FMO DATABASE

FMODB ID: 721JK

Calculation Name: 1Y9W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y9W

Chain ID: A

ChEMBL ID:

UniProt ID: Q81CG1

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	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	140
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1208395.046433
FMO2-HF: Nuclear repulsion	1150425.726354
FMO2-HF: Total energy	-57969.320079
FMO2-MP2: Total energy	-58137.577791

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-4.926	-1.076	-0.001	-2.077	-1.771	0.007

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.001

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	3	MET	0	-0.020	-0.002	3.445	-4.830	-1.008	0.000	-2.071	-1.750	0.007
4	A	4	LYS	1	0.922	0.952	5.453	-0.555	-0.527	-0.001	-0.006	-0.021	0.000
5	A	5	HIS	0	-0.043	-0.016	9.090	0.259	0.259	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.002	-0.006	11.830	-0.111	-0.111	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.884	-0.929	14.927	0.342	0.342	0.000	0.000	0.000	0.000
8	A	8	ASN	0	-0.039	-0.018	17.980	-0.034	-0.034	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.053	0.041	20.745	0.003	0.003	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.036	-0.062	22.317	-0.011	-0.011	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.990	0.980	24.769	-0.045	-0.045	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.023	0.005	24.130	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.778	-0.854	19.567	0.078	0.078	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.016	-0.005	23.662	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.804	-0.893	26.118	-0.006	-0.006	0.000	0.000	0.000	0.000
16	A	16	TYR	0	0.002	0.006	19.519	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.005	0.001	20.924	-0.013	-0.013	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.888	0.933	24.734	-0.008	-0.008	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.021	-0.028	27.738	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.853	0.939	21.999	0.095	0.095	0.000	0.000	0.000	0.000
21	A	21	VAL	0	0.017	0.007	25.727	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	22	ILE	0	0.021	0.015	27.696	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	23	GLN	0	0.010	0.008	25.454	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	24	TYR	0	-0.004	0.001	26.009	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	25	ASN	0	0.043	0.024	28.209	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	26	MET	0	-0.014	-0.009	31.603	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.115	-0.068	28.904	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.022	-0.005	29.728	-0.006	-0.006	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.012	0.011	32.527	0.004	0.004	0.000	0.000	0.000	0.000
30	A	30	THR	0	0.032	0.008	36.130	-0.003	-0.003	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.823	-0.937	38.845	-0.054	-0.054	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.969	-0.966	40.968	-0.036	-0.036	0.000	0.000	0.000	0.000
33	A	33	VAL	0	0.014	-0.003	39.993	0.003	0.003	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.775	0.888	35.931	0.061	0.061	0.000	0.000	0.000	0.000
35	A	35	GLN	0	-0.003	0.023	41.223	0.000	0.000	0.000	0.000	0.000	0.000
36	A	36	PRO	0	-0.030	-0.018	42.120	0.000	0.000	0.000	0.000	0.000	0.000
37	A	37	MET	0	-0.020	-0.019	39.369	0.002	0.002	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.818	-0.884	42.609	-0.015	-0.015	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.940	-0.951	44.257	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.006	-0.006	46.840	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	41	SER	0	-0.004	-0.021	50.523	0.002	0.002	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.021	0.010	52.852	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.008	-0.011	56.090	0.001	0.001	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.016	0.023	58.648	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	45	LYS	1	0.852	0.910	61.051	0.000	0.000	0.000	0.000	0.000	0.000
46	A	46	ASN	0	0.012	-0.004	63.600	-0.001	-0.001	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.870	-0.949	65.166	0.000	0.000	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.932	-0.949	65.894	0.004	0.004	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.023	-0.005	62.348	0.000	0.000	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.827	0.919	61.364	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	51	ILE	0	-0.003	-0.011	57.066	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	52	PHE	0	0.022	0.001	60.958	0.001	0.001	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.041	0.019	59.461	0.001	0.001	0.000	0.000	0.000	0.000
54	A	54	GLY	0	-0.011	-0.006	56.480	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.037	-0.013	53.193	0.001	0.001	0.000	0.000	0.000	0.000
56	A	56	THR	0	0.039	0.006	48.390	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.021	0.015	47.823	0.001	0.001	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.014	0.010	43.318	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	59	MET	0	-0.033	-0.019	45.710	0.000	0.000	0.000	0.000	0.000	0.000
60	A	60	TYR	0	0.078	0.019	39.698	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	61	PHE	0	-0.047	-0.014	36.403	0.001	0.001	0.000	0.000	0.000	0.000
62	A	62	TYR	0	-0.003	0.003	42.687	0.001	0.001	0.000	0.000	0.000	0.000
63	A	63	HIS	0	-0.069	-0.044	42.827	0.002	0.002	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.065	0.028	46.471	0.000	0.000	0.000	0.000	0.000	0.000
65	A	65	HIS	0	-0.044	-0.016	44.588	0.001	0.001	0.000	0.000	0.000	0.000
66	A	66	ILE	0	-0.025	-0.029	46.752	0.000	0.000	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.862	-0.922	44.809	0.003	0.003	0.000	0.000	0.000	0.000
