FMO DATABASE

FMODB ID: VR8L1

Calculation Name: 2YAD-E-Xray320

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	79
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-494708.846424
FMO2-HF: Nuclear repulsion	463157.93421
FMO2-HF: Total energy	-31550.912214
FMO2-MP2: Total energy	-31638.487348

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:88:ACE )

Summations of interaction energy for fragment #1(E:88:ACE )

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.
-0.534	0.958	0.445	-0.876	-1.06	-0.006

Interaction energy analysis for fragmet #1(E:88:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.014

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	90	THR	0	-0.039	-0.007	3.836	1.122	1.884	-0.005	-0.307	-0.449	0.000
4	E	91	THR	0	-0.022	0.000	6.625	-0.034	-0.034	0.000	0.000	0.000	0.000
5	E	92	ALA	0	0.029	0.025	9.527	0.013	0.013	0.000	0.000	0.000	0.000
6	E	93	THR	0	-0.019	-0.011	12.848	0.063	0.063	0.000	0.000	0.000	0.000
7	E	94	PHE	0	-0.016	-0.013	15.717	-0.010	-0.010	0.000	0.000	0.000	0.000
8	E	95	SER	0	0.027	0.016	19.503	0.014	0.014	0.000	0.000	0.000	0.000
9	E	96	ILE	0	-0.031	-0.017	22.838	-0.007	-0.007	0.000	0.000	0.000	0.000
10	E	97	GLY	0	0.014	0.015	25.596	0.009	0.009	0.000	0.000	0.000	0.000
11	E	98	SER	0	-0.032	-0.026	28.734	-0.004	-0.004	0.000	0.000	0.000	0.000
12	E	99	THR	0	-0.027	-0.031	28.732	0.001	0.001	0.000	0.000	0.000	0.000
13	E	100	GLY	0	0.035	0.044	26.209	0.003	0.003	0.000	0.000	0.000	0.000
14	E	101	LEU	0	-0.041	-0.027	21.093	-0.010	-0.010	0.000	0.000	0.000	0.000
15	E	102	VAL	0	-0.001	-0.002	17.930	0.010	0.010	0.000	0.000	0.000	0.000
16	E	103	VAL	0	-0.003	0.005	13.542	-0.020	-0.020	0.000	0.000	0.000	0.000
17	E	104	TYR	0	-0.016	-0.021	13.031	0.033	0.033	0.000	0.000	0.000	0.000
18	E	105	ASP	-1	-0.846	-0.947	8.711	-0.229	-0.229	0.000	0.000	0.000	0.000
19	E	106	TYR	0	0.031	-0.003	7.759	0.067	0.067	0.000	0.000	0.000	0.000
20	E	107	GLN	0	-0.016	-0.008	2.998	-1.621	-0.891	0.450	-0.569	-0.611	-0.006
21	E	108	GLN	0	-0.001	0.001	6.525	0.151	0.151	0.000	0.000	0.000	0.000
22	E	109	LEU	0	-0.018	0.002	9.847	0.032	0.032	0.000	0.000	0.000	0.000
23	E	110	LEU	0	-0.018	-0.008	11.688	0.044	0.044	0.000	0.000	0.000	0.000
24	E	111	ILE	0	0.006	0.002	13.757	-0.042	-0.042	0.000	0.000	0.000	0.000
25	E	112	ALA	0	0.010	0.014	16.563	0.028	0.028	0.000	0.000	0.000	0.000
26	E	113	TYR	0	0.007	-0.005	18.547	-0.018	-0.018	0.000	0.000	0.000	0.000
27	E	114	LYS	1	0.926	0.955	21.797	0.046	0.046	0.000	0.000	0.000	0.000
28	E	115	PRO	0	0.037	0.029	24.113	-0.007	-0.007	0.000	0.000	0.000	0.000
29	E	116	ALA	0	0.054	0.033	27.496	-0.002	-0.002	0.000	0.000	0.000	0.000
30	E	117	PRO	0	-0.020	-0.015	27.825	0.004	0.004	0.000	0.000	0.000	0.000
31	E	118	GLY	0	0.014	0.008	28.538	0.001	0.001	0.000	0.000	0.000	0.000
32	E	119	THR	0	-0.008	-0.002	28.871	0.001	0.001	0.000	0.000	0.000	0.000
33	E	148	CYS	0	-0.125	-0.070	27.212	0.006	0.006	0.000	0.000	0.000	0.000
34	E	189	CYS	0	-0.056	-0.041	19.714	-0.014	-0.014	0.000	0.000	0.000	0.000
35	E	122	TYR	0	0.054	0.044	23.470	0.008	0.008	0.000	0.000	0.000	0.000
36	E	123	ILE	0	-0.030	-0.016	18.156	-0.012	-0.012	0.000	0.000	0.000	0.000
