FMO DATABASE

FMODB ID: M3J9Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-917728.404968
FMO2-HF: Nuclear repulsion	870606.166365
FMO2-HF: Total energy	-47122.238603
FMO2-MP2: Total energy	-47260.736522

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.
-4.858	-10.994	23.591	-9.277	-8.181	-0.043

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 : -0.051 / q_NPA : -0.052

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	0.067	0.036	3.292	2.620	4.974	0.044	-1.106	-1.292	0.000
4	A	5	LEU	0	0.055	0.023	5.857	-0.700	-0.700	0.000	0.000	0.000	0.000
5	A	6	SER	0	-0.013	-0.006	6.634	-0.620	-0.620	0.000	0.000	0.000	0.000
6	A	7	ASP	-1	-0.828	-0.919	7.980	-0.812	-0.812	0.000	0.000	0.000	0.000
7	A	8	LEU	0	0.005	0.017	3.405	-0.707	-0.318	0.014	-0.099	-0.305	0.000
8	A	9	HIS	0	0.034	0.011	6.564	-0.051	-0.051	0.000	0.000	0.000	0.000
9	A	10	ARG	1	0.938	0.979	9.816	0.181	0.181	0.000	0.000	0.000	0.000
10	A	11	GLN	0	-0.085	-0.059	7.486	-0.381	-0.381	0.000	0.000	0.000	0.000
11	A	12	VAL	0	0.035	0.012	8.217	-0.011	-0.011	0.000	0.000	0.000	0.000
12	A	13	SER	0	0.000	-0.003	10.888	0.077	0.077	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.917	0.965	13.003	0.739	0.739	0.000	0.000	0.000	0.000
14	A	15	LEU	0	0.001	0.000	11.239	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	16	VAL	0	0.026	0.017	14.642	0.038	0.038	0.000	0.000	0.000	0.000
16	A	17	GLN	0	-0.061	-0.040	16.903	0.050	0.050	0.000	0.000	0.000	0.000
17	A	18	GLN	0	-0.071	-0.032	16.992	-0.019	-0.019	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.919	-0.951	19.868	-0.203	-0.203	0.000	0.000	0.000	0.000
19	A	20	SER	0	-0.025	-0.017	16.696	-0.017	-0.017	0.000	0.000	0.000	0.000
20	A	21	GLY	0	-0.032	-0.029	16.697	-0.030	-0.030	0.000	0.000	0.000	0.000
21	A	22	ASP	-1	-0.905	-0.935	17.115	-0.066	-0.066	0.000	0.000	0.000	0.000
22	A	23	CYS	0	-0.104	-0.033	16.226	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	24	THR	0	0.013	0.012	13.878	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	25	GLY	0	0.020	0.011	10.157	-0.077	-0.077	0.000	0.000	0.000	0.000
25	A	26	LYS	1	0.936	0.953	9.409	1.111	1.111	0.000	0.000	0.000	0.000
26	A	27	LEU	0	0.011	0.011	2.045	-0.227	-0.773	4.175	-1.923	-1.706	0.000
27	A	28	ARG	1	0.959	0.982	6.105	2.425	2.425	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.042	0.019	4.854	-0.406	-0.406	0.000	0.000	0.000	0.000
29	A	30	ASN	0	-0.038	-0.029	5.817	0.674	0.674	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.016	0.023	8.002	-0.213	-0.213	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.014	0.011	9.539	0.351	0.351	0.000	0.000	0.000	0.000
32	A	33	ALA	0	-0.020	-0.015	12.594	0.001	0.001	0.000	0.000	0.000	0.000
33	A	34	ASN	0	0.029	0.003	14.604	-0.038	-0.038	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.913	0.946	16.211	0.765	0.765	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.926	-0.943	18.979	-0.486	-0.486	0.000	0.000	0.000	0.000
36	A	37	THR	0	0.008	0.015	17.703	0.039	0.039	0.000	0.000	0.000	0.000
37	A	38	THR	0	0.006	-0.007	19.028	-0.038	-0.038	0.000	0.000	0.000	0.000
38	A	39	PHE	0	-0.037	-0.023	15.947	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	40	GLN	0	-0.035	-0.028	18.440	0.015	0.015	0.000	0.000	0.000	0.000
