FMO DATABASE

FMODB ID: 6Y5GZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-984275.984499
FMO2-HF: Nuclear repulsion	936897.198833
FMO2-HF: Total energy	-47378.785665
FMO2-MP2: Total energy	-47518.869286

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.
-304.545	-304.635	53.803	-21.805	-31.911	-0.255

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 : 0.786 / q_NPA : 0.884

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	0.061	-0.007	2.562	-12.576	-8.747	0.969	-2.232	-2.566	-0.011
4	A	5	SER	0	0.045	0.027	5.231	-1.781	-1.642	-0.001	-0.003	-0.135	0.000
5	A	6	SER	0	0.061	0.034	2.236	-1.249	0.005	1.564	-1.082	-1.736	-0.008
6	A	7	LEU	0	-0.053	-0.020	2.092	-10.884	-8.718	5.663	-2.873	-4.957	-0.007
7	A	8	LEU	0	0.040	0.015	2.632	5.984	2.815	0.325	3.169	-0.325	0.000
8	A	9	GLU	-1	-0.883	-0.939	5.962	-30.199	-30.199	0.000	0.000	0.000	0.000
9	A	10	GLU	-1	-0.797	-0.869	1.734	-119.101	-127.269	24.334	-8.711	-7.455	-0.112
10	A	11	PHE	0	0.010	-0.023	5.590	3.867	3.867	0.000	0.000	0.000	0.000
11	A	12	ALA	0	0.000	0.010	7.668	2.830	2.830	0.000	0.000	0.000	0.000
12	A	13	THR	0	-0.003	-0.014	8.687	2.879	2.879	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.832	-0.864	8.118	-29.031	-29.031	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.066	-0.033	10.168	2.141	2.141	0.000	0.000	0.000	0.000
15	A	16	GLY	0	-0.042	-0.006	13.175	1.707	1.707	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.074	-0.036	13.414	1.488	1.488	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.962	-0.986	13.491	-16.557	-16.557	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.945	-0.975	12.169	-20.521	-20.521	0.000	0.000	0.000	0.000
19	A	20	ILE	0	-0.075	-0.043	9.830	0.655	0.655	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.917	-0.945	11.870	-16.808	-16.808	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.049	-0.040	11.498	-0.998	-0.998	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.010	0.002	14.715	-0.161	-0.161	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.893	-0.961	15.803	-15.216	-15.216	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.094	-0.044	16.090	-0.056	-0.056	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.020	0.017	12.426	-0.930	-0.930	0.000	0.000	0.000	0.000
26	A	27	HIS	0	-0.021	-0.014	12.576	-0.877	-0.877	0.000	0.000	0.000	0.000
27	A	28	GLY	0	0.098	0.051	13.795	0.760	0.760	0.000	0.000	0.000	0.000
28	A	29	ALA	0	-0.072	-0.035	14.693	0.108	0.108	0.000	0.000	0.000	0.000
29	A	30	VAL	0	0.056	0.035	13.676	-0.104	-0.104	0.000	0.000	0.000	0.000
30	A	31	THR	0	-0.024	-0.014	16.668	0.207	0.207	0.000	0.000	0.000	0.000
31	A	32	ILE	0	-0.003	-0.003	18.334	-0.168	-0.168	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.878	-0.952	21.768	-12.577	-12.577	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.868	0.923	24.742	12.366	12.366	0.000	0.000	0.000	0.000
34	A	35	ILE	0	-0.018	0.001	25.929	0.292	0.292	0.000	0.000	0.000	0.000
35	A	36	TRP	0	0.024	0.026	22.607	0.106	0.106	0.000	0.000	0.000	0.000
36	A	37	VAL	0	0.009	-0.012	19.587	-0.137	-0.137	0.000	0.000	0.000	0.000
37	A	38	VAL	0	-0.022	0.001	14.845	0.213	0.213	0.000	0.000	0.000	0.000
