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: JQ499

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 OptAll
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 -1928327.493437
FMO2-HF: Nuclear repulsion 1857960.302649
FMO2-HF: Total energy -70367.190788
FMO2-MP2: Total energy -70567.327853


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.
-1.866-0.082000000000001-0.017-0.853-0.9110.004
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 : 0.003 / q_NPA : 0.001
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].
3A4LYS10.7840.8953.8790.8322.443-0.015-0.830-0.7650.004
4A5VAL0-0.041-0.0356.3260.0630.0630.0000.0000.0000.000
5A6LEU00.0020.01810.0770.1420.1420.0000.0000.0000.000
6A7VAL0-0.005-0.01413.351-0.008-0.0080.0000.0000.0000.000
7A8PRO0-0.0190.00516.2510.0420.0420.0000.0000.0000.000
8A9VAL0-0.022-0.02319.4570.0060.0060.0000.0000.0000.000
9A10ALA00.0470.02222.2220.0050.0050.0000.0000.0000.000
10A11HIS00.0180.00925.9190.0050.0050.0000.0000.0000.000
11A12ASP-1-0.844-0.92429.303-0.090-0.0900.0000.0000.0000.000
12A13SER00.0130.00824.721-0.006-0.0060.0000.0000.0000.000
13A14GLU-1-0.782-0.88925.672-0.098-0.0980.0000.0000.0000.000
14A15GLU-1-0.733-0.85824.464-0.101-0.1010.0000.0000.0000.000
15A16ILE0-0.015-0.00723.540-0.005-0.0050.0000.0000.0000.000
16A17GLU-1-0.769-0.90722.258-0.188-0.1880.0000.0000.0000.000
17A18ALA00.0470.02519.969-0.025-0.0250.0000.0000.0000.000
18A19VAL00.0110.00318.552-0.020-0.0200.0000.0000.0000.000
19A20SER0-0.020-0.01718.1770.0050.0050.0000.0000.0000.000
20A21ILE0-0.018-0.00515.010-0.019-0.0190.0000.0000.0000.000
21A22ILE00.0070.00114.121-0.050-0.0500.0000.0000.0000.000
22A23ASP-1-0.815-0.88213.308-0.039-0.0390.0000.0000.0000.000
23A24THR0-0.031-0.03113.5930.0340.0340.0000.0000.0000.000
24A25LEU00.0190.00010.015-0.018-0.0180.0000.0000.0000.000
25A26ARG10.8170.8939.0020.0840.0840.0000.0000.0000.000
26A27ARG10.7960.8799.4870.1330.1330.0000.0000.0000.000
27A28ALA0-0.047-0.0158.5160.1170.1170.0000.0000.0000.000
28A29GLY0-0.004-0.0075.8950.0250.0250.0000.0000.0000.000
29A30ALA0-0.039-0.0034.4440.1110.250-0.001-0.015-0.1220.000
30A31GLU-1-0.831-0.9155.189-0.015-0.0150.0000.0000.0000.000
31A32VAL0-0.051-0.0226.951-0.208-0.2080.0000.0000.0000.000
32A33VAL00.0070.01310.1710.1520.1520.0000.0000.0000.000
33A34VAL0-0.001-0.00412.546-0.039-0.0390.0000.0000.0000.000
34A35ALA0-0.010-0.01916.2080.0300.0300.0000.0000.0000.000
35A36SER00.004-0.00918.355-0.010-0.0100.0000.0000.0000.000
36A37VAL0-0.038-0.03522.180-0.007-0.0070.0000.0000.0000.000
37A38GLU-1-0.772-0.84024.124-0.112-0.1120.0000.0000.0000.000
38A39ASP-1-0.914-0.95926.272-0.081-0.0810.0000.0000.0000.000
39A40THR0-0.035-0.01727.7170.0080.0080.0000.0000.0000.000
40A41GLU-1-0.768-0.89422.374-0.055-0.0550.0000.0000.0000.000
41A42ILE0-0.050-0.01023.652-0.006-0.0060.0000.0000.0000.000
