FMO DATABASE

FMODB ID: 228LR

Calculation Name: 1K46-A-Xray372

Preferred Name: Tyrosine-protein phosphatase yopH

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1K46

Chain ID: A

ChEMBL ID: CHEMBL5835

UniProt ID: P08538

Base Structure: X-ray

Registration Date: 2023-06-19

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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-918763.314878
FMO2-HF: Nuclear repulsion	871640.047055
FMO2-HF: Total energy	-47123.267823
FMO2-MP2: Total energy	-47261.606454

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:2:ASN)

Summations of interaction energy for fragment #1(A:2:ASN)

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.
-11.189	-8.074	12.073	-6.68	-8.504	-0.031

Interaction energy analysis for fragmet #1(A:2:ASN)

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 : -0.023

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	4	SER	0	0.060	0.009	3.567	1.961	4.786	0.018	-1.408	-1.435	0.004
4	A	5	LEU	0	0.038	0.012	5.658	-0.707	-0.707	0.000	0.000	0.000	0.000
5	A	6	SER	0	-0.015	-0.006	6.494	-0.612	-0.612	0.000	0.000	0.000	0.000
6	A	7	ASP	-1	-0.795	-0.873	7.642	0.150	0.150	0.000	0.000	0.000	0.000
7	A	8	LEU	0	0.020	0.012	3.122	-0.855	-0.298	0.066	-0.161	-0.462	0.000
8	A	9	HIS	0	0.029	0.020	6.241	-0.092	-0.092	0.000	0.000	0.000	0.000
9	A	10	ARG	1	0.876	0.939	9.722	-0.509	-0.509	0.000	0.000	0.000	0.000
10	A	11	GLN	0	-0.061	-0.033	7.093	-0.139	-0.139	0.000	0.000	0.000	0.000
11	A	12	VAL	0	0.030	0.007	7.968	-0.031	-0.031	0.000	0.000	0.000	0.000
12	A	13	SER	0	0.003	-0.007	10.647	-0.012	-0.012	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.940	0.980	12.737	0.148	0.148	0.000	0.000	0.000	0.000
14	A	15	LEU	0	0.008	0.000	10.838	-0.022	-0.022	0.000	0.000	0.000	0.000
15	A	16	VAL	0	0.010	0.004	14.593	0.001	0.001	0.000	0.000	0.000	0.000
16	A	17	GLN	0	-0.046	-0.031	16.789	0.001	0.001	0.000	0.000	0.000	0.000
17	A	18	GLN	0	-0.077	-0.033	16.529	-0.025	-0.025	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.915	-0.951	19.510	-0.017	-0.017	0.000	0.000	0.000	0.000
19	A	20	SER	0	-0.027	-0.016	16.884	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	21	GLY	0	-0.026	-0.025	16.116	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.914	-0.942	16.505	0.088	0.088	0.000	0.000	0.000	0.000
22	A	23	CYS	0	-0.083	-0.028	16.246	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	24	THR	0	0.000	-0.001	14.081	0.021	0.021	0.000	0.000	0.000	0.000
24	A	25	GLY	0	0.018	0.010	10.279	-0.066	-0.066	0.000	0.000	0.000	0.000
25	A	26	LYS	1	0.923	0.951	9.010	0.317	0.317	0.000	0.000	0.000	0.000
26	A	27	LEU	0	0.011	0.009	2.259	-1.326	-1.123	3.664	-1.616	-2.251	-0.004
27	A	28	ARG	1	0.907	0.947	5.559	1.630	1.630	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.059	0.029	5.759	-0.221	-0.221	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.030	-0.012	6.454	0.271	0.271	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.054	0.037	8.345	-0.059	-0.059	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.009	0.002	10.073	0.214	0.214	0.000	0.000	0.000	0.000
32	A	33	ALA	0	-0.017	-0.010	13.269	0.015	0.015	0.000	0.000	0.000	0.000
33	A	34	ASN	0	0.010	-0.003	15.200	0.005	0.005	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.920	0.948	16.727	0.414	0.414	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.874	-0.902	19.069	-0.136	-0.136	0.000	0.000	0.000	0.000
