FMO DATABASE

FMODB ID: 43Z2N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-498503.069342
FMO2-HF: Nuclear repulsion	466911.200211
FMO2-HF: Total energy	-31591.869131
FMO2-MP2: Total energy	-31679.68634

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.
0.391	1.775	-0.007	-0.563	-0.814	0.001

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 : 0.021 / q_NPA : -0.002

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	-0.021	-0.014	3.876	-0.445	0.939	-0.007	-0.563	-0.814	0.001
4	D	91	THR	0	0.018	0.002	5.624	0.507	0.507	0.000	0.000	0.000	0.000
5	D	92	ALA	0	-0.029	-0.008	9.135	-0.119	-0.119	0.000	0.000	0.000	0.000
6	D	93	THR	0	-0.011	-0.006	11.909	0.026	0.026	0.000	0.000	0.000	0.000
7	D	94	PHE	0	-0.018	-0.002	13.637	0.002	0.002	0.000	0.000	0.000	0.000
8	D	95	SER	0	0.034	0.010	18.693	-0.012	-0.012	0.000	0.000	0.000	0.000
9	D	96	ILE	0	-0.025	-0.016	22.147	0.014	0.014	0.000	0.000	0.000	0.000
10	D	97	GLY	0	0.020	0.013	25.141	-0.004	-0.004	0.000	0.000	0.000	0.000
11	D	98	SER	0	-0.001	-0.008	28.150	-0.003	-0.003	0.000	0.000	0.000	0.000
12	D	99	THR	0	-0.049	-0.038	28.727	-0.005	-0.005	0.000	0.000	0.000	0.000
13	D	100	GLY	0	0.028	0.045	26.347	-0.006	-0.006	0.000	0.000	0.000	0.000
14	D	101	LEU	0	-0.033	-0.019	21.539	-0.004	-0.004	0.000	0.000	0.000	0.000
15	D	102	VAL	0	0.010	-0.005	17.634	0.012	0.012	0.000	0.000	0.000	0.000
16	D	103	VAL	0	-0.001	-0.001	13.951	-0.031	-0.031	0.000	0.000	0.000	0.000
17	D	104	TYR	0	-0.049	-0.038	12.693	0.025	0.025	0.000	0.000	0.000	0.000
18	D	105	ASP	-1	-0.806	-0.908	10.482	-0.183	-0.183	0.000	0.000	0.000	0.000
19	D	106	TYR	0	0.014	-0.007	7.587	0.064	0.064	0.000	0.000	0.000	0.000
20	D	107	GLN	0	-0.025	0.006	6.426	0.170	0.170	0.000	0.000	0.000	0.000
21	D	108	GLN	0	-0.076	-0.071	8.516	0.057	0.057	0.000	0.000	0.000	0.000
22	D	109	LEU	0	0.002	0.011	11.548	-0.016	-0.016	0.000	0.000	0.000	0.000
23	D	110	LEU	0	-0.032	-0.015	13.364	-0.043	-0.043	0.000	0.000	0.000	0.000
24	D	111	ILE	0	0.003	0.006	14.723	0.008	0.008	0.000	0.000	0.000	0.000
25	D	112	ALA	0	-0.013	0.000	17.396	-0.004	-0.004	0.000	0.000	0.000	0.000
26	D	113	TYR	0	0.003	-0.009	19.851	-0.007	-0.007	0.000	0.000	0.000	0.000
27	D	114	LYS	1	0.889	0.953	22.683	0.064	0.064	0.000	0.000	0.000	0.000
28	D	115	PRO	0	0.024	0.017	25.159	-0.005	-0.005	0.000	0.000	0.000	0.000
29	D	116	ALA	0	0.059	0.038	28.245	-0.001	-0.001	0.000	0.000	0.000	0.000
30	D	117	PRO	0	0.006	-0.002	27.824	-0.001	-0.001	0.000	0.000	0.000	0.000
31	D	118	GLY	0	0.021	0.013	29.096	0.004	0.004	0.000	0.000	0.000	0.000
32	D	119	THR	0	-0.020	-0.012	29.688	0.005	0.005	0.000	0.000	0.000	0.000
33	D	148	CYS	0	-0.086	-0.030	28.944	-0.004	-0.004	0.000	0.000	0.000	0.000
34	D	121	CYS	0	-0.047	-0.045	20.536	0.011	0.011	0.000	0.000	0.000	0.000
35	D	122	TYR	0	0.057	0.050	25.298	0.003	0.003	0.000	0.000	0.000	0.000
36	D	123	ILE	0	-0.022	-0.015	20.226	-0.001	-0.001	0.000	0.000	0.000	0.000
37	D	124	MET	0	-0.004	0.018	20.406	0.017	0.017	0.000	0.000	0.000	0.000
