FMO DATABASE

FMODB ID: MV1VZ

Calculation Name: 1NYU-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NYU

Chain ID: B

ChEMBL ID:

UniProt ID: P38444

Base Structure: X-ray

Registration Date: 2023-09-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

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. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	83
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-550775.121325
FMO2-HF: Nuclear repulsion	513316.786599
FMO2-HF: Total energy	-37458.334726
FMO2-MP2: Total energy	-37558.283486

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:2:LEU)

Summations of interaction energy for fragment #1(B:2:LEU)

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.
-4.901	0.905	3.569	-2.987	-6.387	-0.017

Interaction energy analysis for fragmet #1(B:2:LEU)

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 : -0.012

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	B	4	CYS	0	-0.115	-0.018	2.621	-4.556	-0.470	2.705	-2.620	-4.171	-0.017
4	B	5	ASP	-1	-0.847	-0.934	4.617	-0.898	-0.733	-0.001	-0.012	-0.151	0.000
5	B	6	GLY	0	-0.020	-0.003	7.317	0.027	0.027	0.000	0.000	0.000	0.000
6	B	7	LYS	1	0.729	0.847	8.069	0.233	0.233	0.000	0.000	0.000	0.000
7	B	8	VAL	0	0.112	0.056	5.987	0.109	0.109	0.000	0.000	0.000	0.000
8	B	9	ASN	0	0.059	0.090	8.144	0.131	0.131	0.000	0.000	0.000	0.000
9	B	10	ILE	0	-0.115	-0.130	2.576	-0.574	-0.099	0.864	-0.207	-1.132	0.000
10	B	11	CYS	0	0.014	0.070	3.886	-0.236	0.020	0.001	-0.049	-0.208	0.000
11	B	13	LYS	1	0.850	0.903	3.967	1.224	1.671	0.004	-0.064	-0.388	0.000
12	B	14	LYS	1	0.809	0.893	6.069	0.252	0.252	0.000	0.000	0.000	0.000
13	B	15	GLN	0	-0.047	-0.041	7.946	0.281	0.281	0.000	0.000	0.000	0.000
14	B	16	PHE	0	0.019	0.019	11.022	-0.019	-0.019	0.000	0.000	0.000	0.000
15	B	17	PHE	0	0.023	0.009	14.605	0.031	0.031	0.000	0.000	0.000	0.000
16	B	18	VAL	0	-0.003	0.006	17.395	0.000	0.000	0.000	0.000	0.000	0.000
17	B	19	SER	0	0.022	0.019	20.703	0.010	0.010	0.000	0.000	0.000	0.000
18	B	20	PHE	0	0.066	0.013	22.751	0.002	0.002	0.000	0.000	0.000	0.000
19	B	21	LYS	1	0.885	0.945	25.993	0.045	0.045	0.000	0.000	0.000	0.000
20	B	22	ASP	-1	-0.891	-0.958	25.457	-0.065	-0.065	0.000	0.000	0.000	0.000
21	B	23	ILE	0	-0.059	-0.025	24.103	0.001	0.001	0.000	0.000	0.000	0.000
22	B	24	GLY	0	-0.005	0.006	27.418	0.005	0.005	0.000	0.000	0.000	0.000
23	B	25	TRP	0	-0.014	-0.023	25.547	0.005	0.005	0.000	0.000	0.000	0.000
24	B	26	ASN	0	-0.049	-0.030	29.408	0.001	0.001	0.000	0.000	0.000	0.000
25	B	27	ASP	-1	-0.880	-0.931	30.241	-0.019	-0.019	0.000	0.000	0.000	0.000
26	B	28	TRP	0	0.003	0.010	28.444	0.001	0.001	0.000	0.000	0.000	0.000
27	B	29	ILE	0	-0.020	-0.014	26.248	0.003	0.003	0.000	0.000	0.000	0.000
28	B	30	ILE	0	-0.019	0.018	29.981	-0.004	-0.004	0.000	0.000	0.000	0.000
29	B	31	ALA	0	-0.023	-0.007	26.785	-0.006	-0.006	0.000	0.000	0.000	0.000
30	B	32	PRO	0	-0.019	-0.011	21.905	0.006	0.006	0.000	0.000	0.000	0.000
31	B	33	SER	0	0.055	0.001	24.481	0.002	0.002	0.000	0.000	0.000	0.000
32	B	34	GLY	0	0.016	0.005	22.383	0.000	0.000	0.000	0.000	0.000	0.000
33	B	35	TYR	0	-0.021	-0.005	17.451	0.000	0.000	0.000	0.000	0.000	0.000
34	B	36	HIS	0	-0.019	-0.012	13.396	-0.030	-0.030	0.000	0.000	0.000	0.000
35	B	37	ALA	0	-0.024	0.014	14.818	0.037	0.037	0.000	0.000	0.000	0.000
36	B	38	ASN	0	0.031	0.008	9.687	-0.084	-0.084	0.000	0.000	0.000	0.000
37	B	39	TYR	0	0.012	-0.001	11.455	0.110	0.110	0.000	0.000	0.000	0.000
