FMO DATABASE

FMODB ID: VRGM1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1713905.565861
FMO2-HF: Nuclear repulsion	1647815.153208
FMO2-HF: Total energy	-66090.412653
FMO2-MP2: Total energy	-66282.754026

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.
-13.785	-5.194	12.605	-6.945	-14.25	-0.043

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 : -0.020 / q_NPA : -0.008

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	0.036	0.012	3.792	-2.175	-0.352	-0.024	-0.849	-0.950	0.005
4	A	6	TYR	0	-0.039	-0.035	6.256	0.202	0.202	0.000	0.000	0.000	0.000
5	A	7	PHE	0	0.000	0.000	9.828	-0.015	-0.015	0.000	0.000	0.000	0.000
6	A	8	ALA	0	-0.010	-0.013	12.877	0.024	0.024	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.795	-0.876	15.086	0.041	0.041	0.000	0.000	0.000	0.000
8	A	10	ILE	0	0.020	0.012	18.202	0.014	0.014	0.000	0.000	0.000	0.000
9	A	11	ASP	-1	-0.753	-0.854	20.400	0.066	0.066	0.000	0.000	0.000	0.000
10	A	12	SER	0	0.030	-0.015	23.658	0.002	0.002	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.863	-0.895	25.790	0.075	0.075	0.000	0.000	0.000	0.000
12	A	14	LYS	1	0.825	0.870	21.436	-0.086	-0.086	0.000	0.000	0.000	0.000
13	A	15	ILE	0	0.002	0.014	18.900	0.006	0.006	0.000	0.000	0.000	0.000
14	A	16	ASN	0	-0.053	-0.035	21.891	-0.001	-0.001	0.000	0.000	0.000	0.000
15	A	17	GLN	0	0.031	0.035	22.255	0.004	0.004	0.000	0.000	0.000	0.000
16	A	18	LEU	0	0.018	0.005	16.472	0.002	0.002	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.045	-0.046	19.568	0.002	0.002	0.000	0.000	0.000	0.000
18	A	20	GLU	-1	-0.979	-0.984	21.642	0.056	0.056	0.000	0.000	0.000	0.000
19	A	21	SER	0	-0.071	-0.020	20.745	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	22	THR	0	-0.032	-0.039	18.501	-0.011	-0.011	0.000	0.000	0.000	0.000
21	A	23	GLU	-1	-0.789	-0.868	14.540	0.161	0.161	0.000	0.000	0.000	0.000
22	A	24	LYS	1	0.753	0.874	17.184	-0.083	-0.083	0.000	0.000	0.000	0.000
23	A	25	PRO	0	-0.016	-0.016	14.897	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	26	LEU	0	0.018	-0.004	12.258	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	27	MET	0	0.035	0.036	7.895	0.034	0.034	0.000	0.000	0.000	0.000
26	A	28	ASP	-1	-0.911	-0.946	10.693	0.265	0.265	0.000	0.000	0.000	0.000
27	A	29	ASN	0	-0.071	-0.040	11.099	0.008	0.008	0.000	0.000	0.000	0.000
28	A	30	ILE	0	0.059	0.034	9.420	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	31	HIS	0	-0.084	-0.045	6.938	0.118	0.118	0.000	0.000	0.000	0.000
30	A	32	ASP	-1	-0.912	-0.981	11.472	0.271	0.271	0.000	0.000	0.000	0.000
31	A	33	THR	0	0.034	0.015	15.215	-0.014	-0.014	0.000	0.000	0.000	0.000
32	A	34	LEU	0	-0.008	-0.005	12.095	-0.022	-0.022	0.000	0.000	0.000	0.000
33	A	35	SER	0	-0.049	0.011	14.485	0.005	0.005	0.000	0.000	0.000	0.000
34	A	36	GLY	0	0.008	0.012	15.383	0.004	0.004	0.000	0.000	0.000	0.000
35	A	37	LEU	0	-0.047	-0.010	16.197	-0.020	-0.020	0.000	0.000	0.000	0.000
36	A	38	ARG	1	0.953	0.975	16.484	-0.065	-0.065	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.882	0.941	11.560	-0.276	-0.276	0.000	0.000	0.000	0.000
38	A	40	LEU	0	-0.092	-0.008	13.863	0.023	0.023	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.825	-0.931	9.468	0.388	0.388	0.000	0.000	0.000	0.000
