FMO DATABASE

FMODB ID: 828MY

Calculation Name: 2YAD-B-Xray320

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YAD

Chain ID: B

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	80
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-503913.101532
FMO2-HF: Nuclear repulsion	472041.470052
FMO2-HF: Total energy	-31871.63148
FMO2-MP2: Total energy	-31960.126544

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(B:88:ACE )

Summations of interaction energy for fragment #1(B: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.
1.447	2.102	-0.005	-0.254	-0.396	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / 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

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].
3	B	90	THR	0	-0.031	0.009	3.841	1.376	2.031	-0.005	-0.254	-0.396
4	B	91	THR	0	-0.014	-0.010	6.566	0.091	0.091	0.000	0.000	0.000
5	B	92	ALA	0	0.019	0.008	9.928	0.105	0.105	0.000	0.000	0.000
6	B	93	THR	0	-0.020	-0.001	13.269	-0.023	-0.023	0.000	0.000	0.000
7	B	94	PHE	0	-0.022	-0.007	16.253	0.028	0.028	0.000	0.000	0.000
8	B	95	SER	0	0.035	0.013	19.966	-0.005	-0.005	0.000	0.000	0.000
9	B	96	ILE	0	-0.031	-0.022	23.509	0.001	0.001	0.000	0.000	0.000
10	B	97	GLY	0	0.005	0.012	26.289	0.001	0.001	0.000	0.000	0.000
11	B	98	SER	0	-0.021	-0.019	29.616	0.002	0.002	0.000	0.000	0.000
12	B	99	THR	0	-0.038	-0.047	28.504	0.004	0.004	0.000	0.000	0.000
13	B	100	GLY	0	0.021	0.039	26.282	-0.005	-0.005	0.000	0.000	0.000
14	B	101	LEU	0	-0.027	-0.016	20.901	0.003	0.003	0.000	0.000	0.000
15	B	102	VAL	0	-0.002	-0.007	18.822	-0.007	-0.007	0.000	0.000	0.000
16	B	103	VAL	0	0.001	0.006	13.643	0.000	0.000	0.000	0.000	0.000
17	B	104	TYR	0	-0.041	-0.039	14.557	0.003	0.003	0.000	0.000	0.000
18	B	105	ASP	-1	-0.829	-0.942	9.780	-1.059	-1.059	0.000	0.000	0.000
19	B	106	TYR	0	0.007	-0.022	9.976	0.048	0.048	0.000	0.000	0.000
20	B	107	GLN	0	-0.025	0.005	6.148	-0.126	-0.126	0.000	0.000	0.000
21	B	108	GLN	0	-0.008	-0.006	9.087	0.235	0.235	0.000	0.000	0.000
22	B	109	LEU	0	-0.009	0.007	11.754	0.131	0.131	0.000	0.000	0.000
23	B	110	LEU	0	-0.042	-0.015	14.303	0.078	0.078	0.000	0.000	0.000
24	B	111	ILE	0	0.004	0.002	15.337	-0.033	-0.033	0.000	0.000	0.000
25	B	112	ALA	0	0.007	0.018	17.665	0.018	0.018	0.000	0.000	0.000
26	B	113	TYR	0	0.005	-0.008	19.234	0.003	0.003	0.000	0.000	0.000
27	B	114	LYS	1	0.978	0.996	22.355	0.122	0.122	0.000	0.000	0.000
28	B	115	PRO	0	0.035	0.029	24.337	0.005	0.005	0.000	0.000	0.000
29	B	116	ALA	0	0.074	0.045	27.808	0.008	0.008	0.000	0.000	0.000
30	B	117	PRO	0	-0.024	-0.001	26.871	-0.007	-0.007	0.000	0.000	0.000
31	B	118	GLY	0	0.030	0.018	27.685	0.005	0.005	0.000	0.000	0.000
32	B	119	THR	0	-0.018	-0.026	28.448	0.000	0.000	0.000	0.000	0.000
33	B	148	CYS	0	-0.095	-0.057	27.066	0.002	0.002	0.000	0.000	0.000
34	B	189	CYS	0	-0.086	-0.066	18.838	0.014	0.014	0.000	0.000	0.000
35	B	122	TYR	0	0.046	0.046	23.898	0.004	0.004	0.000	0.000	0.000
36	B	123	ILE	0	-0.023	-0.019	18.868	-0.020	-0.020	0.000	0.000	0.000
