FMO DATABASE

FMODB ID: Z65ZN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1059546.169151
FMO2-HF: Nuclear repulsion	1006391.728966
FMO2-HF: Total energy	-53154.440185
FMO2-MP2: Total energy	-53298.019629

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.
-7.012	-2.472	6.89	-5.23	-6.202	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 : 0.050 / 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	0.028	0.024	3.442	0.331	3.210	-0.008	-1.469	-1.402	-0.001
4	A	32	GLN	0	-0.012	-0.005	2.465	-1.608	-1.008	3.291	-1.662	-2.230	0.016
5	A	33	LEU	0	0.031	0.009	2.167	-2.505	-1.530	3.601	-2.067	-2.510	-0.001
6	A	34	VAL	0	0.053	0.032	3.906	-1.192	-1.106	0.006	-0.032	-0.060	0.000
7	A	35	VAL	0	0.052	0.025	6.834	-0.048	-0.048	0.000	0.000	0.000	0.000
8	A	36	ASN	0	-0.109	-0.065	6.916	0.008	0.008	0.000	0.000	0.000	0.000
9	A	37	ALA	0	0.072	0.046	8.123	-0.267	-0.267	0.000	0.000	0.000	0.000
10	A	38	VAL	0	0.026	-0.001	9.930	-0.174	-0.174	0.000	0.000	0.000	0.000
11	A	39	ARG	1	0.914	0.963	11.404	-0.777	-0.777	0.000	0.000	0.000	0.000
12	A	40	LYS	1	0.933	0.977	10.331	-1.350	-1.350	0.000	0.000	0.000	0.000
13	A	41	LEU	0	-0.028	0.003	13.974	-0.079	-0.079	0.000	0.000	0.000	0.000
14	A	42	GLN	0	-0.028	-0.024	15.886	-0.022	-0.022	0.000	0.000	0.000	0.000
15	A	43	GLU	-1	-0.921	-0.965	16.251	0.508	0.508	0.000	0.000	0.000	0.000
16	A	44	SER	0	-0.079	-0.037	18.529	-0.037	-0.037	0.000	0.000	0.000	0.000
17	A	45	GLY	0	0.022	0.018	20.177	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	46	PHE	0	0.015	-0.013	20.587	-0.022	-0.022	0.000	0.000	0.000	0.000
19	A	47	TYR	0	-0.126	-0.098	20.106	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	48	TRP	0	0.008	-0.003	22.245	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	49	SER	0	-0.002	-0.003	22.698	-0.013	-0.013	0.000	0.000	0.000	0.000
22	A	50	ALA	0	-0.005	-0.008	24.164	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	51	VAL	0	0.048	0.042	26.459	-0.003	-0.003	0.000	0.000	0.000	0.000
24	A	52	THR	0	-0.031	-0.027	26.982	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	53	GLY	0	-0.006	-0.025	29.226	0.006	0.006	0.000	0.000	0.000	0.000
26	A	54	GLY	0	-0.008	-0.009	30.145	0.003	0.003	0.000	0.000	0.000	0.000
27	A	55	GLU	-1	-0.784	-0.901	31.387	0.042	0.042	0.000	0.000	0.000	0.000
28	A	56	ALA	0	0.033	0.025	29.290	0.005	0.005	0.000	0.000	0.000	0.000
29	A	57	ASN	0	-0.038	-0.027	31.326	0.006	0.006	0.000	0.000	0.000	0.000
30	A	58	LEU	0	-0.029	-0.013	34.547	0.001	0.001	0.000	0.000	0.000	0.000
31	A	59	LEU	0	0.000	-0.001	30.785	0.001	0.001	0.000	0.000	0.000	0.000
32	A	60	LEU	0	0.011	0.009	30.147	0.003	0.003	0.000	0.000	0.000	0.000
33	A	61	SER	0	-0.036	-0.005	34.654	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	62	ALA	0	-0.006	-0.014	38.239	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	63	GLU	-1	-0.880	-0.924	34.803	0.079	0.079	0.000	0.000	0.000	0.000
36	A	64	PRO	0	-0.006	0.009	36.452	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	65	ALA	0	0.006	0.000	35.676	0.004	0.004	0.000	0.000	0.000	0.000
38	A	66	GLY	0	0.011	-0.019	32.160	0.003	0.003	0.000	0.000	0.000	0.000
39	A	67	THR	0	0.013	-0.004	31.088	0.012	0.012	0.000	0.000	0.000	0.000
40	A	68	PHE	0	-0.050	-0.024	24.110	-0.007	-0.007	0.000	0.000	0.000	0.000
