FMO DATABASE

FMODB ID: 764MK

Calculation Name: 4GF3-A-Xray372

Preferred Name: Tyrosine-protein phosphatase yopH

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4GF3

Chain ID: A

ChEMBL ID: CHEMBL4404

UniProt ID: P15273

Base Structure: X-ray

Registration Date: 2023-09-23

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	123
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-984692.768114
FMO2-HF: Nuclear repulsion	937314.989904
FMO2-HF: Total energy	-47377.778211
FMO2-MP2: Total energy	-47517.924345

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:ARG)

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

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.
-264.475	-269.721	60.801	-24.391	-31.162	-0.227

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.815 / q_NPA : 0.910

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	4	TYR	0	0.062	-0.007	2.464	-10.757	-7.345	1.406	-2.180	-2.637	-0.012
4	A	5	SER	0	0.069	0.021	4.844	-1.226	-1.112	-0.001	-0.002	-0.111	0.000
5	A	6	SER	0	0.068	0.040	2.034	0.028	0.927	2.146	-1.191	-1.854	-0.007
6	A	7	LEU	0	-0.044	-0.018	1.913	-6.000	-6.075	5.442	-1.485	-3.882	-0.009
7	A	8	LEU	0	0.016	0.001	3.056	3.455	2.988	0.090	0.684	-0.306	-0.002
8	A	9	GLU	-1	-0.915	-0.943	6.754	-27.519	-27.519	0.000	0.000	0.000	0.000
9	A	10	GLU	-1	-0.841	-0.937	2.011	-111.860	-106.100	6.953	-6.473	-6.241	-0.098
10	A	11	PHE	0	-0.015	-0.018	6.041	3.406	3.406	0.000	0.000	0.000	0.000
11	A	12	ALA	0	0.015	0.023	8.163	2.505	2.505	0.000	0.000	0.000	0.000
12	A	13	THR	0	0.010	0.000	9.204	2.730	2.730	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.866	-0.902	8.526	-28.674	-28.674	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.076	-0.043	10.517	2.090	2.090	0.000	0.000	0.000	0.000
15	A	16	GLY	0	-0.025	0.010	13.477	1.632	1.632	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.092	-0.052	14.394	1.465	1.465	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.947	-0.981	14.285	-16.238	-16.238	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.924	-0.967	13.239	-19.654	-19.654	0.000	0.000	0.000	0.000
19	A	20	ILE	0	-0.099	-0.036	10.572	0.728	0.728	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.920	-0.951	12.524	-16.565	-16.565	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.040	-0.040	11.523	-0.959	-0.959	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.003	0.009	14.615	-0.159	-0.159	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.881	-0.956	15.604	-14.819	-14.819	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.098	-0.044	15.778	-0.281	-0.281	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.015	0.007	12.268	-0.958	-0.958	0.000	0.000	0.000	0.000
26	A	27	HIS	0	-0.029	-0.010	12.432	-0.991	-0.991	0.000	0.000	0.000	0.000
27	A	28	GLY	0	0.104	0.052	13.571	0.601	0.601	0.000	0.000	0.000	0.000
28	A	29	ALA	0	-0.052	-0.030	14.535	0.156	0.156	0.000	0.000	0.000	0.000
29	A	30	VAL	0	0.052	0.042	14.205	0.083	0.083	0.000	0.000	0.000	0.000
30	A	31	THR	0	-0.031	-0.018	17.059	0.616	0.616	0.000	0.000	0.000	0.000
31	A	32	ILE	0	0.003	-0.014	17.869	-0.142	-0.142	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.864	-0.934	21.777	-12.355	-12.355	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.846	0.912	24.711	12.116	12.116	0.000	0.000	0.000	0.000
34	A	35	ILE	0	-0.006	-0.005	26.001	0.211	0.211	0.000	0.000	0.000	0.000