40	A	41	GLY	0	0.029	0.023	17.276	0.038	0.038	0.000	0.000	0.000	0.000
41	A	42	LEU	0	-0.057	-0.016	16.754	0.064	0.064	0.000	0.000	0.000	0.000
42	A	43	THR	0	0.047	0.012	14.817	0.061	0.061	0.000	0.000	0.000	0.000
43	A	44	ILE	0	-0.015	-0.014	11.462	-0.083	-0.083	0.000	0.000	0.000	0.000
44	A	45	ALA	0	-0.042	-0.022	15.291	-0.094	-0.094	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.020	-0.002	18.338	-0.029	-0.029	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.053	0.021	18.601	-0.036	-0.036	0.000	0.000	0.000	0.000
47	A	48	ALA	0	-0.037	0.005	13.406	-0.092	-0.092	0.000	0.000	0.000	0.000
48	A	49	ARG	1	0.905	0.929	12.985	0.423	0.423	0.000	0.000	0.000	0.000
49	A	50	GLU	-1	-0.841	-0.943	10.243	0.330	0.330	0.000	0.000	0.000	0.000
50	A	51	SER	0	-0.044	-0.029	8.107	0.097	0.097	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.803	-0.871	7.853	-0.994	-0.994	0.000	0.000	0.000	0.000
52	A	53	LYS	1	1.018	1.017	7.963	-1.812	-1.812	0.000	0.000	0.000	0.000
53	A	54	VAL	0	-0.038	-0.003	2.862	-0.244	0.530	0.455	-0.322	-0.908	0.003
54	A	55	PHE	0	-0.035	0.006	3.628	-2.388	-1.729	0.004	-0.465	-0.199	-0.003
55	A	56	ALA	0	0.045	0.013	5.665	0.166	0.166	0.000	0.000	0.000	0.000
56	A	57	GLN	0	0.056	0.007	5.111	0.916	0.916	0.000	0.000	0.000	0.000
57	A	58	THR	0	0.006	0.009	1.688	-6.369	-16.644	18.890	-5.086	-3.529	-0.041
58	A	59	VAL	0	-0.016	-0.008	3.514	0.538	1.047	0.009	-0.276	-0.242	-0.002
59	A	60	LEU	0	-0.019	-0.010	7.174	0.118	0.118	0.000	0.000	0.000	0.000
60	A	61	SER	0	-0.035	-0.025	5.253	0.550	0.550	0.000	0.000	0.000	0.000
61	A	62	HIS	0	-0.063	-0.033	5.883	-0.405	-0.405	0.000	0.000	0.000	0.000
62	A	63	VAL	0	-0.012	-0.006	8.994	-0.316	-0.316	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.030	0.030	10.812	-0.115	-0.115	0.000	0.000	0.000	0.000
64	A	65	ASN	0	-0.089	-0.061	12.611	-0.165	-0.165	0.000	0.000	0.000	0.000
65	A	66	VAL	0	-0.035	0.014	14.161	-0.124	-0.124	0.000	0.000	0.000	0.000
66	A	67	VAL	0	-0.036	-0.019	16.709	0.000	0.000	0.000	0.000	0.000	0.000
67	A	68	LEU	0	-0.032	-0.009	16.379	-0.057	-0.057	0.000	0.000	0.000	0.000
68	A	69	THR	0	0.016	-0.001	20.317	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	70	GLN	0	0.066	0.041	23.314	0.025	0.025	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.857	-0.952	24.909	0.083	0.083	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.798	-0.852	19.771	0.108	0.108	0.000	0.000	0.000	0.000
72	A	73	THR	0	-0.002	-0.012	21.427	0.002	0.002	0.000	0.000	0.000	0.000
73	A	74	ALA	0	-0.007	0.005	22.430	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	75	LYS	1	0.934	0.963	21.488	0.031	0.031	0.000	0.000	0.000	0.000
75	A	76	LEU	0	0.027	0.019	16.680	-0.026	-0.026	0.000	0.000	0.000	0.000
76	A	77	LEU	0	0.019	0.023	20.537	-0.005	-0.005	0.000	0.000	0.000	0.000
77	A	78	GLN	0	0.005	0.004	23.784	-0.032	-0.032	0.000	0.000	0.000	0.000
78	A	79	SER	0	-0.019	-0.001	18.960	-0.022	-0.022	0.000	0.000	0.000	0.000
79	A	80	THR	0	-0.033	-0.022	21.398	0.011	0.011	0.000	0.000	0.000	0.000
80	A	81	VAL	0	-0.015	-0.011	22.679	0.000	0.000	0.000	0.000	0.000	0.000
81	A	82	LYS	1	0.901	0.952	23.524	0.152	0.152	0.000	0.000	0.000	0.000
82	A	83	HIS	0	-0.070	-0.044	20.218	-0.060	-0.060	0.000	0.000	0.000	0.000
