FMO DATABASE

FMODB ID: 7G5MK

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	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	124
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-917550.087051
FMO2-HF: Nuclear repulsion	870427.071829
FMO2-HF: Total energy	-47123.015221
FMO2-MP2: Total energy	-47261.406015

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.
-4.461	-2.327	10.263	-5.314	-7.085	-0.03

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 : -0.057 / q_NPA : -0.046

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	0.039	0.025	3.466	3.633	5.908	0.035	-1.000	-1.310	0.001
4	A	5	LEU	0	0.065	0.024	5.856	-0.776	-0.776	0.000	0.000	0.000	0.000
5	A	6	SER	0	0.011	0.008	6.677	-0.766	-0.766	0.000	0.000	0.000	0.000
6	A	7	ASP	-1	-0.805	-0.902	8.011	-0.152	-0.152	0.000	0.000	0.000	0.000
7	A	8	LEU	0	0.005	0.015	3.052	-0.937	-0.412	0.049	-0.143	-0.431	0.000
8	A	9	HIS	0	0.035	0.011	6.600	-0.179	-0.179	0.000	0.000	0.000	0.000
9	A	10	ARG	1	0.886	0.954	9.698	-0.359	-0.359	0.000	0.000	0.000	0.000
10	A	11	GLN	0	-0.063	-0.046	7.186	-0.168	-0.168	0.000	0.000	0.000	0.000
11	A	12	VAL	0	0.027	0.006	8.204	-0.054	-0.054	0.000	0.000	0.000	0.000
12	A	13	SER	0	-0.008	-0.008	10.903	0.030	0.030	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.946	0.977	12.920	0.434	0.434	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.003	-0.001	11.158	-0.016	-0.016	0.000	0.000	0.000	0.000
15	A	16	VAL	0	0.021	0.010	14.672	0.019	0.019	0.000	0.000	0.000	0.000
16	A	17	GLN	0	-0.052	-0.033	16.914	0.025	0.025	0.000	0.000	0.000	0.000
17	A	18	GLN	0	-0.084	-0.039	17.115	-0.034	-0.034	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.919	-0.952	19.854	-0.141	-0.141	0.000	0.000	0.000	0.000
19	A	20	SER	0	-0.034	-0.019	16.767	-0.023	-0.023	0.000	0.000	0.000	0.000
20	A	21	GLY	0	-0.022	-0.024	16.708	-0.031	-0.031	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.915	-0.941	17.132	-0.079	-0.079	0.000	0.000	0.000	0.000
22	A	23	CYS	0	-0.093	-0.031	16.362	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	24	THR	0	0.035	0.027	13.809	0.021	0.021	0.000	0.000	0.000	0.000
24	A	25	GLY	0	-0.006	-0.006	10.147	-0.053	-0.053	0.000	0.000	0.000	0.000
25	A	26	LYS	1	0.933	0.953	9.384	0.909	0.909	0.000	0.000	0.000	0.000
26	A	27	LEU	0	0.004	0.004	2.278	-0.973	-0.204	1.845	-1.164	-1.450	-0.002
27	A	28	ARG	1	0.936	0.970	6.116	2.079	2.079	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.049	0.023	4.853	-0.303	-0.303	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.036	-0.026	5.816	0.469	0.469	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.040	0.030	7.938	-0.094	-0.094	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.010	0.010	9.545	0.230	0.230	0.000	0.000	0.000	0.000
32	A	33	ALA	0	-0.015	-0.009	12.642	0.016	0.016	0.000	0.000	0.000	0.000
33	A	34	ASN	0	0.005	-0.006	14.916	-0.026	-0.026	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.928	0.950	16.615	0.519	0.519	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.893	-0.916	19.378	-0.247	-0.247	0.000	0.000	0.000	0.000
36	A	37	THR	0	0.006	0.006	18.296	0.025	0.025	0.000	0.000	0.000	0.000
37	A	38	THR	0	0.012	0.006	19.393	-0.035	-0.035	0.000	0.000	0.000	0.000
38	A	39	PHE	0	-0.060	-0.035	15.702	0.010	0.010	0.000	0.000	0.000	0.000
