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: VQ241

Calculation Name: 4XAH-A-Xray372

Preferred Name:

Target Type:

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

ligand 3-letter code: CME

PDB ID: 4XAH

Chain ID: A

ChEMBL ID:

UniProt ID: Q03705

Base Structure: X-ray

Registration Date: 2023-09-20

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 177
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1983798.965774
FMO2-HF: Nuclear repulsion 1911364.958036
FMO2-HF: Total energy -72434.007738
FMO2-MP2: Total energy -72641.038311


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.
-30.485-24.74929.299-13.193-21.838-0.078
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 : -0.061 / q_NPA : -0.032
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].
3A3VAL0-0.008-0.0132.391-0.6230.5592.398-1.129-2.451-0.001
4A4SER0-0.035-0.0154.6590.2280.320-0.001-0.017-0.0740.000
5A5ILE00.0530.0158.1990.1540.1540.0000.0000.0000.000
6A6ILE00.0240.02011.236-0.002-0.0020.0000.0000.0000.000
7A7PRO00.0470.02014.7410.0480.0480.0000.0000.0000.000
8A8GLN00.0000.01217.5930.0150.0150.0000.0000.0000.000
9A9PHE0-0.088-0.05415.9940.0300.0300.0000.0000.0000.000
10A10PRO00.0410.02515.095-0.024-0.0240.0000.0000.0000.000
11A11ASP-1-0.926-0.95614.469-0.056-0.0560.0000.0000.0000.000
12A12ILE0-0.068-0.02511.6010.0340.0340.0000.0000.0000.000
13A13LYS10.9050.9667.418-0.061-0.0610.0000.0000.0000.000
14A14VAL0-0.004-0.0027.3090.1300.1300.0000.0000.0000.000
15A15SER00.0020.0182.305-0.838-0.3601.040-0.564-0.9540.000
16A16LEU0-0.037-0.0193.6280.4100.8920.003-0.100-0.3840.000
17A17ALA00.0500.0272.426-3.956-1.9253.303-2.496-2.838-0.020
18A18LEU00.0120.0113.5040.5790.5980.0270.084-0.1300.000
19A19PHE00.0050.0055.721-0.394-0.3940.0000.0000.0000.000
20A20GLU-1-0.822-0.9168.787-0.409-0.4090.0000.0000.0000.000
21A21GLN0-0.069-0.05711.9290.1360.1360.0000.0000.0000.000
22A22VAL0-0.028-0.02512.3390.0500.0500.0000.0000.0000.000
23A23LYS10.9170.95614.9750.1190.1190.0000.0000.0000.000
24A24ASN0-0.035-0.03215.415-0.024-0.0240.0000.0000.0000.000
25A25ALA00.0720.04616.9000.0230.0230.0000.0000.0000.000
26A26LYS10.8920.93317.8580.0190.0190.0000.0000.0000.000
27A27GLU-1-0.887-0.92718.7920.1780.1780.0000.0000.0000.000
28A28ILE00.0260.02613.5370.0110.0110.0000.0000.0000.000
29A29ARG10.8590.91217.5220.0350.0350.0000.0000.0000.000
30A30SER0-0.106-0.05919.6460.0020.0020.0000.0000.0000.000
31A31LYS10.8870.92819.227-0.179-0.1790.0000.0000.0000.000
32A32MET0-0.0030.02217.0330.0140.0140.0000.0000.0000.000
33A33SER00.003-0.01318.1850.0150.0150.0000.0000.0000.000
34A34GLU-1-0.836-0.89819.8750.1870.1870.0000.0000.0000.000
35A35LEU00.0320.00415.0700.0280.0280.0000.0000.0000.000
36A36SER00.0170.03214.9030.0500.0500.0000.0000.0000.000
37A37THR0-0.051-0.02414.9980.0040.0040.0000.0000.0000.000
