FMO DATABASE

FMODB ID: QYG1Y

Calculation Name: 1I3Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name: o-phosphotyrosine

ligand 3-letter code: PTR

PDB ID: 1I3Z

Chain ID: A

ChEMBL ID:

UniProt ID: O35324

Base Structure: X-ray

Registration Date: 2023-09-19

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	102
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-792275.247527
FMO2-HF: Nuclear repulsion	751049.269151
FMO2-HF: Total energy	-41225.978376
FMO2-MP2: Total energy	-41344.039626

3D Structure

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-20.241	-17.608	16.501	-7.758	-11.374	0.021

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : 0.021

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

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

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].
3	A	3	LEU	0	-0.044	-0.013	2.872	-1.041	2.513	0.155	-1.677	-2.031	0.002
4	A	4	PRO	0	0.059	0.022	5.322	-0.284	-0.281	-0.001	-0.003	0.001	0.000
5	A	5	TYR	0	0.043	0.031	7.875	-0.098	-0.098	0.000	0.000	0.000	0.000
6	A	6	TYR	0	-0.126	-0.087	2.286	-2.227	0.466	1.301	-1.188	-2.805	-0.012
7	A	7	HIS	1	0.832	0.903	6.345	0.853	0.853	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.083	0.052	6.247	0.402	0.402	0.000	0.000	0.000	0.000
9	A	9	CYS	0	-0.023	-0.019	7.057	0.641	0.641	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.046	-0.026	10.269	0.103	0.103	0.000	0.000	0.000	0.000
11	A	11	THR	0	-0.001	-0.019	11.917	0.100	0.100	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.852	0.921	14.505	0.140	0.140	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.966	0.982	15.836	0.395	0.395	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.797	-0.861	15.885	-0.535	-0.535	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.009	-0.001	13.722	0.014	0.014	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.902	-0.961	15.595	-0.099	-0.099	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.000	-0.002	18.991	0.023	0.023	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.045	-0.033	15.480	0.022	0.022	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.015	0.004	15.052	0.023	0.023	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.016	0.011	19.012	0.039	0.039	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.942	0.975	21.922	0.378	0.378	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.056	0.032	21.639	-0.016	-0.016	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.028	-0.002	22.644	0.017	0.017	0.000	0.000	0.000	0.000
24	A	24	VAL	0	0.034	0.011	23.522	0.020	0.020	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.829	-0.879	23.318	0.033	0.033	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.066	0.022	20.497	0.001	0.001	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.064	-0.028	18.739	0.010	0.010	0.000	0.000	0.000	0.000
28	A	28	PHE	0	-0.011	-0.017	11.861	0.045	0.045	0.000	0.000	0.000	0.000
29	A	29	LEU	0	0.009	0.012	10.649	-0.127	-0.127	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.018	-0.011	5.930	0.315	0.315	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.908	0.951	7.108	-0.247	-0.247	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.736	-0.851	4.885	-2.281	-2.228	-0.001	-0.004	-0.049	0.000
33	A	33	SER	0	-0.063	-0.036	7.161	0.117	0.117	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.761	-0.895	9.532	-0.213	-0.213	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.032	-0.010	12.736	0.008	0.008	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.051	-0.022	10.812	0.054	0.054	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.067	0.028	9.572	0.081	0.081	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.027	0.024	6.362	0.124	0.124	0.000	0.000	0.000	0.000
39	A	39	ALA	0	-0.059	-0.015	5.236	0.502	0.502	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.015	0.003	2.286	-0.812	-0.691	2.088	-0.346	-1.863	-0.001
41	A	41	CYS	0	-0.031	-0.025	5.942	0.116	0.116	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.012	0.030	9.318	-0.160	-0.160	0.000	0.000	0.000	0.000
43	A	43	CYS	0	-0.063	-0.002	10.822	-0.070	-0.070	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.051	0.022	13.709	-0.051	-0.051	0.000	0.000	0.000	0.000
45	A	45	SER	0	-0.015	-0.014	16.951	0.003	0.003	0.000	0.000	0.000	0.000
