FMO DATABASE

FMODB ID: R52Z8

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

Total energy (hartree)

FMO2-HF: Electronic energy	-489834.891486
FMO2-HF: Nuclear repulsion	458605.878172
FMO2-HF: Total energy	-31229.013314
FMO2-MP2: Total energy	-31315.685033

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.
-9.066	-4.383	7.454	-4.498	-7.638	-0.032

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 : -0.025 / 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

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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	-0.019	-0.004	2.796	-3.225	-0.644	0.426	-1.383	-1.624	-0.007
4	E	92	ALA	0	0.023	0.032	4.964	0.370	0.473	-0.001	-0.004	-0.098	0.000
5	E	93	THR	0	-0.014	-0.015	6.619	-0.014	-0.014	0.000	0.000	0.000	0.000
6	E	94	PHE	0	-0.036	-0.017	9.271	0.047	0.047	0.000	0.000	0.000	0.000
7	E	95	SER	0	0.037	0.013	13.393	0.009	0.009	0.000	0.000	0.000	0.000
8	E	96	ILE	0	-0.020	-0.012	16.687	-0.009	-0.009	0.000	0.000	0.000	0.000
9	E	97	GLY	0	0.016	0.009	19.689	0.008	0.008	0.000	0.000	0.000	0.000
10	E	98	SER	0	-0.007	-0.011	22.738	0.001	0.001	0.000	0.000	0.000	0.000
11	E	99	THR	0	-0.055	-0.040	23.594	0.010	0.010	0.000	0.000	0.000	0.000
12	E	100	GLY	0	0.035	0.048	20.841	0.000	0.000	0.000	0.000	0.000	0.000
13	E	101	LEU	0	-0.035	-0.021	16.524	0.002	0.002	0.000	0.000	0.000	0.000
14	E	102	VAL	0	0.013	-0.006	11.974	-0.012	-0.012	0.000	0.000	0.000	0.000
15	E	103	VAL	0	-0.006	0.006	9.003	0.010	0.010	0.000	0.000	0.000	0.000
16	E	104	TYR	0	-0.047	-0.042	7.008	0.051	0.051	0.000	0.000	0.000	0.000
17	E	105	ASP	-1	-0.806	-0.927	6.085	-1.699	-1.699	0.000	0.000	0.000	0.000
18	E	106	TYR	0	0.033	-0.009	2.396	-0.933	0.202	1.010	-0.437	-1.708	0.001
19	E	107	GLN	0	-0.001	0.012	2.217	-5.129	-4.387	6.020	-2.665	-4.096	-0.026
20	E	108	GLN	0	-0.031	-0.015	4.823	0.581	0.703	-0.001	-0.009	-0.112	0.000
21	E	109	LEU	0	-0.020	-0.004	7.091	0.295	0.295	0.000	0.000	0.000	0.000
22	E	110	LEU	0	-0.026	-0.007	8.684	0.239	0.239	0.000	0.000	0.000	0.000
23	E	111	ILE	0	0.011	0.009	9.668	-0.123	-0.123	0.000	0.000	0.000	0.000
24	E	112	ALA	0	-0.005	0.003	12.049	0.058	0.058	0.000	0.000	0.000	0.000
25	E	113	TYR	0	-0.029	-0.038	14.358	-0.016	-0.016	0.000	0.000	0.000	0.000
26	E	114	LYS	1	0.904	0.965	17.216	0.122	0.122	0.000	0.000	0.000	0.000
27	E	115	PRO	0	0.035	0.028	19.934	0.006	0.006	0.000	0.000	0.000	0.000
28	E	116	ALA	0	0.040	0.029	22.795	0.010	0.010	0.000	0.000	0.000	0.000
29	E	117	PRO	0	0.008	-0.002	23.623	-0.006	-0.006	0.000	0.000	0.000	0.000
30	E	118	GLY	0	0.015	0.009	24.619	0.002	0.002	0.000	0.000	0.000	0.000
31	E	119	THR	0	-0.025	-0.017	24.421	-0.004	-0.004	0.000	0.000	0.000	0.000
32	E	148	CYS	0	-0.126	-0.050	23.881	0.015	0.015	0.000	0.000	0.000	0.000
33	E	121	CYS	0	-0.066	-0.049	16.545	-0.005	-0.005	0.000	0.000	0.000	0.000
34	E	122	TYR	0	0.046	0.031	19.850	0.001	0.001	0.000	0.000	0.000	0.000
35	E	123	ILE	0	-0.024	-0.015	15.410	-0.033	-0.033	0.000	0.000	0.000	0.000
