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: 8232Y

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 OptAll
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 -2538109.516393
FMO2-HF: Nuclear repulsion 2444372.106907
FMO2-HF: Total energy -93737.409486
FMO2-MP2: Total energy -94007.372358


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.
-26.491-14.6520.992-10.755-22.076-0.075
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 : -0.008 / q_NPA : 0.016
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].
3A3ILE00.003-0.0152.296-2.681-0.0543.705-1.876-4.455-0.007
4A4ASP-1-0.754-0.8574.726-1.885-1.841-0.001-0.015-0.0290.000
5A5TYR0-0.029-0.0337.9390.2230.2230.0000.0000.0000.000
6A6LEU00.0250.03411.020-0.001-0.0010.0000.0000.0000.000
7A7THR00.013-0.02814.3980.0890.0890.0000.0000.0000.000
8A8LEU0-0.035-0.01017.015-0.029-0.0290.0000.0000.0000.000
9A9PHE0-0.007-0.00218.8930.0120.0120.0000.0000.0000.000
10A10PRO00.0320.02016.1850.0080.0080.0000.0000.0000.000
11A11GLU-1-0.824-0.92816.341-0.225-0.2250.0000.0000.0000.000
12A12MET0-0.095-0.04317.3420.0310.0310.0000.0000.0000.000
13A13PHE00.018-0.00511.2740.0260.0260.0000.0000.0000.000
14A14ASP-1-0.888-0.93413.992-0.326-0.3260.0000.0000.0000.000
15A15GLY00.0110.00115.618-0.010-0.0100.0000.0000.0000.000
16A16VAL00.0260.00311.1880.0200.0200.0000.0000.0000.000
17A17LEU00.0150.0239.2450.0240.0240.0000.0000.0000.000
18A18ASN0-0.078-0.03911.638-0.111-0.1110.0000.0000.0000.000
19A19HIS0-0.006-0.01114.2930.0160.0160.0000.0000.0000.000
20A20SER0-0.020-0.00811.7790.0670.0670.0000.0000.0000.000
21A21ILE0-0.027-0.03110.935-0.045-0.0450.0000.0000.0000.000
22A22MET00.0560.0396.5430.0670.0670.0000.0000.0000.000
23A23LYS10.9250.9618.7030.3040.3040.0000.0000.0000.000
24A24ARG10.8650.94010.065-0.125-0.1250.0000.0000.0000.000
25A25ALA00.0400.0225.6410.0650.0650.0000.0000.0000.000
26A26GLN00.0250.0037.080-0.173-0.1730.0000.0000.0000.000
27A27GLU-1-0.871-0.9328.729-0.420-0.4200.0000.0000.0000.000
28A28ASN0-0.122-0.0679.4440.0460.0460.0000.0000.0000.000
29A29ASN0-0.033-0.0167.350-0.073-0.0730.0000.0000.0000.000
30A30LYS10.8550.9314.745-1.190-1.042-0.001-0.032-0.1140.000
31A31LEU00.0030.0082.227-4.494-3.0575.005-2.056-4.386-0.013
32A32GLN0-0.033-0.0073.4151.4662.0840.016-0.117-0.5160.000
33A33ILE00.0140.0033.766-0.969-0.7780.002-0.063-0.1300.000
34A34ASN0-0.0030.0046.3000.4630.4630.0000.0000.0000.000
35A35THR0-0.009-0.0039.7680.0300.0300.0000.0000.0000.000
36A36VAL00.0540.02512.103-0.025-0.0250.0000.0000.0000.000
37A37ASN0-0.028-0.02714.8320.0950.0950.0000.0000.0000.000
38A38PHE00.0620.01717.7840.0080.0080.0000.0000.0000.000