46	A	46	PHE	0	0.061	0.010	20.404	0.025	0.025	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.860	0.911	23.572	-0.091	-0.091	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.809	0.902	25.038	0.075	0.075	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.048	0.041	23.398	-0.016	-0.016	0.000	0.000	0.000	0.000
50	A	50	VAL	0	-0.011	-0.022	16.786	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	51	TYR	0	0.006	0.010	18.402	0.015	0.015	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.029	-0.053	13.616	0.002	0.002	0.000	0.000	0.000	0.000
53	A	53	TYR	0	0.054	0.034	13.468	-0.015	-0.015	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.905	0.925	10.523	-0.356	-0.356	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.026	-0.019	6.839	0.115	0.115	0.000	0.000	0.000	0.000
56	A	56	PHE	0	0.019	0.010	6.835	0.133	0.133	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.898	0.948	4.138	-8.159	-7.613	0.112	-0.187	-0.470	0.001
58	A	58	GLU	-1	-0.795	-0.883	7.752	0.777	0.777	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.944	0.956	10.880	-0.608	-0.608	0.000	0.000	0.000	0.000
60	A	60	HIS	0	0.028	0.026	13.303	0.038	0.038	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.048	0.032	8.825	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	62	TYR	0	0.026	0.019	8.108	0.937	0.937	0.000	0.000	0.000	0.000
63	A	63	TYR	0	-0.017	-0.026	2.174	-5.792	-10.629	12.750	-4.229	-3.684	0.030
64	A	64	ARG	1	0.874	0.926	8.681	-1.734	-1.734	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.012	0.002	10.764	0.024	0.024	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.866	-0.931	12.278	0.527	0.527	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.042	-0.009	14.709	-0.045	-0.045	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.798	-0.887	18.082	0.424	0.424	0.000	0.000	0.000	0.000
69	A	69	ALA	0	-0.022	-0.020	21.308	0.025	0.025	0.000	0.000	0.000	0.000
70	A	70	HIS	0	-0.022	0.000	23.946	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	71	THR	0	-0.044	-0.031	20.808	-0.010	-0.010	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.014	-0.013	21.474	0.047	0.047	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.895	0.938	15.633	-0.936	-0.936	0.000	0.000	0.000	0.000
74	A	74	THR	0	0.013	0.014	16.500	0.047	0.047	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.022	-0.028	13.179	0.125	0.125	0.000	0.000	0.000	0.000
76	A	76	PHE	0	0.009	0.003	10.431	-0.237	-0.237	0.000	0.000	0.000	0.000
77	A	77	PRO	0	0.033	0.013	10.272	0.551	0.551	0.000	0.000	0.000	0.000
78	A	78	ASN	0	-0.047	-0.034	7.437	0.483	0.483	0.000	0.000	0.000	0.000
79	A	79	LEU	0	0.056	0.026	3.916	-1.174	-0.674	0.097	-0.124	-0.473	0.001
80	A	80	GLN	0	0.076	0.028	7.079	-0.167	-0.167	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.843	-0.915	9.250	1.011	1.011	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.049	-0.005	8.978	-0.249	-0.249	0.000	0.000	0.000	0.000
83	A	83	VAL	0	-0.003	-0.016	9.924	-0.297	-0.297	0.000	0.000	0.000	0.000
84	A	84	SER	0	-0.009	0.005	12.359	-0.250	-0.250	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.848	0.933	14.920	-0.870	-0.870	0.000	0.000	0.000	0.000
86	A	86	TYR	0	0.027	-0.001	14.069	-0.171	-0.171	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.029	0.040	16.513	-0.085	-0.085	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.857	0.926	17.848	-0.600	-0.600	0.000	0.000	0.000	0.000
89	A	89	PRO	0	0.056	0.023	21.360	0.030	0.030	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.027	0.000	24.295	0.022	0.022	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.052	-0.013	19.890	0.083	0.083	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.050	0.020	20.806	0.061	0.061	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.062	-0.017	15.925	0.015	0.015	0.000	0.000	0.000	0.000
94	A	94	VAL	0	-0.015	-0.010	20.098	-0.027	-0.027	0.000	0.000	0.000	0.000
95	A	95	VAL	0	-0.029	-0.014	20.859	-0.039	-0.039	0.000	0.000	0.000	0.000
96	A	96	HIS	0	-0.026	0.008	19.995	0.064	0.064	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.032	-0.028	13.590	-0.046	-0.046	0.000	0.000	0.000	0.000
98	A	98	SER	0	-0.009	-0.005	17.610	0.008	0.008	0.000	0.000	0.000	0.000
99	A	99	ASN	0	-0.019	-0.021	18.397	0.006	0.006	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.012	0.017	13.189	-0.013	-0.013	0.000	0.000	0.000	0.000
101	A	101	ILE	0	0.013	0.003	14.622	-0.089	-0.089	0.000	0.000	0.000	0.000
102	A	102	MET	0	-0.032	-0.023	11.027	-0.139	-0.139	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:MET)