FMO DATABASE

FMODB ID: 3J9KL

Calculation Name: 2P58-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P58

Chain ID: C

ChEMBL ID:

UniProt ID: O68690

Base Structure: X-ray

Registration Date: 2023-09-21

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	112
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-872544.060696
FMO2-HF: Nuclear repulsion	827879.848701
FMO2-HF: Total energy	-44664.211995
FMO2-MP2: Total energy	-44794.28886

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(C:3:TYR)

Summations of interaction energy for fragment #1(C:3:TYR)

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.
-54.586	-45.097	15.797	-11.015	-14.269	-0.099

Interaction energy analysis for fragmet #1(C:3:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.052 / q_NPA : -0.044

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	C	5	LEU	0	0.071	0.023	2.822	-3.361	-0.475	0.441	-1.496	-1.831	-0.003
4	C	6	ASN	0	0.072	0.025	4.701	-0.087	0.067	-0.001	-0.004	-0.149	0.000
5	C	7	VAL	0	0.002	0.013	2.770	-0.748	0.324	0.239	-0.228	-1.082	0.000
6	C	8	LEU	0	0.022	0.019	2.096	-4.876	-1.962	3.204	-1.690	-4.427	0.006
7	C	9	LEU	0	-0.001	-0.003	3.797	-1.049	-0.697	0.027	-0.083	-0.295	0.000
8	C	10	ALA	0	0.046	0.022	7.082	0.023	0.023	0.000	0.000	0.000	0.000
9	C	11	GLU	-1	-0.846	-0.920	1.769	-45.762	-43.651	11.887	-7.514	-6.485	-0.102
10	C	12	ILE	0	-0.004	-0.005	6.017	0.662	0.662	0.000	0.000	0.000	0.000
11	C	13	ALA	0	0.030	0.019	8.004	0.328	0.328	0.000	0.000	0.000	0.000
12	C	14	LEU	0	-0.007	0.002	8.394	0.290	0.290	0.000	0.000	0.000	0.000
13	C	15	ILE	0	0.002	0.010	6.042	0.343	0.343	0.000	0.000	0.000	0.000
14	C	16	GLY	0	0.035	0.019	10.085	0.281	0.281	0.000	0.000	0.000	0.000
15	C	17	THR	0	-0.083	-0.037	13.089	0.147	0.147	0.000	0.000	0.000	0.000
16	C	18	GLY	0	-0.007	-0.002	13.425	0.110	0.110	0.000	0.000	0.000	0.000
17	C	19	ASN	0	-0.117	-0.070	12.810	0.177	0.177	0.000	0.000	0.000	0.000
18	C	20	HIS	0	-0.036	-0.023	16.092	0.059	0.059	0.000	0.000	0.000	0.000
19	C	21	TYR	0	-0.009	0.024	15.761	0.076	0.076	0.000	0.000	0.000	0.000
20	C	22	HIS	0	0.046	0.019	16.688	-0.096	-0.096	0.000	0.000	0.000	0.000
21	C	23	GLU	-1	-0.847	-0.905	18.739	-0.461	-0.461	0.000	0.000	0.000	0.000
22	C	24	GLU	-1	-0.840	-0.933	16.139	-0.514	-0.514	0.000	0.000	0.000	0.000
23	C	25	ALA	0	-0.010	-0.014	14.331	-0.055	-0.055	0.000	0.000	0.000	0.000
24	C	26	ASN	0	-0.102	-0.055	15.280	-0.090	-0.090	0.000	0.000	0.000	0.000
25	C	27	CYS	0	0.013	0.017	17.084	0.028	0.028	0.000	0.000	0.000	0.000
26	C	28	ILE	0	-0.044	-0.019	10.803	0.009	0.009	0.000	0.000	0.000	0.000
27	C	29	ALA	0	-0.009	-0.015	13.780	-0.022	-0.022	0.000	0.000	0.000	0.000
28	C	30	GLU	-1	-0.860	-0.925	15.419	-0.382	-0.382	0.000	0.000	0.000	0.000
29	C	31	TRP	0	-0.035	-0.023	10.532	0.119	0.119	0.000	0.000	0.000	0.000
30	C	32	LEU	0	-0.046	-0.045	9.721	0.025	0.025	0.000	0.000	0.000	0.000
31	C	33	HIS	0	-0.068	-0.038	13.796	0.065	0.065	0.000	0.000	0.000	0.000
