FMO DATABASE

FMODB ID: LZL89

Calculation Name: 1YKH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YKH

Chain ID: A

ChEMBL ID:

UniProt ID: P47822

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	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	95
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-598265.589992
FMO2-HF: Nuclear repulsion	558137.356964
FMO2-HF: Total energy	-40128.233028
FMO2-MP2: Total energy	-40245.884489

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:111:ASN)

Summations of interaction energy for fragment #1(A:111:ASN)

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.
-30.165	-25.847	9.231	-5.163	-8.386	0.047

Interaction energy analysis for fragmet #1(A:111:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.068 / q_NPA : 0.022

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	113	GLN	0	0.042	0.031	2.359	-8.929	-5.995	2.629	-2.223	-3.340	0.021
4	A	114	TYR	0	-0.060	-0.053	2.036	-12.180	-11.582	6.585	-2.660	-4.522	0.025
5	A	115	LYS	1	0.823	0.899	4.011	-6.258	-5.472	0.017	-0.280	-0.524	0.001
6	A	116	ILE	0	0.026	0.013	5.938	-1.124	-1.124	0.000	0.000	0.000	0.000
7	A	117	GLN	0	-0.013	-0.006	6.590	-1.060	-1.060	0.000	0.000	0.000	0.000
8	A	118	GLU	-1	-0.740	-0.853	7.550	-0.421	-0.421	0.000	0.000	0.000	0.000
9	A	119	LEU	0	-0.008	0.017	9.791	-0.254	-0.254	0.000	0.000	0.000	0.000
10	A	120	ARG	1	0.938	0.958	10.914	-1.816	-1.816	0.000	0.000	0.000	0.000
11	A	121	LYS	1	0.816	0.909	9.708	-0.297	-0.297	0.000	0.000	0.000	0.000
12	A	122	LEU	0	0.029	0.016	12.683	-0.094	-0.094	0.000	0.000	0.000	0.000
13	A	123	LEU	0	0.038	0.017	15.377	-0.087	-0.087	0.000	0.000	0.000	0.000
14	A	124	LYS	1	0.950	0.982	17.138	-0.481	-0.481	0.000	0.000	0.000	0.000
15	A	125	SER	0	-0.003	-0.012	18.094	-0.058	-0.058	0.000	0.000	0.000	0.000
16	A	126	LEU	0	0.008	0.015	19.739	-0.040	-0.040	0.000	0.000	0.000	0.000
17	A	127	LEU	0	0.008	0.007	21.565	-0.030	-0.030	0.000	0.000	0.000	0.000
18	A	128	LEU	0	-0.014	0.002	23.162	-0.022	-0.022	0.000	0.000	0.000	0.000
19	A	129	ASN	0	0.054	0.007	22.718	-0.039	-0.039	0.000	0.000	0.000	0.000
20	A	130	TYR	0	-0.002	0.004	25.708	-0.014	-0.014	0.000	0.000	0.000	0.000
21	A	131	LEU	0	0.007	-0.013	27.595	-0.012	-0.012	0.000	0.000	0.000	0.000
22	A	132	GLU	-1	-0.808	-0.896	27.088	0.092	0.092	0.000	0.000	0.000	0.000
23	A	133	LEU	0	-0.039	-0.014	29.828	-0.008	-0.008	0.000	0.000	0.000	0.000
24	A	134	ILE	0	-0.081	-0.033	31.583	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	135	GLY	0	0.014	0.009	33.681	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	136	VAL	0	-0.054	-0.019	32.364	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	137	LEU	0	-0.052	-0.025	28.885	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	138	SER	0	-0.009	-0.009	32.970	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	139	ILE	0	0.015	0.008	31.010	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	140	ASN	0	-0.034	-0.021	33.964	0.004	0.004	0.000	0.000	0.000	0.000
31	A	141	PRO	0	0.061	0.012	35.209	0.003	0.003	0.000	0.000	0.000	0.000
32	A	142	ASP	-1	-0.845	-0.907	35.797	0.029	0.029	0.000	0.000	0.000	0.000
33	A	143	MET	0	-0.039	-0.024	31.222	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	144	TYR	0	-0.006	0.004	31.291	0.013	0.013	0.000	0.000	0.000	0.000
35	A	145	GLU	-1	-0.871	-0.954	31.583	0.085	0.085	0.000	0.000	0.000	0.000
36	A	146	ARG	1	0.848	0.894	28.230	-0.034	-0.034	0.000	0.000	0.000	0.000
37	A	147	LYS	1	0.807	0.913	26.474	-0.083	-0.083	0.000	0.000	0.000	0.000
38	A	148	VAL	0	0.020	0.010	26.731	0.024	0.024	0.000	0.000	0.000	0.000
39	A	149	GLU	-1	-0.816	-0.877	26.209	0.074	0.074	0.000	0.000	0.000	0.000
40	A	150	ASN	0	-0.041	-0.014	22.937	0.012	0.012	0.000	0.000	0.000	0.000
41	A	151	ILE	0	0.022	0.005	22.078	0.034	0.034	0.000	0.000	0.000	0.000
42	A	152	ARG	1	0.949	0.974	22.658	-0.114	-0.114	0.000	0.000	0.000	0.000
43	A	153	THR	0	-0.015	-0.012	18.955	0.021	0.021	0.000	0.000	0.000	0.000
