FMO DATABASE

FMODB ID: R8KK8

Calculation Name: 1YA9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1YA9

Chain ID: A

ChEMBL ID:

UniProt ID: P08226

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	174
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1740275.289073
FMO2-HF: Nuclear repulsion	1668880.272644
FMO2-HF: Total energy	-71395.01643
FMO2-MP2: Total energy	-71602.408073

3D Structure Molmil

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:4:PRO)

Summations of interaction energy for fragment #1(A:4:PRO)

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.
-1.996	1.208	0.009	-1.434	-1.78	0

Interaction energy analysis for fragmet #1(A:4:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.008

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].
3	A	6	VAL	0	-0.025	-0.013	3.217	-1.153	1.807	0.010	-1.400	-1.570
4	A	7	THR	0	0.017	0.015	4.299	-0.346	-0.102	-0.001	-0.034	-0.210
5	A	8	ASP	-1	-0.891	-0.936	5.957	0.549	0.549	0.000	0.000	0.000
6	A	9	GLN	0	-0.049	-0.034	8.242	0.032	0.032	0.000	0.000	0.000
7	A	10	LEU	0	0.018	0.021	11.924	0.027	0.027	0.000	0.000	0.000
8	A	11	GLU	-1	-0.847	-0.907	14.070	-0.115	-0.115	0.000	0.000	0.000
9	A	12	TRP	0	-0.047	-0.044	15.432	-0.030	-0.030	0.000	0.000	0.000
10	A	13	GLN	0	-0.054	-0.045	9.479	-0.025	-0.025	0.000	0.000	0.000
11	A	14	SER	0	0.055	0.025	11.884	-0.023	-0.023	0.000	0.000	0.000
12	A	15	ASN	0	-0.101	-0.061	13.026	-0.056	-0.056	0.000	0.000	0.000
13	A	16	GLN	0	0.017	0.013	9.935	0.057	0.057	0.000	0.000	0.000
14	A	17	PRO	0	0.072	0.047	7.466	0.109	0.109	0.000	0.000	0.000
15	A	18	TRP	0	0.039	0.004	8.695	0.032	0.032	0.000	0.000	0.000
16	A	19	GLU	-1	-0.824	-0.889	11.726	0.061	0.061	0.000	0.000	0.000
17	A	20	GLN	0	-0.030	-0.030	6.776	0.111	0.111	0.000	0.000	0.000
18	A	21	ALA	0	0.018	0.032	9.348	0.075	0.075	0.000	0.000	0.000
19	A	22	LEU	0	0.004	-0.003	10.402	0.045	0.045	0.000	0.000	0.000
20	A	23	ASN	0	-0.019	-0.019	11.989	-0.013	-0.013	0.000	0.000	0.000
21	A	24	ARG	1	0.933	0.971	6.205	0.092	0.092	0.000	0.000	0.000
22	A	25	PHE	0	0.007	-0.001	11.707	0.002	0.002	0.000	0.000	0.000
23	A	26	TRP	0	-0.012	-0.032	14.635	0.005	0.005	0.000	0.000	0.000
24	A	27	ASP	-1	-0.838	-0.913	14.086	0.310	0.310	0.000	0.000	0.000
25	A	28	TYR	0	-0.005	-0.022	14.173	-0.010	-0.010	0.000	0.000	0.000
26	A	29	LEU	0	0.011	-0.004	16.418	-0.010	-0.010	0.000	0.000	0.000
27	A	30	ARG	1	0.749	0.858	17.501	-0.243	-0.243	0.000	0.000	0.000
