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: YVQ22

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 OptH
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 -1981890.250123
FMO2-HF: Nuclear repulsion 1909457.087705
FMO2-HF: Total energy -72433.162418
FMO2-MP2: Total energy -72640.153194


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.
-34.449-31.50134.503-13.07-24.374-0.097
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 : -0.063 / q_NPA : -0.030
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].
3A3VAL0-0.030-0.0262.228-0.5970.7712.359-1.092-2.635-0.002
4A4SER0-0.037-0.0154.7470.1390.235-0.001-0.025-0.0690.000
5A5ILE00.0660.0208.3470.1530.1530.0000.0000.0000.000
6A6ILE00.0180.01911.201-0.018-0.0180.0000.0000.0000.000
7A7PRO00.0460.02014.8240.0410.0410.0000.0000.0000.000
8A8GLN00.0060.03417.4990.0090.0090.0000.0000.0000.000
9A9PHE0-0.078-0.05516.0930.0220.0220.0000.0000.0000.000
10A10PRO00.0370.02014.975-0.009-0.0090.0000.0000.0000.000
11A11ASP-1-0.902-0.94014.0660.0280.0280.0000.0000.0000.000
12A12ILE0-0.080-0.03111.7440.0340.0340.0000.0000.0000.000
13A13LYS10.9160.9846.916-0.187-0.1870.0000.0000.0000.000
14A14VAL0-0.002-0.0017.6610.1320.1320.0000.0000.0000.000
15A15SER0-0.0080.0063.051-1.266-0.5180.487-0.351-0.8830.001
16A16LEU0-0.038-0.0203.7410.1980.6600.001-0.101-0.3620.000
17A17ALA00.0540.0332.496-4.724-2.7063.393-2.510-2.901-0.024
18A18LEU00.0130.0103.5020.9410.9420.0350.110-0.1460.000
19A19PHE0-0.0010.0035.995-0.403-0.4030.0000.0000.0000.000
20A20GLU-1-0.860-0.9468.766-0.485-0.4850.0000.0000.0000.000
21A21GLN0-0.039-0.03111.9130.1260.1260.0000.0000.0000.000
22A22VAL0-0.019-0.01812.4670.0480.0480.0000.0000.0000.000
23A23LYS10.9260.95414.9580.1550.1550.0000.0000.0000.000
24A24ASN0-0.020-0.01315.548-0.025-0.0250.0000.0000.0000.000
25A25ALA00.0700.04517.1390.0240.0240.0000.0000.0000.000
26A26LYS10.9350.97218.0950.0400.0400.0000.0000.0000.000
27A27GLU-1-0.917-0.96019.4060.1290.1290.0000.0000.0000.000
28A28ILE00.0250.03113.9320.0140.0140.0000.0000.0000.000
29A29ARG10.8980.94517.6750.0480.0480.0000.0000.0000.000
30A30SER0-0.115-0.06819.5640.0070.0070.0000.0000.0000.000
31A31LYS11.0191.01119.077-0.164-0.1640.0000.0000.0000.000
32A32MET0-0.0060.02016.7390.0170.0170.0000.0000.0000.000
33A33SER00.004-0.01318.0130.0200.0200.0000.0000.0000.000
34A34GLU-1-0.932-0.96719.8720.1690.1690.0000.0000.0000.000
35A35LEU00.025-0.00114.5340.0290.0290.0000.0000.0000.000
36A36SER0-0.0260.01514.9460.0510.0510.0000.0000.0000.000
37A37THR0-0.056-0.03115.4860.0180.0180.0000.0000.0000.000
38A38SER0-0.051-0.02511.8220.0350.0350.0000.0000.0000.000
39A39PHE00.021-0.0186.8140.1180.1180.0000.0000.0000.000
40A40ALA0-0.0120.01210.925-0.083-0.0830.0000.0000.0000.000
