FMO DATABASE

FMODB ID: 82M9Y

Calculation Name: 1YLM-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 1YLM

Chain ID: A

ChEMBL ID:
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UniProt ID: O32126

Base Structure: X-ray

Registration Date: 2023-06-20

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	143
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1374132.748966
FMO2-HF: Nuclear repulsion	1316159.419804
FMO2-HF: Total energy	-57973.329162
FMO2-MP2: Total energy	-58142.466783

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:1:MET)

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

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.
-4.873	-1.314	1.946	-1.65	-3.856	-0.007

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.053 / q_NPA : -0.039

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	A	3	PHE	0	-0.067	-0.048	2.502	-2.295	0.398	1.886	-1.300	-3.280	-0.004
4	A	4	VAL	0	0.080	0.049	5.969	0.222	0.222	0.000	0.000	0.000	0.000
5	A	5	ASP	-1	-0.858	-0.928	8.775	-0.241	-0.241	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.837	0.882	10.500	0.047	0.047	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.023	-0.020	12.669	0.072	0.072	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.850	0.937	15.611	0.351	0.351	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.064	0.032	13.071	0.039	0.039	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.880	-0.934	15.332	-0.014	-0.014	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.892	0.928	18.252	0.132	0.132	0.000	0.000	0.000	0.000
12	A	12	THR	0	-0.004	0.012	19.954	0.019	0.019	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.027	0.014	18.449	0.014	0.014	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.032	0.024	22.179	0.013	0.013	0.000	0.000	0.000	0.000
15	A	15	PHE	0	-0.045	-0.026	24.506	0.008	0.008	0.000	0.000	0.000	0.000
16	A	16	PHE	0	0.029	-0.002	24.940	0.006	0.006	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.794	-0.876	25.172	-0.026	-0.026	0.000	0.000	0.000	0.000
18	A	18	HIS	0	-0.029	0.000	28.036	0.007	0.007	0.000	0.000	0.000	0.000
19	A	19	GLN	0	-0.023	-0.023	29.777	0.007	0.007	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.000	0.006	29.509	0.003	0.003	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.002	-0.003	32.129	0.004	0.004	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.034	-0.011	34.052	0.003	0.003	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.039	-0.003	35.265	0.002	0.002	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.938	-0.958	36.087	-0.022	-0.022	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.041	-0.020	37.944	0.004	0.004	0.000	0.000	0.000	0.000
26	A	26	GLN	0	-0.043	-0.044	40.439	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	27	THR	0	-0.022	-0.008	42.299	0.001	0.001	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.906	-0.954	44.875	-0.030	-0.030	0.000	0.000	0.000	0.000
29	A	29	TRP	0	-0.031	-0.044	39.419	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	30	GLN	0	-0.012	-0.014	45.265	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	31	SER	0	0.005	0.031	47.736	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.846	-0.904	47.722	-0.041	-0.041	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.029	-0.014	45.086	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.023	0.007	44.283	-0.002	-0.002	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.947	-0.982	43.149	-0.046	-0.046	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.009	0.004	42.460	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.022	-0.011	39.904	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.010	0.006	38.210	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	39	GLN	0	0.008	-0.002	37.732	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.916	0.969	32.656	0.084	0.084	0.000	0.000	0.000	0.000
