FMO DATABASE

FMODB ID: Z65YN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-790586.094912
FMO2-HF: Nuclear repulsion	749361.695459
FMO2-HF: Total energy	-41224.399454
FMO2-MP2: Total energy	-41342.473407

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.
-4.8	-10.691	29.823	-8.16	-15.774	-0.026

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 : -0.064 / q_NPA : -0.039

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 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	-0.022	-0.008	2.709	-3.730	1.370	0.424	-2.183	-3.341	-0.008
4	A	4	PRO	0	0.040	0.017	5.114	-0.155	-0.146	-0.001	-0.002	-0.006	0.000
5	A	5	TYR	0	0.068	0.016	7.795	-0.102	-0.102	0.000	0.000	0.000	0.000
6	A	6	TYR	0	-0.155	-0.120	1.883	4.707	-3.590	18.387	-3.515	-6.576	-0.018
7	A	7	HIS	1	0.832	0.905	5.727	-0.330	-0.330	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.067	0.031	6.613	0.369	0.369	0.000	0.000	0.000	0.000
9	A	9	CYS	0	0.006	-0.005	7.461	0.241	0.241	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.069	-0.040	10.733	0.030	0.030	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.073	0.061	12.906	0.135	0.135	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.980	0.996	15.828	-0.196	-0.196	0.000	0.000	0.000	0.000
13	A	13	ARG	1	1.031	1.020	17.234	0.024	0.024	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.899	-0.957	16.422	-0.194	-0.194	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.015	-0.023	14.344	0.011	0.011	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.912	-0.957	16.312	0.156	0.156	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.040	-0.028	19.698	-0.008	-0.008	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.058	-0.040	14.804	-0.017	-0.017	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.018	0.008	15.178	0.001	0.001	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.022	0.014	19.022	0.002	0.002	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.862	0.949	22.010	0.101	0.101	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.020	0.011	21.502	-0.022	-0.022	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.027	-0.030	22.337	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.010	0.003	23.162	0.009	0.009	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.815	-0.877	22.756	0.146	0.146	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.012	-0.021	20.116	-0.012	-0.012	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.017	-0.002	18.067	-0.010	-0.010	0.000	0.000	0.000	0.000
28	A	28	PHE	0	0.004	0.000	11.367	0.046	0.046	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.007	0.004	10.569	-0.099	-0.099	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.008	-0.005	6.082	0.144	0.144	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.962	0.989	8.071	-0.860	-0.860	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.738	-0.813	6.180	1.767	1.767	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.040	-0.045	8.763	-0.343	-0.343	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.944	-0.981	11.524	0.166	0.166	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.063	-0.027	14.688	-0.038	-0.038	0.000	0.000	0.000	0.000
36	A	36	VAL	0	-0.019	-0.014	11.765	-0.049	-0.049	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.057	0.021	11.277	0.163	0.163	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.029	0.022	7.748	-0.040	-0.040	0.000	0.000	0.000	0.000
39	A	39	ALA	0	-0.063	-0.014	6.366	0.413	0.413	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.021	0.003	3.528	-0.782	-0.013	0.249	-0.197	-0.821	0.001
41	A	41	CYS	0	-0.077	-0.037	7.808	-0.386	-0.386	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.045	0.039	10.411	0.031	0.031	0.000	0.000	0.000	0.000
43	A	43	CYS	0	-0.067	-0.039	11.681	-0.107	-0.107	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.072	0.026	14.654	-0.030	-0.030	0.000	0.000	0.000	0.000
45	A	45	SER	0	-0.043	-0.002	17.374	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	46	PHE	0	0.062	0.007	20.594	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.911	0.955	23.848	-0.144	-0.144	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.886	0.952	26.040	-0.070	-0.070	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.078	0.034	24.187	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	50	VAL	0	0.005	0.003	17.616	0.005	0.005	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.005	0.004	19.429	0.009	0.009	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.032	-0.025	15.295	0.045	0.045	0.000	0.000	0.000	0.000
