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: YZ5V2

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 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 563
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -12347230.351093
FMO2-HF: Nuclear repulsion 12118559.668351
FMO2-HF: Total energy -228670.682742
FMO2-MP2: Total energy -229334.169881


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.
-8.399-2.4913.847-4.115-5.641-0.015
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 : -0.012 / q_NPA : -0.008
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].
3A829PRO00.009-0.0063.8600.7712.144-0.014-0.645-0.7140.001
4A830VAL00.0660.0156.490-0.632-0.6320.0000.0000.0000.000
5A831LYS10.9090.9568.549-0.460-0.4600.0000.0000.0000.000
6A832GLN0-0.033-0.0168.3030.0100.0100.0000.0000.0000.000
7A833PHE00.0620.0237.030-0.144-0.1440.0000.0000.0000.000
8A834VAL00.0400.01110.404-0.060-0.0600.0000.0000.0000.000
9A835LYS10.8160.89911.8380.3220.3220.0000.0000.0000.000
10A836HIS00.0130.0067.1200.0030.0030.0000.0000.0000.000
11A837ILE0-0.006-0.00410.619-0.034-0.0340.0000.0000.0000.000
12A838GLY00.0250.02013.0160.0120.0120.0000.0000.0000.000
13A839GLU-1-0.817-0.90712.151-0.387-0.3870.0000.0000.0000.000
14A840LEU0-0.050-0.0079.905-0.003-0.0030.0000.0000.0000.000
15A841TYR0-0.035-0.07314.1200.0140.0140.0000.0000.0000.000
16A842SER0-0.089-0.02117.3170.0250.0250.0000.0000.0000.000
17A843ASN0-0.005-0.01718.8880.0030.0030.0000.0000.0000.000
18A844ASN00.002-0.01320.949-0.004-0.0040.0000.0000.0000.000
19A845GLN00.0100.01218.2980.0130.0130.0000.0000.0000.000
20A846HIS00.0380.03617.329-0.001-0.0010.0000.0000.0000.000
21A847GLY00.0380.01914.136-0.016-0.0160.0000.0000.0000.000
22A848PHE00.010-0.02512.933-0.051-0.0510.0000.0000.0000.000
23A849SER0-0.0060.01014.734-0.009-0.0090.0000.0000.0000.000
24A850GLU-1-0.927-0.96214.810-0.295-0.2950.0000.0000.0000.000
25A851ASP-1-0.850-0.9159.811-0.675-0.6750.0000.0000.0000.000
26A852PHE0-0.067-0.04812.6050.0000.0000.0000.0000.0000.000
27A853GLU-1-0.876-0.94114.832-0.192-0.1920.0000.0000.0000.000
28A854GLU-1-0.807-0.86910.804-0.595-0.5950.0000.0000.0000.000
29A855VAL0-0.060-0.05811.6510.0070.0070.0000.0000.0000.000
30A856GLN0-0.024-0.00814.0800.0280.0280.0000.0000.0000.000
31A857ARG10.9350.97117.4270.1990.1990.0000.0000.0000.000
32A858CYS0-0.097-0.02714.0380.0030.0030.0000.0000.0000.000
33A859THR00.011-0.02116.056-0.001-0.0010.0000.0000.0000.000
34A860ALA0-0.037-0.00818.4320.0180.0180.0000.0000.0000.000
35A861ASP-1-0.852-0.93220.277-0.163-0.1630.0000.0000.0000.000
36A862MET0-0.109-0.04415.3310.0120.0120.0000.0000.0000.000
37A863ASN0-0.045-0.00621.4680.0110.0110.0000.0000.0000.000
