FMO DATABASE

FMODB ID: 17Y3Z

Calculation Name: 2YWX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YWX

Chain ID: A

ChEMBL ID:

UniProt ID: Q58033

Base Structure: X-ray

Registration Date: 2023-06-22

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	157
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1378085.256309
FMO2-HF: Nuclear repulsion	1318713.910833
FMO2-HF: Total energy	-59371.345476
FMO2-MP2: Total energy	-59544.002794

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.
-8.074	-1.82	13.869	-4.199	-15.921	-0.042

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 : 0.023 / q_NPA : 0.047

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	CYS	0	-0.009	-0.003	3.612	0.440	4.325	0.516	-1.757	-2.644	-0.001
4	A	4	ILE	0	-0.002	0.005	4.979	-0.946	-0.898	-0.001	-0.013	-0.034	0.000
5	A	5	ILE	0	0.008	0.000	8.580	0.043	0.043	0.000	0.000	0.000	0.000
6	A	6	MET	0	-0.020	0.003	11.204	-0.092	-0.092	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.025	0.014	14.716	-0.011	-0.011	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.065	-0.057	17.670	-0.023	-0.023	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.866	-0.921	18.398	0.102	0.102	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.032	-0.022	19.444	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.885	-0.959	17.491	0.109	0.109	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.064	0.025	15.776	0.024	0.024	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.982	0.998	17.214	-0.058	-0.058	0.000	0.000	0.000	0.000
14	A	14	ILE	0	-0.047	-0.032	17.045	0.000	0.000	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.054	0.013	13.315	0.007	0.007	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.899	-0.958	13.372	0.199	0.199	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.813	0.917	15.299	-0.090	-0.090	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.000	0.006	11.641	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.037	0.018	9.870	0.013	0.013	0.000	0.000	0.000	0.000
20	A	20	ASN	0	-0.004	-0.009	11.499	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	21	ILE	0	0.033	0.037	11.631	-0.015	-0.015	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.007	-0.009	6.222	-0.028	-0.028	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.889	0.937	9.190	-0.142	-0.142	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.979	-0.978	11.187	0.107	0.107	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.070	-0.044	9.447	-0.038	-0.038	0.000	0.000	0.000	0.000
26	A	26	GLY	0	-0.027	-0.001	9.833	0.026	0.026	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.030	-0.014	4.465	-0.023	0.060	-0.001	-0.005	-0.077	0.000
28	A	28	GLU	-1	-0.892	-0.951	2.227	-4.505	-2.899	2.108	-1.301	-2.412	-0.008
29	A	29	PHE	0	-0.052	-0.059	2.601	-1.170	0.055	7.314	-4.547	-3.992	-0.018
30	A	30	GLU	-1	-0.831	-0.897	3.216	-0.282	-3.077	0.524	4.095	-1.824	-0.008
31	A	31	VAL	0	-0.030	-0.024	4.954	-0.099	-0.043	0.000	-0.004	-0.053	0.000
32	A	32	ARG	1	0.886	0.938	7.501	-0.540	-0.540	0.000	0.000	0.000	0.000
33	A	33	VAL	0	0.009	0.013	10.800	-0.013	-0.013	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.025	0.008	14.212	-0.023	-0.023	0.000	0.000	0.000	0.000
35	A	35	SER	0	-0.042	-0.003	15.978	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.042	0.013	18.404	-0.006	-0.006	0.000	0.000	0.000	0.000
37	A	37	HIS	0	0.030	0.010	19.477	-0.008	-0.008	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.884	0.925	21.300	-0.066	-0.066	0.000	0.000	0.000	0.000
39	A	39	THR	0	0.019	0.020	18.439	0.001	0.001	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.032	0.023	18.546	0.011	0.011	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.805	-0.925	18.109	0.022	0.022	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.021	0.021	14.547	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.031	-0.024	13.665	0.024	0.024	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.831	-0.897	12.891	-0.018	-0.018	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.961	-0.970	13.183	-0.035	-0.035	0.000	0.000	0.000	0.000
