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: NNZGQ

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 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 184
LigandCharge CSD=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1924154.691101
FMO2-HF: Nuclear repulsion 1853787.796121
FMO2-HF: Total energy -70366.89498
FMO2-MP2: Total energy -70566.982085


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.
-2.267-0.397-0.026-0.818-1.0260.004
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 : -0.007 / q_NPA : -0.003
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].
3A4LYS10.8260.9253.7990.9112.615-0.024-0.801-0.8790.004
4A5VAL0-0.036-0.0366.1610.1350.1350.0000.0000.0000.000
5A6LEU00.0050.0249.9050.1400.1400.0000.0000.0000.000
6A7VAL0-0.008-0.01613.026-0.007-0.0070.0000.0000.0000.000
7A8PRO0-0.021-0.00216.0700.0410.0410.0000.0000.0000.000
8A9VAL0-0.026-0.02419.1570.0100.0100.0000.0000.0000.000
9A10ALA00.0460.02322.0150.0040.0040.0000.0000.0000.000
10A11HIS00.0300.01125.6580.0040.0040.0000.0000.0000.000
11A12ASP-1-0.861-0.94128.940-0.095-0.0950.0000.0000.0000.000
12A13SER00.0090.00224.480-0.006-0.0060.0000.0000.0000.000
13A14GLU-1-0.801-0.90225.842-0.096-0.0960.0000.0000.0000.000
14A15GLU-1-0.723-0.85624.384-0.105-0.1050.0000.0000.0000.000
15A16ILE0-0.017-0.00223.264-0.003-0.0030.0000.0000.0000.000
16A17GLU-1-0.780-0.90622.312-0.181-0.1810.0000.0000.0000.000
17A18ALA00.0320.00619.925-0.024-0.0240.0000.0000.0000.000
18A19VAL0-0.0050.00018.322-0.024-0.0240.0000.0000.0000.000
19A20SER0-0.003-0.01618.1080.0080.0080.0000.0000.0000.000
20A21ILE0-0.0230.00214.857-0.014-0.0140.0000.0000.0000.000
21A22ILE0-0.009-0.01213.970-0.036-0.0360.0000.0000.0000.000
22A23ASP-1-0.831-0.89113.196-0.014-0.0140.0000.0000.0000.000
23A24THR0-0.024-0.03313.7410.0440.0440.0000.0000.0000.000
24A25LEU00.008-0.0049.926-0.002-0.0020.0000.0000.0000.000
25A26ARG10.8560.9219.1650.1150.1150.0000.0000.0000.000
26A27ARG10.8080.9049.6470.1190.1190.0000.0000.0000.000
27A28ALA0-0.052-0.0208.7730.1100.1100.0000.0000.0000.000
28A29GLY0-0.002-0.0076.1140.1130.1130.0000.0000.0000.000
29A30ALA0-0.070-0.0174.6870.1300.240-0.001-0.007-0.1020.000
30A31GLU-1-0.865-0.9365.123-0.167-0.1670.0000.0000.0000.000
31A32VAL0-0.037-0.0306.839-0.294-0.2940.0000.0000.0000.000
32A33VAL00.0010.01610.0260.1410.1410.0000.0000.0000.000
33A34VAL0-0.008-0.00712.464-0.038-0.0380.0000.0000.0000.000
34A35ALA00.005-0.01416.0780.0360.0360.0000.0000.0000.000
35A36SER00.017-0.01018.066-0.013-0.0130.0000.0000.0000.000
36A37VAL0-0.054-0.04121.849-0.008-0.0080.0000.0000.0000.000
37A38GLU-1-0.732-0.81223.930-0.115-0.1150.0000.0000.0000.000
38A39ASP-1-0.945-0.97326.011-0.088-0.0880.0000.0000.0000.000
39A40THR0-0.017-0.00227.3180.0100.0100.0000.0000.0000.000
40A41GLU-1-0.837-0.92122.392-0.067-0.0670.0000.0000.0000.000
