Manual

About

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

tag_button

FMODB ID: PLLZ9

Calculation Name: 3OT1-B-Xray13

Preferred Name:

Target Type:

Ligand Name: s-oxy cysteine

ligand 3-letter code: CSX

PDB ID: 3OT1

Chain ID: B

ChEMBL ID:

UniProt ID: Q9KPQ8

Base Structure: X-ray

Registration Date: 2018-02-14

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 201
LigandCharge CL-=-1,NA+=1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2114744.635769
FMO2-HF: Nuclear repulsion 2039707.833725
FMO2-HF: Total energy -75036.802044
FMO2-MP2: Total energy -75249.624114


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(B:4:ACE)


Summations of interaction energy for fragment #1(B:4: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.
0.8121.678-0.012-0.381-0.4720
Interaction energy analysis for fragmet #1(B:4:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / q_NPA : -0.010
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].
3B6SER0-0.046-0.0293.8231.0151.881-0.012-0.381-0.4720.000
4B7LYS10.9320.9705.850-0.016-0.0160.0000.0000.0000.000
5B8ARG10.8980.9529.1410.6250.6250.0000.0000.0000.000
6B9ILE0-0.013-0.00811.9410.0660.0660.0000.0000.0000.000
7B10LEU00.0120.01915.350-0.007-0.0070.0000.0000.0000.000
8B11VAL00.007-0.00418.5860.0220.0220.0000.0000.0000.000
9B12PRO0-0.018-0.01121.7620.0000.0000.0000.0000.0000.000
10B13VAL0-0.0030.00224.9180.0070.0070.0000.0000.0000.000
11B14ALA00.0420.00728.105-0.001-0.0010.0000.0000.0000.000
12B15HIS00.0320.01331.726-0.002-0.0020.0000.0000.0000.000
13B16GLY0-0.0020.00035.2160.0030.0030.0000.0000.0000.000
14B17SER00.006-0.01130.3850.0020.0020.0000.0000.0000.000
15B18GLU-1-0.844-0.91831.601-0.047-0.0470.0000.0000.0000.000
16B19GLU-1-0.744-0.85330.370-0.058-0.0580.0000.0000.0000.000
17B20MET0-0.010-0.00329.583-0.004-0.0040.0000.0000.0000.000
18B21GLU-1-0.789-0.91528.333-0.045-0.0450.0000.0000.0000.000
19B22THR0-0.038-0.03425.787-0.006-0.0060.0000.0000.0000.000
20B23VAL0-0.001-0.00524.705-0.010-0.0100.0000.0000.0000.000
21B24ILE0-0.0020.01124.506-0.006-0.0060.0000.0000.0000.000
22B25ILE0-0.016-0.00320.838-0.003-0.0030.0000.0000.0000.000
23B26VAL00.007-0.01120.339-0.011-0.0110.0000.0000.0000.000
24B27ASP-1-0.880-0.92319.662-0.118-0.1180.0000.0000.0000.000
25B28THR00.017-0.01519.280-0.005-0.0050.0000.0000.0000.000
26B29LEU0-0.014-0.01815.812-0.003-0.0030.0000.0000.0000.000
27B30VAL0-0.012-0.00315.123-0.031-0.0310.0000.0000.0000.000
28B31ARG10.7770.86715.8300.0580.0580.0000.0000.0000.000
29B32ALA0-0.022-0.00313.3210.0140.0140.0000.0000.0000.000
30B33GLY0-0.0090.00111.531-0.014-0.0140.0000.0000.0000.000
31B34PHE0-0.036-0.00510.050-0.133-0.1330.0000.0000.0000.000
32B35GLN0-0.040-0.02110.8480.0670.0670.0000.0000.0000.000
33B36VAL00.0010.00013.4870.0100.0100.0000.0000.0000.000
34B37THR00.0210.02316.814-0.005-0.0050.0000.0000.0000.000
35B38MET00.0130.01619.1810.0170.0170.0000.0000.0000.000
36B39ALA00.0510.01422.792-0.005-0.0050.0000.0000.0000.000
37B40ALA00.2110.20124.5980.0090.0090.0000.0000.0000.000
38B41VAL00.2720.19428.359-0.002-0.0020.0000.0000.0000.000
39B42GLY00.1170.14930.4680.0030.0030.0000.0000.0000.000
40B43ASP-1-0.722-0.85532.326-0.074-0.0740.0000.0000.0000.000
