FMO DATABASE

FMODB ID: 39NYL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-598495.66854
FMO2-HF: Nuclear repulsion	558368.010369
FMO2-HF: Total energy	-40127.658171
FMO2-MP2: Total energy	-40245.435185

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.
-31.573	-25.235	7.08	-5.221	-8.196	0.053

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 : 0.059 / q_NPA : 0.013

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	0.056	0.042	2.175	-12.544	-8.729	3.616	-3.202	-4.229	0.028
4	A	114	TYR	0	-0.046	-0.036	2.214	-11.236	-9.235	3.456	-1.866	-3.591	0.024
5	A	115	LYS	1	0.848	0.904	4.191	-5.586	-5.064	0.008	-0.153	-0.376	0.001
6	A	116	ILE	0	0.036	0.019	5.993	-0.972	-0.972	0.000	0.000	0.000	0.000
7	A	117	GLN	0	-0.024	-0.008	6.959	-0.976	-0.976	0.000	0.000	0.000	0.000
8	A	118	GLU	-1	-0.734	-0.855	8.088	-0.498	-0.498	0.000	0.000	0.000	0.000
9	A	119	LEU	0	-0.004	0.011	9.978	-0.206	-0.206	0.000	0.000	0.000	0.000
10	A	120	ARG	1	0.939	0.956	11.181	-1.637	-1.637	0.000	0.000	0.000	0.000
11	A	121	LYS	1	0.807	0.906	9.698	-0.052	-0.052	0.000	0.000	0.000	0.000
12	A	122	LEU	0	0.022	0.013	13.199	-0.082	-0.082	0.000	0.000	0.000	0.000
13	A	123	LEU	0	0.044	0.017	15.821	-0.063	-0.063	0.000	0.000	0.000	0.000
14	A	124	LYS	1	0.950	0.986	16.827	-0.444	-0.444	0.000	0.000	0.000	0.000
15	A	125	SER	0	0.004	-0.006	18.733	-0.041	-0.041	0.000	0.000	0.000	0.000
16	A	126	LEU	0	0.003	0.016	20.337	-0.031	-0.031	0.000	0.000	0.000	0.000
17	A	127	LEU	0	0.012	0.003	21.944	-0.024	-0.024	0.000	0.000	0.000	0.000
18	A	128	LEU	0	-0.044	-0.011	23.513	-0.019	-0.019	0.000	0.000	0.000	0.000
19	A	129	ASN	0	0.068	0.012	23.099	-0.030	-0.030	0.000	0.000	0.000	0.000
20	A	130	TYR	0	-0.008	0.011	26.202	-0.010	-0.010	0.000	0.000	0.000	0.000
21	A	131	LEU	0	0.038	0.004	27.853	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	132	GLU	-1	-0.839	-0.892	27.762	0.060	0.060	0.000	0.000	0.000	0.000
23	A	133	LEU	0	0.007	0.011	30.395	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	134	ILE	0	-0.114	-0.060	32.045	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	135	GLY	0	-0.009	-0.007	34.001	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	136	VAL	0	-0.056	-0.020	32.755	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	137	LEU	0	-0.044	-0.014	29.108	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	138	SER	0	0.023	-0.001	33.341	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	139	ILE	0	0.002	-0.008	31.447	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	140	ASN	0	-0.068	-0.023	34.382	0.005	0.005	0.000	0.000	0.000	0.000
31	A	141	PRO	0	0.103	0.014	35.948	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	142	ASP	-1	-0.869	-0.905	36.383	0.006	0.006	0.000	0.000	0.000	0.000
33	A	143	MET	0	-0.028	-0.025	31.877	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	144	TYR	0	-0.047	-0.018	31.990	0.009	0.009	0.000	0.000	0.000	0.000
35	A	145	GLU	-1	-0.871	-0.940	32.452	0.054	0.054	0.000	0.000	0.000	0.000
36	A	146	ARG	1	0.878	0.908	28.451	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	147	LYS	1	0.807	0.905	26.918	-0.050	-0.050	0.000	0.000	0.000	0.000
38	A	148	VAL	0	0.044	0.020	27.026	0.017	0.017	0.000	0.000	0.000	0.000
39	A	149	GLU	-1	-0.832	-0.891	26.624	0.037	0.037	0.000	0.000	0.000	0.000
40	A	150	ASN	0	0.015	-0.005	23.238	0.010	0.010	0.000	0.000	0.000	0.000
41	A	151	ILE	0	-0.065	-0.029	22.519	0.029	0.029	0.000	0.000	0.000	0.000
42	A	152	ARG	1	0.947	0.973	23.805	-0.095	-0.095	0.000	0.000	0.000	0.000
43	A	153	THR	0	-0.018	0.000	18.972	0.015	0.015	0.000	0.000	0.000	0.000
44	A	154	ILE	0	0.028	0.013	17.881	0.035	0.035	0.000	0.000	0.000	0.000
45	A	155	LEU	0	0.024	0.011	17.829	0.066	0.066	0.000	0.000	0.000	0.000
46	A	156	VAL	0	0.023	0.028	18.090	0.060	0.060	0.000	0.000	0.000	0.000
