Manual

About

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: GN9N1

Calculation Name: 3KY7-A-Xray372

Preferred Name:

Target Type:

Ligand Name: cysteinesulfonic acid

ligand 3-letter code: OCS

PDB ID: 3KY7

Chain ID: A

ChEMBL ID:

UniProt ID: Q6GHJ5

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 230
LigandCharge OCS=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2535880.709662
FMO2-HF: Nuclear repulsion 2442144.46324
FMO2-HF: Total energy -93736.246422
FMO2-MP2: Total energy -94006.256468


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-24.869-14.69423.624-11.612-22.188-0.083
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : 0.005
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].
3A3ILE0-0.001-0.0242.113-2.779-0.1094.584-2.432-4.821-0.008
4A4ASP-1-0.756-0.8564.806-1.723-1.649-0.001-0.017-0.0560.000
5A5TYR00.000-0.0247.4230.1740.1740.0000.0000.0000.000
6A6LEU00.0130.02611.048-0.030-0.0300.0000.0000.0000.000
7A7THR00.014-0.02514.5130.0750.0750.0000.0000.0000.000
8A8LEU0-0.055-0.02416.842-0.030-0.0300.0000.0000.0000.000
9A9PHE0-0.020-0.02418.6490.0140.0140.0000.0000.0000.000
10A10PRO00.0110.01116.1000.0090.0090.0000.0000.0000.000
11A11GLU-1-0.813-0.91716.485-0.201-0.2010.0000.0000.0000.000
12A12MET0-0.112-0.05117.4480.0210.0210.0000.0000.0000.000
13A13PHE00.021-0.00611.3450.0250.0250.0000.0000.0000.000
14A14ASP-1-0.899-0.92814.195-0.320-0.3200.0000.0000.0000.000
15A15GLY0-0.036-0.03216.100-0.008-0.0080.0000.0000.0000.000
16A16VAL0-0.007-0.01111.4560.0140.0140.0000.0000.0000.000
17A17LEU00.0260.0219.4130.0060.0060.0000.0000.0000.000
18A18ASN0-0.053-0.02511.429-0.110-0.1100.0000.0000.0000.000
19A19HIS00.017-0.00414.1530.0100.0100.0000.0000.0000.000
20A20SER00.0300.03911.9990.0630.0630.0000.0000.0000.000
21A21ILE0-0.061-0.02411.579-0.053-0.0530.0000.0000.0000.000
22A22MET00.029-0.0076.9770.1070.1070.0000.0000.0000.000
23A23LYS10.9050.9338.7960.3510.3510.0000.0000.0000.000
24A24ARG10.8630.9489.730-0.073-0.0730.0000.0000.0000.000
25A25ALA00.0760.0255.7970.0160.0160.0000.0000.0000.000
26A26GLN00.0310.0197.146-0.209-0.2090.0000.0000.0000.000
27A27GLU-1-0.864-0.9188.715-0.525-0.5250.0000.0000.0000.000
28A28ASN0-0.129-0.0749.1280.0760.0760.0000.0000.0000.000
29A29ASN0-0.034-0.0197.306-0.086-0.0860.0000.0000.0000.000
30A30LYS10.8850.9554.134-1.175-0.820-0.001-0.130-0.2250.000
31A31LEU00.017-0.0071.999-6.454-7.6428.375-3.106-4.082-0.021
32A32GLN0-0.032-0.0143.5751.6302.2420.009-0.142-0.4780.000
33A33ILE00.0120.0124.095-0.528-0.400-0.001-0.031-0.0960.000
34A34ASN0-0.003-0.0036.4950.4330.4330.0000.0000.0000.000
35A35THR00.0050.0029.8340.0280.0280.0000.0000.0000.000