36	A	37	THR	0	0.013	0.003	18.607	0.017	0.017	0.000	0.000	0.000	0.000
37	A	38	THR	0	-0.003	-0.010	19.622	-0.038	-0.038	0.000	0.000	0.000	0.000
38	A	39	PHE	0	-0.054	-0.019	15.750	0.015	0.015	0.000	0.000	0.000	0.000
39	A	40	GLN	0	0.002	-0.015	19.045	-0.016	-0.016	0.000	0.000	0.000	0.000
40	A	41	GLY	0	0.042	0.032	17.782	0.020	0.020	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.025	0.003	17.259	0.048	0.048	0.000	0.000	0.000	0.000
42	A	43	THR	0	0.067	0.017	14.830	0.033	0.033	0.000	0.000	0.000	0.000
43	A	44	ILE	0	-0.001	-0.002	11.337	-0.071	-0.071	0.000	0.000	0.000	0.000
44	A	45	ALA	0	-0.051	-0.024	15.103	-0.067	-0.067	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.027	-0.021	18.215	-0.052	-0.052	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.047	0.030	18.224	-0.045	-0.045	0.000	0.000	0.000	0.000
47	A	48	ALA	0	-0.012	0.012	13.686	-0.062	-0.062	0.000	0.000	0.000	0.000
48	A	49	ARG	1	0.780	0.874	13.222	0.089	0.089	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.827	-0.951	8.749	1.617	1.617	0.000	0.000	0.000	0.000
50	A	51	SER	0	-0.018	-0.009	8.179	0.335	0.335	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.798	-0.878	8.510	-0.373	-0.373	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.898	0.949	7.455	-1.664	-1.664	0.000	0.000	0.000	0.000
53	A	54	VAL	0	-0.004	0.005	3.205	-1.088	0.004	0.084	-0.473	-0.703	0.004
54	A	55	PHE	0	-0.025	0.008	4.099	-1.723	-1.492	-0.001	-0.095	-0.135	0.000
55	A	56	ALA	0	0.027	0.008	6.095	-0.459	-0.459	0.000	0.000	0.000	0.000
56	A	57	GLN	0	0.055	0.010	4.919	-0.312	-0.209	-0.001	-0.003	-0.098	0.000
57	A	58	THR	0	-0.013	-0.001	1.880	-10.078	-12.362	8.236	-2.764	-3.187	-0.034
58	A	59	VAL	0	-0.003	0.003	3.457	0.438	0.768	0.008	-0.158	-0.179	-0.001
59	A	60	LEU	0	0.005	0.003	7.126	0.144	0.144	0.000	0.000	0.000	0.000
60	A	61	SER	0	-0.041	-0.036	5.164	0.406	0.406	0.000	0.000	0.000	0.000
61	A	62	HIS	0	-0.083	-0.050	4.626	0.212	0.270	-0.001	-0.002	-0.054	0.000
62	A	63	VAL	0	-0.010	-0.009	8.592	0.076	0.076	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.022	0.026	10.772	0.095	0.095	0.000	0.000	0.000	0.000
64	A	65	ASN	0	-0.077	-0.046	12.476	-0.018	-0.018	0.000	0.000	0.000	0.000
65	A	66	VAL	0	0.000	0.023	13.733	-0.022	-0.022	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.031	-0.026	16.288	0.026	0.026	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.031	-0.003	15.845	-0.037	-0.037	0.000	0.000	0.000	0.000
68	A	69	THR	0	0.012	-0.019	19.771	0.030	0.030	0.000	0.000	0.000	0.000
69	A	70	GLN	0	0.038	0.035	23.181	0.012	0.012	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.818	-0.929	25.239	-0.092	-0.092	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.802	-0.858	19.560	-0.214	-0.214	0.000	0.000	0.000	0.000
72	A	73	THR	0	-0.005	-0.008	21.062	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	74	ALA	0	0.000	-0.001	22.491	0.006	0.006	0.000	0.000	0.000	0.000
74	A	75	LYS	1	0.843	0.924	21.140	0.208	0.208	0.000	0.000	0.000	0.000
75	A	76	LEU	0	0.031	0.021	16.532	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	77	LEU	0	0.003	0.014	20.387	0.019	0.019	0.000	0.000	0.000	0.000
77	A	78	GLN	0	0.000	-0.004	23.785	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	79	SER	0	-0.046	-0.042	18.944	0.012	0.012	0.000	0.000	0.000	0.000
79	A	80	THR	0	-0.037	-0.024	21.286	0.021	0.021	0.000	0.000	0.000	0.000