41	A	69	LEU	0	0.041	0.038	25.887	0.006	0.006	0.000	0.000	0.000	0.000
42	A	70	ILE	0	-0.016	-0.016	19.505	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	71	ARG	1	0.910	0.970	22.731	-0.049	-0.049	0.000	0.000	0.000	0.000
44	A	72	ASP	-1	-0.757	-0.848	20.550	0.107	0.107	0.000	0.000	0.000	0.000
45	A	73	SER	0	-0.085	-0.045	21.128	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	74	SER	0	0.036	0.007	22.813	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	75	ASP	-1	-0.966	-0.991	22.921	-0.074	-0.074	0.000	0.000	0.000	0.000
48	A	76	GLN	0	0.031	0.008	21.842	-0.020	-0.020	0.000	0.000	0.000	0.000
49	A	77	ARG	1	0.924	0.962	19.095	0.150	0.150	0.000	0.000	0.000	0.000
50	A	78	HIS	0	-0.047	-0.019	17.812	0.004	0.004	0.000	0.000	0.000	0.000
51	A	79	PHE	0	0.037	0.033	12.782	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	80	PHE	0	0.075	0.028	14.201	0.013	0.013	0.000	0.000	0.000	0.000
53	A	81	THR	0	-0.060	-0.043	19.168	-0.024	-0.024	0.000	0.000	0.000	0.000
54	A	82	LEU	0	0.018	0.025	22.284	0.012	0.012	0.000	0.000	0.000	0.000
55	A	83	SER	0	-0.021	-0.026	23.873	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	84	VAL	0	0.034	0.007	27.631	0.009	0.009	0.000	0.000	0.000	0.000
57	A	85	LYS	1	0.861	0.951	29.873	-0.065	-0.065	0.000	0.000	0.000	0.000
58	A	86	THR	0	-0.029	-0.035	32.409	0.002	0.002	0.000	0.000	0.000	0.000
59	A	87	GLN	0	0.035	-0.008	34.869	-0.005	-0.005	0.000	0.000	0.000	0.000
60	A	88	SER	0	0.008	0.018	37.237	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	89	GLY	0	0.035	0.020	37.390	-0.004	-0.004	0.000	0.000	0.000	0.000
62	A	90	THR	0	0.000	0.015	31.905	0.004	0.004	0.000	0.000	0.000	0.000
63	A	91	LYS	1	0.866	0.961	30.760	-0.041	-0.041	0.000	0.000	0.000	0.000
64	A	92	ASN	0	0.034	0.027	27.357	0.013	0.013	0.000	0.000	0.000	0.000
65	A	93	LEU	0	0.021	0.019	24.347	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	94	ARG	1	0.960	0.994	21.353	0.027	0.027	0.000	0.000	0.000	0.000
67	A	95	ILE	0	0.004	0.001	16.166	0.006	0.006	0.000	0.000	0.000	0.000
68	A	96	GLN	0	-0.036	-0.017	16.181	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	97	CAS	0	-0.014	-0.010	10.997	0.036	0.036	0.000	0.000	0.000	0.000
70	A	98	GLU	-1	-0.821	-0.917	10.320	-0.070	-0.070	0.000	0.000	0.000	0.000
71	A	99	GLY	0	0.004	0.002	7.373	0.097	0.097	0.000	0.000	0.000	0.000
72	A	100	GLY	0	-0.044	-0.012	6.407	0.214	0.214	0.000	0.000	0.000	0.000
73	A	101	SER	0	-0.031	-0.009	7.438	0.231	0.231	0.000	0.000	0.000	0.000
74	A	102	PHE	0	-0.035	-0.031	10.429	-0.115	-0.115	0.000	0.000	0.000	0.000
75	A	103	SER	0	0.075	0.031	13.948	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	104	LEU	0	-0.023	0.007	17.209	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	105	GLN	0	0.004	0.005	20.649	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	106	SER	0	0.014	0.009	22.075	0.010	0.010	0.000	0.000	0.000	0.000
79	A	107	ASP	-1	-0.803	-0.868	24.056	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	108	PRO	0	0.036	0.016	26.727	0.005	0.005	0.000	0.000	0.000	0.000
81	A	109	ARG	1	0.823	0.884	27.719	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	110	SER	0	-0.084	-0.042	26.538	0.008	0.008	0.000	0.000	0.000	0.000
83	A	111	THR	0	0.011	0.002	28.444	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	112	GLN	0	-0.031	-0.009	25.531	0.004	0.004	0.000	0.000	0.000	0.000
