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: 89GVY

Calculation Name: 4XLL-A-Xray372

Preferred Name:

Target Type:

Ligand Name: 3-sulfinoalanine

ligand 3-letter code: CSD

PDB ID: 4XLL

Chain ID: A

ChEMBL ID:

UniProt ID: B9PZH8

Base Structure: X-ray

Registration Date: 2023-09-22

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 184
LigandCharge CSD=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1921734.594526
FMO2-HF: Nuclear repulsion 1851368.620358
FMO2-HF: Total energy -70365.974168
FMO2-MP2: Total energy -70566.003041


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:2:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-1.329-0.030999999999999-0.022-0.467-0.810.002
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / 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].
3A4LYS10.9160.9663.7991.3202.504-0.021-0.460-0.7030.002
4A5VAL0-0.034-0.0336.0420.1930.1930.0000.0000.0000.000
5A6LEU00.0020.0199.7820.0670.0670.0000.0000.0000.000
6A7VAL0-0.009-0.01612.9050.0270.0270.0000.0000.0000.000
7A8PRO0-0.026-0.00515.9440.0130.0130.0000.0000.0000.000
8A9VAL0-0.016-0.01719.0340.0220.0220.0000.0000.0000.000
9A10ALA00.0240.01521.892-0.008-0.0080.0000.0000.0000.000
10A11HIS00.0300.00225.5360.0110.0110.0000.0000.0000.000
11A12ASP-1-0.920-0.98528.817-0.028-0.0280.0000.0000.0000.000
12A13SER0-0.004-0.00624.452-0.004-0.0040.0000.0000.0000.000
13A14GLU-1-0.838-0.92025.8990.0200.0200.0000.0000.0000.000
14A15GLU-1-0.741-0.88824.3670.0030.0030.0000.0000.0000.000
15A16ILE0-0.036-0.01323.2480.0080.0080.0000.0000.0000.000
16A17GLU-1-0.789-0.91822.2900.0080.0080.0000.0000.0000.000
17A18ALA00.0270.00719.9150.0030.0030.0000.0000.0000.000
18A19VAL0-0.015-0.00518.3060.0010.0010.0000.0000.0000.000
19A20SER00.000-0.01818.0930.0270.0270.0000.0000.0000.000
20A21ILE0-0.0290.00214.8070.0360.0360.0000.0000.0000.000
21A22ILE0-0.019-0.01813.9480.0240.0240.0000.0000.0000.000
22A23ASP-1-0.908-0.93613.1830.2450.2450.0000.0000.0000.000
23A24THR00.003-0.02413.7300.0740.0740.0000.0000.0000.000
24A25LEU00.011-0.0059.6680.1000.1000.0000.0000.0000.000
25A26ARG10.8600.9229.1520.1300.1300.0000.0000.0000.000
26A27ARG10.8520.9349.641-0.142-0.1420.0000.0000.0000.000
27A28ALA0-0.065-0.0238.8230.0920.0920.0000.0000.0000.000
28A29GLY00.0120.0026.1080.5070.5070.0000.0000.0000.000
29A30ALA0-0.046-0.0154.6670.0930.207-0.001-0.007-0.1070.000
30A31GLU-1-0.904-0.9475.116-0.663-0.6630.0000.0000.0000.000
31A32VAL0-0.038-0.0266.780-0.223-0.2230.0000.0000.0000.000
32A33VAL0-0.0050.0119.9550.0610.0610.0000.0000.0000.000
33A34VAL00.0020.00512.347-0.010-0.0100.0000.0000.0000.000
34A35ALA00.007-0.01415.9580.0050.0050.0000.0000.0000.000
35A36SER00.020-0.00817.9510.0050.0050.0000.0000.0000.000
36A37VAL0-0.058-0.03921.735-0.016-0.0160.0000.0000.0000.000
37A38GLU-1-0.725-0.82523.817-0.062-0.0620.0000.0000.0000.000
38A39ASP-1-0.961-0.98125.904-0.069-0.0690.0000.0000.0000.000
