FMO DATABASE

FMODB ID: ZY8JN

Calculation Name: 2YAD-E-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YAD

Chain ID: E

ChEMBL ID:

UniProt ID: P11686

Base Structure: X-ray

Registration Date: 2023-06-20

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	76
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-487324.340665
FMO2-HF: Nuclear repulsion	456095.512181
FMO2-HF: Total energy	-31228.828484
FMO2-MP2: Total energy	-31315.476257

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(E:89:VAL)

Summations of interaction energy for fragment #1(E:89:VAL)

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.
-6.976	-1.12	3.919	-3.218	-6.558	-0.015

Interaction energy analysis for fragmet #1(E:89:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.019

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	E	91	THR	0	-0.022	-0.001	2.979	-2.487	-0.150	0.237	-1.140	-1.435	-0.003
4	E	92	ALA	0	0.011	0.011	4.726	0.357	0.442	-0.001	-0.005	-0.079	0.000
5	E	93	THR	0	-0.012	-0.006	6.934	-0.022	-0.022	0.000	0.000	0.000	0.000
6	E	94	PHE	0	-0.020	-0.014	9.386	0.049	0.049	0.000	0.000	0.000	0.000
7	E	95	SER	0	0.034	0.019	13.530	-0.003	-0.003	0.000	0.000	0.000	0.000
8	E	96	ILE	0	-0.037	-0.022	16.545	-0.004	-0.004	0.000	0.000	0.000	0.000
9	E	97	GLY	0	0.015	0.015	19.585	0.004	0.004	0.000	0.000	0.000	0.000
10	E	98	SER	0	-0.016	-0.017	22.820	0.001	0.001	0.000	0.000	0.000	0.000
11	E	99	THR	0	-0.027	-0.025	23.584	0.009	0.009	0.000	0.000	0.000	0.000
12	E	100	GLY	0	0.033	0.040	20.820	-0.002	-0.002	0.000	0.000	0.000	0.000
13	E	101	LEU	0	-0.039	-0.023	16.251	0.005	0.005	0.000	0.000	0.000	0.000
14	E	102	VAL	0	0.003	-0.005	12.104	-0.012	-0.012	0.000	0.000	0.000	0.000
15	E	103	VAL	0	0.002	0.010	9.214	0.005	0.005	0.000	0.000	0.000	0.000
16	E	104	TYR	0	-0.037	-0.041	7.217	0.019	0.019	0.000	0.000	0.000	0.000
17	E	105	ASP	-1	-0.836	-0.935	5.958	-1.890	-1.890	0.000	0.000	0.000	0.000
18	E	106	TYR	0	0.033	-0.003	2.623	-0.874	0.068	0.581	-0.292	-1.231	0.002
19	E	107	GLN	0	-0.007	-0.002	2.214	-3.566	-1.217	3.103	-1.761	-3.691	-0.014
20	E	108	GLN	0	-0.014	-0.008	4.609	0.461	0.604	-0.001	-0.020	-0.122	0.000
21	E	109	LEU	0	-0.013	0.001	7.363	0.291	0.291	0.000	0.000	0.000	0.000
22	E	110	LEU	0	-0.038	-0.014	9.034	0.215	0.215	0.000	0.000	0.000	0.000
23	E	111	ILE	0	0.022	0.015	9.940	-0.094	-0.094	0.000	0.000	0.000	0.000
24	E	112	ALA	0	-0.003	0.004	12.293	0.055	0.055	0.000	0.000	0.000	0.000
25	E	113	TYR	0	0.006	-0.003	14.471	-0.003	-0.003	0.000	0.000	0.000	0.000
26	E	114	LYS	1	0.919	0.954	17.104	0.134	0.134	0.000	0.000	0.000	0.000
27	E	115	PRO	0	0.033	0.026	19.621	0.006	0.006	0.000	0.000	0.000	0.000
28	E	116	ALA	0	0.045	0.022	22.567	0.011	0.011	0.000	0.000	0.000	0.000
29	E	117	PRO	0	-0.012	-0.011	23.825	-0.007	-0.007	0.000	0.000	0.000	0.000
30	E	118	GLY	0	0.015	0.009	24.746	0.003	0.003	0.000	0.000	0.000	0.000
31	E	119	THR	0	-0.006	-0.003	24.728	-0.002	-0.002	0.000	0.000	0.000	0.000
32	E	148	CYS	0	-0.133	-0.049	23.820	0.013	0.013	0.000	0.000	0.000	0.000
33	E	121	CYS	0	-0.051	-0.039	16.803	0.006	0.006	0.000	0.000	0.000	0.000