35	A	36	TRP	0	0.031	0.033	22.392	0.099	0.099	0.000	0.000	0.000	0.000
36	A	37	VAL	0	0.001	-0.003	19.550	-0.240	-0.240	0.000	0.000	0.000	0.000
37	A	38	VAL	0	-0.042	-0.008	14.634	0.084	0.084	0.000	0.000	0.000	0.000
38	A	39	HIS	0	-0.004	-0.008	16.088	-0.697	-0.697	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.004	-0.011	9.887	-0.891	-0.891	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.037	0.018	12.103	1.025	1.025	0.000	0.000	0.000	0.000
41	A	42	PRO	0	0.020	0.031	9.741	-1.236	-1.236	0.000	0.000	0.000	0.000
42	A	43	ILE	0	-0.039	-0.026	11.263	1.926	1.926	0.000	0.000	0.000	0.000
43	A	44	ASN	0	-0.071	-0.057	12.254	0.098	0.098	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.931	-0.969	9.966	-23.285	-23.285	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.916	0.964	7.336	26.109	26.109	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.841	-0.888	7.923	-26.816	-26.816	0.000	0.000	0.000	0.000
47	A	48	LEU	0	0.003	0.001	6.419	0.951	0.951	0.000	0.000	0.000	0.000
48	A	49	VAL	0	-0.023	-0.013	10.085	0.434	0.434	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.030	0.021	11.665	-0.437	-0.437	0.000	0.000	0.000	0.000
50	A	51	PHE	0	-0.026	-0.029	13.427	0.934	0.934	0.000	0.000	0.000	0.000
51	A	52	MET	0	0.038	0.037	17.200	-0.166	-0.166	0.000	0.000	0.000	0.000
52	A	53	ARG	1	0.867	0.952	20.349	11.181	11.181	0.000	0.000	0.000	0.000
53	A	54	ALA	0	0.026	0.014	24.073	-0.023	-0.023	0.000	0.000	0.000	0.000
54	A	55	GLY	0	0.009	-0.002	26.120	0.292	0.292	0.000	0.000	0.000	0.000
55	A	56	ILE	0	0.005	-0.001	29.966	-0.215	-0.215	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.024	0.001	32.650	-0.024	-0.024	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.017	-0.021	33.436	0.259	0.259	0.000	0.000	0.000	0.000
58	A	59	GLY	0	0.056	0.012	35.834	0.346	0.346	0.000	0.000	0.000	0.000
59	A	60	GLN	0	0.024	-0.001	36.028	-0.224	-0.224	0.000	0.000	0.000	0.000
60	A	61	SER	0	0.017	-0.004	35.731	-0.116	-0.116	0.000	0.000	0.000	0.000
61	A	62	GLN	0	0.111	0.085	31.640	-0.200	-0.200	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.025	0.023	31.458	-0.337	-0.337	0.000	0.000	0.000	0.000
63	A	64	TYR	0	-0.034	-0.013	31.707	-0.224	-0.224	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.957	-0.964	30.439	-10.009	-10.009	0.000	0.000	0.000	0.000
65	A	66	ILE	0	-0.018	-0.021	26.062	-0.388	-0.388	0.000	0.000	0.000	0.000
66	A	67	LEU	0	0.004	-0.008	27.102	-0.412	-0.412	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.887	0.939	28.694	9.209	9.209	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.954	0.981	24.717	11.815	11.815	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.037	0.003	23.653	-1.156	-1.156	0.000	0.000	0.000	0.000
70	A	71	LEU	0	0.002	0.014	23.878	0.180	0.180	0.000	0.000	0.000	0.000
71	A	72	PHE	0	0.041	0.013	20.774	-0.671	-0.671	0.000	0.000	0.000	0.000
72	A	73	SER	0	-0.005	-0.018	17.641	0.385	0.385	0.000	0.000	0.000	0.000
73	A	74	PRO	0	0.014	0.009	16.600	-0.450	-0.450	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.019	0.007	13.912	-1.016	-1.016	0.000	0.000	0.000	0.000
75	A	76	SER	0	0.071	0.038	8.850	0.778	0.778	0.000	0.000	0.000	0.000
76	A	77	GLY	0	0.020	-0.004	11.193	0.456	0.456	0.000	0.000	0.000	0.000
77	A	78	VAL	0	-0.039	-0.007	12.018	1.258	1.258	0.000	0.000	0.000	0.000
78	A	79	ILE	0	0.026	0.019	15.781	-0.355	-0.355	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.810	0.905	18.098	16.784	16.784	0.000	0.000	0.000	0.000