44	A	154	ILE	0	0.022	0.006	17.480	0.042	0.042	0.000	0.000	0.000	0.000
45	A	155	LEU	0	0.002	0.002	17.566	0.081	0.081	0.000	0.000	0.000	0.000
46	A	156	VAL	0	0.033	0.030	18.174	0.062	0.062	0.000	0.000	0.000	0.000
47	A	157	ASN	0	-0.013	-0.006	14.093	0.014	0.014	0.000	0.000	0.000	0.000
48	A	158	ILE	0	0.019	0.006	13.848	0.132	0.132	0.000	0.000	0.000	0.000
49	A	159	HIS	0	-0.029	-0.021	14.330	0.117	0.117	0.000	0.000	0.000	0.000
50	A	160	HIS	0	-0.054	-0.020	12.701	0.021	0.021	0.000	0.000	0.000	0.000
51	A	161	LEU	0	-0.007	0.003	7.868	0.077	0.077	0.000	0.000	0.000	0.000
52	A	162	LEU	0	0.018	0.005	9.551	0.303	0.303	0.000	0.000	0.000	0.000
53	A	163	ASN	0	-0.027	-0.020	11.798	-0.029	-0.029	0.000	0.000	0.000	0.000
54	A	164	GLU	-1	-0.778	-0.873	7.028	1.727	1.727	0.000	0.000	0.000	0.000
55	A	165	TYR	0	0.003	-0.012	7.031	-0.031	-0.031	0.000	0.000	0.000	0.000
56	A	166	ARG	1	0.919	0.952	8.601	-0.584	-0.584	0.000	0.000	0.000	0.000
57	A	167	PRO	0	-0.009	-0.003	7.802	-0.025	-0.025	0.000	0.000	0.000	0.000
58	A	168	HIS	0	-0.062	-0.034	6.444	0.542	0.542	0.000	0.000	0.000	0.000
59	A	169	GLN	0	0.072	0.026	9.156	0.089	0.089	0.000	0.000	0.000	0.000
60	A	170	SER	0	-0.010	-0.009	12.412	-0.148	-0.148	0.000	0.000	0.000	0.000
61	A	171	ARG	1	0.906	0.959	6.903	-0.932	-0.932	0.000	0.000	0.000	0.000
62	A	172	GLU	-1	-0.887	-0.942	12.382	1.292	1.292	0.000	0.000	0.000	0.000
63	A	173	SER	0	-0.008	-0.003	14.914	-0.098	-0.098	0.000	0.000	0.000	0.000
64	A	174	LEU	0	-0.038	-0.010	16.902	-0.067	-0.067	0.000	0.000	0.000	0.000
65	A	175	ILE	0	0.002	-0.008	14.035	-0.060	-0.060	0.000	0.000	0.000	0.000
66	A	176	MET	0	0.019	0.017	18.279	-0.032	-0.032	0.000	0.000	0.000	0.000
67	A	177	LEU	0	0.025	0.026	20.739	-0.049	-0.049	0.000	0.000	0.000	0.000
68	A	178	LEU	0	-0.036	-0.028	19.666	-0.046	-0.046	0.000	0.000	0.000	0.000
69	A	179	GLU	-1	-0.940	-0.973	20.581	0.495	0.495	0.000	0.000	0.000	0.000
70	A	180	GLU	-1	-0.927	-0.966	23.839	0.342	0.342	0.000	0.000	0.000	0.000
71	A	181	GLN	0	-0.009	-0.011	26.268	-0.041	-0.041	0.000	0.000	0.000	0.000
72	A	182	LEU	0	-0.017	-0.006	25.058	-0.026	-0.026	0.000	0.000	0.000	0.000
73	A	183	GLU	-1	-0.786	-0.868	27.875	0.220	0.220	0.000	0.000	0.000	0.000
74	A	184	TYR	0	0.001	0.010	29.686	-0.016	-0.016	0.000	0.000	0.000	0.000
75	A	185	LYS	1	0.782	0.872	30.797	-0.194	-0.194	0.000	0.000	0.000	0.000
76	A	186	ARG	1	0.866	0.920	26.648	-0.269	-0.269	0.000	0.000	0.000	0.000
77	A	187	GLY	0	-0.008	-0.001	33.621	-0.010	-0.010	0.000	0.000	0.000	0.000
78	A	188	GLU	-1	-0.751	-0.866	35.732	0.152	0.152	0.000	0.000	0.000	0.000
79	A	189	ILE	0	-0.014	-0.004	34.856	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	190	ARG	1	0.841	0.904	32.515	-0.203	-0.203	0.000	0.000	0.000	0.000
81	A	191	GLU	-1	-0.926	-0.953	39.501	0.129	0.129	0.000	0.000	0.000	0.000
82	A	192	ILE	0	0.024	0.006	40.849	-0.009	-0.009	0.000	0.000	0.000	0.000
83	A	193	GLU	-1	-0.867	-0.922	40.539	0.107	0.107	0.000	0.000	0.000	0.000
84	A	194	GLN	0	-0.061	-0.028	41.438	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	195	VAL	0	0.024	0.014	45.337	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	196	CYS	0	-0.042	-0.029	46.605	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	197	LYS	1	0.848	0.908	43.543	-0.110	-0.110	0.000	0.000	0.000	0.000
88	A	198	GLN	0	-0.007	-0.006	47.597	0.000	0.000	0.000	0.000	0.000	0.000
89	A	199	VAL	0	0.001	-0.001	51.239	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	200	HIS	0	0.010	0.003	52.453	-0.006	-0.006	0.000	0.000	0.000	0.000
91	A	201	ASP	-1	-0.784	-0.875	53.118	0.078	0.078	0.000	0.000	0.000	0.000
92	A	202	LYS	1	0.774	0.891	53.579	-0.083	-0.083	0.000	0.000	0.000	0.000
93	A	203	LEU	0	-0.021	-0.002	57.219	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	204	THR	0	-0.060	-0.025	57.369	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	205	SER	0	-0.091	-0.054	58.289	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:111:ASN)