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: 171NZ

Calculation Name: 2NLK-A-Xray372

Preferred Name: Receptor-type tyrosine-protein phosphatase gamma

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2NLK

Chain ID: A

ChEMBL ID: CHEMBL4905

UniProt ID: P23470

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 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 563
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -12363805.08221
FMO2-HF: Nuclear repulsion 12135129.621617
FMO2-HF: Total energy -228675.460593
FMO2-MP2: Total energy -229338.988821


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:827:ALA)


Summations of interaction energy for fragment #1(A:827: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.
-11.206-7.9269.076-5.497-6.86-0.028
Interaction energy analysis for fragmet #1(A:827:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : 0.004
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].
3A829PRO00.021-0.0023.8840.1381.521-0.010-0.680-0.6940.002
4A830VAL00.0610.0156.1630.3010.3010.0000.0000.0000.000
5A831LYS10.9020.9448.4971.1131.1130.0000.0000.0000.000
6A832GLN00.0010.0078.2100.3390.3390.0000.0000.0000.000
7A833PHE00.0250.0176.9290.1100.1100.0000.0000.0000.000
8A834VAL00.0380.0119.5660.1370.1370.0000.0000.0000.000
9A835LYS10.8050.89511.8010.8720.8720.0000.0000.0000.000
10A836HIS00.0270.0116.491-0.185-0.1850.0000.0000.0000.000
11A837ILE0-0.019-0.01310.0070.1120.1120.0000.0000.0000.000
12A838GLY00.0150.01512.5300.0830.0830.0000.0000.0000.000
13A839GLU-1-0.786-0.89211.916-0.675-0.6750.0000.0000.0000.000
14A840LEU0-0.0450.0049.1520.0460.0460.0000.0000.0000.000
15A841TYR0-0.019-0.04413.4390.0650.0650.0000.0000.0000.000
16A842SER0-0.091-0.04416.3750.0420.0420.0000.0000.0000.000
17A843ASN00.003-0.01218.4610.0170.0170.0000.0000.0000.000
18A844ASN0-0.007-0.00920.8690.0130.0130.0000.0000.0000.000
19A845GLN00.0040.00217.8720.0110.0110.0000.0000.0000.000
20A846HIS0-0.033-0.01417.1830.0020.0020.0000.0000.0000.000
21A847GLY00.0210.01713.9810.0140.0140.0000.0000.0000.000
22A848PHE00.012-0.02512.3450.0050.0050.0000.0000.0000.000
23A849SER0-0.014-0.02414.2610.0370.0370.0000.0000.0000.000
24A850GLU-1-0.891-0.91814.257-0.004-0.0040.0000.0000.0000.000
25A851ASP-1-0.823-0.8929.166-0.070-0.0700.0000.0000.0000.000
26A852PHE0-0.056-0.02711.9780.0910.0910.0000.0000.0000.000
27A853GLU-1-0.789-0.89714.5810.1500.1500.0000.0000.0000.000
28A854GLU-1-0.778-0.86411.0160.4350.4350.0000.0000.0000.000
29A855VAL0-0.007-0.02611.2940.0750.0750.0000.0000.0000.000
30A856GLN0-0.036-0.00413.7000.0500.0500.0000.0000.0000.000
31A857ARG10.8640.92017.158-0.142-0.1420.0000.0000.0000.000
32A858CYS0-0.100-0.03313.3700.0340.0340.0000.0000.0000.000
