FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-09-03

All entries: 45600

Number of unique PDB entries: 8613

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FMODB ID: MRZ2Z

Calculation Name: 1F2F-A-Xray547

Preferred Name: Tyrosine-protein kinase SRC

Target Type: SINGLE PROTEIN

Ligand Name: phosphate ion

Ligand 3-letter code: PO4

Ligand of Interest (LOI):

PDB ID: 1F2F

Chain ID: A

ChEMBL ID: CHEMBL3655

UniProt ID: P00523

Base Structure: X-ray

Registration Date: 2025-09-02

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 104
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -837323.001337
FMO2-HF: Nuclear repulsion 794936.715267
FMO2-HF: Total energy -42386.28607
FMO2-MP2: Total energy -42509.443693


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:144:MET)


Summations of interaction energy for fragment #1(A:144:MET)
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.
19.30721.6060.764-0.583-2.48-0.011
Interaction energy analysis for fragmet #1(A:144:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.835 / q_NPA : 0.912
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].
3A146GLU-1-0.822-0.9213.526-31.905-29.6570.765-0.580-2.433-0.011
4A147GLU-1-0.907-0.9495.766-24.886-24.835-0.001-0.003-0.0470.000
5A148TRP00.0730.0367.2901.0541.0540.0000.0000.0000.000
6A149TYR0-0.057-0.0337.3003.4623.4620.0000.0000.0000.000
7A150PHE00.0820.0307.981-3.608-3.6080.0000.0000.0000.000
8A151GLY0-0.021-0.0089.4900.4910.4910.0000.0000.0000.000
9A152LYS10.8020.87910.24827.02727.0270.0000.0000.0000.000
10A153ILE00.0380.04112.9021.3391.3390.0000.0000.0000.000
11A154THR0-0.007-0.01015.1460.7300.7300.0000.0000.0000.000
12A155ARG10.9020.94918.90212.02212.0220.0000.0000.0000.000
13A156ARG11.0191.01221.25113.03813.0380.0000.0000.0000.000
14A157GLU-1-0.800-0.84217.054-16.113-16.1130.0000.0000.0000.000
15A158SER0-0.020-0.03617.614-0.074-0.0740.0000.0000.0000.000
16A159GLU-1-0.834-0.92018.802-12.252-12.2520.0000.0000.0000.000
17A160ARG10.8350.87518.46315.62415.6240.0000.0000.0000.000
18A161LEU0-0.0030.00715.3180.2820.2820.0000.0000.0000.000
19A162LEU0-0.024-0.02218.0570.2600.2600.0000.0000.0000.000
20A163LEU0-0.042-0.01721.0510.4390.4390.0000.0000.0000.000
21A164ASN00.0160.02021.2720.9900.9900.0000.0000.0000.000
22A165PRO00.005-0.01423.987-0.164-0.1640.0000.0000.0000.000
23A166GLU-1-0.940-0.95422.785-12.484-12.4840.0000.0000.0000.000
24A167ASN0-0.056-0.02818.964-0.539-0.5390.0000.0000.0000.000
25A168PRO0-0.0030.00521.4030.4970.4970.0000.0000.0000.000
26A169ARG10.8670.94223.2119.7709.7700.0000.0000.0000.000
27A170GLY00.0290.02222.6130.0450.0450.0000.0000.0000.000
28A171THR0-0.002-0.01018.095-0.803-0.8030.0000.0000.0000.000
29A172PHE0-0.026-0.03013.9740.3150.3150.0000.0000.0000.000
30A173LEU00.0220.02413.502-0.803-0.8030.0000.0000.0000.000
31A174VAL0-0.026-0.02013.0501.4451.4450.0000.0000.0000.000
32A175ARG10.8880.96412.51914.92014.9200.0000.0000.0000.000
33A176GLU-1-0.804-0.90411.824-22.770-22.7700.0000.0000.0000.000
34A177SER0-0.040-0.01715.1451.1431.1430.0000.0000.0000.000
35A178GLU-1-0.837-0.92918.955-14.504-14.5040.0000.0000.0000.000
36A179THR00.0070.00220.6170.3420.3420.0000.0000.0000.000
37A180THR0-0.071-0.03521.7440.6890.6890.0000.0000.0000.000
38A181LYS11.0491.02118.99114.98614.9860.0000.0000.0000.000
39A182GLY00.0380.02017.7970.5510.5510.0000.0000.0000.000
40A183ALA0-0.0320.00218.646-0.023-0.0230.0000.0000.0000.000
41A184TYR00.013-0.00212.790-0.074-0.0740.0000.0000.0000.000
42A185CYS0-0.103-0.04617.1231.5051.5050.0000.0000.0000.000
43A186LEU00.0650.04717.213-1.100-1.1000.0000.0000.0000.000
