FMO DATABASE

FMODB ID: YY682

Calculation Name: 2YAD-F-Xray320

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YAD

Chain ID: F

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	78
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-482393.632162
FMO2-HF: Nuclear repulsion	451318.089922
FMO2-HF: Total energy	-31075.54224
FMO2-MP2: Total energy	-31161.632993

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(F:88:ACE )

Summations of interaction energy for fragment #1(F: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.
1.375	1.967	-0.005	-0.218	-0.369	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.005

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].
3	F	90	THR	0	-0.006	0.014	3.843	1.404	1.996	-0.005	-0.218	-0.369
4	F	91	THR	0	-0.022	-0.009	6.665	0.147	0.147	0.000	0.000	0.000
5	F	92	ALA	0	0.018	0.007	10.357	-0.086	-0.086	0.000	0.000	0.000
6	F	93	THR	0	-0.015	-0.002	12.813	0.044	0.044	0.000	0.000	0.000
7	F	94	PHE	0	0.000	0.000	14.608	-0.006	-0.006	0.000	0.000	0.000
8	F	95	SER	0	0.027	0.015	19.405	0.015	0.015	0.000	0.000	0.000
9	F	96	ILE	0	-0.032	-0.022	22.871	-0.007	-0.007	0.000	0.000	0.000
10	F	97	GLY	0	0.014	0.018	25.493	0.009	0.009	0.000	0.000	0.000
11	F	98	SER	0	-0.014	-0.016	28.927	-0.004	-0.004	0.000	0.000	0.000
12	F	99	THR	0	-0.034	-0.030	29.484	0.002	0.002	0.000	0.000	0.000
13	F	100	GLY	0	0.024	0.034	26.883	0.000	0.000	0.000	0.000	0.000
14	F	101	LEU	0	-0.029	-0.019	22.124	-0.011	-0.011	0.000	0.000	0.000
15	F	102	VAL	0	-0.009	-0.005	18.334	0.011	0.011	0.000	0.000	0.000
16	F	103	VAL	0	0.004	0.005	14.965	-0.022	-0.022	0.000	0.000	0.000
17	F	104	TYR	0	-0.038	-0.027	13.054	0.038	0.038	0.000	0.000	0.000
18	F	105	ASP	-1	-0.845	-0.943	11.104	-0.402	-0.402	0.000	0.000	0.000
19	F	106	TYR	0	0.023	-0.010	7.750	0.055	0.055	0.000	0.000	0.000
20	F	107	GLN	0	-0.033	0.001	6.889	-0.045	-0.045	0.000	0.000	0.000
21	F	108	GLN	0	-0.047	-0.032	8.081	0.138	0.138	0.000	0.000	0.000
22	F	109	LEU	0	-0.038	0.003	10.758	0.039	0.039	0.000	0.000	0.000
23	F	110	LEU	0	-0.012	-0.020	12.736	0.058	0.058	0.000	0.000	0.000
24	F	111	ILE	0	-0.011	-0.008	14.851	-0.051	-0.051	0.000	0.000	0.000
25	F	112	ALA	0	0.001	0.010	17.510	0.033	0.033	0.000	0.000	0.000
26	F	113	TYR	0	-0.001	-0.008	20.080	-0.020	-0.020	0.000	0.000	0.000
27	F	114	LYS	1	0.954	0.982	22.999	0.112	0.112	0.000	0.000	0.000
28	F	115	PRO	0	0.021	0.021	25.671	-0.006	-0.006	0.000	0.000	0.000
29	F	116	ALA	0	0.058	0.029	28.625	0.000	0.000	0.000	0.000	0.000
30	F	117	PRO	0	-0.017	-0.011	29.612	0.001	0.001	0.000	0.000	0.000
31	F	118	GLY	0	0.016	0.011	30.557	0.004	0.004	0.000	0.000	0.000
32	F	119	THR	0	-0.013	-0.009	30.558	0.002	0.002	0.000	0.000	0.000
33	F	148	CYS	0	-0.101	-0.052	29.593	0.005	0.005	0.000	0.000	0.000
34	F	189	CYS	0	-0.064	-0.056	22.021	-0.007	-0.007	0.000	0.000	0.000
35	F	122	TYR	0	0.051	0.036	25.065	0.008	0.008	0.000	0.000	0.000
