FMO DATABASE

FMODB ID: 2J6GR

Calculation Name: 1Y0O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y0O

Chain ID: A

ChEMBL ID:

UniProt ID: Q9SCY2

Base Structure: X-ray

Registration Date: 2023-09-20

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	125
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-972728.197638
FMO2-HF: Nuclear repulsion	926382.782779
FMO2-HF: Total energy	-46345.414859
FMO2-MP2: Total energy	-46479.79678

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:5:CYS)

Summations of interaction energy for fragment #1(A:5:CYS)

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.
-5.225	-1.401	7	-3.587	-7.238	-0.009

Interaction energy analysis for fragmet #1(A:5:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.018

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

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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	7	PHE	0	-0.058	-0.041	2.949	-0.973	1.592	1.034	-1.334	-2.266	-0.005
4	A	8	SER	0	0.031	0.035	5.135	0.587	0.638	-0.001	-0.003	-0.047	0.000
5	A	9	VAL	0	-0.012	-0.028	8.436	0.043	0.043	0.000	0.000	0.000	0.000
6	A	10	SER	0	0.003	0.007	10.809	0.137	0.137	0.000	0.000	0.000	0.000
7	A	11	PRO	0	0.023	-0.006	14.060	-0.054	-0.054	0.000	0.000	0.000	0.000
8	A	12	SER	0	-0.022	-0.003	15.644	0.031	0.031	0.000	0.000	0.000	0.000
9	A	13	GLY	0	0.017	0.003	13.736	0.035	0.035	0.000	0.000	0.000	0.000
10	A	14	LEU	0	-0.073	-0.027	11.521	-0.115	-0.115	0.000	0.000	0.000	0.000
11	A	15	ALA	0	0.029	0.030	7.655	-0.060	-0.060	0.000	0.000	0.000	0.000
12	A	16	PHE	0	-0.028	-0.021	6.534	0.233	0.233	0.000	0.000	0.000	0.000
13	A	17	CYS	0	0.015	-0.001	3.130	0.557	-0.076	3.780	-1.163	-1.984	-0.004
14	A	18	ASP	-1	-0.813	-0.900	5.165	2.077	2.222	-0.001	-0.025	-0.119	0.000
15	A	19	LYS	1	0.781	0.884	2.894	-8.941	-8.429	1.311	-0.491	-1.332	0.001
16	A	20	VAL	0	-0.017	-0.003	6.695	-0.318	-0.318	0.000	0.000	0.000	0.000
17	A	21	VAL	0	0.060	0.035	10.457	-0.104	-0.104	0.000	0.000	0.000	0.000
18	A	22	GLY	0	0.001	0.002	12.531	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	23	TYR	0	-0.004	0.000	15.770	-0.079	-0.079	0.000	0.000	0.000	0.000
20	A	24	GLY	0	0.009	0.001	19.188	-0.056	-0.056	0.000	0.000	0.000	0.000
21	A	25	PRO	0	-0.007	-0.016	20.320	0.009	0.009	0.000	0.000	0.000	0.000
22	A	26	GLU	-1	-0.864	-0.913	19.343	0.211	0.211	0.000	0.000	0.000	0.000
23	A	27	ALA	0	-0.047	-0.004	18.811	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	28	VAL	0	0.019	-0.002	20.545	-0.032	-0.032	0.000	0.000	0.000	0.000
