FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 893QY

Calculation Name: 4CS6-A-Xray372

Preferred Name:

Target Type:

Ligand Name: s-mercaptocysteine

ligand 3-letter code: CSS

PDB ID: 4CS6

Chain ID: A

ChEMBL ID:

UniProt ID: Q8ZPX9

Base Structure: X-ray

Registration Date: 2023-09-24

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 260
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3474762.835095
FMO2-HF: Nuclear repulsion 3372707.081828
FMO2-HF: Total energy -102055.753267
FMO2-MP2: Total energy -102353.96952


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:3:LEU)


Summations of interaction energy for fragment #1(A:3:LEU)
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.
-10.618-3.0575.723-4.094-9.191-0.021
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.020
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].
3A5ILE00.0290.0143.787-2.1850.112-0.040-1.112-1.1450.003
4A6PRO00.0060.0076.2590.3730.3730.0000.0000.0000.000
5A7PRO00.0630.0138.936-0.144-0.1440.0000.0000.0000.000
6A8SER0-0.030-0.01012.192-0.080-0.0800.0000.0000.0000.000
7A9ILE00.0600.0358.868-0.027-0.0270.0000.0000.0000.000
8A10GLN0-0.0230.00010.750-0.111-0.1110.0000.0000.0000.000
9A11CYS0-0.002-0.01512.671-0.035-0.0350.0000.0000.0000.000
10A12GLN00.0070.00515.584-0.008-0.0080.0000.0000.0000.000
11A13THR00.028-0.00810.281-0.046-0.0460.0000.0000.0000.000
12A14GLU-1-0.833-0.90013.661-0.133-0.1330.0000.0000.0000.000
13A15ALA0-0.053-0.02515.3880.0040.0040.0000.0000.0000.000
14A16ALA00.0860.04615.9320.0070.0070.0000.0000.0000.000
15A17CYS0-0.048-0.01813.704-0.026-0.0260.0000.0000.0000.000
16A18ARG10.8490.91916.4190.1370.1370.0000.0000.0000.000
17A19LEU00.0050.01519.6760.0120.0120.0000.0000.0000.000
18A20ILE00.0480.01116.8520.0080.0080.0000.0000.0000.000
19A21THR0-0.0110.01718.1160.0020.0020.0000.0000.0000.000
20A22ARG10.7820.90020.6570.1400.1400.0000.0000.0000.000
21A23VAL00.0000.00524.0410.0100.0100.0000.0000.0000.000
22A24THR0-0.037-0.04921.1610.0020.0020.0000.0000.0000.000
23A25GLY0-0.010-0.00823.7000.0080.0080.0000.0000.0000.000
24A26ASP-1-0.935-0.97423.039-0.184-0.1840.0000.0000.0000.000
25A27THR0-0.057-0.01123.419-0.018-0.0180.0000.0000.0000.000
26A28LEU00.0080.00816.980-0.022-0.0220.0000.0000.0000.000
27A29ARG10.9270.96416.5180.3220.3220.0000.0000.0000.000
28A30ALA0-0.031-0.03812.578-0.020-0.0200.0000.0000.0000.000
29A31ILE0-0.010-0.00112.2160.0520.0520.0000.0000.0000.000
30A32HIS0-0.037-0.0247.842-0.035-0.0350.0000.0000.0000.000
31A33LEU00.0130.0196.0970.1600.1600.0000.0000.0000.000
32A34TYR00.038-0.0105.842-0.418-0.4180.0000.0000.0000.000
33A35GLY00.0710.0397.0880.1640.1640.0000.0000.0000.000
34A36SER0-0.008-0.0346.781-0.200-0.2000.0000.0000.0000.000