38A38SER0-0.062-0.02811.6200.0310.0310.0000.0000.0000.000
39A39PHE00.055-0.0016.8600.0690.0690.0000.0000.0000.000
40A40ALA0-0.0150.01211.067-0.054-0.0540.0000.0000.0000.000
41A41PHE00.029-0.00310.2760.0050.0050.0000.0000.0000.000
42A42ILE0-0.006-0.01111.8990.0140.0140.0000.0000.0000.000
43A43ASP-1-0.759-0.88712.931-0.304-0.3040.0000.0000.0000.000
44A44PRO00.0110.00111.777-0.006-0.0060.0000.0000.0000.000
45A45ARG10.8140.89714.0210.1950.1950.0000.0000.0000.000
46A46LEU0-0.038-0.02116.9300.0180.0180.0000.0000.0000.000
47A47VAL0-0.059-0.02712.2560.0080.0080.0000.0000.0000.000
48A48CYS00.0050.00814.626-0.026-0.0260.0000.0000.0000.000
49A49SER0-0.004-0.01413.736-0.021-0.0210.0000.0000.0000.000
50A50GLY00.0260.00110.939-0.024-0.0240.0000.0000.0000.000
51A51GLU-1-0.854-0.88811.696-0.414-0.4140.0000.0000.0000.000
52A52GLN00.0390.02814.9400.0260.0260.0000.0000.0000.000
53A53MET0-0.0100.0069.9350.0690.0690.0000.0000.0000.000
54A54TYR00.023-0.0127.6560.0500.0500.0000.0000.0000.000
55A55SER0-0.005-0.00113.6730.0810.0810.0000.0000.0000.000
56A56ALA00.0500.02315.4490.0480.0480.0000.0000.0000.000
57A57ILE0-0.033-0.00310.4680.0570.0570.0000.0000.0000.000
58A58TYR0-0.018-0.02814.7510.0490.0490.0000.0000.0000.000
59A59LYS10.8970.94817.2950.2270.2270.0000.0000.0000.000
60A60THR00.003-0.04316.1740.0350.0350.0000.0000.0000.000
61A61LEU0-0.017-0.00813.8630.0340.0340.0000.0000.0000.000
62A62ILE00.0010.00318.1710.0280.0280.0000.0000.0000.000
63A63GLU-1-0.869-0.93721.638-0.095-0.0950.0000.0000.0000.000
64A64VAL0-0.054-0.02919.1040.0190.0190.0000.0000.0000.000
65A65LYS10.8860.96220.8660.0970.0970.0000.0000.0000.000
66A66TYR0-0.038-0.03322.6270.0080.0080.0000.0000.0000.000
67A67ASN0-0.022-0.01725.1990.0150.0150.0000.0000.0000.000
68A68LYS10.8940.95226.0180.0610.0610.0000.0000.0000.000
69A69MET0-0.0330.00720.031-0.010-0.0100.0000.0000.0000.000
70A70ARG10.8960.94323.3940.0800.0800.0000.0000.0000.000
71A71THR0-0.057-0.05820.6560.0140.0140.0000.0000.0000.000
72A72ARG10.9410.95220.610-0.064-0.0640.0000.0000.0000.000
73A73ASN00.0010.01416.6120.0020.0020.0000.0000.0000.000
74A74LEU00.1260.06214.266-0.012-0.0120.0000.0000.0000.000
75A75ASN00.0070.01411.504-0.077-0.0770.0000.0000.0000.000
76A76SER0-0.025-0.04114.035-0.031-0.0310.0000.0000.0000.000
77A77GLU-1-0.750-0.83617.571-0.090-0.0900.0000.0000.0000.000
78A78CYS0-0.0240.00214.258-0.041-0.0410.0000.0000.0000.000
79A79VAL00.0130.00515.364-0.027-0.0270.0000.0000.0000.000
80A80LEU0-0.072-0.05217.237-0.004-0.0040.0000.0000.0000.000
81A81CME0-0.099-0.03518.6150.0030.0030.0000.0000.0000.000
82A82LEU00.0290.03415.081-0.013-0.0130.0000.0000.0000.000
83A83SER0-0.0050.01918.698-0.005-0.0050.0000.0000.0000.000
84A84PRO00.0270.00921.8920.0100.0100.0000.0000.0000.000
85A85THR0-0.112-0.04424.4670.0160.0160.0000.0000.0000.000
