FMO DATABASE

FMODB ID: 142KZ

Calculation Name: 2YAD-D-Xray320

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: 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	-503952.850776
FMO2-HF: Nuclear repulsion	472039.103663
FMO2-HF: Total energy	-31913.747113
FMO2-MP2: Total energy	-32002.495711

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:87:ACE )

Summations of interaction energy for fragment #1(D:87: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.
0.963	2.045	-0.006	-0.499	-0.578	-0.001

Interaction energy analysis for fragmet #1(D:87: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 : -0.009

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	D	89	VAL	0	0.007	0.020	3.820	0.875	1.957	-0.006	-0.499	-0.578	-0.001
4	D	90	THR	0	-0.002	-0.001	5.777	-0.020	-0.020	0.000	0.000	0.000	0.000
5	D	91	THR	0	0.006	-0.009	9.417	0.082	0.082	0.000	0.000	0.000	0.000
6	D	92	ALA	0	-0.003	0.007	11.834	-0.003	-0.003	0.000	0.000	0.000	0.000
7	D	93	THR	0	-0.027	-0.001	13.966	0.002	0.002	0.000	0.000	0.000	0.000
8	D	94	PHE	0	0.011	0.004	14.477	0.017	0.017	0.000	0.000	0.000	0.000
9	D	95	SER	0	0.021	0.012	20.030	-0.010	-0.010	0.000	0.000	0.000	0.000
10	D	96	ILE	0	-0.030	-0.024	22.459	0.010	0.010	0.000	0.000	0.000	0.000
11	D	97	GLY	0	0.010	0.017	25.797	-0.005	-0.005	0.000	0.000	0.000	0.000
12	D	98	SER	0	-0.006	-0.013	29.115	0.001	0.001	0.000	0.000	0.000	0.000
13	D	99	THR	0	-0.044	-0.042	30.623	-0.001	-0.001	0.000	0.000	0.000	0.000
14	D	100	GLY	0	0.020	0.037	27.779	-0.005	-0.005	0.000	0.000	0.000	0.000
15	D	101	LEU	0	-0.027	-0.017	23.581	0.003	0.003	0.000	0.000	0.000	0.000
16	D	102	VAL	0	-0.001	-0.004	19.254	-0.002	-0.002	0.000	0.000	0.000	0.000
17	D	103	VAL	0	-0.007	-0.007	17.081	-0.004	-0.004	0.000	0.000	0.000	0.000
18	D	104	TYR	0	-0.054	-0.042	13.930	0.003	0.003	0.000	0.000	0.000	0.000
19	D	105	ASP	-1	-0.842	-0.948	13.568	-0.288	-0.288	0.000	0.000	0.000	0.000
20	D	106	TYR	0	0.012	-0.020	9.248	0.044	0.044	0.000	0.000	0.000	0.000
21	D	107	GLN	0	-0.055	-0.003	10.022	-0.107	-0.107	0.000	0.000	0.000	0.000
22	D	108	GLN	0	0.011	0.000	11.018	0.044	0.044	0.000	0.000	0.000	0.000
23	D	109	LEU	0	0.003	0.010	12.451	0.039	0.039	0.000	0.000	0.000	0.000
24	D	110	LEU	0	-0.017	0.003	15.008	0.024	0.024	0.000	0.000	0.000	0.000
25	D	111	ILE	0	0.021	0.014	16.648	-0.003	-0.003	0.000	0.000	0.000	0.000
26	D	112	ALA	0	0.001	0.015	19.191	0.001	0.001	0.000	0.000	0.000	0.000
27	D	113	TYR	0	-0.002	-0.014	21.885	0.005	0.005	0.000	0.000	0.000	0.000
28	D	114	LYS	1	0.952	0.982	24.451	0.041	0.041	0.000	0.000	0.000	0.000
29	D	115	PRO	0	0.027	0.026	27.340	0.003	0.003	0.000	0.000	0.000	0.000
30	D	116	ALA	0	0.065	0.038	30.027	0.003	0.003	0.000	0.000	0.000	0.000
31	D	117	PRO	0	-0.021	-0.014	31.667	-0.004	-0.004	0.000	0.000	0.000	0.000
32	D	118	GLY	0	0.019	0.011	32.557	0.002	0.002	0.000	0.000	0.000	0.000
33	D	119	THR	0	-0.003	-0.007	32.562	0.001	0.001	0.000	0.000	0.000	0.000
34	D	148	CYS	0	-0.109	-0.060	31.775	-0.003	-0.003	0.000	0.000	0.000	0.000
35	D	189	CYS	0	-0.085	-0.062	24.849	0.010	0.010	0.000	0.000	0.000	0.000
36	D	122	TYR	0	0.061	0.044	26.798	0.000	0.000	0.000	0.000	0.000	0.000
37	D	123	ILE	0	-0.039	-0.025	22.266	-0.004	-0.004	0.000	0.000	0.000	0.000