36A36VAL00.0560.02712.287-0.032-0.0320.0000.0000.0000.000
37A37ASN0-0.048-0.03114.8070.0900.0900.0000.0000.0000.000
38A38PHE00.0760.02218.1480.0030.0030.0000.0000.0000.000
39A39ARG10.8860.93419.5670.1840.1840.0000.0000.0000.000
40A40ASP-1-0.888-0.92920.721-0.310-0.3100.0000.0000.0000.000
41A41TYR0-0.057-0.04217.3610.0200.0200.0000.0000.0000.000
42A42ALA0-0.0120.02122.8950.0190.0190.0000.0000.0000.000
43A43ILE0-0.035-0.07026.0570.0000.0000.0000.0000.0000.000
44A44ASN0-0.005-0.00827.4450.0000.0000.0000.0000.0000.000
45A45LYS10.8830.99130.8350.0870.0870.0000.0000.0000.000
46A46HIS00.0430.04331.345-0.003-0.0030.0000.0000.0000.000
47A47ASN00.0410.00828.4520.0080.0080.0000.0000.0000.000
48A48GLN0-0.035-0.02428.161-0.003-0.0030.0000.0000.0000.000
49A49VAL00.0340.00922.912-0.002-0.0020.0000.0000.0000.000
50A50ASP-1-0.868-0.94325.656-0.055-0.0550.0000.0000.0000.000
51A51ASP-1-0.821-0.90628.040-0.078-0.0780.0000.0000.0000.000
52A52TYR0-0.011-0.01031.1320.0060.0060.0000.0000.0000.000
53A53PRO00.0140.03732.755-0.003-0.0030.0000.0000.0000.000
54A54TYR00.0260.00133.2260.0000.0000.0000.0000.0000.000
55A55GLY0-0.048-0.02135.5920.0040.0040.0000.0000.0000.000
56A56GLY0-0.034-0.01337.3550.0030.0030.0000.0000.0000.000
57A57GLY00.010-0.01135.9250.0040.0040.0000.0000.0000.000
58A58GLN0-0.081-0.04736.161-0.002-0.0020.0000.0000.0000.000
59A59GLY00.0200.01932.165-0.001-0.0010.0000.0000.0000.000
60A60MET0-0.071-0.01730.0170.0000.0000.0000.0000.0000.000
61A61VAL0-0.036-0.02727.3850.0080.0080.0000.0000.0000.000
62A62LEU0-0.0020.00920.582-0.011-0.0110.0000.0000.0000.000
63A63LYS10.7970.86525.1950.1020.1020.0000.0000.0000.000
64A64PRO00.014-0.00223.465-0.010-0.0100.0000.0000.0000.000
65A65GLU-1-0.943-0.97622.675-0.139-0.1390.0000.0000.0000.000
66A66PRO0-0.0080.00322.435-0.019-0.0190.0000.0000.0000.000
67A67VAL00.0200.00717.625-0.032-0.0320.0000.0000.0000.000
68A68PHE00.004-0.01318.088-0.027-0.0270.0000.0000.0000.000
69A69ASN0-0.024-0.01119.021-0.024-0.0240.0000.0000.0000.000
70A70ALA00.0030.00316.335-0.031-0.0310.0000.0000.0000.000
71A71MET0-0.041-0.02613.184-0.091-0.0910.0000.0000.0000.000
72A72GLU-1-0.948-0.96714.782-0.378-0.3780.0000.0000.0000.000
73A73ASP-1-0.844-0.89916.402-0.560-0.5600.0000.0000.0000.000
74A74LEU0-0.097-0.03411.423-0.089-0.0890.0000.0000.0000.000
75A75ASP-1-0.968-0.98611.362-0.989-0.9890.0000.0000.0000.000
76A76VAL0-0.046-0.0299.913-0.088-0.0880.0000.0000.0000.000
77A77THR00.0070.01310.4410.0760.0760.0000.0000.0000.000
78A78GLU-1-0.943-0.97811.628-0.137-0.1370.0000.0000.0000.000
79A79GLN0-0.094-0.0489.2020.0630.0630.0000.0000.0000.000
80A80ALA0-0.0220.0067.272-0.102-0.1020.0000.0000.0000.000