25	A	29	LYS	1	0.932	0.944	23.659	-0.049	-0.049	0.000	0.000	0.000	0.000
26	A	30	GLY	0	0.000	0.007	25.114	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	31	GLN	0	-0.027	-0.006	24.123	0.019	0.019	0.000	0.000	0.000	0.000
28	A	32	LEU	0	-0.005	0.001	24.996	0.006	0.006	0.000	0.000	0.000	0.000
29	A	33	ILE	0	-0.013	-0.004	19.176	0.004	0.004	0.000	0.000	0.000	0.000
30	A	34	LYS	1	0.896	0.945	21.496	-0.332	-0.332	0.000	0.000	0.000	0.000
31	A	35	ALA	0	0.023	0.010	16.179	0.032	0.032	0.000	0.000	0.000	0.000
32	A	36	HIS	0	0.051	0.048	15.978	-0.070	-0.070	0.000	0.000	0.000	0.000
33	A	37	TYR	0	-0.033	-0.058	13.100	0.068	0.068	0.000	0.000	0.000	0.000
34	A	38	VAL	0	-0.015	-0.018	11.534	-0.120	-0.120	0.000	0.000	0.000	0.000
35	A	39	GLY	0	0.016	0.018	11.292	0.177	0.177	0.000	0.000	0.000	0.000
36	A	40	LYS	1	0.923	0.955	9.733	-1.090	-1.090	0.000	0.000	0.000	0.000
37	A	41	LEU	0	0.038	0.019	12.171	-0.063	-0.063	0.000	0.000	0.000	0.000
38	A	42	GLU	-1	-0.755	-0.860	10.014	-0.748	-0.748	0.000	0.000	0.000	0.000
39	A	43	ASN	0	-0.001	0.004	11.334	-0.031	-0.031	0.000	0.000	0.000	0.000
40	A	44	GLY	0	0.017	0.012	11.143	0.035	0.035	0.000	0.000	0.000	0.000
41	A	45	LYS	1	0.855	0.941	12.074	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	46	VAL	0	0.011	-0.003	13.948	0.007	0.007	0.000	0.000	0.000	0.000
43	A	47	PHE	0	-0.019	-0.015	14.158	-0.062	-0.062	0.000	0.000	0.000	0.000
44	A	48	ASP	-1	-0.790	-0.867	16.574	0.330	0.330	0.000	0.000	0.000	0.000
45	A	49	SER	0	0.007	0.001	15.893	0.091	0.091	0.000	0.000	0.000	0.000
46	A	50	SER	0	0.015	0.016	17.134	-0.038	-0.038	0.000	0.000	0.000	0.000
47	A	51	TYR	0	-0.049	-0.052	14.999	-0.096	-0.096	0.000	0.000	0.000	0.000
48	A	52	ASN	0	-0.031	-0.010	19.437	-0.054	-0.054	0.000	0.000	0.000	0.000
49	A	53	ARG	1	0.845	0.917	20.718	-0.351	-0.351	0.000	0.000	0.000	0.000
50	A	54	GLY	0	0.010	0.017	23.017	-0.028	-0.028	0.000	0.000	0.000	0.000
51	A	55	LYS	1	0.912	0.954	22.890	-0.275	-0.275	0.000	0.000	0.000	0.000
52	A	56	PRO	0	-0.004	-0.002	20.200	0.014	0.014	0.000	0.000	0.000	0.000
53	A	57	LEU	0	-0.005	0.011	19.557	-0.045	-0.045	0.000	0.000	0.000	0.000
54	A	58	THR	0	-0.060	-0.044	21.429	0.020	0.020	0.000	0.000	0.000	0.000
55	A	59	PHE	0	0.030	0.017	18.366	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	60	ARG	1	0.883	0.939	23.896	-0.137	-0.137	0.000	0.000	0.000	0.000