39	A	40	GLN	0	-0.026	-0.032	18.674	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	41	GLY	0	0.034	0.031	17.434	0.027	0.027	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.029	0.006	17.069	0.047	0.047	0.000	0.000	0.000	0.000
42	A	43	THR	0	0.053	0.014	14.986	0.039	0.039	0.000	0.000	0.000	0.000
43	A	44	ILE	0	-0.003	0.000	11.541	-0.074	-0.074	0.000	0.000	0.000	0.000
44	A	45	ALA	0	-0.046	-0.025	15.271	-0.088	-0.088	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.018	-0.009	18.435	-0.058	-0.058	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.054	0.032	18.870	-0.045	-0.045	0.000	0.000	0.000	0.000
47	A	48	ALA	0	-0.007	0.016	13.709	-0.080	-0.080	0.000	0.000	0.000	0.000
48	A	49	ARG	1	0.828	0.890	13.439	0.177	0.177	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.831	-0.946	9.550	1.150	1.150	0.000	0.000	0.000	0.000
50	A	51	SER	0	-0.026	-0.020	8.545	0.232	0.232	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.811	-0.884	8.277	-0.514	-0.514	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.913	0.952	7.789	-1.733	-1.733	0.000	0.000	0.000	0.000
53	A	54	VAL	0	-0.026	-0.001	3.411	-0.203	0.436	0.032	-0.205	-0.467	0.001
54	A	55	PHE	0	-0.037	0.010	3.888	-1.816	-1.519	0.000	-0.164	-0.133	-0.001
55	A	56	ALA	0	0.037	0.010	5.806	-0.158	-0.158	0.000	0.000	0.000	0.000
56	A	57	GLN	0	0.056	0.010	4.995	0.259	0.259	0.000	0.000	0.000	0.000
57	A	58	THR	0	0.001	-0.004	1.929	-6.507	-9.150	8.287	-2.546	-3.099	-0.028
58	A	59	VAL	0	-0.008	0.002	3.359	0.811	1.083	0.015	-0.092	-0.195	-0.001
59	A	60	LEU	0	-0.002	0.000	7.054	0.119	0.119	0.000	0.000	0.000	0.000
60	A	61	SER	0	-0.048	-0.035	5.319	0.605	0.605	0.000	0.000	0.000	0.000
61	A	62	HIS	0	-0.071	-0.047	4.876	-0.285	-0.285	0.000	0.000	0.000	0.000
62	A	63	VAL	0	-0.015	-0.003	8.651	-0.138	-0.138	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.036	0.034	10.923	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	65	ASN	0	-0.094	-0.063	12.537	-0.110	-0.110	0.000	0.000	0.000	0.000
65	A	66	VAL	0	-0.022	0.018	13.907	-0.077	-0.077	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.038	-0.025	16.363	0.016	0.016	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.031	-0.007	16.055	-0.049	-0.049	0.000	0.000	0.000	0.000
68	A	69	THR	0	0.010	-0.003	20.072	0.011	0.011	0.000	0.000	0.000	0.000
69	A	70	GLN	0	0.065	0.043	23.123	0.019	0.019	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.838	-0.950	25.050	0.017	0.017	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.804	-0.855	19.600	-0.032	-0.032	0.000	0.000	0.000	0.000
72	A	73	THR	0	-0.001	-0.012	21.330	0.005	0.005	0.000	0.000	0.000	0.000
73	A	74	ALA	0	-0.003	0.008	22.296	0.003	0.003	0.000	0.000	0.000	0.000
74	A	75	LYS	1	0.862	0.929	21.349	0.067	0.067	0.000	0.000	0.000	0.000
75	A	76	LEU	0	0.011	0.011	16.757	-0.010	-0.010	0.000	0.000	0.000	0.000
76	A	77	LEU	0	0.020	0.017	20.508	0.007	0.007	0.000	0.000	0.000	0.000
77	A	78	GLN	0	0.011	0.007	23.755	-0.013	-0.013	0.000	0.000	0.000	0.000
78	A	79	SER	0	-0.030	-0.013	18.997	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	80	THR	0	-0.024	-0.018	21.160	0.016	0.016	0.000	0.000	0.000	0.000
80	A	81	VAL	0	-0.015	-0.012	22.724	0.006	0.006	0.000	0.000	0.000	0.000
81	A	82	LYS	1	0.888	0.951	23.415	0.116	0.116	0.000	0.000	0.000	0.000
