FMO DATABASE

FMODB ID: 14LRZ

Calculation Name: 1RYL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1RYL

Chain ID: A

ChEMBL ID:

UniProt ID: P76483

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	OptAll
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	164
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1715476.010638
FMO2-HF: Nuclear repulsion	1649385.173202
FMO2-HF: Total energy	-66090.837436
FMO2-MP2: Total energy	-66283.073474

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:3:MET)

Summations of interaction energy for fragment #1(A:3: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.
-13.67	-4.669	13.56	-7.347	-15.212	-0.051

Interaction energy analysis for fragmet #1(A:3:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : 0.000

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	5	GLY	0	0.026	0.004	3.798	-2.379	-0.559	-0.004	-0.956	-0.860	0.003
4	A	6	TYR	0	-0.060	-0.044	6.046	0.194	0.194	0.000	0.000	0.000	0.000
5	A	7	PHE	0	0.020	0.005	9.732	0.002	0.002	0.000	0.000	0.000	0.000
6	A	8	ALA	0	0.005	-0.005	12.880	0.026	0.026	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.804	-0.885	15.052	-0.002	-0.002	0.000	0.000	0.000	0.000
8	A	10	ILE	0	0.017	0.009	18.207	0.014	0.014	0.000	0.000	0.000	0.000
9	A	11	ASP	-1	-0.745	-0.854	20.374	0.039	0.039	0.000	0.000	0.000	0.000
10	A	12	SER	0	0.041	-0.012	23.438	0.001	0.001	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.890	-0.901	25.996	0.051	0.051	0.000	0.000	0.000	0.000
12	A	14	LYS	1	0.807	0.862	21.299	-0.057	-0.057	0.000	0.000	0.000	0.000
13	A	15	ILE	0	0.002	0.012	18.771	0.005	0.005	0.000	0.000	0.000	0.000
14	A	16	ASN	0	-0.046	-0.029	21.559	0.001	0.001	0.000	0.000	0.000	0.000
15	A	17	GLN	0	0.057	0.036	22.110	0.004	0.004	0.000	0.000	0.000	0.000
16	A	18	LEU	0	0.016	0.024	16.231	0.005	0.005	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.012	-0.018	19.244	0.004	0.004	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.989	-0.996	21.244	0.046	0.046	0.000	0.000	0.000	0.000
19	A	21	SER	0	-0.056	-0.037	20.882	0.001	0.001	0.000	0.000	0.000	0.000
20	A	22	THR	0	-0.047	-0.035	18.101	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	23	GLU	-1	-0.782	-0.875	14.223	0.125	0.125	0.000	0.000	0.000	0.000
22	A	24	LYS	1	0.742	0.872	16.790	-0.074	-0.074	0.000	0.000	0.000	0.000
23	A	25	PRO	0	-0.023	-0.021	14.814	-0.007	-0.007	0.000	0.000	0.000	0.000
24	A	26	LEU	0	0.018	-0.005	12.020	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	27	MET	0	0.031	0.035	7.299	0.042	0.042	0.000	0.000	0.000	0.000
26	A	28	ASP	-1	-0.849	-0.919	10.509	0.269	0.269	0.000	0.000	0.000	0.000
27	A	29	ASN	0	-0.124	-0.068	11.522	0.013	0.013	0.000	0.000	0.000	0.000
28	A	30	ILE	0	0.021	0.020	9.451	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	31	HIS	0	-0.017	-0.016	6.647	0.079	0.079	0.000	0.000	0.000	0.000
30	A	32	ASP	-1	-0.945	-0.955	11.319	0.228	0.228	0.000	0.000	0.000	0.000
31	A	33	THR	0	0.041	0.004	15.112	-0.017	-0.017	0.000	0.000	0.000	0.000
32	A	34	LEU	0	-0.001	0.007	12.354	-0.026	-0.026	0.000	0.000	0.000	0.000
33	A	35	SER	0	-0.017	0.003	14.493	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	36	GLY	0	-0.030	-0.015	15.419	-0.005	-0.005	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.018	0.007	16.311	-0.020	-0.020	0.000	0.000	0.000	0.000