32	C	34	LEU	0	0.010	0.022	17.156	0.055	0.055	0.000	0.000	0.000	0.000
33	C	35	LYS	1	0.759	0.872	13.138	0.347	0.347	0.000	0.000	0.000	0.000
34	C	36	GLY	0	0.047	0.032	15.545	0.017	0.017	0.000	0.000	0.000	0.000
35	C	37	GLU	-1	-0.956	-0.959	11.398	-0.788	-0.788	0.000	0.000	0.000	0.000
36	C	38	GLU	-1	-0.839	-0.931	14.463	-0.600	-0.600	0.000	0.000	0.000	0.000
37	C	39	GLU	-1	-0.898	-0.948	15.259	-0.752	-0.752	0.000	0.000	0.000	0.000
38	C	40	ALA	0	0.012	0.003	11.350	-0.081	-0.081	0.000	0.000	0.000	0.000
39	C	41	VAL	0	0.012	0.011	13.222	-0.078	-0.078	0.000	0.000	0.000	0.000
40	C	42	GLN	0	-0.001	0.002	15.855	0.010	0.010	0.000	0.000	0.000	0.000
41	C	43	LEU	0	-0.018	-0.008	11.547	0.024	0.024	0.000	0.000	0.000	0.000
42	C	44	ILE	0	0.005	0.002	11.420	-0.006	-0.006	0.000	0.000	0.000	0.000
43	C	45	ARG	1	0.984	1.000	14.855	0.562	0.562	0.000	0.000	0.000	0.000
44	C	46	LEU	0	-0.014	-0.015	18.143	0.063	0.063	0.000	0.000	0.000	0.000
45	C	47	SER	0	0.011	-0.004	14.276	0.078	0.078	0.000	0.000	0.000	0.000
46	C	48	SER	0	-0.009	-0.019	16.744	0.082	0.082	0.000	0.000	0.000	0.000
47	C	49	LEU	0	-0.058	-0.035	18.359	0.064	0.064	0.000	0.000	0.000	0.000
48	C	50	MET	0	-0.033	-0.017	19.502	0.041	0.041	0.000	0.000	0.000	0.000
49	C	51	ASN	0	-0.056	-0.031	15.802	0.073	0.073	0.000	0.000	0.000	0.000
50	C	52	ARG	1	0.866	0.951	19.826	0.536	0.536	0.000	0.000	0.000	0.000
51	C	53	GLY	0	-0.008	0.004	22.992	0.044	0.044	0.000	0.000	0.000	0.000
52	C	54	ASP	-1	-0.850	-0.900	24.578	-0.331	-0.331	0.000	0.000	0.000	0.000
53	C	55	TYR	0	0.076	0.005	22.774	-0.005	-0.005	0.000	0.000	0.000	0.000
54	C	56	ALA	0	0.026	0.023	26.331	-0.002	-0.002	0.000	0.000	0.000	0.000
55	C	57	SER	0	-0.044	-0.042	26.716	0.014	0.014	0.000	0.000	0.000	0.000
56	C	58	ALA	0	-0.015	0.000	22.970	-0.007	-0.007	0.000	0.000	0.000	0.000
57	C	59	LEU	0	0.014	0.007	24.693	-0.006	-0.006	0.000	0.000	0.000	0.000
58	C	60	GLN	0	-0.008	0.006	27.049	0.018	0.018	0.000	0.000	0.000	0.000
59	C	61	GLN	0	0.009	-0.015	24.339	-0.012	-0.012	0.000	0.000	0.000	0.000
60	C	62	GLY	0	0.043	0.018	23.565	-0.008	-0.008	0.000	0.000	0.000	0.000
61	C	63	ASN	0	-0.060	-0.027	24.478	0.011	0.011	0.000	0.000	0.000	0.000
62	C	64	LYS	1	0.847	0.920	26.951	0.304	0.304	0.000	0.000	0.000	0.000
63	C	65	LEU	0	-0.022	-0.006	22.656	0.015	0.015	0.000	0.000	0.000	0.000
64	C	66	ALA	0	-0.013	-0.002	23.819	-0.027	-0.027	0.000	0.000	0.000	0.000
65	C	67	TYR	0	0.077	0.037	19.242	0.011	0.011	0.000	0.000	0.000	0.000
66	C	68	PRO	0	0.009	-0.003	21.221	-0.023	-0.023	0.000	0.000	0.000	0.000
67	C	69	ASP	-1	-0.786	-0.872	16.165	-0.653	-0.653	0.000	0.000	0.000	0.000
68	C	70	LEU	0	-0.015	-0.009	15.405	-0.062	-0.062	0.000	0.000	0.000	0.000
69	C	71	GLU	-1	-0.775	-0.854	18.974	-0.347	-0.347	0.000	0.000	0.000	0.000
70	C	72	PRO	0	-0.008	-0.010	19.715	0.027	0.027	0.000	0.000	0.000	0.000
71	C	73	TRP	0	0.045	0.026	14.046	0.046	0.046	0.000	0.000	0.000	0.000
72	C	74	LEU	0	0.002	0.013	20.657	0.033	0.033	0.000	0.000	0.000	0.000
