FMO DATABASE

FMODB ID: Q16RY

Calculation Name: 2YAD-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YAD

Chain ID: D

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	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	77
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-496543.852172
FMO2-HF: Nuclear repulsion	464952.310213
FMO2-HF: Total energy	-31591.541959
FMO2-MP2: Total energy	-31679.323556

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(D:88:LEU)

Summations of interaction energy for fragment #1(D:88:LEU)

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.
0.05	1.278	-0.012	-0.488	-0.728	0.002

Interaction energy analysis for fragmet #1(D:88:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.008

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	D	90	THR	0	-0.005	-0.002	3.857	-0.637	0.591	-0.012	-0.488	-0.728	0.002
4	D	91	THR	0	-0.001	-0.013	6.269	0.357	0.357	0.000	0.000	0.000	0.000
5	D	92	ALA	0	0.000	0.010	9.379	-0.146	-0.146	0.000	0.000	0.000	0.000
6	D	93	THR	0	-0.026	-0.002	12.214	0.054	0.054	0.000	0.000	0.000	0.000
7	D	94	PHE	0	0.010	0.005	13.670	0.002	0.002	0.000	0.000	0.000	0.000
8	D	95	SER	0	0.027	0.014	18.765	-0.008	-0.008	0.000	0.000	0.000	0.000
9	D	96	ILE	0	-0.034	-0.026	21.939	0.014	0.014	0.000	0.000	0.000	0.000
10	D	97	GLY	0	0.011	0.017	24.910	-0.004	-0.004	0.000	0.000	0.000	0.000
11	D	98	SER	0	-0.001	-0.010	28.039	-0.004	-0.004	0.000	0.000	0.000	0.000
12	D	99	THR	0	-0.039	-0.040	28.765	-0.005	-0.005	0.000	0.000	0.000	0.000
13	D	100	GLY	0	0.017	0.035	26.445	-0.007	-0.007	0.000	0.000	0.000	0.000
14	D	101	LEU	0	-0.026	-0.016	21.240	-0.007	-0.007	0.000	0.000	0.000	0.000
15	D	102	VAL	0	-0.006	-0.006	18.104	0.013	0.013	0.000	0.000	0.000	0.000
16	D	103	VAL	0	0.001	-0.002	14.314	-0.033	-0.033	0.000	0.000	0.000	0.000
17	D	104	TYR	0	-0.060	-0.046	13.023	0.027	0.027	0.000	0.000	0.000	0.000
18	D	105	ASP	-1	-0.840	-0.946	11.129	-0.273	-0.273	0.000	0.000	0.000	0.000
19	D	106	TYR	0	0.015	-0.020	8.120	0.071	0.071	0.000	0.000	0.000	0.000
20	D	107	GLN	0	-0.050	-0.001	6.380	0.139	0.139	0.000	0.000	0.000	0.000
21	D	108	GLN	0	0.013	0.003	8.749	0.067	0.067	0.000	0.000	0.000	0.000
22	D	109	LEU	0	0.008	0.012	11.979	-0.014	-0.014	0.000	0.000	0.000	0.000
23	D	110	LEU	0	-0.023	-0.002	13.826	-0.021	-0.021	0.000	0.000	0.000	0.000
24	D	111	ILE	0	0.024	0.017	15.202	-0.003	-0.003	0.000	0.000	0.000	0.000
25	D	112	ALA	0	-0.008	0.011	17.921	0.001	0.001	0.000	0.000	0.000	0.000
26	D	113	TYR	0	0.008	-0.010	20.087	-0.009	-0.009	0.000	0.000	0.000	0.000
27	D	114	LYS	1	0.946	0.980	22.964	0.086	0.086	0.000	0.000	0.000	0.000
28	D	115	PRO	0	0.022	0.023	25.246	-0.004	-0.004	0.000	0.000	0.000	0.000
29	D	116	ALA	0	0.068	0.040	28.417	-0.001	-0.001	0.000	0.000	0.000	0.000
30	D	117	PRO	0	-0.016	-0.012	28.540	-0.002	-0.002	0.000	0.000	0.000	0.000
31	D	118	GLY	0	0.022	0.013	29.509	0.005	0.005	0.000	0.000	0.000	0.000
32	D	119	THR	0	-0.001	-0.007	30.064	0.005	0.005	0.000	0.000	0.000	0.000
33	D	148	CYS	0	-0.080	-0.027	29.097	-0.003	-0.003	0.000	0.000	0.000	0.000
34	D	121	CYS	0	-0.084	-0.061	21.029	0.011	0.011	0.000	0.000	0.000	0.000
