FMO DATABASE

FMODB ID: R9G98

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	OptAll
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	-456564.879353
FMO2-HF: Nuclear repulsion	423209.833
FMO2-HF: Total energy	-33355.046353
FMO2-MP2: Total energy	-33443.516106

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.
-13.315	-5.13	3.255	-5.057	-6.384	-0.016

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 : -0.008 / q_NPA : -0.015

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	-0.019	-0.004	3.102	-3.140	-0.662	0.111	-1.174	-1.415	-0.004
4	D	13	LYS	1	0.885	0.935	5.327	1.089	1.150	-0.001	-0.005	-0.054	0.000
5	D	14	LYS	1	0.839	0.906	9.064	0.027	0.027	0.000	0.000	0.000	0.000
6	D	15	GLN	0	0.002	-0.017	10.830	0.103	0.103	0.000	0.000	0.000	0.000
7	D	16	PHE	0	0.011	0.001	14.199	0.034	0.034	0.000	0.000	0.000	0.000
8	D	17	PHE	0	-0.001	-0.001	17.057	-0.011	-0.011	0.000	0.000	0.000	0.000
9	D	18	VAL	0	-0.003	0.021	20.810	0.017	0.017	0.000	0.000	0.000	0.000
10	D	19	SER	0	-0.011	-0.029	23.801	-0.007	-0.007	0.000	0.000	0.000	0.000
11	D	20	PHE	0	0.063	0.018	27.626	0.007	0.007	0.000	0.000	0.000	0.000
12	D	21	LYS	1	0.867	0.916	30.415	0.033	0.033	0.000	0.000	0.000	0.000
13	D	22	ASP	-1	-0.864	-0.905	28.097	-0.019	-0.019	0.000	0.000	0.000	0.000
14	D	23	ILE	0	-0.026	-0.015	25.798	0.006	0.006	0.000	0.000	0.000	0.000
15	D	24	GLY	0	0.006	0.017	30.180	0.004	0.004	0.000	0.000	0.000	0.000
16	D	25	TRP	0	-0.010	-0.018	31.260	-0.003	-0.003	0.000	0.000	0.000	0.000
17	D	26	ASN	0	-0.063	-0.040	34.080	-0.003	-0.003	0.000	0.000	0.000	0.000
18	D	27	ASP	-1	-0.868	-0.928	35.414	-0.015	-0.015	0.000	0.000	0.000	0.000
19	D	28	TRP	0	-0.029	0.000	35.891	0.000	0.000	0.000	0.000	0.000	0.000
20	D	29	ILE	0	-0.051	-0.035	31.742	-0.002	-0.002	0.000	0.000	0.000	0.000
21	D	30	ILE	0	0.000	0.012	35.060	-0.001	-0.001	0.000	0.000	0.000	0.000
22	D	31	ALA	0	-0.026	-0.004	33.701	-0.003	-0.003	0.000	0.000	0.000	0.000
23	D	32	PRO	0	0.011	0.004	28.431	0.001	0.001	0.000	0.000	0.000	0.000
24	D	33	SER	0	0.068	0.016	30.889	0.003	0.003	0.000	0.000	0.000	0.000
25	D	34	GLY	0	0.002	-0.006	27.221	0.009	0.009	0.000	0.000	0.000	0.000
26	D	35	TYR	0	-0.020	-0.002	22.041	-0.001	-0.001	0.000	0.000	0.000	0.000
27	D	36	HIS	0	0.051	0.024	19.255	0.015	0.015	0.000	0.000	0.000	0.000
28	D	37	ALA	0	0.013	0.007	19.525	-0.021	-0.021	0.000	0.000	0.000	0.000
29	D	38	ASN	0	-0.051	-0.041	14.147	-0.035	-0.035	0.000	0.000	0.000	0.000
30	D	39	TYR	0	0.027	0.021	13.502	0.057	0.057	0.000	0.000	0.000	0.000
31	D	40	CYS	0	-0.047	-0.003	7.855	0.013	0.013	0.000	0.000	0.000	0.000
32	D	41	GLU	-1	-0.793	-0.874	8.002	0.288	0.288	0.000	0.000	0.000	0.000
33	D	42	GLY	0	0.047	0.018	4.057	-1.376	-1.101	0.003	-0.143	-0.136	0.000
34	D	43	GLU	-1	-0.846	-0.909	2.733	-2.826	-0.326	0.846	-1.319	-2.027	0.014
35	D	44	CYS	0	-0.091	-0.054	2.483	-5.550	-2.831	2.296	-2.394	-2.622	-0.026