38	A	39	HIS	0	0.017	0.006	16.057	-0.848	-0.848	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.011	-0.007	10.650	-0.936	-0.936	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.044	0.020	12.415	1.007	1.007	0.000	0.000	0.000	0.000
41	A	42	PRO	0	0.017	0.027	10.313	-1.261	-1.261	0.000	0.000	0.000	0.000
42	A	43	ILE	0	-0.043	-0.026	11.585	1.940	1.940	0.000	0.000	0.000	0.000
43	A	44	ASN	0	-0.066	-0.056	12.431	0.308	0.308	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.837	-0.899	9.576	-25.838	-25.838	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.826	0.899	7.784	24.275	24.275	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.825	-0.874	7.876	-27.509	-27.509	0.000	0.000	0.000	0.000
47	A	48	LEU	0	0.015	0.005	6.479	1.325	1.325	0.000	0.000	0.000	0.000
48	A	49	VAL	0	-0.023	-0.013	9.883	0.233	0.233	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.024	0.017	11.919	-0.539	-0.539	0.000	0.000	0.000	0.000
50	A	51	PHE	0	-0.023	-0.029	13.690	0.963	0.963	0.000	0.000	0.000	0.000
51	A	52	MET	0	0.015	0.029	17.525	-0.127	-0.127	0.000	0.000	0.000	0.000
52	A	53	ARG	1	0.770	0.863	20.852	11.162	11.162	0.000	0.000	0.000	0.000
53	A	54	ALA	0	0.035	0.020	24.627	-0.126	-0.126	0.000	0.000	0.000	0.000
54	A	55	GLY	0	0.027	0.015	26.843	0.294	0.294	0.000	0.000	0.000	0.000
55	A	56	ILE	0	0.001	0.004	30.386	-0.232	-0.232	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.030	-0.005	32.801	-0.019	-0.019	0.000	0.000	0.000	0.000
57	A	58	THR	0	0.003	-0.010	33.798	0.320	0.320	0.000	0.000	0.000	0.000
58	A	59	GLY	0	0.032	0.007	36.012	0.342	0.342	0.000	0.000	0.000	0.000
59	A	60	GLN	0	0.008	-0.006	36.089	-0.249	-0.249	0.000	0.000	0.000	0.000
60	A	61	SER	0	-0.004	0.002	36.204	-0.126	-0.126	0.000	0.000	0.000	0.000
61	A	62	GLN	0	0.102	0.049	31.708	-0.196	-0.196	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.033	0.030	31.269	-0.350	-0.350	0.000	0.000	0.000	0.000
63	A	64	TYR	0	0.005	-0.002	31.665	-0.272	-0.272	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.906	-0.940	30.646	-9.925	-9.925	0.000	0.000	0.000	0.000
65	A	66	ILE	0	-0.002	0.008	25.867	-0.410	-0.410	0.000	0.000	0.000	0.000
66	A	67	LEU	0	0.011	-0.004	27.309	-0.339	-0.339	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.814	0.879	28.775	9.318	9.318	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.933	0.966	25.243	11.277	11.277	0.000	0.000	0.000	0.000
69	A	70	ASN	0	0.014	0.036	23.162	-1.134	-1.134	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.004	0.019	24.312	0.023	0.023	0.000	0.000	0.000	0.000
71	A	72	PHE	0	0.053	0.023	21.059	-0.678	-0.678	0.000	0.000	0.000	0.000
72	A	73	SER	0	0.013	-0.014	18.202	0.263	0.263	0.000	0.000	0.000	0.000
73	A	74	PRO	0	-0.004	0.005	16.711	-0.385	-0.385	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.013	0.005	13.990	-1.072	-1.072	0.000	0.000	0.000	0.000
75	A	76	SER	0	0.063	0.033	8.996	0.599	0.599	0.000	0.000	0.000	0.000
76	A	77	GLY	0	0.042	0.008	11.438	-0.202	-0.202	0.000	0.000	0.000	0.000
77	A	78	VAL	0	-0.045	-0.014	12.023	1.256	1.256	0.000	0.000	0.000	0.000
78	A	79	ILE	0	-0.003	0.023	15.776	-0.165	-0.165	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.800	0.898	17.994	16.561	16.561	0.000	0.000	0.000	0.000
80	A	81	CYS	0	-0.026	-0.024	20.368	0.033	0.033	0.000	0.000	0.000	0.000
