FMO DATABASE

FMODB ID: N1QNQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1375500.133032
FMO2-HF: Nuclear repulsion	1317525.913675
FMO2-HF: Total energy	-57974.219357
FMO2-MP2: Total energy	-58143.366113

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	-1.647	1.66	-1.551	-3.335	-0.006

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 : -0.051 / q_NPA : -0.038

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	-0.039	2.694	-2.194	0.193	1.616	-1.241	-2.762	-0.003
4	A	4	VAL	0	0.082	0.047	6.117	0.229	0.229	0.000	0.000	0.000	0.000
5	A	5	ASP	-1	-0.856	-0.921	8.839	-0.259	-0.259	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.843	0.892	10.775	0.095	0.095	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.001	-0.007	12.751	0.068	0.068	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.759	0.871	15.701	0.387	0.387	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.064	0.037	13.105	0.041	0.041	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.839	-0.917	15.314	-0.037	-0.037	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.842	0.905	18.326	0.164	0.164	0.000	0.000	0.000	0.000
12	A	12	THR	0	0.004	-0.002	19.790	0.018	0.018	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.005	0.009	18.605	0.016	0.016	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.034	0.026	22.239	0.013	0.013	0.000	0.000	0.000	0.000
15	A	15	PHE	0	-0.036	-0.021	24.576	0.009	0.009	0.000	0.000	0.000	0.000
16	A	16	PHE	0	0.036	0.005	24.978	0.008	0.008	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.781	-0.856	24.850	-0.040	-0.040	0.000	0.000	0.000	0.000
18	A	18	HIS	0	-0.031	-0.002	28.093	0.008	0.008	0.000	0.000	0.000	0.000
19	A	19	GLN	0	-0.041	-0.036	29.806	0.007	0.007	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.003	0.002	29.591	0.004	0.004	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.004	0.000	32.182	0.005	0.005	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.029	-0.008	34.107	0.004	0.004	0.000	0.000	0.000	0.000
23	A	23	PHE	0	-0.031	-0.007	35.282	0.002	0.002	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.903	-0.943	36.089	-0.029	-0.029	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.051	-0.027	37.990	0.005	0.005	0.000	0.000	0.000	0.000
26	A	26	GLN	0	-0.052	-0.045	40.493	0.000	0.000	0.000	0.000	0.000	0.000
27	A	27	THR	0	-0.006	0.001	42.472	0.001	0.001	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.879	-0.934	44.930	-0.034	-0.034	0.000	0.000	0.000	0.000
29	A	29	TRP	0	-0.013	-0.029	39.338	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	30	GLN	0	-0.029	-0.025	45.312	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.005	0.012	47.999	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.879	-0.921	47.773	-0.043	-0.043	0.000	0.000	0.000	0.000
33	A	33	ILE	0	-0.022	-0.013	45.117	-0.003	-0.003	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.050	0.024	44.341	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.948	-0.986	43.201	-0.051	-0.051	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.006	0.001	42.508	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.021	-0.012	39.967	-0.005	-0.005	0.000	0.000	0.000	0.000
38	A	38	LEU	0	0.006	0.005	38.202	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	39	GLN	0	0.006	-0.006	37.777	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.894	0.962	32.593	0.094	0.094	0.000	0.000	0.000	0.000
41	A	41	ILE	0	0.036	0.014	33.922	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.040	0.017	32.824	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	43	HIS	0	-0.040	-0.022	31.271	-0.004	-0.004	0.000	0.000	0.000	0.000
44	A	44	LEU	0	-0.013	-0.021	29.843	-0.010	-0.010	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.003	0.007	28.259	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	46	ILE	0	0.000	0.002	27.368	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.788	-0.861	26.577	-0.177	-0.177	0.000	0.000	0.000	0.000