37	E	124	MET	0	0.018	0.024	19.214	0.005	0.005	0.000	0.000	0.000	0.000
38	E	125	LYS	1	0.891	0.945	14.056	0.027	0.027	0.000	0.000	0.000	0.000
39	E	126	ILE	0	-0.035	-0.018	13.196	-0.008	-0.008	0.000	0.000	0.000	0.000
40	E	127	ALA	0	0.009	0.012	15.408	0.007	0.007	0.000	0.000	0.000	0.000
41	E	128	PRO	0	-0.016	-0.007	13.099	-0.025	-0.025	0.000	0.000	0.000	0.000
42	E	129	GLU	-1	-0.883	-0.949	14.552	-0.182	-0.182	0.000	0.000	0.000	0.000
43	E	130	SER	0	-0.055	-0.037	17.599	0.012	0.012	0.000	0.000	0.000	0.000
44	E	131	ILE	0	-0.008	0.000	12.846	0.009	0.009	0.000	0.000	0.000	0.000
45	E	132	PRO	0	-0.013	0.015	17.039	0.002	0.002	0.000	0.000	0.000	0.000
46	E	133	SER	0	0.056	0.014	18.764	-0.019	-0.019	0.000	0.000	0.000	0.000
47	E	134	LEU	0	0.106	0.047	20.208	0.011	0.011	0.000	0.000	0.000	0.000
48	E	135	GLU	-1	-0.911	-0.960	21.508	-0.108	-0.108	0.000	0.000	0.000	0.000
49	E	136	ALA	0	-0.076	-0.040	23.408	0.015	0.015	0.000	0.000	0.000	0.000
50	E	137	LEU	0	-0.007	0.002	19.902	0.013	0.013	0.000	0.000	0.000	0.000
51	E	138	THR	0	0.019	-0.007	23.645	0.013	0.013	0.000	0.000	0.000	0.000
52	E	139	ARG	1	0.957	0.985	26.383	0.111	0.111	0.000	0.000	0.000	0.000
53	E	140	LYS	1	0.944	0.993	24.186	0.091	0.091	0.000	0.000	0.000	0.000
54	E	141	VAL	0	0.038	0.016	25.155	0.008	0.008	0.000	0.000	0.000	0.000
55	E	142	HIS	0	0.059	0.047	27.851	0.006	0.006	0.000	0.000	0.000	0.000
56	E	143	ASN	0	-0.054	-0.042	31.081	0.007	0.007	0.000	0.000	0.000	0.000
57	E	144	PHE	0	-0.048	-0.037	29.056	0.003	0.003	0.000	0.000	0.000	0.000
58	E	145	GLN	0	-0.067	-0.024	31.365	0.007	0.007	0.000	0.000	0.000	0.000
59	E	146	MET	0	-0.060	-0.015	24.619	0.004	0.004	0.000	0.000	0.000	0.000
60	E	147	GLU	-1	-0.862	-0.954	29.153	-0.054	-0.054	0.000	0.000	0.000	0.000
61	E	149	NME	0	0.002	0.023	31.566	0.004	0.004	0.000	0.000	0.000	0.000
62	E	179	ACE	0	0.026	0.001	17.340	-0.004	-0.004	0.000	0.000	0.000	0.000
63	E	180	PHE	0	-0.047	-0.031	15.583	0.021	0.021	0.000	0.000	0.000	0.000
64	E	181	LEU	0	0.030	0.022	14.548	-0.005	-0.005	0.000	0.000	0.000	0.000
65	E	182	GLY	0	0.094	0.059	11.544	-0.017	-0.017	0.000	0.000	0.000	0.000
66	E	183	MET	0	-0.015	-0.010	11.453	-0.045	-0.045	0.000	0.000	0.000	0.000
67	E	184	ALA	0	0.018	0.015	12.059	-0.023	-0.023	0.000	0.000	0.000	0.000
68	E	185	VAL	0	0.073	0.027	13.747	-0.010	-0.010	0.000	0.000	0.000	0.000
69	E	186	SER	0	-0.034	-0.034	15.663	0.004	0.004	0.000	0.000	0.000	0.000
70	E	187	THR	0	-0.040	-0.011	16.356	0.002	0.002	0.000	0.000	0.000	0.000
71	E	188	LEU	0	-0.009	0.001	18.112	-0.002	-0.002	0.000	0.000	0.000	0.000
72	E	190	GLY	0	0.043	0.044	21.506	0.007	0.007	0.000	0.000	0.000	0.000
73	E	191	GLU	-1	-0.977	-0.996	22.922	0.007	0.007	0.000	0.000	0.000	0.000
74	E	192	VAL	0	-0.047	-0.008	24.699	-0.004	-0.004	0.000	0.000	0.000	0.000
75	E	193	PRO	0	-0.012	0.001	25.754	0.004	0.004	0.000	0.000	0.000	0.000
76	E	194	LEU	0	-0.015	-0.014	21.206	-0.007	-0.007	0.000	0.000	0.000	0.000
77	E	195	TYR	0	0.003	-0.007	24.857	0.004	0.004	0.000	0.000	0.000	0.000
78	E	196	TYR	0	-0.023	-0.022	19.748	-0.006	-0.006	0.000	0.000	0.000	0.000
79	E	197	ILE	-1	-0.924	-0.968	23.197	-0.045	-0.045	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(E:88:ACE )