83	A	84	ASN	0	-0.041	-0.010	23.790	0.027	0.027	0.000	0.000	0.000	0.000
84	A	85	LEU	0	0.037	0.020	19.172	0.017	0.017	0.000	0.000	0.000	0.000
85	A	86	ASN	0	0.009	0.000	20.977	-0.018	-0.018	0.000	0.000	0.000	0.000
86	A	87	ASN	0	0.014	0.016	13.725	0.089	0.089	0.000	0.000	0.000	0.000
87	A	88	TYR	0	-0.021	-0.058	13.696	0.094	0.094	0.000	0.000	0.000	0.000
88	A	89	ASP	-1	-0.807	-0.853	16.744	0.697	0.697	0.000	0.000	0.000	0.000
89	A	90	LEU	0	0.015	-0.007	17.885	0.087	0.087	0.000	0.000	0.000	0.000
90	A	91	ARG	1	0.948	0.975	19.034	-0.766	-0.766	0.000	0.000	0.000	0.000
91	A	92	SER	0	0.026	-0.004	22.127	0.004	0.004	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.061	-0.027	22.205	0.019	0.019	0.000	0.000	0.000	0.000
93	A	94	GLY	0	0.017	0.003	25.320	-0.013	-0.013	0.000	0.000	0.000	0.000
94	A	95	ASN	0	-0.027	-0.014	27.855	0.015	0.015	0.000	0.000	0.000	0.000
95	A	96	GLY	0	0.045	0.026	28.397	-0.006	-0.006	0.000	0.000	0.000	0.000
96	A	97	ASN	0	-0.003	-0.006	24.063	-0.030	-0.030	0.000	0.000	0.000	0.000
97	A	98	SER	0	-0.006	-0.005	21.407	0.013	0.013	0.000	0.000	0.000	0.000
98	A	99	VAL	0	0.019	0.018	17.279	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	100	LEU	0	-0.002	0.011	12.511	-0.037	-0.037	0.000	0.000	0.000	0.000
100	A	101	VAL	0	-0.048	-0.034	14.866	0.120	0.120	0.000	0.000	0.000	0.000
101	A	102	SER	0	-0.029	-0.040	12.847	0.233	0.233	0.000	0.000	0.000	0.000
102	A	103	LEU	0	-0.016	-0.007	9.820	-0.185	-0.185	0.000	0.000	0.000	0.000
103	A	104	ARG	1	0.819	0.918	13.846	-0.511	-0.511	0.000	0.000	0.000	0.000
104	A	105	SER	0	-0.018	-0.024	14.388	-0.120	-0.120	0.000	0.000	0.000	0.000
105	A	106	ASP	-1	-0.859	-0.935	11.135	1.202	1.202	0.000	0.000	0.000	0.000
106	A	107	GLN	0	0.002	-0.012	11.140	-0.162	-0.162	0.000	0.000	0.000	0.000
107	A	108	MET	0	0.031	0.012	10.290	0.071	0.071	0.000	0.000	0.000	0.000
108	A	109	THR	0	-0.010	0.015	12.429	-0.225	-0.225	0.000	0.000	0.000	0.000
109	A	110	LEU	0	0.051	-0.001	12.040	0.017	0.017	0.000	0.000	0.000	0.000
110	A	111	GLN	0	-0.029	-0.012	14.290	0.015	0.015	0.000	0.000	0.000	0.000
111	A	112	ASP	-1	-0.734	-0.845	14.958	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	113	ALA	0	0.011	0.002	10.763	0.071	0.071	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.848	0.940	12.541	0.364	0.364	0.000	0.000	0.000	0.000
114	A	115	VAL	0	0.003	-0.003	15.116	0.044	0.044	0.000	0.000	0.000	0.000
115	A	116	LEU	0	0.013	0.000	12.425	0.047	0.047	0.000	0.000	0.000	0.000
116	A	117	LEU	0	0.005	-0.007	8.999	0.062	0.062	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-0.892	-0.944	13.072	-0.242	-0.242	0.000	0.000	0.000	0.000
118	A	119	ALA	0	-0.024	0.004	16.440	0.023	0.023	0.000	0.000	0.000	0.000
119	A	120	ALA	0	0.001	-0.015	13.277	0.043	0.043	0.000	0.000	0.000	0.000
120	A	121	LEU	0	0.008	0.009	14.918	0.003	0.003	0.000	0.000	0.000	0.000
121	A	122	ARG	1	0.780	0.867	16.959	-0.091	-0.091	0.000	0.000	0.000	0.000
122	A	123	GLN	0	-0.012	-0.005	17.886	-0.007	-0.007	0.000	0.000	0.000	0.000
123	A	124	GLU	-1	-0.982	-0.978	15.468	0.009	0.009	0.000	0.000	0.000	0.000
124	A	125	SER	0	-0.065	-0.029	18.943	-0.017	-0.017	0.000	0.000	0.000	0.000

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