36	A	38	ARG	1	0.937	0.968	16.639	-0.014	-0.014	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.874	0.942	11.605	-0.143	-0.143	0.000	0.000	0.000	0.000
38	A	40	LEU	0	-0.093	-0.015	14.084	0.026	0.026	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.831	-0.938	9.767	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.041	-0.015	9.121	0.056	0.056	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.821	-0.890	7.562	0.318	0.318	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.857	0.894	3.726	-1.320	-1.049	0.000	-0.101	-0.170	0.000
43	A	45	ARG	1	0.858	0.914	6.291	0.101	0.101	0.000	0.000	0.000	0.000
44	A	46	TRP	0	0.021	-0.002	2.248	-0.887	0.511	2.034	-0.921	-2.511	-0.001
45	A	47	ASP	-1	-0.719	-0.823	6.294	-0.776	-0.776	0.000	0.000	0.000	0.000
46	A	48	PHE	0	0.013	0.003	8.371	0.155	0.155	0.000	0.000	0.000	0.000
47	A	49	LEU	0	-0.025	-0.016	11.482	0.099	0.099	0.000	0.000	0.000	0.000
48	A	50	HIS	0	0.025	0.028	10.775	0.123	0.123	0.000	0.000	0.000	0.000
49	A	51	PHE	0	0.026	0.012	12.102	0.068	0.068	0.000	0.000	0.000	0.000
50	A	52	GLY	0	-0.063	-0.041	13.884	0.047	0.047	0.000	0.000	0.000	0.000
51	A	53	LEU	0	-0.048	-0.033	16.137	0.041	0.041	0.000	0.000	0.000	0.000
52	A	54	THR	0	-0.020	0.006	14.655	0.018	0.018	0.000	0.000	0.000	0.000
53	A	55	GLY	0	-0.030	0.008	17.045	0.016	0.016	0.000	0.000	0.000	0.000
54	A	56	THR	0	0.033	-0.002	14.211	0.002	0.002	0.000	0.000	0.000	0.000
55	A	57	SER	0	0.055	0.009	8.120	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	58	ALA	0	-0.015	-0.024	7.560	0.078	0.078	0.000	0.000	0.000	0.000
57	A	59	PHE	0	-0.005	-0.019	2.292	-1.169	-0.551	1.517	-0.472	-1.662	-0.004
58	A	60	ASP	-1	-0.988	-0.981	8.144	-0.257	-0.257	0.000	0.000	0.000	0.000
59	A	61	PRO	0	0.011	0.031	11.427	0.006	0.006	0.000	0.000	0.000	0.000
60	A	62	ALA	0	0.026	0.008	14.167	0.027	0.027	0.000	0.000	0.000	0.000
61	A	63	LYS	1	0.957	0.952	17.944	0.124	0.124	0.000	0.000	0.000	0.000
62	A	64	ASN	0	-0.054	-0.034	19.847	0.003	0.003	0.000	0.000	0.000	0.000
63	A	65	ASP	-1	-0.729	-0.850	17.815	-0.171	-0.171	0.000	0.000	0.000	0.000
64	A	66	PRO	0	-0.030	-0.025	19.238	0.003	0.003	0.000	0.000	0.000	0.000
65	A	67	LEU	0	-0.013	-0.019	19.085	0.009	0.009	0.000	0.000	0.000	0.000
66	A	68	SER	0	-0.004	-0.020	13.880	0.000	0.000	0.000	0.000	0.000	0.000
67	A	69	ARG	1	0.845	0.910	14.526	0.069	0.069	0.000	0.000	0.000	0.000
68	A	70	ALA	0	-0.015	0.005	16.430	0.010	0.010	0.000	0.000	0.000	0.000
69	A	71	VAL	0	-0.018	0.004	11.063	0.000	0.000	0.000	0.000	0.000	0.000
70	A	72	LEU	0	0.032	0.006	9.326	-0.017	-0.017	0.000	0.000	0.000	0.000
71	A	73	GLY	0	0.020	0.023	12.158	0.032	0.032	0.000	0.000	0.000	0.000
72	A	74	GLU	-1	-0.849	-0.921	15.340	-0.072	-0.072	0.000	0.000	0.000	0.000
73	A	75	HIS	1	0.760	0.849	17.469	0.025	0.025	0.000	0.000	0.000	0.000
74	A	76	SER	0	0.052	0.022	12.044	-0.014	-0.014	0.000	0.000	0.000	0.000
75	A	77	LEU	0	-0.106	-0.056	14.359	-0.004	-0.004	0.000	0.000	0.000	0.000
76	A	78	GLU	-1	-0.824	-0.936	10.774	0.210	0.210	0.000	0.000	0.000	0.000
77	A	79	ASP	-1	-0.908	-0.949	8.837	0.199	0.199	0.000	0.000	0.000	0.000
78	A	80	GLY	0	-0.010	0.009	6.784	0.022	0.022	0.000	0.000	0.000	0.000
