FMO DATABASE

FMODB ID: 4NM1N

Calculation Name: 1YLX-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YLX

Chain ID: A

ChEMBL ID:

UniProt ID: Q5KZY7

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	101
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-793742.943496
FMO2-HF: Nuclear repulsion	751562.318257
FMO2-HF: Total energy	-42180.62524
FMO2-MP2: Total energy	-42300.747848

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:0:ACE )

Summations of interaction energy for fragment #1(A:0:ACE )

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.
-1.195	-0.266	-0.004	-0.354	-0.569	0

Interaction energy analysis for fragmet #1(A:0:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.028

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].
3	A	2	GLU	-1	-0.944	-0.965	3.833	0.103	0.962	-0.005	-0.338	-0.515
4	A	3	PHE	0	-0.035	-0.026	4.001	0.010	0.080	0.001	-0.016	-0.054
5	A	4	ALA	0	0.085	0.048	8.433	0.109	0.109	0.000	0.000	0.000
6	A	5	PRO	0	0.013	-0.001	12.224	0.003	0.003	0.000	0.000	0.000
7	A	6	ARG	1	0.868	0.892	15.017	0.100	0.100	0.000	0.000	0.000
8	A	7	SER	0	-0.046	-0.029	16.543	-0.012	-0.012	0.000	0.000	0.000
9	A	8	VAL	0	0.038	0.022	16.206	0.008	0.008	0.000	0.000	0.000
10	A	9	VAL	0	0.053	0.032	13.696	-0.004	-0.004	0.000	0.000	0.000
11	A	10	ILE	0	-0.044	-0.027	16.865	0.004	0.004	0.000	0.000	0.000
12	A	11	GLU	-1	-0.911	-0.972	20.252	-0.107	-0.107	0.000	0.000	0.000
13	A	12	GLU	-1	-0.901	-0.927	16.478	-0.310	-0.310	0.000	0.000	0.000
14	A	13	PHE	0	-0.077	-0.039	16.932	0.001	0.001	0.000	0.000	0.000
15	A	14	ILE	0	-0.021	-0.005	21.856	0.014	0.014	0.000	0.000	0.000
16	A	15	ASP	-1	-0.911	-0.948	23.485	-0.135	-0.135	0.000	0.000	0.000
17	A	16	THR	0	-0.063	-0.037	23.321	0.005	0.005	0.000	0.000	0.000
18	A	17	LEU	0	-0.037	-0.012	25.769	0.005	0.005	0.000	0.000	0.000
19	A	18	GLU	-1	-0.882	-0.942	28.083	-0.077	-0.077	0.000	0.000	0.000
20	A	19	PRO	0	-0.003	-0.005	28.551	0.004	0.004	0.000	0.000	0.000
21	A	20	MET	0	-0.034	-0.005	27.463	-0.001	-0.001	0.000	0.000	0.000
22	A	21	MET	0	-0.025	-0.016	29.952	0.003	0.003	0.000	0.000	0.000
23	A	22	GLU	-1	-0.929	-0.950	33.008	-0.073	-0.073	0.000	0.000	0.000
24	A	23	ALA	0	-0.060	-0.034	31.915	0.004	0.004	0.000	0.000	0.000
25	A	24	TYR	0	-0.050	-0.041	29.595	-0.003	-0.003	0.000	0.000	0.000
26	A	25	GLY	0	-0.019	0.009	34.681	0.004	0.004	0.000	0.000	0.000
27	A	26	LEU	0	-0.078	-0.047	31.812	0.002	0.002	0.000	0.000	0.000