81A81ARG10.7520.8376.822-0.260-0.2600.0000.0000.0000.000
82A82VAL00.0430.0398.555-0.058-0.0580.0000.0000.0000.000
83A83ILE00.010-0.0058.2190.1070.1070.0000.0000.0000.000
84A84LEU00.0140.02412.370-0.072-0.0720.0000.0000.0000.000
85A85MET0-0.080-0.03012.4680.0650.0650.0000.0000.0000.000
86A86OCS-1-0.876-0.96116.6910.0570.0570.0000.0000.0000.000
87A87PRO00.0380.01719.9800.0270.0270.0000.0000.0000.000
88A88GLN0-0.065-0.02822.5700.0160.0160.0000.0000.0000.000
89A89GLY00.0450.03819.0660.0050.0050.0000.0000.0000.000
90A90GLU-1-0.909-0.96916.6970.4290.4290.0000.0000.0000.000
91A91PRO0-0.022-0.00717.5660.0260.0260.0000.0000.0000.000
92A92PHE00.0290.0119.5340.0320.0320.0000.0000.0000.000
93A93SER0-0.004-0.01514.266-0.031-0.0310.0000.0000.0000.000
94A94HIS00.0480.01413.3320.1000.1000.0000.0000.0000.000
95A95GLN0-0.027-0.01012.9790.1540.1540.0000.0000.0000.000
96A96LYS10.8740.94711.449-0.516-0.5160.0000.0000.0000.000
97A97ALA00.0340.0139.2100.1740.1740.0000.0000.0000.000
98A98VAL0-0.044-0.0378.1900.4390.4390.0000.0000.0000.000
99A99GLU-1-0.854-0.8968.9420.9720.9720.0000.0000.0000.000
100A100LEU00.0640.0156.053-0.006-0.0060.0000.0000.0000.000
101A101SER0-0.105-0.0324.077-0.1340.4950.043-0.180-0.4930.000
102A102LYS10.8740.9264.775-0.801-0.4830.008-0.044-0.2820.000
103A103ALA00.0100.0294.428-0.447-0.175-0.001-0.071-0.2000.000
104A104ASP-1-0.883-0.9492.424-5.707-2.4922.254-2.256-3.212-0.030
105A105HIS0-0.076-0.0632.581-5.464-2.7421.639-2.008-2.353-0.025
106A106ILE0-0.0260.0003.4230.4031.2680.734-0.232-1.3670.000
107A107VAL00.0380.0225.677-0.339-0.3390.0000.0000.0000.000
108A108PHE00.007-0.0076.3470.2200.2200.0000.0000.0000.000
109A109ILE00.0300.01111.292-0.097-0.0970.0000.0000.0000.000
110A110CYS0-0.063-0.03813.4810.0600.0600.0000.0000.0000.000
111A111GLY00.0170.01915.9210.0240.0240.0000.0000.0000.000
112A112HIS0-0.037-0.01218.9480.0260.0260.0000.0000.0000.000
113A113TYR00.0220.01521.216-0.022-0.0220.0000.0000.0000.000
114A114GLU-1-0.896-0.94025.103-0.002-0.0020.0000.0000.0000.000
115A115GLY00.003-0.00226.7220.0100.0100.0000.0000.0000.000
116A116TYR00.0330.00420.749-0.011-0.0110.0000.0000.0000.000
117A117ASP-1-0.747-0.84124.510-0.047-0.0470.0000.0000.0000.000
118A118GLU-1-0.792-0.90124.0570.0250.0250.0000.0000.0000.000
119A119ARG10.7910.86724.0470.0670.0670.0000.0000.0000.000
120A120ILE0-0.0060.00419.127-0.011-0.0110.0000.0000.0000.000
121A121ARG10.7670.83919.423-0.070-0.0700.0000.0000.0000.000
122A122THR0-0.059-0.02920.0260.0040.0040.0000.0000.0000.000
123A123HIS0-0.093-0.05520.2910.0020.0020.0000.0000.0000.000
124A124LEU0-0.0020.01416.404-0.018-0.0180.0000.0000.0000.000
125A125VAL0-0.039-0.02914.998-0.013-0.0130.0000.0000.0000.000