40	A	42	ILE	0	-0.061	-0.035	9.146	0.039	0.039	0.000	0.000	0.000	0.000
41	A	43	ASP	-1	-0.805	-0.886	7.403	0.999	0.999	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.854	0.908	3.404	-2.905	-2.354	0.014	-0.222	-0.342	0.000
43	A	45	ARG	1	0.844	0.902	6.170	-0.135	-0.135	0.000	0.000	0.000	0.000
44	A	46	TRP	0	0.004	-0.018	2.505	-1.363	0.679	1.103	-0.953	-2.193	0.000
45	A	47	ASP	-1	-0.696	-0.810	6.467	-0.770	-0.770	0.000	0.000	0.000	0.000
46	A	48	PHE	0	-0.002	0.003	8.542	0.134	0.134	0.000	0.000	0.000	0.000
47	A	49	LEU	0	-0.016	-0.008	11.392	0.084	0.084	0.000	0.000	0.000	0.000
48	A	50	HIS	0	0.034	0.035	10.794	0.106	0.106	0.000	0.000	0.000	0.000
49	A	51	PHE	0	0.014	0.011	12.139	0.065	0.065	0.000	0.000	0.000	0.000
50	A	52	GLY	0	-0.054	-0.031	13.839	0.044	0.044	0.000	0.000	0.000	0.000
51	A	53	LEU	0	-0.050	-0.034	16.172	0.036	0.036	0.000	0.000	0.000	0.000
52	A	54	THR	0	-0.018	-0.004	14.983	0.014	0.014	0.000	0.000	0.000	0.000
53	A	55	GLY	0	-0.038	-0.003	16.780	0.014	0.014	0.000	0.000	0.000	0.000
54	A	56	THR	0	0.009	-0.011	14.393	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	57	SER	0	0.058	0.010	8.250	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	58	ALA	0	-0.016	-0.024	7.851	0.068	0.068	0.000	0.000	0.000	0.000
57	A	59	PHE	0	-0.026	-0.031	2.274	-0.965	-0.431	1.319	-0.383	-1.469	-0.004
58	A	60	ASP	-1	-0.985	-0.981	8.257	-0.281	-0.281	0.000	0.000	0.000	0.000
59	A	61	PRO	0	-0.003	0.028	11.700	0.013	0.013	0.000	0.000	0.000	0.000
60	A	62	ALA	0	0.022	0.013	14.413	0.020	0.020	0.000	0.000	0.000	0.000
61	A	63	LYS	1	0.949	0.947	18.125	0.126	0.126	0.000	0.000	0.000	0.000
62	A	64	ASN	0	-0.069	-0.040	20.016	0.005	0.005	0.000	0.000	0.000	0.000
63	A	65	ASP	-1	-0.717	-0.855	18.215	-0.149	-0.149	0.000	0.000	0.000	0.000
64	A	66	PRO	0	-0.026	-0.033	19.119	0.000	0.000	0.000	0.000	0.000	0.000
65	A	67	LEU	0	0.022	0.005	19.149	0.010	0.010	0.000	0.000	0.000	0.000
66	A	68	SER	0	-0.008	-0.010	14.120	0.003	0.003	0.000	0.000	0.000	0.000
67	A	69	ARG	1	0.829	0.896	14.691	0.056	0.056	0.000	0.000	0.000	0.000
68	A	70	ALA	0	-0.030	0.002	16.589	0.013	0.013	0.000	0.000	0.000	0.000
69	A	71	VAL	0	-0.029	-0.003	11.108	0.010	0.010	0.000	0.000	0.000	0.000
70	A	72	LEU	0	0.032	0.005	9.455	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	73	GLY	0	0.026	0.026	12.309	0.035	0.035	0.000	0.000	0.000	0.000
72	A	74	GLU	-1	-0.869	-0.936	15.415	-0.048	-0.048	0.000	0.000	0.000	0.000
73	A	75	HIS	1	0.742	0.845	17.663	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	76	SER	0	0.081	0.054	13.037	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	77	LEU	0	-0.084	-0.051	14.541	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	78	GLU	-1	-0.824	-0.938	10.977	0.232	0.232	0.000	0.000	0.000	0.000
77	A	79	ASP	-1	-0.897	-0.953	8.510	0.238	0.238	0.000	0.000	0.000	0.000
78	A	80	GLY	0	0.007	-0.007	7.371	0.001	0.001	0.000	0.000	0.000	0.000
79	A	81	ILE	0	-0.126	-0.075	8.310	-0.177	-0.177	0.000	0.000	0.000	0.000
80	A	82	ASP	-1	-0.952	-0.951	5.693	0.664	0.742	-0.001	-0.006	-0.070	0.000
81	A	83	GLY	0	0.020	0.005	4.424	-0.291	-0.070	0.006	-0.060	-0.168	0.000
