FMO DATABASE

FMODB ID: QYGYY

Calculation Name: 1NYS-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NYS

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:

Apendix: None

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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-547434.245633
FMO2-HF: Nuclear repulsion	509975.315036
FMO2-HF: Total energy	-37458.930597
FMO2-MP2: Total energy	-37558.711944

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.
-4.277	2.375	2.264	-2.887	-6.026	-0.007

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 : -0.035 / q_NPA : -0.020

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	0.010	0.030	3.356	-0.174	2.612	0.025	-1.188	-1.622	-0.003
4	B	5	ASP	-1	-0.821	-0.908	6.207	0.373	0.373	0.000	0.000	0.000	0.000
5	B	6	GLY	0	-0.035	-0.020	8.856	-0.071	-0.071	0.000	0.000	0.000	0.000
6	B	7	LYS	1	0.839	0.899	9.523	-0.841	-0.841	0.000	0.000	0.000	0.000
7	B	8	VAL	0	0.052	0.033	8.897	0.348	0.348	0.000	0.000	0.000	0.000
8	B	9	ASN	0	-0.038	-0.002	8.566	-0.301	-0.301	0.000	0.000	0.000	0.000
9	B	10	ILE	0	0.069	0.027	5.772	-0.287	-0.287	0.000	0.000	0.000	0.000
10	B	11	CYS	0	-0.036	0.002	5.025	0.839	0.839	0.000	0.000	0.000	0.000
11	B	13	LYS	1	0.941	0.951	3.851	-0.252	0.173	0.002	-0.047	-0.379	0.000
12	B	14	LYS	1	0.852	0.934	5.292	-0.656	-0.671	-0.001	-0.003	0.020	0.000
13	B	15	GLN	0	-0.010	-0.020	8.694	-0.146	-0.146	0.000	0.000	0.000	0.000
14	B	16	PHE	0	-0.011	-0.001	10.743	0.036	0.036	0.000	0.000	0.000	0.000
15	B	17	PHE	0	-0.010	0.007	14.290	-0.020	-0.020	0.000	0.000	0.000	0.000
16	B	18	VAL	0	0.004	0.007	17.221	0.022	0.022	0.000	0.000	0.000	0.000
17	B	19	SER	0	0.033	0.034	20.083	-0.014	-0.014	0.000	0.000	0.000	0.000
18	B	20	PHE	0	0.082	0.008	22.397	0.007	0.007	0.000	0.000	0.000	0.000
19	B	21	LYS	1	0.945	0.965	25.389	-0.003	-0.003	0.000	0.000	0.000	0.000
20	B	22	ASP	-1	-0.988	-0.991	24.647	0.018	0.018	0.000	0.000	0.000	0.000
21	B	23	ILE	0	-0.012	-0.016	21.991	0.006	0.006	0.000	0.000	0.000	0.000
22	B	24	GLY	0	-0.016	0.000	26.532	0.002	0.002	0.000	0.000	0.000	0.000
23	B	25	TRP	0	-0.016	-0.020	24.080	-0.003	-0.003	0.000	0.000	0.000	0.000
24	B	26	ASN	0	-0.035	-0.015	28.823	-0.002	-0.002	0.000	0.000	0.000	0.000
25	B	27	ASP	-1	-0.868	-0.927	29.879	-0.006	-0.006	0.000	0.000	0.000	0.000
26	B	28	TRP	0	-0.050	-0.010	27.228	-0.003	-0.003	0.000	0.000	0.000	0.000
27	B	29	ILE	0	-0.052	-0.028	25.417	-0.003	-0.003	0.000	0.000	0.000	0.000
28	B	30	ILE	0	0.003	0.004	29.367	0.000	0.000	0.000	0.000	0.000	0.000
29	B	31	ALA	0	-0.042	-0.005	26.658	-0.003	-0.003	0.000	0.000	0.000	0.000
30	B	32	PRO	0	-0.010	-0.009	21.406	0.000	0.000	0.000	0.000	0.000	0.000
31	B	33	SER	0	0.056	0.017	24.488	0.004	0.004	0.000	0.000	0.000	0.000
32	B	34	GLY	0	0.035	-0.006	22.031	0.010	0.010	0.000	0.000	0.000	0.000
33	B	35	TYR	0	-0.017	-0.010	17.126	-0.011	-0.011	0.000	0.000	0.000	0.000
34	B	36	HIS	0	-0.021	-0.015	13.119	-0.001	-0.001	0.000	0.000	0.000	0.000
35	B	37	ALA	0	0.009	0.033	14.024	-0.003	-0.003	0.000	0.000	0.000	0.000
36	B	38	ASN	0	-0.012	-0.013	8.885	0.033	0.033	0.000	0.000	0.000	0.000
37	B	39	TYR	0	0.002	-0.010	9.775	0.021	0.021	0.000	0.000	0.000	0.000
38	B	40	CYS	0	-0.072	0.003	2.419	-1.511	-0.448	0.484	-0.477	-1.070	0.005
39	B	41	GLU	-1	-0.868	-0.937	7.681	0.603	0.603	0.000	0.000	0.000	0.000