38A864ILE0-0.020-0.00119.3180.0090.0090.0000.0000.0000.000
39A865THR00.0350.01624.0340.0020.0020.0000.0000.0000.000
40A866ALA00.010-0.01826.715-0.001-0.0010.0000.0000.0000.000
41A867GLU-1-0.917-0.96128.980-0.052-0.0520.0000.0000.0000.000
42A868HIS0-0.102-0.05731.6420.0080.0080.0000.0000.0000.000
43A869SER00.011-0.01530.2180.0020.0020.0000.0000.0000.000
44A870ASN00.0280.01631.7070.0030.0030.0000.0000.0000.000
45A871HIS00.0380.04834.6540.0020.0020.0000.0000.0000.000
46A872PRO00.0400.00037.6030.0010.0010.0000.0000.0000.000
47A873GLU-1-0.833-0.91940.654-0.020-0.0200.0000.0000.0000.000
48A874ASN0-0.032-0.04535.8530.0050.0050.0000.0000.0000.000
49A875LYS10.9971.01036.8510.0380.0380.0000.0000.0000.000
50A876HIS0-0.005-0.01637.804-0.001-0.0010.0000.0000.0000.000
51A877LYS10.8140.91436.2190.0240.0240.0000.0000.0000.000
52A878ASN00.0070.01833.1430.0000.0000.0000.0000.0000.000
53A879ARG10.8140.92231.8480.0300.0300.0000.0000.0000.000
54A880TYR0-0.022-0.03830.1910.0010.0010.0000.0000.0000.000
55A881ILE00.0010.00032.219-0.001-0.0010.0000.0000.0000.000
56A882ASN00.0530.01928.7670.0040.0040.0000.0000.0000.000
57A883ILE0-0.061-0.01425.822-0.007-0.0070.0000.0000.0000.000
58A884LEU0-0.0050.01427.1010.0080.0080.0000.0000.0000.000
59A885ALA0-0.027-0.02325.948-0.004-0.0040.0000.0000.0000.000
60A886TYR00.0050.00120.3570.0080.0080.0000.0000.0000.000
61A887ASP-1-0.764-0.89425.457-0.052-0.0520.0000.0000.0000.000
62A888HIS0-0.038-0.01719.8130.0170.0170.0000.0000.0000.000
63A889SER0-0.020-0.01821.4170.0080.0080.0000.0000.0000.000
64A890ARG10.8470.96123.4170.0420.0420.0000.0000.0000.000
65A891VAL0-0.006-0.00625.9180.0040.0040.0000.0000.0000.000
66A892LYS10.9100.95628.0520.0270.0270.0000.0000.0000.000
67A893LEU0-0.0200.00031.4900.0050.0050.0000.0000.0000.000
68A894ARG10.8610.92931.9500.0010.0010.0000.0000.0000.000
69A895PRO00.0320.01736.9300.0000.0000.0000.0000.0000.000
70A896LEU0-0.022-0.00939.9570.0020.0020.0000.0000.0000.000
71A897PRO00.0200.01643.095-0.001-0.0010.0000.0000.0000.000
72A898GLY00.0130.00246.7200.0010.0010.0000.0000.0000.000
73A899LYS10.8840.93743.2220.0070.0070.0000.0000.0000.000
74A900ASP-1-0.811-0.89641.585-0.017-0.0170.0000.0000.0000.000
75A901SER00.0460.03942.4990.0010.0010.0000.0000.0000.000
76A902LYS10.8610.92936.3040.0220.0220.0000.0000.0000.000
77A903HIS10.8310.90438.1410.0240.0240.0000.0000.0000.000
78A904SER00.0450.02738.374-0.001-0.0010.0000.0000.0000.000
79A905ASP-1-0.839-0.93734.767-0.024-0.0240.0000.0000.0000.000
80A906TYR0-0.071-0.01331.068-0.002-0.0020.0000.0000.0000.000
81A907ILE00.0730.03730.4500.0020.0020.0000.0000.0000.000
82A908ASN0-0.0210.00328.372-0.006-0.0060.0000.0000.0000.000
