FMO DATABASE

FMODB ID: R9RJ8

Calculation Name: 2NYX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NYX

Chain ID: A

ChEMBL ID:

UniProt ID: P71672

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	146
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1133293.082847
FMO2-HF: Nuclear repulsion	1078615.006584
FMO2-HF: Total energy	-54678.076262
FMO2-MP2: Total energy	-54840.021334

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:7:PRO)

Summations of interaction energy for fragment #1(A:7:PRO)

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.
13.983	-1.32	-0.148	16.519	-1.07	-0.007

Interaction energy analysis for fragmet #1(A:7:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.034 / q_NPA : -0.017

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	9	THR	0	-0.083	-0.079	2.520	15.942	0.592	-0.147	16.531	-1.035	-0.007
4	A	10	ALA	0	0.000	0.017	5.256	-0.671	-0.624	-0.001	-0.012	-0.035	0.000
5	A	11	GLU	-1	-0.960	-1.004	8.117	0.062	0.062	0.000	0.000	0.000	0.000
6	A	12	GLU	-1	-0.909	-0.945	8.671	-0.463	-0.463	0.000	0.000	0.000	0.000
7	A	13	SER	0	-0.006	-0.017	12.309	0.069	0.069	0.000	0.000	0.000	0.000
8	A	14	VAL	0	0.084	0.016	16.086	-0.006	-0.006	0.000	0.000	0.000	0.000
9	A	15	ASP	-1	-0.862	-0.899	18.578	-0.118	-0.118	0.000	0.000	0.000	0.000
10	A	16	VAL	0	0.048	0.016	14.170	-0.003	-0.003	0.000	0.000	0.000	0.000
11	A	17	ILE	0	-0.005	0.011	13.799	-0.011	-0.011	0.000	0.000	0.000	0.000
12	A	18	THR	0	-0.034	-0.037	16.135	0.028	0.028	0.000	0.000	0.000	0.000
13	A	19	ASP	-1	-0.890	-0.939	18.871	-0.153	-0.153	0.000	0.000	0.000	0.000
14	A	20	ALA	0	-0.042	-0.023	15.359	0.004	0.004	0.000	0.000	0.000	0.000
15	A	21	LEU	0	-0.001	-0.005	17.350	0.018	0.018	0.000	0.000	0.000	0.000
16	A	22	LEU	0	-0.001	0.015	19.243	0.015	0.015	0.000	0.000	0.000	0.000
17	A	23	THR	0	-0.012	0.001	19.790	0.010	0.010	0.000	0.000	0.000	0.000
18	A	24	ALA	0	0.013	0.005	18.483	0.008	0.008	0.000	0.000	0.000	0.000
19	A	25	SER	0	-0.053	-0.042	20.591	0.016	0.016	0.000	0.000	0.000	0.000
20	A	26	ARG	1	0.965	0.971	23.901	0.087	0.087	0.000	0.000	0.000	0.000
21	A	27	LEU	0	0.020	0.022	20.890	0.004	0.004	0.000	0.000	0.000	0.000
22	A	28	LEU	0	0.027	0.011	22.137	0.009	0.009	0.000	0.000	0.000	0.000
23	A	29	VAL	0	-0.010	0.001	25.530	0.007	0.007	0.000	0.000	0.000	0.000
24	A	30	ALA	0	0.008	0.015	27.373	0.003	0.003	0.000	0.000	0.000	0.000
25	A	31	ILE	0	0.022	0.021	24.298	0.004	0.004	0.000	0.000	0.000	0.000
26	A	32	SER	0	-0.055	-0.042	28.762	0.008	0.008	0.000	0.000	0.000	0.000
27	A	33	ALA	0	-0.017	0.002	31.286	0.002	0.002	0.000	0.000	0.000	0.000
28	A	34	HIS	0	0.049	0.023	31.054	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	35	SER	0	-0.030	-0.034	31.741	0.004	0.004	0.000	0.000	0.000	0.000
