FMO DATABASE

FMODB ID: 2NGLR

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

Total energy (hartree)

FMO2-HF: Electronic energy	-984503.945657
FMO2-HF: Nuclear repulsion	937125.503675
FMO2-HF: Total energy	-47378.441982
FMO2-MP2: Total energy	-47518.547209

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.
-280.502	-273.881	41.149	-18.984	-28.784	-0.21

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 : 0.811 / q_NPA : 0.905

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	0.075	-0.004	2.491	-11.940	-7.610	1.264	-2.629	-2.965	-0.009
4	A	5	SER	0	0.068	0.022	5.006	-1.710	-1.581	-0.001	-0.003	-0.125	0.000
5	A	6	SER	0	0.025	0.036	2.298	-1.219	0.157	1.454	-1.085	-1.745	-0.007
6	A	7	LEU	0	-0.042	-0.022	2.079	-7.616	-6.789	6.356	-2.615	-4.568	-0.008
7	A	8	LEU	0	0.027	0.004	2.662	5.707	2.885	0.246	2.961	-0.385	-0.002
8	A	9	GLU	-1	-0.894	-0.938	6.315	-29.414	-29.414	0.000	0.000	0.000	0.000
9	A	10	GLU	-1	-0.800	-0.876	1.713	-124.052	-129.265	22.132	-9.281	-7.639	-0.122
10	A	11	PHE	0	0.009	-0.012	5.887	3.594	3.594	0.000	0.000	0.000	0.000
11	A	12	ALA	0	0.017	0.022	7.836	2.641	2.641	0.000	0.000	0.000	0.000
12	A	13	THR	0	-0.004	-0.014	9.033	2.773	2.773	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.838	-0.863	8.164	-29.457	-29.457	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.065	-0.038	10.233	2.126	2.126	0.000	0.000	0.000	0.000
15	A	16	GLY	0	-0.032	0.006	13.212	1.662	1.662	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.092	-0.048	13.944	1.492	1.492	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.959	-0.985	14.053	-16.348	-16.348	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.928	-0.970	12.693	-20.145	-20.145	0.000	0.000	0.000	0.000
19	A	20	ILE	0	-0.097	-0.037	10.032	0.829	0.829	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.918	-0.953	12.197	-16.567	-16.567	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.048	-0.036	11.431	-0.889	-0.889	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.011	0.003	14.621	-0.119	-0.119	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.880	-0.957	15.666	-15.005	-15.005	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.095	-0.042	15.918	-0.275	-0.275	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.015	0.002	12.419	-0.917	-0.917	0.000	0.000	0.000	0.000
26	A	27	HIS	0	-0.029	-0.013	12.584	-0.887	-0.887	0.000	0.000	0.000	0.000
27	A	28	GLY	0	0.108	0.055	13.506	0.573	0.573	0.000	0.000	0.000	0.000
28	A	29	ALA	0	-0.054	-0.032	14.493	0.178	0.178	0.000	0.000	0.000	0.000
29	A	30	VAL	0	0.058	0.042	14.040	0.034	0.034	0.000	0.000	0.000	0.000
30	A	31	THR	0	-0.022	-0.016	16.956	0.247	0.247	0.000	0.000	0.000	0.000
31	A	32	ILE	0	-0.019	-0.018	17.986	-0.147	-0.147	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.852	-0.933	21.709	-12.525	-12.525	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.849	0.913	24.588	12.213	12.213	0.000	0.000	0.000	0.000
34	A	35	ILE	0	-0.009	-0.002	25.915	0.223	0.223	0.000	0.000	0.000	0.000
35	A	36	TRP	0	0.025	0.031	22.624	0.098	0.098	0.000	0.000	0.000	0.000
36	A	37	VAL	0	0.006	-0.002	19.461	-0.243	-0.243	0.000	0.000	0.000	0.000
37	A	38	VAL	0	-0.045	-0.007	14.769	0.103	0.103	0.000	0.000	0.000	0.000
