FMO DATABASE

FMODB ID: N1VQQ

Calculation Name: 2YAD-A-Xray320

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YAD

Chain ID: A

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	DGL=-1
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-480435.554856
FMO2-HF: Nuclear repulsion	449363.276091
FMO2-HF: Total energy	-31072.278765
FMO2-MP2: Total energy	-31158.249775

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(A:89:ACE )

Summations of interaction energy for fragment #1(A:89: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.
1.807	2.231	3.697	-1.689	-2.431	-0.002

Interaction energy analysis for fragmet #1(A:89:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / 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

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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	91	THR	0	-0.013	-0.002	3.831	0.855	1.696	-0.005	-0.406	-0.429	0.000
4	A	92	ALA	0	0.028	0.021	7.038	0.005	0.005	0.000	0.000	0.000	0.000
5	A	93	THR	0	-0.024	-0.001	10.432	0.064	0.064	0.000	0.000	0.000	0.000
6	A	94	PHE	0	0.012	0.007	12.473	0.005	0.005	0.000	0.000	0.000	0.000
7	A	95	SER	0	0.034	0.015	16.926	0.005	0.005	0.000	0.000	0.000	0.000
8	A	96	ILE	0	-0.030	-0.019	19.236	0.004	0.004	0.000	0.000	0.000	0.000
9	A	97	GLY	0	0.005	0.007	22.457	0.004	0.004	0.000	0.000	0.000	0.000
10	A	98	SER	0	0.000	-0.007	25.780	-0.006	-0.006	0.000	0.000	0.000	0.000
11	A	99	THR	0	-0.051	-0.037	26.286	-0.003	-0.003	0.000	0.000	0.000	0.000
12	A	100	GLY	0	0.025	0.041	23.250	-0.004	-0.004	0.000	0.000	0.000	0.000
13	A	101	LEU	0	-0.024	-0.018	18.666	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	102	VAL	0	-0.010	-0.006	14.758	0.019	0.019	0.000	0.000	0.000	0.000
15	A	103	VAL	0	-0.009	0.002	10.641	-0.043	-0.043	0.000	0.000	0.000	0.000
16	A	104	TYR	0	-0.037	-0.029	9.243	0.071	0.071	0.000	0.000	0.000	0.000
17	A	105	ASP	-1	-0.843	-0.931	5.853	-0.435	-0.435	0.000	0.000	0.000	0.000
18	A	106	TYR	0	0.019	-0.015	3.663	0.135	0.293	0.005	-0.045	-0.117	0.000
19	A	107	GLN	0	-0.072	-0.016	2.335	0.622	0.753	3.503	-1.917	-1.718	-0.002
20	A	108	GLN	0	0.016	-0.003	3.015	0.670	-0.036	0.194	0.679	-0.167	0.000
21	A	109	LEU	0	-0.027	-0.005	6.131	-0.100	-0.100	0.000	0.000	0.000	0.000
22	A	110	LEU	0	-0.023	-0.006	7.959	-0.056	-0.056	0.000	0.000	0.000	0.000
23	A	111	ILE	0	-0.009	-0.003	9.899	-0.065	-0.065	0.000	0.000	0.000	0.000
24	A	112	ALA	0	0.023	0.016	12.675	0.024	0.024	0.000	0.000	0.000	0.000
25	A	113	TYR	0	0.009	-0.007	15.045	-0.030	-0.030	0.000	0.000	0.000	0.000
26	A	114	LYS	1	0.954	0.978	18.272	0.108	0.108	0.000	0.000	0.000	0.000
27	A	115	PRO	0	0.016	0.024	21.093	-0.009	-0.009	0.000	0.000	0.000	0.000
28	A	116	ALA	0	0.060	0.027	24.269	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	117	PRO	0	-0.029	-0.015	25.518	0.000	0.000	0.000	0.000	0.000	0.000
30	A	118	GLY	0	0.023	0.016	26.236	0.006	0.006	0.000	0.000	0.000	0.000
31	A	119	THR	0	-0.002	-0.009	26.040	0.006	0.006	0.000	0.000	0.000	0.000
32	A	148	CYS	0	-0.105	-0.052	24.382	0.001	0.001	0.000	0.000	0.000	0.000
33	A	189	CYS	0	-0.069	-0.056	17.726	0.002	0.002	0.000	0.000	0.000	0.000
34	A	122	TYR	0	0.042	0.036	19.924	0.012	0.012	0.000	0.000	0.000	0.000
35	A	123	ILE	0	-0.017	-0.008	14.509	-0.014	-0.014	0.000	0.000	0.000	0.000
