FMO DATABASE

FMODB ID: Z656N

Calculation Name: 1NYS-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NYS

Chain ID: D

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	OptHSide
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	74
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-455229.878204
FMO2-HF: Nuclear repulsion	421875.427508
FMO2-HF: Total energy	-33354.450696
FMO2-MP2: Total energy	-33442.898181

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:10:ILE)

Summations of interaction energy for fragment #1(D:10:ILE)

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.
-9.831	-2.11	2.237	-4.293	-5.665	-0.019

Interaction energy analysis for fragmet #1(D:10:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.011

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	D	12	CYS	0	-0.043	-0.020	3.217	-3.254	-0.939	0.083	-1.087	-1.311	-0.002
4	D	13	LYS	1	0.877	0.960	5.333	0.955	1.032	-0.001	-0.007	-0.069	0.000
5	D	14	LYS	1	0.875	0.923	8.971	-0.056	-0.056	0.000	0.000	0.000	0.000
6	D	15	GLN	0	0.009	-0.029	10.775	0.069	0.069	0.000	0.000	0.000	0.000
7	D	16	PHE	0	0.034	0.014	14.264	0.031	0.031	0.000	0.000	0.000	0.000
8	D	17	PHE	0	0.022	0.015	16.963	-0.008	-0.008	0.000	0.000	0.000	0.000
9	D	18	VAL	0	-0.002	0.016	20.515	0.016	0.016	0.000	0.000	0.000	0.000
10	D	19	SER	0	0.018	-0.005	23.546	-0.007	-0.007	0.000	0.000	0.000	0.000
11	D	20	PHE	0	0.082	0.024	27.361	0.005	0.005	0.000	0.000	0.000	0.000
12	D	21	LYS	1	0.853	0.932	30.414	0.016	0.016	0.000	0.000	0.000	0.000
13	D	22	ASP	-1	-0.870	-0.935	27.969	-0.005	-0.005	0.000	0.000	0.000	0.000
14	D	23	ILE	0	-0.010	0.012	25.328	0.007	0.007	0.000	0.000	0.000	0.000
15	D	24	GLY	0	-0.006	-0.008	29.787	0.004	0.004	0.000	0.000	0.000	0.000
16	D	25	TRP	0	-0.014	-0.021	31.336	-0.001	-0.001	0.000	0.000	0.000	0.000
17	D	26	ASN	0	-0.062	-0.029	34.182	-0.001	-0.001	0.000	0.000	0.000	0.000
18	D	27	ASP	-1	-0.852	-0.919	35.293	-0.006	-0.006	0.000	0.000	0.000	0.000
19	D	28	TRP	0	-0.044	-0.012	35.801	-0.001	-0.001	0.000	0.000	0.000	0.000
20	D	29	ILE	0	-0.062	-0.054	31.903	-0.002	-0.002	0.000	0.000	0.000	0.000
21	D	30	ILE	0	-0.007	-0.005	35.155	-0.001	-0.001	0.000	0.000	0.000	0.000
22	D	31	ALA	0	-0.032	0.003	33.576	-0.003	-0.003	0.000	0.000	0.000	0.000
23	D	32	PRO	0	-0.010	-0.019	28.368	0.001	0.001	0.000	0.000	0.000	0.000
24	D	33	SER	0	0.048	0.012	30.272	0.003	0.003	0.000	0.000	0.000	0.000
25	D	34	GLY	0	0.019	0.001	26.924	0.008	0.008	0.000	0.000	0.000	0.000
26	D	35	TYR	0	-0.016	-0.006	21.635	-0.003	-0.003	0.000	0.000	0.000	0.000
27	D	36	HIS	0	0.037	0.010	19.124	0.009	0.009	0.000	0.000	0.000	0.000
28	D	37	ALA	0	0.017	0.007	19.261	-0.010	-0.010	0.000	0.000	0.000	0.000
29	D	38	ASN	0	-0.138	-0.078	13.874	-0.025	-0.025	0.000	0.000	0.000	0.000
30	D	39	TYR	0	0.034	0.023	13.343	0.050	0.050	0.000	0.000	0.000	0.000
31	D	40	CYS	0	-0.047	-0.003	7.709	-0.007	-0.007	0.000	0.000	0.000	0.000
32	D	41	GLU	-1	-0.779	-0.859	7.996	0.339	0.339	0.000	0.000	0.000	0.000
33	D	42	GLY	0	0.037	-0.013	4.544	-1.075	-0.988	0.000	-0.049	-0.038	0.000