41A42ILE0-0.061-0.02923.607-0.007-0.0070.0000.0000.0000.000
42A43VAL00.0280.02624.1450.0000.0000.0000.0000.0000.000
43A44ARG10.8860.92626.8230.0790.0790.0000.0000.0000.000
44A45MET0-0.034-0.00422.318-0.005-0.0050.0000.0000.0000.000
45A46SER00.0000.00828.5600.0090.0090.0000.0000.0000.000
46A47ARG10.7630.83130.4800.0940.0940.0000.0000.0000.000
47A48GLY0-0.029-0.00831.8320.0070.0070.0000.0000.0000.000
48A49VAL00.0100.00926.5960.0070.0070.0000.0000.0000.000
49A50CYS0-0.061-0.02828.003-0.009-0.0090.0000.0000.0000.000
50A51VAL00.0090.00621.5080.0090.0090.0000.0000.0000.000
51A52LYS10.8690.94222.0200.0300.0300.0000.0000.0000.000
52A53ALA0-0.023-0.01219.5730.0030.0030.0000.0000.0000.000
53A54ASP-1-0.819-0.90814.476-0.126-0.1260.0000.0000.0000.000
54A55LYS10.9040.94914.6510.1230.1230.0000.0000.0000.000
55A56LEU00.0470.04318.355-0.012-0.0120.0000.0000.0000.000
56A57ILE00.020-0.00617.926-0.014-0.0140.0000.0000.0000.000
57A58SER00.0370.01719.445-0.019-0.0190.0000.0000.0000.000
58A59ALA0-0.077-0.02818.6430.0000.0000.0000.0000.0000.000
59A60VAL0-0.029-0.02514.325-0.004-0.0040.0000.0000.0000.000
60A61GLU-1-0.842-0.94015.866-0.254-0.2540.0000.0000.0000.000
61A62ASN0-0.067-0.03217.335-0.015-0.0150.0000.0000.0000.000
62A63GLU-1-0.892-0.93410.709-0.494-0.4940.0000.0000.0000.000
63A64THR0-0.059-0.04010.7320.0120.0120.0000.0000.0000.000
64A65TYR00.0430.0149.002-0.109-0.1090.0000.0000.0000.000
65A66ASP-1-0.820-0.9146.203-3.135-3.1350.0000.0000.0000.000
66A67CYS0-0.088-0.0449.5220.2320.2320.0000.0000.0000.000
67A68ILE00.0220.03112.0420.0080.0080.0000.0000.0000.000
68A69ALA00.006-0.00814.8470.0310.0310.0000.0000.0000.000
69A70ILE0-0.021-0.02716.4680.0300.0300.0000.0000.0000.000
70A71PRO00.0070.00919.4840.0100.0100.0000.0000.0000.000
71A72GLY00.0490.04821.961-0.001-0.0010.0000.0000.0000.000
72A73GLY0-0.0100.00025.6950.0040.0040.0000.0000.0000.000
73A74MET0-0.0250.00328.744-0.011-0.0110.0000.0000.0000.000
74A75PRO00.0490.00831.8210.0070.0070.0000.0000.0000.000
75A76GLY00.0290.02628.282-0.005-0.0050.0000.0000.0000.000
76A77ALA00.046-0.00226.917-0.009-0.0090.0000.0000.0000.000
77A78GLU-1-0.856-0.93327.990-0.126-0.1260.0000.0000.0000.000
78A79ARG10.8180.88328.4990.1110.1110.0000.0000.0000.000
79A80CYS0-0.048-0.01924.075-0.010-0.0100.0000.0000.0000.000
80A81ARG10.6900.80325.6340.1260.1260.0000.0000.0000.000
81A82ASP-1-0.788-0.86127.767-0.142-0.1420.0000.0000.0000.000
82A83SER00.0140.02224.6970.0020.0020.0000.0000.0000.000
83A84ALA00.010-0.00325.745-0.016-0.0160.0000.0000.0000.000
84A85ALA00.0630.04822.080-0.013-0.0130.0000.0000.0000.000
85A86LEU00.0250.00519.531-0.029-0.0290.0000.0000.0000.000
86A87THR0-0.008-0.00521.336-0.028-0.0280.0000.0000.0000.000
87A88ALA0-0.005-0.00322.838-0.015-0.0150.0000.0000.0000.000
88A89MET0-0.0090.02015.305-0.012-0.0120.0000.0000.0000.000
89A90LEU00.0060.00218.547-0.051-0.0510.0000.0000.0000.000
