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: PJ89P

Calculation Name: 4EKF-A-Xray13

Preferred Name:

Target Type:

Ligand Name: 3-sulfinoalanine

ligand 3-letter code: CSD

PDB ID: 4EKF

Chain ID: A

ChEMBL ID:

UniProt ID: P03252

Base Structure: X-ray

Registration Date: 2017-11-22

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water No
Procedure Auto-FMO protocol ver. 1.20171117
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 199
LigandResidueName
LigandFragmentNumber 0
LigandCharge CSD=-1,NA+=1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -2341546.677945
FMO2-HF: Nuclear repulsion 2260871.87727
FMO2-HF: Total energy -80674.800674
FMO2-MP2: Total energy -80902.806059


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.
18.87622.04319.315-7.67-14.811-0.059
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 : 1 / q_Mulliken : 0.819 / q_NPA : 0.913
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].
3A3SER0-0.011-0.0193.458-3.224-1.8210.012-0.436-0.9790.002
4A4SER00.0280.0126.4651.7881.7880.0000.0000.0000.000
5A5GLU-1-0.787-0.9068.082-19.616-19.6160.0000.0000.0000.000
6A6GLN00.003-0.00211.344-0.260-0.2600.0000.0000.0000.000
7A7GLU-1-0.826-0.8857.903-35.961-35.9610.0000.0000.0000.000
8A8LEU00.0200.00210.3662.0682.0680.0000.0000.0000.000
9A9LYS10.8670.93713.04520.30120.3010.0000.0000.0000.000
10A10ALA0-0.0180.00314.6731.3731.3730.0000.0000.0000.000
11A11ILE00.0300.01412.4191.1381.1380.0000.0000.0000.000
12A12VAL00.0430.00916.3721.1801.1800.0000.0000.0000.000
13A13LYS10.9170.96018.78014.49214.4920.0000.0000.0000.000
14A14ASP-1-0.823-0.90118.798-15.637-15.6370.0000.0000.0000.000
15A15LEU0-0.088-0.02918.1040.6790.6790.0000.0000.0000.000
16A16GLY00.0370.02322.0680.5120.5120.0000.0000.0000.000
17A17CYS0-0.021-0.01822.2640.3260.3260.0000.0000.0000.000
18A18GLY0-0.026-0.00823.9390.1310.1310.0000.0000.0000.000
19A19PRO0-0.003-0.00624.7850.0320.0320.0000.0000.0000.000
20A20TYR00.0100.00726.2790.4450.4450.0000.0000.0000.000
21A21PHE0-0.023-0.01317.891-0.193-0.1930.0000.0000.0000.000
22A22LEU0-0.004-0.01223.3780.1910.1910.0000.0000.0000.000
23A23GLY00.0070.01320.3320.1230.1230.0000.0000.0000.000
24A24THR0-0.014-0.01614.858-0.100-0.1000.0000.0000.0000.000
25A25TYR0-0.044-0.01816.8040.7140.7140.0000.0000.0000.000
26A26ASP-1-0.771-0.87414.328-22.063-22.0630.0000.0000.0000.000
27A27LYS10.8240.93415.13819.39419.3940.0000.0000.0000.000
28A28ARG10.9630.97517.10012.92112.9210.0000.0000.0000.000
29A29PHE0-0.006-0.02519.944-0.481-0.4810.0000.0000.0000.000
30A30PRO00.0430.04921.7020.2000.2000.0000.0000.0000.000
31A31GLY00.0290.02924.1730.3440.3440.0000.0000.0000.000
32A32PHE0-0.032-0.02827.4910.3510.3510.0000.0000.0000.000
33A33VAL00.0680.04828.014-0.381-0.3810.0000.0000.0000.000
34A34SER00.0140.01330.4010.3700.3700.0000.0000.0000.000
35A35PRO00.010-0.01033.711-0.171-0.1710.0000.0000.0000.000
36A36HIS00.0370.00835.9340.0630.0630.0000.0000.0000.000
37A37LYS10.9290.96132.1009.7949.7940.0000.0000.0000.000
38A38LEU00.0090.02029.489-0.072-0.0720.0000.0000.0000.000
39A39ALA0-0.022-0.00526.778-0.035-0.0350.0000.0000.0000.000
40A40CYS0-0.0230.00322.437-0.068-0.0680.0000.0000.0000.000