57	A	61	ILE	0	0.000	0.024	18.361	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	62	GLY	0	0.048	-0.005	21.965	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	63	VAL	0	-0.093	-0.057	23.274	-0.022	-0.022	0.000	0.000	0.000	0.000
60	A	64	GLY	0	0.018	0.024	23.817	-0.011	-0.011	0.000	0.000	0.000	0.000
61	A	65	GLU	-1	-0.868	-0.932	24.394	0.170	0.170	0.000	0.000	0.000	0.000
62	A	66	VAL	0	-0.054	-0.013	19.231	0.021	0.021	0.000	0.000	0.000	0.000
63	A	67	ILE	0	-0.019	0.003	15.628	-0.028	-0.028	0.000	0.000	0.000	0.000
64	A	68	LYS	1	0.904	0.946	18.615	0.130	0.130	0.000	0.000	0.000	0.000
65	A	69	GLY	0	0.052	0.018	14.869	0.000	0.000	0.000	0.000	0.000	0.000
66	A	70	TRP	0	-0.026	-0.021	14.024	0.062	0.062	0.000	0.000	0.000	0.000
67	A	71	ASP	-1	-0.753	-0.891	15.811	0.174	0.174	0.000	0.000	0.000	0.000
68	A	72	GLN	0	-0.012	-0.020	16.355	0.025	0.025	0.000	0.000	0.000	0.000
69	A	73	GLY	0	0.028	0.026	12.950	-0.029	-0.029	0.000	0.000	0.000	0.000
70	A	74	ILE	0	-0.035	-0.017	12.827	0.116	0.116	0.000	0.000	0.000	0.000
71	A	75	LEU	0	-0.023	-0.002	15.371	0.014	0.014	0.000	0.000	0.000	0.000
72	A	76	GLY	0	0.038	0.034	15.700	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	77	SER	0	-0.050	-0.043	16.756	-0.013	-0.013	0.000	0.000	0.000	0.000
74	A	78	ASP	-1	-0.869	-0.924	17.643	-0.185	-0.185	0.000	0.000	0.000	0.000
75	A	79	GLY	0	0.009	-0.009	15.628	-0.055	-0.055	0.000	0.000	0.000	0.000
76	A	80	ILE	0	-0.087	-0.038	12.043	-0.076	-0.076	0.000	0.000	0.000	0.000
77	A	81	PRO	0	0.052	0.038	13.015	0.042	0.042	0.000	0.000	0.000	0.000
78	A	82	PRO	0	0.052	0.039	14.495	0.047	0.047	0.000	0.000	0.000	0.000
79	A	83	MET	0	-0.056	-0.017	11.534	0.036	0.036	0.000	0.000	0.000	0.000
80	A	84	LEU	0	0.010	0.014	14.854	-0.062	-0.062	0.000	0.000	0.000	0.000
81	A	85	THR	0	-0.067	-0.070	16.168	0.086	0.086	0.000	0.000	0.000	0.000
82	A	86	GLY	0	0.010	-0.003	17.416	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	87	GLY	0	0.022	0.026	13.619	0.060	0.060	0.000	0.000	0.000	0.000
84	A	88	LYS	1	0.753	0.860	8.217	-2.207	-2.207	0.000	0.000	0.000	0.000
85	A	89	ARG	1	0.758	0.848	7.411	-0.298	-0.298	0.000	0.000	0.000	0.000
86	A	90	THR	0	-0.035	-0.037	3.263	0.462	1.464	0.879	-0.558	-1.323	-0.001
87	A	91	LEU	0	-0.041	-0.014	5.540	-0.878	-0.860	-0.001	-0.007	-0.010	0.000
88	A	92	ARG	1	0.861	0.893	6.350	1.571	1.571	0.000	0.000	0.000	0.000
89	A	93	ILE	0	-0.009	0.000	8.205	-0.094	-0.094	0.000	0.000	0.000	0.000
90	A	94	PRO	0	0.069	0.034	11.999	0.028	0.028	0.000	0.000	0.000	0.000
91	A	95	PRO	0	0.053	0.028	14.679	0.074	0.074	0.000	0.000	0.000	0.000
92	A	96	GLU	-1	-0.862	-0.936	17.736	-0.139	-0.139	0.000	0.000	0.000	0.000