41	A	41	ILE	0	0.036	0.016	33.685	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.034	0.013	32.777	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	43	HIS	0	-0.047	-0.020	31.268	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.020	-0.024	29.808	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.008	0.010	28.211	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.002	0.000	27.331	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.795	-0.878	26.546	-0.169	-0.169	0.000	0.000	0.000	0.000
48	A	48	CYS	0	-0.024	0.004	23.886	-0.014	-0.014	0.000	0.000	0.000	0.000
49	A	49	ILE	0	-0.020	0.000	22.418	-0.013	-0.013	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.025	-0.015	21.914	-0.017	-0.017	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.926	-0.954	21.049	-0.253	-0.253	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.038	-0.026	17.444	-0.034	-0.034	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.013	-0.010	17.008	-0.028	-0.028	0.000	0.000	0.000	0.000
54	A	54	ASN	0	0.037	0.005	17.038	-0.047	-0.047	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.833	-0.899	14.540	-0.455	-0.455	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.107	-0.046	12.842	-0.086	-0.086	0.000	0.000	0.000	0.000
57	A	57	ILE	0	0.040	0.001	12.249	-0.067	-0.067	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.916	-0.952	11.942	-0.789	-0.789	0.000	0.000	0.000	0.000
59	A	59	GLY	0	-0.063	-0.035	9.007	-0.281	-0.281	0.000	0.000	0.000	0.000
60	A	60	PHE	0	-0.063	-0.053	7.377	-0.579	-0.579	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.062	-0.012	4.886	-0.042	-0.042	0.000	0.000	0.000	0.000
62	A	62	MET	0	0.002	0.034	9.463	0.164	0.164	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.908	0.947	12.858	0.241	0.241	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.869	-0.947	15.738	-0.491	-0.491	0.000	0.000	0.000	0.000
65	A	65	PRO	0	-0.049	-0.011	16.918	0.057	0.057	0.000	0.000	0.000	0.000
66	A	66	GLY	0	-0.004	0.008	20.331	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.086	-0.058	23.260	0.011	0.011	0.000	0.000	0.000	0.000
68	A	68	TYR	0	0.045	-0.013	23.928	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.930	-0.978	24.997	-0.141	-0.141	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.863	-0.911	23.019	-0.200	-0.200	0.000	0.000	0.000	0.000
71	A	71	ILE	0	-0.032	0.004	20.245	0.002	0.002	0.000	0.000	0.000	0.000
72	A	72	MET	0	-0.028	-0.019	21.032	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.804	-0.889	22.851	-0.125	-0.125	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.024	0.027	17.020	0.013	0.013	0.000	0.000	0.000	0.000
75	A	75	LEU	0	0.020	-0.003	17.331	0.012	0.012	0.000	0.000	0.000	0.000
76	A	76	VAL	0	-0.043	-0.009	19.356	0.031	0.031	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.954	-0.969	19.212	-0.134	-0.134	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.971	-1.003	13.855	-0.199	-0.199	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.815	0.910	16.560	0.089	0.089	0.000	0.000	0.000	0.000
80	A	80	VAL	0	0.019	0.028	15.826	0.028	0.028	0.000	0.000	0.000	0.000
81	A	81	VAL	0	-0.032	-0.022	18.429	0.017	0.017	0.000	0.000	0.000	0.000
82	A	82	THR	0	-0.034	-0.028	22.206	0.002	0.002	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.831	-0.925	25.300	-0.066	-0.066	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.918	0.951	27.162	0.019	0.019	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.801	-0.872	25.230	-0.032	-0.032	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.077	0.040	26.153	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.896	-0.946	26.808	-0.083	-0.083	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.952	-0.977	30.346	-0.046	-0.046	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.003	-0.007	25.423	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.893	0.938	27.708	0.115	0.115	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.874	0.941	30.058	0.067	0.067	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.005	0.009	30.496	0.003	0.003	0.000	0.000	0.000	0.000