42A43VAL00.0230.01624.514-0.001-0.0010.0000.0000.0000.000
43A44ARG10.8380.89827.1780.0770.0770.0000.0000.0000.000
44A45MET0-0.0210.00322.339-0.005-0.0050.0000.0000.0000.000
45A46SER0-0.044-0.02928.5630.0090.0090.0000.0000.0000.000
46A47ARG10.7840.85029.8010.0970.0970.0000.0000.0000.000
47A48GLY0-0.0210.00131.4620.0070.0070.0000.0000.0000.000
48A49VAL0-0.034-0.01026.6360.0060.0060.0000.0000.0000.000
49A50CYS0-0.034-0.01428.085-0.009-0.0090.0000.0000.0000.000
50A51VAL00.0120.00621.8530.0100.0100.0000.0000.0000.000
51A52LYS10.8000.89722.0350.0260.0260.0000.0000.0000.000
52A53ALA00.0020.00419.4540.0000.0000.0000.0000.0000.000
53A54ASP-1-0.815-0.89514.587-0.115-0.1150.0000.0000.0000.000
54A55LYS10.8830.94214.6430.0990.0990.0000.0000.0000.000
55A56LEU00.0590.04318.596-0.004-0.0040.0000.0000.0000.000
56A57ILE00.027-0.00618.379-0.012-0.0120.0000.0000.0000.000
57A58SER00.0600.02619.479-0.018-0.0180.0000.0000.0000.000
58A59ALA0-0.105-0.04218.8900.0060.0060.0000.0000.0000.000
59A60VAL0-0.019-0.02314.4610.0040.0040.0000.0000.0000.000
60A61GLU-1-0.856-0.95516.259-0.228-0.2280.0000.0000.0000.000
61A62ASN0-0.071-0.02817.782-0.008-0.0080.0000.0000.0000.000
62A63GLU-1-0.825-0.88311.033-0.418-0.4180.0000.0000.0000.000
63A64THR0-0.079-0.05811.4790.0120.0120.0000.0000.0000.000
64A65TYR0-0.007-0.0229.360-0.085-0.0850.0000.0000.0000.000
65A66ASP-1-0.816-0.9076.344-2.911-2.9110.0000.0000.0000.000
66A67CYS0-0.090-0.0439.7260.1980.1980.0000.0000.0000.000
67A68ILE00.0220.03012.3870.0130.0130.0000.0000.0000.000
68A69ALA00.012-0.00515.0510.0250.0250.0000.0000.0000.000
69A70ILE0-0.002-0.00916.7550.0290.0290.0000.0000.0000.000
70A71PRO00.0090.00619.8960.0050.0050.0000.0000.0000.000
71A72GLY00.0190.03622.303-0.001-0.0010.0000.0000.0000.000
72A73GLY00.0060.00226.0870.0050.0050.0000.0000.0000.000
73A74MET0-0.029-0.00829.094-0.011-0.0110.0000.0000.0000.000
74A75PRO00.0550.02232.1100.0070.0070.0000.0000.0000.000
75A76GLY00.0270.02428.331-0.005-0.0050.0000.0000.0000.000
76A77ALA00.0590.00827.081-0.010-0.0100.0000.0000.0000.000
77A78GLU-1-0.865-0.93028.152-0.121-0.1210.0000.0000.0000.000
78A79ARG10.8350.88928.5620.1050.1050.0000.0000.0000.000
79A80CYS0-0.048-0.02224.427-0.010-0.0100.0000.0000.0000.000
80A81ARG10.6930.80925.8610.1210.1210.0000.0000.0000.000
81A82ASP-1-0.773-0.85728.230-0.136-0.1360.0000.0000.0000.000
82A83SER00.0140.01924.9910.0010.0010.0000.0000.0000.000
83A84ALA00.0110.00225.737-0.018-0.0180.0000.0000.0000.000
84A85ALA00.0470.03922.607-0.012-0.0120.0000.0000.0000.000
85A86LEU00.0310.00719.810-0.027-0.0270.0000.0000.0000.000
86A87THR0-0.035-0.02621.592-0.028-0.0280.0000.0000.0000.000
87A88ALA00.0080.00523.048-0.013-0.0130.0000.0000.0000.000
88A89MET0-0.0090.03415.459-0.013-0.0130.0000.0000.0000.000
89A90LEU00.0260.00618.845-0.045-0.0450.0000.0000.0000.000
90A91LYS10.8510.93220.2440.1880.1880.0000.0000.0000.000
