FMO DATABASE

FMODB ID: R9G58

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

Total energy (hartree)

FMO2-HF: Electronic energy	-791181.632808
FMO2-HF: Nuclear repulsion	749956.170769
FMO2-HF: Total energy	-41225.462038
FMO2-MP2: Total energy	-41343.514397

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.
-22.758	-18.565	16.04	-7.476	-12.755	0.032

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 : -0.024 / q_NPA : -0.005

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	-0.051	-0.018	3.123	-2.602	1.743	0.050	-1.792	-2.602	-0.003
4	A	4	PRO	0	0.061	0.020	5.251	-0.279	-0.287	-0.001	-0.002	0.012	0.000
5	A	5	TYR	0	0.060	0.015	7.597	-0.300	-0.300	0.000	0.000	0.000	0.000
6	A	6	TYR	0	-0.142	-0.090	2.335	-1.543	-0.118	4.061	-1.326	-4.160	-0.012
7	A	7	HIS	1	0.832	0.903	5.910	-0.189	-0.189	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.069	0.035	6.587	0.221	0.221	0.000	0.000	0.000	0.000
9	A	9	CYS	0	-0.005	-0.007	7.379	0.356	0.356	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.060	-0.045	10.672	0.135	0.135	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.044	0.020	12.596	0.123	0.123	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.910	0.958	15.260	0.036	0.036	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.968	0.986	16.389	0.266	0.266	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.817	-0.885	16.550	-0.419	-0.419	0.000	0.000	0.000	0.000
15	A	15	CYS	0	-0.044	-0.029	14.279	0.031	0.031	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.903	-0.963	16.222	0.070	0.070	0.000	0.000	0.000	0.000
17	A	17	ALA	0	-0.036	-0.024	19.468	0.016	0.016	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.058	-0.038	15.402	0.001	0.001	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.026	0.004	15.499	0.020	0.020	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.031	0.028	19.184	0.026	0.026	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.882	0.959	22.001	0.203	0.203	0.000	0.000	0.000	0.000
22	A	22	GLY	0	0.021	0.008	21.671	-0.026	-0.026	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.024	-0.027	22.517	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.006	0.000	23.382	0.007	0.007	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.860	-0.905	22.896	0.178	0.178	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.030	-0.007	20.213	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	27	ASN	0	-0.051	-0.022	18.215	0.025	0.025	0.000	0.000	0.000	0.000
28	A	28	PHE	0	0.013	0.002	11.731	0.039	0.039	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.019	-0.003	10.784	-0.093	-0.093	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.009	-0.004	6.229	0.212	0.212	0.000	0.000	0.000	0.000
31	A	31	ARG	1	0.969	0.994	7.653	-0.480	-0.480	0.000	0.000	0.000	0.000
32	A	32	ASP	-1	-0.737	-0.844	4.869	-1.538	-1.486	-0.001	-0.004	-0.046	0.000
33	A	33	SER	0	-0.120	-0.061	7.371	0.040	0.040	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.828	-0.927	10.097	-0.206	-0.206	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.036	-0.016	13.228	-0.002	-0.002	0.000	0.000	0.000	0.000
36	A	36	VAL	0	0.005	-0.007	11.110	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	37	PRO	0	0.053	0.024	10.163	0.069	0.069	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.023	0.018	6.823	0.089	0.089	0.000	0.000	0.000	0.000
39	A	39	ALA	0	-0.062	-0.016	5.608	0.328	0.328	0.000	0.000	0.000	0.000
40	A	40	LEU	0	0.024	0.006	2.320	-0.611	-0.066	1.053	-0.242	-1.357	-0.001
41	A	41	CYS	0	-0.068	-0.034	6.491	-0.122	-0.122	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.033	0.030	9.800	0.025	0.025	0.000	0.000	0.000	0.000
43	A	43	CYS	0	-0.050	-0.032	11.346	-0.150	-0.150	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.048	0.014	14.352	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	45	SER	0	-0.021	0.004	17.466	-0.022	-0.022	0.000	0.000	0.000	0.000
46	A	46	PHE	0	0.117	0.034	20.707	0.017	0.017	0.000	0.000	0.000	0.000
47	A	47	LYS	1	0.877	0.938	23.944	-0.200	-0.200	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.865	0.943	25.973	-0.065	-0.065	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.082	0.040	23.726	-0.018	-0.018	0.000	0.000	0.000	0.000
