FMO DATABASE

FMODB ID: YYG32

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1713119.340013
FMO2-HF: Nuclear repulsion	1647029.9597
FMO2-HF: Total energy	-66089.380313
FMO2-MP2: Total energy	-66281.806289

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.
-23.086	-13.78	14.937	-8.079	-16.167	-0.029

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 : -0.017 / q_NPA : -0.012

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	0.041	0.014	3.792	-2.250	-0.531	-0.024	-0.791	-0.905	0.005
4	A	6	TYR	0	-0.046	-0.039	6.197	0.311	0.311	0.000	0.000	0.000	0.000
5	A	7	PHE	0	0.007	0.008	9.838	-0.031	-0.031	0.000	0.000	0.000	0.000
6	A	8	ALA	0	0.003	-0.011	12.925	0.037	0.037	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.789	-0.905	15.070	0.038	0.038	0.000	0.000	0.000	0.000
8	A	10	ILE	0	-0.006	-0.001	18.413	0.014	0.014	0.000	0.000	0.000	0.000
9	A	11	ASP	-1	-0.794	-0.891	20.379	0.045	0.045	0.000	0.000	0.000	0.000
10	A	12	SER	0	0.016	-0.022	23.610	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.921	-0.949	25.519	0.050	0.050	0.000	0.000	0.000	0.000
12	A	14	LYS	1	0.951	0.973	21.441	-0.073	-0.073	0.000	0.000	0.000	0.000
13	A	15	ILE	0	0.002	0.010	18.754	0.001	0.001	0.000	0.000	0.000	0.000
14	A	16	ASN	0	-0.029	-0.024	21.533	-0.006	-0.006	0.000	0.000	0.000	0.000
15	A	17	GLN	0	0.014	0.024	22.659	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	18	LEU	0	0.004	-0.003	16.190	0.001	0.001	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.046	-0.046	19.019	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.981	-0.982	21.230	0.022	0.022	0.000	0.000	0.000	0.000
19	A	21	SER	0	-0.057	-0.002	20.402	0.000	0.000	0.000	0.000	0.000	0.000
20	A	22	THR	0	-0.052	-0.051	18.195	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	23	GLU	-1	-0.772	-0.868	14.283	0.023	0.023	0.000	0.000	0.000	0.000
22	A	24	LYS	1	0.751	0.877	17.050	-0.020	-0.020	0.000	0.000	0.000	0.000
23	A	25	PRO	0	-0.022	-0.019	14.976	0.004	0.004	0.000	0.000	0.000	0.000
24	A	26	LEU	0	0.030	0.000	12.057	0.008	0.008	0.000	0.000	0.000	0.000
25	A	27	MET	0	0.042	0.037	7.753	0.002	0.002	0.000	0.000	0.000	0.000
26	A	28	ASP	-1	-0.915	-0.945	10.592	0.065	0.065	0.000	0.000	0.000	0.000
27	A	29	ASN	0	-0.056	-0.037	11.219	0.038	0.038	0.000	0.000	0.000	0.000
28	A	30	ILE	0	0.065	0.038	9.012	0.016	0.016	0.000	0.000	0.000	0.000
29	A	31	HIS	0	-0.084	-0.049	6.884	0.141	0.141	0.000	0.000	0.000	0.000
30	A	32	ASP	-1	-0.915	-0.983	11.485	0.262	0.262	0.000	0.000	0.000	0.000
31	A	33	THR	0	0.001	0.006	15.230	-0.013	-0.013	0.000	0.000	0.000	0.000
32	A	34	LEU	0	-0.001	-0.003	11.651	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	35	SER	0	-0.058	0.006	14.509	0.012	0.012	0.000	0.000	0.000	0.000
34	A	36	GLY	0	0.009	0.012	15.405	0.011	0.011	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.047	-0.010	16.043	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	38	ARG	1	0.967	0.988	16.499	-0.068	-0.068	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.878	0.932	11.607	-0.254	-0.254	0.000	0.000	0.000	0.000
