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: V53Q1

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 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 563
LigandResidueName
LigandFragmentNumber 0
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -12350473.566624
FMO2-HF: Nuclear repulsion 12121799.994231
FMO2-HF: Total energy -228673.572392
FMO2-MP2: Total energy -229337.065686


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.
-7.931-1.4842.655-3.932-5.17-0.012
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 : -0.020 / q_NPA : -0.015
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].
3A829PRO00.0170.0013.8600.8142.170-0.014-0.629-0.7130.001
4A830VAL00.0650.0156.469-0.595-0.5950.0000.0000.0000.000
5A831LYS10.9110.9548.465-0.331-0.3310.0000.0000.0000.000
6A832GLN0-0.034-0.0128.2870.0530.0530.0000.0000.0000.000
7A833PHE00.0570.0237.342-0.122-0.1220.0000.0000.0000.000
8A834VAL00.0360.00810.343-0.045-0.0450.0000.0000.0000.000
9A835LYS10.7920.88312.1330.3970.3970.0000.0000.0000.000
10A836HIS00.0120.0107.481-0.025-0.0250.0000.0000.0000.000
11A837ILE0-0.007-0.00710.601-0.026-0.0260.0000.0000.0000.000
12A838GLY00.0240.01713.0100.0200.0200.0000.0000.0000.000
13A839GLU-1-0.780-0.88812.490-0.419-0.4190.0000.0000.0000.000
14A840LEU0-0.047-0.0029.807-0.002-0.0020.0000.0000.0000.000
15A841TYR0-0.025-0.05014.1330.0210.0210.0000.0000.0000.000
16A842SER0-0.087-0.02217.2320.0270.0270.0000.0000.0000.000
17A843ASN0-0.002-0.01618.9110.0030.0030.0000.0000.0000.000
18A844ASN0-0.002-0.01420.9750.0000.0000.0000.0000.0000.000
19A845GLN00.0010.00318.3130.0110.0110.0000.0000.0000.000
20A846HIS0-0.0100.01117.4050.0020.0020.0000.0000.0000.000
21A847GLY00.0320.01814.165-0.014-0.0140.0000.0000.0000.000
22A848PHE00.004-0.02613.063-0.050-0.0500.0000.0000.0000.000
23A849SER0-0.008-0.01414.740-0.006-0.0060.0000.0000.0000.000
24A850GLU-1-0.895-0.93814.746-0.283-0.2830.0000.0000.0000.000
25A851ASP-1-0.822-0.8769.831-0.662-0.6620.0000.0000.0000.000
26A852PHE0-0.056-0.03612.6220.0040.0040.0000.0000.0000.000
27A853GLU-1-0.857-0.93814.831-0.172-0.1720.0000.0000.0000.000
28A854GLU-1-0.799-0.88910.834-0.519-0.5190.0000.0000.0000.000
29A855VAL0-0.047-0.04611.6480.0130.0130.0000.0000.0000.000
30A856GLN0-0.0080.00414.0800.0340.0340.0000.0000.0000.000
31A857ARG10.9050.95817.4100.1870.1870.0000.0000.0000.000
32A858CYS0-0.087-0.02214.0210.0070.0070.0000.0000.0000.000
33A859THR00.021-0.02316.0500.0010.0010.0000.0000.0000.000
34A860ALA0-0.043-0.00718.4200.0160.0160.0000.0000.0000.000
35A861ASP-1-0.848-0.93120.356-0.143-0.1430.0000.0000.0000.000
36A862MET0-0.098-0.03715.2380.0120.0120.0000.0000.0000.000
37A863ASN0-0.078-0.02621.4620.0140.0140.0000.0000.0000.000