44A187SER0-0.025-0.02717.9620.8050.8050.0000.0000.0000.000
45A188VAL00.0370.00318.809-0.696-0.6960.0000.0000.0000.000
46A189SER00.0390.02321.4300.4910.4910.0000.0000.0000.000
47A190ASP-1-0.813-0.91623.999-10.505-10.5050.0000.0000.0000.000
48A191PHE00.010-0.00627.4070.0000.0000.0000.0000.0000.000
49A192ASP-1-0.831-0.90930.705-9.002-9.0020.0000.0000.0000.000
50A193ASN00.010-0.01634.299-0.036-0.0360.0000.0000.0000.000
51A194ALA0-0.043-0.00937.1140.1860.1860.0000.0000.0000.000
52A195LYS10.8850.94132.8079.4609.4600.0000.0000.0000.000
53A196GLY00.0490.04533.361-0.107-0.1070.0000.0000.0000.000
54A197LEU0-0.007-0.00625.595-0.035-0.0350.0000.0000.0000.000
55A198ASN0-0.102-0.05228.170-0.088-0.0880.0000.0000.0000.000
56A199VAL00.0530.02322.680-0.294-0.2940.0000.0000.0000.000
57A200LYS10.8930.95524.61310.89210.8920.0000.0000.0000.000
58A201HIS0-0.022-0.02021.789-1.144-1.1440.0000.0000.0000.000
59A202TYR00.0120.01322.2860.6010.6010.0000.0000.0000.000
60A203LYS10.8160.89621.59612.61312.6130.0000.0000.0000.000
61A204ILE00.0160.01517.2380.4500.4500.0000.0000.0000.000
62A205ARG10.9280.96120.54211.98011.9800.0000.0000.0000.000
63A206LYS10.9600.98115.90018.37418.3740.0000.0000.0000.000
64A207LEU0-0.0100.00321.2330.5500.5500.0000.0000.0000.000
65A208ASP-1-0.865-0.93322.366-12.863-12.8630.0000.0000.0000.000
66A209SER0-0.039-0.01923.632-0.338-0.3380.0000.0000.0000.000
67A210GLY0-0.019-0.01219.493-0.265-0.2650.0000.0000.0000.000
68A211GLY00.0080.01318.365-0.872-0.8720.0000.0000.0000.000
69A212PHE00.001-0.02015.050-0.274-0.2740.0000.0000.0000.000
70A213TYR00.0210.00520.0130.5270.5270.0000.0000.0000.000
71A214ILE00.0250.02520.871-0.392-0.3920.0000.0000.0000.000
72A215TRP00.0300.00624.3510.3250.3250.0000.0000.0000.000
73A216SER00.0050.00026.881-0.126-0.1260.0000.0000.0000.000
74A217ARG10.9620.99228.4239.5989.5980.0000.0000.0000.000
75A218THR0-0.0020.00523.9350.2570.2570.0000.0000.0000.000
76A219GLN0-0.054-0.02823.035-0.594-0.5940.0000.0000.0000.000
77A220PHE0-0.001-0.00518.028-0.021-0.0210.0000.0000.0000.000
78A221SER00.019-0.00416.872-0.318-0.3180.0000.0000.0000.000
79A222SER0-0.002-0.00512.473-0.835-0.8350.0000.0000.0000.000
80A223LEU00.0170.01112.1830.9520.9520.0000.0000.0000.000
81A224GLN00.0850.0377.7352.3342.3340.0000.0000.0000.000
82A225GLN00.0330.03611.9930.6360.6360.0000.0000.0000.000
83A226LEU0-0.0270.00015.3860.8070.8070.0000.0000.0000.000
84A227VAL00.0380.01013.3170.9510.9510.0000.0000.0000.000
85A228ALA00.0230.02714.7710.6920.6920.0000.0000.0000.000
86A229TYR0-0.077-0.06816.4150.7440.7440.0000.0000.0000.000
87A230TYR00.005-0.00819.4280.4250.4250.0000.0000.0000.000
88A231SER00.0140.01817.2230.1860.1860.0000.0000.0000.000
89A232LYS10.8590.95019.78613.43113.4310.0000.0000.0000.000
90A233HIS00.005-0.00722.6480.6580.6580.0000.0000.0000.000
91A234ALA00.0340.01724.150-0.373-0.3730.0000.0000.0000.000
92A235ASP-1-0.866-0.92326.069-10.992-10.9920.0000.0000.0000.000
93A236GLY00.0490.02827.315-0.171-0.1710.0000.0000.0000.000
94A237LEU0-0.068-0.03421.9670.0010.0010.0000.0000.0000.000
95A238CYS0-0.107-0.03526.5290.1840.1840.0000.0000.0000.000
96A239HIS00.0240.00124.1230.7050.7050.0000.0000.0000.000
97A240ARG10.8810.94421.63612.18912.1890.0000.0000.0000.000
98A241LEU0-0.033-0.01817.1370.0850.0850.0000.0000.0000.000
99A242THR0-0.059-0.05219.9190.2540.2540.0000.0000.0000.000
100A243ASN0-0.0030.00917.3840.3270.3270.0000.0000.0000.000
101A244VAL00.0390.02710.9840.2550.2550.0000.0000.0000.000
102A245CYS0-0.049-0.02614.1721.0471.0470.0000.0000.0000.000
103A246PRO0-0.015-0.00413.172-1.517-1.5170.0000.0000.0000.000
104A247THR-1-0.909-0.94410.753-23.671-23.6710.0000.0000.0000.000