30	A	36	ILE	0	-0.047	-0.035	34.401	0.003	0.003	0.000	0.000	0.000	0.000
31	A	37	ALA	0	0.024	0.021	36.976	0.001	0.001	0.000	0.000	0.000	0.000
32	A	38	GLN	0	-0.035	-0.007	36.380	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	39	VAL	0	-0.121	-0.049	38.407	0.002	0.002	0.000	0.000	0.000	0.000
34	A	40	ASP	-1	-0.898	-0.978	40.770	0.008	0.008	0.000	0.000	0.000	0.000
35	A	41	GLU	-1	-0.933	-0.961	41.566	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	42	ASN	0	-0.037	-0.013	42.842	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	43	ILE	0	-0.100	-0.019	40.457	0.001	0.001	0.000	0.000	0.000	0.000
38	A	44	THR	0	0.019	-0.022	41.349	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	45	ILE	0	0.060	0.013	36.070	0.003	0.003	0.000	0.000	0.000	0.000
40	A	46	PRO	0	-0.012	-0.013	38.901	0.004	0.004	0.000	0.000	0.000	0.000
41	A	47	GLN	0	0.092	0.062	41.048	0.002	0.002	0.000	0.000	0.000	0.000
42	A	48	PHE	0	0.070	0.037	34.686	0.003	0.003	0.000	0.000	0.000	0.000
43	A	49	ARG	1	0.886	0.933	36.048	-0.031	-0.031	0.000	0.000	0.000	0.000
44	A	50	THR	0	-0.020	-0.018	38.368	0.004	0.004	0.000	0.000	0.000	0.000
45	A	51	LEU	0	0.030	0.006	40.737	0.003	0.003	0.000	0.000	0.000	0.000
46	A	52	VAL	0	0.006	0.006	34.572	0.003	0.003	0.000	0.000	0.000	0.000
47	A	53	ILE	0	-0.013	0.003	38.002	0.005	0.005	0.000	0.000	0.000	0.000
48	A	54	LEU	0	0.021	0.004	39.190	0.003	0.003	0.000	0.000	0.000	0.000
49	A	55	SER	0	-0.027	-0.009	37.762	0.001	0.001	0.000	0.000	0.000	0.000
50	A	56	ASN	0	-0.100	-0.053	34.110	0.002	0.002	0.000	0.000	0.000	0.000
51	A	57	HIS	0	-0.005	0.002	37.207	0.004	0.004	0.000	0.000	0.000	0.000
52	A	58	GLY	0	-0.001	0.017	40.720	0.000	0.000	0.000	0.000	0.000	0.000
53	A	59	PRO	0	-0.047	-0.041	43.841	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	60	ILE	0	0.042	0.039	43.142	0.001	0.001	0.000	0.000	0.000	0.000
55	A	61	ASN	0	-0.012	0.000	47.320	-0.002	-0.002	0.000	0.000	0.000	0.000
56	A	62	LEU	0	0.047	0.003	47.959	0.001	0.001	0.000	0.000	0.000	0.000
57	A	63	ALA	0	-0.011	0.006	48.077	0.000	0.000	0.000	0.000	0.000	0.000
58	A	64	THR	0	0.037	0.008	43.787	0.001	0.001	0.000	0.000	0.000	0.000
59	A	65	LEU	0	0.026	0.002	42.914	0.001	0.001	0.000	0.000	0.000	0.000
60	A	66	ALA	0	-0.009	-0.002	43.224	0.000	0.000	0.000	0.000	0.000	0.000
61	A	67	THR	0	-0.023	-0.014	41.843	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	68	LEU	0	0.006	0.003	37.811	0.001	0.001	0.000	0.000	0.000	0.000
63	A	69	LEU	0	-0.053	-0.022	38.692	0.000	0.000	0.000	0.000	0.000	0.000
64	A	70	GLY	0	0.021	0.033	39.850	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	71	VAL	0	-0.069	-0.029	40.991	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	72	GLN	0	0.077	0.032	44.258	0.003	0.003	0.000	0.000	0.000	0.000
