FMO DATABASE

FMODB ID: 1JQ8Z

Calculation Name: 1RYL-A-Xray315

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	166
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1723744.648526
FMO2-HF: Nuclear repulsion	1657484.302899
FMO2-HF: Total energy	-66260.345627
FMO2-MP2: Total energy	-66453.316563

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:2:ACE )

Summations of interaction energy for fragment #1(A:2:ACE )

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.
-4.126	-2.324	0.208	-0.955	-1.054	0

Interaction energy analysis for fragmet #1(A:2:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.039 / q_NPA : -0.034

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	4	ILE	0	-0.031	0.018	3.856	1.150	2.127	-0.005	-0.463	-0.509	-0.001
4	A	5	GLY	0	0.045	0.016	6.590	-0.151	-0.151	0.000	0.000	0.000	0.000
5	A	6	TYR	0	-0.048	-0.040	10.216	0.196	0.196	0.000	0.000	0.000	0.000
6	A	7	PHE	0	0.013	0.010	13.336	-0.027	-0.027	0.000	0.000	0.000	0.000
7	A	8	ALA	0	-0.001	-0.013	16.968	0.040	0.040	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.785	-0.904	18.741	-0.090	-0.090	0.000	0.000	0.000	0.000
9	A	10	ILE	0	-0.012	-0.003	22.176	0.005	0.005	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.796	-0.892	24.143	-0.094	-0.094	0.000	0.000	0.000	0.000
11	A	12	SER	0	0.019	-0.022	27.489	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.917	-0.946	29.529	-0.084	-0.084	0.000	0.000	0.000	0.000
13	A	14	LYS	1	0.948	0.972	24.860	0.095	0.095	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.003	0.006	23.237	-0.011	-0.011	0.000	0.000	0.000	0.000
15	A	16	ASN	0	-0.029	-0.023	25.798	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	17	GLN	0	0.013	0.025	26.034	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.009	-0.010	20.213	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	19	LEU	0	-0.056	-0.053	23.846	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	20	GLU	-1	-0.975	-0.977	25.857	-0.097	-0.097	0.000	0.000	0.000	0.000
20	A	21	SER	0	-0.058	0.005	24.429	0.007	0.007	0.000	0.000	0.000	0.000
21	A	22	THR	0	-0.037	-0.054	23.372	0.004	0.004	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.887	-0.927	21.497	-0.183	-0.183	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.824	0.891	16.293	0.287	0.287	0.000	0.000	0.000	0.000
24	A	25	PRO	0	0.013	0.008	18.284	-0.028	-0.028	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.035	0.023	18.140	-0.019	-0.019	0.000	0.000	0.000	0.000
26	A	27	MET	0	0.066	0.000	12.365	0.013	0.013	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.917	-0.937	13.968	-0.421	-0.421	0.000	0.000	0.000	0.000
28	A	29	ASN	0	-0.022	-0.021	13.544	0.041	0.041	0.000	0.000	0.000	0.000
29	A	30	ILE	0	0.075	0.045	12.570	0.041	0.041	0.000	0.000	0.000	0.000
30	A	31	HIS	0	-0.071	-0.041	10.033	0.016	0.016	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.919	-0.985	13.876	-0.106	-0.106	0.000	0.000	0.000	0.000
32	A	33	THR	0	0.003	0.008	17.376	0.015	0.015	0.000	0.000	0.000	0.000
33	A	34	LEU	0	0.003	-0.002	15.222	0.025	0.025	0.000	0.000	0.000	0.000
34	A	35	SER	0	-0.061	0.005	16.713	0.015	0.015	0.000	0.000	0.000	0.000
35	A	36	GLY	0	0.013	0.014	17.665	0.018	0.018	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.046	-0.010	19.386	0.015	0.015	0.000	0.000	0.000	0.000