53	A	53	TYR	0	0.081	0.043	14.258	-0.050	-0.050	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.965	0.974	11.959	-0.481	-0.481	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.019	-0.004	7.101	-0.040	-0.040	0.000	0.000	0.000	0.000
56	A	56	PHE	0	0.021	0.007	8.068	0.229	0.229	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.936	0.988	2.891	-2.777	-1.998	0.331	-0.235	-0.876	0.000
58	A	58	GLU	-1	-0.884	-0.956	6.592	0.537	0.537	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.951	0.953	9.033	-0.415	-0.415	0.000	0.000	0.000	0.000
60	A	60	HIS	0	0.028	0.027	11.075	-0.007	-0.007	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.039	0.023	6.855	-0.023	-0.023	0.000	0.000	0.000	0.000
62	A	62	TYR	0	0.026	0.019	7.167	0.181	0.181	0.000	0.000	0.000	0.000
63	A	63	TYR	0	0.014	0.003	1.866	-0.732	-5.575	10.045	-1.827	-3.375	-0.003
64	A	64	ARG	1	0.892	0.942	7.866	-1.113	-1.113	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.037	-0.006	10.989	0.099	0.099	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.958	-0.988	12.452	0.545	0.545	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.016	0.010	15.223	-0.014	-0.014	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.832	-0.899	18.449	0.341	0.341	0.000	0.000	0.000	0.000
69	A	69	ALA	0	-0.018	-0.037	21.862	0.009	0.009	0.000	0.000	0.000	0.000
70	A	70	HIS	0	-0.051	-0.011	24.143	-0.017	-0.017	0.000	0.000	0.000	0.000
71	A	71	THR	0	-0.033	-0.024	20.859	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.003	-0.006	21.383	0.021	0.021	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.970	0.979	15.231	-0.558	-0.558	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.038	-0.007	16.058	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	75	ILE	0	0.002	-0.017	12.301	0.107	0.107	0.000	0.000	0.000	0.000
76	A	76	PHE	0	0.027	0.016	10.224	-0.122	-0.122	0.000	0.000	0.000	0.000
77	A	77	PRO	0	0.049	0.012	9.754	0.217	0.217	0.000	0.000	0.000	0.000
78	A	78	ASN	0	0.014	-0.003	6.814	0.071	0.071	0.000	0.000	0.000	0.000
79	A	79	LEU	0	0.069	0.026	3.543	-0.832	-0.240	0.388	-0.201	-0.779	0.002
80	A	80	GLN	0	0.051	0.033	6.757	0.102	0.102	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.925	-0.972	8.813	0.394	0.394	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.050	0.004	9.315	-0.087	-0.087	0.000	0.000	0.000	0.000
83	A	83	VAL	0	-0.012	-0.030	10.105	-0.128	-0.128	0.000	0.000	0.000	0.000
84	A	84	SER	0	-0.005	0.004	11.928	-0.148	-0.148	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.888	0.957	14.404	-0.559	-0.559	0.000	0.000	0.000	0.000
86	A	86	TYR	0	0.003	-0.015	14.131	-0.096	-0.096	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.098	0.072	16.771	-0.034	-0.034	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.870	0.945	18.053	-0.389	-0.389	0.000	0.000	0.000	0.000
89	A	89	PRO	0	0.051	0.018	21.209	0.034	0.034	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.053	0.022	23.892	0.005	0.005	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.095	-0.053	20.228	0.022	0.022	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.052	0.026	20.799	0.037	0.037	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.078	-0.030	16.670	0.020	0.020	0.000	0.000	0.000	0.000
94	A	94	VAL	0	-0.017	0.001	20.928	-0.035	-0.035	0.000	0.000	0.000	0.000
95	A	95	VAL	0	-0.026	-0.010	21.056	-0.036	-0.036	0.000	0.000	0.000	0.000
96	A	96	HIS	0	-0.026	0.003	20.176	0.053	0.053	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.058	-0.042	13.920	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	98	SER	0	-0.021	-0.009	17.854	-0.022	-0.022	0.000	0.000	0.000	0.000
99	A	99	ASN	0	-0.024	-0.035	17.985	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.052	0.030	12.719	0.018	0.018	0.000	0.000	0.000	0.000
101	A	101	ILE	0	0.002	0.015	13.846	-0.074	-0.074	0.000	0.000	0.000	0.000
102	A	102	MET	0	0.004	0.020	11.355	0.006	0.006	0.000	0.000	0.000	0.000

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