39A39ARG10.8700.91419.1800.2200.2200.0000.0000.0000.000
40A40ASP-1-0.908-0.94320.738-0.335-0.3350.0000.0000.0000.000
41A41TYR0-0.076-0.05217.0160.0220.0220.0000.0000.0000.000
42A42ALA0-0.041-0.01822.5670.0210.0210.0000.0000.0000.000
43A43ILE0-0.074-0.03525.880-0.003-0.0030.0000.0000.0000.000
44A44ASN00.0680.04827.497-0.001-0.0010.0000.0000.0000.000
45A45LYS10.8950.93430.8280.1070.1070.0000.0000.0000.000
46A46HIS00.0560.04030.8430.0020.0020.0000.0000.0000.000
47A47ASN0-0.009-0.00928.3090.0050.0050.0000.0000.0000.000
48A48GLN0-0.003-0.00227.744-0.006-0.0060.0000.0000.0000.000
49A49VAL00.0400.01522.4580.0010.0010.0000.0000.0000.000
50A50ASP-1-0.883-0.95225.317-0.086-0.0860.0000.0000.0000.000
51A51ASP-1-0.818-0.90027.760-0.098-0.0980.0000.0000.0000.000
52A52TYR0-0.004-0.01031.0560.0060.0060.0000.0000.0000.000
53A53PRO00.0060.02532.663-0.004-0.0040.0000.0000.0000.000
54A54TYR00.014-0.00833.1680.0020.0020.0000.0000.0000.000
55A55GLY0-0.050-0.01735.4710.0050.0050.0000.0000.0000.000
56A56GLY0-0.018-0.00937.0370.0030.0030.0000.0000.0000.000
57A57GLY00.012-0.00535.6400.0020.0020.0000.0000.0000.000
58A58GLN0-0.100-0.05635.8370.0000.0000.0000.0000.0000.000
59A59GLY00.0270.01232.5310.0030.0030.0000.0000.0000.000
60A60MET0-0.068-0.01829.7530.0030.0030.0000.0000.0000.000
61A61VAL0-0.028-0.01627.5820.0090.0090.0000.0000.0000.000
62A62LEU0-0.0060.01120.631-0.010-0.0100.0000.0000.0000.000
63A63LYS10.7960.87825.2100.1310.1310.0000.0000.0000.000
64A64PRO00.0070.00623.539-0.013-0.0130.0000.0000.0000.000
65A65GLU-1-0.876-0.94922.684-0.175-0.1750.0000.0000.0000.000
66A66PRO0-0.030-0.01222.546-0.024-0.0240.0000.0000.0000.000
67A67VAL00.0070.00117.580-0.035-0.0350.0000.0000.0000.000
68A68PHE0-0.009-0.01318.095-0.031-0.0310.0000.0000.0000.000
69A69ASN0-0.027-0.02119.098-0.035-0.0350.0000.0000.0000.000
70A70ALA0-0.026-0.00416.465-0.036-0.0360.0000.0000.0000.000
71A71MET0-0.044-0.02313.454-0.079-0.0790.0000.0000.0000.000
72A72GLU-1-0.926-0.96414.675-0.479-0.4790.0000.0000.0000.000
73A73ASP-1-0.860-0.90716.428-0.676-0.6760.0000.0000.0000.000
74A74LEU0-0.069-0.02211.024-0.096-0.0960.0000.0000.0000.000
75A75ASP-1-0.947-0.97410.896-1.268-1.2680.0000.0000.0000.000
76A76VAL0-0.044-0.0269.535-0.136-0.1360.0000.0000.0000.000
77A77THR0-0.031-0.01010.4490.1190.1190.0000.0000.0000.000
78A78GLU-1-0.907-0.95911.295-0.206-0.2060.0000.0000.0000.000
79A79GLN0-0.094-0.0529.247-0.018-0.0180.0000.0000.0000.000
80A80ALA0-0.0110.0207.0990.0080.0080.0000.0000.0000.000
81A81ARG10.7450.8286.669-0.147-0.1470.0000.0000.0000.000
82A82VAL00.0510.0228.377-0.182-0.1820.0000.0000.0000.000
