FMO DATABASE

FMODB ID: 2JK6R

Calculation Name: 1Y12-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y12

Chain ID: A

ChEMBL ID:

UniProt ID: Q9I747

Base Structure: X-ray

Registration Date: 2023-06-21

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	161
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1407955.426514
FMO2-HF: Nuclear repulsion	1346445.231321
FMO2-HF: Total energy	-61510.195193
FMO2-MP2: Total energy	-61686.812684

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:ALA)

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

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.
-5.084	-2.852	0.511	-1.173	-1.568	0.004

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.017

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	ASP	-1	-0.810	-0.886	3.734	-5.012	-3.650	-0.003	-0.679	-0.679	0.002
4	A	5	MET	0	-0.071	-0.037	5.582	0.784	0.784	0.000	0.000	0.000	0.000
5	A	6	PHE	0	0.030	0.024	8.656	0.012	0.012	0.000	0.000	0.000	0.000
6	A	7	ILE	0	0.008	0.002	12.289	0.080	0.080	0.000	0.000	0.000	0.000
7	A	8	LYS	1	0.944	1.002	15.581	0.234	0.234	0.000	0.000	0.000	0.000
8	A	9	ILE	0	0.028	0.009	19.119	0.029	0.029	0.000	0.000	0.000	0.000
9	A	10	GLY	0	0.021	0.005	21.876	0.003	0.003	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.984	-0.993	24.438	-0.167	-0.167	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.062	-0.029	22.714	0.000	0.000	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.927	0.974	22.203	0.225	0.225	0.000	0.000	0.000	0.000
13	A	14	GLY	0	0.035	0.010	18.706	0.012	0.012	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.903	-0.959	17.918	-0.315	-0.315	0.000	0.000	0.000	0.000
15	A	16	SER	0	-0.041	0.007	13.002	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	17	LYS	1	0.955	0.956	14.170	0.578	0.578	0.000	0.000	0.000	0.000
17	A	18	ASP	-1	-0.774	-0.863	11.819	-0.839	-0.839	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.953	0.974	13.847	0.443	0.443	0.000	0.000	0.000	0.000
19	A	20	THR	0	-0.013	-0.015	15.222	0.030	0.030	0.000	0.000	0.000	0.000
20	A	21	HIS	1	0.767	0.868	14.018	0.537	0.537	0.000	0.000	0.000	0.000
21	A	22	ALA	0	0.029	0.021	16.208	-0.019	-0.019	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.986	-1.005	18.041	-0.226	-0.226	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.866	-0.920	16.079	-0.363	-0.363	0.000	0.000	0.000	0.000
24	A	25	ILE	0	-0.022	-0.026	14.787	-0.013	-0.013	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.843	-0.925	10.973	-0.896	-0.896	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.059	-0.034	9.794	0.101	0.101	0.000	0.000	0.000	0.000
27	A	28	LEU	0	-0.007	-0.014	8.033	-0.225	-0.225	0.000	0.000	0.000	0.000
28	A	29	ALA	0	0.000	-0.002	7.648	-0.043	-0.043	0.000	0.000	0.000	0.000
29	A	30	TRP	0	0.006	-0.006	9.643	0.060	0.060	0.000	0.000	0.000	0.000
30	A	31	SER	0	-0.017	-0.001	12.330	0.040	0.040	0.000	0.000	0.000	0.000
31	A	32	TRP	0	-0.004	-0.019	15.069	-0.016	-0.016	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.025	0.016	18.109	0.025	0.025	0.000	0.000	0.000	0.000
33	A	34	MET	0	-0.006	0.000	20.939	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	35	SER	0	0.006	0.018	24.478	0.013	0.013	0.000	0.000	0.000	0.000