38	A	40	LEU	0	-0.089	-0.009	13.670	0.033	0.033	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.850	-0.935	9.684	0.421	0.421	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.055	-0.028	8.809	0.054	0.054	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.852	-0.922	7.459	1.021	1.021	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.904	0.943	2.959	-10.245	-8.160	0.115	-1.115	-1.085	0.012
43	A	45	ARG	1	0.822	0.899	6.143	-0.150	-0.150	0.000	0.000	0.000	0.000
44	A	46	TRP	0	0.006	-0.017	2.507	-1.340	0.522	1.258	-0.891	-2.228	0.001
45	A	47	ASP	-1	-0.681	-0.816	6.916	-0.383	-0.383	0.000	0.000	0.000	0.000
46	A	48	PHE	0	-0.006	0.003	8.578	0.061	0.061	0.000	0.000	0.000	0.000
47	A	49	LEU	0	-0.008	-0.002	11.015	0.051	0.051	0.000	0.000	0.000	0.000
48	A	50	HIS	0	0.035	0.044	10.640	0.066	0.066	0.000	0.000	0.000	0.000
49	A	51	PHE	0	0.015	0.006	12.386	0.034	0.034	0.000	0.000	0.000	0.000
50	A	52	GLY	0	-0.056	-0.032	14.349	0.023	0.023	0.000	0.000	0.000	0.000
51	A	53	LEU	0	-0.057	-0.036	15.923	0.022	0.022	0.000	0.000	0.000	0.000
52	A	54	THR	0	-0.015	-0.010	15.349	0.007	0.007	0.000	0.000	0.000	0.000
53	A	55	GLY	0	-0.019	0.006	17.304	0.006	0.006	0.000	0.000	0.000	0.000
54	A	56	THR	0	-0.015	-0.028	14.389	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	57	SER	0	0.051	0.009	8.406	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	58	ALA	0	-0.016	-0.023	8.032	0.026	0.026	0.000	0.000	0.000	0.000
57	A	59	PHE	0	-0.027	-0.031	2.208	-0.966	-0.367	1.476	-0.472	-1.603	-0.003
58	A	60	ASP	-1	-0.984	-0.981	8.203	-0.294	-0.294	0.000	0.000	0.000	0.000
59	A	61	PRO	0	-0.012	0.022	11.634	0.012	0.012	0.000	0.000	0.000	0.000
60	A	62	ALA	0	0.034	0.020	14.352	0.004	0.004	0.000	0.000	0.000	0.000
61	A	63	LYS	1	0.956	0.949	18.063	0.125	0.125	0.000	0.000	0.000	0.000
62	A	64	ASN	0	-0.077	-0.045	19.957	0.007	0.007	0.000	0.000	0.000	0.000
63	A	65	ASP	-1	-0.752	-0.871	18.173	-0.105	-0.105	0.000	0.000	0.000	0.000
64	A	66	PRO	0	-0.024	-0.036	18.933	0.002	0.002	0.000	0.000	0.000	0.000
65	A	67	LEU	0	0.016	0.006	18.787	0.007	0.007	0.000	0.000	0.000	0.000
66	A	68	SER	0	-0.012	-0.019	13.962	0.001	0.001	0.000	0.000	0.000	0.000
67	A	69	ARG	1	0.860	0.920	14.647	0.057	0.057	0.000	0.000	0.000	0.000
68	A	70	ALA	0	-0.034	0.001	16.609	0.007	0.007	0.000	0.000	0.000	0.000
69	A	71	VAL	0	-0.023	-0.003	10.957	0.005	0.005	0.000	0.000	0.000	0.000
70	A	72	LEU	0	0.027	0.001	9.591	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	73	GLY	0	0.027	0.025	12.354	0.011	0.011	0.000	0.000	0.000	0.000
72	A	74	GLU	-1	-0.908	-0.956	15.524	-0.042	-0.042	0.000	0.000	0.000	0.000
73	A	75	HIS	1	0.724	0.840	17.853	0.019	0.019	0.000	0.000	0.000	0.000
74	A	76	SER	0	0.051	0.041	13.193	0.007	0.007	0.000	0.000	0.000	0.000
75	A	77	LEU	0	-0.055	-0.044	14.076	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	78	GLU	-1	-0.839	-0.951	10.518	0.024	0.024	0.000	0.000	0.000	0.000
77	A	79	ASP	-1	-0.884	-0.955	8.379	0.156	0.156	0.000	0.000	0.000	0.000
78	A	80	GLY	0	0.016	0.027	7.496	-0.032	-0.032	0.000	0.000	0.000	0.000
79	A	81	ILE	0	-0.137	-0.094	8.378	-0.106	-0.106	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.934	-0.938	6.062	-0.158	-0.158	0.000	0.000	0.000	0.000
81	A	83	GLY	0	0.003	-0.006	4.253	-0.305	-0.048	0.011	-0.066	-0.203	0.000