83A83ILE0-0.002-0.0068.1440.1260.1260.0000.0000.0000.000
84A84LEU00.0160.01712.370-0.073-0.0730.0000.0000.0000.000
85A85MET0-0.080-0.01912.5140.0790.0790.0000.0000.0000.000
86A86OCS-1-0.854-0.93516.7200.0260.0260.0000.0000.0000.000
87A87PRO00.024-0.00120.0850.0300.0300.0000.0000.0000.000
88A88GLN0-0.061-0.03322.4340.0150.0150.0000.0000.0000.000
89A89GLY00.0060.01719.0350.0040.0040.0000.0000.0000.000
90A90GLU-1-0.848-0.94216.5020.4480.4480.0000.0000.0000.000
91A91PRO0-0.0210.00117.3400.0190.0190.0000.0000.0000.000
92A92PHE00.0400.0129.2860.0360.0360.0000.0000.0000.000
93A93SER0-0.001-0.00914.006-0.024-0.0240.0000.0000.0000.000
94A94HIS00.000-0.00913.2050.0910.0910.0000.0000.0000.000
95A95GLN0-0.044-0.02412.8540.1510.1510.0000.0000.0000.000
96A96LYS10.8660.94011.238-0.476-0.4760.0000.0000.0000.000
97A97ALA00.0350.0198.8100.1930.1930.0000.0000.0000.000
98A98VAL0-0.028-0.0108.3120.4650.4650.0000.0000.0000.000
99A99GLU-1-0.815-0.86610.1860.7690.7690.0000.0000.0000.000
100A100LEU00.0450.0106.0000.0730.0730.0000.0000.0000.000
101A101SER0-0.087-0.0484.3350.2540.8000.019-0.143-0.4220.000
102A102LYS10.7960.8845.338-1.048-0.905-0.001-0.012-0.1310.000
103A103ALA00.0210.0314.547-0.499-0.277-0.001-0.053-0.1680.000
104A104ASP-1-0.892-0.9552.440-6.159-3.0961.914-2.074-2.904-0.026
105A105HIS0-0.060-0.0422.336-7.307-5.3503.753-3.056-2.654-0.032
106A106ILE0-0.0260.0003.2520.8251.5851.293-0.338-1.7160.000
107A107VAL00.0420.0275.526-0.438-0.4380.0000.0000.0000.000
108A108PHE00.013-0.0116.3950.2660.2660.0000.0000.0000.000
109A109ILE00.0360.01511.366-0.090-0.0900.0000.0000.0000.000
110A110CYS0-0.080-0.03713.3890.0690.0690.0000.0000.0000.000
111A111GLY00.0410.03215.5980.0350.0350.0000.0000.0000.000
112A112HIS0-0.054-0.01819.0320.0220.0220.0000.0000.0000.000
113A113TYR00.0190.00221.203-0.026-0.0260.0000.0000.0000.000
114A114GLU-1-0.901-0.94025.239-0.025-0.0250.0000.0000.0000.000
115A115GLY00.0150.01326.5910.0100.0100.0000.0000.0000.000
116A116TYR00.009-0.01820.495-0.009-0.0090.0000.0000.0000.000
117A117ASP-1-0.752-0.84424.699-0.079-0.0790.0000.0000.0000.000
118A118GLU-1-0.796-0.89423.771-0.008-0.0080.0000.0000.0000.000
119A119ARG10.7990.87823.8890.1010.1010.0000.0000.0000.000
120A120ILE00.0050.01118.798-0.011-0.0110.0000.0000.0000.000
121A121ARG10.7750.82919.193-0.041-0.0410.0000.0000.0000.000
122A122THR0-0.048-0.03619.8740.0070.0070.0000.0000.0000.000
123A123HIS0-0.112-0.05820.1690.0070.0070.0000.0000.0000.000
124A124LEU0-0.0130.00716.221-0.030-0.0300.0000.0000.0000.000
125A125VAL0-0.038-0.01414.660-0.031-0.0310.0000.0000.0000.000
126A126THR0-0.019-0.02111.571-0.018-0.0180.0000.0000.0000.000