38	A	39	HIS	0	-0.010	-0.011	16.184	-0.638	-0.638	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.012	-0.011	10.246	-0.874	-0.874	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.046	0.023	12.412	1.012	1.012	0.000	0.000	0.000	0.000
41	A	42	PRO	0	0.029	0.039	9.979	-1.214	-1.214	0.000	0.000	0.000	0.000
42	A	43	ILE	0	-0.037	-0.026	11.561	1.885	1.885	0.000	0.000	0.000	0.000
43	A	44	ASN	0	-0.069	-0.057	12.567	0.344	0.344	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.838	-0.902	9.893	-24.901	-24.901	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.831	0.899	8.079	23.635	23.635	0.000	0.000	0.000	0.000
46	A	47	GLU	-1	-0.822	-0.871	8.109	-25.902	-25.902	0.000	0.000	0.000	0.000
47	A	48	LEU	0	-0.001	-0.005	6.376	1.017	1.017	0.000	0.000	0.000	0.000
48	A	49	VAL	0	-0.020	-0.013	10.038	0.476	0.476	0.000	0.000	0.000	0.000
49	A	50	ALA	0	0.026	0.023	11.964	-0.437	-0.437	0.000	0.000	0.000	0.000
50	A	51	PHE	0	-0.016	-0.028	13.741	0.978	0.978	0.000	0.000	0.000	0.000
51	A	52	MET	0	0.037	0.037	17.528	-0.173	-0.173	0.000	0.000	0.000	0.000
52	A	53	ARG	1	0.821	0.910	20.621	11.071	11.071	0.000	0.000	0.000	0.000
53	A	54	ALA	0	0.030	0.015	24.353	-0.021	-0.021	0.000	0.000	0.000	0.000
54	A	55	GLY	0	0.024	0.011	26.393	0.293	0.293	0.000	0.000	0.000	0.000
55	A	56	ILE	0	-0.002	-0.004	30.242	-0.205	-0.205	0.000	0.000	0.000	0.000
56	A	57	LEU	0	-0.029	-0.004	32.680	-0.019	-0.019	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.008	-0.018	33.652	0.286	0.286	0.000	0.000	0.000	0.000
58	A	59	GLY	0	0.047	0.015	36.005	0.340	0.340	0.000	0.000	0.000	0.000
59	A	60	GLN	0	0.024	0.004	36.325	-0.232	-0.232	0.000	0.000	0.000	0.000
60	A	61	SER	0	0.002	-0.006	36.678	-0.165	-0.165	0.000	0.000	0.000	0.000
61	A	62	GLN	0	0.097	0.055	32.180	-0.198	-0.198	0.000	0.000	0.000	0.000
62	A	63	LEU	0	0.034	0.031	31.926	-0.344	-0.344	0.000	0.000	0.000	0.000
63	A	64	TYR	0	-0.014	-0.009	32.141	-0.225	-0.225	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.912	-0.932	31.089	-9.874	-9.874	0.000	0.000	0.000	0.000
65	A	66	ILE	0	-0.001	-0.009	26.565	-0.375	-0.375	0.000	0.000	0.000	0.000
66	A	67	LEU	0	-0.003	-0.010	27.545	-0.411	-0.411	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.832	0.897	29.107	9.244	9.244	0.000	0.000	0.000	0.000
68	A	69	LYS	1	0.952	0.978	25.287	11.457	11.457	0.000	0.000	0.000	0.000
69	A	70	ASN	0	0.000	0.024	23.741	-1.168	-1.168	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.010	0.012	24.279	0.173	0.173	0.000	0.000	0.000	0.000
71	A	72	PHE	0	0.050	0.025	21.102	-0.655	-0.655	0.000	0.000	0.000	0.000
72	A	73	SER	0	0.001	-0.021	18.093	0.332	0.332	0.000	0.000	0.000	0.000
73	A	74	PRO	0	0.008	0.017	16.899	-0.424	-0.424	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.011	0.009	14.335	-1.003	-1.003	0.000	0.000	0.000	0.000
75	A	76	SER	0	0.066	0.030	9.206	0.384	0.384	0.000	0.000	0.000	0.000
76	A	77	GLY	0	0.022	0.004	11.627	0.391	0.391	0.000	0.000	0.000	0.000
77	A	78	VAL	0	-0.036	-0.007	12.507	1.179	1.179	0.000	0.000	0.000	0.000
78	A	79	ILE	0	0.016	0.025	16.257	-0.342	-0.342	0.000	0.000	0.000	0.000
79	A	80	ARG	1	0.795	0.891	18.574	16.440	16.440	0.000	0.000	0.000	0.000
80	A	81	CYS	0	-0.041	-0.028	21.034	-0.146	-0.146	0.000	0.000	0.000	0.000