50	A	50	VAL	0	0.000	-0.005	17.036	0.017	0.017	0.000	0.000	0.000	0.000
51	A	51	TYR	0	0.002	0.009	18.925	0.004	0.004	0.000	0.000	0.000	0.000
52	A	52	SER	0	-0.016	-0.020	14.223	0.035	0.035	0.000	0.000	0.000	0.000
53	A	53	TYR	0	0.064	0.038	13.702	-0.046	-0.046	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.916	0.936	10.930	-0.370	-0.370	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.027	-0.011	6.756	0.118	0.118	0.000	0.000	0.000	0.000
56	A	56	PHE	0	0.018	0.005	7.463	-0.020	-0.020	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.918	0.973	4.253	-5.616	-5.331	0.003	-0.044	-0.244	0.000
58	A	58	GLU	-1	-0.827	-0.912	7.206	0.664	0.664	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.947	0.949	10.303	-0.519	-0.519	0.000	0.000	0.000	0.000
60	A	60	HIS	0	0.024	0.025	12.501	0.000	0.000	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.049	0.033	8.475	0.055	0.055	0.000	0.000	0.000	0.000
62	A	62	TYR	0	0.033	0.021	8.612	0.639	0.639	0.000	0.000	0.000	0.000
63	A	63	TYR	0	-0.040	-0.034	2.276	-7.868	-10.859	10.634	-3.927	-3.715	0.047
64	A	64	ARG	1	0.858	0.925	8.631	-1.517	-1.517	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.018	-0.002	11.020	0.023	0.023	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.888	-0.944	12.347	0.563	0.563	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.030	-0.001	14.900	-0.012	-0.012	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.811	-0.891	18.271	0.452	0.452	0.000	0.000	0.000	0.000
69	A	69	ALA	0	-0.024	-0.039	21.586	0.023	0.023	0.000	0.000	0.000	0.000
70	A	70	HIS	0	-0.050	-0.010	24.025	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	71	THR	0	-0.019	-0.015	20.920	-0.007	-0.007	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.008	-0.006	21.910	0.027	0.027	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.945	0.965	15.644	-0.825	-0.825	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.009	0.002	16.631	0.033	0.033	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.022	-0.025	13.144	0.128	0.128	0.000	0.000	0.000	0.000
76	A	76	PHE	0	0.008	0.008	10.458	-0.207	-0.207	0.000	0.000	0.000	0.000
77	A	77	PRO	0	0.043	0.013	10.523	0.418	0.418	0.000	0.000	0.000	0.000
78	A	78	ASN	0	-0.054	-0.038	7.478	0.468	0.468	0.000	0.000	0.000	0.000
79	A	79	LEU	0	0.066	0.027	3.650	-1.120	-0.580	0.241	-0.139	-0.643	0.001
80	A	80	GLN	0	0.068	0.030	6.872	-0.017	-0.017	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.848	-0.928	9.532	1.028	1.028	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.054	-0.002	8.981	-0.253	-0.253	0.000	0.000	0.000	0.000
83	A	83	VAL	0	-0.023	-0.032	9.601	-0.309	-0.309	0.000	0.000	0.000	0.000
84	A	84	SER	0	-0.012	0.007	12.146	-0.302	-0.302	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.881	0.944	14.573	-1.024	-1.024	0.000	0.000	0.000	0.000
86	A	86	TYR	0	0.024	-0.005	13.812	-0.188	-0.188	0.000	0.000	0.000	0.000
87	A	87	GLY	0	0.097	0.073	16.875	-0.078	-0.078	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.821	0.923	18.359	-0.780	-0.780	0.000	0.000	0.000	0.000
89	A	89	PRO	0	0.044	0.009	21.249	0.041	0.041	0.000	0.000	0.000	0.000
90	A	90	GLY	0	0.041	0.011	23.887	0.012	0.012	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.060	-0.018	19.850	0.070	0.070	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.058	0.027	20.666	0.058	0.058	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.073	-0.023	16.369	0.013	0.013	0.000	0.000	0.000	0.000
94	A	94	VAL	0	0.000	0.006	20.597	-0.038	-0.038	0.000	0.000	0.000	0.000
95	A	95	VAL	0	-0.039	-0.019	21.189	-0.047	-0.047	0.000	0.000	0.000	0.000
96	A	96	HIS	0	-0.032	0.003	20.018	0.060	0.060	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.050	-0.037	13.908	-0.030	-0.030	0.000	0.000	0.000	0.000
98	A	98	SER	0	-0.012	-0.007	17.923	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	99	ASN	0	-0.015	-0.026	18.125	0.012	0.012	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.042	0.023	12.687	0.000	0.000	0.000	0.000	0.000	0.000
101	A	101	ILE	0	-0.002	0.010	14.029	-0.104	-0.104	0.000	0.000	0.000	0.000
102	A	102	MET	0	-0.006	0.019	10.711	-0.045	-0.045	0.000	0.000	0.000	0.000

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