127A127ASP-1-0.819-0.87511.7850.5560.5560.0000.0000.0000.000
128A128GLU-1-0.766-0.84414.2420.0340.0340.0000.0000.0000.000
129A129ILE0-0.067-0.03512.0020.0550.0550.0000.0000.0000.000
130A130SER00.0480.03816.149-0.043-0.0430.0000.0000.0000.000
131A131MET0-0.008-0.02014.3360.0710.0710.0000.0000.0000.000
132A132GLY0-0.054-0.02418.0910.0150.0150.0000.0000.0000.000
133A133ASP-1-0.902-0.94421.7230.1360.1360.0000.0000.0000.000
134A134TYR0-0.096-0.04719.756-0.019-0.0190.0000.0000.0000.000
135A135VAL00.0300.01823.3210.0070.0070.0000.0000.0000.000
136A136LEU0-0.015-0.01819.2490.0010.0010.0000.0000.0000.000
137A137THR0-0.023-0.02223.083-0.004-0.0040.0000.0000.0000.000
138A138GLY00.0120.00620.703-0.019-0.0190.0000.0000.0000.000
139A139GLY00.0690.04017.1390.0280.0280.0000.0000.0000.000
140A140GLU-1-0.786-0.89714.439-0.067-0.0670.0000.0000.0000.000
141A141LEU00.0010.00013.6980.0140.0140.0000.0000.0000.000
142A142PRO00.0130.01313.7960.0410.0410.0000.0000.0000.000
143A143ALA00.1030.04710.7870.0910.0910.0000.0000.0000.000
144A144MET0-0.081-0.0169.1080.0730.0730.0000.0000.0000.000
145A145THR0-0.061-0.0459.3680.0690.0690.0000.0000.0000.000
146A146MET0-0.031-0.0128.8490.0460.0460.0000.0000.0000.000
147A147THR00.0390.0133.9580.3090.4580.000-0.017-0.1310.000
148A148ASP-1-0.954-0.9625.0910.5870.623-0.0010.000-0.0350.000
149A149ALA0-0.020-0.0137.2880.1480.1480.0000.0000.0000.000
150A150ILE00.0080.0042.954-0.5160.0780.109-0.121-0.5810.000
151A151VAL00.0510.0142.2910.1270.1601.436-0.246-1.2220.000
152A152ARG10.8550.9334.154-0.725-0.6440.000-0.020-0.0610.000
153A153LEU0-0.058-0.0376.721-0.302-0.3020.0000.0000.0000.000
154A154ILE00.0340.0392.457-0.616-1.4243.745-0.516-2.4210.003
155A155PRO0-0.027-0.0096.579-0.626-0.6260.0000.0000.0000.000
156A156GLY0-0.035-0.0088.238-0.220-0.2200.0000.0000.0000.000
157A170SER00.000-0.01723.173-0.008-0.0080.0000.0000.0000.000
158A171ASP-1-0.814-0.89625.0890.2210.2210.0000.0000.0000.000
159A172GLY00.0110.00528.216-0.010-0.0100.0000.0000.0000.000
160A173LEU0-0.066-0.02829.893-0.012-0.0120.0000.0000.0000.000
161A174LEU00.000-0.00428.9450.0130.0130.0000.0000.0000.000
162A175GLU-1-0.863-0.92125.4560.2140.2140.0000.0000.0000.000
163A176PHE0-0.019-0.00229.768-0.013-0.0130.0000.0000.0000.000
164A177PRO0-0.067-0.03231.5070.0040.0040.0000.0000.0000.000
165A178GLN00.001-0.01027.185-0.011-0.0110.0000.0000.0000.000
166A179TYR00.027-0.00432.210-0.005-0.0050.0000.0000.0000.000
167A180THR00.000-0.00632.5790.0030.0030.0000.0000.0000.000
168A181ARG10.9360.98734.951-0.090-0.0900.0000.0000.0000.000
169A182PRO00.0370.01336.8520.0010.0010.0000.0000.0000.000