91A92THR0-0.019-0.00718.3420.0030.0030.0000.0000.0000.000
92A93HIS00.0160.00813.782-0.089-0.0890.0000.0000.0000.000
93A94LYS10.8310.91417.4140.3120.3120.0000.0000.0000.000
94A95ALA0-0.024-0.00620.099-0.004-0.0040.0000.0000.0000.000
95A96GLN0-0.033-0.02015.683-0.026-0.0260.0000.0000.0000.000
96A97GLY0-0.0290.00416.213-0.052-0.0520.0000.0000.0000.000
97A98LYS10.8470.9209.2841.3651.3650.0000.0000.0000.000
98A99LEU0-0.014-0.00412.9760.1050.1050.0000.0000.0000.000
99A100ILE00.0080.00615.005-0.010-0.0100.0000.0000.0000.000
100A101ALA00.014-0.00617.0850.0240.0240.0000.0000.0000.000
101A102ALA0-0.0200.00018.9410.0100.0100.0000.0000.0000.000
102A103ILE0-0.052-0.01221.6090.0000.0000.0000.0000.0000.000
103A104CSD-1-0.779-0.89023.829-0.133-0.1330.0000.0000.0000.000
104A105ALA00.0500.02827.569-0.002-0.0020.0000.0000.0000.000
105A106SER0-0.030-0.03524.4770.0050.0050.0000.0000.0000.000
106A107PRO0-0.038-0.01024.626-0.010-0.0100.0000.0000.0000.000
107A108ALA00.0040.01226.366-0.003-0.0030.0000.0000.0000.000
108A109VAL00.0290.00829.5660.0000.0000.0000.0000.0000.000
109A110VAL0-0.0040.01424.4220.0040.0040.0000.0000.0000.000
110A111LEU0-0.015-0.01522.111-0.002-0.0020.0000.0000.0000.000
111A112GLN00.0220.01126.053-0.011-0.0110.0000.0000.0000.000
112A113THR0-0.047-0.03329.5530.0080.0080.0000.0000.0000.000
113A114HIS0-0.014-0.00726.5390.0050.0050.0000.0000.0000.000
114A115GLY00.0150.00827.831-0.008-0.0080.0000.0000.0000.000
115A116LEU0-0.029-0.02322.569-0.008-0.0080.0000.0000.0000.000
116A117LEU00.014-0.00224.481-0.029-0.0290.0000.0000.0000.000
117A118GLN00.0120.00126.8930.0130.0130.0000.0000.0000.000
118A119GLY00.0080.00928.212-0.010-0.0100.0000.0000.0000.000
119A120GLU-1-0.823-0.86423.427-0.346-0.3460.0000.0000.0000.000
120A121LYS10.8270.88226.2480.1880.1880.0000.0000.0000.000
121A122ALA0-0.009-0.00425.775-0.023-0.0230.0000.0000.0000.000
122A123VAL00.002-0.00326.0330.0200.0200.0000.0000.0000.000
123A124ALA00.0400.00227.175-0.015-0.0150.0000.0000.0000.000
124A125TYR00.021-0.00329.1050.0100.0100.0000.0000.0000.000
125A126PRO0-0.012-0.01031.1280.0010.0010.0000.0000.0000.000
126A127CYS0-0.043-0.02434.3830.0020.0020.0000.0000.0000.000
127A128PHE00.0310.01232.2770.0030.0030.0000.0000.0000.000
128A129MET0-0.0210.01131.549-0.010-0.0100.0000.0000.0000.000
129A130ASP-1-0.832-0.91534.348-0.109-0.1090.0000.0000.0000.000
130A131GLN0-0.054-0.01633.380-0.004-0.0040.0000.0000.0000.000
131A132PHE0-0.0010.00228.620-0.008-0.0080.0000.0000.0000.000
132A133PRO00.0580.02333.6250.0100.0100.0000.0000.0000.000
133A134ALA00.009-0.00335.134-0.006-0.0060.0000.0000.0000.000
134A135ASP-1-0.899-0.94935.408-0.145-0.1450.0000.0000.0000.000
135A136MET00.0100.02529.743-0.007-0.0070.0000.0000.0000.000
136A137ARG10.7650.89130.6630.1100.1100.0000.0000.0000.000
137A138GLY00.0230.00828.8910.0020.0020.0000.0000.0000.000