41B44LYS10.8740.95433.7950.0620.0620.0000.0000.0000.000
42B45LEU00.0660.03327.7940.0000.0000.0000.0000.0000.000
43B46GLN0-0.044-0.01730.0170.0000.0000.0000.0000.0000.000
44B47VAL0-0.0060.00031.0840.0050.0050.0000.0000.0000.000
45B48GLN0-0.044-0.01533.489-0.001-0.0010.0000.0000.0000.000
46B49GLY00.0520.02634.2590.0010.0010.0000.0000.0000.000
47B50SER0-0.052-0.03734.8310.0040.0040.0000.0000.0000.000
48B51ARG10.8390.89036.6770.0410.0410.0000.0000.0000.000
49B52GLY0-0.0030.00638.0400.0010.0010.0000.0000.0000.000
50B53VAL0-0.001-0.00232.790-0.001-0.0010.0000.0000.0000.000
51B54TRP0-0.009-0.00334.138-0.002-0.0020.0000.0000.0000.000
52B55LEU00.0030.00428.648-0.004-0.0040.0000.0000.0000.000
53B56THR0-0.020-0.01428.0820.0050.0050.0000.0000.0000.000
54B57ALA0-0.029-0.00225.756-0.008-0.0080.0000.0000.0000.000
55B58GLU-1-0.902-0.95220.331-0.243-0.2430.0000.0000.0000.000
56B59GLN0-0.004-0.01720.1290.0040.0040.0000.0000.0000.000
57B60THR00.1770.05625.1590.0090.0090.0000.0000.0000.000
58B61LEU00.2630.11024.247-0.008-0.0080.0000.0000.0000.000
59B62GLU-1-0.199-0.44925.323-0.090-0.0900.0000.0000.0000.000
60B63ALA00.1570.29625.5620.0040.0040.0000.0000.0000.000
61B64CYS0-0.056-0.00121.025-0.010-0.0100.0000.0000.0000.000
62B65SER00.0060.00119.4770.0180.0180.0000.0000.0000.000
63B66ALA00.0480.01618.049-0.024-0.0240.0000.0000.0000.000
64B67GLU-1-0.884-0.95315.431-0.152-0.1520.0000.0000.0000.000
65B68ALA0-0.093-0.02813.830-0.043-0.0430.0000.0000.0000.000
66B69PHE0-0.016-0.02013.136-0.062-0.0620.0000.0000.0000.000
67B70ASP-1-0.831-0.9219.280-0.537-0.5370.0000.0000.0000.000
68B71ALA0-0.0090.00112.1020.0620.0620.0000.0000.0000.000
69B72LEU0-0.0110.01315.399-0.029-0.0290.0000.0000.0000.000
70B73ALA00.004-0.01019.0050.0190.0190.0000.0000.0000.000
71B74LEU0-0.022-0.01821.173-0.007-0.0070.0000.0000.0000.000
72B75PRO00.0210.00324.7630.0100.0100.0000.0000.0000.000
73B76GLY00.0390.04127.3440.0020.0020.0000.0000.0000.000
74B77GLY00.0440.03030.899-0.004-0.0040.0000.0000.0000.000
75B78VAL0-0.005-0.03834.215-0.001-0.0010.0000.0000.0000.000
76B79GLY00.0110.00436.7230.0000.0000.0000.0000.0000.000
77B80GLY00.0300.02333.002-0.001-0.0010.0000.0000.0000.000
78B81ALA00.0240.00532.183-0.002-0.0020.0000.0000.0000.000
79B82GLN0-0.023-0.02733.2210.0000.0000.0000.0000.0000.000
80B83ALA00.0180.01433.7160.0000.0000.0000.0000.0000.000
81B84PHE0-0.054-0.03727.847-0.002-0.0020.0000.0000.0000.000
82B85ALA0-0.029-0.02731.6470.0000.0000.0000.0000.0000.000
83B86ASP-1-0.956-0.96333.896-0.038-0.0380.0000.0000.0000.000
84B87SER00.0040.03130.899-0.002-0.0020.0000.0000.0000.000
85B88THR00.029-0.01331.4640.0000.0000.0000.0000.0000.000
86B89ALA00.0040.00628.0690.0000.0000.0000.0000.0000.000
87B90LEU00.0230.01425.817-0.005-0.0050.0000.0000.0000.000
88B91LEU0-0.004-0.00926.7440.0000.0000.0000.0000.0000.000
89B92ALA00.000-0.00127.5850.0030.0030.0000.0000.0000.000
90B93LEU0-0.0020.00221.1450.0000.0000.0000.0000.0000.000
91B94ILE0-0.010-0.00422.544-0.003-0.0030.0000.0000.0000.000
92B95ASP-1-0.798-0.88423.027-0.030-0.0300.0000.0000.0000.000
93B96ALA0-0.025-0.00821.3400.0050.0050.0000.0000.0000.000
94B97PHE00.026-0.00516.119-0.001-0.0010.0000.0000.0000.000
95B98SER00.0020.00118.5560.0110.0110.0000.0000.0000.000