68	A	68	PHE	0	-0.012	-0.010	45.165	0.002	0.002	0.000	0.000	0.000	0.000
69	A	69	LEU	0	-0.002	0.003	50.302	-0.002	-0.002	0.000	0.000	0.000	0.000
70	A	70	TRP	0	-0.035	-0.013	54.057	0.001	0.001	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.009	-0.015	56.341	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.812	-0.858	60.076	0.009	0.009	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.905	-0.980	61.877	0.009	0.009	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.056	-0.043	63.578	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.031	-0.010	64.895	0.000	0.000	0.000	0.000	0.000	0.000
76	A	76	ARG	1	0.887	0.945	63.203	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	77	HIS	0	-0.023	-0.025	65.143	0.000	0.000	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.840	-0.904	67.643	0.003	0.003	0.000	0.000	0.000	0.000
79	A	79	GLY	0	-0.020	0.000	65.769	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	80	TYR	0	0.019	-0.017	63.359	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.047	0.023	60.323	0.000	0.000	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.061	-0.046	60.177	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	83	GLN	0	0.028	0.015	61.894	0.000	0.000	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.013	0.015	58.116	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.019	0.005	55.536	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	86	HIS	0	-0.008	-0.013	57.834	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.921	-0.968	59.779	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	88	ILE	0	-0.005	-0.007	52.292	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	89	GLU	-1	-0.768	-0.858	55.049	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	90	GLY	0	-0.069	-0.024	56.121	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.045	0.027	53.833	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	92	ALA	0	0.037	0.011	51.946	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.855	0.915	53.148	0.008	0.008	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.935	-0.955	55.627	-0.015	-0.015	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.775	0.871	51.127	0.013	0.013	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.007	0.009	51.105	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	97	CYS	0	-0.079	-0.017	49.784	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.899	0.947	44.888	0.023	0.023	0.000	0.000	0.000	0.000
99	A	99	LEU	0	-0.076	-0.033	46.263	0.001	0.001	0.000	0.000	0.000	0.000
100	A	100	ILE	0	0.012	0.023	49.521	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.041	-0.027	44.189	0.000	0.000	0.000	0.000	0.000	0.000
102	A	102	LEU	0	0.056	0.042	47.484	0.000	0.000	0.000	0.000	0.000	0.000
103	A	103	ASP	-1	-0.886	-0.922	44.864	0.012	0.012	0.000	0.000	0.000	0.000
104	A	104	SER	0	0.000	0.004	47.854	0.000	0.000	0.000	0.000	0.000	0.000
105	A	105	PHE	0	0.049	0.006	44.099	0.000	0.000	0.000	0.000	0.000	0.000
106	A	106	SER	0	0.034	-0.001	50.033	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	107	PHE	0	-0.114	-0.055	48.552	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	108	GLN	0	-0.023	-0.015	49.092	0.000	0.000	0.000	0.000	0.000	0.000
109	A	109	ALA	0	0.012	0.019	54.187	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	110	PRO	0	0.095	0.055	53.315	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	111	GLU	-1	-0.882	-0.969	55.259	0.007	0.007	0.000	0.000	0.000	0.000
112	A	112	PHE	0	0.007	0.003	57.264	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	113	TYR	0	0.080	0.036	54.281	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.962	1.006	56.878	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.829	0.916	58.025	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	116	HIS	0	-0.040	-0.017	58.938	-0.001	-0.001	0.000	0.000	0.000	0.000
117	A	117	GLY	0	0.014	0.004	59.107	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	118	TYR	0	-0.036	-0.031	52.374	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	119	ARG	1	0.813	0.888	49.237	0.004	0.004	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.847	-0.918	50.767	0.008	0.008	0.000	0.000	0.000	0.000
121	A	121	TYR	0	-0.095	-0.064	43.898	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	122	GLY	0	0.015	0.004	45.947	0.000	0.000	0.000	0.000	0.000	0.000
123	A	123	VAL	0	0.006	0.010	46.416	0.000	0.000	0.000	0.000	0.000	0.000
124	A	124	VAL	0	-0.045	0.000	42.160	0.001	0.001	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.896	-0.972	44.947	0.017	0.017	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.908	-0.957	45.487	0.032	0.032	0.000	0.000	0.000	0.000
127	A	127	HIS	0	-0.024	0.005	41.615	0.005	0.005	0.000	0.000	0.000	0.000
128	A	128	PRO	0	0.030	-0.013	44.412	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	129	LYS	1	0.956	0.979	45.208	-0.035	-0.035	0.000	0.000	0.000	0.000
130	A	130	GLY	0	-0.074	-0.037	46.856	0.000	0.000	0.000	0.000	0.000	0.000
131	A	131	HIS	1	0.840	0.915	49.091	-0.025	-0.025	0.000	0.000	0.000	0.000
132	A	132	SER	0	0.051	0.060	48.041	0.001	0.001	0.000	0.000	0.000	0.000
133	A	133	GLN	0	-0.014	-0.019	43.216	0.002	0.002	0.000	0.000	0.000	0.000
134	A	134	HIS	0	-0.009	-0.009	47.362	0.001	0.001	0.000	0.000	0.000	0.000
135	A	135	PHE	0	0.027	0.016	42.835	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	136	PHE	0	0.005	-0.008	47.679	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.761	-0.856	48.729	-0.008	-0.008	0.000	0.000	0.000	0.000
138	A	138	LYS	1	0.811	0.907	50.590	0.004	0.004	0.000	0.000	0.000	0.000
139	A	139	ARG	1	0.824	0.904	47.202	0.011	0.011	0.000	0.000	0.000	0.000
140	A	140	LEU	0	-0.007	-0.013	52.750	0.000	0.000	0.000	0.000	0.000	0.000

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