41A41ALA00.0040.01520.2410.0900.0900.0000.0000.0000.000
42A42ILE0-0.013-0.00113.710-0.117-0.1170.0000.0000.0000.000
43A43VAL00.0100.00415.6900.1840.1840.0000.0000.0000.000
44A44ASN00.0110.0078.6720.0270.0270.0000.0000.0000.000
45A45THR00.004-0.02312.1880.5440.5440.0000.0000.0000.000
46A46ALA00.0050.0149.9870.9180.9180.0000.0000.0000.000
47A47GLY0-0.020-0.00112.0691.1541.1540.0000.0000.0000.000
48A48ARG10.8280.86211.23021.85121.8510.0000.0000.0000.000
49A49GLU-1-0.842-0.92311.032-21.162-21.1620.0000.0000.0000.000
50A50THR0-0.0420.0057.415-1.231-1.2310.0000.0000.0000.000
51A51GLY00.0240.0184.860-2.673-2.6730.0000.0000.0000.000
52A52GLY00.012-0.0023.8990.4650.681-0.001-0.050-0.1650.000
53A53VAL00.0130.0173.064-0.959-0.0910.097-0.187-0.7780.000
54A54HIS10.8490.9145.48931.00831.0080.0000.0000.0000.000
55A55TRP0-0.049-0.0067.4804.0064.0060.0000.0000.0000.000
56A56MET00.0400.01811.0730.6310.6310.0000.0000.0000.000
57A57ALA0-0.022-0.01214.731-0.237-0.2370.0000.0000.0000.000
58A58PHE00.0010.00217.6920.6530.6530.0000.0000.0000.000
59A59ALA00.0320.00121.137-0.189-0.1890.0000.0000.0000.000
60A60TRP00.0060.00424.4020.2740.2740.0000.0000.0000.000
61A61ASN00.0500.01128.0620.2410.2410.0000.0000.0000.000
62A62PRO0-0.0030.00931.2450.1730.1730.0000.0000.0000.000
63A63ARG10.9620.97434.3328.3558.3550.0000.0000.0000.000
64A64SER0-0.016-0.01532.7220.2140.2140.0000.0000.0000.000
65A65LYS10.9450.99434.1198.3608.3600.0000.0000.0000.000
66A66THR00.0080.00528.9430.0940.0940.0000.0000.0000.000
67A67CYS0-0.081-0.01925.722-0.250-0.2500.0000.0000.0000.000
68A68TYR00.0440.01623.9340.1500.1500.0000.0000.0000.000
69A69LEU0-0.037-0.02620.273-0.392-0.3920.0000.0000.0000.000
70A70PHE00.0470.02114.9230.2710.2710.0000.0000.0000.000
71A71GLU-1-0.798-0.92613.049-19.493-19.4930.0000.0000.0000.000
72A72PRO00.0090.00711.2330.9860.9860.0000.0000.0000.000
73A73PHE00.0440.0288.2340.5530.5530.0000.0000.0000.000
74A74GLY00.0510.03313.7070.7820.7820.0000.0000.0000.000
75A75PHE0-0.090-0.05716.4420.8920.8920.0000.0000.0000.000
76A76SER0-0.069-0.04215.1700.5810.5810.0000.0000.0000.000
77A77ASP-1-0.839-0.90214.360-16.105-16.1050.0000.0000.0000.000
78A78GLN00.045-0.00716.5690.4170.4170.0000.0000.0000.000
79A79ARG10.9570.99918.28213.29113.2910.0000.0000.0000.000
80A80LEU00.0360.01714.0850.3420.3420.0000.0000.0000.000
81A81LYS10.9400.95817.78512.14512.1450.0000.0000.0000.000
82A82GLN00.0050.00820.5430.0150.0150.0000.0000.0000.000
83A83VAL0-0.034-0.02019.5630.4490.4490.0000.0000.0000.000
84A84TYR0-0.015-0.04516.985-0.066-0.0660.0000.0000.0000.000
85A85GLN0-0.029-0.00921.975-0.002-0.0020.0000.0000.0000.000
86A86PHE00.0490.02425.1750.3750.3750.0000.0000.0000.000
87A87GLU-1-0.917-0.96521.507-12.551-12.5510.0000.0000.0000.000
88A88TYR00.023-0.00224.8640.2480.2480.0000.0000.0000.000
89A89GLU-1-0.864-0.93026.690-9.672-9.6720.0000.0000.0000.000
90A90SER0-0.046-0.04127.6390.4830.4830.0000.0000.0000.000
91A91LEU0-0.0200.01326.1110.1820.1820.0000.0000.0000.000
92A92LEU0-0.006-0.00328.8280.2640.2640.0000.0000.0000.000
93A93ARG10.9050.95930.7339.7569.7560.0000.0000.0000.000
94A94ARG10.7870.87626.18611.34311.3430.0000.0000.0000.000