126A126THR00.004-0.00311.753-0.018-0.0180.0000.0000.0000.000
127A127ASP-1-0.845-0.89711.8340.5670.5670.0000.0000.0000.000
128A128GLU-1-0.775-0.84614.3860.0780.0780.0000.0000.0000.000
129A129ILE0-0.075-0.04811.9700.0560.0560.0000.0000.0000.000
130A130SER00.0350.04116.159-0.034-0.0340.0000.0000.0000.000
131A131MET0-0.030-0.03114.3950.0690.0690.0000.0000.0000.000
132A132GLY0-0.019-0.02318.0280.0200.0200.0000.0000.0000.000
133A133ASP-1-0.950-0.96321.5700.1470.1470.0000.0000.0000.000
134A134TYR0-0.051-0.01019.671-0.019-0.0190.0000.0000.0000.000
135A135VAL00.0140.00223.5700.0070.0070.0000.0000.0000.000
136A136LEU0-0.015-0.01519.248-0.005-0.0050.0000.0000.0000.000
137A137THR0-0.023-0.02323.016-0.003-0.0030.0000.0000.0000.000
138A138GLY00.0280.01220.698-0.017-0.0170.0000.0000.0000.000
139A139GLY00.0590.03617.0700.0300.0300.0000.0000.0000.000
140A140GLU-1-0.813-0.91514.633-0.033-0.0330.0000.0000.0000.000
141A141LEU0-0.008-0.00613.7260.0220.0220.0000.0000.0000.000
142A142PRO00.0160.01013.6910.0410.0410.0000.0000.0000.000
143A143ALA00.1120.05210.7700.0930.0930.0000.0000.0000.000
144A144MET0-0.045-0.0079.2140.0860.0860.0000.0000.0000.000
145A145THR0-0.075-0.0439.5630.0570.0570.0000.0000.0000.000
146A146MET0-0.005-0.0059.0490.0500.0500.0000.0000.0000.000
147A147THR00.0130.0304.2130.0920.199-0.001-0.009-0.0970.000
148A148ASP-1-0.936-0.9565.2680.6960.6960.0000.0000.0000.000
149A149ALA0-0.049-0.0307.4610.1390.1390.0000.0000.0000.000
150A150ILE00.0130.0043.241-0.4120.1240.069-0.114-0.4910.000
151A151VAL00.0680.0292.2710.1380.3281.230-0.249-1.1710.000
152A152ARG10.8610.9584.103-0.619-0.5370.000-0.015-0.0670.000
153A153LEU0-0.048-0.0386.643-0.364-0.3640.0000.0000.0000.000
154A154ILE0-0.0010.0042.387-0.288-1.7004.684-0.576-2.6970.001
155A155PRO0-0.062-0.0226.533-0.599-0.5990.0000.0000.0000.000
156A156GLY00.0060.0118.769-0.159-0.1590.0000.0000.0000.000
157A170SER0-0.007-0.01823.090-0.005-0.0050.0000.0000.0000.000
158A171ASP-1-0.800-0.87725.1180.2180.2180.0000.0000.0000.000
159A172GLY0-0.003-0.01227.834-0.013-0.0130.0000.0000.0000.000
160A173LEU0-0.044-0.01729.579-0.012-0.0120.0000.0000.0000.000
161A174LEU0-0.010-0.00629.0380.0120.0120.0000.0000.0000.000
162A175GLU-1-0.880-0.94725.2440.2120.2120.0000.0000.0000.000
163A176PHE0-0.038-0.01229.670-0.012-0.0120.0000.0000.0000.000
164A177PRO0-0.044-0.01831.2930.0040.0040.0000.0000.0000.000
165A178GLN0-0.009-0.01227.241-0.010-0.0100.0000.0000.0000.000
166A179TYR00.0320.00032.613-0.004-0.0040.0000.0000.0000.000
167A180THR00.0160.00832.3670.0020.0020.0000.0000.0000.000
168A181ARG10.9060.98034.869-0.080-0.0800.0000.0000.0000.000
169A182PRO00.0500.01336.6160.0010.0010.0000.0000.0000.000