138A139GLU-1-0.951-0.97728.861-0.126-0.1260.0000.0000.0000.000
139A140GLY00.0160.00427.717-0.014-0.0140.0000.0000.0000.000
140A141ARG10.8170.86526.0400.1370.1370.0000.0000.0000.000
141A142VAL0-0.030-0.00820.490-0.011-0.0110.0000.0000.0000.000
142A143CYS0-0.0230.02423.7020.0140.0140.0000.0000.0000.000
143A144VAL0-0.030-0.02718.993-0.028-0.0280.0000.0000.0000.000
144A145SER0-0.014-0.01321.4920.0380.0380.0000.0000.0000.000
145A146ASN0-0.032-0.02920.991-0.023-0.0230.0000.0000.0000.000
146A147LYS10.8720.93315.5910.6120.6120.0000.0000.0000.000
147A148ILE0-0.0040.01518.430-0.031-0.0310.0000.0000.0000.000
148A149VAL0-0.010-0.00416.6760.0080.0080.0000.0000.0000.000
149A150THR00.0080.00619.8540.0100.0100.0000.0000.0000.000
150A151SER00.012-0.02222.6230.0080.0080.0000.0000.0000.000
151A152VAL00.0410.01824.4730.0040.0040.0000.0000.0000.000
152A153GLY00.0380.01926.3520.0120.0120.0000.0000.0000.000
153A154PRO00.0540.03525.655-0.007-0.0070.0000.0000.0000.000
154A155SER0-0.022-0.00625.450-0.005-0.0050.0000.0000.0000.000
155A156SER0-0.015-0.01024.6240.0130.0130.0000.0000.0000.000
156A157ALA00.0440.03221.511-0.024-0.0240.0000.0000.0000.000
157A158ILE00.0460.02319.135-0.031-0.0310.0000.0000.0000.000
158A159GLU-1-0.808-0.86518.734-0.189-0.1890.0000.0000.0000.000
159A160PHE00.005-0.00718.619-0.033-0.0330.0000.0000.0000.000
160A161ALA00.0290.01715.220-0.056-0.0560.0000.0000.0000.000
161A162LEU0-0.006-0.00614.361-0.074-0.0740.0000.0000.0000.000
162A163LYS10.8310.91814.7410.2720.2720.0000.0000.0000.000
163A164LEU00.0430.01412.961-0.054-0.0540.0000.0000.0000.000
164A165ILE00.0130.0119.591-0.168-0.1680.0000.0000.0000.000
165A166GLU-1-0.828-0.88210.478-0.399-0.3990.0000.0000.0000.000
166A167VAL0-0.036-0.02212.5710.0180.0180.0000.0000.0000.000
167A168LEU0-0.0140.0057.964-0.055-0.0550.0000.0000.0000.000
168A169TYR0-0.0070.0084.515-1.033-0.999-0.001-0.008-0.0240.000
169A170ASN00.024-0.0017.7860.2900.2900.0000.0000.0000.000
170A171LYS10.9010.93711.3200.2720.2720.0000.0000.0000.000
171A172GLU-1-0.854-0.90312.8330.0390.0390.0000.0000.0000.000
172A173GLN00.0220.0107.7420.1400.1400.0000.0000.0000.000
173A174ALA00.0130.01111.3190.0410.0410.0000.0000.0000.000
174A175LYS10.8550.90913.7790.1020.1020.0000.0000.0000.000
175A176LYS10.8860.95112.636-0.083-0.0830.0000.0000.0000.000
176A177ILE0-0.0040.00411.5000.0390.0390.0000.0000.0000.000
177A178ALA00.011-0.00315.0210.0090.0090.0000.0000.0000.000
178A179ALA0-0.011-0.01018.2790.0130.0130.0000.0000.0000.000
179A180GLN0-0.013-0.00813.610-0.007-0.0070.0000.0000.0000.000
180A181LEU0-0.034-0.00817.0610.0060.0060.0000.0000.0000.000
181A182LEU0-0.048-0.01620.564-0.007-0.0070.0000.0000.0000.000
182A183TYR0-0.032-0.02321.077-0.006-0.0060.0000.0000.0000.000
183A184ALA00.0110.00322.292-0.001-0.0010.0000.0000.0000.000
184A185TYR0-0.068-0.06617.074-0.008-0.0080.0000.0000.0000.000