40	B	42	GLY	0	-0.007	-0.003	7.556	0.439	0.439	0.000	0.000	0.000	0.000
41	B	43	GLU	-1	-0.954	-0.973	8.772	0.451	0.451	0.000	0.000	0.000	0.000
42	B	44	CYS	0	-0.065	-0.042	5.246	0.321	0.378	-0.002	-0.003	-0.051	0.000
43	B	45	PRO	0	0.020	0.006	9.511	-0.078	-0.078	0.000	0.000	0.000	0.000
44	B	46	SER	0	0.019	0.016	12.599	-0.010	-0.010	0.000	0.000	0.000	0.000
45	B	47	HIS	0	-0.034	-0.017	14.648	-0.026	-0.026	0.000	0.000	0.000	0.000
46	B	48	ILE	0	-0.007	0.010	17.176	-0.004	-0.004	0.000	0.000	0.000	0.000
47	B	77	LEU	0	0.030	-0.003	18.820	-0.002	-0.002	0.000	0.000	0.000	0.000
48	B	78	LYS	1	0.959	0.987	17.201	-0.208	-0.208	0.000	0.000	0.000	0.000
49	B	79	SER	0	0.019	-0.007	11.592	-0.027	-0.027	0.000	0.000	0.000	0.000
50	B	80	CYS	0	-0.051	-0.031	12.291	0.021	0.021	0.000	0.000	0.000	0.000
51	B	82	VAL	0	-0.018	-0.008	8.494	-0.055	-0.055	0.000	0.000	0.000	0.000
52	B	83	PRO	0	0.055	-0.006	7.003	0.061	0.061	0.000	0.000	0.000	0.000
53	B	84	THR	0	-0.057	-0.013	5.050	-0.004	-0.004	0.000	0.000	0.000	0.000
54	B	85	LYS	1	0.964	0.980	6.585	0.330	0.330	0.000	0.000	0.000	0.000
55	B	86	LEU	0	-0.003	0.013	8.250	0.007	0.007	0.000	0.000	0.000	0.000
56	B	87	ARG	1	0.965	0.988	11.266	0.254	0.254	0.000	0.000	0.000	0.000
57	B	88	PRO	0	-0.019	-0.021	13.231	0.018	0.018	0.000	0.000	0.000	0.000
58	B	89	MET	0	-0.016	0.003	16.691	-0.020	-0.020	0.000	0.000	0.000	0.000
59	B	90	SER	0	-0.037	-0.021	19.021	0.006	0.006	0.000	0.000	0.000	0.000
60	B	91	MET	0	-0.009	-0.010	22.623	0.000	0.000	0.000	0.000	0.000	0.000
61	B	92	LEU	0	-0.030	-0.012	25.300	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	93	TYR	0	-0.022	-0.016	27.620	0.002	0.002	0.000	0.000	0.000	0.000
63	B	94	TYR	0	0.034	0.028	30.616	-0.002	-0.002	0.000	0.000	0.000	0.000
64	B	95	ASP	-1	-0.862	-0.927	32.998	-0.016	-0.016	0.000	0.000	0.000	0.000
65	B	96	ASP	-1	-0.797	-0.922	34.449	-0.007	-0.007	0.000	0.000	0.000	0.000
66	B	97	GLY	0	-0.082	-0.024	37.390	0.001	0.001	0.000	0.000	0.000	0.000
67	B	98	GLN	0	-0.107	-0.065	38.522	-0.002	-0.002	0.000	0.000	0.000	0.000
68	B	99	ASN	0	-0.021	-0.003	38.103	0.000	0.000	0.000	0.000	0.000	0.000
69	B	100	ILE	0	-0.016	-0.013	33.432	-0.001	-0.001	0.000	0.000	0.000	0.000
70	B	101	ILE	0	-0.004	0.016	29.946	-0.002	-0.002	0.000	0.000	0.000	0.000
71	B	102	LYS	1	0.916	0.946	25.348	0.070	0.070	0.000	0.000	0.000	0.000
72	B	103	LYS	1	0.913	0.958	25.310	0.034	0.034	0.000	0.000	0.000	0.000
73	B	104	ASP	-1	-0.814	-0.894	21.682	-0.087	-0.087	0.000	0.000	0.000	0.000
74	B	105	ILE	0	-0.047	-0.027	20.445	0.004	0.004	0.000	0.000	0.000	0.000
75	B	106	GLN	0	0.027	-0.007	18.505	-0.015	-0.015	0.000	0.000	0.000	0.000
76	B	107	ASN	0	-0.042	-0.033	14.919	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	108	MET	0	0.045	0.028	15.927	0.020	0.020	0.000	0.000	0.000	0.000
78	B	109	ILE	0	-0.026	0.004	11.301	-0.002	-0.002	0.000	0.000	0.000	0.000
79	B	110	VAL	0	0.012	0.016	7.651	-0.015	-0.015	0.000	0.000	0.000	0.000
80	B	111	GLU	-1	-0.958	-0.991	7.212	-0.484	-0.484	0.000	0.000	0.000	0.000
81	B	112	GLU	-1	-0.898	-0.969	2.393	-2.220	-1.036	0.904	-0.416	-1.672	0.000
82	B	114	GLY	0	0.078	0.021	2.841	-0.956	0.196	0.852	-0.753	-1.252	-0.009
83	B	116	SER	0	0.003	0.033	8.472	-0.082	-0.082	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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