FMO DATABASE

FMODB ID: JLMJ9

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	OptH
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	-598814.595843
FMO2-HF: Nuclear repulsion	558687.95658
FMO2-HF: Total energy	-40126.639263
FMO2-MP2: Total energy	-40244.514401

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.
-37.514	-32.481	10.683	-6.371	-9.344	0.066

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 : 0.075 / q_NPA : 0.025

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	0.048	0.034	2.003	-16.941	-14.250	6.300	-4.072	-4.918	0.038
4	A	114	TYR	0	-0.009	0.002	2.260	-12.881	-11.096	4.370	-2.162	-3.992	0.027
5	A	115	LYS	1	0.887	0.936	4.089	-5.543	-4.986	0.013	-0.137	-0.434	0.001
6	A	116	ILE	0	0.027	0.022	5.948	-1.083	-1.083	0.000	0.000	0.000	0.000
7	A	117	GLN	0	-0.047	-0.023	6.860	-1.121	-1.121	0.000	0.000	0.000	0.000
8	A	118	GLU	-1	-0.792	-0.899	8.014	-0.995	-0.995	0.000	0.000	0.000	0.000
9	A	119	LEU	0	0.007	0.020	9.984	-0.143	-0.143	0.000	0.000	0.000	0.000
10	A	120	ARG	1	0.954	0.963	11.038	-1.606	-1.606	0.000	0.000	0.000	0.000
11	A	121	LYS	1	0.802	0.905	10.154	0.659	0.659	0.000	0.000	0.000	0.000
12	A	122	LEU	0	0.029	0.015	13.264	-0.053	-0.053	0.000	0.000	0.000	0.000
13	A	123	LEU	0	0.054	0.018	16.124	-0.045	-0.045	0.000	0.000	0.000	0.000
14	A	124	LYS	1	0.929	0.981	16.092	-0.292	-0.292	0.000	0.000	0.000	0.000
15	A	125	SER	0	0.017	-0.005	18.759	-0.031	-0.031	0.000	0.000	0.000	0.000
16	A	126	LEU	0	0.014	0.030	20.214	-0.023	-0.023	0.000	0.000	0.000	0.000
17	A	127	LEU	0	0.011	0.004	21.824	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	128	LEU	0	-0.023	-0.005	23.178	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	129	ASN	0	0.046	-0.013	23.001	-0.021	-0.021	0.000	0.000	0.000	0.000
20	A	130	TYR	0	-0.011	0.008	26.081	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	131	LEU	0	0.033	0.001	27.495	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	132	GLU	-1	-0.897	-0.939	28.168	-0.024	-0.024	0.000	0.000	0.000	0.000
23	A	133	LEU	0	-0.004	0.006	30.284	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	134	ILE	0	-0.112	-0.056	31.929	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	135	GLY	0	-0.013	-0.012	33.880	0.003	0.003	0.000	0.000	0.000	0.000
26	A	136	VAL	0	-0.053	-0.018	32.429	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	137	LEU	0	-0.048	-0.017	28.803	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	138	SER	0	-0.007	-0.012	33.087	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	139	ILE	0	0.051	0.008	31.025	-0.007	-0.007	0.000	0.000	0.000	0.000
30	A	140	ASN	0	-0.059	-0.018	34.282	0.006	0.006	0.000	0.000	0.000	0.000
31	A	141	PRO	0	0.090	0.019	35.848	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	142	ASP	-1	-0.869	-0.914	36.428	-0.051	-0.051	0.000	0.000	0.000	0.000
33	A	143	MET	0	-0.028	-0.028	31.634	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	144	TYR	0	-0.056	-0.023	31.883	0.007	0.007	0.000	0.000	0.000	0.000
35	A	145	GLU	-1	-0.838	-0.922	32.340	0.014	0.014	0.000	0.000	0.000	0.000
36	A	146	ARG	1	0.928	0.962	28.111	0.068	0.068	0.000	0.000	0.000	0.000
37	A	147	LYS	1	0.864	0.962	26.907	0.036	0.036	0.000	0.000	0.000	0.000
38	A	148	VAL	0	0.064	0.035	26.908	0.015	0.015	0.000	0.000	0.000	0.000
39	A	149	GLU	-1	-0.901	-0.959	26.291	-0.005	-0.005	0.000	0.000	0.000	0.000
40	A	150	ASN	0	-0.017	-0.018	23.202	0.007	0.007	0.000	0.000	0.000	0.000
41	A	151	ILE	0	-0.066	-0.027	22.398	0.024	0.024	0.000	0.000	0.000	0.000
42	A	152	ARG	1	0.954	0.974	23.692	-0.060	-0.060	0.000	0.000	0.000	0.000
43	A	153	THR	0	-0.009	0.007	18.777	0.020	0.020	0.000	0.000	0.000	0.000
44	A	154	ILE	0	0.015	0.008	17.776	0.032	0.032	0.000	0.000	0.000	0.000
45	A	155	LEU	0	0.017	0.001	17.697	0.072	0.072	0.000	0.000	0.000	0.000