95A95SER0-0.026-0.01631.197-0.024-0.0240.0000.0000.0000.000
96A96ALA0-0.0190.01933.7680.1820.1820.0000.0000.0000.000
97A97NME0-0.0010.00036.594-0.141-0.1410.0000.0000.0000.000
98A104ACE00.0140.00038.7880.0540.0540.0000.0000.0000.000
99A105ILE0-0.051-0.04432.278-0.063-0.0630.0000.0000.0000.000
100A106THR00.0360.03730.8690.1230.1230.0000.0000.0000.000
101A107LEU0-0.031-0.01524.717-0.236-0.2360.0000.0000.0000.000
102A108GLU-1-0.920-0.96125.807-10.604-10.6040.0000.0000.0000.000
103A109LYS10.9150.95621.96611.15011.1500.0000.0000.0000.000
104A110SER00.0510.02318.4280.4370.4370.0000.0000.0000.000
105A111THR0-0.018-0.00920.818-0.115-0.1150.0000.0000.0000.000
106A112GLN0-0.038-0.01619.9070.0780.0780.0000.0000.0000.000
107A113SER00.0160.00814.626-0.666-0.6660.0000.0000.0000.000
108A114VAL00.0000.00114.3180.6100.6100.0000.0000.0000.000
109A115GLN00.0110.0036.9121.1251.1250.0000.0000.0000.000
110A116GLY00.0260.00410.6590.8400.8400.0000.0000.0000.000
111A117PRO00.0170.0058.542-2.004-2.0040.0000.0000.0000.000
112A118ASN0-0.010-0.0095.984-1.402-1.4020.0000.0000.0000.000
113A119SER0-0.041-0.0264.883-4.071-3.984-0.001-0.004-0.0820.000
114A120ALA00.0140.0132.042-0.801-2.1784.535-1.155-2.0020.001
115A121ALA00.0330.0104.076-2.957-2.8480.003-0.065-0.0470.000
116A122CSD-1-0.740-0.8456.434-30.161-30.1610.0000.0000.0000.000
117A123GLY00.010-0.0148.2712.5532.5530.0000.0000.0000.000
118A124LEU00.0210.0049.3632.6692.6690.0000.0000.0000.000
119A125PHE00.0290.00611.0292.2262.2260.0000.0000.0000.000
120A126CYS0-0.075-0.01612.7531.9231.9230.0000.0000.0000.000
121A127CYS0-0.044-0.01313.6851.2641.2640.0000.0000.0000.000
122A128MET0-0.0050.01715.9030.8300.8300.0000.0000.0000.000
123A129PHE00.0680.01117.5261.0411.0410.0000.0000.0000.000
124A130LEU0-0.043-0.03518.5940.9260.9260.0000.0000.0000.000
125A131HIS00.0270.03320.3940.5370.5370.0000.0000.0000.000
126A132ALA00.0310.01422.0940.7020.7020.0000.0000.0000.000
127A133PHE0-0.031-0.02623.3910.6370.6370.0000.0000.0000.000
128A134ALA0-0.016-0.01524.7130.4660.4660.0000.0000.0000.000
129A135ASN0-0.068-0.03025.7610.8170.8170.0000.0000.0000.000
130A136TRP0-0.014-0.00726.0090.3690.3690.0000.0000.0000.000
131A137PRO00.0260.02528.473-0.069-0.0690.0000.0000.0000.000
132A138GLN0-0.020-0.02229.525-0.147-0.1470.0000.0000.0000.000
133A139THR0-0.025-0.01529.4870.2910.2910.0000.0000.0000.000
134A140PRO0-0.0040.02824.801-0.197-0.1970.0000.0000.0000.000
135A141MET0-0.011-0.01921.112-0.713-0.7130.0000.0000.0000.000
136A142ASP-1-0.595-0.68823.448-11.481-11.4810.0000.0000.0000.000
137A143HIS00.3900.41626.1130.2690.2690.0000.0000.0000.000
138A144ASN0-0.017-0.00125.349-0.068-0.0680.0000.0000.0000.000
139A145PRO00.009-0.00726.922-0.272-0.2720.0000.0000.0000.000
140A146THR00.0280.01221.551-0.034-0.0340.0000.0000.0000.000
141A147MET00.1310.09519.133-0.686-0.6860.0000.0000.0000.000
142A148ASN00.078-0.01922.805-0.347-0.3470.0000.0000.0000.000
143A149LEU0-0.0100.02721.4470.1110.1110.0000.0000.0000.000
144A150ILE00.0290.06917.337-0.441-0.4410.0000.0000.0000.000
145A151THR00.083-0.01519.6970.7920.7920.0000.0000.0000.000
146A152GLY00.0220.02619.100-0.701-0.7010.0000.0000.0000.000
147A153VAL0-0.022-0.01317.3340.5740.5740.0000.0000.0000.000