35	A	36	GLN	0	0.041	0.010	27.363	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	37	SER	0	0.024	0.013	30.554	0.003	0.003	0.000	0.000	0.000	0.000
37	A	38	GLY	0	-0.028	0.002	33.907	0.000	0.000	0.000	0.000	0.000	0.000
38	A	39	SER	0	-0.015	-0.016	34.772	0.005	0.005	0.000	0.000	0.000	0.000
39	A	40	MET	0	0.010	-0.010	35.179	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	41	HIS	0	-0.019	-0.009	36.146	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	42	MET	0	-0.031	0.007	40.412	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	43	GLY	0	0.027	0.019	42.213	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	44	GLY	0	0.007	-0.002	43.927	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.007	0.020	43.656	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	46	GLY	0	-0.033	-0.034	40.913	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.103	0.054	40.560	-0.003	-0.003	0.000	0.000	0.000	0.000
47	A	48	ALA	0	-0.050	-0.030	38.519	0.002	0.002	0.000	0.000	0.000	0.000
48	A	49	GLY	0	0.000	0.003	36.452	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	50	LYS	1	0.947	0.966	34.564	0.002	0.002	0.000	0.000	0.000	0.000
50	A	51	VAL	0	0.009	0.006	27.943	0.004	0.004	0.000	0.000	0.000	0.000
51	A	52	ASN	0	-0.067	-0.028	28.356	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	53	VAL	0	0.017	-0.007	24.161	0.006	0.006	0.000	0.000	0.000	0.000
53	A	54	GLN	0	-0.015	0.000	21.471	0.008	0.008	0.000	0.000	0.000	0.000
54	A	55	ASP	-1	-0.725	-0.860	22.959	-0.088	-0.088	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.078	-0.025	15.892	0.006	0.006	0.000	0.000	0.000	0.000
56	A	57	SER	0	0.016	0.004	17.069	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	58	PHE	0	-0.017	-0.022	13.563	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	59	THR	0	0.013	0.004	12.067	0.039	0.039	0.000	0.000	0.000	0.000
59	A	60	LYS	1	0.789	0.890	12.457	0.241	0.241	0.000	0.000	0.000	0.000
60	A	61	TYR	0	0.074	0.019	10.233	0.051	0.051	0.000	0.000	0.000	0.000
61	A	62	ILE	0	-0.047	0.001	15.744	0.014	0.014	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.777	-0.863	18.124	-0.385	-0.385	0.000	0.000	0.000	0.000
63	A	64	LYS	1	0.917	0.944	20.485	0.295	0.295	0.000	0.000	0.000	0.000
64	A	65	SER	0	-0.077	-0.061	20.120	0.024	0.024	0.000	0.000	0.000	0.000
65	A	66	THR	0	-0.028	-0.050	21.337	0.011	0.011	0.000	0.000	0.000	0.000
66	A	67	PRO	0	0.027	0.005	23.313	0.016	0.016	0.000	0.000	0.000	0.000
67	A	68	ASN	0	-0.006	-0.001	25.635	0.025	0.025	0.000	0.000	0.000	0.000
68	A	69	LEU	0	0.012	0.009	20.609	0.013	0.013	0.000	0.000	0.000	0.000
69	A	70	MET	0	0.027	0.016	24.590	0.015	0.015	0.000	0.000	0.000	0.000
70	A	71	MET	0	0.009	0.020	27.563	0.016	0.016	0.000	0.000	0.000	0.000
71	A	72	ALA	0	-0.020	-0.004	27.201	0.010	0.010	0.000	0.000	0.000	0.000
72	A	73	CYS	0	-0.035	-0.012	27.014	0.010	0.010	0.000	0.000	0.000	0.000
73	A	74	SER	0	-0.034	-0.022	28.972	0.010	0.010	0.000	0.000	0.000	0.000
74	A	75	SER	0	-0.118	-0.070	32.385	0.008	0.008	0.000	0.000	0.000	0.000
75	A	76	GLY	0	0.036	0.027	31.966	0.007	0.007	0.000	0.000	0.000	0.000
76	A	77	LYS	1	0.892	0.948	32.320	0.092	0.092	0.000	0.000	0.000	0.000