46	A	46	ILE	0	-0.016	-0.013	8.603	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.039	-0.031	8.702	0.029	0.029	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.831	0.900	9.219	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	49	ASN	0	-0.058	-0.024	9.511	-0.063	-0.063	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.008	0.033	4.570	-0.138	-0.038	-0.001	-0.005	-0.093	0.000
51	A	51	LYS	1	0.853	0.911	3.053	-0.236	0.430	0.040	-0.134	-0.571	0.001
52	A	52	ALA	0	-0.026	-0.003	2.264	-2.869	-0.956	3.100	-2.272	-2.740	-0.006
53	A	53	ASP	-1	-0.817	-0.895	2.873	1.224	0.113	0.159	1.956	-1.004	-0.001
54	A	54	VAL	0	-0.021	-0.014	4.857	0.781	0.781	0.000	0.000	0.000	0.000
55	A	55	PHE	0	0.053	0.022	5.619	0.117	0.117	0.000	0.000	0.000	0.000
56	A	56	ILE	0	-0.007	0.002	7.896	-0.074	-0.074	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.003	0.012	10.325	0.132	0.132	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.028	-0.016	13.010	-0.045	-0.045	0.000	0.000	0.000	0.000
59	A	59	ALA	0	0.044	0.014	15.819	0.010	0.010	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.067	0.033	19.103	-0.009	-0.009	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.036	-0.025	22.830	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.070	0.052	25.080	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	63	ALA	0	-0.024	-0.008	20.513	0.002	0.002	0.000	0.000	0.000	0.000
64	A	64	HIS	0	0.027	0.000	21.126	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.021	-0.001	14.217	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	66	PRO	0	0.026	0.001	15.178	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	67	GLY	0	0.085	0.033	15.881	-0.017	-0.017	0.000	0.000	0.000	0.000
68	A	68	VAL	0	-0.004	-0.004	16.651	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	69	VAL	0	0.006	0.003	11.041	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.032	0.006	13.372	-0.028	-0.028	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.085	-0.037	14.965	-0.014	-0.014	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.033	-0.012	13.829	-0.002	-0.002	0.000	0.000	0.000	0.000
73	A	73	THR	0	-0.037	-0.016	9.886	-0.037	-0.037	0.000	0.000	0.000	0.000
74	A	74	THR	0	0.010	0.012	12.746	0.002	0.002	0.000	0.000	0.000	0.000
75	A	75	LYS	1	0.811	0.911	7.021	0.730	0.730	0.000	0.000	0.000	0.000
76	A	76	PRO	0	0.021	0.004	9.186	0.083	0.083	0.000	0.000	0.000	0.000
77	A	77	VAL	0	0.027	0.023	10.110	-0.061	-0.061	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.023	-0.014	10.706	0.018	0.018	0.000	0.000	0.000	0.000
79	A	79	ALA	0	0.020	0.015	13.251	0.055	0.055	0.000	0.000	0.000	0.000
80	A	80	VAL	0	-0.030	-0.033	14.938	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	81	PRO	0	0.000	0.013	17.659	0.014	0.014	0.000	0.000	0.000	0.000
82	A	82	VAL	0	0.019	0.000	19.760	0.002	0.002	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.843	-0.895	22.449	0.042	0.042	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.030	-0.002	25.669	0.002	0.002	0.000	0.000	0.000	0.000
85	A	85	LYS	1	0.925	0.940	27.564	-0.026	-0.026	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.019	0.005	29.865	0.001	0.001	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.882	-0.943	30.474	0.019	0.019	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.012	0.001	26.905	0.001	0.001	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.015	-0.011	26.792	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	90	ASP	-1	-0.884	-0.941	27.803	0.017	0.017	0.000	0.000	0.000	0.000
91	A	91	ALA	0	-0.013	-0.010	22.610	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	92	LEU	0	-0.013	0.009	22.996	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	93	LEU	0	0.048	0.011	24.092	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	94	SER	0	-0.035	-0.020	23.589	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	95	SER	0	-0.070	-0.041	19.675	-0.002	-0.002	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.015	-0.013	21.113	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	97	GLN	0	-0.055	-0.012	23.026	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	98	MET	0	-0.027	0.011	19.370	0.006	0.006	0.000	0.000	0.000	0.000
99	A	99	PRO	0	0.002	0.008	23.164	0.000	0.000	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.004	-0.029	24.083	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	101	GLY	0	-0.008	0.004	23.413	0.002	0.002	0.000	0.000	0.000	0.000
