FMO DATABASE

FMODB ID: R9GL8

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	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	125
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1059947.218154
FMO2-HF: Nuclear repulsion	1006792.152355
FMO2-HF: Total energy	-53155.065799
FMO2-MP2: Total energy	-53298.62092

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.
-9.449	-4.894	6.846	-5.214	-6.187	0.016

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 : 0.040 / q_NPA : -0.006

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	31	TYR	0	0.026	0.025	3.432	-0.007	2.859	-0.007	-1.465	-1.394	-0.001
4	A	32	GLN	0	0.023	0.010	2.422	-2.065	-1.683	3.558	-1.716	-2.224	0.019
5	A	33	LEU	0	0.037	0.014	2.228	-3.189	-1.973	3.289	-1.992	-2.513	-0.002
6	A	34	VAL	0	0.046	0.024	3.918	-1.165	-1.074	0.006	-0.041	-0.056	0.000
7	A	35	VAL	0	0.044	0.024	6.854	-0.130	-0.130	0.000	0.000	0.000	0.000
8	A	36	ASN	0	-0.050	-0.030	6.541	-0.869	-0.869	0.000	0.000	0.000	0.000
9	A	37	ALA	0	0.027	0.030	8.149	-0.306	-0.306	0.000	0.000	0.000	0.000
10	A	38	VAL	0	0.030	0.000	9.941	-0.182	-0.182	0.000	0.000	0.000	0.000
11	A	39	ARG	1	0.846	0.910	11.631	-0.839	-0.839	0.000	0.000	0.000	0.000
12	A	40	LYS	1	0.880	0.938	10.444	-1.336	-1.336	0.000	0.000	0.000	0.000
13	A	41	LEU	0	-0.040	-0.004	13.985	-0.088	-0.088	0.000	0.000	0.000	0.000
14	A	42	GLN	0	-0.020	-0.012	15.900	-0.017	-0.017	0.000	0.000	0.000	0.000
15	A	43	GLU	-1	-0.837	-0.908	15.874	0.611	0.611	0.000	0.000	0.000	0.000
16	A	44	SER	0	-0.072	-0.039	18.563	-0.040	-0.040	0.000	0.000	0.000	0.000
17	A	45	GLY	0	0.014	0.014	20.186	-0.019	-0.019	0.000	0.000	0.000	0.000
18	A	46	PHE	0	0.014	-0.019	20.561	-0.022	-0.022	0.000	0.000	0.000	0.000
19	A	47	TYR	0	-0.102	-0.072	20.118	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	48	TRP	0	-0.004	-0.011	22.258	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	49	SER	0	-0.002	-0.005	22.442	-0.013	-0.013	0.000	0.000	0.000	0.000
22	A	50	ALA	0	-0.021	-0.010	24.183	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	51	VAL	0	0.032	0.034	26.471	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	52	THR	0	-0.037	-0.060	27.000	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	53	GLY	0	-0.006	-0.024	29.244	0.005	0.005	0.000	0.000	0.000	0.000
26	A	54	GLY	0	-0.010	-0.011	30.162	0.002	0.002	0.000	0.000	0.000	0.000
27	A	55	GLU	-1	-0.765	-0.856	31.501	0.054	0.054	0.000	0.000	0.000	0.000
28	A	56	ALA	0	0.032	0.024	29.321	0.005	0.005	0.000	0.000	0.000	0.000
29	A	57	ASN	0	-0.039	-0.031	31.341	0.005	0.005	0.000	0.000	0.000	0.000
30	A	58	LEU	0	-0.014	-0.005	34.561	0.000	0.000	0.000	0.000	0.000	0.000
31	A	59	LEU	0	-0.005	-0.001	30.879	0.000	0.000	0.000	0.000	0.000	0.000
32	A	60	LEU	0	0.017	0.012	30.141	0.003	0.003	0.000	0.000	0.000	0.000
33	A	61	SER	0	-0.034	0.007	34.666	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	62	ALA	0	-0.002	-0.008	38.251	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	63	GLU	-1	-0.866	-0.917	34.765	0.083	0.083	0.000	0.000	0.000	0.000
36	A	64	PRO	0	0.004	0.007	36.777	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	65	ALA	0	0.006	0.001	35.683	0.004	0.004	0.000	0.000	0.000	0.000
38	A	66	GLY	0	0.016	-0.001	32.164	0.002	0.002	0.000	0.000	0.000	0.000
39	A	67	THR	0	-0.007	-0.005	31.094	0.011	0.011	0.000	0.000	0.000	0.000