77	A	78	HIS	0	-0.012	0.005	29.513	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	79	TYR	0	0.008	-0.002	25.981	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	80	PRO	0	0.040	0.017	28.379	0.005	0.005	0.000	0.000	0.000	0.000
80	A	81	GLN	0	-0.031	-0.032	23.391	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	82	ALA	0	0.026	0.028	20.511	-0.011	-0.011	0.000	0.000	0.000	0.000
82	A	83	LYS	1	0.926	0.966	17.727	0.213	0.213	0.000	0.000	0.000	0.000
83	A	84	LEU	0	0.037	0.032	11.982	-0.032	-0.032	0.000	0.000	0.000	0.000
84	A	85	THR	0	-0.023	-0.014	12.568	0.094	0.094	0.000	0.000	0.000	0.000
85	A	86	ILE	0	-0.001	0.005	7.960	-0.157	-0.157	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.801	0.882	8.643	1.305	1.305	0.000	0.000	0.000	0.000
87	A	88	LYS	1	0.857	0.923	6.644	-1.327	-1.327	0.000	0.000	0.000	0.000
88	A	89	ALA	0	0.073	0.032	2.691	-1.192	-0.484	0.515	-0.475	-0.748	0.002
89	A	90	GLY	0	0.016	0.012	4.416	0.765	0.927	-0.001	-0.019	-0.141	0.000
90	A	91	GLY	0	0.036	0.027	6.992	0.117	0.117	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.935	-0.988	9.549	-0.402	-0.402	0.000	0.000	0.000	0.000
92	A	93	ASN	0	-0.013	-0.006	12.705	0.047	0.047	0.000	0.000	0.000	0.000
93	A	94	GLN	0	-0.103	-0.035	7.861	0.096	0.096	0.000	0.000	0.000	0.000
94	A	95	VAL	0	-0.008	-0.010	11.395	-0.067	-0.067	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.842	-0.914	11.250	-0.379	-0.379	0.000	0.000	0.000	0.000
96	A	97	TYR	0	-0.029	-0.019	6.846	0.210	0.210	0.000	0.000	0.000	0.000
97	A	98	LEU	0	0.025	0.022	11.864	0.071	0.071	0.000	0.000	0.000	0.000
98	A	99	ILE	0	0.004	0.010	13.367	-0.092	-0.092	0.000	0.000	0.000	0.000
99	A	100	ILE	0	0.007	0.007	15.429	0.051	0.051	0.000	0.000	0.000	0.000
100	A	101	THR	0	-0.054	-0.027	18.031	-0.037	-0.037	0.000	0.000	0.000	0.000
101	A	102	LEU	0	0.003	0.007	19.919	0.023	0.023	0.000	0.000	0.000	0.000
102	A	103	LYS	1	0.939	0.951	23.265	0.069	0.069	0.000	0.000	0.000	0.000
103	A	104	GLU	-1	-0.950	-0.987	26.878	-0.071	-0.071	0.000	0.000	0.000	0.000
104	A	105	VAL	0	-0.024	-0.020	23.248	0.004	0.004	0.000	0.000	0.000	0.000
105	A	106	LEU	0	0.064	0.033	26.629	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	107	VAL	0	-0.008	-0.008	23.639	-0.007	-0.007	0.000	0.000	0.000	0.000
107	A	108	SER	0	-0.010	-0.001	24.964	0.002	0.002	0.000	0.000	0.000	0.000
108	A	109	SER	0	-0.022	-0.025	23.517	0.008	0.008	0.000	0.000	0.000	0.000
109	A	110	VAL	0	0.042	0.007	22.400	-0.016	-0.016	0.000	0.000	0.000	0.000
110	A	111	SER	0	-0.048	-0.013	21.678	0.021	0.021	0.000	0.000	0.000	0.000
111	A	112	THR	0	0.019	-0.016	21.041	-0.019	-0.019	0.000	0.000	0.000	0.000
112	A	113	GLY	0	-0.002	0.000	22.159	0.020	0.020	0.000	0.000	0.000	0.000
113	A	114	GLY	0	0.018	0.007	21.557	-0.022	-0.022	0.000	0.000	0.000	0.000
114	A	115	SER	0	-0.099	-0.039	19.446	0.023	0.023	0.000	0.000	0.000	0.000
115	A	116	GLY	0	0.013	0.008	22.319	0.017	0.017	0.000	0.000	0.000	0.000
116	A	117	GLY	0	-0.032	-0.027	21.670	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	118	GLU	-1	-0.865	-0.923	17.926	-0.260	-0.260	0.000	0.000	0.000	0.000
118	A	119	ASP	-1	-0.915	-0.958	16.363	-0.376	-0.376	0.000	0.000	0.000	0.000
119	A	120	ARG	1	0.888	0.942	12.735	0.581	0.581	0.000	0.000	0.000	0.000