38	B	40	CYS	0	-0.057	0.015	4.666	-1.416	-1.289	-0.002	-0.020	-0.105	0.000
39	B	41	GLU	-1	-0.852	-0.945	7.893	-0.396	-0.396	0.000	0.000	0.000	0.000
40	B	42	GLY	0	0.133	0.050	6.931	-0.214	-0.214	0.000	0.000	0.000	0.000
41	B	43	GLU	-1	-0.869	-0.934	7.437	-0.036	-0.036	0.000	0.000	0.000	0.000
42	B	44	CYS	0	-0.094	-0.049	6.959	-0.249	-0.249	0.000	0.000	0.000	0.000
43	B	45	PRO	0	0.006	-0.001	7.780	-0.055	-0.055	0.000	0.000	0.000	0.000
44	B	46	SER	0	0.013	-0.022	10.972	0.015	0.015	0.000	0.000	0.000	0.000
45	B	47	HIS	0	0.020	0.024	14.573	0.005	0.005	0.000	0.000	0.000	0.000
46	B	48	ILE	0	-0.025	0.045	14.004	-0.009	-0.009	0.000	0.000	0.000	0.000
47	B	77	LEU	0	-0.011	-0.013	18.321	0.004	0.004	0.000	0.000	0.000	0.000
48	B	78	LYS	1	0.943	0.940	13.689	-0.153	-0.153	0.000	0.000	0.000	0.000
49	B	79	SER	0	-0.024	-0.020	11.674	0.029	0.029	0.000	0.000	0.000	0.000
50	B	80	CYS	0	0.003	-0.016	11.935	-0.066	-0.066	0.000	0.000	0.000	0.000
51	B	82	VAL	0	-0.014	-0.014	9.191	-0.118	-0.118	0.000	0.000	0.000	0.000
52	B	83	PRO	0	0.034	0.000	9.183	0.258	0.258	0.000	0.000	0.000	0.000
53	B	84	THR	0	-0.016	-0.019	7.954	-0.135	-0.135	0.000	0.000	0.000	0.000
54	B	85	LYS	1	0.927	0.975	8.578	-0.514	-0.514	0.000	0.000	0.000	0.000
55	B	86	LEU	0	-0.031	0.002	10.140	0.000	0.000	0.000	0.000	0.000	0.000
56	B	87	ARG	1	1.007	1.007	10.376	0.023	0.023	0.000	0.000	0.000	0.000
57	B	88	PRO	0	-0.015	-0.026	14.165	-0.012	-0.012	0.000	0.000	0.000	0.000
58	B	89	MET	0	-0.023	0.011	17.210	-0.019	-0.019	0.000	0.000	0.000	0.000
59	B	90	SER	0	-0.053	-0.037	19.185	0.005	0.005	0.000	0.000	0.000	0.000
60	B	91	MET	0	-0.009	-0.013	22.527	-0.008	-0.008	0.000	0.000	0.000	0.000
61	B	92	LEU	0	0.013	0.000	25.376	0.004	0.004	0.000	0.000	0.000	0.000
62	B	93	TYR	0	-0.026	-0.021	28.154	-0.003	-0.003	0.000	0.000	0.000	0.000
63	B	94	TYR	0	0.025	0.022	30.993	0.002	0.002	0.000	0.000	0.000	0.000
64	B	95	ASP	-1	-0.862	-0.936	33.622	0.011	0.011	0.000	0.000	0.000	0.000
65	B	96	ASP	-1	-0.880	-0.975	35.197	0.011	0.011	0.000	0.000	0.000	0.000
66	B	97	GLY	0	-0.074	-0.021	37.920	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	98	GLN	0	-0.064	-0.035	38.792	-0.002	-0.002	0.000	0.000	0.000	0.000
68	B	99	ASN	0	0.004	0.020	37.784	-0.002	-0.002	0.000	0.000	0.000	0.000
69	B	100	ILE	0	-0.023	-0.002	33.875	0.001	0.001	0.000	0.000	0.000	0.000
70	B	101	ILE	0	-0.014	0.000	30.753	0.002	0.002	0.000	0.000	0.000	0.000
71	B	102	LYS	1	0.923	0.962	25.713	-0.013	-0.013	0.000	0.000	0.000	0.000
72	B	103	LYS	1	0.876	0.947	25.062	-0.045	-0.045	0.000	0.000	0.000	0.000
73	B	104	ASP	-1	-0.816	-0.898	22.267	0.021	0.021	0.000	0.000	0.000	0.000
74	B	105	ILE	0	-0.045	-0.031	20.982	0.010	0.010	0.000	0.000	0.000	0.000
75	B	106	GLN	0	0.030	0.004	19.740	0.013	0.013	0.000	0.000	0.000	0.000
76	B	107	ASN	0	-0.037	-0.026	16.452	0.014	0.014	0.000	0.000	0.000	0.000
77	B	108	MET	0	0.061	0.025	17.007	-0.004	-0.004	0.000	0.000	0.000	0.000
78	B	109	ILE	0	-0.054	-0.010	11.718	-0.019	-0.019	0.000	0.000	0.000	0.000
79	B	110	VAL	0	0.012	0.005	8.925	0.044	0.044	0.000	0.000	0.000	0.000
80	B	111	GLU	-1	-0.959	-0.993	7.539	0.096	0.096	0.000	0.000	0.000	0.000
81	B	112	GLU	-1	-0.882	-0.953	4.308	0.654	0.780	-0.001	-0.007	-0.118	0.000
82	B	114	GLY	0	0.064	0.037	4.897	1.394	1.518	-0.001	-0.008	-0.114	0.000
83	B	116	SER	0	0.043	0.047	9.277	-0.053	-0.053	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:2:LEU)