40	A	68	PHE	0	-0.033	-0.017	24.212	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	69	LEU	0	0.033	0.030	25.886	0.006	0.006	0.000	0.000	0.000	0.000
42	A	70	ILE	0	-0.011	-0.015	19.534	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	71	ARG	1	0.912	0.972	22.738	-0.059	-0.059	0.000	0.000	0.000	0.000
44	A	72	ASP	-1	-0.748	-0.859	20.777	0.138	0.138	0.000	0.000	0.000	0.000
45	A	73	SER	0	-0.080	-0.040	21.138	-0.010	-0.010	0.000	0.000	0.000	0.000
46	A	74	SER	0	0.038	0.012	22.830	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	75	ASP	-1	-0.898	-0.938	22.806	-0.067	-0.067	0.000	0.000	0.000	0.000
48	A	76	GLN	0	0.034	0.005	21.885	-0.014	-0.014	0.000	0.000	0.000	0.000
49	A	77	ARG	1	0.920	0.961	19.119	0.143	0.143	0.000	0.000	0.000	0.000
50	A	78	HIS	0	-0.060	-0.035	17.836	-0.002	-0.002	0.000	0.000	0.000	0.000
51	A	79	PHE	0	0.037	0.034	12.188	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	80	PHE	0	0.066	0.023	14.171	0.012	0.012	0.000	0.000	0.000	0.000
53	A	81	THR	0	-0.053	-0.035	19.183	-0.027	-0.027	0.000	0.000	0.000	0.000
54	A	82	LEU	0	0.013	0.021	22.298	0.014	0.014	0.000	0.000	0.000	0.000
55	A	83	SER	0	-0.024	-0.019	23.884	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	84	VAL	0	0.046	0.011	27.642	0.009	0.009	0.000	0.000	0.000	0.000
57	A	85	LYS	1	0.837	0.925	29.881	-0.069	-0.069	0.000	0.000	0.000	0.000
58	A	86	THR	0	-0.012	-0.022	32.382	0.002	0.002	0.000	0.000	0.000	0.000
59	A	87	GLN	0	0.048	0.002	34.875	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	88	SER	0	0.028	0.025	37.245	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	89	GLY	0	0.039	0.023	37.399	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	90	THR	0	0.002	0.009	31.890	0.003	0.003	0.000	0.000	0.000	0.000
63	A	91	LYS	1	0.827	0.935	30.853	-0.042	-0.042	0.000	0.000	0.000	0.000
64	A	92	ASN	0	0.030	0.019	27.459	0.013	0.013	0.000	0.000	0.000	0.000
65	A	93	LEU	0	0.020	0.018	24.380	-0.011	-0.011	0.000	0.000	0.000	0.000
66	A	94	ARG	1	0.904	0.962	21.407	0.031	0.031	0.000	0.000	0.000	0.000
67	A	95	ILE	0	0.009	0.000	16.316	0.003	0.003	0.000	0.000	0.000	0.000
68	A	96	GLN	0	-0.058	-0.042	16.068	0.002	0.002	0.000	0.000	0.000	0.000
69	A	97	CAS	0	-0.006	-0.013	9.815	0.063	0.063	0.000	0.000	0.000	0.000
70	A	98	GLU	-1	-0.789	-0.886	10.329	-0.078	-0.078	0.000	0.000	0.000	0.000
71	A	99	GLY	0	0.017	0.005	7.375	0.088	0.088	0.000	0.000	0.000	0.000
72	A	100	GLY	0	-0.041	-0.011	6.414	0.173	0.173	0.000	0.000	0.000	0.000
73	A	101	SER	0	-0.035	-0.012	7.445	0.230	0.230	0.000	0.000	0.000	0.000
74	A	102	PHE	0	-0.030	-0.025	10.429	-0.106	-0.106	0.000	0.000	0.000	0.000
75	A	103	SER	0	0.073	0.031	13.952	-0.010	-0.010	0.000	0.000	0.000	0.000
76	A	104	LEU	0	-0.026	0.007	17.211	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	105	GLN	0	0.015	0.011	20.654	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	106	SER	0	0.002	0.000	22.081	0.012	0.012	0.000	0.000	0.000	0.000
79	A	107	ASP	-1	-0.809	-0.867	24.059	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	108	PRO	0	0.034	0.019	26.840	0.004	0.004	0.000	0.000	0.000	0.000
81	A	109	ARG	1	0.816	0.884	27.799	0.000	0.000	0.000	0.000	0.000	0.000
82	A	110	SER	0	-0.077	-0.046	26.557	0.008	0.008	0.000	0.000	0.000	0.000