36	F	123	ILE	0	-0.037	-0.029	20.119	-0.017	-0.017	0.000	0.000	0.000
37	F	124	MET	0	0.034	0.036	20.612	0.012	0.012	0.000	0.000	0.000
38	F	125	LYS	1	0.955	0.982	17.796	0.067	0.067	0.000	0.000	0.000
39	F	126	ILE	0	-0.033	-0.012	13.495	-0.001	-0.001	0.000	0.000	0.000
40	F	127	ALA	0	0.036	0.015	15.495	0.007	0.007	0.000	0.000	0.000
41	F	128	PRO	0	0.015	-0.010	11.872	-0.032	-0.032	0.000	0.000	0.000
42	F	129	GLU	-1	-0.901	-0.946	13.578	-0.167	-0.167	0.000	0.000	0.000
43	F	130	SER	0	-0.075	-0.041	16.464	0.021	0.021	0.000	0.000	0.000
44	F	131	ILE	0	0.010	0.020	11.670	-0.003	-0.003	0.000	0.000	0.000
45	F	132	PRO	0	-0.032	0.001	15.927	-0.002	-0.002	0.000	0.000	0.000
46	F	133	SER	0	0.076	0.022	17.650	-0.028	-0.028	0.000	0.000	0.000
47	F	134	LEU	0	0.091	0.042	19.094	0.016	0.016	0.000	0.000	0.000
48	F	135	GLU	-1	-0.835	-0.906	20.377	-0.133	-0.133	0.000	0.000	0.000
49	F	136	ALA	0	-0.003	0.004	21.901	0.019	0.019	0.000	0.000	0.000
50	F	137	LEU	0	0.004	0.009	19.611	0.017	0.017	0.000	0.000	0.000
51	F	138	THR	0	0.017	-0.004	22.918	0.015	0.015	0.000	0.000	0.000
52	F	139	ARG	1	0.805	0.887	25.791	0.144	0.144	0.000	0.000	0.000
53	F	140	LYS	1	0.916	0.961	23.560	0.132	0.132	0.000	0.000	0.000
54	F	141	VAL	0	0.033	-0.003	25.136	0.009	0.009	0.000	0.000	0.000
55	F	142	HIS	0	0.018	0.022	27.751	0.006	0.006	0.000	0.000	0.000
56	F	143	ASN	0	-0.047	-0.038	29.766	0.008	0.008	0.000	0.000	0.000
57	F	144	PHE	0	-0.055	-0.034	28.055	0.004	0.004	0.000	0.000	0.000
58	F	145	GLN	0	-0.024	0.014	31.148	0.005	0.005	0.000	0.000	0.000
59	F	146	MET	0	-0.078	-0.014	25.477	-0.001	-0.001	0.000	0.000	0.000
60	F	147	GLU	-1	-0.884	-0.971	30.278	-0.074	-0.074	0.000	0.000	0.000
61	F	149	NME	0	0.013	0.022	33.211	0.004	0.004	0.000	0.000	0.000
62	F	180	ACE	0	0.003	-0.008	19.647	0.003	0.003	0.000	0.000	0.000
63	F	181	LEU	0	0.009	-0.009	18.209	-0.006	-0.006	0.000	0.000	0.000
64	F	182	GLY	0	0.093	0.062	14.924	-0.020	-0.020	0.000	0.000	0.000
65	F	183	MET	0	-0.006	-0.005	14.751	-0.004	-0.004	0.000	0.000	0.000
66	F	184	ALA	0	0.046	0.031	14.376	0.006	0.006	0.000	0.000	0.000
67	F	185	VAL	0	0.059	0.022	15.874	0.007	0.007	0.000	0.000	0.000
68	F	186	SER	0	-0.022	-0.028	18.216	0.019	0.019	0.000	0.000	0.000
69	F	187	THR	0	-0.047	-0.020	19.108	0.012	0.012	0.000	0.000	0.000
70	F	188	LEU	0	-0.041	-0.017	20.297	0.008	0.008	0.000	0.000	0.000
71	F	190	GLY	0	0.039	0.045	24.037	0.009	0.009	0.000	0.000	0.000
72	F	191	GLU	-1	-0.981	-1.000	25.789	-0.051	-0.051	0.000	0.000	0.000
73	F	192	VAL	0	-0.044	0.000	27.328	0.001	0.001	0.000	0.000	0.000
74	F	193	PRO	0	-0.020	-0.003	28.728	0.000	0.000	0.000	0.000	0.000
75	F	194	LEU	0	-0.004	-0.010	24.459	-0.008	-0.008	0.000	0.000	0.000
76	F	195	TYR	0	0.004	-0.002	27.172	0.007	0.007	0.000	0.000	0.000
77	F	196	TYR	0	-0.018	-0.012	22.405	-0.008	-0.008	0.000	0.000	0.000
78	F	197	ILE	-1	-0.920	-0.961	24.281	-0.086	-0.086	0.000	0.000	0.000

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