000.000
124A774PRO0-0.0030.00628.365-0.010-0.0100.0000.0000.0000.000
125A775VAL00.0000.00524.1820.0030.0030.0000.0000.0000.000
126A776GLN0-0.060-0.02127.3810.0060.0060.0000.0000.0000.000
127A777GLY00.0550.00827.408-0.001-0.0010.0000.0000.0000.000
128A778MET0-0.005-0.00426.222-0.011-0.0110.0000.0000.0000.000
129A779PHE0-0.0030.01120.2520.0070.0070.0000.0000.0000.000
130A780GLU-1-0.870-0.94826.378-0.085-0.0850.0000.0000.0000.000
131A781ASN0-0.038-0.02128.552-0.001-0.0010.0000.0000.0000.000
132A782PHE0-0.0330.00025.9600.0000.0000.0000.0000.0000.000
133A783ASN00.013-0.00325.7310.0040.0040.0000.0000.0000.000
134A784ILE0-0.023-0.03227.161-0.010-0.0100.0000.0000.0000.000
135A785ASP-1-0.874-0.90727.799-0.076-0.0760.0000.0000.0000.000
136A786GLY00.0190.02226.303-0.010-0.0100.0000.0000.0000.000
137A787LEU0-0.062-0.03525.9780.0020.0020.0000.0000.0000.000
138A788PHE00.0230.00023.387-0.013-0.0130.0000.0000.0000.000
139A789PHE00.0070.01217.2110.0070.0070.0000.0000.0000.000
140A790PRO0-0.020-0.02020.564-0.017-0.0170.0000.0000.0000.000
141A791VAL00.0060.00514.354-0.002-0.0020.0000.0000.0000.000
142A792VAL00.0050.00712.7450.0140.0140.0000.0000.0000.000
143A793SER00.0410.0528.848-0.010-0.0100.0000.0000.0000.000
144A794PHE00.003-0.0188.0960.1760.1760.0000.0000.0000.000
145A795SER00.1150.0694.564-0.434-0.374-0.001-0.043-0.0150.000
146A796ALA00.014-0.0094.5600.4090.555-0.001-0.017-0.1280.000
147A797GLY0-0.0100.0016.0210.1190.1190.0000.0000.0000.000
148A798ILE00.0220.0219.0030.0990.0990.0000.0000.0000.000
149A799LYS10.8630.95011.0140.2510.2510.0000.0000.0000.000
150A800VAL00.0470.01713.6360.0250.0250.0000.0000.0000.000
151A801ARG10.8090.88515.9020.1810.1810.0000.0000.0000.000
152A802PHE00.0120.01316.6790.0050.0050.0000.0000.0000.000
153A803LEU0-0.056-0.01720.7310.0180.0180.0000.0000.0000.000
154A804LEU00.0340.00122.6300.0000.0000.0000.0000.0000.000
155A805GLY00.0620.04926.1020.0080.0080.0000.0000.0000.000
156A806GLY00.015-0.00928.916-0.002-0.0020.0000.0000.0000.000
157A807ARG10.9440.96930.5830.0700.0700.0000.0000.0000.000
158A808HIS0-0.008-0.00925.7670.0100.0100.0000.0000.0000.000
159A809GLY00.005-0.00126.524-0.008-0.0080.0000.0000.0000.000
160A810GLU-1-0.968-0.97227.179-0.087-0.0870.0000.0000.0000.000
161A811PHE0-0.044-0.02327.198-0.006-0.0060.0000.0000.0000.000
162A812LYS10.9250.95926.6250.1240.1240.0000.0000.0000.000
163A813PHE0-0.033-0.00627.3940.0090.0090.0000.0000.0000.000
164A814LEU00.0230.00431.477-0.002-0.0020.0000.0000.0000.000
165A815PRO00.0160.02531.655-0.003-0.0030.0000.0000.0000.000
166A816PRO0-0.0150.00531.4030.0060.0060.0000.0000.0000.000
167A817PRO00.0460.00234.5810.0000.0000.0000.0000.0000.000
168A818GLY0-0.033-0.02136.915-0.001-0.0010.0000.0000.0000.000
169A819TYR0-0.027-0.00930.125-0.003-0.0030.0000.0000.0000.000
170A820ALA00.0350.03133.1520.0030.0030.0000.0000.0000.000
171A821ALA00.009-0.00730.304-0.008-0.0080.0000.0000.0000.000
172A822CYS00.0120.00425.0660.0050.0050.0000.0000.0000.000
173A823TYR0-0.024-0.00328.3870.0060.0060.0000.0000.0000.000
174A824GLU-1-0.961-0.98629.491-0.076-0.0760.0000.0000.0000.000
175A825ALA0-0.013-0.00329.4280.0050.0050.0000.0000.0000.000
176A826VAL0-0.087-0.02428.189-0.002-0.0020.0000.0000.0000.000
177A827LEU00.0620.04829.0710.0070.0070.0000.0000.0000.000
178A828PRO00.009-0.02232.3020.0020.0020.0000.0000.0000.000
179A829LYS10.8910.93830.4310.0570.0570.0000.0000.0000.000
180A830GLU-1-0.854-0.91527.064-0.074-0.0740.0000.0000.0000.000
181A831LYS10.9330.94428.1010.0550.0550.0000.0000.0000.000
182A832LEU00.0070.02724.6630.0020.0020.0000.0000.0000.000
183A833LYS10.8380.91222.3440.0930.0930.0000.0000.0000.000
184A834VAL00.0090.00216.916-0.003-0.0030.0000.0000.0000.000
185A835GLU-1-0.900-0.92716.783-0.154-0.1540.0000.0000.0000.000
186A836HIS00.015-0.0179.181-0.026-0.0260.0000.0000.0000.000
187A837SER0-0.0240.00710.8480.0920.0920.0000.0000.0000.000
188A838ARG11.0020.9837.200-0.091-0.0910.0000.0000.0000.000
189A839GLU-1-0.807-0.8952.601-0.1120.2882.996-2.081-1.314-0.018
190A840TYR0-0.055-0.0436.9020.0390.0390.0000.0000.0000.000
191A841LYS10.9140.9578.583-0.370-0.3700.0000.0000.0000.000
192A842NME00.0610.0417.6740.1230.1230.0000.0000.0000.000
193A901IPA0-0.033-0.0129.9850.0320.0320.0000.0000.0000.000
194A902CL--1-0.929-0.9658.218-0.588-0.5880.0000.0000.0000.000