33A859THR00.028-0.01515.3760.0330.0330.0000.0000.0000.000
34A860ALA0-0.032-0.00517.909-0.014-0.0140.0000.0000.0000.000
35A861ASP-1-0.862-0.93420.4380.1880.1880.0000.0000.0000.000
36A862MET0-0.094-0.03215.2110.0030.0030.0000.0000.0000.000
37A863ASN0-0.079-0.03721.427-0.015-0.0150.0000.0000.0000.000
38A864ILE0-0.0190.00419.361-0.005-0.0050.0000.0000.0000.000
39A865THR00.0300.01024.085-0.008-0.0080.0000.0000.0000.000
40A866ALA00.039-0.00726.6360.0150.0150.0000.0000.0000.000
41A867GLU-1-0.909-0.94528.8780.1200.1200.0000.0000.0000.000
42A868HIS0-0.096-0.07731.757-0.015-0.0150.0000.0000.0000.000
43A869SER0-0.039-0.01729.982-0.007-0.0070.0000.0000.0000.000
44A870ASN0-0.005-0.01430.772-0.013-0.0130.0000.0000.0000.000
45A871HIS00.0390.04534.287-0.007-0.0070.0000.0000.0000.000
46A872PRO00.0460.00537.4430.0000.0000.0000.0000.0000.000
47A873GLU-1-0.831-0.92640.4600.0790.0790.0000.0000.0000.000
48A874ASN0-0.005-0.01935.541-0.004-0.0040.0000.0000.0000.000
49A875LYS10.9590.99436.869-0.076-0.0760.0000.0000.0000.000
50A876HIS00.001-0.00237.662-0.001-0.0010.0000.0000.0000.000
51A877LYS10.8300.91235.691-0.100-0.1000.0000.0000.0000.000
52A878ASN00.0250.03532.7980.0140.0140.0000.0000.0000.000
53A879ARG10.7620.86232.306-0.083-0.0830.0000.0000.0000.000
54A880TYR0-0.021-0.03430.116-0.009-0.0090.0000.0000.0000.000
55A881ILE0-0.002-0.00931.8100.0070.0070.0000.0000.0000.000
56A882ASN00.0540.02828.301-0.001-0.0010.0000.0000.0000.000
57A883ILE0-0.052-0.01525.6620.0090.0090.0000.0000.0000.000
58A884LEU00.0380.03926.793-0.005-0.0050.0000.0000.0000.000
59A885ALA00.004-0.01225.6330.0130.0130.0000.0000.0000.000
60A886TYR00.016-0.00219.568-0.027-0.0270.0000.0000.0000.000
61A887ASP-1-0.736-0.84225.4470.1720.1720.0000.0000.0000.000
62A888HIS0-0.0080.00120.051-0.038-0.0380.0000.0000.0000.000
63A889SER0-0.043-0.04021.359-0.004-0.0040.0000.0000.0000.000
64A890ARG10.7820.89723.296-0.159-0.1590.0000.0000.0000.000
65A891VAL00.000-0.01226.2330.0020.0020.0000.0000.0000.000
66A892LYS10.8400.92728.009-0.213-0.2130.0000.0000.0000.000
67A893LEU0-0.0100.01931.2840.0020.0020.0000.0000.0000.000
68A894ARG10.8180.88632.792-0.139-0.1390.0000.0000.0000.000
69A895PRO00.0200.02037.266-0.002-0.0020.0000.0000.0000.000
70A896LEU0-0.006-0.01339.916-0.002-0.0020.0000.0000.0000.000
71A897PRO00.0130.01443.1330.0000.0000.0000.0000.0000.000
72A898GLY00.0150.00946.853-0.001-0.0010.0000.0000.0000.000
73A899LYS10.8440.91141.994-0.080-0.0800.0000.0000.0000.000
74A900ASP-1-0.812-0.89141.0720.0880.0880.0000.0000.0000.000
75A901SER00.0620.03642.1280.0050.0050.0000.0000.0000.000
76A902LYS10.8460.92636.208-0.118-0.1180.0000.0000.0000.000
77A903HIS10.8270.90637.801-0.090-0.0900.0000.0000.0000.000
78A904SER00.0290.01937.8630.0050.0050.0000.0000.0000.000