41A41PHE00.024-0.00510.6200.0200.0200.0000.0000.0000.000
42A42ILE00.003-0.00711.4230.0140.0140.0000.0000.0000.000
43A43ASP-1-0.788-0.90512.928-0.335-0.3350.0000.0000.0000.000
44A44PRO00.005-0.00311.7730.0010.0010.0000.0000.0000.000
45A45ARG10.8920.95714.0200.2140.2140.0000.0000.0000.000
46A46LEU0-0.032-0.01516.9400.0210.0210.0000.0000.0000.000
47A47VAL0-0.058-0.02812.2610.0150.0150.0000.0000.0000.000
48A48CYS0-0.032-0.00314.623-0.039-0.0390.0000.0000.0000.000
49A49SER00.020-0.00513.710-0.026-0.0260.0000.0000.0000.000
50A50GLY00.0440.01010.931-0.018-0.0180.0000.0000.0000.000
51A51GLU-1-0.869-0.89611.690-0.356-0.3560.0000.0000.0000.000
52A52GLN00.0470.03314.9310.0250.0250.0000.0000.0000.000
53A53MET0-0.0120.0009.9780.0720.0720.0000.0000.0000.000
54A54TYR00.018-0.0147.7430.0370.0370.0000.0000.0000.000
55A55SER0-0.0050.00213.6610.0840.0840.0000.0000.0000.000
56A56ALA00.0460.02215.3860.0470.0470.0000.0000.0000.000
57A57ILE0-0.029-0.00710.4700.0560.0560.0000.0000.0000.000
58A58TYR0-0.031-0.06014.9380.0510.0510.0000.0000.0000.000
59A59LYS10.9090.95117.7820.1800.1800.0000.0000.0000.000
60A60THR00.008-0.02616.7380.0330.0330.0000.0000.0000.000
61A61LEU0-0.023-0.01214.1150.0290.0290.0000.0000.0000.000
62A62ILE00.0070.00818.5040.0220.0220.0000.0000.0000.000
63A63GLU-1-0.907-0.97122.030-0.067-0.0670.0000.0000.0000.000
64A64VAL0-0.031-0.02419.5160.0150.0150.0000.0000.0000.000
65A65LYS10.8750.95921.0150.0480.0480.0000.0000.0000.000
66A66TYR0-0.040-0.03322.7860.0050.0050.0000.0000.0000.000
67A67ASN0-0.040-0.01325.4670.0070.0070.0000.0000.0000.000
68A68LYS10.9360.97126.3240.0310.0310.0000.0000.0000.000
69A69MET0-0.0150.01920.318-0.005-0.0050.0000.0000.0000.000
70A70ARG10.9210.95923.7730.0470.0470.0000.0000.0000.000
71A71THR0-0.067-0.04921.1400.0110.0110.0000.0000.0000.000
72A72ARG10.9480.95521.335-0.077-0.0770.0000.0000.0000.000
73A73ASN00.0080.00516.9340.0100.0100.0000.0000.0000.000
74A74LEU00.1250.06214.656-0.014-0.0140.0000.0000.0000.000
75A75ASN00.0170.02711.922-0.051-0.0510.0000.0000.0000.000
76A76SER0-0.012-0.02314.514-0.045-0.0450.0000.0000.0000.000
77A77GLU-1-0.758-0.86317.678-0.051-0.0510.0000.0000.0000.000
78A78CYS00.0040.01412.839-0.038-0.0380.0000.0000.0000.000
79A79VAL0-0.010-0.00115.181-0.034-0.0340.0000.0000.0000.000
80A80LEU0-0.065-0.04817.122-0.012-0.0120.0000.0000.0000.000
81A81CME0-0.093-0.01618.832-0.002-0.0020.0000.0000.0000.000
82A82LEU00.0210.03514.932-0.015-0.0150.0000.0000.0000.000
83A83SER0-0.0050.01518.597-0.011-0.0110.0000.0000.0000.000
84A84PRO00.0330.01221.7570.0110.0110.0000.0000.0000.000
85A85THR0-0.083-0.01224.4010.0160.0160.0000.0000.0000.000
86A86SER00.0550.01825.5720.0000.0000.0000.0000.0000.000
87A87ASN0-0.019-0.00927.0980.0100.0100.0000.0000.0000.000