102	A	102	ILE	0	-0.029	-0.009	18.364	-0.011	-0.011	0.000	0.000	0.000	0.000
103	A	103	PRO	0	0.011	0.009	17.973	0.010	0.010	0.000	0.000	0.000	0.000
104	A	104	VAL	0	0.028	0.004	16.269	-0.012	-0.012	0.000	0.000	0.000	0.000
105	A	105	ALA	0	-0.026	0.008	15.064	0.009	0.009	0.000	0.000	0.000	0.000
106	A	106	THR	0	0.044	0.015	16.593	0.008	0.008	0.000	0.000	0.000	0.000
107	A	107	VAL	0	-0.030	0.001	16.467	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	108	GLY	0	0.010	-0.009	19.512	0.006	0.006	0.000	0.000	0.000	0.000
109	A	109	ILE	0	0.092	0.040	21.196	0.008	0.008	0.000	0.000	0.000	0.000
110	A	110	ASH	0	-0.098	-0.104	20.914	0.003	0.003	0.000	0.000	0.000	0.000
111	A	111	ARG	1	0.857	0.940	19.508	-0.032	-0.032	0.000	0.000	0.000	0.000
112	A	112	GLY	0	0.075	0.032	15.862	-0.008	-0.008	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.919	-0.959	14.451	0.093	0.093	0.000	0.000	0.000	0.000
114	A	114	ASN	0	0.010	-0.022	14.751	0.000	0.000	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.026	0.025	13.715	-0.032	-0.032	0.000	0.000	0.000	0.000
116	A	116	ALA	0	0.016	0.012	10.355	-0.052	-0.052	0.000	0.000	0.000	0.000
117	A	117	ILE	0	0.005	0.001	10.050	-0.077	-0.077	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.016	0.015	11.763	-0.040	-0.040	0.000	0.000	0.000	0.000
119	A	119	ALA	0	0.032	0.002	7.427	-0.050	-0.050	0.000	0.000	0.000	0.000
120	A	120	LEU	0	0.004	0.002	6.789	-0.246	-0.246	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.877	-0.934	8.427	-0.048	-0.048	0.000	0.000	0.000	0.000
122	A	122	ILE	0	-0.021	-0.004	8.255	0.022	0.022	0.000	0.000	0.000	0.000
123	A	123	LEU	0	0.005	-0.002	2.895	-0.626	-0.048	0.111	-0.212	-0.477	-0.001
124	A	124	ALA	0	-0.027	-0.008	6.898	0.232	0.232	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.054	-0.016	9.842	0.077	0.077	0.000	0.000	0.000	0.000
126	A	126	LYS	1	0.838	0.911	5.960	0.147	0.147	0.000	0.000	0.000	0.000
127	A	127	ASP	-1	-0.814	-0.890	7.200	0.807	0.807	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.852	-0.951	9.283	0.068	0.068	0.000	0.000	0.000	0.000
129	A	129	ASN	0	-0.039	-0.024	9.082	-0.124	-0.124	0.000	0.000	0.000	0.000
130	A	130	ILE	0	-0.023	-0.008	5.671	-0.052	-0.052	0.000	0.000	0.000	0.000
131	A	131	ALA	0	0.044	0.024	10.219	-0.042	-0.042	0.000	0.000	0.000	0.000
132	A	132	LYS	1	0.867	0.922	13.088	-0.131	-0.131	0.000	0.000	0.000	0.000
133	A	133	LYS	1	0.897	0.945	11.136	-0.296	-0.296	0.000	0.000	0.000	0.000
134	A	134	LEU	0	0.001	0.018	11.264	-0.005	-0.005	0.000	0.000	0.000	0.000
135	A	135	ILE	0	-0.014	-0.002	14.775	-0.005	-0.005	0.000	0.000	0.000	0.000
136	A	136	GLU	-1	-0.873	-0.933	17.511	0.112	0.112	0.000	0.000	0.000	0.000
137	A	137	TYR	0	-0.030	-0.015	15.937	-0.010	-0.010	0.000	0.000	0.000	0.000
138	A	138	ARG	1	0.923	0.935	17.322	0.005	0.005	0.000	0.000	0.000	0.000
139	A	139	GLU	-1	-0.795	-0.868	20.498	0.031	0.031	0.000	0.000	0.000	0.000
140	A	140	LYS	1	0.941	0.960	18.237	-0.094	-0.094	0.000	0.000	0.000	0.000
141	A	141	MET	0	-0.017	-0.008	20.219	-0.004	-0.004	0.000	0.000	0.000	0.000
142	A	142	LYS	1	0.862	0.925	23.564	-0.029	-0.029	0.000	0.000	0.000	0.000
143	A	143	LYS	1	0.874	0.935	26.038	-0.039	-0.039	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.962	0.996	22.703	-0.060	-0.060	0.000	0.000	0.000	0.000
145	A	145	VAL	0	0.021	0.020	27.430	-0.002	-0.002	0.000	0.000	0.000	0.000
146	A	146	TYR	0	0.030	0.002	29.851	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	147	ALA	0	0.027	0.022	31.179	-0.001	-0.001	0.000	0.000	0.000	0.000
148	A	148	SER	0	-0.067	-0.039	31.101	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	149	ASP	-1	-0.852	-0.925	33.704	0.019	0.019	0.000	0.000	0.000	0.000
150	A	150	GLU	-1	-0.846	-0.919	35.849	0.021	0.021	0.000	0.000	0.000	0.000
151	A	151	LYS	1	0.922	0.969	35.305	-0.029	-0.029	0.000	0.000	0.000	0.000
152	A	152	VAL	0	-0.005	-0.029	37.146	-0.001	-0.001	0.000	0.000	0.000	0.000
153	A	153	LYS	1	0.806	0.901	38.183	-0.021	-0.021	0.000	0.000	0.000	0.000
154	A	154	GLU	-1	-0.849	-0.900	41.705	0.016	0.016	0.000	0.000	0.000	0.000
155	A	155	MET	0	-0.101	-0.033	39.366	0.000	0.000	0.000	0.000	0.000	0.000
156	A	156	PHE	0	-0.015	-0.009	42.312	0.000	0.000	0.000	0.000	0.000	0.000
157	A	157	LYS	1	0.804	0.896	45.549	-0.017	-0.017	0.000	0.000	0.000	0.000

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