37	A	38	ARG	1	0.969	0.990	19.216	0.067	0.067	0.000	0.000	0.000	0.000
38	A	39	ARG	1	0.874	0.930	14.100	0.188	0.188	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.084	-0.007	16.899	0.032	0.032	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.852	-0.935	11.426	-0.219	-0.219	0.000	0.000	0.000	0.000
41	A	42	ILE	0	-0.054	-0.028	12.242	0.060	0.060	0.000	0.000	0.000	0.000
42	A	43	ASP	-1	-0.851	-0.922	8.393	0.377	0.377	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.896	0.940	2.886	-3.005	-2.636	0.102	-0.205	-0.265	0.002
44	A	45	ARG	1	0.824	0.900	7.785	0.029	0.029	0.000	0.000	0.000	0.000
45	A	46	TRP	0	0.005	-0.018	6.812	0.186	0.186	0.000	0.000	0.000	0.000
46	A	47	ASP	-1	-0.679	-0.816	10.643	-0.289	-0.289	0.000	0.000	0.000	0.000
47	A	48	PHE	0	-0.003	0.004	11.667	0.051	0.051	0.000	0.000	0.000	0.000
48	A	49	LEU	0	-0.009	-0.001	14.552	0.021	0.021	0.000	0.000	0.000	0.000
49	A	50	HIS	0	0.041	0.046	15.334	0.007	0.007	0.000	0.000	0.000	0.000
50	A	51	PHE	0	0.007	0.004	16.239	0.030	0.030	0.000	0.000	0.000	0.000
51	A	52	GLY	0	-0.052	-0.030	18.042	0.018	0.018	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.062	-0.037	20.122	0.013	0.013	0.000	0.000	0.000	0.000
53	A	54	THR	0	-0.014	-0.010	19.766	0.005	0.005	0.000	0.000	0.000	0.000
54	A	55	GLY	0	-0.019	0.006	21.263	0.007	0.007	0.000	0.000	0.000	0.000
55	A	56	THR	0	-0.014	-0.028	19.594	0.002	0.002	0.000	0.000	0.000	0.000
56	A	57	SER	0	0.052	0.009	13.325	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	58	ALA	0	-0.019	-0.024	13.142	0.010	0.010	0.000	0.000	0.000	0.000
58	A	59	PHE	0	-0.028	-0.031	8.403	-0.037	-0.037	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.981	-0.979	14.494	-0.147	-0.147	0.000	0.000	0.000	0.000
60	A	61	PRO	0	-0.016	0.020	17.670	0.032	0.032	0.000	0.000	0.000	0.000
61	A	62	ALA	0	0.036	0.021	20.255	0.012	0.012	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.955	0.948	23.963	0.124	0.124	0.000	0.000	0.000	0.000
63	A	64	ASN	0	-0.074	-0.043	26.083	0.004	0.004	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.751	-0.871	23.615	-0.116	-0.116	0.000	0.000	0.000	0.000
65	A	66	PRO	0	-0.025	-0.037	24.350	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	67	LEU	0	0.015	0.006	23.667	-0.005	-0.005	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.007	-0.018	19.300	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	69	ARG	1	0.856	0.920	20.031	0.117	0.117	0.000	0.000	0.000	0.000
69	A	70	ALA	0	-0.032	0.002	22.096	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	71	VAL	0	-0.019	0.000	16.193	0.001	0.001	0.000	0.000	0.000	0.000
71	A	72	LEU	0	0.027	0.000	14.997	-0.028	-0.028	0.000	0.000	0.000	0.000
72	A	73	GLY	0	0.022	0.023	17.866	-0.019	-0.019	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.905	-0.954	20.904	-0.136	-0.136	0.000	0.000	0.000	0.000
74	A	75	HIS	1	0.729	0.843	23.075	0.164	0.164	0.000	0.000	0.000	0.000
75	A	76	SER	0	0.052	0.041	19.223	-0.024	-0.024	0.000	0.000	0.000	0.000
76	A	77	LEU	0	-0.044	-0.040	19.261	0.021	0.021	0.000	0.000	0.000	0.000
77	A	78	GLU	-1	-0.864	-0.963	15.402	-0.410	-0.410	0.000	0.000	0.000	0.000
78	A	79	ASP	-1	-0.858	-0.936	14.433	-0.490	-0.490	0.000	0.000	0.000	0.000
79	A	80	GLY	0	-0.014	0.030	13.504	0.021	0.021	0.000	0.000	0.000	0.000