80	A	81	VAL	0	-0.017	-0.011	22.850	0.014	0.014	0.000	0.000	0.000	0.000
81	A	82	LYS	1	0.864	0.937	23.038	0.163	0.163	0.000	0.000	0.000	0.000
82	A	83	HIS	0	-0.021	-0.016	20.993	-0.027	-0.027	0.000	0.000	0.000	0.000
83	A	84	ASN	0	-0.036	-0.010	24.092	0.014	0.014	0.000	0.000	0.000	0.000
84	A	85	LEU	0	0.022	0.019	19.658	0.019	0.019	0.000	0.000	0.000	0.000
85	A	86	ASN	0	0.007	-0.001	20.553	-0.033	-0.033	0.000	0.000	0.000	0.000
86	A	87	ASN	0	0.006	0.008	14.075	0.105	0.105	0.000	0.000	0.000	0.000
87	A	88	TYR	0	0.001	-0.018	13.983	0.047	0.047	0.000	0.000	0.000	0.000
88	A	89	ASP	-1	-0.788	-0.841	16.697	0.306	0.306	0.000	0.000	0.000	0.000
89	A	90	LEU	0	0.001	-0.007	17.990	0.008	0.008	0.000	0.000	0.000	0.000
90	A	91	ARG	1	0.957	0.997	19.582	-0.185	-0.185	0.000	0.000	0.000	0.000
91	A	92	SER	0	0.035	0.007	21.809	-0.012	-0.012	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.069	-0.050	21.882	0.020	0.020	0.000	0.000	0.000	0.000
93	A	94	GLY	0	0.028	0.014	25.050	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	95	ASN	0	-0.039	-0.025	27.831	0.001	0.001	0.000	0.000	0.000	0.000
95	A	96	GLY	0	0.055	0.040	28.225	0.002	0.002	0.000	0.000	0.000	0.000
96	A	97	ASN	0	-0.011	-0.007	23.986	-0.017	-0.017	0.000	0.000	0.000	0.000
97	A	98	SER	0	0.025	0.006	21.350	0.028	0.028	0.000	0.000	0.000	0.000
98	A	99	VAL	0	-0.010	0.006	16.604	-0.023	-0.023	0.000	0.000	0.000	0.000
99	A	100	LEU	0	-0.015	0.003	12.397	0.019	0.019	0.000	0.000	0.000	0.000
100	A	101	VAL	0	-0.046	-0.025	14.677	0.018	0.018	0.000	0.000	0.000	0.000
101	A	102	SER	0	-0.027	-0.034	13.356	0.106	0.106	0.000	0.000	0.000	0.000
102	A	103	LEU	0	-0.008	-0.013	10.140	-0.122	-0.122	0.000	0.000	0.000	0.000
103	A	104	ARG	1	0.826	0.901	14.152	-0.163	-0.163	0.000	0.000	0.000	0.000
104	A	105	SER	0	-0.026	-0.021	14.798	-0.050	-0.050	0.000	0.000	0.000	0.000
105	A	106	ASP	-1	-0.813	-0.889	11.314	1.167	1.167	0.000	0.000	0.000	0.000
106	A	107	GLN	0	0.020	-0.004	11.723	-0.055	-0.055	0.000	0.000	0.000	0.000
107	A	108	MET	0	0.012	0.009	10.178	-0.038	-0.038	0.000	0.000	0.000	0.000
108	A	109	THR	0	-0.024	-0.014	13.059	-0.115	-0.115	0.000	0.000	0.000	0.000
109	A	110	LEU	0	0.035	-0.011	12.766	-0.046	-0.046	0.000	0.000	0.000	0.000
110	A	111	GLN	0	0.008	0.012	14.674	-0.067	-0.067	0.000	0.000	0.000	0.000
111	A	112	ASP	-1	-0.730	-0.828	15.046	-0.202	-0.202	0.000	0.000	0.000	0.000
112	A	113	ALA	0	0.029	0.007	10.864	0.001	0.001	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.814	0.901	12.533	0.349	0.349	0.000	0.000	0.000	0.000
114	A	115	VAL	0	-0.005	-0.003	14.959	0.012	0.012	0.000	0.000	0.000	0.000
115	A	116	LEU	0	-0.004	-0.004	12.201	0.034	0.034	0.000	0.000	0.000	0.000
116	A	117	LEU	0	0.024	0.003	8.652	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-0.841	-0.902	12.771	-0.381	-0.381	0.000	0.000	0.000	0.000
118	A	119	ALA	0	-0.031	-0.012	16.239	0.050	0.050	0.000	0.000	0.000	0.000
119	A	120	ALA	0	0.001	-0.002	12.715	0.049	0.049	0.000	0.000	0.000	0.000
120	A	121	LEU	0	0.028	0.015	14.187	0.042	0.042	0.000	0.000	0.000	0.000
121	A	122	ARG	1	0.845	0.922	16.392	0.258	0.258	0.000	0.000	0.000	0.000
122	A	123	GLN	0	-0.031	-0.007	17.241	0.033	0.033	0.000	0.000	0.000	0.000
123	A	124	GLU	-1	-0.973	-0.976	14.974	-0.395	-0.395	0.000	0.000	0.000	0.000
124	A	125	SER	0	-0.114	-0.079	18.007	0.059	0.059	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ASN)