38A864ILE0-0.0120.00719.3330.0080.0080.0000.0000.0000.000
39A865THR00.0380.01824.0150.0000.0000.0000.0000.0000.000
40A866ALA00.014-0.02126.6880.0000.0000.0000.0000.0000.000
41A867GLU-1-0.910-0.95428.951-0.041-0.0410.0000.0000.0000.000
42A868HIS0-0.109-0.07031.8610.0060.0060.0000.0000.0000.000
43A869SER00.0360.02930.3610.0020.0020.0000.0000.0000.000
44A870ASN0-0.014-0.00831.3400.0020.0020.0000.0000.0000.000
45A871HIS00.0510.05934.6220.0010.0010.0000.0000.0000.000
46A872PRO00.038-0.00137.5710.0010.0010.0000.0000.0000.000
47A873GLU-1-0.842-0.93340.620-0.015-0.0150.0000.0000.0000.000
48A874ASN0-0.035-0.03535.7910.0050.0050.0000.0000.0000.000
49A875LYS10.9791.00036.8100.0330.0330.0000.0000.0000.000
50A876HIS00.006-0.00537.765-0.001-0.0010.0000.0000.0000.000
51A877LYS10.8330.91136.2030.0170.0170.0000.0000.0000.000
52A878ASN0-0.0200.01132.9030.0000.0000.0000.0000.0000.000
53A879ARG10.7610.87032.1560.0250.0250.0000.0000.0000.000
54A880TYR0-0.014-0.03530.2580.0000.0000.0000.0000.0000.000
55A881ILE00.006-0.00532.1840.0000.0000.0000.0000.0000.000
56A882ASN00.0430.01528.5890.0040.0040.0000.0000.0000.000
57A883ILE0-0.058-0.01125.919-0.006-0.0060.0000.0000.0000.000
58A884LEU00.0120.02327.0210.0070.0070.0000.0000.0000.000
59A885ALA00.002-0.00625.906-0.004-0.0040.0000.0000.0000.000
60A886TYR0-0.003-0.00620.0030.0070.0070.0000.0000.0000.000
61A887ASP-1-0.744-0.86325.424-0.037-0.0370.0000.0000.0000.000
62A888HIS0-0.046-0.01619.8430.0150.0150.0000.0000.0000.000
63A889SER0-0.031-0.02621.3990.0080.0080.0000.0000.0000.000
64A890ARG10.8000.91623.3800.0280.0280.0000.0000.0000.000
65A891VAL0-0.007-0.00425.9330.0040.0040.0000.0000.0000.000
66A892LYS10.8990.95328.0070.0160.0160.0000.0000.0000.000
67A893LEU0-0.036-0.00531.4470.0040.0040.0000.0000.0000.000
68A894ARG10.8350.89632.214-0.006-0.0060.0000.0000.0000.000
69A895PRO00.0050.01036.899-0.001-0.0010.0000.0000.0000.000
70A896LEU0-0.003-0.00239.9240.0020.0020.0000.0000.0000.000
71A897PRO00.0180.01543.062-0.001-0.0010.0000.0000.0000.000
72A898GLY00.0120.00546.6860.0000.0000.0000.0000.0000.000
73A899LYS10.8460.91442.5700.0020.0020.0000.0000.0000.000
74A900ASP-1-0.802-0.88741.538-0.011-0.0110.0000.0000.0000.000
75A901SER00.0560.03942.5250.0010.0010.0000.0000.0000.000
76A902LYS10.8530.92136.5730.0140.0140.0000.0000.0000.000
77A903HIS10.8210.90338.2170.0170.0170.0000.0000.0000.000
78A904SER00.0420.02338.332-0.001-0.0010.0000.0000.0000.000
79A905ASP-1-0.818-0.89534.662-0.015-0.0150.0000.0000.0000.000
80A906TYR0-0.057-0.04430.8240.0010.0010.0000.0000.0000.000
81A907ILE00.0700.02230.5080.0010.0010.0000.0000.0000.000
82A908ASN0-0.0150.00428.454-0.004-0.0040.0000.0000.0000.000