28	A	27	ASP	-1	-0.914	-0.955	35.888	-0.059	-0.059	0.000	0.000	0.000
29	A	28	GLN	0	-0.005	-0.006	34.791	-0.001	-0.001	0.000	0.000	0.000
30	A	29	VAL	0	0.004	-0.005	28.966	-0.003	-0.003	0.000	0.000	0.000
31	A	30	GLY	0	0.010	0.014	29.217	0.004	0.004	0.000	0.000	0.000
32	A	31	ILE	0	-0.012	-0.009	22.918	-0.007	-0.007	0.000	0.000	0.000
33	A	32	PHE	0	-0.040	-0.005	21.614	0.010	0.010	0.000	0.000	0.000
34	A	33	GLU	-1	-0.722	-0.838	20.080	-0.154	-0.154	0.000	0.000	0.000
35	A	34	GLU	-1	-0.798	-0.876	19.809	-0.095	-0.095	0.000	0.000	0.000
36	A	35	HIS	0	-0.078	-0.032	18.079	-0.012	-0.012	0.000	0.000	0.000
37	A	36	GLY	0	0.035	0.011	17.186	0.012	0.012	0.000	0.000	0.000
38	A	37	GLU	-1	-0.947	-0.970	17.801	-0.033	-0.033	0.000	0.000	0.000
39	A	38	GLY	0	-0.045	-0.030	14.835	-0.017	-0.017	0.000	0.000	0.000
40	A	39	ASN	0	-0.013	-0.007	8.669	-0.029	-0.029	0.000	0.000	0.000
41	A	40	ARG	1	0.964	0.992	11.512	0.060	0.060	0.000	0.000	0.000
42	A	41	TYR	0	-0.030	-0.023	13.601	0.058	0.058	0.000	0.000	0.000
43	A	42	TYR	0	-0.007	-0.002	14.752	-0.043	-0.043	0.000	0.000	0.000
44	A	43	VAL	0	0.027	0.018	16.358	0.029	0.029	0.000	0.000	0.000
45	A	44	GLY	0	0.020	-0.001	18.760	-0.024	-0.024	0.000	0.000	0.000
46	A	45	TYR	0	-0.043	-0.032	21.667	0.004	0.004	0.000	0.000	0.000
47	A	46	THR	0	-0.014	-0.025	25.422	-0.003	-0.003	0.000	0.000	0.000
48	A	47	ILE	0	0.009	-0.007	28.466	0.003	0.003	0.000	0.000	0.000
49	A	48	ASN	0	0.009	0.010	31.597	0.003	0.003	0.000	0.000	0.000
50	A	49	LYS	1	0.920	0.955	35.053	0.071	0.071	0.000	0.000	0.000
51	A	50	ASP	-1	-0.943	-0.974	37.121	-0.049	-0.049	0.000	0.000	0.000
52	A	51	ASP	-1	-0.922	-0.958	39.359	-0.047	-0.047	0.000	0.000	0.000
53	A	52	GLU	-1	-0.955	-0.972	35.361	-0.070	-0.070	0.000	0.000	0.000
54	A	53	MET	0	-0.073	-0.036	32.390	-0.005	-0.005	0.000	0.000	0.000
55	A	54	ILE	0	-0.008	0.006	29.613	-0.003	-0.003	0.000	0.000	0.000
56	A	55	THR	0	-0.013	0.013	24.649	-0.002	-0.002	0.000	0.000	0.000
57	A	56	ILE	0	-0.022	0.008	24.262	-0.003	-0.003	0.000	0.000	0.000
58	A	57	HIS	0	-0.046	-0.041	19.842	-0.022	-0.022	0.000	0.000	0.000
59	A	58	MET	0	0.010	0.017	15.803	-0.006	-0.006	0.000	0.000	0.000
60	A	59	PRO	0	-0.039	-0.010	13.383	0.025	0.025	0.000	0.000	0.000
61	A	60	PHE	0	0.063	0.018	11.075	-0.111	-0.111	0.000	0.000	0.000
62	A	61	VAL	0	0.004	0.007	6.633	0.100	0.100	0.000	0.000	0.000
63	A	62	LYS	1	0.943	0.979	9.218	0.044	0.044	0.000	0.000	0.000
64	A	63	ASN	0	-0.046	-0.007	7.348	0.085	0.085	0.000	0.000	0.000