73	C	75	ALA	0	0.016	0.015	24.129	0.036	0.036	0.000	0.000	0.000	0.000
74	C	76	LEU	0	0.002	0.001	19.992	0.034	0.034	0.000	0.000	0.000	0.000
75	C	77	CYS	0	-0.042	-0.027	23.105	0.019	0.019	0.000	0.000	0.000	0.000
76	C	78	GLU	-1	-0.786	-0.885	25.472	-0.297	-0.297	0.000	0.000	0.000	0.000
77	C	79	TYR	0	-0.020	-0.008	25.645	0.029	0.029	0.000	0.000	0.000	0.000
78	C	80	ARG	1	0.886	0.944	24.390	0.420	0.420	0.000	0.000	0.000	0.000
79	C	81	LEU	0	-0.034	-0.009	27.805	0.015	0.015	0.000	0.000	0.000	0.000
80	C	82	GLY	0	0.012	0.026	30.611	0.020	0.020	0.000	0.000	0.000	0.000
81	C	83	LEU	0	-0.033	-0.014	31.353	0.020	0.020	0.000	0.000	0.000	0.000
82	C	84	GLY	0	0.025	-0.003	33.090	-0.008	-0.008	0.000	0.000	0.000	0.000
83	C	85	SER	0	0.017	0.000	34.745	0.002	0.002	0.000	0.000	0.000	0.000
84	C	86	ALA	0	-0.018	-0.002	32.551	0.004	0.004	0.000	0.000	0.000	0.000
85	C	87	LEU	0	0.064	0.042	28.159	-0.006	-0.006	0.000	0.000	0.000	0.000
86	C	88	GLU	-1	-0.791	-0.875	31.203	-0.217	-0.217	0.000	0.000	0.000	0.000
87	C	89	SER	0	-0.047	-0.025	33.558	0.003	0.003	0.000	0.000	0.000	0.000
88	C	90	ARG	1	0.729	0.813	26.368	0.355	0.355	0.000	0.000	0.000	0.000
89	C	91	LEU	0	0.020	0.007	27.513	-0.009	-0.009	0.000	0.000	0.000	0.000
90	C	92	ASN	0	-0.027	-0.014	30.096	0.006	0.006	0.000	0.000	0.000	0.000
91	C	93	ARG	1	0.787	0.876	27.684	0.314	0.314	0.000	0.000	0.000	0.000
92	C	94	LEU	0	0.017	0.001	24.470	0.004	0.004	0.000	0.000	0.000	0.000
93	C	95	ALA	0	0.014	0.016	27.559	-0.002	-0.002	0.000	0.000	0.000	0.000
94	C	96	ARG	1	0.907	0.960	29.800	0.193	0.193	0.000	0.000	0.000	0.000
95	C	97	SER	0	-0.011	0.009	24.114	0.020	0.020	0.000	0.000	0.000	0.000
96	C	98	GLN	0	0.022	0.005	26.600	0.008	0.008	0.000	0.000	0.000	0.000
97	C	99	ASP	-1	-0.789	-0.862	19.934	-0.431	-0.431	0.000	0.000	0.000	0.000
98	C	100	PRO	0	0.044	0.016	20.951	-0.012	-0.012	0.000	0.000	0.000	0.000
99	C	101	ARG	1	0.804	0.860	14.873	0.632	0.632	0.000	0.000	0.000	0.000
100	C	102	ILE	0	0.003	0.005	20.131	-0.020	-0.020	0.000	0.000	0.000	0.000
101	C	103	GLN	0	-0.043	-0.037	22.475	0.008	0.008	0.000	0.000	0.000	0.000
102	C	104	THR	0	-0.050	-0.030	21.147	0.021	0.021	0.000	0.000	0.000	0.000
103	C	105	PHE	0	0.009	0.010	21.040	0.003	0.003	0.000	0.000	0.000	0.000
104	C	106	VAL	0	0.004	-0.002	22.821	0.013	0.013	0.000	0.000	0.000	0.000
105	C	107	ASN	0	-0.009	-0.008	26.473	0.023	0.023	0.000	0.000	0.000	0.000
106	C	108	GLY	0	0.028	0.020	24.482	0.016	0.016	0.000	0.000	0.000	0.000
107	C	109	MET	0	-0.002	-0.004	24.498	0.014	0.014	0.000	0.000	0.000	0.000
108	C	110	ARG	1	0.831	0.880	26.903	0.237	0.237	0.000	0.000	0.000	0.000
109	C	111	GLU	-1	-0.852	-0.910	28.196	-0.190	-0.190	0.000	0.000	0.000	0.000
110	C	112	GLN	0	-0.082	-0.042	26.490	-0.010	-0.010	0.000	0.000	0.000	0.000
111	C	113	LEU	0	-0.038	-0.028	28.925	0.009	0.009	0.000	0.000	0.000	0.000
112	C	114	LYS	1	0.788	0.919	31.962	0.212	0.212	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(C:3:TYR)