46	A	156	VAL	0	0.018	0.021	17.779	0.075	0.075	0.000	0.000	0.000	0.000
47	A	157	ASN	0	0.003	-0.012	13.855	0.022	0.022	0.000	0.000	0.000	0.000
48	A	158	ILE	0	0.020	0.017	13.664	0.132	0.132	0.000	0.000	0.000	0.000
49	A	159	HIS	0	0.001	0.011	14.327	0.176	0.176	0.000	0.000	0.000	0.000
50	A	160	HIS	0	-0.046	-0.004	13.158	0.064	0.064	0.000	0.000	0.000	0.000
51	A	161	LEU	0	0.033	0.011	8.109	0.164	0.164	0.000	0.000	0.000	0.000
52	A	162	LEU	0	0.000	-0.015	10.068	0.366	0.366	0.000	0.000	0.000	0.000
53	A	163	ASN	0	-0.071	-0.056	11.586	0.126	0.126	0.000	0.000	0.000	0.000
54	A	164	GLU	-1	-0.856	-0.918	7.289	1.332	1.332	0.000	0.000	0.000	0.000
55	A	165	TYR	0	0.023	-0.017	6.730	-0.032	-0.032	0.000	0.000	0.000	0.000
56	A	166	ARG	1	0.952	0.971	8.612	-0.693	-0.693	0.000	0.000	0.000	0.000
57	A	167	PRO	0	0.002	0.001	7.680	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	168	HIS	0	-0.035	-0.028	6.771	0.428	0.428	0.000	0.000	0.000	0.000
59	A	169	GLN	0	0.065	0.018	8.699	0.204	0.204	0.000	0.000	0.000	0.000
60	A	170	SER	0	-0.016	0.009	11.882	-0.212	-0.212	0.000	0.000	0.000	0.000
61	A	171	ARG	1	0.918	0.970	7.374	-1.519	-1.519	0.000	0.000	0.000	0.000
62	A	172	GLU	-1	-0.881	-0.936	12.191	1.608	1.608	0.000	0.000	0.000	0.000
63	A	173	SER	0	-0.011	-0.001	14.584	-0.140	-0.140	0.000	0.000	0.000	0.000
64	A	174	LEU	0	-0.036	-0.015	16.274	-0.091	-0.091	0.000	0.000	0.000	0.000
65	A	175	ILE	0	-0.017	-0.017	13.792	-0.085	-0.085	0.000	0.000	0.000	0.000
66	A	176	MET	0	0.043	0.030	18.034	-0.038	-0.038	0.000	0.000	0.000	0.000
67	A	177	LEU	0	0.036	0.029	20.469	-0.070	-0.070	0.000	0.000	0.000	0.000
68	A	178	LEU	0	-0.055	-0.038	19.348	-0.054	-0.054	0.000	0.000	0.000	0.000
69	A	179	GLU	-1	-0.927	-0.969	19.602	0.743	0.743	0.000	0.000	0.000	0.000
70	A	180	GLU	-1	-0.923	-0.950	23.449	0.462	0.462	0.000	0.000	0.000	0.000
71	A	181	GLN	0	-0.059	-0.035	25.867	-0.047	-0.047	0.000	0.000	0.000	0.000
72	A	182	LEU	0	-0.044	-0.031	24.845	-0.036	-0.036	0.000	0.000	0.000	0.000
73	A	183	GLU	-1	-0.836	-0.904	27.554	0.326	0.326	0.000	0.000	0.000	0.000
74	A	184	TYR	0	0.015	0.009	29.375	-0.026	-0.026	0.000	0.000	0.000	0.000
75	A	185	LYS	1	0.936	0.962	30.147	-0.317	-0.317	0.000	0.000	0.000	0.000
76	A	186	ARG	1	0.916	0.963	26.941	-0.384	-0.384	0.000	0.000	0.000	0.000
77	A	187	GLY	0	0.003	0.006	33.429	-0.014	-0.014	0.000	0.000	0.000	0.000
78	A	188	GLU	-1	-0.861	-0.931	35.398	0.223	0.223	0.000	0.000	0.000	0.000
79	A	189	ILE	0	-0.046	-0.023	35.175	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	190	ARG	1	0.855	0.916	32.407	-0.294	-0.294	0.000	0.000	0.000	0.000
81	A	191	GLU	-1	-0.946	-0.969	39.195	0.191	0.191	0.000	0.000	0.000	0.000
82	A	192	ILE	0	0.002	-0.005	41.186	-0.013	-0.013	0.000	0.000	0.000	0.000
83	A	193	GLU	-1	-0.951	-0.990	40.270	0.175	0.175	0.000	0.000	0.000	0.000
84	A	194	GLN	0	-0.072	-0.029	41.960	0.001	0.001	0.000	0.000	0.000	0.000
85	A	195	VAL	0	0.029	0.022	45.286	-0.010	-0.010	0.000	0.000	0.000	0.000
86	A	196	CYS	0	-0.009	0.006	46.850	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	197	LYS	1	0.976	0.989	44.427	-0.161	-0.161	0.000	0.000	0.000	0.000
88	A	198	GLN	0	0.014	-0.001	47.828	0.000	0.000	0.000	0.000	0.000	0.000
89	A	199	VAL	0	-0.033	-0.010	51.414	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	200	HIS	0	0.000	-0.012	52.378	-0.007	-0.007	0.000	0.000	0.000	0.000
91	A	201	ASP	-1	-0.917	-0.958	52.923	0.113	0.113	0.000	0.000	0.000	0.000
92	A	202	LYS	1	0.867	0.918	53.377	-0.121	-0.121	0.000	0.000	0.000	0.000
93	A	203	LEU	0	-0.032	-0.007	57.189	-0.004	-0.004	0.000	0.000	0.000	0.000
94	A	204	THR	0	-0.059	-0.002	57.024	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	205	SER	0	-0.060	-0.030	57.838	-0.002	-0.002	0.000	0.000	0.000	0.000

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