82	A	84	PHE	0	0.024	0.010	5.254	-0.420	-0.279	-0.001	-0.025	-0.115	0.000
83	A	85	LEU	0	-0.001	-0.002	8.037	-0.121	-0.121	0.000	0.000	0.000	0.000
84	A	86	GLY	0	0.015	0.018	10.886	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	87	LEU	0	-0.057	-0.033	13.455	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	88	THR	0	-0.029	-0.009	16.836	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	89	TRP	0	0.024	0.010	19.439	0.007	0.007	0.000	0.000	0.000	0.000
88	A	90	ASN	0	-0.017	-0.009	22.843	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	91	GLN	0	-0.050	-0.043	25.085	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	92	GLU	-1	-0.818	-0.888	22.515	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	93	LEU	0	0.005	0.004	20.101	-0.007	-0.007	0.000	0.000	0.000	0.000
92	A	94	ALA	0	0.008	0.010	23.660	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	95	ALA	0	0.024	0.016	25.574	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	96	THR	0	0.007	0.009	19.343	-0.007	-0.007	0.000	0.000	0.000	0.000
95	A	97	ILE	0	-0.040	-0.025	22.582	-0.008	-0.008	0.000	0.000	0.000	0.000
96	A	98	ASP	-1	-0.931	-0.959	23.923	-0.040	-0.040	0.000	0.000	0.000	0.000
97	A	99	ARG	1	0.910	0.966	22.012	0.049	0.049	0.000	0.000	0.000	0.000
98	A	100	LEU	0	-0.001	-0.002	18.704	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	101	GLU	-1	-0.840	-0.917	22.848	-0.029	-0.029	0.000	0.000	0.000	0.000
100	A	102	SER	0	-0.023	-0.011	25.970	0.002	0.002	0.000	0.000	0.000	0.000
101	A	103	LEU	0	-0.060	-0.009	21.551	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	104	ASP	-1	-0.759	-0.874	26.016	-0.067	-0.067	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.815	0.875	24.198	0.059	0.059	0.000	0.000	0.000	0.000
104	A	106	ASN	0	-0.080	-0.047	26.103	-0.009	-0.009	0.000	0.000	0.000	0.000
105	A	107	GLU	-1	-0.929	-0.956	26.691	-0.101	-0.101	0.000	0.000	0.000	0.000
106	A	108	LEU	0	0.032	0.009	21.325	-0.009	-0.009	0.000	0.000	0.000	0.000
107	A	109	ARG	1	0.777	0.873	22.839	0.120	0.120	0.000	0.000	0.000	0.000
108	A	110	LYS	1	0.879	0.935	24.478	0.088	0.088	0.000	0.000	0.000	0.000
109	A	111	GLN	0	0.008	0.004	22.567	-0.009	-0.009	0.000	0.000	0.000	0.000
110	A	112	PHE	0	-0.036	0.001	16.403	-0.014	-0.014	0.000	0.000	0.000	0.000
111	A	113	SER	0	-0.004	-0.012	19.724	0.012	0.012	0.000	0.000	0.000	0.000
112	A	114	ILE	0	0.011	-0.001	17.169	-0.026	-0.026	0.000	0.000	0.000	0.000
113	A	115	LYS	1	0.792	0.879	18.134	0.141	0.141	0.000	0.000	0.000	0.000
114	A	116	ARG	1	0.907	0.949	17.837	0.247	0.247	0.000	0.000	0.000	0.000
115	A	117	LEU	0	-0.008	0.016	12.899	-0.019	-0.019	0.000	0.000	0.000	0.000
116	A	118	ASN	0	-0.008	-0.027	13.770	-0.088	-0.088	0.000	0.000	0.000	0.000
117	A	119	GLU	-1	-0.990	-0.990	15.003	-0.355	-0.355	0.000	0.000	0.000	0.000
118	A	120	MET	0	-0.020	-0.008	13.431	0.006	0.006	0.000	0.000	0.000	0.000
119	A	121	GLU	-1	-0.981	-0.972	10.519	-0.713	-0.713	0.000	0.000	0.000	0.000
120	A	122	ILE	0	-0.037	0.002	9.220	-0.141	-0.141	0.000	0.000	0.000	0.000
121	A	123	TYR	0	0.056	0.039	2.095	-3.882	-3.807	8.120	-2.331	-5.865	-0.023
122	A	124	PRO	0	-0.097	-0.085	5.351	0.266	0.266	0.000	0.000	0.000	0.000