83A909ALA00.0190.00426.6560.0010.0010.0000.0000.0000.000
84A910ASN0-0.0080.00722.367-0.002-0.0020.0000.0000.0000.000
85A911TYR0-0.048-0.04721.2650.0030.0030.0000.0000.0000.000
86A912VAL00.0150.00716.396-0.013-0.0130.0000.0000.0000.000
87A913ASP-1-0.816-0.88013.7980.0030.0030.0000.0000.0000.000
88A914GLY00.041-0.00113.624-0.018-0.0180.0000.0000.0000.000
89A915TYR0-0.067-0.0676.9370.0450.0450.0000.0000.0000.000
90A916ASN0-0.026-0.00810.421-0.014-0.0140.0000.0000.0000.000
91A917LYS10.9220.97611.982-0.100-0.1000.0000.0000.0000.000
92A918ALA00.0500.03315.093-0.025-0.0250.0000.0000.0000.000
93A919LYS10.9320.94616.8370.0100.0100.0000.0000.0000.000
94A920ALA0-0.035-0.00216.6540.0070.0070.0000.0000.0000.000
95A921TYR0-0.025-0.04915.0930.0060.0060.0000.0000.0000.000
96A922ILE0-0.009-0.00420.392-0.007-0.0070.0000.0000.0000.000
97A923ALA00.0010.01420.9650.0030.0030.0000.0000.0000.000
98A924THR0-0.016-0.04723.078-0.002-0.0020.0000.0000.0000.000
99A925GLN0-0.0010.00126.630-0.005-0.0050.0000.0000.0000.000
100A926GLY00.0270.00428.9580.0050.0050.0000.0000.0000.000
101A927PRO00.0000.01331.351-0.002-0.0020.0000.0000.0000.000
102A928LEU00.0320.01834.1260.0000.0000.0000.0000.0000.000
103A929LYS10.9650.97437.5110.0110.0110.0000.0000.0000.000
104A930SER0-0.0110.01040.0360.0020.0020.0000.0000.0000.000
105A931THR00.0370.01535.6650.0000.0000.0000.0000.0000.000
106A932PHE0-0.021-0.00136.8010.0010.0010.0000.0000.0000.000
107A933GLU-1-0.797-0.89937.7630.0010.0010.0000.0000.0000.000
108A934ASP-1-0.839-0.91735.878-0.004-0.0040.0000.0000.0000.000
109A935PHE00.0190.00430.3370.0020.0020.0000.0000.0000.000
110A936TRP00.028-0.00633.4840.0040.0040.0000.0000.0000.000
111A937ARG10.8130.91635.4790.0030.0030.0000.0000.0000.000
112A938MET00.0180.02129.3640.0020.0020.0000.0000.0000.000
113A939ILE0-0.010-0.00230.4540.0030.0030.0000.0000.0000.000
114A940TRP0-0.004-0.00731.8670.0040.0040.0000.0000.0000.000
115A941GLU-1-0.831-0.93033.1930.0100.0100.0000.0000.0000.000
116A942GLN0-0.0140.01827.7580.0000.0000.0000.0000.0000.000
117A943ASN0-0.010-0.00228.3360.0020.0020.0000.0000.0000.000
118A944THR0-0.0230.01026.8770.0040.0040.0000.0000.0000.000
119A945GLY00.0460.01927.835-0.002-0.0020.0000.0000.0000.000
120A946ILE0-0.030-0.01424.848-0.001-0.0010.0000.0000.0000.000
121A947ILE00.0040.01126.539-0.003-0.0030.0000.0000.0000.000
122A948VAL0-0.012-0.00822.4640.0030.0030.0000.0000.0000.000
123A949MET0-0.047-0.00325.560-0.006-0.0060.0000.0000.0000.000
124A950ILE0-0.017-0.01322.1880.0030.0030.0000.0000.0000.000
125A951THR0-0.002-0.02826.478-0.009-0.0090.0000.0000.0000.000
126A952ASN00.0030.01529.6710.0080.0080.0000.0000.0000.000
127A953LEU0-0.001-0.00133.277-0.003-0.0030.0000.0000.0000.000