81	A	82	ALA	0	-0.007	0.005	23.955	0.304	0.304	0.000	0.000	0.000	0.000
82	A	83	LEU	0	0.014	0.011	25.665	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.764	-0.871	27.596	-10.775	-10.775	0.000	0.000	0.000	0.000
84	A	85	LYS	1	0.882	0.933	29.251	9.779	9.779	0.000	0.000	0.000	0.000
85	A	86	ASP	-1	-0.934	-0.974	32.081	-9.147	-9.147	0.000	0.000	0.000	0.000
86	A	87	ASP	-1	-0.875	-0.929	32.732	-8.987	-8.987	0.000	0.000	0.000	0.000
87	A	88	HIS	0	-0.104	-0.060	28.977	0.318	0.318	0.000	0.000	0.000	0.000
88	A	89	TRP	0	0.016	-0.002	26.550	-0.333	-0.333	0.000	0.000	0.000	0.000
89	A	90	LEU	0	-0.007	0.005	21.185	-0.132	-0.132	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.025	-0.010	21.328	-0.028	-0.028	0.000	0.000	0.000	0.000
91	A	92	TRP	0	0.036	-0.005	16.917	-0.661	-0.661	0.000	0.000	0.000	0.000
92	A	93	SER	0	-0.006	-0.010	13.739	-0.219	-0.219	0.000	0.000	0.000	0.000
93	A	94	GLN	0	-0.067	-0.048	12.843	0.422	0.422	0.000	0.000	0.000	0.000
94	A	95	LEU	0	-0.019	-0.009	8.313	0.299	0.299	0.000	0.000	0.000	0.000
95	A	96	ASN	0	0.027	0.016	6.933	-2.411	-2.411	0.000	0.000	0.000	0.000
96	A	97	ILE	0	0.014	0.001	3.350	-5.775	-5.261	0.017	-0.088	-0.443	0.000
97	A	98	ASN	0	-0.053	-0.038	2.390	-22.254	-17.910	1.385	-2.440	-3.289	-0.022
98	A	99	ASP	-1	-0.884	-0.941	2.638	-50.090	-48.036	0.933	-1.121	-1.865	-0.016
99	A	100	THR	0	-0.057	-0.016	3.532	1.605	2.422	0.026	-0.235	-0.608	-0.001
100	A	101	SER	0	-0.009	-0.029	2.268	-20.745	-20.903	7.009	-2.894	-3.957	-0.025
101	A	102	GLY	0	0.060	0.017	3.386	10.251	9.882	0.064	0.701	-0.395	0.001
102	A	103	THR	0	-0.030	-0.034	5.551	4.333	4.333	0.000	0.000	0.000	0.000
103	A	104	GLN	0	-0.038	-0.005	6.618	0.340	0.340	0.000	0.000	0.000	0.000
104	A	105	LEU	0	0.027	0.010	6.081	3.963	3.963	0.000	0.000	0.000	0.000
105	A	106	ALA	0	0.056	0.029	9.281	3.419	3.419	0.000	0.000	0.000	0.000
106	A	107	SER	0	-0.032	-0.019	11.069	2.676	2.676	0.000	0.000	0.000	0.000
107	A	108	VAL	0	-0.015	-0.001	11.734	2.128	2.128	0.000	0.000	0.000	0.000
108	A	109	LEU	0	0.017	0.019	13.385	1.843	1.843	0.000	0.000	0.000	0.000
109	A	110	THR	0	0.045	0.002	15.223	1.093	1.093	0.000	0.000	0.000	0.000
110	A	111	SER	0	-0.032	-0.018	16.178	1.327	1.327	0.000	0.000	0.000	0.000
111	A	112	LEU	0	-0.079	-0.033	15.842	1.192	1.192	0.000	0.000	0.000	0.000
112	A	113	VAL	0	0.035	0.007	19.440	1.021	1.021	0.000	0.000	0.000	0.000
113	A	114	ASP	-1	-0.865	-0.924	21.136	-13.629	-13.629	0.000	0.000	0.000	0.000
114	A	115	LYS	1	0.817	0.930	22.334	13.485	13.485	0.000	0.000	0.000	0.000
115	A	116	ALA	0	0.017	-0.007	23.732	0.674	0.674	0.000	0.000	0.000	0.000
116	A	117	VAL	0	0.017	0.025	25.532	0.604	0.604	0.000	0.000	0.000	0.000
117	A	118	THR	0	-0.094	-0.037	26.174	0.502	0.502	0.000	0.000	0.000	0.000
118	A	119	LEU	0	-0.128	-0.073	26.473	0.746	0.746	0.000	0.000	0.000	0.000
119	A	133	ARG	1	0.885	0.932	2.662	47.081	47.873	0.264	-0.255	-0.800	0.001
120	A	134	PRO	0	-0.025	-0.016	6.134	-0.669	-0.669	0.000	0.000	0.000	0.000
121	A	135	SER	0	0.051	0.005	7.527	-2.186	-2.186	0.000	0.000	0.000	0.000
122	A	136	SER	0	-0.055	-0.030	8.192	-0.241	-0.241	0.000	0.000	0.000	0.000
123	A	137	SER	0	-0.041	-0.009	10.024	2.367	2.367	0.000	0.000	0.000	0.000

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