48	A	48	CYS	0	-0.038	0.002	23.928	-0.016	-0.016	0.000	0.000	0.000	0.000
49	A	49	ILE	0	-0.023	0.010	22.460	-0.015	-0.015	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.018	-0.013	21.939	-0.018	-0.018	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.849	-0.909	21.088	-0.301	-0.301	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.033	-0.022	17.637	-0.035	-0.035	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.012	-0.012	17.037	-0.031	-0.031	0.000	0.000	0.000	0.000
54	A	54	ASN	0	0.020	-0.002	17.035	-0.041	-0.041	0.000	0.000	0.000	0.000
55	A	55	ASP	-1	-0.792	-0.873	14.521	-0.466	-0.466	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.102	-0.045	12.907	-0.091	-0.091	0.000	0.000	0.000	0.000
57	A	57	ILE	0	0.044	-0.001	12.230	-0.072	-0.072	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.931	-0.955	11.763	-0.842	-0.842	0.000	0.000	0.000	0.000
59	A	59	GLY	0	-0.062	-0.035	9.029	-0.289	-0.289	0.000	0.000	0.000	0.000
60	A	60	PHE	0	-0.060	-0.056	7.375	-0.593	-0.593	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.066	-0.016	4.556	-0.126	-0.035	-0.001	-0.010	-0.079	0.000
62	A	62	MET	0	0.003	0.042	9.246	0.168	0.168	0.000	0.000	0.000	0.000
63	A	63	ARG	1	0.900	0.943	12.672	0.242	0.242	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.872	-0.946	15.566	-0.496	-0.496	0.000	0.000	0.000	0.000
65	A	65	PRO	0	-0.045	-0.014	16.720	0.058	0.058	0.000	0.000	0.000	0.000
66	A	66	GLY	0	-0.001	0.012	20.140	-0.009	-0.009	0.000	0.000	0.000	0.000
67	A	67	SER	0	-0.087	-0.069	23.075	0.011	0.011	0.000	0.000	0.000	0.000
68	A	68	TYR	0	-0.003	-0.030	23.767	-0.007	-0.007	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.877	-0.954	24.837	-0.150	-0.150	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.863	-0.904	22.720	-0.215	-0.215	0.000	0.000	0.000	0.000
71	A	71	ILE	0	-0.024	0.003	20.146	0.002	0.002	0.000	0.000	0.000	0.000
72	A	72	MET	0	-0.025	-0.015	20.854	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	73	ASP	-1	-0.806	-0.893	22.698	-0.127	-0.127	0.000	0.000	0.000	0.000
74	A	74	ILE	0	0.021	0.026	16.895	0.016	0.016	0.000	0.000	0.000	0.000
75	A	75	LEU	0	0.031	0.002	17.189	0.013	0.013	0.000	0.000	0.000	0.000
76	A	76	VAL	0	-0.041	-0.008	19.166	0.031	0.031	0.000	0.000	0.000	0.000
77	A	77	ASP	-1	-0.931	-0.964	18.775	-0.133	-0.133	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.922	-0.974	13.897	-0.242	-0.242	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.740	0.871	16.359	0.112	0.112	0.000	0.000	0.000	0.000
80	A	80	VAL	0	0.022	0.031	15.797	0.027	0.027	0.000	0.000	0.000	0.000
81	A	81	VAL	0	-0.034	-0.023	18.409	0.017	0.017	0.000	0.000	0.000	0.000
82	A	82	THR	0	-0.011	-0.036	22.190	0.001	0.001	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.854	-0.930	25.273	-0.070	-0.070	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.846	0.910	26.961	0.026	0.026	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.756	-0.836	25.573	-0.035	-0.035	0.000	0.000	0.000	0.000
86	A	86	GLY	0	0.076	0.037	26.129	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.813	-0.894	26.716	-0.093	-0.093	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.923	-0.951	30.155	-0.052	-0.052	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.006	-0.010	25.385	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.850	0.912	26.952	0.115	0.115	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.798	0.888	29.942	0.076	0.076	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.005	0.004	30.657	0.003	0.003	0.000	0.000	0.000	0.000
93	A	93	ILE	0	0.040	0.017	26.556	0.000	0.000	0.000	0.000	0.000	0.000