67	A	73	PRO	0	0.068	0.013	47.877	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	74	SER	0	-0.033	-0.010	49.938	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	75	ALA	0	0.024	0.003	48.292	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	76	THR	0	0.000	0.001	46.592	0.000	0.000	0.000	0.000	0.000	0.000
71	A	77	GLY	0	0.026	0.016	48.627	0.000	0.000	0.000	0.000	0.000	0.000
72	A	78	ARG	1	0.972	0.986	51.725	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	79	MET	0	-0.017	0.001	44.012	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	80	VAL	0	0.024	0.001	48.017	0.000	0.000	0.000	0.000	0.000	0.000
75	A	81	ASP	-1	-0.821	-0.889	49.828	0.015	0.015	0.000	0.000	0.000	0.000
76	A	82	ARG	1	0.930	0.968	50.053	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	83	LEU	0	0.005	0.002	45.348	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	84	VAL	0	-0.030	-0.004	49.512	0.001	0.001	0.000	0.000	0.000	0.000
79	A	85	GLY	0	0.001	0.013	52.575	0.000	0.000	0.000	0.000	0.000	0.000
80	A	86	ALA	0	-0.058	-0.023	49.581	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	87	GLU	-1	-0.928	-0.956	50.644	0.015	0.015	0.000	0.000	0.000	0.000
82	A	88	LEU	0	-0.051	-0.041	45.239	0.002	0.002	0.000	0.000	0.000	0.000
83	A	89	ILE	0	-0.059	-0.037	45.821	0.003	0.003	0.000	0.000	0.000	0.000
84	A	90	ASP	-1	-0.811	-0.878	49.376	0.023	0.023	0.000	0.000	0.000	0.000
85	A	91	ARG	1	0.808	0.857	51.445	-0.018	-0.018	0.000	0.000	0.000	0.000
86	A	92	LEU	0	0.012	0.006	51.694	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	93	PRO	0	0.014	0.002	55.206	0.000	0.000	0.000	0.000	0.000	0.000
88	A	94	HIS	0	0.031	0.008	53.521	0.000	0.000	0.000	0.000	0.000	0.000
89	A	95	PRO	0	-0.002	0.020	53.898	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	96	THR	0	0.034	-0.008	56.991	0.001	0.001	0.000	0.000	0.000	0.000
91	A	97	SER	0	-0.046	-0.001	57.307	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	98	ARG	1	0.897	0.935	59.319	-0.024	-0.024	0.000	0.000	0.000	0.000
93	A	99	ARG	1	0.914	0.981	58.439	-0.027	-0.027	0.000	0.000	0.000	0.000
94	A	100	GLU	-1	-0.793	-0.882	53.475	0.034	0.034	0.000	0.000	0.000	0.000
95	A	101	LEU	0	-0.033	-0.031	53.775	0.000	0.000	0.000	0.000	0.000	0.000
96	A	102	LEU	0	0.013	-0.009	50.461	0.001	0.001	0.000	0.000	0.000	0.000
97	A	103	ALA	0	0.002	0.014	48.156	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	104	ALA	0	0.040	0.007	47.105	0.003	0.003	0.000	0.000	0.000	0.000
99	A	105	LEU	0	-0.026	0.003	42.020	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	106	THR	0	0.043	0.018	46.736	0.001	0.001	0.000	0.000	0.000	0.000