96B99GLN0-0.071-0.03820.3190.0140.0140.0000.0000.0000.000
97B100GLN0-0.049-0.01416.143-0.010-0.0100.0000.0000.0000.000
98B101GLY0-0.0210.00015.7600.0050.0050.0000.0000.0000.000
99B102LYS10.7970.91212.7190.1900.1900.0000.0000.0000.000
100B103LEU0-0.006-0.00415.4390.0060.0060.0000.0000.0000.000
101B104VAL00.0060.01517.345-0.026-0.0260.0000.0000.0000.000
102B105ALA00.0120.00120.2960.0150.0150.0000.0000.0000.000
103B106ALA0-0.019-0.00422.079-0.010-0.0100.0000.0000.0000.000
104B107ILE0-0.021-0.00325.5980.0090.0090.0000.0000.0000.000
105B108CYS0-0.061-0.03528.225-0.001-0.0010.0000.0000.0000.000
106B109ALA00.0280.00632.0310.0030.0030.0000.0000.0000.000
107B110THR0-0.004-0.01528.1780.0030.0030.0000.0000.0000.000
108B111PRO00.0050.01128.7290.0010.0010.0000.0000.0000.000
109B112ALA00.0020.00930.8930.0030.0030.0000.0000.0000.000
110B113LEU0-0.030-0.03234.5020.0010.0010.0000.0000.0000.000
111B114VAL00.0060.01529.572-0.001-0.0010.0000.0000.0000.000
112B115PHE0-0.004-0.01125.5830.0020.0020.0000.0000.0000.000
113B116ALA00.0300.02331.3380.0020.0020.0000.0000.0000.000
114B117LYS10.8730.95034.7480.0220.0220.0000.0000.0000.000
115B118GLN0-0.005-0.01332.9600.0010.0010.0000.0000.0000.000
116B119GLN0-0.060-0.01033.5990.0020.0020.0000.0000.0000.000
117B120LYS10.8520.91728.3550.0330.0330.0000.0000.0000.000
118B121PHE00.0170.00023.7100.0020.0020.0000.0000.0000.000
119B122VAL00.0820.04828.9720.0030.0030.0000.0000.0000.000
120B123GLY00.002-0.00330.9220.0030.0030.0000.0000.0000.000
121B124ALA0-0.032-0.00627.9240.0050.0050.0000.0000.0000.000
122B125ARG10.8580.93729.396-0.019-0.0190.0000.0000.0000.000
123B126MET00.0500.02828.732-0.001-0.0010.0000.0000.0000.000
124B127THR0-0.012-0.01229.5370.0010.0010.0000.0000.0000.000
125B128CYS0-0.015-0.00731.016-0.002-0.0020.0000.0000.0000.000
126B129HIS00.0700.04732.9320.0030.0030.0000.0000.0000.000
127B130PRO00.018-0.00935.4100.0010.0010.0000.0000.0000.000
128B131ASN0-0.043-0.03038.5280.0030.0030.0000.0000.0000.000
129B132PHE00.0210.00636.794-0.001-0.0010.0000.0000.0000.000
130B133PHE0-0.005-0.00535.5090.0010.0010.0000.0000.0000.000
131B134ASP-1-0.903-0.94038.876-0.010-0.0100.0000.0000.0000.000
132B135HIS0-0.052-0.04137.857-0.002-0.0020.0000.0000.0000.000
133B136ILE0-0.037-0.01534.1060.0000.0000.0000.0000.0000.000
134B137PRO00.0450.03136.2400.0010.0010.0000.0000.0000.000
135B138SER00.0050.00537.8550.0010.0010.0000.0000.0000.000
136B139GLU-1-0.884-0.95237.6430.0070.0070.0000.0000.0000.000
137B140ARG10.7870.87031.804-0.014-0.0140.0000.0000.0000.000
138B141LEU00.0010.02733.5880.0000.0000.0000.0000.0000.000
139B142SER0-0.083-0.05631.3360.0020.0020.0000.0000.0000.000
140B143ARG10.9790.98033.778-0.006-0.0060.0000.0000.0000.000
141B144GLN00.0410.03528.534-0.001-0.0010.0000.0000.0000.000
142B145ARG10.8610.91430.2720.0030.0030.0000.0000.0000.000
143B146VAL00.0530.04424.128-0.006-0.0060.0000.0000.0000.000
144B147CYS0-0.097-0.03427.0030.0070.0070.0000.0000.0000.000
145B148TYR00.0830.03218.688-0.008-0.0080.0000.0000.0000.000
146B149TYR0-0.009-0.00524.1690.0070.0070.0000.0000.0000.000
147B150ALA00.0480.00521.269-0.003-0.0030.0000.0000.0000.000
148B151THR0-0.044-0.01921.4160.0040.0040.0000.0000.0000.000