35	D	122	TYR	0	0.055	0.039	25.116	0.005	0.005	0.000	0.000	0.000	0.000
36	D	123	ILE	0	-0.022	-0.014	20.266	-0.004	-0.004	0.000	0.000	0.000	0.000
37	D	124	MET	0	-0.004	0.006	20.960	0.017	0.017	0.000	0.000	0.000	0.000
38	D	125	LYS	1	0.862	0.925	16.462	-0.134	-0.134	0.000	0.000	0.000	0.000
39	D	126	ILE	0	-0.055	-0.026	14.241	-0.006	-0.006	0.000	0.000	0.000	0.000
40	D	127	ALA	0	0.028	0.013	17.130	0.004	0.004	0.000	0.000	0.000	0.000
41	D	128	PRO	0	-0.008	-0.016	14.057	0.008	0.008	0.000	0.000	0.000	0.000
42	D	129	GLU	-1	-0.878	-0.935	13.835	0.683	0.683	0.000	0.000	0.000	0.000
43	D	130	SER	0	-0.072	-0.038	16.295	-0.021	-0.021	0.000	0.000	0.000	0.000
44	D	131	ILE	0	0.016	0.008	11.681	-0.063	-0.063	0.000	0.000	0.000	0.000
45	D	132	PRO	0	-0.023	0.004	15.930	-0.002	-0.002	0.000	0.000	0.000	0.000
46	D	133	SER	0	0.078	0.035	17.547	-0.011	-0.011	0.000	0.000	0.000	0.000
47	D	134	LEU	0	0.112	0.047	18.423	-0.009	-0.009	0.000	0.000	0.000	0.000
48	D	135	GLU	-1	-0.895	-0.940	20.154	0.048	0.048	0.000	0.000	0.000	0.000
49	D	136	ALA	0	-0.017	-0.011	21.612	-0.009	-0.009	0.000	0.000	0.000	0.000
50	D	137	LEU	0	-0.002	0.011	19.814	-0.007	-0.007	0.000	0.000	0.000	0.000
51	D	138	THR	0	0.016	-0.012	22.931	-0.015	-0.015	0.000	0.000	0.000	0.000
52	D	139	ARG	1	0.900	0.950	25.769	-0.071	-0.071	0.000	0.000	0.000	0.000
53	D	140	LYS	1	0.916	0.976	23.153	-0.110	-0.110	0.000	0.000	0.000	0.000
54	D	141	VAL	0	0.030	-0.011	25.205	-0.003	-0.003	0.000	0.000	0.000	0.000
55	D	142	HIS	0	0.018	0.029	27.940	-0.007	-0.007	0.000	0.000	0.000	0.000
56	D	143	ASN	0	-0.040	-0.035	29.829	-0.006	-0.006	0.000	0.000	0.000	0.000
57	D	144	PHE	0	-0.060	-0.043	28.345	0.003	0.003	0.000	0.000	0.000	0.000
58	D	145	GLN	0	0.011	0.029	31.444	-0.006	-0.006	0.000	0.000	0.000	0.000
59	D	146	MET	0	-0.084	-0.028	25.836	-0.004	-0.004	0.000	0.000	0.000	0.000
60	D	147	GLU	-1	-0.923	-0.972	30.272	0.005	0.005	0.000	0.000	0.000	0.000
61	D	180	PHE	0	0.008	-0.022	15.345	0.000	0.000	0.000	0.000	0.000	0.000
62	D	181	LEU	0	-0.002	0.000	17.378	0.014	0.014	0.000	0.000	0.000	0.000
63	D	182	GLY	0	0.107	0.073	14.050	-0.009	-0.009	0.000	0.000	0.000	0.000
64	D	183	MET	0	0.014	-0.002	13.327	0.036	0.036	0.000	0.000	0.000	0.000
65	D	184	ALA	0	0.006	0.011	13.187	0.025	0.025	0.000	0.000	0.000	0.000
66	D	185	VAL	0	0.061	0.028	15.062	0.030	0.030	0.000	0.000	0.000	0.000
67	D	186	SER	0	-0.006	-0.017	17.577	0.029	0.029	0.000	0.000	0.000	0.000
68	D	187	THR	0	-0.050	-0.024	17.715	0.012	0.012	0.000	0.000	0.000	0.000
69	D	188	LEU	0	-0.027	-0.009	19.248	0.015	0.015	0.000	0.000	0.000	0.000
70	D	190	GLY	0	0.037	0.040	23.081	0.011	0.011	0.000	0.000	0.000	0.000
71	D	191	GLU	-1	-0.959	-0.989	24.768	-0.086	-0.086	0.000	0.000	0.000	0.000
72	D	192	VAL	0	-0.053	-0.002	26.562	0.007	0.007	0.000	0.000	0.000	0.000
73	D	193	PRO	0	-0.013	-0.004	27.952	-0.001	-0.001	0.000	0.000	0.000	0.000
74	D	194	LEU	0	0.001	-0.003	23.856	0.000	0.000	0.000	0.000	0.000	0.000
75	D	195	TYR	0	0.017	-0.004	27.143	0.004	0.004	0.000	0.000	0.000	0.000
76	D	196	TYR	0	0.018	0.009	22.795	0.001	0.001	0.000	0.000	0.000	0.000
77	D	197	ILE	0	-0.028	-0.014	24.971	0.006	0.006	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(D:88:LEU)