86A86SER00.0820.03425.673-0.002-0.0020.0000.0000.0000.000
87A87ASN0-0.0160.00427.2170.0120.0120.0000.0000.0000.000
88A88ILE00.0800.03720.269-0.006-0.0060.0000.0000.0000.000
89A89SER0-0.033-0.02723.212-0.003-0.0030.0000.0000.0000.000
90A90ASP-1-0.782-0.86424.984-0.101-0.1010.0000.0000.0000.000
91A91ALA00.0250.01521.172-0.010-0.0100.0000.0000.0000.000
92A92PHE00.019-0.00416.920-0.014-0.0140.0000.0000.0000.000
93A93LEU0-0.0410.00020.923-0.007-0.0070.0000.0000.0000.000
94A94LYS10.8690.90622.8210.1040.1040.0000.0000.0000.000
95A95PHE00.0370.00717.659-0.009-0.0090.0000.0000.0000.000
96A96GLY00.0240.02616.925-0.027-0.0270.0000.0000.0000.000
97A97ILE0-0.043-0.00914.420-0.015-0.0150.0000.0000.0000.000
98A98LYS10.8050.87917.4620.2000.2000.0000.0000.0000.000
99A99ASP-1-0.790-0.88819.809-0.020-0.0200.0000.0000.0000.000
100A100ASP-1-0.814-0.88721.737-0.132-0.1320.0000.0000.0000.000
101A101SER0-0.0110.01416.522-0.008-0.0080.0000.0000.0000.000
102A102SER00.0310.01917.0750.0290.0290.0000.0000.0000.000
103A103GLN0-0.0050.00412.2700.0170.0170.0000.0000.0000.000
104A104LEU0-0.061-0.0319.3110.0910.0910.0000.0000.0000.000
105A105ILE00.0400.0317.703-0.160-0.1600.0000.0000.0000.000
106A106CYS0-0.054-0.0196.3420.2070.2070.0000.0000.0000.000
107A107LEU00.0240.0145.919-0.002-0.0020.0000.0000.0000.000
108A108LYS10.8750.9406.393-0.344-0.3440.0000.0000.0000.000
109A109PHE00.015-0.0037.180-0.156-0.1560.0000.0000.0000.000
110A110HIS0-0.057-0.0474.8350.1210.1210.0000.0000.0000.000
111A111THR00.018-0.0129.609-0.058-0.0580.0000.0000.0000.000
112A112ASN00.0110.00112.879-0.035-0.0350.0000.0000.0000.000
113A113THR0-0.061-0.0137.6670.0100.0100.0000.0000.0000.000
114A114ASP-1-0.829-0.91010.7290.2060.2060.0000.0000.0000.000
115A115ASP-1-0.932-0.9959.1470.1210.1210.0000.0000.0000.000
116A116VAL0-0.062-0.0122.921-0.3580.0330.129-0.103-0.417-0.001
117A117ASP-1-0.779-0.8735.7271.6571.6570.0000.0000.0000.000
118A118LYS10.8890.9182.205-5.353-4.0671.615-0.510-2.3910.002
119A119GLU-1-0.765-0.8763.8166.5617.4030.122-0.195-0.769-0.003
120A120GLN0-0.0430.0016.699-0.272-0.2720.0000.0000.0000.000
121A121LEU0-0.002-0.0122.261-1.171-0.8792.004-0.433-1.862-0.003
122A122ARG10.8470.8801.994-8.774-7.3494.804-2.354-3.8760.002
123A123THR0-0.012-0.0014.974-1.403-1.3790.002-0.025-0.0010.000
124A124ILE0-0.0040.0068.247-0.404-0.4040.0000.0000.0000.000
125A125MET0-0.015-0.0132.739-1.535-1.2911.587-0.376-1.4540.003
126A126THR0-0.025-0.0227.304-0.505-0.5050.0000.0000.0000.000
127A127SER0-0.033-0.0089.587-0.222-0.2220.0000.0000.0000.000
128A128ILE0-0.044-0.01511.258-0.157-0.1570.0000.0000.0000.000
129A129VAL0-0.043-0.0289.546-0.129-0.1290.0000.0000.0000.000
130A130LYS10.8540.92911.836-0.252-0.2520.0000.0000.0000.000
131A131GLY00.0600.02112.184-0.049-0.0490.0000.0000.0000.000