94	A	94	ALA	0	0.010	0.014	30.885	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	95	TYR	0	-0.047	-0.057	33.686	0.001	0.001	0.000	0.000	0.000	0.000
96	A	96	ARG	1	0.810	0.880	28.636	0.168	0.168	0.000	0.000	0.000	0.000
97	A	97	LYS	1	0.921	0.960	33.533	0.106	0.106	0.000	0.000	0.000	0.000
98	A	98	THR	0	0.006	-0.002	35.418	0.001	0.001	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.005	0.008	35.107	0.003	0.003	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.037	-0.012	32.646	0.002	0.002	0.000	0.000	0.000	0.000
101	A	101	GLN	0	-0.052	-0.027	35.237	0.003	0.003	0.000	0.000	0.000	0.000
102	A	102	GLN	0	-0.042	-0.024	37.788	0.002	0.002	0.000	0.000	0.000	0.000
103	A	103	TYR	0	0.099	0.049	39.966	0.005	0.005	0.000	0.000	0.000	0.000
104	A	104	LEU	0	-0.050	-0.029	41.831	0.003	0.003	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.049	-0.029	43.402	0.003	0.003	0.000	0.000	0.000	0.000
106	A	106	ALA	0	-0.025	0.006	41.591	0.001	0.001	0.000	0.000	0.000	0.000
107	A	107	ASP	-1	-0.807	-0.893	42.863	-0.049	-0.049	0.000	0.000	0.000	0.000
108	A	108	SER	0	0.028	-0.007	42.424	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	109	GLY	0	0.032	0.024	42.930	0.001	0.001	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.937	-0.969	41.638	-0.062	-0.062	0.000	0.000	0.000	0.000
111	A	111	LEU	0	0.006	0.014	36.339	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	112	TYR	0	0.004	0.001	38.848	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	113	ARG	1	0.924	0.963	39.942	0.048	0.048	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.034	0.003	35.941	0.002	0.002	0.000	0.000	0.000	0.000
115	A	115	ILE	0	0.012	-0.004	34.085	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.845	0.923	35.631	0.039	0.039	0.000	0.000	0.000	0.000
117	A	117	ALA	0	-0.047	-0.016	37.549	0.003	0.003	0.000	0.000	0.000	0.000
118	A	118	HIS	1	0.835	0.900	32.530	0.061	0.061	0.000	0.000	0.000	0.000
119	A	119	GLN	0	0.053	0.032	32.321	-0.005	-0.005	0.000	0.000	0.000	0.000
120	A	120	THR	0	0.002	-0.009	31.477	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	121	ALA	0	0.023	0.015	28.905	0.002	0.002	0.000	0.000	0.000	0.000
122	A	122	LEU	0	-0.006	-0.004	27.562	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	123	GLN	0	0.014	-0.008	27.414	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	124	ASP	-1	-0.800	-0.874	26.166	-0.010	-0.010	0.000	0.000	0.000	0.000
125	A	125	PHE	0	0.038	0.034	21.001	0.008	0.008	0.000	0.000	0.000	0.000
126	A	126	PRO	0	0.041	0.011	21.518	-0.005	-0.005	0.000	0.000	0.000	0.000
127	A	127	LYS	1	0.814	0.890	20.543	0.010	0.010	0.000	0.000	0.000	0.000
128	A	128	ARG	1	0.747	0.855	20.236	0.037	0.037	0.000	0.000	0.000	0.000
129	A	129	ILE	0	0.031	0.013	16.174	0.012	0.012	0.000	0.000	0.000	0.000
130	A	130	ARG	1	0.811	0.866	15.782	0.045	0.045	0.000	0.000	0.000	0.000
131	A	131	SER	0	0.024	0.019	15.904	0.019	0.019	0.000	0.000	0.000	0.000
132	A	132	TYR	0	0.031	0.038	11.535	0.053	0.053	0.000	0.000	0.000	0.000
133	A	133	LEU	0	0.009	0.001	11.159	0.057	0.057	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.982	-0.999	11.118	0.142	0.142	0.000	0.000	0.000	0.000
135	A	135	THR	0	-0.100	-0.064	12.546	0.059	0.059	0.000	0.000	0.000	0.000
136	A	136	GLU	-1	-0.922	-0.959	8.360	0.781	0.781	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.079	-0.031	5.829	0.353	0.353	0.000	0.000	0.000	0.000
138	A	138	GLY	0	-0.004	0.012	8.146	-0.031	-0.031	0.000	0.000	0.000	0.000
139	A	139	PRO	0	-0.041	-0.034	11.270	-0.074	-0.074	0.000	0.000	0.000	0.000
140	A	140	VAL	0	-0.037	-0.021	12.289	-0.033	-0.033	0.000	0.000	0.000	0.000
141	A	141	SER	0	-0.017	0.003	7.011	-0.078	-0.078	0.000	0.000	0.000	0.000
142	A	142	ALA	0	0.067	0.025	8.671	0.051	0.051	0.000	0.000	0.000	0.000
143	A	143	PHE	0	0.006	0.015	3.168	-1.167	-0.419	0.045	-0.300	-0.494	-0.003

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