79	A	81	ILE	0	-0.106	-0.079	7.718	-0.214	-0.214	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.918	-0.944	5.492	0.700	0.807	-0.001	-0.009	-0.096	0.000
81	A	83	GLY	0	-0.015	-0.011	4.308	-0.800	-0.400	0.009	-0.110	-0.299	0.000
82	A	84	PHE	0	0.012	0.015	5.004	-0.249	-0.022	0.000	-0.032	-0.195	0.000
83	A	85	LEU	0	-0.014	-0.003	7.796	-0.180	-0.180	0.000	0.000	0.000	0.000
84	A	86	GLY	0	0.038	0.028	10.601	0.017	0.017	0.000	0.000	0.000	0.000
85	A	87	LEU	0	-0.040	-0.012	13.314	-0.015	-0.015	0.000	0.000	0.000	0.000
86	A	88	THR	0	-0.032	-0.014	16.652	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	89	TRP	0	0.030	0.014	19.384	0.003	0.003	0.000	0.000	0.000	0.000
88	A	90	ASN	0	-0.044	-0.032	22.666	-0.008	-0.008	0.000	0.000	0.000	0.000
89	A	91	GLN	0	-0.041	-0.037	25.080	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	92	GLU	-1	-0.816	-0.880	22.430	-0.028	-0.028	0.000	0.000	0.000	0.000
91	A	93	LEU	0	0.009	0.000	19.687	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	94	ALA	0	0.001	0.005	23.319	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.033	0.014	25.850	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	96	THR	0	-0.010	-0.006	19.289	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	97	ILE	0	-0.030	-0.012	22.322	-0.010	-0.010	0.000	0.000	0.000	0.000
96	A	98	ASP	-1	-0.941	-0.958	23.921	-0.066	-0.066	0.000	0.000	0.000	0.000
97	A	99	ARG	1	0.865	0.932	21.564	0.076	0.076	0.000	0.000	0.000	0.000
98	A	100	LEU	0	0.019	0.015	18.573	-0.008	-0.008	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.836	-0.915	22.783	-0.064	-0.064	0.000	0.000	0.000	0.000
100	A	102	SER	0	-0.026	-0.016	26.090	0.003	0.003	0.000	0.000	0.000	0.000
101	A	103	LEU	0	-0.047	-0.002	21.606	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	104	ASP	-1	-0.742	-0.858	26.044	-0.093	-0.093	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.807	0.859	24.141	0.097	0.097	0.000	0.000	0.000	0.000
104	A	106	ASN	0	-0.111	-0.067	25.872	-0.009	-0.009	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.895	-0.943	26.749	-0.125	-0.125	0.000	0.000	0.000	0.000
106	A	108	LEU	0	0.036	0.017	21.177	-0.009	-0.009	0.000	0.000	0.000	0.000
107	A	109	ARG	1	0.786	0.880	22.608	0.145	0.145	0.000	0.000	0.000	0.000
108	A	110	LYS	1	0.873	0.937	24.447	0.108	0.108	0.000	0.000	0.000	0.000
109	A	111	GLN	0	-0.031	-0.022	22.465	-0.005	-0.005	0.000	0.000	0.000	0.000
110	A	112	PHE	0	-0.029	-0.003	16.187	-0.013	-0.013	0.000	0.000	0.000	0.000
111	A	113	SER	0	-0.042	-0.047	19.586	0.018	0.018	0.000	0.000	0.000	0.000
112	A	114	ILE	0	0.011	-0.003	16.860	-0.027	-0.027	0.000	0.000	0.000	0.000
113	A	115	LYS	1	0.773	0.870	17.983	0.150	0.150	0.000	0.000	0.000	0.000
114	A	116	ARG	1	0.919	0.948	17.608	0.264	0.264	0.000	0.000	0.000	0.000
115	A	117	LEU	0	-0.031	0.012	12.660	-0.020	-0.020	0.000	0.000	0.000	0.000
116	A	118	ASN	0	-0.009	-0.021	13.493	-0.096	-0.096	0.000	0.000	0.000	0.000
117	A	119	GLU	-1	-0.963	-0.981	14.921	-0.341	-0.341	0.000	0.000	0.000	0.000
118	A	120	MET	0	-0.038	-0.014	12.979	0.011	0.011	0.000	0.000	0.000	0.000
119	A	121	GLU	-1	-0.957	-0.968	10.333	-0.671	-0.671	0.000	0.000	0.000	0.000
120	A	122	ILE	0	-0.021	0.003	8.916	-0.183	-0.183	0.000	0.000	0.000	0.000
121	A	123	TYR	0	0.011	0.009	2.200	-4.256	-3.148	6.580	-2.158	-5.530	-0.025