132A132GLN0-0.033-0.0129.9070.1250.1250.0000.0000.0000.000
133A133GLU-1-0.800-0.8591.785-12.235-15.79612.266-4.899-3.805-0.057
134A134ILE0-0.015-0.0016.1240.2310.2310.0000.0000.0000.000
135A135GLU-1-0.868-0.9263.928-2.921-2.659-0.001-0.027-0.2340.000
136A136PHE0-0.004-0.0063.9410.6700.9370.002-0.048-0.2210.000
137A137ASN0-0.002-0.0235.3480.0440.024-0.001-0.0010.0230.000
138A138ASP-1-0.749-0.8938.743-0.747-0.7470.0000.0000.0000.000
139A139ASP-1-0.846-0.89812.184-0.538-0.5380.0000.0000.0000.000
140A140ASN0-0.006-0.0218.1150.3340.3340.0000.0000.0000.000
141A141LEU0-0.037-0.0119.4210.1010.1010.0000.0000.0000.000
142A142SER0-0.051-0.02812.3670.1230.1230.0000.0000.0000.000
143A143ARG10.7890.88312.4200.7530.7530.0000.0000.0000.000
144A144PHE0-0.037-0.02211.7880.0640.0640.0000.0000.0000.000
145A145TYR0-0.0300.00716.1760.0430.0430.0000.0000.0000.000
146A146ASP-1-0.818-0.91517.799-0.194-0.1940.0000.0000.0000.000
147A147GLU-1-0.785-0.88821.446-0.215-0.2150.0000.0000.0000.000
148A148ALA0-0.023-0.00523.6680.0150.0150.0000.0000.0000.000
149A149LEU00.011-0.00921.2400.0150.0150.0000.0000.0000.000
150A150ILE00.0330.01618.9020.0140.0140.0000.0000.0000.000
151A151ARG10.7590.86523.2230.1930.1930.0000.0000.0000.000
152A152LYS10.8850.95726.7780.1620.1620.0000.0000.0000.000
153A153ILE0-0.040-0.01923.0690.0130.0130.0000.0000.0000.000
154A154TYR0-0.034-0.05019.6410.0000.0000.0000.0000.0000.000
155A155LYS10.8580.94325.8170.1360.1360.0000.0000.0000.000
156A156LEU00.0090.01224.8570.0010.0010.0000.0000.0000.000
157A157SER0-0.012-0.03229.3150.0080.0080.0000.0000.0000.000
158A158ASP-1-0.905-0.95831.976-0.139-0.1390.0000.0000.0000.000
159A159ASP-1-0.874-0.91633.904-0.118-0.1180.0000.0000.0000.000
160A160PHE0-0.029-0.01026.431-0.001-0.0010.0000.0000.0000.000
161A161LYS10.8810.93431.0270.1360.1360.0000.0000.0000.000
162A162PRO0-0.0160.00826.1470.0030.0030.0000.0000.0000.000
163A163GLN00.009-0.01028.0600.0010.0010.0000.0000.0000.000
164A164ASP-1-0.817-0.89623.808-0.299-0.2990.0000.0000.0000.000
165A165VAL00.0430.02518.0500.0090.0090.0000.0000.0000.000
166A166ASN0-0.007-0.01420.002-0.040-0.0400.0000.0000.0000.000
167A167GLY0-0.0020.00221.5950.0060.0060.0000.0000.0000.000
168A168LEU0-0.008-0.01221.1760.0130.0130.0000.0000.0000.000
169A169SER0-0.005-0.04418.381-0.009-0.0090.0000.0000.0000.000
170A170ARG10.9760.99620.3040.2310.2310.0000.0000.0000.000
171A171ALA0-0.021-0.01222.8520.0140.0140.0000.0000.0000.000
172A172LEU0-0.011-0.00519.4550.0160.0160.0000.0000.0000.000
173A173VAL00.0080.00318.7540.0090.0090.0000.0000.0000.000
174A174ASP-1-0.996-0.99121.314-0.178-0.1780.0000.0000.0000.000
175A175ALA0-0.0090.00424.0940.0140.0140.0000.0000.0000.000
176A176ILE0-0.098-0.03418.6030.0140.0140.0000.0000.0000.000
177A177GLN0-0.011-0.00522.1400.0110.0110.0000.0000.0000.000