93	A	93	ILE	0	0.050	0.021	26.518	0.000	0.000	0.000	0.000	0.000	0.000
94	A	94	ALA	0	0.001	0.008	30.873	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	95	TYR	0	-0.054	-0.054	33.814	0.001	0.001	0.000	0.000	0.000	0.000
96	A	96	ARG	1	0.832	0.898	28.776	0.158	0.158	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.952	0.979	33.617	0.104	0.104	0.000	0.000	0.000	0.000
98	A	98	THR	0	0.003	0.000	35.554	0.000	0.000	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.002	0.008	35.014	0.003	0.003	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.041	-0.012	32.745	0.001	0.001	0.000	0.000	0.000	0.000
101	A	101	GLN	0	-0.059	-0.030	35.319	0.004	0.004	0.000	0.000	0.000	0.000
102	A	102	GLN	0	-0.064	-0.039	37.900	0.002	0.002	0.000	0.000	0.000	0.000
103	A	103	TYR	0	0.099	0.047	39.940	0.003	0.003	0.000	0.000	0.000	0.000
104	A	104	LEU	0	-0.058	-0.035	41.939	0.003	0.003	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.047	-0.028	43.521	0.003	0.003	0.000	0.000	0.000	0.000
106	A	106	ALA	0	-0.025	0.006	41.512	0.000	0.000	0.000	0.000	0.000	0.000
107	A	107	ASP	-1	-0.833	-0.908	42.846	-0.046	-0.046	0.000	0.000	0.000	0.000
108	A	108	SER	0	0.031	-0.016	42.389	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	109	GLY	0	0.027	0.025	42.897	0.001	0.001	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.932	-0.953	41.664	-0.058	-0.058	0.000	0.000	0.000	0.000
111	A	111	LEU	0	0.011	0.014	36.267	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	112	TYR	0	0.016	0.006	38.822	0.000	0.000	0.000	0.000	0.000	0.000
113	A	113	ARG	1	0.942	0.959	39.916	0.043	0.043	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.034	0.003	35.983	0.002	0.002	0.000	0.000	0.000	0.000
115	A	115	ILE	0	0.012	-0.003	34.218	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.896	0.958	35.609	0.033	0.033	0.000	0.000	0.000	0.000
117	A	117	ALA	0	-0.050	-0.022	37.531	0.003	0.003	0.000	0.000	0.000	0.000
118	A	118	HIS	1	0.825	0.904	32.525	0.057	0.057	0.000	0.000	0.000	0.000
119	A	119	GLN	0	0.033	0.012	32.306	-0.004	-0.004	0.000	0.000	0.000	0.000
120	A	120	THR	0	-0.013	-0.017	31.343	0.000	0.000	0.000	0.000	0.000	0.000
121	A	121	ALA	0	0.058	0.033	28.834	0.002	0.002	0.000	0.000	0.000	0.000
122	A	122	LEU	0	-0.018	-0.010	27.547	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	123	GLN	0	-0.010	-0.025	27.385	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.915	-0.961	26.070	-0.011	-0.011	0.000	0.000	0.000	0.000
125	A	125	PHE	0	0.018	0.018	20.906	0.007	0.007	0.000	0.000	0.000	0.000
126	A	126	PRO	0	0.026	0.006	21.491	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	127	LYS	1	0.922	0.965	20.509	-0.004	-0.004	0.000	0.000	0.000	0.000
128	A	128	ARG	1	0.789	0.876	20.216	0.030	0.030	0.000	0.000	0.000	0.000
129	A	129	ILE	0	0.039	0.016	16.077	0.013	0.013	0.000	0.000	0.000	0.000
130	A	130	ARG	1	0.819	0.878	15.757	0.032	0.032	0.000	0.000	0.000	0.000
131	A	131	SER	0	0.008	0.009	15.874	0.026	0.026	0.000	0.000	0.000	0.000
132	A	132	TYR	0	0.030	0.029	11.366	0.054	0.054	0.000	0.000	0.000	0.000
133	A	133	LEU	0	-0.002	-0.005	11.379	0.057	0.057	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.989	-0.997	11.089	0.169	0.169	0.000	0.000	0.000	0.000
135	A	135	THR	0	-0.102	-0.054	12.529	0.058	0.058	0.000	0.000	0.000	0.000
136	A	136	GLU	-1	-0.923	-0.960	8.435	0.762	0.762	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.081	-0.030	5.788	0.352	0.352	0.000	0.000	0.000	0.000
138	A	138	GLY	0	-0.002	0.014	8.114	-0.028	-0.028	0.000	0.000	0.000	0.000
139	A	139	PRO	0	-0.027	-0.025	11.234	-0.075	-0.075	0.000	0.000	0.000	0.000
140	A	140	VAL	0	-0.033	-0.019	12.248	-0.034	-0.034	0.000	0.000	0.000	0.000
141	A	141	SER	0	0.001	0.009	7.191	-0.086	-0.086	0.000	0.000	0.000	0.000
142	A	142	ALA	0	0.077	0.039	8.573	0.054	0.054	0.000	0.000	0.000	0.000
143	A	143	PHE	0	-0.017	0.011	3.117	-1.253	-0.387	0.060	-0.350	-0.576	-0.003

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