35A37ALA0-0.073-0.0397.3830.1050.1050.0000.0000.0000.000
36A38VAL0-0.023-0.0102.294-0.886-0.0300.861-0.359-1.3570.001
37A39ALA00.0170.0132.675-2.251-0.6630.726-0.963-1.351-0.014
38A40GLY00.0080.0155.3940.0690.072-0.001-0.001-0.0010.000
39A41GLY0-0.0150.0037.7270.1200.1200.0000.0000.0000.000
40A42LEU0-0.012-0.0129.247-0.077-0.0770.0000.0000.0000.000
41A43LYS10.9060.95211.5590.1640.1640.0000.0000.0000.000
42A44PRO00.016-0.01415.185-0.022-0.0220.0000.0000.0000.000
43A45ASN0-0.016-0.03617.812-0.008-0.0080.0000.0000.0000.000
44A46SER00.0060.02712.6210.0000.0000.0000.0000.0000.000
45A47ASP-1-0.743-0.80514.393-0.295-0.2950.0000.0000.0000.000
46A48ILE0-0.066-0.03011.271-0.062-0.0620.0000.0000.0000.000
47A49ASH0-0.008-0.04810.6430.0260.0260.0000.0000.0000.000
48A50LEU0-0.004-0.01810.350-0.134-0.1340.0000.0000.0000.000
49A51LEU00.0060.01211.5080.0670.0670.0000.0000.0000.000
50A52VAL0-0.007-0.00713.137-0.044-0.0440.0000.0000.0000.000
51A53THR0-0.0030.00714.9140.0290.0290.0000.0000.0000.000
52A54ILE00.0400.01017.2530.0010.0010.0000.0000.0000.000
53A55CSS0-0.083-0.03020.757-0.004-0.0040.0000.0000.0000.000
54A56GLN00.0190.00623.5180.0030.0030.0000.0000.0000.000
55A57PRO00.0030.00125.525-0.011-0.0110.0000.0000.0000.000
56A58LEU0-0.0360.00223.7320.0050.0050.0000.0000.0000.000
57A59THR00.010-0.01727.6770.0100.0100.0000.0000.0000.000
58A60GLU-1-0.898-0.96330.012-0.106-0.1060.0000.0000.0000.000
59A61ALA00.0250.01431.533-0.002-0.0020.0000.0000.0000.000
60A62GLN00.0260.03127.0860.0030.0030.0000.0000.0000.000
61A63ARG10.8480.93426.6880.1600.1600.0000.0000.0000.000
62A64ALA00.0500.02227.414-0.005-0.0050.0000.0000.0000.000
63A65THR0-0.055-0.03727.5770.0040.0040.0000.0000.0000.000
64A66LEU0-0.016-0.02321.856-0.002-0.0020.0000.0000.0000.000
65A67MET0-0.0020.00724.243-0.011-0.0110.0000.0000.0000.000
66A68GLN00.006-0.00625.9300.0030.0030.0000.0000.0000.000
67A69GLU-1-0.826-0.91925.144-0.119-0.1190.0000.0000.0000.000
68A70LEU0-0.032-0.01919.531-0.003-0.0030.0000.0000.0000.000
69A71LEU00.0170.01122.7900.0010.0010.0000.0000.0000.000
70A72ALA0-0.0050.01125.2770.0090.0090.0000.0000.0000.000
71A73LEU0-0.068-0.02519.9820.0130.0130.0000.0000.0000.000
72A74SER00.007-0.01220.567-0.017-0.0170.0000.0000.0000.000
73A75SER0-0.009-0.00621.6770.0170.0170.0000.0000.0000.000
74A76PRO00.0330.01622.029-0.012-0.0120.0000.0000.0000.000
75A77PRO00.0260.00419.7040.0070.0070.0000.0000.0000.000
76A78GLY0-0.011-0.00620.9620.0090.0090.0000.0000.0000.000
77A79ALA0-0.0280.01522.8480.0070.0070.0000.0000.0000.000
78A80SER0-0.005-0.03023.6530.0060.0060.0000.0000.0000.000
79A81ALA00.0000.01221.310-0.006-0.0060.0000.0000.0000.000
80A82GLU-1-0.973-0.99619.4810.0070.0070.0000.0000.0000.000