28	A	31	TRP	0	0.032	0.032	19.022	-0.002	-0.002	0.000	0.000	0.000
29	A	32	VAL	0	0.057	0.033	20.139	-0.012	-0.012	0.000	0.000	0.000
30	A	33	GLN	0	-0.071	-0.045	22.592	-0.011	-0.011	0.000	0.000	0.000
31	A	34	THR	0	-0.044	-0.033	24.367	-0.008	-0.008	0.000	0.000	0.000
32	A	35	LEU	0	-0.055	-0.025	26.058	-0.007	-0.007	0.000	0.000	0.000
33	A	36	SER	0	0.055	0.034	25.392	-0.006	-0.006	0.000	0.000	0.000
34	A	37	ASP	-1	-0.864	-0.935	28.212	0.071	0.071	0.000	0.000	0.000
35	A	38	GLN	0	-0.053	-0.035	21.523	0.000	0.000	0.000	0.000	0.000
36	A	39	VAL	0	-0.066	-0.021	22.890	-0.006	-0.006	0.000	0.000	0.000
37	A	40	GLN	0	-0.024	-0.012	24.930	-0.017	-0.017	0.000	0.000	0.000
38	A	41	GLU	-1	-0.833	-0.897	27.293	0.037	0.037	0.000	0.000	0.000
39	A	42	GLU	-1	-0.820	-0.909	20.807	0.103	0.103	0.000	0.000	0.000
40	A	43	LEU	0	-0.051	-0.017	23.730	-0.010	-0.010	0.000	0.000	0.000
41	A	44	GLN	0	-0.097	-0.066	25.419	-0.018	-0.018	0.000	0.000	0.000
42	A	45	SER	0	0.072	0.044	23.817	-0.010	-0.010	0.000	0.000	0.000
43	A	46	SER	0	-0.109	-0.067	23.883	-0.012	-0.012	0.000	0.000	0.000
44	A	47	GLN	0	0.054	0.027	18.011	-0.021	-0.021	0.000	0.000	0.000
45	A	48	VAL	0	0.047	0.036	18.659	-0.006	-0.006	0.000	0.000	0.000
46	A	49	THR	0	-0.003	-0.013	19.015	-0.002	-0.002	0.000	0.000	0.000
47	A	50	GLN	0	-0.042	0.016	18.191	-0.018	-0.018	0.000	0.000	0.000
48	A	51	GLU	-1	-0.782	-0.867	14.646	0.056	0.056	0.000	0.000	0.000
49	A	52	LEU	0	-0.052	-0.029	14.623	-0.017	-0.017	0.000	0.000	0.000
50	A	53	THR	0	0.023	-0.031	16.355	-0.012	-0.012	0.000	0.000	0.000
51	A	54	ALA	0	0.032	0.027	12.287	-0.026	-0.026	0.000	0.000	0.000
52	A	55	LEU	0	-0.006	0.003	10.344	-0.042	-0.042	0.000	0.000	0.000
53	A	56	MET	0	-0.045	-0.022	12.841	-0.012	-0.012	0.000	0.000	0.000
54	A	57	GLU	-1	-0.939	-0.977	14.585	-0.247	-0.247	0.000	0.000	0.000
55	A	58	ASP	-1	-0.845	-0.895	8.499	-0.599	-0.599	0.000	0.000	0.000
56	A	59	THR	0	-0.006	-0.014	11.512	-0.021	-0.021	0.000	0.000	0.000
57	A	60	MET	0	-0.055	-0.032	13.194	-0.011	-0.011	0.000	0.000	0.000
58	A	61	THR	0	-0.033	-0.015	11.775	0.016	0.016	0.000	0.000	0.000
59	A	62	GLU	-1	-0.831	-0.915	7.270	-0.944	-0.944	0.000	0.000	0.000
60	A	63	VAL	0	-0.097	-0.054	11.737	0.039	0.039	0.000	0.000	0.000
61	A	64	LYS	1	0.839	0.912	15.300	0.255	0.255	0.000	0.000	0.000
62	A	65	ALA	0	0.057	0.032	12.360	0.022	0.022	0.000	0.000	0.000
63	A	66	TYR	0	0.056	0.030	13.745	0.044	0.044	0.000	0.000	0.000
64	A	67	LYS	1	0.785	0.879	15.240	0.217	0.217	0.000	0.000	0.000