149B152GLN0-0.024-0.02323.118-0.004-0.0040.0000.0000.0000.000
150B153HIS00.0230.03517.705-0.019-0.0190.0000.0000.0000.000
151B154LEU00.0220.02520.318-0.013-0.0130.0000.0000.0000.000
152B155LEU0-0.021-0.00920.2990.0100.0100.0000.0000.0000.000
153B156THR00.0330.01823.116-0.009-0.0090.0000.0000.0000.000
154B157SER00.019-0.01726.4410.0040.0040.0000.0000.0000.000
155B158GLN0-0.015-0.01628.417-0.004-0.0040.0000.0000.0000.000
156B159GLY00.0410.00430.941-0.001-0.0010.0000.0000.0000.000
157B160PRO00.0530.02530.6330.0000.0000.0000.0000.0000.000
158B161GLY0-0.014-0.00430.566-0.002-0.0020.0000.0000.0000.000
159B162THR0-0.016-0.01528.9240.0030.0030.0000.0000.0000.000
160B163ALA00.0290.01726.6420.0010.0010.0000.0000.0000.000
161B164LEU00.0520.02723.315-0.004-0.0040.0000.0000.0000.000
162B165GLU-1-0.729-0.83923.403-0.007-0.0070.0000.0000.0000.000
163B166PHE0-0.016-0.01523.2240.0060.0060.0000.0000.0000.000
164B167ALA00.0320.01520.3190.0010.0010.0000.0000.0000.000
165B168LEU00.0230.00918.796-0.004-0.0040.0000.0000.0000.000
166B169ALA00.0090.01218.4610.0120.0120.0000.0000.0000.000
167B170MET0-0.034-0.02117.0160.0120.0120.0000.0000.0000.000
168B171ILE0-0.0010.00613.5010.0020.0020.0000.0000.0000.000
169B172ALA0-0.010-0.00213.6590.0250.0250.0000.0000.0000.000
170B173LEU0-0.057-0.02514.6300.0370.0370.0000.0000.0000.000
171B174LEU0-0.061-0.02011.3400.0300.0300.0000.0000.0000.000
172B175ALA0-0.041-0.0349.4580.0460.0460.0000.0000.0000.000
173B176GLY00.0220.03410.3560.0570.0570.0000.0000.0000.000
174B177VAL00.025-0.01012.969-0.039-0.0390.0000.0000.0000.000
175B178GLU-1-0.944-0.96513.9760.1810.1810.0000.0000.0000.000
176B179LEU00.0100.01610.411-0.021-0.0210.0000.0000.0000.000
177B180ALA00.0080.00013.997-0.031-0.0310.0000.0000.0000.000
178B181GLN00.026-0.00616.843-0.023-0.0230.0000.0000.0000.000
179B182HIS0-0.040-0.00915.8300.0050.0050.0000.0000.0000.000
180B183VAL0-0.017-0.01315.832-0.013-0.0130.0000.0000.0000.000
181B184ALA00.013-0.00318.549-0.007-0.0070.0000.0000.0000.000
182B185ALA0-0.038-0.00421.448-0.002-0.0020.0000.0000.0000.000
183B186PRO0-0.054-0.02921.9800.0020.0020.0000.0000.0000.000
184B187MET0-0.0070.00422.495-0.004-0.0040.0000.0000.0000.000
185B188VAL0-0.069-0.02825.8120.0010.0010.0000.0000.0000.000
186B189LEU00.0260.02224.618-0.001-0.0010.0000.0000.0000.000
187B190HIS00.0150.00828.7570.0040.0040.0000.0000.0000.000
188B191PRO00.026-0.00630.2790.0020.0020.0000.0000.0000.000
189B192GLN0-0.012-0.02430.2470.0050.0050.0000.0000.0000.000
190B193GLN0-0.089-0.04428.4090.0010.0010.0000.0000.0000.000
191B194LEU00.0380.02324.078-0.001-0.0010.0000.0000.0000.000
192B195THR0-0.052-0.02026.0140.0060.0060.0000.0000.0000.000
193B196GLU-1-0.921-0.96026.0770.0250.0250.0000.0000.0000.000
194B197LEU0-0.0050.01919.7330.0060.0060.0000.0000.0000.000
195B198SER0-0.048-0.03921.5060.0130.0130.0000.0000.0000.000
196B199GLY00.000-0.00421.6440.0000.0000.0000.0000.0000.000
197B200PHE0-0.042-0.01619.498-0.007-0.0070.0000.0000.0000.000
198B201NME00.0080.01617.4100.0100.0100.0000.0000.0000.000
199B206CL--1-0.900-0.90737.388-0.036-0.0360.0000.0000.0000.000
200B207NA+1-1.258-0.73230.1850.0940.0940.0000.0000.0000.000
201B208CL--1-0.854-0.90925.544-0.050-0.0500.0000.0000.0000.000