81	A	82	ALA	0	-0.015	0.007	23.639	0.216	0.216	0.000	0.000	0.000	0.000
82	A	83	LEU	0	0.014	0.018	25.990	-0.024	-0.024	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.779	-0.868	27.470	-11.117	-11.117	0.000	0.000	0.000	0.000
84	A	85	LYS	1	0.822	0.870	29.276	9.847	9.847	0.000	0.000	0.000	0.000
85	A	86	ASP	-1	-0.830	-0.873	32.098	-9.301	-9.301	0.000	0.000	0.000	0.000
86	A	87	ASP	-1	-0.860	-0.937	32.973	-9.074	-9.074	0.000	0.000	0.000	0.000
87	A	88	HIS	0	-0.089	-0.054	29.088	0.285	0.285	0.000	0.000	0.000	0.000
88	A	89	TRP	0	0.005	-0.009	26.880	-0.301	-0.301	0.000	0.000	0.000	0.000
89	A	90	LEU	0	-0.008	0.001	21.435	-0.172	-0.172	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.030	-0.016	21.570	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	92	TRP	0	0.033	-0.006	16.880	-0.568	-0.568	0.000	0.000	0.000	0.000
92	A	93	SER	0	-0.006	-0.022	13.782	-0.199	-0.199	0.000	0.000	0.000	0.000
93	A	94	GLN	0	-0.047	-0.038	12.559	0.731	0.731	0.000	0.000	0.000	0.000
94	A	95	LEU	0	-0.034	-0.014	7.624	0.410	0.410	0.000	0.000	0.000	0.000
95	A	96	ASN	0	0.020	0.003	6.631	-2.443	-2.443	0.000	0.000	0.000	0.000
96	A	97	ILE	0	0.019	0.001	3.192	-6.056	-5.236	0.038	-0.226	-0.632	-0.001
97	A	98	ASN	0	-0.076	-0.045	2.053	-30.725	-27.546	5.072	-3.607	-4.645	-0.043
98	A	99	ASP	-1	-0.853	-0.923	2.202	-53.909	-53.322	3.502	-1.555	-2.533	-0.022
99	A	100	THR	0	-0.016	0.001	3.394	1.965	3.086	0.034	-0.418	-0.738	-0.002
100	A	101	SER	0	-0.021	-0.034	1.953	-28.838	-30.950	12.133	-4.772	-5.249	-0.050
101	A	102	GLY	0	0.054	0.028	3.233	10.201	9.822	0.072	0.667	-0.361	0.000
102	A	103	THR	0	-0.019	-0.035	5.761	4.150	4.150	0.000	0.000	0.000	0.000
103	A	104	GLN	0	-0.030	0.018	6.577	-0.240	-0.240	0.000	0.000	0.000	0.000
104	A	105	LEU	0	0.029	0.009	6.330	3.955	3.955	0.000	0.000	0.000	0.000
105	A	106	ALA	0	0.036	0.021	9.342	3.220	3.220	0.000	0.000	0.000	0.000
106	A	107	SER	0	-0.019	-0.020	11.100	2.735	2.735	0.000	0.000	0.000	0.000
107	A	108	VAL	0	-0.042	-0.007	11.460	1.992	1.992	0.000	0.000	0.000	0.000
108	A	109	LEU	0	0.025	0.011	13.364	1.761	1.761	0.000	0.000	0.000	0.000
109	A	110	THR	0	0.024	0.006	15.383	0.939	0.939	0.000	0.000	0.000	0.000
110	A	111	SER	0	-0.007	-0.013	16.003	1.368	1.368	0.000	0.000	0.000	0.000
111	A	112	LEU	0	-0.069	-0.025	16.018	1.093	1.093	0.000	0.000	0.000	0.000
112	A	113	VAL	0	0.048	0.022	19.330	0.988	0.988	0.000	0.000	0.000	0.000
113	A	114	ASP	-1	-0.879	-0.936	20.534	-14.052	-14.052	0.000	0.000	0.000	0.000
114	A	115	LYS	1	0.851	0.954	21.837	13.474	13.474	0.000	0.000	0.000	0.000
115	A	116	ALA	0	0.013	-0.016	23.445	0.637	0.637	0.000	0.000	0.000	0.000
116	A	117	VAL	0	-0.014	-0.001	25.422	0.636	0.636	0.000	0.000	0.000	0.000
117	A	118	THR	0	-0.088	-0.060	25.608	0.510	0.510	0.000	0.000	0.000	0.000
118	A	119	LEU	0	-0.111	-0.034	26.278	0.752	0.752	0.000	0.000	0.000	0.000
119	A	133	ARG	1	0.875	0.931	2.748	47.247	47.890	0.098	-0.162	-0.579	0.001
120	A	134	PRO	0	-0.020	-0.010	6.241	-0.334	-0.334	0.000	0.000	0.000	0.000
121	A	135	SER	0	0.055	0.013	7.296	-2.767	-2.767	0.000	0.000	0.000	0.000
122	A	136	SER	0	-0.076	-0.039	8.455	-0.371	-0.371	0.000	0.000	0.000	0.000
123	A	137	SER	0	-0.032	-0.011	10.244	2.604	2.604	0.000	0.000	0.000	0.000

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