90A91LYS10.8680.93720.1530.1990.1990.0000.0000.0000.000
91A92THR0-0.021-0.00518.1750.0050.0050.0000.0000.0000.000
92A93HIS00.0070.00313.500-0.102-0.1020.0000.0000.0000.000
93A94LYS10.8640.94117.1300.3130.3130.0000.0000.0000.000
94A95ALA0-0.041-0.01819.817-0.005-0.0050.0000.0000.0000.000
95A96GLN0-0.027-0.01015.541-0.036-0.0360.0000.0000.0000.000
96A97GLY0-0.037-0.00415.696-0.067-0.0670.0000.0000.0000.000
97A98LYS10.8810.9409.2551.4261.4260.0000.0000.0000.000
98A99LEU0-0.0080.00212.8510.1110.1110.0000.0000.0000.000
99A100ILE00.0180.01414.836-0.024-0.0240.0000.0000.0000.000
100A101ALA00.015-0.00416.7790.0330.0330.0000.0000.0000.000
101A102ALA0-0.017-0.00118.5860.0080.0080.0000.0000.0000.000
102A103ILE0-0.033-0.01121.4320.0010.0010.0000.0000.0000.000
103A104CSD-1-0.811-0.89623.502-0.134-0.1340.0000.0000.0000.000
104A105ALA00.0530.01627.220-0.001-0.0010.0000.0000.0000.000
105A106SER0-0.040-0.02924.3350.0060.0060.0000.0000.0000.000
106A107PRO0-0.0210.00224.519-0.010-0.0100.0000.0000.0000.000
107A108ALA0-0.0120.00126.333-0.002-0.0020.0000.0000.0000.000
108A109VAL00.0330.01629.2280.0010.0010.0000.0000.0000.000
109A110VAL00.0030.01024.0420.0030.0030.0000.0000.0000.000
110A111LEU0-0.014-0.01021.925-0.004-0.0040.0000.0000.0000.000
111A112GLN00.0350.02225.895-0.009-0.0090.0000.0000.0000.000
112A113THR0-0.030-0.02129.3860.0090.0090.0000.0000.0000.000
113A114HIS0-0.044-0.02126.6720.0060.0060.0000.0000.0000.000
114A115GLY00.0020.00627.889-0.009-0.0090.0000.0000.0000.000
115A116LEU0-0.039-0.03222.634-0.011-0.0110.0000.0000.0000.000
116A117LEU00.004-0.00124.574-0.028-0.0280.0000.0000.0000.000
117A118GLN0-0.002-0.01026.8140.0120.0120.0000.0000.0000.000
118A119GLY00.004-0.00727.684-0.014-0.0140.0000.0000.0000.000
119A120GLU-1-0.848-0.88923.477-0.334-0.3340.0000.0000.0000.000
120A121LYS10.8460.89826.4630.1840.1840.0000.0000.0000.000
121A122ALA00.002-0.00925.899-0.024-0.0240.0000.0000.0000.000
122A123VAL00.0010.00425.9630.0200.0200.0000.0000.0000.000
123A124ALA00.031-0.00327.319-0.014-0.0140.0000.0000.0000.000
124A125TYR00.016-0.00628.9200.0120.0120.0000.0000.0000.000
125A126PRO0-0.0060.00330.9340.0010.0010.0000.0000.0000.000
126A127CYS0-0.039-0.01834.1040.0020.0020.0000.0000.0000.000
127A128PHE00.022-0.00732.1540.0030.0030.0000.0000.0000.000
128A129MET0-0.0200.00631.520-0.010-0.0100.0000.0000.0000.000
129A130ASP-1-0.843-0.91534.407-0.107-0.1070.0000.0000.0000.000
130A131GLN0-0.039-0.01333.423-0.003-0.0030.0000.0000.0000.000
131A132PHE0-0.013-0.00228.566-0.008-0.0080.0000.0000.0000.000
132A133PRO00.0770.03233.7950.0100.0100.0000.0000.0000.000
133A134ALA00.022-0.00235.178-0.006-0.0060.0000.0000.0000.000
134A135ASP-1-0.923-0.95535.304-0.144-0.1440.0000.0000.0000.000
135A136MET00.0180.03129.971-0.008-0.0080.0000.0000.0000.000
136A137ARG10.7350.87630.5080.1090.1090.0000.0000.0000.000
137A138GLY00.006-0.00328.8480.0030.0030.0000.0000.0000.000
