FMO DATABASE

FMODB ID: QYGLY

Calculation Name: 2HMH-A-Xray372

Preferred Name:

Target Type:

Ligand Name: o-phosphotyrosine

ligand 3-letter code: PTR

PDB ID: 2HMH

Chain ID: A

ChEMBL ID:

UniProt ID: Q00560

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1061031.013892
FMO2-HF: Nuclear repulsion	1007875.641571
FMO2-HF: Total energy	-53155.372321
FMO2-MP2: Total energy	-53298.902486

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:29:SER)

Summations of interaction energy for fragment #1(A:29:SER)

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.
-9.65	-4.779	5.827	-4.603	-6.093	0.014

Interaction energy analysis for fragmet #1(A:29:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : -0.007

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	31	TYR	0	0.019	0.016	3.929	-0.400	1.804	-0.008	-1.223	-0.972	-0.001
4	A	32	GLN	0	0.029	0.010	2.033	-1.968	-1.176	2.371	-1.374	-1.788	0.006
5	A	33	LEU	0	0.029	0.010	2.273	-3.477	-1.835	3.452	-1.878	-3.216	0.008
6	A	34	VAL	0	0.036	0.025	4.314	-1.961	-1.728	0.012	-0.128	-0.117	0.001
7	A	35	VAL	0	0.039	0.019	7.182	-0.243	-0.243	0.000	0.000	0.000	0.000
8	A	36	ASN	0	-0.082	-0.049	6.197	-0.682	-0.682	0.000	0.000	0.000	0.000
9	A	37	ALA	0	0.033	0.027	8.312	-0.299	-0.299	0.000	0.000	0.000	0.000
10	A	38	VAL	0	0.016	0.000	10.259	-0.179	-0.179	0.000	0.000	0.000	0.000
11	A	39	ARG	1	0.854	0.911	11.701	-0.254	-0.254	0.000	0.000	0.000	0.000
12	A	40	LYS	1	0.836	0.906	11.357	-0.403	-0.403	0.000	0.000	0.000	0.000
13	A	41	LEU	0	-0.034	-0.003	14.298	-0.055	-0.055	0.000	0.000	0.000	0.000
14	A	42	GLN	0	-0.026	-0.010	16.187	-0.026	-0.026	0.000	0.000	0.000	0.000
15	A	43	GLU	-1	-0.758	-0.864	15.119	0.181	0.181	0.000	0.000	0.000	0.000
16	A	44	SER	0	-0.071	-0.043	18.737	-0.026	-0.026	0.000	0.000	0.000	0.000
17	A	45	GLY	0	0.010	0.011	20.186	-0.012	-0.012	0.000	0.000	0.000	0.000
18	A	46	PHE	0	0.002	-0.023	21.297	-0.009	-0.009	0.000	0.000	0.000	0.000
19	A	47	TYR	0	-0.104	-0.067	20.551	0.001	0.001	0.000	0.000	0.000	0.000
20	A	48	TRP	0	0.005	-0.004	22.846	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	49	SER	0	-0.044	-0.041	22.936	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	50	ALA	0	-0.032	-0.019	24.525	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	51	VAL	0	0.023	0.031	27.014	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	52	THR	0	-0.033	-0.059	27.586	0.005	0.005	0.000	0.000	0.000	0.000
25	A	53	GLY	0	0.008	-0.017	29.709	0.001	0.001	0.000	0.000	0.000	0.000
26	A	54	GLY	0	-0.014	-0.004	30.503	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	55	GLU	-1	-0.764	-0.854	32.070	0.041	0.041	0.000	0.000	0.000	0.000
28	A	56	ALA	0	0.029	0.015	29.634	0.000	0.000	0.000	0.000	0.000	0.000
29	A	57	ASN	0	-0.040	-0.032	31.683	0.001	0.001	0.000	0.000	0.000	0.000
30	A	58	LEU	0	-0.020	-0.010	34.744	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	59	LEU	0	-0.001	0.001	31.469	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	60	LEU	0	0.004	0.012	30.491	0.000	0.000	0.000	0.000	0.000	0.000
33	A	61	SER	0	-0.042	-0.001	35.036	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	62	ALA	0	0.011	-0.007	38.711	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	63	GLU	-1	-0.881	-0.920	35.108	0.035	0.035	0.000	0.000	0.000	0.000
36	A	64	PRO	0	0.023	0.025	37.129	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	65	ALA	0	0.024	0.007	36.348	0.003	0.003	0.000	0.000	0.000	0.000