79A905ASP-1-0.796-0.87434.6320.1300.1300.0000.0000.0000.000
80A906TYR0-0.060-0.03330.6230.0150.0150.0000.0000.0000.000
81A907ILE00.0570.01630.593-0.009-0.0090.0000.0000.0000.000
82A908ASN0-0.033-0.00828.4390.0220.0220.0000.0000.0000.000
83A909ALA00.0220.01126.596-0.002-0.0020.0000.0000.0000.000
84A910ASN0-0.0050.01122.355-0.019-0.0190.0000.0000.0000.000
85A911TYR0-0.042-0.03521.8000.0020.0020.0000.0000.0000.000
86A912VAL00.0020.00316.1320.0140.0140.0000.0000.0000.000
87A913ASP-1-0.781-0.86214.3130.5990.5990.0000.0000.0000.000
88A914GLY00.035-0.00213.357-0.029-0.0290.0000.0000.0000.000
89A915TYR0-0.049-0.0626.9650.2790.2790.0000.0000.0000.000
90A916ASN0-0.033-0.00910.659-0.067-0.0670.0000.0000.0000.000
91A917LYS10.8870.94812.221-0.471-0.4710.0000.0000.0000.000
92A918ALA00.0500.03015.6800.0080.0080.0000.0000.0000.000
93A919LYS10.9290.94417.362-0.455-0.4550.0000.0000.0000.000
94A920ALA00.0080.02816.758-0.048-0.0480.0000.0000.0000.000
95A921TYR0-0.046-0.05514.987-0.033-0.0330.0000.0000.0000.000
96A922ILE0-0.015-0.01320.4320.0150.0150.0000.0000.0000.000
97A923ALA00.0100.03120.665-0.018-0.0180.0000.0000.0000.000
98A924THR0-0.032-0.05322.775-0.005-0.0050.0000.0000.0000.000
99A925GLN00.0090.00726.390-0.004-0.0040.0000.0000.0000.000
100A926GLY00.0520.01328.798-0.001-0.0010.0000.0000.0000.000
101A927PRO0-0.0180.01030.994-0.003-0.0030.0000.0000.0000.000
102A928LEU00.0530.02833.672-0.008-0.0080.0000.0000.0000.000
103A929LYS10.9260.94237.080-0.050-0.0500.0000.0000.0000.000
104A930SER0-0.016-0.01139.4290.0000.0000.0000.0000.0000.000
105A931THR00.0250.00535.3660.0030.0030.0000.0000.0000.000
106A932PHE0-0.025-0.00336.3610.0050.0050.0000.0000.0000.000
107A933GLU-1-0.823-0.90537.5200.0790.0790.0000.0000.0000.000
108A934ASP-1-0.802-0.90435.8080.1000.1000.0000.0000.0000.000
109A935PHE00.0130.00530.0610.0090.0090.0000.0000.0000.000
110A936TRP00.015-0.01833.1070.0080.0080.0000.0000.0000.000
111A937ARG10.7550.86735.305-0.103-0.1030.0000.0000.0000.000
112A938MET0-0.0020.01528.9100.0080.0080.0000.0000.0000.000
113A939ILE00.006-0.00130.3060.0070.0070.0000.0000.0000.000
114A940TRP0-0.009-0.01031.7140.0030.0030.0000.0000.0000.000
115A941GLU-1-0.790-0.89933.5430.1230.1230.0000.0000.0000.000
116A942GLN0-0.0280.00128.1580.0220.0220.0000.0000.0000.000
117A943ASN0-0.009-0.00228.7030.0000.0000.0000.0000.0000.000
118A944THR0-0.032-0.00126.8010.0010.0010.0000.0000.0000.000
119A945GLY00.0500.02827.977-0.011-0.0110.0000.0000.0000.000
120A946ILE0-0.038-0.02224.823-0.012-0.0120.0000.0000.0000.000
121A947ILE0-0.002-0.00126.4410.0140.0140.0000.0000.0000.000
122A948VAL0-0.0040.00222.234-0.013-0.0130.0000.0000.0000.000
123A949MET0-0.0410.00225.4040.0090.0090.0000.0000.0000.000