170A183ARG10.9060.92840.098-0.052-0.0520.0000.0000.0000.000
171A184GLU-1-0.828-0.89142.1330.0520.0520.0000.0000.0000.000
172A185PHE00.0140.00039.655-0.003-0.0030.0000.0000.0000.000
173A186LYS10.9540.97742.784-0.043-0.0430.0000.0000.0000.000
174A187GLY00.0430.02144.9990.0000.0000.0000.0000.0000.000
175A188LEU0-0.052-0.01940.6980.0020.0020.0000.0000.0000.000
176A189THR00.021-0.00242.5570.0000.0000.0000.0000.0000.000
177A190VAL0-0.053-0.01338.8980.0040.0040.0000.0000.0000.000
178A191PRO0-0.006-0.01039.633-0.003-0.0030.0000.0000.0000.000
179A192ASP-1-0.845-0.92442.2530.0650.0650.0000.0000.0000.000
180A193VAL0-0.016-0.00341.2110.0000.0000.0000.0000.0000.000
181A194LEU0-0.0090.00437.1560.0020.0020.0000.0000.0000.000
182A195LEU0-0.050-0.03040.1140.0010.0010.0000.0000.0000.000
183A196SER0-0.051-0.03942.610-0.003-0.0030.0000.0000.0000.000
184A197GLY00.0160.01842.116-0.002-0.0020.0000.0000.0000.000
185A198ASN0-0.0170.00643.1350.0050.0050.0000.0000.0000.000
186A199HIS00.0840.00538.3320.0050.0050.0000.0000.0000.000
187A200ALA00.0410.04539.8550.0050.0050.0000.0000.0000.000
188A201ASN0-0.005-0.02041.7310.0030.0030.0000.0000.0000.000
189A202ILE0-0.0230.00037.2110.0010.0010.0000.0000.0000.000
190A203ASP-1-0.853-0.92635.8990.1380.1380.0000.0000.0000.000
191A204ALA00.0020.00537.8450.0040.0040.0000.0000.0000.000
192A205TRP00.0390.01537.3160.0030.0030.0000.0000.0000.000
193A206ARG10.8640.92633.967-0.131-0.1310.0000.0000.0000.000
194A207HIS0-0.013-0.01236.0030.0080.0080.0000.0000.0000.000
195A208GLU-1-0.881-0.95637.0310.0970.0970.0000.0000.0000.000
196A209GLN0-0.025-0.00336.6380.0010.0010.0000.0000.0000.000
197A210LYS10.8070.90230.070-0.190-0.1900.0000.0000.0000.000
198A211LEU00.0080.03134.9320.0020.0020.0000.0000.0000.000
199A212ILE00.003-0.00137.503-0.001-0.0010.0000.0000.0000.000
200A213ARG10.8580.92434.566-0.118-0.1180.0000.0000.0000.000
201A214THR00.0190.00333.0050.0040.0040.0000.0000.0000.000
202A215TYR00.0290.01635.085-0.003-0.0030.0000.0000.0000.000
203A216ASN0-0.035-0.02038.435-0.006-0.0060.0000.0000.0000.000
204A217LYS10.9130.95134.100-0.120-0.1200.0000.0000.0000.000
205A218ARG10.8160.87327.685-0.185-0.1850.0000.0000.0000.000
206A219PRO00.0970.04934.0630.0060.0060.0000.0000.0000.000
207A220ASP-1-0.761-0.85031.6580.1740.1740.0000.0000.0000.000
208A221LEU0-0.039-0.03729.0030.0050.0050.0000.0000.0000.000
209A222ILE0-0.039-0.01133.0720.0020.0020.0000.0000.0000.000
210A223GLU-1-0.935-0.96436.4400.1200.1200.0000.0000.0000.000
211A224LYS10.8560.94829.861-0.204-0.2040.0000.0000.0000.000
212A225TYR00.0220.01433.1420.0130.0130.0000.0000.0000.000
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