82	A	84	PHE	0	0.002	0.001	4.934	-0.335	-0.136	0.000	-0.037	-0.162	0.000
83	A	85	LEU	0	-0.003	0.003	7.733	-0.168	-0.168	0.000	0.000	0.000	0.000
84	A	86	GLY	0	0.016	0.016	10.555	0.015	0.015	0.000	0.000	0.000	0.000
85	A	87	LEU	0	-0.055	-0.033	13.523	-0.003	-0.003	0.000	0.000	0.000	0.000
86	A	88	THR	0	-0.015	-0.003	16.959	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	89	TRP	0	0.013	0.003	19.598	0.007	0.007	0.000	0.000	0.000	0.000
88	A	90	ASN	0	-0.022	-0.017	23.027	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	91	GLN	0	-0.047	-0.040	25.227	0.000	0.000	0.000	0.000	0.000	0.000
90	A	92	GLU	-1	-0.785	-0.869	22.495	-0.020	-0.020	0.000	0.000	0.000	0.000
91	A	93	LEU	0	-0.003	-0.001	20.256	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	94	ALA	0	0.011	0.013	23.708	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.031	0.020	25.561	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	96	THR	0	-0.023	-0.001	19.353	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	97	ILE	0	-0.051	-0.033	22.495	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	98	ASP	-1	-0.896	-0.946	23.842	-0.026	-0.026	0.000	0.000	0.000	0.000
97	A	99	ARG	1	0.930	0.981	22.044	0.042	0.042	0.000	0.000	0.000	0.000
98	A	100	LEU	0	-0.007	-0.009	18.590	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.907	-0.963	22.673	-0.011	-0.011	0.000	0.000	0.000	0.000
100	A	102	SER	0	-0.027	-0.020	25.776	0.002	0.002	0.000	0.000	0.000	0.000
101	A	103	LEU	0	-0.053	-0.006	21.289	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	104	ASP	-1	-0.805	-0.889	25.768	-0.039	-0.039	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.875	0.906	24.200	0.030	0.030	0.000	0.000	0.000	0.000
104	A	106	ASN	0	-0.018	-0.008	25.824	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.967	-0.970	26.964	-0.067	-0.067	0.000	0.000	0.000	0.000
106	A	108	LEU	0	0.040	0.009	21.132	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	109	ARG	1	0.781	0.891	23.056	0.072	0.072	0.000	0.000	0.000	0.000
108	A	110	LYS	1	0.886	0.938	24.684	0.057	0.057	0.000	0.000	0.000	0.000
109	A	111	GLN	0	0.032	0.014	23.156	-0.009	-0.009	0.000	0.000	0.000	0.000
110	A	112	PHE	0	-0.055	-0.006	16.835	-0.011	-0.011	0.000	0.000	0.000	0.000
111	A	113	SER	0	0.005	-0.005	20.381	0.005	0.005	0.000	0.000	0.000	0.000
112	A	114	ILE	0	0.007	-0.016	17.547	-0.019	-0.019	0.000	0.000	0.000	0.000
113	A	115	LYS	1	0.889	0.948	18.641	0.093	0.093	0.000	0.000	0.000	0.000
114	A	116	ARG	1	0.917	0.967	17.996	0.176	0.176	0.000	0.000	0.000	0.000
115	A	117	LEU	0	0.008	0.020	13.592	-0.015	-0.015	0.000	0.000	0.000	0.000
116	A	118	ASN	0	-0.003	-0.022	14.161	-0.066	-0.066	0.000	0.000	0.000	0.000
117	A	119	GLU	-1	-0.994	-0.994	15.170	-0.306	-0.306	0.000	0.000	0.000	0.000
118	A	120	MET	0	-0.019	0.000	13.392	0.001	0.001	0.000	0.000	0.000	0.000
119	A	121	GLU	-1	-0.978	-0.970	10.401	-0.619	-0.619	0.000	0.000	0.000	0.000
120	A	122	ILE	0	-0.036	0.004	9.256	-0.112	-0.112	0.000	0.000	0.000	0.000
121	A	123	TYR	0	0.065	0.045	2.275	-4.308	-5.027	9.765	-2.658	-6.388	-0.024
122	A	124	PRO	0	-0.092	-0.084	5.530	0.187	0.187	0.000	0.000	0.000	0.000