124A950ILE0-0.014-0.01221.798-0.012-0.0120.0000.0000.0000.000
125A951THR00.000-0.02526.020-0.001-0.0010.0000.0000.0000.000
126A952ASN0-0.0240.00229.2850.0010.0010.0000.0000.0000.000
127A953LEU00.005-0.00232.8410.0050.0050.0000.0000.0000.000
128A954VAL0-0.012-0.01335.6000.0020.0020.0000.0000.0000.000
129A955GLU-1-0.715-0.81730.7890.0430.0430.0000.0000.0000.000
130A956LYS10.8860.93334.158-0.010-0.0100.0000.0000.0000.000
131A957GLY00.0640.04037.2760.0000.0000.0000.0000.0000.000
132A958ARG10.9430.97635.068-0.028-0.0280.0000.0000.0000.000
133A959ARG10.9300.94936.529-0.047-0.0470.0000.0000.0000.000
134A960LYS10.8710.94430.319-0.043-0.0430.0000.0000.0000.000
135A961CYS00.0040.02032.3670.0110.0110.0000.0000.0000.000
136A962ASP-1-0.827-0.87034.4090.0520.0520.0000.0000.0000.000
137A963GLN0-0.036-0.03836.2200.0030.0030.0000.0000.0000.000
138A964TYR0-0.010-0.01930.699-0.003-0.0030.0000.0000.0000.000
139A965TRP00.0320.01034.1540.0060.0060.0000.0000.0000.000
140A966PRO00.0120.02938.626-0.002-0.0020.0000.0000.0000.000
141A967THR00.031-0.00141.0170.0020.0020.0000.0000.0000.000
142A968GLU-1-0.833-0.89942.3790.0270.0270.0000.0000.0000.000
143A969ASN0-0.050-0.03744.3620.0030.0030.0000.0000.0000.000
144A970SER0-0.031-0.02144.0040.0030.0030.0000.0000.0000.000
145A971GLU-1-0.837-0.89842.9060.0470.0470.0000.0000.0000.000
146A972GLU-1-0.983-0.99843.7410.0570.0570.0000.0000.0000.000
147A973TYR00.0400.01339.4600.0010.0010.0000.0000.0000.000
148A974GLY00.0880.05141.8800.0050.0050.0000.0000.0000.000
149A975ASN0-0.037-0.03242.565-0.005-0.0050.0000.0000.0000.000
150A976ILE0-0.034-0.00537.9360.0000.0000.0000.0000.0000.000
151A977ILE00.0150.02441.281-0.001-0.0010.0000.0000.0000.000
152A978VAL0-0.001-0.00438.2660.0030.0030.0000.0000.0000.000
153A979THR00.002-0.02440.654-0.003-0.0030.0000.0000.0000.000
154A980LEU00.0030.01838.3960.0030.0030.0000.0000.0000.000
155A981LYS10.8180.89139.281-0.044-0.0440.0000.0000.0000.000
156A982SER00.0430.02437.851-0.002-0.0020.0000.0000.0000.000
157A983THR00.006-0.01736.6050.0050.0050.0000.0000.0000.000
158A984LYS10.8520.93033.952-0.012-0.0120.0000.0000.0000.000
159A985ILE00.0380.01933.9320.0040.0040.0000.0000.0000.000
160A986HIS10.8460.94231.249-0.012-0.0120.0000.0000.0000.000
161A987ALA00.0140.03532.0370.0040.0040.0000.0000.0000.000
162A988CYS00.012-0.00928.046-0.002-0.0020.0000.0000.0000.000
163A989TYR0-0.010-0.00727.7450.0050.0050.0000.0000.0000.000
164A990THR0-0.0020.00629.876-0.006-0.0060.0000.0000.0000.000
165A991VAL0-0.0290.00029.7420.0070.0070.0000.0000.0000.000
166A992ARG10.9080.92732.002-0.050-0.0500.0000.0000.0000.000
167A993ARG10.9570.99633.577-0.044-0.0440.0000.0000.0000.000
168A994PHE00.0480.01234.410-0.005-0.0050.0000.0000.0000.000