83A909ALA00.0260.00726.6950.0020.0020.0000.0000.0000.000
84A910ASN0-0.015-0.00122.313-0.001-0.0010.0000.0000.0000.000
85A911TYR0-0.056-0.05421.2570.0050.0050.0000.0000.0000.000
86A912VAL00.0040.00316.320-0.015-0.0150.0000.0000.0000.000
87A913ASP-1-0.822-0.90313.623-0.043-0.0430.0000.0000.0000.000
88A914GLY00.022-0.01113.633-0.014-0.0140.0000.0000.0000.000
89A915TYR0-0.076-0.0777.2500.0280.0280.0000.0000.0000.000
90A916ASN0-0.017-0.00110.439-0.015-0.0150.0000.0000.0000.000
91A917LYS10.9590.98311.987-0.094-0.0940.0000.0000.0000.000
92A918ALA00.0290.02615.114-0.026-0.0260.0000.0000.0000.000
93A919LYS10.9070.94716.8560.0340.0340.0000.0000.0000.000
94A920ALA0-0.0260.01216.6980.0100.0100.0000.0000.0000.000
95A921TYR0-0.031-0.07615.1030.0090.0090.0000.0000.0000.000
96A922ILE0-0.003-0.00520.395-0.009-0.0090.0000.0000.0000.000
97A923ALA0-0.0060.00720.9640.0050.0050.0000.0000.0000.000
98A924THR0-0.019-0.04523.031-0.003-0.0030.0000.0000.0000.000
99A925GLN00.0090.00926.582-0.005-0.0050.0000.0000.0000.000
100A926GLY00.0280.00429.0120.0050.0050.0000.0000.0000.000
101A927PRO00.0070.01131.313-0.003-0.0030.0000.0000.0000.000
102A928LEU00.009-0.00134.0840.0000.0000.0000.0000.0000.000
103A929LYS10.9790.97337.5060.0120.0120.0000.0000.0000.000
104A930SER0-0.035-0.00140.2000.0020.0020.0000.0000.0000.000
105A931THR00.0390.02035.500-0.001-0.0010.0000.0000.0000.000
106A932PHE0-0.0120.00336.7550.0010.0010.0000.0000.0000.000
107A933GLU-1-0.829-0.92337.723-0.002-0.0020.0000.0000.0000.000
108A934ASP-1-0.900-0.94635.734-0.011-0.0110.0000.0000.0000.000
109A935PHE00.010-0.00830.2960.0010.0010.0000.0000.0000.000
110A936TRP00.027-0.00633.4440.0040.0040.0000.0000.0000.000
111A937ARG10.8460.93435.4900.0090.0090.0000.0000.0000.000
112A938MET00.0200.02029.4730.0010.0010.0000.0000.0000.000
113A939ILE0-0.009-0.00230.2620.0030.0030.0000.0000.0000.000
114A940TRP0-0.006-0.01031.8960.0050.0050.0000.0000.0000.000
115A941GLU-1-0.884-0.97333.2570.0040.0040.0000.0000.0000.000
116A942GLN0-0.0010.03227.7450.0010.0010.0000.0000.0000.000
117A943ASN0-0.016-0.00128.3600.0020.0020.0000.0000.0000.000
118A944THR0-0.029-0.00226.7890.0050.0050.0000.0000.0000.000
119A945GLY00.0470.02227.834-0.002-0.0020.0000.0000.0000.000
120A946ILE0-0.027-0.01124.9300.0000.0000.0000.0000.0000.000
121A947ILE0-0.0010.00726.518-0.005-0.0050.0000.0000.0000.000
122A948VAL0-0.004-0.00422.3820.0040.0040.0000.0000.0000.000
123A949MET0-0.045-0.00125.545-0.007-0.0070.0000.0000.0000.000
124A950ILE0-0.013-0.01622.0940.0040.0040.0000.0000.0000.000
125A951THR0-0.029-0.04026.462-0.010-0.0100.0000.0000.0000.000
126A952ASN00.0210.03329.6520.0080.0080.0000.0000.0000.000
127A953LEU0-0.0110.00433.261-0.004-0.0040.0000.0000.0000.000