123	A	125	GLY	0	0.039	0.010	6.600	-0.033	-0.033	0.000	0.000	0.000	0.000
124	A	126	VAL	0	-0.070	-0.013	9.173	0.111	0.111	0.000	0.000	0.000	0.000
125	A	127	THR	0	-0.005	-0.005	12.042	0.013	0.013	0.000	0.000	0.000	0.000
126	A	128	PHE	0	-0.050	-0.026	12.793	0.041	0.041	0.000	0.000	0.000	0.000
127	A	129	SER	0	0.035	0.013	17.834	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	130	GLU	-1	-0.852	-0.959	21.267	-0.124	-0.124	0.000	0.000	0.000	0.000
129	A	131	GLU	-1	-0.935	-0.976	23.124	-0.060	-0.060	0.000	0.000	0.000	0.000
130	A	132	LEU	0	-0.039	-0.018	19.093	0.011	0.011	0.000	0.000	0.000	0.000
131	A	133	GLU	-1	-0.785	-0.844	20.914	-0.111	-0.111	0.000	0.000	0.000	0.000
132	A	134	GLY	0	-0.001	-0.009	21.406	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	135	GLN	0	0.001	-0.008	21.152	0.000	0.000	0.000	0.000	0.000	0.000
134	A	136	LEU	0	0.018	0.026	14.523	0.013	0.013	0.000	0.000	0.000	0.000
135	A	137	PHE	0	0.056	0.017	17.784	0.000	0.000	0.000	0.000	0.000	0.000
136	A	138	ALA	0	-0.004	-0.013	19.602	0.004	0.004	0.000	0.000	0.000	0.000
137	A	139	SER	0	-0.048	-0.028	15.911	0.015	0.015	0.000	0.000	0.000	0.000
138	A	140	ILE	0	0.047	0.028	14.432	0.006	0.006	0.000	0.000	0.000	0.000
139	A	141	MET	0	-0.014	-0.004	16.480	0.008	0.008	0.000	0.000	0.000	0.000
140	A	142	LEU	0	-0.018	0.007	18.505	0.013	0.013	0.000	0.000	0.000	0.000
141	A	143	ASP	-1	-0.767	-0.885	13.269	-0.031	-0.031	0.000	0.000	0.000	0.000
142	A	144	MET	0	-0.005	0.004	16.023	0.001	0.001	0.000	0.000	0.000	0.000
143	A	145	GLU	-1	-0.868	-0.936	17.648	-0.009	-0.009	0.000	0.000	0.000	0.000
144	A	146	LYS	1	0.875	0.941	16.831	-0.058	-0.058	0.000	0.000	0.000	0.000
145	A	147	LEU	0	0.009	0.009	14.445	0.013	0.013	0.000	0.000	0.000	0.000
146	A	148	ILE	0	0.039	0.027	17.319	0.008	0.008	0.000	0.000	0.000	0.000
147	A	149	SER	0	-0.049	-0.032	20.846	0.007	0.007	0.000	0.000	0.000	0.000
148	A	150	ALA	0	-0.069	-0.029	18.096	0.008	0.008	0.000	0.000	0.000	0.000
149	A	151	TYR	0	0.047	-0.001	15.859	0.009	0.009	0.000	0.000	0.000	0.000
150	A	152	ARG	1	0.899	0.949	21.002	0.002	0.002	0.000	0.000	0.000	0.000
151	A	153	ARG	1	0.755	0.850	19.275	-0.050	-0.050	0.000	0.000	0.000	0.000
152	A	154	MET	0	-0.043	0.062	18.322	0.000	0.000	0.000	0.000	0.000	0.000
153	A	155	LEU	0	0.016	0.013	23.417	0.001	0.001	0.000	0.000	0.000	0.000
154	A	156	ARG	1	0.914	0.963	25.865	-0.030	-0.030	0.000	0.000	0.000	0.000
155	A	157	GLN	0	-0.085	-0.048	26.148	0.000	0.000	0.000	0.000	0.000	0.000
156	A	158	GLY	0	0.006	0.017	27.832	0.002	0.002	0.000	0.000	0.000	0.000
157	A	159	ASN	0	-0.098	-0.057	22.940	-0.001	-0.001	0.000	0.000	0.000	0.000
158	A	160	HIS	0	0.072	0.015	21.219	-0.010	-0.010	0.000	0.000	0.000	0.000
159	A	161	ALA	0	0.009	-0.027	17.033	0.007	0.007	0.000	0.000	0.000	0.000
160	A	162	LEU	0	0.049	0.013	13.939	-0.001	-0.001	0.000	0.000	0.000	0.000
161	A	163	THR	0	-0.033	-0.014	9.358	0.005	0.005	0.000	0.000	0.000	0.000
162	A	164	VAL	0	-0.022	-0.011	7.473	0.037	0.037	0.000	0.000	0.000	0.000
163	A	165	ILE	0	-0.002	-0.002	3.260	-0.892	-0.171	0.117	-0.191	-0.648	-0.001
164	A	166	VAL	0	0.043	0.043	2.460	-2.966	-0.383	2.219	-1.858	-2.945	-0.019

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