38	A	66	GLY	0	0.022	0.019	32.639	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	67	THR	0	-0.023	-0.007	31.656	0.004	0.004	0.000	0.000	0.000	0.000
40	A	68	PHE	0	-0.028	-0.018	24.700	0.000	0.000	0.000	0.000	0.000	0.000
41	A	69	LEU	0	0.039	0.039	26.685	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	70	ILE	0	-0.002	-0.011	20.139	0.002	0.002	0.000	0.000	0.000	0.000
43	A	71	ARG	1	0.891	0.960	23.267	-0.071	-0.071	0.000	0.000	0.000	0.000
44	A	72	ASP	-1	-0.702	-0.822	21.383	0.116	0.116	0.000	0.000	0.000	0.000
45	A	73	SER	0	-0.050	-0.020	21.170	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	74	SER	0	-0.006	-0.014	22.984	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	75	ASP	-1	-0.814	-0.888	22.725	0.055	0.055	0.000	0.000	0.000	0.000
48	A	76	GLN	0	0.029	0.011	22.063	0.004	0.004	0.000	0.000	0.000	0.000
49	A	77	ARG	1	0.890	0.942	18.951	-0.045	-0.045	0.000	0.000	0.000	0.000
50	A	78	HIS	0	-0.022	-0.012	17.817	0.007	0.007	0.000	0.000	0.000	0.000
51	A	79	PHE	0	0.030	0.021	12.156	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	80	PHE	0	0.056	0.018	14.712	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	81	THR	0	-0.071	-0.046	19.580	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	82	LEU	0	0.025	0.037	22.534	0.001	0.001	0.000	0.000	0.000	0.000
55	A	83	SER	0	-0.025	-0.019	24.168	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	84	VAL	0	0.054	0.011	27.935	0.001	0.001	0.000	0.000	0.000	0.000
57	A	85	LYS	1	0.833	0.906	30.255	-0.037	-0.037	0.000	0.000	0.000	0.000
58	A	86	THR	0	-0.021	-0.022	32.230	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	87	GLN	0	0.059	0.008	34.736	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	88	SER	0	0.014	0.020	37.362	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	89	GLY	0	0.065	0.039	37.934	0.000	0.000	0.000	0.000	0.000	0.000
62	A	90	THR	0	-0.009	0.005	32.463	0.001	0.001	0.000	0.000	0.000	0.000
63	A	91	LYS	1	0.803	0.910	31.057	-0.041	-0.041	0.000	0.000	0.000	0.000
64	A	92	ASN	0	0.042	0.020	27.699	0.006	0.006	0.000	0.000	0.000	0.000
65	A	93	LEU	0	0.017	0.017	24.531	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	94	ARG	1	0.876	0.941	21.507	-0.057	-0.057	0.000	0.000	0.000	0.000
67	A	95	ILE	0	-0.013	-0.006	16.339	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	96	GLN	0	-0.044	-0.025	15.818	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	97	CAS	0	-0.038	-0.031	9.660	0.007	0.007	0.000	0.000	0.000	0.000
70	A	98	GLU	-1	-0.770	-0.874	10.160	0.217	0.217	0.000	0.000	0.000	0.000
71	A	99	GLY	0	0.004	-0.004	7.110	0.023	0.023	0.000	0.000	0.000	0.000
72	A	100	GLY	0	-0.023	-0.003	5.892	0.190	0.190	0.000	0.000	0.000	0.000
73	A	101	SER	0	-0.040	-0.016	7.116	0.071	0.071	0.000	0.000	0.000	0.000
74	A	102	PHE	0	0.001	-0.012	10.169	-0.059	-0.059	0.000	0.000	0.000	0.000
75	A	103	SER	0	0.046	0.020	13.802	-0.015	-0.015	0.000	0.000	0.000	0.000
76	A	104	LEU	0	-0.009	0.007	17.069	0.003	0.003	0.000	0.000	0.000	0.000
77	A	105	GLN	0	0.024	0.013	20.368	0.000	0.000	0.000	0.000	0.000	0.000
78	A	106	SER	0	-0.017	-0.014	21.837	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	107	ASP	-1	-0.795	-0.859	24.075	0.038	0.038	0.000	0.000	0.000	0.000
80	A	108	PRO	0	0.031	0.021	26.721	0.001	0.001	0.000	0.000	0.000	0.000
81	A	109	ARG	1	0.801	0.877	27.705	-0.036	-0.036	0.000	0.000	0.000	0.000