39A40THR0-0.021-0.00527.2130.0030.0030.0000.0000.0000.000
40A41GLU-1-0.884-0.95022.503-0.075-0.0750.0000.0000.0000.000
41A42ILE0-0.062-0.03323.4960.0030.0030.0000.0000.0000.000
42A43VAL00.0250.02624.156-0.001-0.0010.0000.0000.0000.000
43A44ARG10.9580.97826.7050.0200.0200.0000.0000.0000.000
44A45MET0-0.0210.00222.509-0.002-0.0020.0000.0000.0000.000
45A46SER0-0.0110.00828.5440.0040.0040.0000.0000.0000.000
46A47ARG10.8560.91130.466-0.002-0.0020.0000.0000.0000.000
47A48GLY0-0.046-0.02231.8320.0040.0040.0000.0000.0000.000
48A49VAL00.0130.01526.3260.0010.0010.0000.0000.0000.000
49A50CYS0-0.053-0.02727.989-0.008-0.0080.0000.0000.0000.000
50A51VAL00.0210.01421.4170.0080.0080.0000.0000.0000.000
51A52LYS10.9370.98221.8200.0190.0190.0000.0000.0000.000
52A53ALA0-0.020-0.01219.4160.0060.0060.0000.0000.0000.000
53A54ASP-1-0.839-0.91914.545-0.075-0.0750.0000.0000.0000.000
54A55LYS10.9000.94314.6620.1800.1800.0000.0000.0000.000
55A56LEU00.0630.05218.2560.0040.0040.0000.0000.0000.000
56A57ILE00.012-0.01217.906-0.021-0.0210.0000.0000.0000.000
57A58SER00.0290.01019.352-0.022-0.0220.0000.0000.0000.000
58A59ALA0-0.058-0.02018.547-0.009-0.0090.0000.0000.0000.000
59A60VAL0-0.036-0.02714.377-0.024-0.0240.0000.0000.0000.000
60A61GLU-1-0.875-0.94715.785-0.224-0.2240.0000.0000.0000.000
61A62ASN0-0.059-0.02717.2750.0000.0000.0000.0000.0000.000
62A63GLU-1-0.959-0.96811.777-0.538-0.5380.0000.0000.0000.000
63A64THR0-0.056-0.04110.4450.0410.0410.0000.0000.0000.000
64A65TYR00.009-0.0078.904-0.153-0.1530.0000.0000.0000.000
65A66ASP-1-0.854-0.9386.153-2.608-2.6080.0000.0000.0000.000
66A67CYS0-0.072-0.0389.5060.2510.2510.0000.0000.0000.000
67A68ILE00.0160.02512.008-0.027-0.0270.0000.0000.0000.000
68A69ALA00.005-0.00914.8090.0370.0370.0000.0000.0000.000
69A70ILE0-0.029-0.03316.4480.0070.0070.0000.0000.0000.000
70A71PRO00.0160.01019.4040.0180.0180.0000.0000.0000.000
71A72GLY00.0580.04721.942-0.011-0.0110.0000.0000.0000.000
72A73GLY0-0.0060.00725.676-0.001-0.0010.0000.0000.0000.000
73A74MET0-0.048-0.01628.725-0.009-0.0090.0000.0000.0000.000
74A75PRO00.0500.01131.8020.0050.0050.0000.0000.0000.000
75A76GLY00.0220.02728.245-0.006-0.0060.0000.0000.0000.000
76A77ALA00.0510.00026.816-0.009-0.0090.0000.0000.0000.000
77A78GLU-1-0.924-0.98427.904-0.054-0.0540.0000.0000.0000.000
78A79ARG10.8140.89328.4110.0520.0520.0000.0000.0000.000
79A80CYS0-0.030-0.00623.972-0.010-0.0100.0000.0000.0000.000
80A81ARG10.7560.84525.5200.0540.0540.0000.0000.0000.000
81A82ASP-1-0.788-0.85827.653-0.079-0.0790.0000.0000.0000.000
82A83SER00.0170.02624.063-0.005-0.0050.0000.0000.0000.000
83A84ALA00.011-0.00625.640-0.009-0.0090.0000.0000.0000.000
84A85ALA00.0600.04021.940-0.009-0.0090.0000.0000.0000.000
85A86LEU00.0190.00419.429-0.023-0.0230.0000.0000.0000.000
86A87THR0-0.0020.00021.235-0.015-0.0150.0000.0000.0000.000
87A88ALA0-0.013-0.00622.753-0.008-0.0080.0000.0000.0000.000
88A89MET0-0.0040.01615.401-0.005-0.0050.0000.0000.0000.000