65	A	68	LYS	1	0.788	0.872	17.635	0.283	0.283	0.000	0.000	0.000
66	A	69	GLU	-1	-0.803	-0.891	14.175	-0.295	-0.295	0.000	0.000	0.000
67	A	70	LEU	0	-0.022	-0.029	17.785	0.029	0.029	0.000	0.000	0.000
68	A	71	GLU	-1	-0.854	-0.911	20.329	-0.173	-0.173	0.000	0.000	0.000
69	A	72	GLU	-1	-0.945	-0.973	19.744	-0.273	-0.273	0.000	0.000	0.000
70	A	73	GLN	0	-0.076	-0.018	17.312	0.030	0.030	0.000	0.000	0.000
71	A	74	LEU	0	-0.041	0.005	22.825	0.019	0.019	0.000	0.000	0.000
72	A	75	GLY	0	-0.036	-0.010	25.762	-0.001	-0.001	0.000	0.000	0.000
73	A	76	PRO	0	0.024	-0.013	28.955	-0.002	-0.002	0.000	0.000	0.000
74	A	77	VAL	0	0.006	-0.006	29.964	0.005	0.005	0.000	0.000	0.000
75	A	78	ALA	0	0.019	0.015	32.840	-0.003	-0.003	0.000	0.000	0.000
76	A	79	GLU	-1	-0.835	-0.908	33.314	-0.098	-0.098	0.000	0.000	0.000
77	A	80	GLU	-1	-0.872	-0.950	33.179	-0.069	-0.069	0.000	0.000	0.000
78	A	81	THR	0	-0.025	-0.029	32.021	0.003	0.003	0.000	0.000	0.000
79	A	82	ARG	1	0.931	0.978	27.682	0.120	0.120	0.000	0.000	0.000
80	A	83	ALA	0	0.018	0.010	28.859	-0.006	-0.006	0.000	0.000	0.000
81	A	84	ARG	1	0.790	0.879	30.449	0.054	0.054	0.000	0.000	0.000
82	A	85	LEU	0	0.079	0.043	27.305	0.002	0.002	0.000	0.000	0.000
83	A	86	GLY	0	0.022	0.021	25.708	-0.003	-0.003	0.000	0.000	0.000
84	A	87	LYS	1	0.913	0.943	26.158	0.081	0.081	0.000	0.000	0.000
85	A	88	GLU	-1	-0.814	-0.886	28.215	-0.054	-0.054	0.000	0.000	0.000
86	A	89	VAL	0	0.056	0.035	21.560	0.004	0.004	0.000	0.000	0.000
87	A	90	GLN	0	-0.066	-0.014	23.702	0.002	0.002	0.000	0.000	0.000
88	A	91	ALA	0	0.037	-0.002	25.017	0.000	0.000	0.000	0.000	0.000
89	A	92	ALA	0	-0.013	-0.001	24.217	0.005	0.005	0.000	0.000	0.000
90	A	93	GLN	0	0.067	0.034	19.637	-0.012	-0.012	0.000	0.000	0.000
91	A	94	ALA	0	-0.003	0.009	22.159	0.000	0.000	0.000	0.000	0.000
92	A	95	ARG	1	0.773	0.855	24.709	0.042	0.042	0.000	0.000	0.000
93	A	96	LEU	0	0.032	0.021	18.244	0.008	0.008	0.000	0.000	0.000
94	A	97	GLY	0	0.047	0.019	21.258	0.005	0.005	0.000	0.000	0.000
95	A	98	ALA	0	0.024	0.002	22.170	0.005	0.005	0.000	0.000	0.000
96	A	99	ASH	0	-0.097	-0.095	23.794	0.009	0.009	0.000	0.000	0.000
97	A	100	MET	0	-0.032	-0.006	16.354	0.004	0.004	0.000	0.000	0.000
98	A	101	GLU	-1	-0.857	-0.923	21.825	-0.076	-0.076	0.000	0.000	0.000
99	A	102	ASP	-1	-0.881	-0.917	24.041	-0.009	-0.009	0.000	0.000	0.000
100	A	103	LEU	0	-0.023	-0.029	21.926	0.008	0.008	0.000	0.000	0.000
101	A	104	ARG	1	0.878	0.928	21.188	0.089	0.089	0.000	0.000	0.000
102	A	105	ASN	0	0.032	0.020	23.445	0.001	0.001	0.000	0.000	0.000