81A83LYS10.8200.91519.8410.0770.0770.0000.0000.0000.000
82A84ARG10.8310.90814.5490.0830.0830.0000.0000.0000.000
83A85ALA00.0470.03518.189-0.010-0.0100.0000.0000.0000.000
84A86LEU0-0.023-0.01816.345-0.031-0.0310.0000.0000.0000.000
85A87GLU-1-0.898-0.94215.189-0.302-0.3020.0000.0000.0000.000
86A88VAL0-0.061-0.03615.092-0.058-0.0580.0000.0000.0000.000
87A89THR00.0380.03615.9350.0480.0480.0000.0000.0000.000
88A90VAL0-0.024-0.00516.719-0.039-0.0390.0000.0000.0000.000
89A91VAL00.012-0.00616.9840.0230.0230.0000.0000.0000.000
90A92LEU00.0500.01919.766-0.011-0.0110.0000.0000.0000.000
91A93TYR00.0530.00017.7810.0030.0030.0000.0000.0000.000
92A94SER0-0.005-0.01120.848-0.008-0.0080.0000.0000.0000.000
93A95GLN00.0060.01622.0300.0130.0130.0000.0000.0000.000
94A96LEU00.0110.00816.3050.0000.0000.0000.0000.0000.000
95A97VAL0-0.063-0.00118.6890.0000.0000.0000.0000.0000.000
96A98PRO0-0.024-0.02621.6460.0090.0090.0000.0000.0000.000
97A99TRP00.016-0.02117.1140.0070.0070.0000.0000.0000.000
98A100CYS0-0.050-0.01223.1810.0230.0230.0000.0000.0000.000
99A101PHE0-0.059-0.01921.640-0.015-0.0150.0000.0000.0000.000
100A102PRO00.0090.00124.5190.0120.0120.0000.0000.0000.000
101A103PRO00.0230.01020.6400.0090.0090.0000.0000.0000.000
102A104SER0-0.001-0.01323.7560.0080.0080.0000.0000.0000.000
103A105ARG10.7710.87220.6140.1940.1940.0000.0000.0000.000
104A106GLU-1-0.819-0.92522.314-0.167-0.1670.0000.0000.0000.000
105A107MET0-0.040-0.03222.2050.0190.0190.0000.0000.0000.000
106A108GLN00.0360.00518.598-0.010-0.0100.0000.0000.0000.000
107A109PHE00.0300.02119.8380.0210.0210.0000.0000.0000.000
108A110GLY00.1100.03619.851-0.030-0.0300.0000.0000.0000.000
109A111GLU-1-0.767-0.83121.503-0.114-0.1140.0000.0000.0000.000
110A112TRP00.0170.02219.3540.0160.0160.0000.0000.0000.000
111A113LEU00.0320.02024.5890.0070.0070.0000.0000.0000.000
112A114ARG10.7870.87224.7910.1140.1140.0000.0000.0000.000
113A115GLU-1-0.919-0.96628.334-0.070-0.0700.0000.0000.0000.000
114A116ASP-1-0.839-0.92230.137-0.101-0.1010.0000.0000.0000.000
115A117ILE0-0.009-0.02026.0870.0020.0020.0000.0000.0000.000
116A118CYS0-0.108-0.04530.5930.0050.0050.0000.0000.0000.000
117A119GLN0-0.066-0.02533.2270.0080.0080.0000.0000.0000.000
118A120GLY0-0.047-0.01433.4460.0030.0030.0000.0000.0000.000
119A121ILE0-0.049-0.02232.529-0.001-0.0010.0000.0000.0000.000
120A122TYR0-0.015-0.01729.158-0.006-0.0060.0000.0000.0000.000
121A123GLU-1-0.838-0.89126.107-0.166-0.1660.0000.0000.0000.000
122A124PRO0-0.015-0.01428.085-0.009-0.0090.0000.0000.0000.000
123A125ALA00.0040.00226.496-0.008-0.0080.0000.0000.0000.000
124A126GLN0-0.063-0.03625.8310.0130.0130.0000.0000.0000.000
125A127GLN0-0.025-0.01325.452-0.016-0.0160.0000.0000.0000.000