128A954VAL00.0310.01135.944-0.002-0.0020.0000.0000.0000.000
129A955GLU-1-0.725-0.82231.345-0.029-0.0290.0000.0000.0000.000
130A956LYS10.9070.93634.6720.0350.0350.0000.0000.0000.000
131A957GLY00.0460.02637.852-0.001-0.0010.0000.0000.0000.000
132A958ARG10.9380.97735.7170.0360.0360.0000.0000.0000.000
133A959ARG10.9260.95337.1310.0150.0150.0000.0000.0000.000
134A960LYS10.8720.93630.6620.0350.0350.0000.0000.0000.000
135A961CYS0-0.023-0.00432.775-0.001-0.0010.0000.0000.0000.000
136A962ASP-1-0.860-0.90234.822-0.014-0.0140.0000.0000.0000.000
137A963GLN0-0.039-0.03536.403-0.001-0.0010.0000.0000.0000.000
138A964TYR0-0.025-0.02331.0860.0020.0020.0000.0000.0000.000
139A965TRP00.0520.02134.5900.0010.0010.0000.0000.0000.000
140A966PRO00.0250.03338.735-0.002-0.0020.0000.0000.0000.000
141A967THR00.022-0.00641.2580.0010.0010.0000.0000.0000.000
142A968GLU-1-0.874-0.93542.9610.0100.0100.0000.0000.0000.000
143A969ASN0-0.023-0.00544.8310.0000.0000.0000.0000.0000.000
144A970SER0-0.015-0.02043.9900.0020.0020.0000.0000.0000.000
145A971GLU-1-0.844-0.90443.1050.0030.0030.0000.0000.0000.000
146A972GLU-1-0.995-0.98943.5130.0080.0080.0000.0000.0000.000
147A973TYR00.0390.00940.250-0.001-0.0010.0000.0000.0000.000
148A974GLY00.0510.02641.9320.0010.0010.0000.0000.0000.000
149A975ASN0-0.016-0.01342.7520.0010.0010.0000.0000.0000.000
150A976ILE0-0.015-0.01138.2570.0020.0020.0000.0000.0000.000
151A977ILE0-0.0090.00941.621-0.001-0.0010.0000.0000.0000.000
152A978VAL00.0160.00438.1700.0030.0030.0000.0000.0000.000
153A979THR0-0.004-0.03340.795-0.001-0.0010.0000.0000.0000.000
154A980LEU0-0.0010.01438.6090.0020.0020.0000.0000.0000.000
155A981LYS10.7980.88339.341-0.021-0.0210.0000.0000.0000.000
156A982SER00.0410.01738.1440.0000.0000.0000.0000.0000.000
157A983THR00.0400.00637.154-0.001-0.0010.0000.0000.0000.000
158A984LYS10.8580.93134.083-0.041-0.0410.0000.0000.0000.000
159A985ILE00.0500.02634.6180.0010.0010.0000.0000.0000.000
160A986HIS10.8350.94131.581-0.033-0.0330.0000.0000.0000.000
161A987ALA00.0230.03832.196-0.003-0.0030.0000.0000.0000.000
162A988CYS0-0.005-0.00928.428-0.003-0.0030.0000.0000.0000.000
163A989TYR00.0320.02128.066-0.002-0.0020.0000.0000.0000.000
164A990THR00.0150.00830.2170.0020.0020.0000.0000.0000.000
165A991VAL0-0.054-0.03030.0730.0000.0000.0000.0000.0000.000
166A992ARG10.9020.94432.494-0.011-0.0110.0000.0000.0000.000
167A993ARG10.9781.00533.622-0.042-0.0420.0000.0000.0000.000
168A994PHE00.0350.01334.559-0.003-0.0030.0000.0000.0000.000
169A995SER0-0.018-0.01036.5900.0040.0040.0000.0000.0000.000
170A996ILE0-0.0070.00735.305-0.003-0.0030.0000.0000.0000.000
171A997ARG10.9700.98539.136-0.014-0.0140.0000.0000.0000.000
172A998ASN00.0220.02139.208-0.003-0.0030.0000.0000.0000.000