103	A	106	ARG	1	0.810	0.910	26.990	-0.005	-0.005	0.000	0.000	0.000
104	A	107	LEU	0	-0.009	-0.018	22.859	0.005	0.005	0.000	0.000	0.000
105	A	108	GLY	0	0.043	0.035	26.767	0.002	0.002	0.000	0.000	0.000
106	A	109	GLN	0	-0.080	-0.039	27.972	0.004	0.004	0.000	0.000	0.000
107	A	110	TYR	0	0.021	0.004	29.255	0.003	0.003	0.000	0.000	0.000
108	A	111	ARG	1	0.884	0.956	24.585	0.012	0.012	0.000	0.000	0.000
109	A	112	ASN	0	0.000	-0.022	30.318	0.001	0.001	0.000	0.000	0.000
110	A	113	GLU	-1	-0.757	-0.870	33.157	0.009	0.009	0.000	0.000	0.000
111	A	114	VAL	0	0.030	0.026	32.544	0.001	0.001	0.000	0.000	0.000
112	A	115	HIS	0	0.022	0.011	30.473	0.002	0.002	0.000	0.000	0.000
113	A	116	THR	0	-0.079	-0.044	35.455	-0.001	-0.001	0.000	0.000	0.000
114	A	117	MET	0	-0.057	-0.015	37.974	0.001	0.001	0.000	0.000	0.000
115	A	118	LEU	0	-0.041	-0.027	38.071	0.003	0.003	0.000	0.000	0.000
116	A	119	GLY	0	0.038	0.018	34.764	0.001	0.001	0.000	0.000	0.000
117	A	120	GLN	0	-0.061	-0.012	35.381	0.007	0.007	0.000	0.000	0.000
118	A	121	SER	0	0.027	0.005	33.756	-0.002	-0.002	0.000	0.000	0.000
119	A	122	THR	0	0.044	0.010	36.152	0.002	0.002	0.000	0.000	0.000
120	A	123	GLU	-1	-0.883	-0.959	36.706	0.043	0.043	0.000	0.000	0.000
121	A	124	GLU	-1	-0.833	-0.913	37.568	0.019	0.019	0.000	0.000	0.000
122	A	125	ILE	0	0.011	-0.006	35.090	0.001	0.001	0.000	0.000	0.000
123	A	126	ARG	1	0.920	0.966	32.496	-0.046	-0.046	0.000	0.000	0.000
124	A	127	ALA	0	0.008	0.024	32.919	0.003	0.003	0.000	0.000	0.000
125	A	128	ARG	1	0.800	0.885	34.625	-0.012	-0.012	0.000	0.000	0.000
126	A	129	LEU	0	-0.011	0.010	27.932	-0.002	-0.002	0.000	0.000	0.000
127	A	130	SER	0	0.065	0.029	29.780	0.001	0.001	0.000	0.000	0.000
128	A	131	THR	0	-0.062	-0.052	30.196	0.004	0.004	0.000	0.000	0.000
129	A	132	HIS	0	-0.036	-0.027	30.498	0.002	0.002	0.000	0.000	0.000
130	A	133	LEU	0	0.075	0.028	25.096	-0.003	-0.003	0.000	0.000	0.000
131	A	134	ARG	1	0.893	0.973	26.696	-0.057	-0.057	0.000	0.000	0.000
132	A	135	LYS	1	0.929	0.956	28.143	-0.013	-0.013	0.000	0.000	0.000
133	A	136	MET	0	-0.043	-0.008	26.300	-0.003	-0.003	0.000	0.000	0.000
134	A	137	ARG	1	0.960	0.988	22.481	-0.089	-0.089	0.000	0.000	0.000
135	A	138	LYS	1	0.954	0.974	24.307	-0.058	-0.058	0.000	0.000	0.000
136	A	139	ARG	1	0.768	0.888	26.757	0.008	0.008	0.000	0.000	0.000
137	A	140	LEU	0	0.056	0.026	19.439	-0.004	-0.004	0.000	0.000	0.000
138	A	141	MET	0	-0.041	-0.005	21.998	-0.004	-0.004	0.000	0.000	0.000