169A995SER0-0.005-0.01136.4710.0020.0020.0000.0000.0000.000
170A996ILE0-0.033-0.00135.270-0.002-0.0020.0000.0000.0000.000
171A997ARG10.9490.97339.155-0.052-0.0520.0000.0000.0000.000
172A998ASN00.0390.03439.453-0.005-0.0050.0000.0000.0000.000
173A999THR0-0.013-0.02141.922-0.002-0.0020.0000.0000.0000.000
174A1000LYS10.9250.96044.490-0.064-0.0640.0000.0000.0000.000
175A1001VAL0-0.0250.00840.3320.0000.0000.0000.0000.0000.000
176A1002LYS10.9040.93943.696-0.068-0.0680.0000.0000.0000.000
177A1003LYS11.0000.99643.971-0.047-0.0470.0000.0000.0000.000
178A1004GLY00.0410.03444.6260.0010.0010.0000.0000.0000.000
179A1005GLN00.0080.00145.610-0.001-0.0010.0000.0000.0000.000
180A1006LYS10.9720.95846.502-0.038-0.0380.0000.0000.0000.000
181A1007GLY00.0430.03447.759-0.001-0.0010.0000.0000.0000.000
182A1008ASN0-0.0030.01240.5490.0000.0000.0000.0000.0000.000
183A1009PRO00.0540.02540.2300.0000.0000.0000.0000.0000.000
184A1010LYS10.8560.92433.735-0.092-0.0920.0000.0000.0000.000
185A1011GLY00.0360.02939.2490.0020.0020.0000.0000.0000.000
186A1012ARG10.7750.84142.079-0.047-0.0470.0000.0000.0000.000
187A1013GLN00.008-0.01438.6050.0060.0060.0000.0000.0000.000
188A1014ASN0-0.054-0.02639.9360.0030.0030.0000.0000.0000.000
189A1015GLU-1-0.821-0.88740.3590.0540.0540.0000.0000.0000.000
190A1016ARG10.9100.95733.771-0.105-0.1050.0000.0000.0000.000
191A1017VAL00.0030.01133.636-0.003-0.0030.0000.0000.0000.000
192A1018VAL0-0.013-0.00330.9430.0070.0070.0000.0000.0000.000
193A1019ILE0-0.021-0.00529.576-0.009-0.0090.0000.0000.0000.000
194A1020GLN00.0250.02029.3070.0040.0040.0000.0000.0000.000
195A1021TYR0-0.006-0.01026.142-0.010-0.0100.0000.0000.0000.000
196A1022HIS00.0330.01227.2360.0070.0070.0000.0000.0000.000
197A1023TYR00.0220.00725.367-0.008-0.0080.0000.0000.0000.000
198A1024THR00.008-0.00827.7260.0040.0040.0000.0000.0000.000
199A1025GLN00.0010.03129.014-0.006-0.0060.0000.0000.0000.000
200A1026TRP0-0.006-0.01920.126-0.003-0.0030.0000.0000.0000.000
201A1027PRO00.0280.03526.4110.0040.0040.0000.0000.0000.000
202A1028ASP-1-0.848-0.93428.5010.0240.0240.0000.0000.0000.000
203A1029MET0-0.038-0.01429.1070.0090.0090.0000.0000.0000.000
204A1030GLY00.0580.03424.875-0.007-0.0070.0000.0000.0000.000
205A1031VAL0-0.011-0.00220.3220.0150.0150.0000.0000.0000.000
206A1032PRO0-0.008-0.01922.103-0.005-0.0050.0000.0000.0000.000
207A1033GLU-1-0.793-0.85923.457-0.066-0.0660.0000.0000.0000.000
208A1034TYR00.0240.00223.853-0.011-0.0110.0000.0000.0000.000
209A1035ALA00.0160.01918.7910.0150.0150.0000.0000.0000.000
210A1036LEU00.0120.01020.9060.0140.0140.0000.0000.0000.000
211A1037PRO00.0560.03222.5290.0080.0080.0000.0000.0000.000
212A1038VAL00.0010.00119.4290.0160.0160.0000.0000.0000.000
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