170A183ARG10.8500.90640.038-0.057-0.0570.0000.0000.0000.000
171A184GLU-1-0.835-0.88742.2280.0560.0560.0000.0000.0000.000
172A185PHE00.0250.01339.837-0.003-0.0030.0000.0000.0000.000
173A186LYS10.9180.94842.572-0.047-0.0470.0000.0000.0000.000
174A187GLY00.0360.02444.828-0.001-0.0010.0000.0000.0000.000
175A188LEU0-0.035-0.00840.5510.0010.0010.0000.0000.0000.000
176A189THR00.017-0.00542.5220.0010.0010.0000.0000.0000.000
177A190VAL0-0.036-0.01838.7240.0040.0040.0000.0000.0000.000
178A191PRO0-0.008-0.01239.683-0.003-0.0030.0000.0000.0000.000
179A192ASP-1-0.780-0.89741.9510.0710.0710.0000.0000.0000.000
180A193VAL00.0070.00941.4040.0000.0000.0000.0000.0000.000
181A194LEU0-0.0170.00037.1560.0020.0020.0000.0000.0000.000
182A195LEU0-0.041-0.02339.8050.0020.0020.0000.0000.0000.000
183A196SER0-0.065-0.03942.431-0.003-0.0030.0000.0000.0000.000
184A197GLY00.0160.01242.201-0.002-0.0020.0000.0000.0000.000
185A198ASN0-0.0070.00142.7450.0070.0070.0000.0000.0000.000
186A199HIS00.0750.01538.3960.0040.0040.0000.0000.0000.000
187A200ALA00.0360.03839.6150.0050.0050.0000.0000.0000.000
188A201ASN00.011-0.01041.5440.0030.0030.0000.0000.0000.000
189A202ILE0-0.0320.00037.2450.0010.0010.0000.0000.0000.000
190A203ASP-1-0.820-0.90735.5470.1460.1460.0000.0000.0000.000
191A204ALA0-0.025-0.00337.7140.0040.0040.0000.0000.0000.000
192A205TRP00.0400.01437.6090.0040.0040.0000.0000.0000.000
193A206ARG10.8290.90033.586-0.140-0.1400.0000.0000.0000.000
194A207HIS00.0170.00035.7160.0080.0080.0000.0000.0000.000
195A208GLU-1-0.899-0.96037.0190.0990.0990.0000.0000.0000.000
196A209GLN0-0.023-0.00136.6370.0000.0000.0000.0000.0000.000
197A210LYS10.8000.89930.108-0.195-0.1950.0000.0000.0000.000
198A211LEU00.0090.02834.8400.0020.0020.0000.0000.0000.000
199A212ILE00.0120.00537.446-0.001-0.0010.0000.0000.0000.000
200A213ARG10.8490.91034.743-0.119-0.1190.0000.0000.0000.000
201A214THR00.0150.00433.0050.0050.0050.0000.0000.0000.000
202A215TYR00.0400.01534.867-0.003-0.0030.0000.0000.0000.000
203A216ASN0-0.022-0.01038.176-0.006-0.0060.0000.0000.0000.000
204A217LYS10.9080.95533.999-0.121-0.1210.0000.0000.0000.000
205A218ARG10.8320.88727.641-0.184-0.1840.0000.0000.0000.000
206A219PRO00.0610.03633.9100.0060.0060.0000.0000.0000.000
207A220ASP-1-0.780-0.86231.8290.1700.1700.0000.0000.0000.000
208A221LEU0-0.011-0.01829.1530.0060.0060.0000.0000.0000.000
209A222ILE0-0.035-0.01433.1440.0020.0020.0000.0000.0000.000
210A223GLU-1-0.945-0.96836.5890.1200.1200.0000.0000.0000.000
211A224LYS10.8700.94829.650-0.208-0.2080.0000.0000.0000.000
212A225TYR00.0330.02632.9970.0150.0150.0000.0000.0000.000
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