88A88ILE00.0610.03120.118-0.007-0.0070.0000.0000.0000.000
89A89SER0-0.048-0.03423.055-0.003-0.0030.0000.0000.0000.000
90A90ASP-1-0.790-0.89924.787-0.092-0.0920.0000.0000.0000.000
91A91ALA00.0220.01420.997-0.011-0.0110.0000.0000.0000.000
92A92PHE00.009-0.00316.807-0.015-0.0150.0000.0000.0000.000
93A93LEU0-0.037-0.00120.685-0.010-0.0100.0000.0000.0000.000
94A94LYS10.8590.91422.6400.0950.0950.0000.0000.0000.000
95A95PHE00.0450.01217.439-0.012-0.0120.0000.0000.0000.000
96A96GLY00.0190.02716.676-0.027-0.0270.0000.0000.0000.000
97A97ILE0-0.046-0.01514.372-0.018-0.0180.0000.0000.0000.000
98A98LYS10.8070.87517.2000.2030.2030.0000.0000.0000.000
99A99ASP-1-0.841-0.94319.843-0.042-0.0420.0000.0000.0000.000
100A100ASP-1-0.871-0.93021.983-0.145-0.1450.0000.0000.0000.000
101A101SER0-0.0130.01116.545-0.006-0.0060.0000.0000.0000.000
102A102SER00.0350.01917.0800.0250.0250.0000.0000.0000.000
103A103GLN0-0.0140.00212.2440.0100.0100.0000.0000.0000.000
104A104LEU0-0.063-0.0319.3280.1080.1080.0000.0000.0000.000
105A105ILE00.0500.0377.685-0.198-0.1980.0000.0000.0000.000
106A106CYS0-0.048-0.0166.1430.2340.2340.0000.0000.0000.000
107A107LEU00.0190.0115.7150.0530.0530.0000.0000.0000.000
108A108LYS10.9060.9546.852-0.581-0.5810.0000.0000.0000.000
109A109PHE00.014-0.0027.610-0.045-0.0450.0000.0000.0000.000
110A110HIS0-0.044-0.0364.984-0.100-0.1000.0000.0000.0000.000
111A111THR00.011-0.0109.654-0.052-0.0520.0000.0000.0000.000
112A112ASN00.0130.00013.111-0.035-0.0350.0000.0000.0000.000
113A113THR0-0.082-0.0308.1390.0110.0110.0000.0000.0000.000
114A114ASP-1-0.838-0.91210.9220.2270.2270.0000.0000.0000.000
115A115ASP-1-0.908-0.9909.1540.2630.2630.0000.0000.0000.000
116A116VAL0-0.082-0.0302.971-0.429-0.0050.230-0.112-0.541-0.001
117A117ASP-1-0.781-0.8855.4811.1181.1180.0000.0000.0000.000
118A118LYS10.9310.9362.061-4.920-7.1379.231-2.162-4.8520.002
119A119GLU-1-0.801-0.9033.0305.5164.630-0.0091.485-0.590-0.002
120A120GLN0-0.0470.0216.135-0.099-0.0990.0000.0000.0000.000
121A121LEU0-0.019-0.0172.159-0.639-1.1373.766-0.694-2.573-0.005
122A122ARG10.9020.9452.453-8.434-5.8341.116-1.284-2.4300.006
123A123THR0-0.012-0.0075.306-1.106-1.0880.000-0.017-0.0020.000
124A124ILE0-0.0060.0008.202-0.304-0.3040.0000.0000.0000.000
125A125MET0-0.016-0.0162.781-1.270-0.5430.854-0.292-1.2880.001
126A126THR0-0.025-0.0287.311-0.435-0.4350.0000.0000.0000.000
127A127SER0-0.045-0.0109.625-0.186-0.1860.0000.0000.0000.000
128A128ILE0-0.069-0.02911.217-0.123-0.1230.0000.0000.0000.000
129A129VAL0-0.037-0.0219.774-0.107-0.1070.0000.0000.0000.000
130A130LYS10.8980.95711.945-0.161-0.1610.0000.0000.0000.000
131A131GLY00.0600.01912.197-0.034-0.0340.0000.0000.0000.000
132A132GLN0-0.036-0.0149.8890.1240.1240.0000.0000.0000.000