89A90LEU00.0120.00518.461-0.033-0.0330.0000.0000.0000.000
90A91LYS10.9450.97120.0590.1290.1290.0000.0000.0000.000
91A92THR00.0000.01217.7340.0040.0040.0000.0000.0000.000
92A93HIS0-0.001-0.00513.374-0.086-0.0860.0000.0000.0000.000
93A94LYS10.8980.95417.0560.1500.1500.0000.0000.0000.000
94A95ALA0-0.034-0.01919.7730.0040.0040.0000.0000.0000.000
95A96GLN0-0.027-0.00815.464-0.036-0.0360.0000.0000.0000.000
96A97GLY0-0.053-0.01615.696-0.052-0.0520.0000.0000.0000.000
97A98LYS10.9660.99010.1130.9140.9140.0000.0000.0000.000
98A99LEU0-0.0140.00113.0230.0780.0780.0000.0000.0000.000
99A100ILE00.0070.01014.836-0.027-0.0270.0000.0000.0000.000
100A101ALA00.011-0.00416.7300.0360.0360.0000.0000.0000.000
101A102ALA0-0.017-0.00118.565-0.011-0.0110.0000.0000.0000.000
102A103ILE0-0.032-0.01021.4110.0130.0130.0000.0000.0000.000
103A104CSD-1-0.803-0.87223.482-0.022-0.0220.0000.0000.0000.000
104A105ALA00.0560.00627.200-0.003-0.0030.0000.0000.0000.000
105A106SER0-0.045-0.03424.351-0.004-0.0040.0000.0000.0000.000
106A107PRO0-0.0130.00424.728-0.012-0.0120.0000.0000.0000.000
107A108ALA0-0.0030.00326.312-0.006-0.0060.0000.0000.0000.000
108A109VAL00.0430.02229.314-0.005-0.0050.0000.0000.0000.000
109A110VAL00.0110.02423.850-0.005-0.0050.0000.0000.0000.000
110A111LEU0-0.026-0.01721.910-0.008-0.0080.0000.0000.0000.000
111A112GLN00.0270.01225.871-0.007-0.0070.0000.0000.0000.000
112A113THR0-0.036-0.03029.3860.0020.0020.0000.0000.0000.000
113A114HIS0-0.073-0.03726.291-0.001-0.0010.0000.0000.0000.000
114A115GLY0-0.015-0.00227.797-0.009-0.0090.0000.0000.0000.000
115A116LEU0-0.038-0.03322.510-0.008-0.0080.0000.0000.0000.000
116A117LEU0-0.0040.00424.574-0.010-0.0100.0000.0000.0000.000
117A118GLN0-0.013-0.01226.8140.0110.0110.0000.0000.0000.000
118A119GLY00.002-0.00827.462-0.008-0.0080.0000.0000.0000.000
119A120GLU-1-0.868-0.87224.019-0.106-0.1060.0000.0000.0000.000
120A121LYS10.8790.92726.5690.0420.0420.0000.0000.0000.000
121A122ALA00.003-0.01126.117-0.006-0.0060.0000.0000.0000.000
122A123VAL0-0.0090.00426.1280.0060.0060.0000.0000.0000.000
123A124ALA00.031-0.00727.298-0.008-0.0080.0000.0000.0000.000
124A125TYR00.012-0.00228.8990.0080.0080.0000.0000.0000.000
125A126PRO0-0.0080.00130.914-0.004-0.0040.0000.0000.0000.000
126A127CYS0-0.045-0.02334.084-0.001-0.0010.0000.0000.0000.000
127A128PHE00.014-0.00932.130-0.002-0.0020.0000.0000.0000.000
128A129MET0-0.0190.00331.876-0.006-0.0060.0000.0000.0000.000
129A130ASP-1-0.904-0.95234.386-0.021-0.0210.0000.0000.0000.000
130A131GLN0-0.054-0.02433.548-0.006-0.0060.0000.0000.0000.000
131A132PHE0-0.016-0.00928.723-0.007-0.0070.0000.0000.0000.000
132A133PRO00.0630.02633.8500.0060.0060.0000.0000.0000.000
133A134ALA00.0260.00035.2850.0000.0000.0000.0000.0000.000
134A135ASP-1-0.923-0.95535.359-0.041-0.0410.0000.0000.0000.000
135A136MET0-0.0210.02030.124-0.003-0.0030.0000.0000.0000.000
136A137ARG10.8300.91630.7260.0250.0250.0000.0000.0000.000