65	A	64	GLU	-1	-0.922	-0.990	9.257	0.246	0.246	0.000	0.000	0.000
66	A	65	ARG	1	0.865	0.937	10.549	-0.274	-0.274	0.000	0.000	0.000
67	A	66	GLY	0	-0.053	-0.026	12.662	-0.022	-0.022	0.000	0.000	0.000
68	A	67	GLU	-1	-0.945	-0.966	10.127	-0.064	-0.064	0.000	0.000	0.000
69	A	68	LEU	0	-0.018	-0.027	10.528	0.004	0.004	0.000	0.000	0.000
70	A	69	ALA	0	0.051	0.032	6.730	-0.034	-0.034	0.000	0.000	0.000
71	A	70	LEU	0	0.026	0.020	8.619	0.058	0.058	0.000	0.000	0.000
72	A	71	GLU	-1	-0.984	-1.001	8.460	-0.814	-0.814	0.000	0.000	0.000
73	A	72	LYS	1	0.891	0.935	9.548	0.309	0.309	0.000	0.000	0.000
74	A	73	GLN	0	-0.001	0.002	12.191	0.016	0.016	0.000	0.000	0.000
75	A	74	GLU	-1	-0.903	-0.993	15.059	-0.204	-0.204	0.000	0.000	0.000
76	A	75	TRP	0	0.045	0.025	17.614	-0.014	-0.014	0.000	0.000	0.000
77	A	76	THR	0	-0.064	-0.038	19.901	0.016	0.016	0.000	0.000	0.000
78	A	77	VAL	0	0.024	0.009	22.337	0.000	0.000	0.000	0.000	0.000
79	A	78	ARG	1	0.721	0.809	23.512	0.122	0.122	0.000	0.000	0.000
80	A	79	LYS	1	0.908	0.956	27.586	0.088	0.088	0.000	0.000	0.000
81	A	80	ASP	-1	-0.853	-0.919	31.353	-0.066	-0.066	0.000	0.000	0.000
82	A	81	GLY	0	-0.059	-0.024	31.219	0.004	0.004	0.000	0.000	0.000
83	A	82	ARG	1	0.865	0.924	29.425	0.064	0.064	0.000	0.000	0.000
84	A	83	GLU	-1	-0.781	-0.874	23.184	-0.142	-0.142	0.000	0.000	0.000
85	A	84	LYS	1	0.854	0.936	26.205	0.103	0.103	0.000	0.000	0.000
86	A	85	LYS	1	0.923	0.972	18.062	0.215	0.215	0.000	0.000	0.000
87	A	86	GLY	0	-0.029	-0.013	21.466	0.015	0.015	0.000	0.000	0.000
88	A	87	PHE	0	-0.010	0.012	22.657	-0.001	-0.001	0.000	0.000	0.000
89	A	88	HIS	1	0.860	0.915	18.899	0.212	0.212	0.000	0.000	0.000
90	A	89	SER	0	0.041	0.037	20.116	-0.022	-0.022	0.000	0.000	0.000
91	A	90	LEU	0	0.064	0.041	22.095	0.008	0.008	0.000	0.000	0.000
92	A	91	GLN	0	0.047	0.011	23.881	0.003	0.003	0.000	0.000	0.000
93	A	92	GLU	-1	-0.859	-0.929	24.148	-0.174	-0.174	0.000	0.000	0.000
94	A	93	ALA	0	0.001	0.000	24.161	0.009	0.009	0.000	0.000	0.000
95	A	94	MET	0	0.001	0.001	26.246	0.009	0.009	0.000	0.000	0.000
96	A	95	GLU	-1	-0.898	-0.954	29.172	-0.088	-0.088	0.000	0.000	0.000
97	A	96	GLU	-1	-0.883	-0.925	28.908	-0.094	-0.094	0.000	0.000	0.000
98	A	97	VAL	0	-0.045	-0.038	28.940	0.007	0.007	0.000	0.000	0.000
99	A	98	ILE	0	-0.026	-0.011	31.667	0.007	0.007	0.000	0.000	0.000
100	A	99	HIS	0	-0.100	-0.027	34.239	0.010	0.010	0.000	0.000	0.000
101	A	100	SER	-1	-0.962	-0.982	34.475	-0.074	-0.074	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:ACE )