126A128ASP-1-0.735-0.86721.843-0.224-0.2240.0000.0000.0000.000
127A129TRP0-0.001-0.01121.981-0.020-0.0200.0000.0000.0000.000
128A130ASP-1-0.814-0.90118.626-0.265-0.2650.0000.0000.0000.000
129A131MET0-0.052-0.01316.422-0.043-0.0430.0000.0000.0000.000
130A132VAL0-0.019-0.01416.606-0.039-0.0390.0000.0000.0000.000
131A133LEU00.0220.02216.173-0.034-0.0340.0000.0000.0000.000
132A134LEU0-0.0140.00011.820-0.059-0.0590.0000.0000.0000.000
133A135ILE0-0.011-0.02311.874-0.089-0.0890.0000.0000.0000.000
134A136THR0-0.011-0.02511.727-0.064-0.0640.0000.0000.0000.000
135A137GLN00.000-0.0049.249-0.079-0.0790.0000.0000.0000.000
136A138ILE0-0.034-0.0227.286-0.160-0.1600.0000.0000.0000.000
137A139LEU0-0.049-0.0087.187-0.170-0.1700.0000.0000.0000.000
138A140GLU-1-0.849-0.8977.600-0.607-0.6070.0000.0000.0000.000
139A141THR0-0.083-0.0612.500-0.745-0.5481.589-0.293-1.494-0.001
140A142SER0-0.019-0.0123.210-0.5050.1310.070-0.240-0.466-0.001
141A143ILE0-0.0010.0122.256-2.944-1.0922.518-1.107-3.263-0.009
142A144PRO0-0.002-0.0084.2950.2920.4240.000-0.019-0.1140.000
143A145LEU00.0110.0117.5640.0970.0970.0000.0000.0000.000
144A146LYS10.8560.9389.9850.5000.5000.0000.0000.0000.000
145A147GLY00.0450.03412.466-0.020-0.0200.0000.0000.0000.000
146A148GLU-1-0.842-0.93211.418-0.646-0.6460.0000.0000.0000.000
147A149ARG10.8990.9577.1610.6950.6950.0000.0000.0000.000
148A150ALA00.0670.0317.8670.1640.1640.0000.0000.0000.000
149A151GLU-1-0.841-0.9457.248-1.077-1.0770.0000.0000.0000.000
150A152ARG10.8180.93410.6310.5060.5060.0000.0000.0000.000
151A153LEU0-0.058-0.02112.5130.0820.0820.0000.0000.0000.000
152A154PHE00.025-0.00211.4790.0660.0660.0000.0000.0000.000
153A155THR00.0310.01414.839-0.005-0.0050.0000.0000.0000.000
154A156PRO00.0560.04615.604-0.003-0.0030.0000.0000.0000.000
155A157ALA0-0.0130.01217.5410.0220.0220.0000.0000.0000.000
156A158PRO00.016-0.00419.6630.0000.0000.0000.0000.0000.000
157A159ALA00.0780.02621.5990.0020.0020.0000.0000.0000.000
158A160ALA00.005-0.00222.6010.0010.0010.0000.0000.0000.000
159A161GLN00.007-0.00622.9580.0060.0060.0000.0000.0000.000
160A162LEU0-0.0020.01717.7540.0010.0010.0000.0000.0000.000
161A163LEU0-0.014-0.00521.2890.0010.0010.0000.0000.0000.000
162A164LYS10.9170.96024.1670.1440.1440.0000.0000.0000.000
163A165ALA0-0.009-0.01121.1990.0070.0070.0000.0000.0000.000
164A166LEU00.0030.01218.6460.0000.0000.0000.0000.0000.000
165A167ARG10.9000.93422.4050.1270.1270.0000.0000.0000.000
166A168TYR0-0.0140.00925.4350.0140.0140.0000.0000.0000.000
167A169PRO00.0660.01723.7890.0100.0100.0000.0000.0000.000
168A170LEU00.0030.01327.1190.0090.0090.0000.0000.0000.000
169A171ASP-1-0.978-0.98529.473-0.099-0.0990.0000.0000.0000.000
170A172LEU0-0.033-0.01327.8620.0050.0050.0000.0000.0000.000