85	A	113	PRO	0	0.033	0.015	20.800	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	114	VAL	0	-0.001	-0.007	19.027	0.009	0.009	0.000	0.000	0.000	0.000
87	A	115	PRO	0	-0.010	0.018	18.965	0.009	0.009	0.000	0.000	0.000	0.000
88	A	116	ARG	1	0.846	0.897	11.727	-0.127	-0.127	0.000	0.000	0.000	0.000
89	A	117	PHE	0	0.002	-0.001	14.553	0.015	0.015	0.000	0.000	0.000	0.000
90	A	118	ASP	-1	-0.831	-0.904	10.365	0.645	0.645	0.000	0.000	0.000	0.000
91	A	119	CAS	0	-0.038	-0.034	11.400	0.058	0.058	0.000	0.000	0.000	0.000
92	A	120	VAL	0	0.061	0.029	14.074	-0.065	-0.065	0.000	0.000	0.000	0.000
93	A	121	LEU	0	0.050	0.022	16.981	-0.042	-0.042	0.000	0.000	0.000	0.000
94	A	122	LYS	1	0.917	0.960	15.115	-0.518	-0.518	0.000	0.000	0.000	0.000
95	A	123	LEU	0	-0.016	0.007	17.110	-0.030	-0.030	0.000	0.000	0.000	0.000
96	A	124	VAL	0	0.022	-0.011	19.302	-0.030	-0.030	0.000	0.000	0.000	0.000
97	A	125	HIS	0	0.002	0.001	22.250	-0.012	-0.012	0.000	0.000	0.000	0.000
98	A	126	HIS	0	0.032	0.043	21.727	-0.031	-0.031	0.000	0.000	0.000	0.000
99	A	127	TYR	0	-0.030	-0.018	21.223	-0.015	-0.015	0.000	0.000	0.000	0.000
100	A	128	MET	0	-0.047	-0.013	25.948	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	129	PRO	0	-0.026	0.009	28.428	0.002	0.002	0.000	0.000	0.000	0.000
102	A	130	PRO	0	0.023	0.010	31.157	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	131	GLN	0	-0.009	-0.007	34.407	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	141	ALA	0	0.051	0.029	30.023	0.002	0.002	0.000	0.000	0.000	0.000
105	A	142	TYR	0	-0.046	-0.045	25.023	-0.011	-0.011	0.000	0.000	0.000	0.000
106	A	143	TYR	0	-0.030	-0.006	30.075	0.000	0.000	0.000	0.000	0.000	0.000
107	A	144	ILE	0	0.006	0.008	29.227	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	145	TYR	0	0.002	-0.002	31.767	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	146	SER	0	-0.079	-0.039	34.051	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	147	GLY	0	0.008	-0.002	36.806	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	148	GLY	0	-0.004	-0.020	39.647	0.000	0.000	0.000	0.000	0.000	0.000
112	A	149	GLU	-1	-0.857	-0.925	39.204	0.019	0.019	0.000	0.000	0.000	0.000
113	A	150	LYS	1	0.925	0.984	33.110	-0.039	-0.039	0.000	0.000	0.000	0.000
114	A	151	ILE	0	0.046	0.022	34.493	0.002	0.002	0.000	0.000	0.000	0.000
115	A	152	PRO	0	-0.038	-0.036	33.629	0.002	0.002	0.000	0.000	0.000	0.000
116	A	153	LEU	0	-0.055	-0.022	26.219	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	154	VAL	0	-0.005	-0.017	30.323	0.004	0.004	0.000	0.000	0.000	0.000
118	A	155	LEU	0	-0.039	-0.010	24.786	-0.005	-0.005	0.000	0.000	0.000	0.000
119	A	156	SER	0	-0.032	-0.016	29.213	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	157	ARG	1	0.915	0.947	30.055	-0.084	-0.084	0.000	0.000	0.000	0.000
121	A	158	PRO	0	0.027	0.029	26.442	-0.006	-0.006	0.000	0.000	0.000	0.000
122	A	159	LEU	0	0.014	0.005	28.353	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	160	SER	0	0.002	0.012	29.405	0.010	0.010	0.000	0.000	0.000	0.000
124	A	161	SER	0	0.014	-0.003	31.388	-0.010	-0.010	0.000	0.000	0.000	0.000
125	A	162	ASN	0	-0.011	0.002	33.038	0.002	0.002	0.000	0.000	0.000	0.000

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