80	A	81	ILE	0	-0.150	-0.066	13.613	0.060	0.060	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.914	-0.978	9.790	-0.798	-0.798	0.000	0.000	0.000	0.000
82	A	83	GLY	0	-0.011	-0.017	9.598	-0.139	-0.139	0.000	0.000	0.000	0.000
83	A	84	PHE	0	0.000	0.002	10.180	0.152	0.152	0.000	0.000	0.000	0.000
84	A	85	LEU	0	0.002	-0.001	12.960	-0.033	-0.033	0.000	0.000	0.000	0.000
85	A	86	GLY	0	0.014	0.017	15.732	0.038	0.038	0.000	0.000	0.000	0.000
86	A	87	LEU	0	-0.052	-0.031	18.685	0.006	0.006	0.000	0.000	0.000	0.000
87	A	88	THR	0	-0.012	-0.001	21.948	0.004	0.004	0.000	0.000	0.000	0.000
88	A	89	TRP	0	0.015	0.004	24.657	0.006	0.006	0.000	0.000	0.000	0.000
89	A	90	ASN	0	-0.022	-0.016	27.894	0.008	0.008	0.000	0.000	0.000	0.000
90	A	91	GLN	0	-0.043	-0.037	29.982	0.006	0.006	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.786	-0.870	27.661	-0.131	-0.131	0.000	0.000	0.000	0.000
92	A	93	LEU	0	-0.003	-0.003	25.150	0.000	0.000	0.000	0.000	0.000	0.000
93	A	94	ALA	0	0.012	0.013	28.795	0.002	0.002	0.000	0.000	0.000	0.000
94	A	95	ALA	0	0.034	0.022	30.955	0.003	0.003	0.000	0.000	0.000	0.000
95	A	96	THR	0	-0.023	-0.002	24.629	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	97	ILE	0	-0.055	-0.034	27.603	0.001	0.001	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.897	-0.946	28.822	-0.058	-0.058	0.000	0.000	0.000	0.000
98	A	99	ARG	1	0.932	0.983	27.388	0.107	0.107	0.000	0.000	0.000	0.000
99	A	100	LEU	0	-0.008	-0.009	23.493	0.003	0.003	0.000	0.000	0.000	0.000
100	A	101	GLU	-1	-0.909	-0.963	27.446	-0.053	-0.053	0.000	0.000	0.000	0.000
101	A	102	SER	0	-0.027	-0.019	30.324	0.007	0.007	0.000	0.000	0.000	0.000
102	A	103	LEU	0	-0.052	-0.006	25.912	0.004	0.004	0.000	0.000	0.000	0.000
103	A	104	ASP	-1	-0.805	-0.889	30.179	-0.028	-0.028	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.874	0.905	27.978	0.049	0.049	0.000	0.000	0.000	0.000
105	A	106	ASN	0	-0.018	-0.009	29.171	0.003	0.003	0.000	0.000	0.000	0.000
106	A	107	GLU	-1	-0.966	-0.969	30.820	-0.046	-0.046	0.000	0.000	0.000	0.000
107	A	108	LEU	0	0.041	0.009	25.042	0.000	0.000	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.779	0.891	26.288	0.008	0.008	0.000	0.000	0.000	0.000
109	A	110	LYS	1	0.887	0.939	27.566	0.019	0.019	0.000	0.000	0.000	0.000
110	A	111	GLN	0	0.033	0.015	26.674	0.004	0.004	0.000	0.000	0.000	0.000
111	A	112	PHE	0	-0.058	-0.007	19.354	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	113	SER	0	0.008	-0.004	23.089	0.008	0.008	0.000	0.000	0.000	0.000
113	A	114	ILE	0	0.005	-0.018	18.905	-0.007	-0.007	0.000	0.000	0.000	0.000
114	A	115	LYS	1	0.890	0.949	20.563	-0.011	-0.011	0.000	0.000	0.000	0.000
115	A	116	ARG	1	0.920	0.968	21.749	0.060	0.060	0.000	0.000	0.000	0.000
116	A	117	LEU	0	0.002	0.018	15.290	-0.006	-0.006	0.000	0.000	0.000	0.000
117	A	118	ASN	0	0.000	-0.020	16.875	0.005	0.005	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.993	-0.993	17.615	-0.031	-0.031	0.000	0.000	0.000	0.000
119	A	120	MET	0	-0.018	0.000	17.856	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	121	GLU	-1	-0.977	-0.970	13.546	-0.014	-0.014	0.000	0.000	0.000	0.000
121	A	122	ILE	0	-0.041	0.002	12.651	-0.038	-0.038	0.000	0.000	0.000	0.000
122	A	123	TYR	0	0.060	0.042	2.927	-0.461	-0.088	0.109	-0.226	-0.256	-0.001
123	A	124	PRO	0	-0.096	-0.084	6.379	0.014	0.014	0.000	0.000	0.000	0.000