83	A	111	THR	0	0.019	0.009	28.611	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	112	GLN	0	-0.044	-0.016	25.700	0.003	0.003	0.000	0.000	0.000	0.000
85	A	113	PRO	0	0.029	0.014	20.914	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	114	VAL	0	0.001	-0.009	19.083	0.011	0.011	0.000	0.000	0.000	0.000
87	A	115	PRO	0	0.004	0.027	18.959	0.004	0.004	0.000	0.000	0.000	0.000
88	A	116	ARG	1	0.835	0.884	11.815	-0.082	-0.082	0.000	0.000	0.000	0.000
89	A	117	PHE	0	0.011	0.005	14.526	0.014	0.014	0.000	0.000	0.000	0.000
90	A	118	ASP	-1	-0.779	-0.854	10.577	0.569	0.569	0.000	0.000	0.000	0.000
91	A	119	CAS	0	-0.013	-0.017	11.399	0.075	0.075	0.000	0.000	0.000	0.000
92	A	120	VAL	0	0.063	0.031	14.074	-0.066	-0.066	0.000	0.000	0.000	0.000
93	A	121	LEU	0	0.051	0.017	16.985	-0.042	-0.042	0.000	0.000	0.000	0.000
94	A	122	LYS	1	0.827	0.896	14.591	-0.517	-0.517	0.000	0.000	0.000	0.000
95	A	123	LEU	0	-0.010	0.002	17.271	-0.030	-0.030	0.000	0.000	0.000	0.000
96	A	124	VAL	0	0.004	-0.017	19.301	-0.029	-0.029	0.000	0.000	0.000	0.000
97	A	125	HIS	0	0.007	0.002	22.252	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	126	HIS	0	0.032	0.039	21.694	-0.031	-0.031	0.000	0.000	0.000	0.000
99	A	127	TYR	0	-0.028	-0.018	21.307	-0.016	-0.016	0.000	0.000	0.000	0.000
100	A	128	MET	0	-0.049	-0.008	25.947	-0.004	-0.004	0.000	0.000	0.000	0.000
101	A	129	PRO	0	-0.025	0.009	28.427	0.002	0.002	0.000	0.000	0.000	0.000
102	A	130	PRO	0	0.020	0.008	31.153	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	131	GLN	0	-0.009	-0.006	34.404	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	141	ALA	0	0.043	0.025	30.012	0.002	0.002	0.000	0.000	0.000	0.000
105	A	142	TYR	0	-0.050	-0.046	24.963	-0.012	-0.012	0.000	0.000	0.000	0.000
106	A	143	TYR	0	-0.020	-0.017	30.073	0.000	0.000	0.000	0.000	0.000	0.000
107	A	144	ILE	0	0.002	0.001	29.136	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	145	TYR	0	-0.033	-0.033	31.770	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	146	SER	0	-0.067	-0.035	34.057	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	147	GLY	0	0.003	-0.009	36.842	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	148	GLY	0	-0.006	-0.016	39.549	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	149	GLU	-1	-0.801	-0.895	39.018	0.013	0.013	0.000	0.000	0.000	0.000
113	A	150	LYS	1	0.897	0.983	33.683	-0.028	-0.028	0.000	0.000	0.000	0.000
114	A	151	ILE	0	0.031	0.014	34.568	0.002	0.002	0.000	0.000	0.000	0.000
115	A	152	PRO	0	-0.031	-0.007	33.663	0.001	0.001	0.000	0.000	0.000	0.000
116	A	153	LEU	0	-0.057	-0.021	26.195	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	154	VAL	0	-0.002	-0.017	30.323	0.003	0.003	0.000	0.000	0.000	0.000
118	A	155	LEU	0	-0.040	-0.008	24.731	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	156	SER	0	-0.028	-0.032	29.216	0.001	0.001	0.000	0.000	0.000	0.000
120	A	157	ARG	1	0.892	0.933	29.979	-0.086	-0.086	0.000	0.000	0.000	0.000
121	A	158	PRO	0	0.021	0.024	26.335	-0.006	-0.006	0.000	0.000	0.000	0.000
122	A	159	LEU	0	0.013	0.002	28.360	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	160	SER	0	0.007	0.015	29.415	0.010	0.010	0.000	0.000	0.000	0.000
124	A	161	SER	0	-0.001	-0.009	31.379	-0.010	-0.010	0.000	0.000	0.000	0.000
125	A	162	ASN	0	0.005	0.007	33.050	-0.001	-0.001	0.000	0.000	0.000	0.000

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