38	D	124	MET	0	0.024	0.025	21.911	0.009	0.009	0.000	0.000	0.000	0.000
39	D	125	LYS	1	0.863	0.924	18.130	0.081	0.081	0.000	0.000	0.000	0.000
40	D	126	ILE	0	-0.057	-0.027	14.806	0.016	0.016	0.000	0.000	0.000	0.000
41	D	127	ALA	0	0.028	0.013	17.510	-0.015	-0.015	0.000	0.000	0.000	0.000
42	D	128	PRO	0	-0.010	-0.016	13.591	0.007	0.007	0.000	0.000	0.000	0.000
43	D	129	GLU	-1	-0.887	-0.940	12.733	0.145	0.145	0.000	0.000	0.000	0.000
44	D	130	SER	0	-0.072	-0.038	14.927	0.021	0.021	0.000	0.000	0.000	0.000
45	D	131	ILE	0	0.020	0.010	11.214	-0.027	-0.027	0.000	0.000	0.000	0.000
46	D	132	PRO	0	-0.021	0.004	15.235	0.025	0.025	0.000	0.000	0.000	0.000
47	D	133	SER	0	0.071	0.031	17.217	-0.007	-0.007	0.000	0.000	0.000	0.000
48	D	134	LEU	0	0.109	0.046	18.343	-0.015	-0.015	0.000	0.000	0.000	0.000
49	D	135	GLU	-1	-0.894	-0.940	20.262	0.062	0.062	0.000	0.000	0.000	0.000
50	D	136	ALA	0	-0.018	-0.011	21.079	-0.009	-0.009	0.000	0.000	0.000	0.000
51	D	137	LEU	0	0.005	0.015	20.236	-0.009	-0.009	0.000	0.000	0.000	0.000
52	D	138	THR	0	0.010	-0.015	22.867	-0.009	-0.009	0.000	0.000	0.000	0.000
53	D	139	ARG	1	0.895	0.947	25.892	-0.056	-0.056	0.000	0.000	0.000	0.000
54	D	140	LYS	1	0.926	0.981	23.382	-0.012	-0.012	0.000	0.000	0.000	0.000
55	D	141	VAL	0	0.033	-0.008	25.615	-0.004	-0.004	0.000	0.000	0.000	0.000
56	D	142	HIS	0	0.010	0.025	28.263	-0.004	-0.004	0.000	0.000	0.000	0.000
57	D	143	ASN	0	-0.044	-0.038	29.366	-0.002	-0.002	0.000	0.000	0.000	0.000
58	D	144	PHE	0	-0.045	-0.034	28.191	-0.001	-0.001	0.000	0.000	0.000	0.000
59	D	145	GLN	0	0.001	0.024	31.712	-0.004	-0.004	0.000	0.000	0.000	0.000
60	D	146	MET	0	-0.073	-0.021	26.347	-0.004	-0.004	0.000	0.000	0.000	0.000
61	D	147	GLU	-1	-0.936	-0.984	31.303	0.001	0.001	0.000	0.000	0.000	0.000
62	D	149	NME	0	0.027	0.035	34.822	0.001	0.001	0.000	0.000	0.000	0.000
63	D	179	ACE	0	0.018	-0.001	26.877	0.001	0.001	0.000	0.000	0.000	0.000
64	D	180	PHE	0	-0.013	-0.027	20.731	-0.003	-0.003	0.000	0.000	0.000	0.000
65	D	181	LEU	0	0.005	0.008	20.917	-0.006	-0.006	0.000	0.000	0.000	0.000
66	D	182	GLY	0	0.107	0.074	18.423	-0.013	-0.013	0.000	0.000	0.000	0.000
67	D	183	MET	0	0.010	-0.004	18.932	0.024	0.024	0.000	0.000	0.000	0.000
68	D	184	ALA	0	0.007	0.011	17.613	0.018	0.018	0.000	0.000	0.000	0.000
69	D	185	VAL	0	0.063	0.029	18.866	0.020	0.020	0.000	0.000	0.000	0.000
70	D	186	SER	0	-0.004	-0.015	21.348	0.016	0.016	0.000	0.000	0.000	0.000
71	D	187	THR	0	-0.054	-0.026	22.746	0.010	0.010	0.000	0.000	0.000	0.000
72	D	188	LEU	0	-0.031	-0.011	22.567	0.010	0.010	0.000	0.000	0.000	0.000
73	D	190	GLY	0	0.037	0.040	27.057	0.003	0.003	0.000	0.000	0.000	0.000
74	D	191	GLU	-1	-0.965	-0.993	29.206	-0.046	-0.046	0.000	0.000	0.000	0.000
75	D	192	VAL	0	-0.056	-0.004	30.092	0.005	0.005	0.000	0.000	0.000	0.000
76	D	193	PRO	0	-0.014	-0.005	31.502	-0.004	-0.004	0.000	0.000	0.000	0.000
77	D	194	LEU	0	-0.003	-0.006	26.909	0.000	0.000	0.000	0.000	0.000	0.000
78	D	195	TYR	0	0.002	-0.014	29.328	0.002	0.002	0.000	0.000	0.000	0.000
79	D	196	TYR	0	-0.013	-0.012	25.154	0.000	0.000	0.000	0.000	0.000	0.000
80	D	197	ILE	-1	-0.936	-0.966	26.002	-0.015	-0.015	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:87:ACE )