34	D	43	GLU	-1	-0.890	-0.925	2.877	-0.339	1.728	0.517	-0.944	-1.640	0.008
35	D	44	CYS	0	-0.126	-0.066	2.523	-4.714	-1.690	1.638	-2.187	-2.475	-0.025
36	D	45	PRO	0	0.039	0.024	4.123	-0.263	-0.112	0.000	-0.019	-0.132	0.000
37	D	46	SER	0	-0.015	-0.002	7.146	-0.211	-0.211	0.000	0.000	0.000	0.000
38	D	77	LEU	0	-0.013	-0.013	13.792	-0.006	-0.006	0.000	0.000	0.000	0.000
39	D	78	LYS	1	0.944	0.971	9.568	-0.943	-0.943	0.000	0.000	0.000	0.000
40	D	79	SER	0	0.005	-0.002	7.861	-0.115	-0.115	0.000	0.000	0.000	0.000
41	D	80	CYS	0	-0.007	-0.010	8.975	0.241	0.241	0.000	0.000	0.000	0.000
42	D	82	VAL	0	0.013	0.013	7.686	0.001	0.001	0.000	0.000	0.000	0.000
43	D	83	PRO	0	0.048	-0.011	10.225	-0.116	-0.116	0.000	0.000	0.000	0.000
44	D	84	THR	0	-0.041	-0.018	10.897	0.047	0.047	0.000	0.000	0.000	0.000
45	D	85	LYS	1	0.827	0.912	12.963	0.357	0.357	0.000	0.000	0.000	0.000
46	D	86	LEU	0	-0.016	-0.002	15.171	-0.009	-0.009	0.000	0.000	0.000	0.000
47	D	87	ARG	1	0.882	0.937	18.128	0.173	0.173	0.000	0.000	0.000	0.000
48	D	88	PRO	0	0.007	0.014	20.999	0.008	0.008	0.000	0.000	0.000	0.000
49	D	89	MET	0	-0.011	-0.018	24.524	-0.013	-0.013	0.000	0.000	0.000	0.000
50	D	90	SER	0	-0.054	-0.050	26.415	0.006	0.006	0.000	0.000	0.000	0.000
51	D	91	MET	0	-0.034	-0.015	29.368	-0.001	-0.001	0.000	0.000	0.000	0.000
52	D	92	LEU	0	-0.014	0.004	32.329	0.001	0.001	0.000	0.000	0.000	0.000
53	D	93	TYR	0	0.014	0.015	34.485	-0.001	-0.001	0.000	0.000	0.000	0.000
54	D	94	TYR	0	0.021	0.013	37.008	-0.001	-0.001	0.000	0.000	0.000	0.000
55	D	95	ASP	-1	-0.949	-0.952	38.825	-0.007	-0.007	0.000	0.000	0.000	0.000
56	D	96	ASP	-1	-0.874	-0.959	40.439	0.006	0.006	0.000	0.000	0.000	0.000
57	D	97	GLY	0	-0.016	0.007	43.057	0.000	0.000	0.000	0.000	0.000	0.000
58	D	98	GLN	0	-0.077	-0.051	45.392	0.000	0.000	0.000	0.000	0.000	0.000
59	D	99	ASN	0	-0.015	-0.007	44.086	-0.003	-0.003	0.000	0.000	0.000	0.000
60	D	100	ILE	0	0.026	0.018	40.631	0.000	0.000	0.000	0.000	0.000	0.000
61	D	101	ILE	0	-0.008	0.001	37.139	-0.001	-0.001	0.000	0.000	0.000	0.000
62	D	102	LYS	1	0.885	0.923	33.098	0.049	0.049	0.000	0.000	0.000	0.000
63	D	103	LYS	1	0.912	0.963	32.805	0.020	0.020	0.000	0.000	0.000	0.000
64	D	104	ASP	-1	-0.819	-0.879	29.596	-0.058	-0.058	0.000	0.000	0.000	0.000
65	D	105	ILE	0	0.001	0.010	27.300	0.003	0.003	0.000	0.000	0.000	0.000
66	D	106	GLN	0	0.044	0.004	24.627	-0.019	-0.019	0.000	0.000	0.000	0.000
67	D	107	ASN	0	-0.051	-0.043	20.988	0.012	0.012	0.000	0.000	0.000	0.000
68	D	108	MET	0	0.070	0.048	21.710	0.009	0.009	0.000	0.000	0.000	0.000
69	D	109	ILE	0	-0.029	0.013	18.528	-0.001	-0.001	0.000	0.000	0.000	0.000
70	D	110	VAL	0	0.023	0.009	13.330	-0.006	-0.006	0.000	0.000	0.000	0.000
71	D	111	GLU	-1	-0.887	-0.940	14.893	-0.282	-0.282	0.000	0.000	0.000	0.000
72	D	112	GLU	-1	-0.839	-0.938	9.826	-0.494	-0.494	0.000	0.000	0.000	0.000
73	D	114	GLY	0	0.073	0.036	6.612	-0.196	-0.196	0.000	0.000	0.000	0.000
74	D	116	SER	0	0.042	0.037	7.160	-0.013	-0.013	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:10:ILE)