82	A	83	HIS	0	-0.058	-0.044	20.637	-0.041	-0.041	0.000	0.000	0.000	0.000
83	A	84	ASN	0	-0.043	-0.012	23.938	0.018	0.018	0.000	0.000	0.000	0.000
84	A	85	LEU	0	0.012	0.009	19.531	0.018	0.018	0.000	0.000	0.000	0.000
85	A	86	ASN	0	-0.003	-0.003	20.568	-0.024	-0.024	0.000	0.000	0.000	0.000
86	A	87	ASN	0	0.001	0.005	13.992	0.100	0.100	0.000	0.000	0.000	0.000
87	A	88	TYR	0	-0.002	-0.016	13.806	0.065	0.065	0.000	0.000	0.000	0.000
88	A	89	ASP	-1	-0.767	-0.827	16.591	0.542	0.542	0.000	0.000	0.000	0.000
89	A	90	LEU	0	0.001	-0.011	17.663	0.045	0.045	0.000	0.000	0.000	0.000
90	A	91	ARG	1	0.953	0.978	19.237	-0.497	-0.497	0.000	0.000	0.000	0.000
91	A	92	SER	0	0.027	0.000	21.955	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.058	-0.036	22.046	0.017	0.017	0.000	0.000	0.000	0.000
93	A	94	GLY	0	0.025	0.013	25.081	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	95	ASN	0	-0.038	-0.015	27.546	0.007	0.007	0.000	0.000	0.000	0.000
95	A	96	GLY	0	0.050	0.033	28.157	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	97	ASN	0	-0.006	-0.017	23.754	-0.024	-0.024	0.000	0.000	0.000	0.000
97	A	98	SER	0	-0.005	-0.005	21.328	0.020	0.020	0.000	0.000	0.000	0.000
98	A	99	VAL	0	0.014	0.014	17.035	-0.012	-0.012	0.000	0.000	0.000	0.000
99	A	100	LEU	0	0.003	0.015	12.330	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	101	VAL	0	-0.050	-0.033	14.680	0.062	0.062	0.000	0.000	0.000	0.000
101	A	102	SER	0	-0.009	-0.022	12.896	0.173	0.173	0.000	0.000	0.000	0.000
102	A	103	LEU	0	-0.019	-0.009	9.727	-0.162	-0.162	0.000	0.000	0.000	0.000
103	A	104	ARG	1	0.826	0.907	13.757	-0.375	-0.375	0.000	0.000	0.000	0.000
104	A	105	SER	0	-0.019	-0.026	14.418	-0.077	-0.077	0.000	0.000	0.000	0.000
105	A	106	ASP	-1	-0.824	-0.902	11.265	1.327	1.327	0.000	0.000	0.000	0.000
106	A	107	GLN	0	0.026	-0.001	11.378	-0.095	-0.095	0.000	0.000	0.000	0.000
107	A	108	MET	0	0.028	0.015	10.067	0.012	0.012	0.000	0.000	0.000	0.000
108	A	109	THR	0	-0.028	-0.006	12.658	-0.166	-0.166	0.000	0.000	0.000	0.000
109	A	110	LEU	0	0.050	-0.003	12.390	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	111	GLN	0	-0.012	-0.005	14.496	-0.029	-0.029	0.000	0.000	0.000	0.000
111	A	112	ASP	-1	-0.744	-0.861	14.987	-0.051	-0.051	0.000	0.000	0.000	0.000
112	A	113	ALA	0	0.020	0.005	10.841	0.035	0.035	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.813	0.902	12.587	0.305	0.305	0.000	0.000	0.000	0.000
114	A	115	VAL	0	-0.003	-0.004	15.151	0.023	0.023	0.000	0.000	0.000	0.000
115	A	116	LEU	0	0.002	-0.005	12.359	0.031	0.031	0.000	0.000	0.000	0.000
116	A	117	LEU	0	0.015	-0.005	8.812	0.026	0.026	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-0.832	-0.893	12.948	-0.303	-0.303	0.000	0.000	0.000	0.000
118	A	119	ALA	0	-0.036	-0.005	16.270	0.027	0.027	0.000	0.000	0.000	0.000
119	A	120	ALA	0	0.002	-0.015	13.013	0.037	0.037	0.000	0.000	0.000	0.000
120	A	121	LEU	0	0.003	0.007	14.519	0.006	0.006	0.000	0.000	0.000	0.000
121	A	122	ARG	1	0.822	0.895	16.739	0.052	0.052	0.000	0.000	0.000	0.000
122	A	123	GLN	0	-0.011	-0.005	17.734	0.008	0.008	0.000	0.000	0.000	0.000
123	A	124	GLU	-1	-0.988	-0.976	15.574	-0.239	-0.239	0.000	0.000	0.000	0.000
124	A	125	SER	0	-0.058	-0.026	18.630	0.005	0.005	0.000	0.000	0.000	0.000

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