137A138GLY00.0040.00129.2260.0010.0010.0000.0000.0000.000
138A139GLU-1-0.945-0.97929.2350.0090.0090.0000.0000.0000.000
139A140GLY00.0010.00127.7790.0010.0010.0000.0000.0000.000
140A141ARG10.9520.96426.812-0.057-0.0570.0000.0000.0000.000
141A142VAL00.0030.02620.767-0.004-0.0040.0000.0000.0000.000
142A143CYS0-0.0400.00923.6420.0030.0030.0000.0000.0000.000
143A144VAL0-0.007-0.01519.237-0.007-0.0070.0000.0000.0000.000
144A145SER0-0.007-0.02321.7250.0120.0120.0000.0000.0000.000
145A146ASN0-0.035-0.03120.600-0.016-0.0160.0000.0000.0000.000
146A147LYS10.8410.92115.3610.3230.3230.0000.0000.0000.000
147A148ILE00.0180.01818.149-0.030-0.0300.0000.0000.0000.000
148A149VAL0-0.0070.00517.1900.0270.0270.0000.0000.0000.000
149A150THR00.0240.01420.050-0.008-0.0080.0000.0000.0000.000
150A151SER0-0.002-0.03922.4220.0200.0200.0000.0000.0000.000
151A152VAL00.0340.02524.237-0.008-0.0080.0000.0000.0000.000
152A153GLY00.0480.00826.364-0.006-0.0060.0000.0000.0000.000
153A154PRO00.0900.05925.6950.0090.0090.0000.0000.0000.000
154A155SER0-0.026-0.01125.3360.0090.0090.0000.0000.0000.000
155A156SER0-0.048-0.03524.4610.0090.0090.0000.0000.0000.000
156A157ALA00.0510.03921.2720.0030.0030.0000.0000.0000.000
157A158ILE00.0520.02819.3710.0040.0040.0000.0000.0000.000
158A159GLU-1-0.947-0.97318.9290.0960.0960.0000.0000.0000.000
159A160PHE0-0.011-0.02618.5950.0120.0120.0000.0000.0000.000
160A161ALA00.0430.01715.135-0.006-0.0060.0000.0000.0000.000
161A162LEU0-0.008-0.00314.4650.0380.0380.0000.0000.0000.000
162A163LYS10.8270.92915.338-0.069-0.0690.0000.0000.0000.000
163A164LEU00.0380.00912.9810.0010.0010.0000.0000.0000.000
164A165ILE0-0.0110.00610.3740.0050.0050.0000.0000.0000.000
165A166GLU-1-0.924-0.95511.3160.2710.2710.0000.0000.0000.000
166A167VAL0-0.062-0.04612.8210.0180.0180.0000.0000.0000.000
167A168LEU0-0.019-0.0028.295-0.065-0.0650.0000.0000.0000.000
168A169TYR0-0.0280.0004.8470.1000.1000.0000.0000.0000.000
169A170ASN00.0510.0208.746-0.158-0.1580.0000.0000.0000.000
170A171LYS11.0111.00412.133-0.184-0.1840.0000.0000.0000.000
171A172GLU-1-0.899-0.96414.2930.4220.4220.0000.0000.0000.000
172A173GLN0-0.011-0.0088.597-0.174-0.1740.0000.0000.0000.000
173A174ALA00.0360.01412.536-0.034-0.0340.0000.0000.0000.000
174A175LYS10.9000.94814.591-0.355-0.3550.0000.0000.0000.000
175A176LYS10.8960.97113.587-0.705-0.7050.0000.0000.0000.000
176A177ILE0-0.0090.00612.052-0.046-0.0460.0000.0000.0000.000
177A178ALA00.007-0.00415.452-0.054-0.0540.0000.0000.0000.000
178A179ALA0-0.006-0.00418.827-0.032-0.0320.0000.0000.0000.000
179A180GLN0-0.040-0.02414.122-0.058-0.0580.0000.0000.0000.000
180A181LEU0-0.001-0.00217.316-0.025-0.0250.0000.0000.0000.000
181A182LEU0-0.045-0.00120.684-0.027-0.0270.0000.0000.0000.000
182A183TYR0-0.0080.00221.373-0.019-0.0190.0000.0000.0000.000
183A184ALA00.005-0.01223.1240.0170.0170.0000.0000.0000.000
184A185TYR0-0.007-0.00317.886-0.001-0.0010.0000.0000.0000.000