36	E	124	MET	0	0.022	0.024	15.494	0.038	0.038	0.000	0.000	0.000	0.000
37	E	125	LYS	1	0.865	0.929	11.616	0.642	0.642	0.000	0.000	0.000	0.000
38	E	126	ILE	0	-0.030	-0.008	8.489	0.051	0.051	0.000	0.000	0.000	0.000
39	E	127	ALA	0	0.026	0.008	12.426	-0.040	-0.040	0.000	0.000	0.000	0.000
40	E	128	PRO	0	0.042	-0.004	9.912	-0.035	-0.035	0.000	0.000	0.000	0.000
41	E	129	GLU	-1	-0.919	-0.953	8.857	-0.750	-0.750	0.000	0.000	0.000	0.000
42	E	130	SER	0	-0.060	-0.013	11.606	0.102	0.102	0.000	0.000	0.000	0.000
43	E	131	ILE	0	-0.028	-0.009	7.191	0.013	0.013	0.000	0.000	0.000	0.000
44	E	132	PRO	0	0.005	0.018	11.361	0.050	0.050	0.000	0.000	0.000	0.000
45	E	133	SER	0	0.082	0.033	12.378	-0.039	-0.039	0.000	0.000	0.000	0.000
46	E	134	LEU	0	0.087	0.038	13.450	0.009	0.009	0.000	0.000	0.000	0.000
47	E	135	GLU	-1	-0.805	-0.867	14.904	-0.140	-0.140	0.000	0.000	0.000	0.000
48	E	136	ALA	0	-0.025	-0.008	16.722	0.017	0.017	0.000	0.000	0.000	0.000
49	E	137	LEU	0	-0.019	-0.006	13.851	0.015	0.015	0.000	0.000	0.000	0.000
50	E	138	THR	0	0.020	-0.003	17.445	0.020	0.020	0.000	0.000	0.000	0.000
51	E	139	ARG	1	0.842	0.888	20.021	0.182	0.182	0.000	0.000	0.000	0.000
52	E	140	LYS	1	0.864	0.940	18.964	0.292	0.292	0.000	0.000	0.000	0.000
53	E	141	VAL	0	0.004	-0.005	19.597	0.007	0.007	0.000	0.000	0.000	0.000
54	E	142	HIS	0	0.059	0.041	22.276	0.010	0.010	0.000	0.000	0.000	0.000
55	E	143	ASN	0	-0.030	-0.026	25.045	0.015	0.015	0.000	0.000	0.000	0.000
56	E	144	PHE	0	-0.050	-0.031	23.997	0.000	0.000	0.000	0.000	0.000	0.000
57	E	145	GLN	0	-0.047	-0.021	26.170	0.010	0.010	0.000	0.000	0.000	0.000
58	E	146	MET	0	-0.046	0.009	19.552	-0.002	-0.002	0.000	0.000	0.000	0.000
59	E	147	GLU	-1	-0.784	-0.911	24.073	-0.146	-0.146	0.000	0.000	0.000	0.000
60	E	180	PHE	0	-0.008	-0.019	15.135	0.006	0.006	0.000	0.000	0.000	0.000
61	E	181	LEU	0	0.016	0.010	13.449	-0.037	-0.037	0.000	0.000	0.000	0.000
62	E	182	GLY	0	0.107	0.066	10.255	-0.105	-0.105	0.000	0.000	0.000	0.000
63	E	183	MET	0	-0.006	0.000	10.268	0.016	0.016	0.000	0.000	0.000	0.000
64	E	184	ALA	0	0.040	0.034	9.503	0.024	0.024	0.000	0.000	0.000	0.000
65	E	185	VAL	0	0.044	0.019	10.644	0.023	0.023	0.000	0.000	0.000	0.000
66	E	186	SER	0	-0.027	-0.034	13.086	0.040	0.040	0.000	0.000	0.000	0.000
67	E	187	THR	0	-0.039	-0.022	14.768	0.040	0.040	0.000	0.000	0.000	0.000
68	E	188	LEU	0	-0.022	-0.003	14.431	0.013	0.013	0.000	0.000	0.000	0.000
69	E	190	GLY	0	0.051	0.041	18.683	0.007	0.007	0.000	0.000	0.000	0.000
70	E	191	GLU	-1	-0.975	-1.004	21.050	-0.025	-0.025	0.000	0.000	0.000	0.000
71	E	192	VAL	0	-0.049	0.000	22.076	0.003	0.003	0.000	0.000	0.000	0.000
72	E	193	PRO	0	0.011	0.013	23.853	-0.007	-0.007	0.000	0.000	0.000	0.000
73	E	194	LEU	0	-0.001	-0.006	19.766	-0.014	-0.014	0.000	0.000	0.000	0.000
74	E	195	TYR	0	-0.012	-0.016	21.877	0.010	0.010	0.000	0.000	0.000	0.000
75	E	196	TYR	0	0.025	0.004	18.046	-0.012	-0.012	0.000	0.000	0.000	0.000
76	E	197	ILE	0	-0.022	-0.010	19.544	0.002	0.002	0.000	0.000	0.000	0.000

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