34	E	122	TYR	0	0.047	0.029	19.494	0.005	0.005	0.000	0.000	0.000	0.000
35	E	123	ILE	0	-0.014	-0.006	15.502	-0.033	-0.033	0.000	0.000	0.000	0.000
36	E	124	MET	0	-0.024	-0.004	15.644	0.037	0.037	0.000	0.000	0.000	0.000
37	E	125	LYS	1	0.889	0.942	11.817	0.618	0.618	0.000	0.000	0.000	0.000
38	E	126	ILE	0	-0.033	-0.013	8.369	0.046	0.046	0.000	0.000	0.000	0.000
39	E	127	ALA	0	0.020	0.007	12.228	-0.048	-0.048	0.000	0.000	0.000	0.000
40	E	128	PRO	0	0.031	-0.006	10.300	-0.015	-0.015	0.000	0.000	0.000	0.000
41	E	129	GLU	-1	-0.916	-0.960	9.138	-0.684	-0.684	0.000	0.000	0.000	0.000
42	E	130	SER	0	-0.047	-0.007	11.819	0.088	0.088	0.000	0.000	0.000	0.000
43	E	131	ILE	0	-0.036	-0.019	7.200	0.024	0.024	0.000	0.000	0.000	0.000
44	E	132	PRO	0	0.001	0.024	11.438	0.048	0.048	0.000	0.000	0.000	0.000
45	E	133	SER	0	0.072	0.029	12.569	-0.031	-0.031	0.000	0.000	0.000	0.000
46	E	134	LEU	0	0.103	0.042	13.677	-0.004	-0.004	0.000	0.000	0.000	0.000
47	E	135	GLU	-1	-0.865	-0.921	15.177	-0.121	-0.121	0.000	0.000	0.000	0.000
48	E	136	ALA	0	-0.048	-0.024	17.192	0.014	0.014	0.000	0.000	0.000	0.000
49	E	137	LEU	0	-0.011	-0.002	14.168	0.009	0.009	0.000	0.000	0.000	0.000
50	E	138	THR	0	0.018	-0.001	17.852	0.014	0.014	0.000	0.000	0.000	0.000
51	E	139	ARG	1	0.898	0.941	20.365	0.160	0.160	0.000	0.000	0.000	0.000
52	E	140	LYS	1	0.933	0.986	19.124	0.268	0.268	0.000	0.000	0.000	0.000
53	E	141	VAL	0	0.018	0.008	19.745	0.005	0.005	0.000	0.000	0.000	0.000
54	E	142	HIS	0	0.058	0.047	22.483	0.008	0.008	0.000	0.000	0.000	0.000
55	E	143	ASN	0	-0.043	-0.037	25.566	0.014	0.014	0.000	0.000	0.000	0.000
56	E	144	PHE	0	-0.053	-0.040	24.356	0.001	0.001	0.000	0.000	0.000	0.000
57	E	145	GLN	0	-0.050	-0.018	26.508	0.007	0.007	0.000	0.000	0.000	0.000
58	E	146	MET	0	-0.067	-0.019	19.960	-0.003	-0.003	0.000	0.000	0.000	0.000
59	E	147	GLU	-1	-0.834	-0.933	24.379	-0.132	-0.132	0.000	0.000	0.000	0.000
60	E	180	PHE	0	-0.006	-0.014	15.251	0.002	0.002	0.000	0.000	0.000	0.000
61	E	181	LEU	0	0.014	0.007	13.525	-0.031	-0.031	0.000	0.000	0.000	0.000
62	E	182	GLY	0	0.098	0.056	10.424	-0.125	-0.125	0.000	0.000	0.000	0.000
63	E	183	MET	0	-0.004	-0.003	10.380	0.042	0.042	0.000	0.000	0.000	0.000
64	E	184	ALA	0	0.032	0.028	9.578	0.049	0.049	0.000	0.000	0.000	0.000
65	E	185	VAL	0	0.059	0.018	10.940	0.043	0.043	0.000	0.000	0.000	0.000
66	E	186	SER	0	-0.023	-0.028	13.326	0.050	0.050	0.000	0.000	0.000	0.000
67	E	187	THR	0	-0.048	-0.022	14.934	0.047	0.047	0.000	0.000	0.000	0.000
68	E	188	LEU	0	-0.002	0.008	14.546	0.020	0.020	0.000	0.000	0.000	0.000
69	E	190	GLY	0	0.047	0.044	18.903	0.004	0.004	0.000	0.000	0.000	0.000
70	E	191	GLU	-1	-0.971	-0.991	21.051	-0.039	-0.039	0.000	0.000	0.000	0.000
71	E	192	VAL	0	-0.045	-0.009	21.951	0.006	0.006	0.000	0.000	0.000	0.000
72	E	193	PRO	0	-0.007	0.005	23.466	-0.010	-0.010	0.000	0.000	0.000	0.000
73	E	194	LEU	0	-0.009	-0.010	19.461	-0.014	-0.014	0.000	0.000	0.000	0.000
74	E	195	TYR	0	0.004	-0.002	22.051	0.010	0.010	0.000	0.000	0.000	0.000
75	E	196	TYR	0	0.013	0.000	18.047	-0.012	-0.012	0.000	0.000	0.000	0.000
76	E	197	ILE	0	-0.017	-0.014	20.178	0.009	0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:89:VAL)