139	A	142	ARG	1	1.032	1.025	23.337	-0.014	-0.014	0.000	0.000	0.000
140	A	143	ASP	-1	-0.795	-0.859	24.614	-0.024	-0.024	0.000	0.000	0.000
141	A	144	ALA	0	0.037	0.025	19.598	-0.013	-0.013	0.000	0.000	0.000
142	A	145	GLU	-1	-0.922	-0.959	20.976	0.038	0.038	0.000	0.000	0.000
143	A	146	ASP	-1	-0.848	-0.919	23.153	-0.036	-0.036	0.000	0.000	0.000
144	A	147	LEU	0	-0.012	-0.010	18.781	-0.006	-0.006	0.000	0.000	0.000
145	A	148	GLN	0	-0.022	-0.017	18.083	-0.010	-0.010	0.000	0.000	0.000
146	A	149	LYS	1	0.889	0.941	20.781	0.016	0.016	0.000	0.000	0.000
147	A	150	ARG	1	0.783	0.882	23.887	0.040	0.040	0.000	0.000	0.000
148	A	151	LEU	0	0.048	0.020	17.797	-0.007	-0.007	0.000	0.000	0.000
149	A	152	ALA	0	0.007	0.006	21.732	-0.007	-0.007	0.000	0.000	0.000
150	A	153	VAL	0	-0.073	-0.029	23.003	-0.001	-0.001	0.000	0.000	0.000
151	A	154	TYR	0	-0.056	-0.031	23.030	-0.004	-0.004	0.000	0.000	0.000
152	A	155	LYS	1	0.890	0.950	17.813	0.101	0.101	0.000	0.000	0.000
153	A	156	ALA	0	0.038	0.013	23.223	0.014	0.014	0.000	0.000	0.000
154	A	157	GLY	0	-0.049	-0.021	26.367	-0.008	-0.008	0.000	0.000	0.000
155	A	158	ALA	0	0.016	0.023	28.349	0.007	0.007	0.000	0.000	0.000
156	A	159	ARG	1	0.870	0.900	29.633	0.056	0.056	0.000	0.000	0.000
157	A	160	GLU	-1	-0.838	-0.891	31.700	-0.033	-0.033	0.000	0.000	0.000
158	A	161	GLY	0	0.001	-0.002	34.609	0.004	0.004	0.000	0.000	0.000
159	A	162	ALA	0	-0.007	0.001	34.930	-0.001	-0.001	0.000	0.000	0.000
160	A	163	GLU	-1	-0.841	-0.900	34.604	-0.050	-0.050	0.000	0.000	0.000
161	A	164	ARG	1	0.819	0.862	28.669	0.040	0.040	0.000	0.000	0.000
162	A	165	GLY	0	0.013	0.031	28.763	-0.001	-0.001	0.000	0.000	0.000
163	A	166	VAL	0	0.043	0.004	29.037	-0.002	-0.002	0.000	0.000	0.000
164	A	167	SER	0	-0.051	-0.043	30.886	0.002	0.002	0.000	0.000	0.000
165	A	168	ALA	0	0.078	0.053	28.729	-0.001	-0.001	0.000	0.000	0.000
166	A	169	ILE	0	-0.007	-0.009	25.936	-0.002	-0.002	0.000	0.000	0.000
167	A	170	ARG	1	0.927	0.947	28.920	0.028	0.028	0.000	0.000	0.000
168	A	171	GLU	-1	-0.879	-0.916	32.445	-0.063	-0.063	0.000	0.000	0.000
169	A	172	ARG	1	0.895	0.951	23.818	0.121	0.121	0.000	0.000	0.000
170	A	173	LEU	0	-0.056	-0.025	27.983	-0.001	-0.001	0.000	0.000	0.000
171	A	174	GLY	0	0.005	0.028	31.386	0.002	0.002	0.000	0.000	0.000
172	A	175	PRO	0	-0.025	-0.054	34.832	0.003	0.003	0.000	0.000	0.000
173	A	176	LEU	0	0.014	0.028	35.404	0.001	0.001	0.000	0.000	0.000
174	A	177	VAL	0	-0.021	0.004	38.255	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:PRO)