93	A	97	LEU	0	0.010	0.012	15.349	0.036	0.036	0.000	0.000	0.000	0.000
94	A	98	ALA	0	0.006	-0.005	15.890	0.055	0.055	0.000	0.000	0.000	0.000
95	A	99	TYR	0	-0.034	-0.027	17.969	0.017	0.017	0.000	0.000	0.000	0.000
96	A	100	GLY	0	0.043	0.030	20.177	0.004	0.004	0.000	0.000	0.000	0.000
97	A	101	ASP	-1	-0.864	-0.939	21.926	-0.130	-0.130	0.000	0.000	0.000	0.000
98	A	102	ARG	1	0.894	0.950	23.335	0.004	0.004	0.000	0.000	0.000	0.000
99	A	103	GLY	0	0.025	0.024	22.104	0.010	0.010	0.000	0.000	0.000	0.000
100	A	104	ALA	0	-0.005	-0.029	21.538	0.011	0.011	0.000	0.000	0.000	0.000
101	A	105	GLY	0	0.011	0.002	23.416	0.007	0.007	0.000	0.000	0.000	0.000
102	A	106	CYS	0	-0.037	-0.017	25.310	0.001	0.001	0.000	0.000	0.000	0.000
103	A	107	LYS	1	0.956	0.975	27.877	-0.079	-0.079	0.000	0.000	0.000	0.000
104	A	108	GLY	0	0.068	0.047	30.994	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	109	GLY	0	0.024	0.014	30.216	0.001	0.001	0.000	0.000	0.000	0.000
106	A	110	SER	0	-0.014	-0.021	27.548	-0.009	-0.009	0.000	0.000	0.000	0.000
107	A	111	CYS	0	-0.058	-0.016	24.121	0.010	0.010	0.000	0.000	0.000	0.000
108	A	112	LEU	0	-0.021	0.001	21.150	-0.008	-0.008	0.000	0.000	0.000	0.000
109	A	113	ILE	0	-0.021	-0.009	17.737	0.018	0.018	0.000	0.000	0.000	0.000
110	A	114	PRO	0	0.043	0.018	19.433	-0.005	-0.005	0.000	0.000	0.000	0.000
111	A	115	PRO	0	0.031	0.020	20.843	-0.005	-0.005	0.000	0.000	0.000	0.000
112	A	116	ALA	0	-0.002	-0.002	20.505	-0.014	-0.014	0.000	0.000	0.000	0.000
113	A	117	SER	0	-0.039	-0.028	16.546	-0.044	-0.044	0.000	0.000	0.000	0.000
114	A	118	VAL	0	-0.011	0.004	11.209	0.029	0.029	0.000	0.000	0.000	0.000
115	A	119	LEU	0	-0.076	-0.034	12.429	0.066	0.066	0.000	0.000	0.000	0.000
116	A	120	LEU	0	0.022	0.020	6.071	-0.117	-0.117	0.000	0.000	0.000	0.000
117	A	121	PHE	0	0.006	-0.013	8.364	-0.054	-0.054	0.000	0.000	0.000	0.000
118	A	122	ASP	-1	-0.756	-0.839	5.887	4.972	5.136	-0.001	-0.006	-0.157	0.000
119	A	123	ILE	0	-0.003	-0.013	8.502	-0.394	-0.394	0.000	0.000	0.000	0.000
120	A	124	GLU	-1	-0.769	-0.860	10.858	1.489	1.489	0.000	0.000	0.000	0.000
121	A	125	TYR	0	0.013	0.010	13.480	-0.151	-0.151	0.000	0.000	0.000	0.000
122	A	126	ILE	0	-0.007	-0.010	16.063	-0.021	-0.021	0.000	0.000	0.000	0.000
123	A	127	GLY	0	0.063	0.039	19.035	-0.025	-0.025	0.000	0.000	0.000	0.000
124	A	128	LYS	1	0.974	0.992	21.377	-0.234	-0.234	0.000	0.000	0.000	0.000
125	A	129	ALA	0	-0.029	-0.017	24.530	0.011	0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:CYS)