37	B	124	MET	0	0.026	0.021	20.480	0.021	0.021	0.000	0.000	0.000
38	B	125	LYS	1	0.896	0.955	16.157	0.342	0.342	0.000	0.000	0.000
39	B	126	ILE	0	-0.043	-0.029	15.740	0.028	0.028	0.000	0.000	0.000
40	B	127	ALA	0	0.017	0.007	18.669	-0.019	-0.019	0.000	0.000	0.000
41	B	128	PRO	0	-0.012	-0.018	16.560	-0.007	-0.007	0.000	0.000	0.000
42	B	129	GLU	-1	-0.887	-0.937	17.527	-0.174	-0.174	0.000	0.000	0.000
43	B	130	SER	0	-0.065	-0.032	20.332	0.020	0.020	0.000	0.000	0.000
44	B	131	ILE	0	0.016	0.011	14.845	-0.007	-0.007	0.000	0.000	0.000
45	B	132	PRO	0	-0.025	0.003	19.274	0.021	0.021	0.000	0.000	0.000
46	B	133	SER	0	0.072	0.028	20.787	-0.012	-0.012	0.000	0.000	0.000
47	B	134	LEU	0	0.111	0.047	21.325	-0.004	-0.004	0.000	0.000	0.000
48	B	135	GLU	-1	-0.897	-0.948	23.159	-0.067	-0.067	0.000	0.000	0.000
49	B	136	ALA	0	-0.016	-0.010	24.925	0.004	0.004	0.000	0.000	0.000
50	B	137	LEU	0	0.001	0.005	21.219	0.003	0.003	0.000	0.000	0.000
51	B	138	THR	0	0.007	-0.008	25.092	0.004	0.004	0.000	0.000	0.000
52	B	139	ARG	1	0.874	0.941	27.801	0.078	0.078	0.000	0.000	0.000
53	B	140	LYS	1	0.944	0.990	24.813	0.151	0.151	0.000	0.000	0.000
54	B	141	VAL	0	0.042	0.010	26.331	0.001	0.001	0.000	0.000	0.000
55	B	142	HIS	0	0.007	0.017	29.029	0.007	0.007	0.000	0.000	0.000
56	B	143	ASN	0	-0.060	-0.052	32.059	0.006	0.006	0.000	0.000	0.000
57	B	144	PHE	0	-0.026	-0.026	29.892	0.001	0.001	0.000	0.000	0.000
58	B	145	GLN	0	-0.033	0.009	32.255	0.000	0.000	0.000	0.000	0.000
59	B	146	MET	0	-0.051	-0.006	26.438	-0.005	-0.005	0.000	0.000	0.000
60	B	147	GLU	-1	-0.881	-0.962	30.102	-0.084	-0.084	0.000	0.000	0.000
61	B	149	SER	0	-0.022	0.005	31.863	0.005	0.005	0.000	0.000	0.000
62	B	150	NME	0	0.003	0.008	34.702	-0.003	-0.003	0.000	0.000	0.000
63	B	179	ACE	0	0.013	-0.005	16.265	0.005	0.005	0.000	0.000	0.000
64	B	180	PHE	0	-0.027	-0.019	15.785	0.014	0.014	0.000	0.000	0.000
65	B	181	LEU	0	0.039	0.031	14.178	-0.069	-0.069	0.000	0.000	0.000
66	B	182	GLY	0	0.088	0.044	10.753	-0.017	-0.017	0.000	0.000	0.000
67	B	183	MET	0	0.021	0.017	6.785	0.149	0.149	0.000	0.000	0.000
68	B	184	ALA	0	0.036	0.026	10.847	0.084	0.084	0.000	0.000	0.000
69	B	185	VAL	0	0.039	0.017	12.664	0.058	0.058	0.000	0.000	0.000
70	B	186	SER	0	-0.003	-0.028	14.395	0.055	0.055	0.000	0.000	0.000
71	B	187	THR	0	-0.058	-0.036	14.441	0.046	0.046	0.000	0.000	0.000
72	B	188	LEU	0	-0.042	-0.011	16.953	0.027	0.027	0.000	0.000	0.000
73	B	190	GLY	0	0.042	0.044	20.288	0.006	0.006	0.000	0.000	0.000
74	B	191	GLU	-1	-0.974	-0.999	21.705	-0.073	-0.073	0.000	0.000	0.000
75	B	192	VAL	0	-0.057	-0.004	24.148	0.010	0.010	0.000	0.000	0.000
76	B	193	PRO	0	-0.018	0.000	25.357	-0.010	-0.010	0.000	0.000	0.000
77	B	194	LEU	0	-0.013	-0.014	21.306	-0.007	-0.007	0.000	0.000	0.000
78	B	195	TYR	0	0.002	-0.011	25.082	0.007	0.007	0.000	0.000	0.000
79	B	196	TYR	0	-0.013	-0.015	20.678	-0.008	-0.008	0.000	0.000	0.000
80	B	197	ILE	-1	-0.940	-0.967	24.865	-0.142	-0.142	0.000	0.000	0.000

Top

Graph

Manual

About

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