80	A	81	CYS	0	-0.037	-0.022	20.617	-0.169	-0.169	0.000	0.000	0.000	0.000
81	A	82	ALA	0	-0.007	0.012	23.768	0.300	0.300	0.000	0.000	0.000	0.000
82	A	83	LEU	0	0.013	0.002	25.667	0.023	0.023	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.784	-0.898	27.391	-10.835	-10.835	0.000	0.000	0.000	0.000
84	A	85	LYS	1	0.901	0.931	29.086	9.929	9.929	0.000	0.000	0.000	0.000
85	A	86	ASP	-1	-0.949	-0.969	31.847	-9.034	-9.034	0.000	0.000	0.000	0.000
86	A	87	ASP	-1	-0.898	-0.937	32.643	-8.972	-8.972	0.000	0.000	0.000	0.000
87	A	88	HIS	0	-0.103	-0.058	28.622	0.311	0.311	0.000	0.000	0.000	0.000
88	A	89	TRP	0	-0.007	-0.018	26.287	-0.363	-0.363	0.000	0.000	0.000	0.000
89	A	90	LEU	0	-0.009	0.003	20.961	-0.130	-0.130	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.019	-0.010	21.015	-0.060	-0.060	0.000	0.000	0.000	0.000
91	A	92	TRP	0	0.042	0.004	16.647	-0.723	-0.723	0.000	0.000	0.000	0.000
92	A	93	SER	0	-0.001	0.003	13.552	-0.327	-0.327	0.000	0.000	0.000	0.000
93	A	94	GLN	0	-0.054	-0.030	12.803	0.430	0.430	0.000	0.000	0.000	0.000
94	A	95	LEU	0	-0.021	-0.009	7.766	0.214	0.214	0.000	0.000	0.000	0.000
95	A	96	ASN	0	0.079	0.050	6.212	-4.204	-4.204	0.000	0.000	0.000	0.000
96	A	97	ILE	0	0.026	0.001	3.090	-6.477	-5.738	0.058	-0.158	-0.640	-0.001
97	A	98	ASN	0	-0.031	-0.031	2.304	-32.153	-27.166	4.688	-4.089	-5.586	-0.047
98	A	99	ASP	-1	-0.928	-0.960	2.819	-47.813	-46.287	0.927	-0.662	-1.791	-0.011
99	A	100	THR	0	-0.072	-0.015	3.202	0.502	2.129	0.147	-0.725	-1.049	-0.001
100	A	101	SER	0	-0.003	-0.014	1.715	-12.286	-37.065	38.752	-7.968	-6.005	-0.041
101	A	102	GLY	0	0.098	0.039	3.792	8.837	9.089	0.025	0.062	-0.338	0.001
102	A	103	THR	0	-0.023	-0.018	6.029	3.863	3.863	0.000	0.000	0.000	0.000
103	A	104	GLN	0	-0.046	-0.025	6.812	0.412	0.412	0.000	0.000	0.000	0.000
104	A	105	LEU	0	0.036	0.009	6.319	3.755	3.755	0.000	0.000	0.000	0.000
105	A	106	ALA	0	0.057	0.038	9.267	3.415	3.415	0.000	0.000	0.000	0.000
106	A	107	SER	0	-0.030	-0.018	11.499	2.831	2.831	0.000	0.000	0.000	0.000
107	A	108	VAL	0	-0.018	-0.011	11.180	2.019	2.019	0.000	0.000	0.000	0.000
108	A	109	LEU	0	0.018	0.015	13.295	1.832	1.832	0.000	0.000	0.000	0.000
109	A	110	THR	0	-0.002	-0.019	15.059	1.593	1.593	0.000	0.000	0.000	0.000
110	A	111	SER	0	0.025	0.018	16.586	1.281	1.281	0.000	0.000	0.000	0.000
111	A	112	LEU	0	-0.092	-0.038	15.463	1.162	1.162	0.000	0.000	0.000	0.000
112	A	113	VAL	0	0.045	0.013	19.152	1.017	1.017	0.000	0.000	0.000	0.000
113	A	114	ASP	-1	-0.888	-0.937	21.264	-13.820	-13.820	0.000	0.000	0.000	0.000
114	A	115	LYS	1	0.849	0.942	22.062	13.659	13.659	0.000	0.000	0.000	0.000
115	A	116	ALA	0	0.021	-0.011	23.457	0.699	0.699	0.000	0.000	0.000	0.000
116	A	117	VAL	0	-0.026	0.006	25.263	0.590	0.590	0.000	0.000	0.000	0.000
117	A	118	THR	0	-0.121	-0.062	25.719	0.424	0.424	0.000	0.000	0.000	0.000
118	A	119	LEU	0	-0.051	-0.018	26.284	0.558	0.558	0.000	0.000	0.000	0.000
119	A	133	ARG	1	0.909	0.930	2.643	46.502	47.261	0.168	-0.204	-0.722	0.001
120	A	134	PRO	0	0.007	0.008	5.785	-0.735	-0.735	0.000	0.000	0.000	0.000
121	A	135	SER	0	-0.007	-0.021	7.488	-2.119	-2.119	0.000	0.000	0.000	0.000
122	A	136	SER	0	-0.034	-0.015	8.265	-0.478	-0.478	0.000	0.000	0.000	0.000
123	A	137	SER	0	-0.038	-0.003	9.957	2.385	2.385	0.000	0.000	0.000	0.000

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