124	A	125	GLY	0	0.041	0.011	7.770	0.105	0.105	0.000	0.000	0.000	0.000
125	A	126	VAL	0	-0.072	-0.014	9.888	0.047	0.047	0.000	0.000	0.000	0.000
126	A	127	THR	0	-0.006	-0.006	12.384	-0.039	-0.039	0.000	0.000	0.000	0.000
127	A	128	PHE	0	-0.047	-0.026	13.424	0.029	0.029	0.000	0.000	0.000	0.000
128	A	129	SER	0	0.035	0.013	18.165	-0.009	-0.009	0.000	0.000	0.000	0.000
129	A	130	GLU	-1	-0.853	-0.958	21.771	0.030	0.030	0.000	0.000	0.000	0.000
130	A	131	GLU	-1	-0.932	-0.974	23.959	0.059	0.059	0.000	0.000	0.000	0.000
131	A	132	LEU	0	-0.040	-0.019	19.455	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	133	GLU	-1	-0.787	-0.845	21.909	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	134	GLY	0	0.003	-0.007	22.932	-0.007	-0.007	0.000	0.000	0.000	0.000
134	A	135	GLN	0	0.001	-0.009	22.007	-0.007	-0.007	0.000	0.000	0.000	0.000
135	A	136	LEU	0	0.019	0.026	16.034	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	137	PHE	0	0.054	0.017	19.675	-0.011	-0.011	0.000	0.000	0.000	0.000
137	A	138	ALA	0	-0.001	-0.012	22.035	-0.009	-0.009	0.000	0.000	0.000	0.000
138	A	139	SER	0	-0.052	-0.029	17.178	-0.009	-0.009	0.000	0.000	0.000	0.000
139	A	140	ILE	0	0.047	0.027	17.222	-0.010	-0.010	0.000	0.000	0.000	0.000
140	A	141	MET	0	-0.015	-0.003	19.260	-0.015	-0.015	0.000	0.000	0.000	0.000
141	A	142	LEU	0	-0.016	0.008	20.704	-0.004	-0.004	0.000	0.000	0.000	0.000
142	A	143	ASP	-1	-0.768	-0.886	15.935	-0.066	-0.066	0.000	0.000	0.000	0.000
143	A	144	MET	0	-0.004	0.004	19.201	-0.017	-0.017	0.000	0.000	0.000	0.000
144	A	145	GLU	-1	-0.867	-0.935	21.535	-0.053	-0.053	0.000	0.000	0.000	0.000
145	A	146	LYS	1	0.875	0.941	19.141	0.020	0.020	0.000	0.000	0.000	0.000
146	A	147	LEU	0	0.009	0.008	19.104	-0.002	-0.002	0.000	0.000	0.000	0.000
147	A	148	ILE	0	0.036	0.026	21.503	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	149	SER	0	-0.043	-0.030	24.939	0.004	0.004	0.000	0.000	0.000	0.000
149	A	150	ALA	0	-0.071	-0.029	21.893	0.003	0.003	0.000	0.000	0.000	0.000
150	A	151	TYR	0	0.046	-0.002	20.971	0.000	0.000	0.000	0.000	0.000	0.000
151	A	152	ARG	1	0.899	0.950	25.467	0.061	0.061	0.000	0.000	0.000	0.000
152	A	153	ARG	1	0.751	0.850	22.514	0.101	0.101	0.000	0.000	0.000	0.000
153	A	154	MET	0	-0.045	0.063	22.275	0.003	0.003	0.000	0.000	0.000	0.000
154	A	155	LEU	0	0.020	0.014	27.397	0.003	0.003	0.000	0.000	0.000	0.000
155	A	156	ARG	1	0.915	0.964	30.215	0.059	0.059	0.000	0.000	0.000	0.000
156	A	157	GLN	0	-0.088	-0.049	29.666	0.009	0.009	0.000	0.000	0.000	0.000
157	A	158	GLY	0	0.008	0.019	31.843	0.001	0.001	0.000	0.000	0.000	0.000
158	A	159	ASN	0	-0.098	-0.058	26.767	-0.002	-0.002	0.000	0.000	0.000	0.000
159	A	160	HIS	0	0.073	0.016	25.572	0.001	0.001	0.000	0.000	0.000	0.000
160	A	161	ALA	0	0.010	-0.027	21.720	-0.001	-0.001	0.000	0.000	0.000	0.000
161	A	162	LEU	0	0.050	0.014	18.275	0.001	0.001	0.000	0.000	0.000	0.000
162	A	163	THR	0	-0.035	-0.014	14.536	0.013	0.013	0.000	0.000	0.000	0.000
163	A	164	VAL	0	-0.023	-0.014	11.496	-0.015	-0.015	0.000	0.000	0.000	0.000
164	A	165	ILE	0	-0.013	-0.004	8.529	-0.005	-0.005	0.000	0.000	0.000	0.000
165	A	166	VAL	0	0.085	0.052	7.294	-0.024	-0.024	0.000	0.000	0.000	0.000
166	A	167	NME	0	-0.022	-0.001	4.080	-0.342	-0.259	0.002	-0.061	-0.024	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ACE )