36	A	124	MET	0	0.007	0.012	15.297	0.016	0.016	0.000	0.000	0.000	0.000
37	A	125	LYS	1	0.908	0.954	10.730	-0.328	-0.328	0.000	0.000	0.000	0.000
38	A	126	ILE	0	-0.031	-0.017	9.077	-0.027	-0.027	0.000	0.000	0.000	0.000
39	A	127	ALA	0	0.030	0.014	11.379	0.072	0.072	0.000	0.000	0.000	0.000
40	A	128	PRO	0	0.007	-0.018	9.084	-0.027	-0.027	0.000	0.000	0.000	0.000
41	A	129	DGL	-1	-0.958	-0.971	10.501	0.250	0.250	0.000	0.000	0.000	0.000
42	A	130	SER	0	-0.016	-0.011	13.501	-0.038	-0.038	0.000	0.000	0.000	0.000
43	A	131	ILE	0	-0.017	0.008	8.963	-0.023	-0.023	0.000	0.000	0.000	0.000
44	A	132	PRO	0	0.007	0.013	12.784	-0.028	-0.028	0.000	0.000	0.000	0.000
45	A	133	SER	0	0.062	0.018	14.545	-0.023	-0.023	0.000	0.000	0.000	0.000
46	A	134	LEU	0	0.093	0.043	16.542	0.006	0.006	0.000	0.000	0.000	0.000
47	A	135	GLU	-1	-0.919	-0.952	17.782	-0.041	-0.041	0.000	0.000	0.000	0.000
48	A	136	ALA	0	-0.048	-0.027	19.128	0.006	0.006	0.000	0.000	0.000	0.000
49	A	137	LEU	0	0.014	0.012	15.887	0.007	0.007	0.000	0.000	0.000	0.000
50	A	138	THR	0	0.025	-0.005	19.466	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	139	ARG	1	0.945	0.979	22.356	0.010	0.010	0.000	0.000	0.000	0.000
52	A	140	LYS	1	0.905	0.971	18.856	-0.029	-0.029	0.000	0.000	0.000	0.000
53	A	141	VAL	0	0.032	0.005	21.228	0.004	0.004	0.000	0.000	0.000	0.000
54	A	142	HIS	0	0.000	0.009	23.956	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	143	ASN	0	-0.041	-0.041	27.072	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	144	PHE	0	-0.059	-0.029	25.779	0.004	0.004	0.000	0.000	0.000	0.000
57	A	145	GLN	0	-0.003	0.016	27.904	0.001	0.001	0.000	0.000	0.000	0.000
58	A	146	MET	0	-0.056	-0.007	22.458	0.000	0.000	0.000	0.000	0.000	0.000
59	A	147	GLU	-1	-0.910	-0.979	25.613	-0.032	-0.032	0.000	0.000	0.000	0.000
60	A	149	DSN	0	0.012	0.010	28.136	0.001	0.001	0.000	0.000	0.000	0.000
61	A	150	NME	0	0.002	0.011	30.977	0.002	0.002	0.000	0.000	0.000	0.000
62	A	180	ACE	0	0.001	-0.007	14.789	0.001	0.001	0.000	0.000	0.000	0.000
63	A	181	LEU	0	0.008	-0.006	12.310	0.014	0.014	0.000	0.000	0.000	0.000
64	A	182	GLY	0	0.059	0.045	9.867	-0.013	-0.013	0.000	0.000	0.000	0.000
65	A	183	MET	0	0.025	0.007	10.860	0.022	0.022	0.000	0.000	0.000	0.000
66	A	184	ALA	0	0.021	0.017	10.769	0.039	0.039	0.000	0.000	0.000	0.000
67	A	185	VAL	0	0.045	0.016	11.149	0.039	0.039	0.000	0.000	0.000	0.000
68	A	186	SER	0	0.004	-0.012	13.559	0.042	0.042	0.000	0.000	0.000	0.000
69	A	187	THR	0	-0.050	-0.025	15.754	0.020	0.020	0.000	0.000	0.000	0.000
70	A	188	LEU	0	-0.044	-0.013	16.289	0.017	0.017	0.000	0.000	0.000	0.000
71	A	190	GLY	0	0.044	0.048	19.476	0.016	0.016	0.000	0.000	0.000	0.000
72	A	191	GLU	-1	-0.970	-0.996	21.342	-0.074	-0.074	0.000	0.000	0.000	0.000
73	A	192	VAL	0	-0.063	-0.008	22.526	0.005	0.005	0.000	0.000	0.000	0.000
74	A	193	PRO	0	-0.011	-0.002	23.395	0.002	0.002	0.000	0.000	0.000	0.000
75	A	194	LEU	0	-0.003	-0.004	18.794	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	195	TYR	0	0.015	-0.008	21.601	0.006	0.006	0.000	0.000	0.000	0.000
77	A	196	TYR	0	-0.022	-0.019	16.350	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	197	ILE	-1	-0.924	-0.966	19.380	0.065	0.065	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:89:ACE )