138A139GLU-1-0.960-0.98128.762-0.118-0.1180.0000.0000.0000.000
139A140GLY00.0090.00427.268-0.014-0.0140.0000.0000.0000.000
140A141ARG10.8220.88626.1820.1270.1270.0000.0000.0000.000
141A142VAL0-0.0260.00020.310-0.012-0.0120.0000.0000.0000.000
142A143CYS0-0.0150.01223.3540.0150.0150.0000.0000.0000.000
143A144VAL0-0.021-0.01418.915-0.026-0.0260.0000.0000.0000.000
144A145SER00.000-0.00421.4800.0400.0400.0000.0000.0000.000
145A146ASN0-0.032-0.02420.608-0.020-0.0200.0000.0000.0000.000
146A147LYS10.8420.91415.6850.6160.6160.0000.0000.0000.000
147A148ILE00.0130.02118.165-0.042-0.0420.0000.0000.0000.000
148A149VAL0-0.017-0.00316.7140.0200.0200.0000.0000.0000.000
149A150THR00.0240.01419.8400.0070.0070.0000.0000.0000.000
150A151SER00.012-0.01822.3760.0090.0090.0000.0000.0000.000
151A152VAL00.0270.02024.2560.0030.0030.0000.0000.0000.000
152A153GLY00.0440.01426.3930.0090.0090.0000.0000.0000.000
153A154PRO00.0890.05325.713-0.006-0.0060.0000.0000.0000.000
154A155SER0-0.020-0.00925.353-0.005-0.0050.0000.0000.0000.000
155A156SER0-0.018-0.01724.6000.0110.0110.0000.0000.0000.000
156A157ALA00.0520.03821.356-0.021-0.0210.0000.0000.0000.000
157A158ILE00.0410.02119.384-0.027-0.0270.0000.0000.0000.000
158A159GLU-1-0.836-0.90418.945-0.176-0.1760.0000.0000.0000.000
159A160PHE00.003-0.01818.869-0.034-0.0340.0000.0000.0000.000
160A161ALA00.0350.01315.183-0.051-0.0510.0000.0000.0000.000
161A162LEU00.0000.00314.482-0.063-0.0630.0000.0000.0000.000
162A163LYS10.8300.92814.8400.2550.2550.0000.0000.0000.000
163A164LEU00.0500.01413.025-0.058-0.0580.0000.0000.0000.000
164A165ILE0-0.0110.0059.774-0.157-0.1570.0000.0000.0000.000
165A166GLU-1-0.854-0.89110.411-0.361-0.3610.0000.0000.0000.000
166A167VAL0-0.049-0.03812.148-0.016-0.0160.0000.0000.0000.000
167A168LEU0-0.0050.0097.881-0.046-0.0460.0000.0000.0000.000
168A169TYR0-0.0050.0034.468-0.964-0.908-0.001-0.010-0.0450.000
169A170ASN00.0430.0137.9390.1910.1910.0000.0000.0000.000
170A171LYS10.9150.94611.3160.2280.2280.0000.0000.0000.000
171A172GLU-1-0.852-0.91913.3370.0770.0770.0000.0000.0000.000
172A173GLN0-0.014-0.0078.1380.1010.1010.0000.0000.0000.000
173A174ALA00.0300.01211.5630.0370.0370.0000.0000.0000.000
174A175LYS10.8670.93013.8550.0570.0570.0000.0000.0000.000
175A176LYS10.8970.95612.833-0.152-0.1520.0000.0000.0000.000
176A177ILE0-0.0040.00911.8710.0270.0270.0000.0000.0000.000
177A178ALA00.001-0.00815.3510.0040.0040.0000.0000.0000.000
178A179ALA0-0.010-0.00518.6020.0080.0080.0000.0000.0000.000
179A180GLN0-0.034-0.02213.912-0.018-0.0180.0000.0000.0000.000
180A181LEU0-0.015-0.01017.2870.0040.0040.0000.0000.0000.000
181A182LEU0-0.0410.00220.692-0.006-0.0060.0000.0000.0000.000
182A183TYR0-0.018-0.00421.261-0.011-0.0110.0000.0000.0000.000
183A184ALA00.006-0.01022.7940.0030.0030.0000.0000.0000.000
184A185TYR0-0.032-0.03717.195-0.012-0.0120.0000.0000.0000.000