122	A	124	PRO	0	-0.095	-0.070	5.425	0.208	0.208	0.000	0.000	0.000	0.000
123	A	125	GLY	0	0.035	0.011	6.444	0.104	0.104	0.000	0.000	0.000	0.000
124	A	126	VAL	0	-0.094	-0.035	9.188	0.178	0.178	0.000	0.000	0.000	0.000
125	A	127	THR	0	0.005	0.005	12.052	0.014	0.014	0.000	0.000	0.000	0.000
126	A	128	PHE	0	-0.027	-0.018	12.742	0.054	0.054	0.000	0.000	0.000	0.000
127	A	129	SER	0	0.027	0.006	17.669	0.001	0.001	0.000	0.000	0.000	0.000
128	A	130	GLU	-1	-0.775	-0.870	21.139	-0.188	-0.188	0.000	0.000	0.000	0.000
129	A	131	GLU	-1	-0.901	-0.971	23.007	-0.144	-0.144	0.000	0.000	0.000	0.000
130	A	132	LEU	0	-0.023	-0.005	19.347	0.009	0.009	0.000	0.000	0.000	0.000
131	A	133	GLU	-1	-0.766	-0.831	20.529	-0.200	-0.200	0.000	0.000	0.000	0.000
132	A	134	GLY	0	-0.002	-0.008	21.200	-0.007	-0.007	0.000	0.000	0.000	0.000
133	A	135	GLN	0	-0.014	-0.015	21.515	0.000	0.000	0.000	0.000	0.000	0.000
134	A	136	LEU	0	0.027	0.020	14.357	0.012	0.012	0.000	0.000	0.000	0.000
135	A	137	PHE	0	0.047	0.024	17.852	-0.011	-0.011	0.000	0.000	0.000	0.000
136	A	138	ALA	0	0.004	-0.002	19.886	0.004	0.004	0.000	0.000	0.000	0.000
137	A	139	SER	0	-0.018	-0.015	16.265	0.016	0.016	0.000	0.000	0.000	0.000
138	A	140	ILE	0	-0.003	0.012	14.709	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	141	MET	0	0.005	0.015	16.943	0.016	0.016	0.000	0.000	0.000	0.000
140	A	142	LEU	0	-0.025	-0.009	19.424	0.015	0.015	0.000	0.000	0.000	0.000
141	A	143	ASP	-1	-0.776	-0.869	14.462	-0.211	-0.211	0.000	0.000	0.000	0.000
142	A	144	MET	0	0.040	0.032	16.703	0.004	0.004	0.000	0.000	0.000	0.000
143	A	145	GLU	-1	-0.806	-0.890	18.158	-0.088	-0.088	0.000	0.000	0.000	0.000
144	A	146	LYS	1	0.795	0.906	16.981	0.137	0.137	0.000	0.000	0.000	0.000
145	A	147	LEU	0	0.016	0.011	14.483	0.019	0.019	0.000	0.000	0.000	0.000
146	A	148	ILE	0	0.030	0.027	17.590	0.018	0.018	0.000	0.000	0.000	0.000
147	A	149	SER	0	-0.065	-0.052	21.184	0.017	0.017	0.000	0.000	0.000	0.000
148	A	150	ALA	0	-0.085	-0.042	18.186	0.015	0.015	0.000	0.000	0.000	0.000
149	A	151	TYR	0	0.039	-0.010	16.051	0.020	0.020	0.000	0.000	0.000	0.000
150	A	152	ARG	1	0.849	0.907	21.105	0.058	0.058	0.000	0.000	0.000	0.000
151	A	153	ARG	1	0.732	0.861	19.461	0.019	0.019	0.000	0.000	0.000	0.000
152	A	154	MET	0	-0.007	0.000	17.472	0.005	0.005	0.000	0.000	0.000	0.000
153	A	155	LEU	0	0.029	0.022	23.212	0.005	0.005	0.000	0.000	0.000	0.000
154	A	156	ARG	1	0.918	0.961	25.750	0.013	0.013	0.000	0.000	0.000	0.000
155	A	157	GLN	0	-0.075	-0.039	25.795	0.000	0.000	0.000	0.000	0.000	0.000
156	A	158	GLY	0	0.006	0.014	27.855	0.004	0.004	0.000	0.000	0.000	0.000
157	A	159	ASN	0	-0.087	-0.046	22.892	0.005	0.005	0.000	0.000	0.000	0.000
158	A	160	HIS	0	0.051	0.015	20.875	-0.013	-0.013	0.000	0.000	0.000	0.000
159	A	161	ALA	0	0.001	-0.017	16.573	0.003	0.003	0.000	0.000	0.000	0.000
160	A	162	LEU	0	0.027	0.007	13.780	0.006	0.006	0.000	0.000	0.000	0.000
161	A	163	THR	0	-0.032	-0.012	9.162	-0.005	-0.005	0.000	0.000	0.000	0.000
162	A	164	VAL	0	-0.012	-0.007	7.900	0.063	0.063	0.000	0.000	0.000	0.000
163	A	165	ILE	0	-0.003	-0.003	2.779	-0.806	-0.205	0.157	-0.182	-0.576	-0.001
164	A	166	VAL	0	0.037	0.032	2.550	-2.688	-0.237	3.268	-2.406	-3.313	-0.023

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:MET)