171A173TRP00.0200.00325.9100.0040.0040.0000.0000.0000.000
172A174GLN0-0.0340.00133.3830.0040.0040.0000.0000.0000.000
173A175SER0-0.063-0.04736.8680.0060.0060.0000.0000.0000.000
174A176THR00.039-0.00536.932-0.002-0.0020.0000.0000.0000.000
175A177ALA0-0.022-0.01837.436-0.001-0.0010.0000.0000.0000.000
176A178ASP-1-0.817-0.87534.548-0.080-0.0800.0000.0000.0000.000
177A179VAL0-0.016-0.01732.267-0.005-0.0050.0000.0000.0000.000
178A180GLN0-0.076-0.03933.1580.0010.0010.0000.0000.0000.000
179A181GLY00.0330.02433.8090.0030.0030.0000.0000.0000.000
180A182ASP-1-0.810-0.89028.126-0.124-0.1240.0000.0000.0000.000
181A183GLU-1-0.879-0.94828.561-0.077-0.0770.0000.0000.0000.000
182A184TYR00.0340.01022.013-0.011-0.0110.0000.0000.0000.000
183A185HIS0-0.041-0.03822.495-0.021-0.0210.0000.0000.0000.000
184A186ILE0-0.0030.02024.063-0.011-0.0110.0000.0000.0000.000
185A187VAL00.0010.00525.248-0.006-0.0060.0000.0000.0000.000
186A188LEU0-0.003-0.00320.408-0.004-0.0040.0000.0000.0000.000
187A189THR0-0.015-0.01621.109-0.022-0.0220.0000.0000.0000.000
188A190LEU0-0.015-0.00522.142-0.010-0.0100.0000.0000.0000.000
189A191ALA0-0.009-0.00121.3310.0000.0000.0000.0000.0000.000
190A192ARG10.8720.93416.9560.1990.1990.0000.0000.0000.000
191A193ILE00.0370.02619.094-0.014-0.0140.0000.0000.0000.000
192A194TRP00.0430.02021.520-0.002-0.0020.0000.0000.0000.000
193A195TYR00.0500.03313.795-0.011-0.0110.0000.0000.0000.000
194A196THR0-0.024-0.01316.1670.0010.0010.0000.0000.0000.000
195A197LEU0-0.059-0.02018.374-0.003-0.0030.0000.0000.0000.000
196A198SER0-0.030-0.03521.4780.0120.0120.0000.0000.0000.000
197A199THR0-0.044-0.04216.958-0.003-0.0030.0000.0000.0000.000
198A200GLY0-0.036-0.00817.376-0.005-0.0050.0000.0000.0000.000
199A201ARG10.8730.9448.1260.4780.4780.0000.0000.0000.000
200A202PHE00.0670.00612.7750.0420.0420.0000.0000.0000.000
201A203THR0-0.092-0.0337.803-0.023-0.0230.0000.0000.0000.000
202A204SER00.0260.01311.1150.0310.0310.0000.0000.0000.000
203A205LYS10.8130.91811.6160.4090.4090.0000.0000.0000.000
204A206ASP-1-0.748-0.85911.015-0.218-0.2180.0000.0000.0000.000
205A207ALA0-0.0050.01112.5420.0410.0410.0000.0000.0000.000
206A208ALA0-0.0040.00314.3420.0310.0310.0000.0000.0000.000
207A209ALA00.0500.01917.5770.0180.0180.0000.0000.0000.000
208A210ASP-1-0.850-0.91817.424-0.023-0.0230.0000.0000.0000.000
209A211TRP0-0.029-0.00917.9300.0080.0080.0000.0000.0000.000
210A212LEU00.0050.01219.8020.0100.0100.0000.0000.0000.000
211A213LEU00.005-0.00922.5180.0090.0090.0000.0000.0000.000
212A214PRO0-0.052-0.01823.4050.0050.0050.0000.0000.0000.000
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214A216LEU0-0.0470.00226.688-0.002-0.0020.0000.0000.0000.000
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