47	A	157	ASN	0	0.011	-0.004	14.311	0.016	0.016	0.000	0.000	0.000	0.000
48	A	158	ILE	0	0.027	0.020	13.799	0.121	0.121	0.000	0.000	0.000	0.000
49	A	159	HIS	0	-0.017	-0.007	14.416	0.124	0.124	0.000	0.000	0.000	0.000
50	A	160	HIS	0	-0.046	-0.008	13.132	0.041	0.041	0.000	0.000	0.000	0.000
51	A	161	LEU	0	0.006	0.003	8.107	0.113	0.113	0.000	0.000	0.000	0.000
52	A	162	LEU	0	0.003	-0.010	10.006	0.253	0.253	0.000	0.000	0.000	0.000
53	A	163	ASN	0	-0.044	-0.037	11.530	0.023	0.023	0.000	0.000	0.000	0.000
54	A	164	GLU	-1	-0.816	-0.881	7.163	1.394	1.394	0.000	0.000	0.000	0.000
55	A	165	TYR	0	-0.013	-0.026	7.123	-0.032	-0.032	0.000	0.000	0.000	0.000
56	A	166	ARG	1	0.922	0.953	8.561	-0.549	-0.549	0.000	0.000	0.000	0.000
57	A	167	PRO	0	0.018	0.007	7.705	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	168	HIS	0	-0.056	-0.040	6.396	0.465	0.465	0.000	0.000	0.000	0.000
59	A	169	GLN	0	0.067	0.026	8.681	0.165	0.165	0.000	0.000	0.000	0.000
60	A	170	SER	0	-0.012	0.007	11.877	-0.108	-0.108	0.000	0.000	0.000	0.000
61	A	171	ARG	1	0.926	0.970	6.617	-0.762	-0.762	0.000	0.000	0.000	0.000
62	A	172	GLU	-1	-0.886	-0.938	12.079	1.196	1.196	0.000	0.000	0.000	0.000
63	A	173	SER	0	-0.009	-0.005	14.578	-0.089	-0.089	0.000	0.000	0.000	0.000
64	A	174	LEU	0	-0.041	-0.017	16.238	-0.064	-0.064	0.000	0.000	0.000	0.000
65	A	175	ILE	0	-0.006	-0.014	13.822	-0.061	-0.061	0.000	0.000	0.000	0.000
66	A	176	MET	0	0.025	0.022	18.001	-0.020	-0.020	0.000	0.000	0.000	0.000
67	A	177	LEU	0	0.020	0.024	20.438	-0.050	-0.050	0.000	0.000	0.000	0.000
68	A	178	LEU	0	-0.035	-0.030	19.232	-0.034	-0.034	0.000	0.000	0.000	0.000
69	A	179	GLU	-1	-0.932	-0.966	19.862	0.516	0.516	0.000	0.000	0.000	0.000
70	A	180	GLU	-1	-0.928	-0.956	23.422	0.326	0.326	0.000	0.000	0.000	0.000
71	A	181	GLN	0	-0.044	-0.029	25.827	-0.040	-0.040	0.000	0.000	0.000	0.000
72	A	182	LEU	0	-0.021	-0.016	24.589	-0.023	-0.023	0.000	0.000	0.000	0.000
73	A	183	GLU	-1	-0.789	-0.870	27.531	0.230	0.230	0.000	0.000	0.000	0.000
74	A	184	TYR	0	0.013	0.012	29.350	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	185	LYS	1	0.782	0.872	30.517	-0.197	-0.197	0.000	0.000	0.000	0.000
76	A	186	ARG	1	0.880	0.935	26.589	-0.276	-0.276	0.000	0.000	0.000	0.000
77	A	187	GLY	0	-0.002	0.008	33.406	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	188	GLU	-1	-0.729	-0.854	35.374	0.154	0.154	0.000	0.000	0.000	0.000
79	A	189	ILE	0	-0.035	-0.017	34.817	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	190	ARG	1	0.834	0.894	32.155	-0.212	-0.212	0.000	0.000	0.000	0.000
81	A	191	GLU	-1	-0.934	-0.970	39.175	0.134	0.134	0.000	0.000	0.000	0.000
82	A	192	ILE	0	0.004	-0.003	40.899	-0.009	-0.009	0.000	0.000	0.000	0.000
83	A	193	GLU	-1	-0.871	-0.930	40.234	0.116	0.116	0.000	0.000	0.000	0.000
84	A	194	GLN	0	-0.075	-0.032	41.535	0.000	0.000	0.000	0.000	0.000	0.000
85	A	195	VAL	0	0.052	0.031	45.266	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	196	CYS	0	-0.039	-0.012	46.495	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	197	LYS	1	0.898	0.942	43.444	-0.117	-0.117	0.000	0.000	0.000	0.000
88	A	198	GLN	0	0.002	0.001	47.667	0.000	0.000	0.000	0.000	0.000	0.000
89	A	199	VAL	0	-0.037	-0.019	51.394	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	200	HIS	0	-0.008	-0.015	52.211	-0.005	-0.005	0.000	0.000	0.000	0.000
91	A	201	ASP	-1	-0.889	-0.939	52.593	0.082	0.082	0.000	0.000	0.000	0.000
92	A	202	LYS	1	0.882	0.932	53.399	-0.087	-0.087	0.000	0.000	0.000	0.000
93	A	203	LEU	0	-0.030	-0.005	57.169	-0.003	-0.003	0.000	0.000	0.000	0.000
94	A	204	THR	0	-0.071	-0.017	56.965	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	205	SER	0	-0.064	-0.035	57.930	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:111:ASN)