123	A	125	GLY	0	0.034	0.009	6.407	0.004	0.004	0.000	0.000	0.000	0.000
124	A	126	VAL	0	-0.070	-0.016	9.015	0.150	0.150	0.000	0.000	0.000	0.000
125	A	127	THR	0	-0.016	-0.008	11.979	0.016	0.016	0.000	0.000	0.000	0.000
126	A	128	PHE	0	-0.031	-0.020	12.607	0.051	0.051	0.000	0.000	0.000	0.000
127	A	129	SER	0	0.036	0.017	17.565	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	130	GLU	-1	-0.760	-0.883	20.938	-0.179	-0.179	0.000	0.000	0.000	0.000
129	A	131	GLU	-1	-0.910	-0.970	22.730	-0.122	-0.122	0.000	0.000	0.000	0.000
130	A	132	LEU	0	-0.040	-0.018	19.128	0.013	0.013	0.000	0.000	0.000	0.000
131	A	133	GLU	-1	-0.767	-0.838	20.668	-0.171	-0.171	0.000	0.000	0.000	0.000
132	A	134	GLY	0	-0.003	-0.006	21.254	-0.003	-0.003	0.000	0.000	0.000	0.000
133	A	135	GLN	0	-0.005	-0.012	21.210	0.000	0.000	0.000	0.000	0.000	0.000
134	A	136	LEU	0	0.030	0.026	14.382	0.014	0.014	0.000	0.000	0.000	0.000
135	A	137	PHE	0	0.051	0.019	17.843	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	138	ALA	0	-0.001	-0.011	19.860	0.005	0.005	0.000	0.000	0.000	0.000
137	A	139	SER	0	-0.014	-0.015	16.229	0.021	0.021	0.000	0.000	0.000	0.000
138	A	140	ILE	0	-0.013	0.004	14.633	0.008	0.008	0.000	0.000	0.000	0.000
139	A	141	MET	0	-0.006	0.007	16.855	0.015	0.015	0.000	0.000	0.000	0.000
140	A	142	LEU	0	-0.013	0.006	19.000	0.019	0.019	0.000	0.000	0.000	0.000
141	A	143	ASP	-1	-0.765	-0.865	13.844	-0.081	-0.081	0.000	0.000	0.000	0.000
142	A	144	MET	0	0.025	0.024	16.339	0.007	0.007	0.000	0.000	0.000	0.000
143	A	145	GLU	-1	-0.817	-0.901	17.922	-0.040	-0.040	0.000	0.000	0.000	0.000
144	A	146	LYS	1	0.815	0.912	16.390	0.023	0.023	0.000	0.000	0.000	0.000
145	A	147	LEU	0	0.000	0.000	14.467	0.019	0.019	0.000	0.000	0.000	0.000
146	A	148	ILE	0	0.035	0.028	17.474	0.014	0.014	0.000	0.000	0.000	0.000
147	A	149	SER	0	-0.064	-0.043	20.994	0.012	0.012	0.000	0.000	0.000	0.000
148	A	150	ALA	0	-0.070	-0.036	18.137	0.012	0.012	0.000	0.000	0.000	0.000
149	A	151	TYR	0	0.039	-0.012	15.951	0.016	0.016	0.000	0.000	0.000	0.000
150	A	152	ARG	1	0.859	0.914	21.026	0.019	0.019	0.000	0.000	0.000	0.000
151	A	153	ARG	1	0.736	0.860	19.444	-0.047	-0.047	0.000	0.000	0.000	0.000
152	A	154	MET	0	-0.008	0.010	17.653	0.003	0.003	0.000	0.000	0.000	0.000
153	A	155	LEU	0	0.018	0.018	23.355	0.002	0.002	0.000	0.000	0.000	0.000
154	A	156	ARG	1	0.908	0.952	25.809	-0.025	-0.025	0.000	0.000	0.000	0.000
155	A	157	GLN	0	-0.070	-0.035	26.070	-0.002	-0.002	0.000	0.000	0.000	0.000
156	A	158	GLY	0	0.005	0.015	27.728	0.003	0.003	0.000	0.000	0.000	0.000
157	A	159	ASN	0	-0.096	-0.053	22.920	0.002	0.002	0.000	0.000	0.000	0.000
158	A	160	HIS	0	0.055	0.011	21.065	-0.013	-0.013	0.000	0.000	0.000	0.000
159	A	161	ALA	0	0.009	-0.017	16.968	0.008	0.008	0.000	0.000	0.000	0.000
160	A	162	LEU	0	0.032	0.014	13.929	-0.001	-0.001	0.000	0.000	0.000	0.000
161	A	163	THR	0	-0.038	-0.016	9.224	0.004	0.004	0.000	0.000	0.000	0.000
162	A	164	VAL	0	-0.016	-0.013	7.617	0.049	0.049	0.000	0.000	0.000	0.000
163	A	165	ILE	0	-0.002	-0.002	3.113	-0.776	-0.203	0.084	-0.171	-0.486	-0.001
164	A	166	VAL	0	0.042	0.048	2.533	-2.599	-0.046	1.985	-1.945	-2.592	-0.020

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