38	D	125	LYS	1	0.858	0.918	16.111	-0.169	-0.169	0.000	0.000	0.000	0.000
39	D	126	ILE	0	-0.026	-0.009	13.917	-0.009	-0.009	0.000	0.000	0.000	0.000
40	D	127	ALA	0	0.030	0.022	16.920	0.003	0.003	0.000	0.000	0.000	0.000
41	D	128	PRO	0	-0.006	-0.006	13.544	0.009	0.009	0.000	0.000	0.000	0.000
42	D	129	GLU	-1	-0.889	-0.949	14.037	0.669	0.669	0.000	0.000	0.000	0.000
43	D	130	SER	0	-0.060	-0.037	16.451	-0.030	-0.030	0.000	0.000	0.000	0.000
44	D	131	ILE	0	0.011	0.009	11.286	-0.065	-0.065	0.000	0.000	0.000	0.000
45	D	132	PRO	0	-0.009	0.020	15.611	-0.008	-0.008	0.000	0.000	0.000	0.000
46	D	133	SER	0	0.074	0.030	17.212	-0.002	-0.002	0.000	0.000	0.000	0.000
47	D	134	LEU	0	0.089	0.037	18.460	-0.013	-0.013	0.000	0.000	0.000	0.000
48	D	135	GLU	-1	-0.784	-0.843	19.978	0.066	0.066	0.000	0.000	0.000	0.000
49	D	136	ALA	0	-0.014	-0.004	21.416	-0.011	-0.011	0.000	0.000	0.000	0.000
50	D	137	LEU	0	-0.015	-0.003	19.270	-0.010	-0.010	0.000	0.000	0.000	0.000
51	D	138	THR	0	0.016	-0.014	22.635	-0.018	-0.018	0.000	0.000	0.000	0.000
52	D	139	ARG	1	0.801	0.862	25.463	-0.093	-0.093	0.000	0.000	0.000	0.000
53	D	140	LYS	1	0.899	0.957	22.871	-0.130	-0.130	0.000	0.000	0.000	0.000
54	D	141	VAL	0	0.014	-0.022	24.778	-0.005	-0.005	0.000	0.000	0.000	0.000
55	D	142	HIS	0	0.027	0.034	27.500	-0.008	-0.008	0.000	0.000	0.000	0.000
56	D	143	ASN	0	-0.009	-0.019	29.904	-0.008	-0.008	0.000	0.000	0.000	0.000
57	D	144	PHE	0	-0.061	-0.049	27.729	0.002	0.002	0.000	0.000	0.000	0.000
58	D	145	GLN	0	-0.014	0.019	30.935	-0.006	-0.006	0.000	0.000	0.000	0.000
59	D	146	MET	0	-0.087	-0.017	25.313	-0.003	-0.003	0.000	0.000	0.000	0.000
60	D	147	GLU	-1	-0.897	-0.972	29.904	0.021	0.021	0.000	0.000	0.000	0.000
61	D	180	PHE	0	0.050	0.022	14.664	-0.003	-0.003	0.000	0.000	0.000	0.000
62	D	181	LEU	0	0.007	-0.008	16.877	0.017	0.017	0.000	0.000	0.000	0.000
63	D	182	GLY	0	0.078	0.055	13.594	-0.005	-0.005	0.000	0.000	0.000	0.000
64	D	183	MET	0	0.018	0.008	12.871	0.034	0.034	0.000	0.000	0.000	0.000
65	D	184	ALA	0	0.026	0.029	12.539	0.030	0.030	0.000	0.000	0.000	0.000
66	D	185	VAL	0	0.053	0.022	14.489	0.030	0.030	0.000	0.000	0.000	0.000
67	D	186	SER	0	-0.026	-0.030	17.010	0.027	0.027	0.000	0.000	0.000	0.000
68	D	187	THR	0	-0.036	-0.026	17.113	0.010	0.010	0.000	0.000	0.000	0.000
69	D	188	LEU	0	-0.026	0.001	18.730	0.013	0.013	0.000	0.000	0.000	0.000
70	D	190	GLY	0	0.044	0.036	22.585	0.008	0.008	0.000	0.000	0.000	0.000
71	D	191	GLU	-1	-0.960	-0.997	24.390	-0.067	-0.067	0.000	0.000	0.000	0.000
72	D	192	VAL	0	-0.048	0.002	26.341	0.006	0.006	0.000	0.000	0.000	0.000
73	D	193	PRO	0	0.009	0.007	27.823	-0.001	-0.001	0.000	0.000	0.000	0.000
74	D	194	LEU	0	-0.004	0.003	23.721	0.000	0.000	0.000	0.000	0.000	0.000
75	D	195	TYR	0	0.001	-0.013	26.787	0.003	0.003	0.000	0.000	0.000	0.000
76	D	196	TYR	0	0.034	0.010	21.988	0.004	0.004	0.000	0.000	0.000	0.000
77	D	197	ILE	0	-0.030	-0.015	24.422	0.008	0.008	0.000	0.000	0.000	0.000

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