148A154PRO00.0310.00719.481-0.298-0.2980.0000.0000.0000.000
149A155ASN00.0910.02517.920-0.611-0.6110.0000.0000.0000.000
150A156SER0-0.032-0.00618.098-0.489-0.4890.0000.0000.0000.000
151A157MET00.0170.00419.653-0.014-0.0140.0000.0000.0000.000
152A158LEU00.0260.03812.065-0.059-0.0590.0000.0000.0000.000
153A159ASN00.005-0.01113.031-1.608-1.6080.0000.0000.0000.000
154A160SER0-0.0150.00015.3810.3190.3190.0000.0000.0000.000
155A161PRO00.0870.01517.279-0.481-0.4810.0000.0000.0000.000
156A162GLN0-0.001-0.00618.319-0.295-0.2950.0000.0000.0000.000
157A163VAL00.0190.02416.5610.1600.1600.0000.0000.0000.000
158A164GLN0-0.030-0.02313.071-1.509-1.5090.0000.0000.0000.000
159A165PRO00.007-0.00715.596-0.701-0.7010.0000.0000.0000.000
160A166THR0-0.0090.00017.902-0.002-0.0020.0000.0000.0000.000
161A167LEU00.0140.02413.431-0.231-0.2310.0000.0000.0000.000
162A168ARG10.9400.98012.51617.65417.6540.0000.0000.0000.000
163A169ARG10.9830.98414.29412.79012.7900.0000.0000.0000.000
164A170ASN0-0.024-0.01915.1670.6390.6390.0000.0000.0000.000
165A171GLN00.0270.0287.7470.8890.8890.0000.0000.0000.000
166A172GLU-1-0.942-0.97613.377-16.898-16.8980.0000.0000.0000.000
167A173GLN0-0.027-0.01315.9000.1530.1530.0000.0000.0000.000
168A174LEU0-0.008-0.00111.9170.3310.3310.0000.0000.0000.000
169A175TYR0-0.027-0.0278.7520.7400.7400.0000.0000.0000.000
170A176SER0-0.028-0.00415.3170.4170.4170.0000.0000.0000.000
171A177PHE00.0530.02018.4810.4760.4760.0000.0000.0000.000
172A178LEU00.021-0.01213.8240.4860.4860.0000.0000.0000.000
173A179GLU-1-0.754-0.85116.470-18.261-18.2610.0000.0000.0000.000
174A180ARG10.9130.96618.88313.06113.0610.0000.0000.0000.000
175A181HIS0-0.050-0.01820.8611.0561.0560.0000.0000.0000.000
176A182SER0-0.064-0.04117.341-0.259-0.2590.0000.0000.0000.000
177A183PRO00.012-0.00218.591-0.529-0.5290.0000.0000.0000.000
178A184TYR00.0510.03311.641-0.919-0.9190.0000.0000.0000.000
179A185PHE00.003-0.00511.539-1.339-1.3390.0000.0000.0000.000
180A186ARG10.9090.94514.64213.85413.8540.0000.0000.0000.000
181A187SER0-0.066-0.02416.4990.1790.1790.0000.0000.0000.000
182A188HIS0-0.064-0.02410.947-0.390-0.3900.0000.0000.0000.000
183A189SER0-0.006-0.00111.269-2.909-2.9090.0000.0000.0000.000
184A190ALA00.0300.00411.477-1.626-1.6260.0000.0000.0000.000
185A191GLN00.007-0.0178.237-1.669-1.6690.0000.0000.0000.000
186A192ILE00.0650.0397.039-5.109-5.1090.0000.0000.0000.000
187A193ARG10.8350.9196.95917.47217.4720.0000.0000.0000.000
188A194SER0-0.031-0.0037.111-2.287-2.2870.0000.0000.0000.000
189A195ALA00.0010.0042.852-4.276-3.6320.212-0.274-0.581-0.002
190A196THR00.031-0.0152.752-12.878-9.9740.572-1.927-1.549-0.020
191A197SER00.0050.0155.5434.5174.5170.0000.0000.0000.000
192A198PHE00.0320.0035.498-1.425-1.4250.0000.0000.0000.000
193A199CYS0-0.058-0.0477.1431.7671.7670.0000.0000.0000.000
194A200HIS0-0.0150.0072.225-9.849-9.1467.085-2.607-5.180-0.029
195A201LEU0-0.026-0.0091.904-1.182-3.7036.798-0.920-3.358-0.011
196A202LYS10.7970.8863.96120.90721.0380.003-0.045-0.0900.000
197A203ASN0-0.004-0.0067.752-0.717-0.7170.0000.0000.0000.000
198A204MET-1-0.814-0.87610.127-16.388-16.3880.0000.0000.0000.000
199A301NA+1-0.2320.07823.23512.68612.6860.0000.0000.0000.000