36	D	45	PRO	0	0.051	0.036	4.202	-0.165	-0.013	0.000	-0.022	-0.130	0.000
37	D	46	SER	0	-0.020	-0.010	7.107	-0.229	-0.229	0.000	0.000	0.000	0.000
38	D	77	LEU	0	-0.004	-0.010	13.651	-0.006	-0.006	0.000	0.000	0.000	0.000
39	D	78	LYS	1	0.862	0.933	8.287	-1.310	-1.310	0.000	0.000	0.000	0.000
40	D	79	SER	0	0.010	0.011	7.639	-0.091	-0.091	0.000	0.000	0.000	0.000
41	D	80	CYS	0	-0.021	-0.031	8.268	0.291	0.291	0.000	0.000	0.000	0.000
42	D	82	VAL	0	0.010	0.005	7.471	0.089	0.089	0.000	0.000	0.000	0.000
43	D	83	PRO	0	0.046	-0.002	10.224	-0.152	-0.152	0.000	0.000	0.000	0.000
44	D	84	THR	0	-0.069	-0.032	10.721	0.042	0.042	0.000	0.000	0.000	0.000
45	D	85	LYS	1	0.826	0.911	12.931	0.427	0.427	0.000	0.000	0.000	0.000
46	D	86	LEU	0	0.000	-0.001	15.286	-0.022	-0.022	0.000	0.000	0.000	0.000
47	D	87	ARG	1	0.878	0.927	18.171	0.210	0.210	0.000	0.000	0.000	0.000
48	D	88	PRO	0	0.005	0.003	21.309	0.008	0.008	0.000	0.000	0.000	0.000
49	D	89	MET	0	-0.020	-0.015	24.484	-0.016	-0.016	0.000	0.000	0.000	0.000
50	D	90	SER	0	-0.068	-0.048	26.603	0.008	0.008	0.000	0.000	0.000	0.000
51	D	91	MET	0	-0.030	-0.006	29.481	-0.003	-0.003	0.000	0.000	0.000	0.000
52	D	92	LEU	0	-0.026	-0.015	32.253	0.002	0.002	0.000	0.000	0.000	0.000
53	D	93	TYR	0	-0.014	-0.016	35.014	-0.002	-0.002	0.000	0.000	0.000	0.000
54	D	94	TYR	0	0.022	0.013	37.147	0.000	0.000	0.000	0.000	0.000	0.000
55	D	95	ASP	-1	-0.940	-0.965	38.838	-0.018	-0.018	0.000	0.000	0.000	0.000
56	D	96	ASP	-1	-0.809	-0.912	40.222	-0.003	-0.003	0.000	0.000	0.000	0.000
57	D	97	GLY	0	-0.030	-0.015	43.023	-0.002	-0.002	0.000	0.000	0.000	0.000
58	D	98	GLN	0	-0.063	-0.040	45.194	0.000	0.000	0.000	0.000	0.000	0.000
59	D	99	ASN	0	-0.032	-0.012	43.768	-0.003	-0.003	0.000	0.000	0.000	0.000
60	D	100	ILE	0	-0.010	0.001	40.900	-0.001	-0.001	0.000	0.000	0.000	0.000
61	D	101	ILE	0	-0.018	-0.003	37.350	-0.001	-0.001	0.000	0.000	0.000	0.000
62	D	102	LYS	1	0.853	0.923	33.178	0.067	0.067	0.000	0.000	0.000	0.000
63	D	103	LYS	1	0.928	0.958	33.104	0.036	0.036	0.000	0.000	0.000	0.000
64	D	104	ASP	-1	-0.799	-0.868	29.906	-0.077	-0.077	0.000	0.000	0.000	0.000
65	D	105	ILE	0	0.006	0.012	27.574	0.001	0.001	0.000	0.000	0.000	0.000
66	D	106	GLN	0	0.058	0.010	24.936	-0.022	-0.022	0.000	0.000	0.000	0.000
67	D	107	ASN	0	-0.028	-0.033	20.946	0.014	0.014	0.000	0.000	0.000	0.000
68	D	108	MET	0	0.035	0.038	21.184	-0.002	-0.002	0.000	0.000	0.000	0.000
69	D	109	ILE	0	-0.024	0.007	18.831	0.000	0.000	0.000	0.000	0.000	0.000
70	D	110	VAL	0	0.031	0.013	13.232	-0.011	-0.011	0.000	0.000	0.000	0.000
71	D	111	GLU	-1	-0.863	-0.920	15.370	-0.318	-0.318	0.000	0.000	0.000	0.000
72	D	112	GLU	-1	-0.849	-0.932	10.474	-0.570	-0.570	0.000	0.000	0.000	0.000
73	D	114	GLY	0	0.075	0.036	6.498	-0.242	-0.242	0.000	0.000	0.000	0.000
74	D	116	SER	0	0.038	0.040	6.894	0.063	0.063	0.000	0.000	0.000	0.000

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