128A954VAL00.0150.00335.922-0.003-0.0030.0000.0000.0000.000
129A955GLU-1-0.743-0.86231.397-0.027-0.0270.0000.0000.0000.000
130A956LYS11.0020.99635.3990.0350.0350.0000.0000.0000.000
131A957GLY00.0330.02037.900-0.002-0.0020.0000.0000.0000.000
132A958ARG10.9360.97736.0350.0370.0370.0000.0000.0000.000
133A959ARG10.9240.95337.1830.0170.0170.0000.0000.0000.000
134A960LYS10.9250.97830.4870.0380.0380.0000.0000.0000.000
135A961CYS0-0.0280.00532.731-0.002-0.0020.0000.0000.0000.000
136A962ASP-1-0.839-0.89434.790-0.016-0.0160.0000.0000.0000.000
137A963GLN0-0.040-0.03536.373-0.001-0.0010.0000.0000.0000.000
138A964TYR0-0.036-0.03131.0360.0020.0020.0000.0000.0000.000
139A965TRP00.0340.01434.7230.0010.0010.0000.0000.0000.000
140A966PRO00.0290.03138.713-0.002-0.0020.0000.0000.0000.000
141A967THR00.017-0.01041.2450.0010.0010.0000.0000.0000.000
142A968GLU-1-0.885-0.93842.9480.0110.0110.0000.0000.0000.000
143A969ASN0-0.009-0.00144.8220.0000.0000.0000.0000.0000.000
144A970SER00.0160.02743.9780.0020.0020.0000.0000.0000.000
145A971GLU-1-0.838-0.89443.1060.0010.0010.0000.0000.0000.000
146A972GLU-1-1.029-1.00043.4870.0050.0050.0000.0000.0000.000
147A973TYR00.0640.02240.627-0.001-0.0010.0000.0000.0000.000
148A974GLY00.0540.03741.8950.0000.0000.0000.0000.0000.000
149A975ASN0-0.045-0.03542.7430.0010.0010.0000.0000.0000.000
150A976ILE0-0.020-0.01938.2690.0020.0020.0000.0000.0000.000
151A977ILE00.0010.01141.602-0.001-0.0010.0000.0000.0000.000
152A978VAL00.0060.00338.3000.0030.0030.0000.0000.0000.000
153A979THR0-0.030-0.08840.774-0.001-0.0010.0000.0000.0000.000
154A980LEU0-0.0100.00638.6210.0020.0020.0000.0000.0000.000
155A981LYS10.8050.89139.158-0.022-0.0220.0000.0000.0000.000
156A982SER00.0390.01038.0790.0010.0010.0000.0000.0000.000
157A983THR00.0570.01837.166-0.001-0.0010.0000.0000.0000.000
158A984LYS10.9040.95833.267-0.048-0.0480.0000.0000.0000.000
159A985ILE00.0610.03334.6290.0010.0010.0000.0000.0000.000
160A986HIS10.8610.94031.592-0.037-0.0370.0000.0000.0000.000
161A987ALA00.0310.04532.203-0.003-0.0030.0000.0000.0000.000
162A988CYS00.018-0.00228.298-0.004-0.0040.0000.0000.0000.000
163A989TYR0-0.0010.02727.968-0.001-0.0010.0000.0000.0000.000
164A990THR00.0350.02130.2270.0020.0020.0000.0000.0000.000
165A991VAL0-0.070-0.03729.9910.0000.0000.0000.0000.0000.000
166A992ARG10.9130.96132.499-0.012-0.0120.0000.0000.0000.000
167A993ARG10.9721.00133.855-0.043-0.0430.0000.0000.0000.000
168A994PHE00.0450.02234.375-0.003-0.0030.0000.0000.0000.000
169A995SER0-0.013-0.01536.5810.0040.0040.0000.0000.0000.000
170A996ILE0-0.0170.00435.189-0.003-0.0030.0000.0000.0000.000
171A997ARG10.9770.98739.116-0.012-0.0120.0000.0000.0000.000