133A133GLU-1-0.815-0.8941.784-15.535-17.93613.041-5.953-4.687-0.073
134A134ILE0-0.0140.0006.0720.2980.2980.0000.0000.0000.000
135A135GLU-1-0.900-0.9563.906-3.001-2.757-0.001-0.025-0.2180.000
136A136PHE0-0.012-0.0133.9520.6990.9630.002-0.046-0.2200.000
137A137ASN00.0240.0085.3490.0470.027-0.001-0.0010.0230.000
138A138ASP-1-0.742-0.8878.743-0.725-0.7250.0000.0000.0000.000
139A139ASP-1-0.906-0.94111.960-0.575-0.5750.0000.0000.0000.000
140A140ASN0-0.067-0.0498.1510.3500.3500.0000.0000.0000.000
141A141LEU0-0.041-0.0159.4160.1020.1020.0000.0000.0000.000
142A142SER0-0.043-0.02712.3670.1260.1260.0000.0000.0000.000
143A143ARG10.8990.95313.2140.7080.7080.0000.0000.0000.000
144A144PHE0-0.031-0.01912.0560.0590.0590.0000.0000.0000.000
145A145TYR0-0.0380.00816.1780.0450.0450.0000.0000.0000.000
146A146ASP-1-0.821-0.92517.798-0.197-0.1970.0000.0000.0000.000
147A147GLU-1-0.804-0.90221.445-0.205-0.2050.0000.0000.0000.000
148A148ALA0-0.0130.00423.6660.0170.0170.0000.0000.0000.000
149A149LEU00.0280.00521.4480.0170.0170.0000.0000.0000.000
150A150ILE00.0350.02118.9890.0160.0160.0000.0000.0000.000
151A151ARG10.7670.87123.2190.1870.1870.0000.0000.0000.000
152A152LYS10.8570.93626.7730.1620.1620.0000.0000.0000.000
153A153ILE0-0.033-0.01322.9250.0140.0140.0000.0000.0000.000
154A154TYR0-0.029-0.04219.6410.0000.0000.0000.0000.0000.000
155A155LYS10.8600.94725.8100.1200.1200.0000.0000.0000.000
156A156LEU00.0000.00624.8670.0020.0020.0000.0000.0000.000
157A157SER00.0220.00729.3090.0060.0060.0000.0000.0000.000
158A158ASP-1-0.893-0.96031.971-0.126-0.1260.0000.0000.0000.000
159A159ASP-1-0.945-0.96733.900-0.106-0.1060.0000.0000.0000.000
160A160PHE0-0.067-0.02726.443-0.002-0.0020.0000.0000.0000.000
161A161LYS10.9560.97231.0430.1260.1260.0000.0000.0000.000
162A162PRO0-0.0210.00126.1850.0030.0030.0000.0000.0000.000
163A163GLN00.011-0.00628.065-0.001-0.0010.0000.0000.0000.000
164A164ASP-1-0.860-0.92323.626-0.268-0.2680.0000.0000.0000.000
165A165VAL00.0370.01617.9980.0100.0100.0000.0000.0000.000
166A166ASN00.0490.02419.911-0.037-0.0370.0000.0000.0000.000
167A167GLY0-0.0090.00121.5920.0080.0080.0000.0000.0000.000
168A168LEU0-0.014-0.01221.1930.0140.0140.0000.0000.0000.000
169A169SER00.007-0.04418.435-0.005-0.0050.0000.0000.0000.000
170A170ARG10.9780.99320.2980.2100.2100.0000.0000.0000.000
171A171ALA0-0.017-0.01122.8450.0150.0150.0000.0000.0000.000
172A172LEU0-0.016-0.00619.4610.0140.0140.0000.0000.0000.000
173A173VAL0-0.0010.00518.8190.0100.0100.0000.0000.0000.000
174A174ASP-1-0.981-0.99221.305-0.151-0.1510.0000.0000.0000.000
175A175ALA0-0.0130.00724.0500.0140.0140.0000.0000.0000.000
176A176ILE0-0.089-0.03018.5470.0140.0140.0000.0000.0000.000
177A177GLN0-0.035-0.02322.1570.0110.0110.0000.0000.0000.000