82	A	110	SER	0	-0.042	-0.030	25.995	0.000	0.000	0.000	0.000	0.000	0.000
83	A	111	THR	0	-0.001	0.005	27.666	0.000	0.000	0.000	0.000	0.000	0.000
84	A	112	GLN	0	-0.035	-0.021	25.518	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	113	PRO	0	0.016	0.013	20.543	0.002	0.002	0.000	0.000	0.000	0.000
86	A	114	VAL	0	0.019	0.002	19.130	0.001	0.001	0.000	0.000	0.000	0.000
87	A	115	PRO	0	-0.001	0.022	18.621	0.006	0.006	0.000	0.000	0.000	0.000
88	A	116	ARG	1	0.839	0.894	11.760	-0.188	-0.188	0.000	0.000	0.000	0.000
89	A	117	PHE	0	0.004	0.001	14.229	-0.015	-0.015	0.000	0.000	0.000	0.000
90	A	118	ASP	-1	-0.789	-0.870	10.637	0.274	0.274	0.000	0.000	0.000	0.000
91	A	119	CAS	0	-0.007	-0.004	11.552	0.066	0.066	0.000	0.000	0.000	0.000
92	A	120	VAL	0	0.050	0.029	14.270	-0.040	-0.040	0.000	0.000	0.000	0.000
93	A	121	LEU	0	0.050	0.014	17.270	-0.024	-0.024	0.000	0.000	0.000	0.000
94	A	122	LYS	1	0.818	0.890	14.503	-0.179	-0.179	0.000	0.000	0.000	0.000
95	A	123	LEU	0	-0.013	0.008	17.268	-0.014	-0.014	0.000	0.000	0.000	0.000
96	A	124	VAL	0	0.008	-0.012	19.323	-0.015	-0.015	0.000	0.000	0.000	0.000
97	A	125	HIS	0	0.012	0.007	22.332	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	126	HIS	0	0.024	0.030	21.515	-0.012	-0.012	0.000	0.000	0.000	0.000
99	A	127	TYR	0	0.000	-0.007	21.350	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	128	MET	0	-0.050	-0.010	26.047	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	129	PRO	0	-0.010	0.012	28.543	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	130	PRO	0	0.006	0.003	31.131	0.000	0.000	0.000	0.000	0.000	0.000
103	A	131	GLN	0	-0.005	-0.004	34.528	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	141	ALA	0	0.041	0.021	30.461	0.000	0.000	0.000	0.000	0.000	0.000
105	A	142	TYR	0	-0.044	-0.042	24.448	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	143	TYR	0	0.000	-0.007	29.678	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	144	ILE	0	-0.008	0.004	28.817	0.003	0.003	0.000	0.000	0.000	0.000
108	A	145	TYR	0	-0.016	-0.045	31.460	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	146	SER	0	-0.073	-0.043	33.970	0.001	0.001	0.000	0.000	0.000	0.000
110	A	147	GLY	0	0.008	-0.001	36.813	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	148	GLY	0	0.001	-0.009	39.736	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	149	GLU	-1	-0.748	-0.846	38.553	0.027	0.027	0.000	0.000	0.000	0.000
113	A	150	LYS	1	0.816	0.928	33.736	-0.029	-0.029	0.000	0.000	0.000	0.000
114	A	151	ILE	0	0.026	0.023	34.419	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	152	PRO	0	-0.010	-0.003	33.619	0.002	0.002	0.000	0.000	0.000	0.000
116	A	153	LEU	0	-0.076	-0.038	26.229	0.000	0.000	0.000	0.000	0.000	0.000
117	A	154	VAL	0	-0.003	-0.012	30.095	0.001	0.001	0.000	0.000	0.000	0.000
118	A	155	LEU	0	-0.045	-0.011	25.040	0.000	0.000	0.000	0.000	0.000	0.000
119	A	156	SER	0	-0.018	-0.026	29.483	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	157	ARG	1	0.865	0.918	30.219	-0.042	-0.042	0.000	0.000	0.000	0.000
121	A	158	PRO	0	0.017	0.015	26.780	0.000	0.000	0.000	0.000	0.000	0.000
122	A	159	LEU	0	0.015	0.002	28.875	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	160	SER	0	-0.003	0.006	29.983	0.004	0.004	0.000	0.000	0.000	0.000
124	A	161	SER	0	0.023	0.003	31.813	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	162	ASN	0	0.004	0.008	33.337	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:29:SER)