172A998ASN00.0190.02039.082-0.003-0.0030.0000.0000.0000.000
173A999THR0-0.036-0.04142.0350.0010.0010.0000.0000.0000.000
174A1000LYS10.9260.96944.323-0.006-0.0060.0000.0000.0000.000
175A1001VAL0-0.0110.02140.2480.0000.0000.0000.0000.0000.000
176A1002LYS10.9650.97043.546-0.014-0.0140.0000.0000.0000.000
177A1003LYS10.9670.97643.749-0.016-0.0160.0000.0000.0000.000
178A1004GLY00.0300.02744.3350.0020.0020.0000.0000.0000.000
179A1005GLN00.0150.01045.224-0.001-0.0010.0000.0000.0000.000
180A1006LYS10.9990.97046.291-0.020-0.0200.0000.0000.0000.000
181A1007GLY00.0140.01247.7930.0000.0000.0000.0000.0000.000
182A1008ASN0-0.0360.00241.2920.0040.0040.0000.0000.0000.000
183A1009PRO00.0930.04040.370-0.001-0.0010.0000.0000.0000.000
184A1010LYS10.9570.98734.784-0.048-0.0480.0000.0000.0000.000
185A1011GLY00.0290.03539.241-0.001-0.0010.0000.0000.0000.000
186A1012ARG10.9340.95742.041-0.022-0.0220.0000.0000.0000.000
187A1013GLN00.029-0.00638.5190.0010.0010.0000.0000.0000.000
188A1014ASN0-0.064-0.02439.7350.0010.0010.0000.0000.0000.000
189A1015GLU-1-0.952-0.98040.2570.0210.0210.0000.0000.0000.000
190A1016ARG10.9150.96133.894-0.025-0.0250.0000.0000.0000.000
191A1017VAL00.0030.00633.854-0.003-0.0030.0000.0000.0000.000
192A1018VAL0-0.0110.00331.0200.0020.0020.0000.0000.0000.000
193A1019ILE0-0.024-0.01429.718-0.002-0.0020.0000.0000.0000.000
194A1020GLN00.0320.01329.4130.0030.0030.0000.0000.0000.000
195A1021TYR00.0120.00626.4160.0020.0020.0000.0000.0000.000
196A1022HIS00.017-0.00627.457-0.001-0.0010.0000.0000.0000.000
197A1023TYR0-0.007-0.00225.5840.0000.0000.0000.0000.0000.000
198A1024THR0-0.052-0.05728.194-0.004-0.0040.0000.0000.0000.000
199A1025GLN00.0590.02629.449-0.004-0.0040.0000.0000.0000.000
200A1026TRP0-0.052-0.02120.9500.0000.0000.0000.0000.0000.000
201A1027PRO00.0160.04026.6950.0020.0020.0000.0000.0000.000
202A1028ASP-1-0.908-0.98228.875-0.036-0.0360.0000.0000.0000.000
203A1029MET0-0.062-0.03429.618-0.006-0.0060.0000.0000.0000.000
204A1030GLY00.0290.02525.5820.0020.0020.0000.0000.0000.000
205A1031VAL0-0.024-0.01720.8550.0020.0020.0000.0000.0000.000
206A1032PRO0-0.021-0.02322.2980.0040.0040.0000.0000.0000.000
207A1033GLU-1-0.829-0.88123.835-0.039-0.0390.0000.0000.0000.000
208A1034TYR00.0610.01324.4510.0010.0010.0000.0000.0000.000
209A1035ALA00.0540.02919.3250.0010.0010.0000.0000.0000.000
210A1036LEU00.0290.02021.1180.0110.0110.0000.0000.0000.000
211A1037PRO00.0610.02723.0620.0110.0110.0000.0000.0000.000
212A1038VAL0-0.024-0.00219.8540.0020.0020.0000.0000.0000.000
213A1039LEU0-0.005-0.00516.3690.0100.0100.0000.0000.0000.000
214A1040THR00.0090.01519.9880.0180.0180.0000.0000.0000.000
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