173A999THR0-0.002-0.01942.0070.0010.0010.0000.0000.0000.000
174A1000LYS10.8830.94044.312-0.009-0.0090.0000.0000.0000.000
175A1001VAL0-0.0150.01340.2380.0000.0000.0000.0000.0000.000
176A1002LYS10.9640.97243.524-0.017-0.0170.0000.0000.0000.000
177A1003LYS11.0030.99143.731-0.018-0.0180.0000.0000.0000.000
178A1004GLY00.0240.02444.3230.0020.0020.0000.0000.0000.000
179A1005GLN00.0060.00545.2130.0000.0000.0000.0000.0000.000
180A1006LYS11.0030.97246.282-0.021-0.0210.0000.0000.0000.000
181A1007GLY00.0160.01247.7880.0000.0000.0000.0000.0000.000
182A1008ASN0-0.0230.01340.8390.0040.0040.0000.0000.0000.000
183A1009PRO00.0840.03240.370-0.001-0.0010.0000.0000.0000.000
184A1010LYS10.8830.94533.246-0.057-0.0570.0000.0000.0000.000
185A1011GLY00.0220.03139.231-0.001-0.0010.0000.0000.0000.000
186A1012ARG10.7710.84942.029-0.024-0.0240.0000.0000.0000.000
187A1013GLN00.023-0.01038.7200.0010.0010.0000.0000.0000.000
188A1014ASN0-0.079-0.03339.7160.0010.0010.0000.0000.0000.000
189A1015GLU-1-0.812-0.88840.2140.0220.0220.0000.0000.0000.000
190A1016ARG10.9180.96133.716-0.030-0.0300.0000.0000.0000.000
191A1017VAL00.0000.00333.641-0.003-0.0030.0000.0000.0000.000
192A1018VAL0-0.024-0.00530.9960.0020.0020.0000.0000.0000.000
193A1019ILE0-0.025-0.01429.740-0.002-0.0020.0000.0000.0000.000
194A1020GLN00.0340.02429.4210.0030.0030.0000.0000.0000.000
195A1021TYR00.0250.01226.4350.0000.0000.0000.0000.0000.000
196A1022HIS00.0090.00127.4630.0000.0000.0000.0000.0000.000
197A1023TYR00.0080.00525.8720.0030.0030.0000.0000.0000.000
198A1024THR0-0.001-0.02528.195-0.004-0.0040.0000.0000.0000.000
199A1025GLN00.0400.04429.495-0.003-0.0030.0000.0000.0000.000
200A1026TRP0-0.046-0.02720.636-0.001-0.0010.0000.0000.0000.000
201A1027PRO00.0280.04226.8080.0020.0020.0000.0000.0000.000
202A1028ASP-1-0.828-0.92428.824-0.038-0.0380.0000.0000.0000.000
203A1029MET0-0.046-0.02029.622-0.003-0.0030.0000.0000.0000.000
204A1030GLY00.0450.03225.5440.0010.0010.0000.0000.0000.000
205A1031VAL0-0.017-0.01320.7490.0030.0030.0000.0000.0000.000
206A1032PRO0-0.019-0.02022.2600.0040.0040.0000.0000.0000.000
207A1033GLU-1-0.803-0.86223.824-0.048-0.0480.0000.0000.0000.000
208A1034TYR00.0460.00524.4300.0000.0000.0000.0000.0000.000
209A1035ALA00.0380.01619.2930.0020.0020.0000.0000.0000.000
210A1036LEU00.0330.02421.0900.0100.0100.0000.0000.0000.000
211A1037PRO00.0550.02723.0260.0100.0100.0000.0000.0000.000
212A1038VAL0-0.0180.00120.0880.0030.0030.0000.0000.0000.000
213A1039LEU0-0.018-0.00816.3760.0120.0120.0000.0000.0000.000
214A1040THR0-0.0010.00519.9600.0190.0190.0000.0000.0000.000
215A1041PHE0-0.014-0.01622.5570.0070.0070.0000.0000.0000.000
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