120	A	121	LEU	0	0.055	0.032	16.729	-0.007	-0.007	0.000	0.000	0.000	0.000
121	A	122	THR	0	-0.030	-0.012	13.707	-0.031	-0.031	0.000	0.000	0.000	0.000
122	A	123	GLU	-1	-0.764	-0.840	16.727	-0.216	-0.216	0.000	0.000	0.000	0.000
123	A	124	ASN	0	0.001	0.010	16.293	-0.064	-0.064	0.000	0.000	0.000	0.000
124	A	125	VAL	0	0.014	0.006	17.877	0.025	0.025	0.000	0.000	0.000	0.000
125	A	126	THR	0	-0.031	-0.016	18.839	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	127	LEU	0	-0.036	-0.017	19.562	0.001	0.001	0.000	0.000	0.000	0.000
127	A	128	ASN	0	-0.009	-0.001	22.708	0.011	0.011	0.000	0.000	0.000	0.000
128	A	129	PHE	0	0.007	-0.005	22.122	-0.007	-0.007	0.000	0.000	0.000	0.000
129	A	130	ALA	0	0.003	0.015	26.783	0.010	0.010	0.000	0.000	0.000	0.000
130	A	131	GLN	0	-0.035	-0.025	27.679	0.011	0.011	0.000	0.000	0.000	0.000
131	A	132	VAL	0	0.013	0.015	21.754	-0.014	-0.014	0.000	0.000	0.000	0.000
132	A	133	GLN	0	-0.052	-0.041	22.516	0.013	0.013	0.000	0.000	0.000	0.000
133	A	134	VAL	0	-0.009	-0.009	17.566	-0.022	-0.022	0.000	0.000	0.000	0.000
134	A	135	ASP	-1	-0.812	-0.892	18.676	-0.012	-0.012	0.000	0.000	0.000	0.000
135	A	136	TYR	0	0.037	0.008	12.689	-0.020	-0.020	0.000	0.000	0.000	0.000
136	A	137	GLN	0	-0.088	-0.057	15.444	-0.030	-0.030	0.000	0.000	0.000	0.000
137	A	138	PRO	0	0.030	0.022	15.099	0.051	0.051	0.000	0.000	0.000	0.000
138	A	139	GLN	0	-0.019	-0.013	11.648	0.018	0.018	0.000	0.000	0.000	0.000
139	A	140	LYS	1	0.943	0.963	16.216	-0.159	-0.159	0.000	0.000	0.000	0.000
140	A	141	ALA	0	0.004	-0.008	16.034	0.049	0.049	0.000	0.000	0.000	0.000
141	A	142	ASP	-1	-0.876	-0.937	15.368	0.351	0.351	0.000	0.000	0.000	0.000
142	A	143	GLY	0	0.003	0.017	13.515	0.013	0.013	0.000	0.000	0.000	0.000
143	A	144	ALA	0	0.015	0.020	14.167	-0.068	-0.068	0.000	0.000	0.000	0.000
144	A	145	LYS	1	0.963	0.977	17.314	0.028	0.028	0.000	0.000	0.000	0.000
145	A	146	ASP	-1	-0.961	-0.978	18.674	0.208	0.208	0.000	0.000	0.000	0.000
146	A	147	GLY	0	0.039	0.025	20.632	-0.004	-0.004	0.000	0.000	0.000	0.000
147	A	148	GLY	0	-0.021	-0.011	21.946	-0.006	-0.006	0.000	0.000	0.000	0.000
148	A	149	PRO	0	0.011	-0.003	19.818	0.016	0.016	0.000	0.000	0.000	0.000
149	A	150	VAL	0	-0.001	-0.003	20.060	-0.007	-0.007	0.000	0.000	0.000	0.000
150	A	151	LYS	1	0.839	0.916	20.585	0.008	0.008	0.000	0.000	0.000	0.000
151	A	152	TYR	0	0.034	0.021	22.082	0.007	0.007	0.000	0.000	0.000	0.000
152	A	153	GLY	0	0.057	0.031	23.660	-0.014	-0.014	0.000	0.000	0.000	0.000
153	A	154	TRP	0	-0.032	-0.011	26.355	0.011	0.011	0.000	0.000	0.000	0.000
154	A	155	ASN	0	0.025	0.011	28.152	-0.011	-0.011	0.000	0.000	0.000	0.000
155	A	156	ILE	0	0.038	0.010	26.257	0.007	0.007	0.000	0.000	0.000	0.000
156	A	157	ARG	1	0.945	0.980	30.788	0.058	0.058	0.000	0.000	0.000	0.000
157	A	158	GLN	0	-0.041	-0.038	33.671	-0.002	-0.002	0.000	0.000	0.000	0.000
158	A	159	ASN	0	-0.031	0.000	33.550	0.004	0.004	0.000	0.000	0.000	0.000
159	A	160	VAL	0	0.010	0.017	33.602	0.005	0.005	0.000	0.000	0.000	0.000
160	A	161	GLN	0	0.018	0.007	30.583	-0.004	-0.004	0.000	0.000	0.000	0.000
161	A	162	ALA	0	-0.051	-0.018	28.567	-0.002	-0.002	0.000	0.000	0.000	0.000

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