101	A	107	LYS	1	0.776	0.858	46.115	-0.025	-0.025	0.000	0.000	0.000	0.000
102	A	108	ARG	1	1.038	1.021	44.049	-0.016	-0.016	0.000	0.000	0.000	0.000
103	A	109	GLY	0	0.087	0.043	44.886	0.000	0.000	0.000	0.000	0.000	0.000
104	A	110	ARG	1	0.897	0.945	42.442	-0.035	-0.035	0.000	0.000	0.000	0.000
105	A	111	ASP	-1	-0.825	-0.893	41.331	0.029	0.029	0.000	0.000	0.000	0.000
106	A	112	VAL	0	0.024	0.015	40.598	0.000	0.000	0.000	0.000	0.000	0.000
107	A	113	VAL	0	0.018	0.007	36.949	0.000	0.000	0.000	0.000	0.000	0.000
108	A	114	ARG	1	0.910	0.954	36.625	-0.055	-0.055	0.000	0.000	0.000	0.000
109	A	115	GLN	0	0.069	0.033	36.400	0.002	0.002	0.000	0.000	0.000	0.000
110	A	116	VAL	0	0.024	0.034	34.153	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	117	THR	0	-0.061	-0.045	31.545	0.001	0.001	0.000	0.000	0.000	0.000
112	A	118	GLU	-1	-0.830	-0.904	31.580	0.050	0.050	0.000	0.000	0.000	0.000
113	A	119	HIS	0	-0.006	0.000	32.309	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	120	ARG	1	0.929	0.965	27.069	-0.045	-0.045	0.000	0.000	0.000	0.000
115	A	121	ARG	1	0.839	0.898	27.346	-0.067	-0.067	0.000	0.000	0.000	0.000
116	A	122	THR	0	0.009	0.009	27.274	0.002	0.002	0.000	0.000	0.000	0.000
117	A	123	GLU	-1	-0.798	-0.865	27.006	-0.031	-0.031	0.000	0.000	0.000	0.000
118	A	124	ILE	0	-0.027	-0.025	22.402	-0.006	-0.006	0.000	0.000	0.000	0.000
119	A	125	ALA	0	-0.016	-0.001	22.964	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	126	ARG	1	0.888	0.916	23.500	0.038	0.038	0.000	0.000	0.000	0.000
121	A	127	ILE	0	-0.040	-0.024	20.141	-0.013	-0.013	0.000	0.000	0.000	0.000
122	A	128	VAL	0	-0.004	-0.021	18.668	-0.011	-0.011	0.000	0.000	0.000	0.000
123	A	129	GLU	-1	-0.972	-0.988	18.834	0.010	0.010	0.000	0.000	0.000	0.000
124	A	130	GLN	0	-0.076	-0.032	19.776	0.001	0.001	0.000	0.000	0.000	0.000
125	A	131	MET	0	-0.041	0.010	14.245	-0.021	-0.021	0.000	0.000	0.000	0.000
126	A	132	ALA	0	0.049	0.016	11.683	0.048	0.048	0.000	0.000	0.000	0.000
127	A	133	PRO	0	0.007	-0.020	13.117	0.043	0.043	0.000	0.000	0.000	0.000
128	A	134	ALA	0	0.016	0.003	8.090	0.062	0.062	0.000	0.000	0.000	0.000
129	A	135	GLU	-1	-0.848	-0.912	9.879	-0.146	-0.146	0.000	0.000	0.000	0.000
130	A	136	ARG	1	0.862	0.937	11.085	-0.015	-0.015	0.000	0.000	0.000	0.000
131	A	137	HIS	0	-0.001	-0.003	11.663	0.064	0.064	0.000	0.000	0.000	0.000
132	A	138	GLY	0	0.025	0.010	10.043	0.066	0.066	0.000	0.000	0.000	0.000
133	A	139	LEU	0	0.000	0.009	10.864	-0.029	-0.029	0.000	0.000	0.000	0.000
134	A	140	VAL	0	0.028	0.007	14.055	-0.019	-0.019	0.000	0.000	0.000	0.000
135	A	141	ARG	1	0.969	1.001	9.438	-0.988	-0.988	0.000	0.000	0.000	0.000
136	A	142	ALA	0	-0.007	-0.003	12.694	-0.017	-0.017	0.000	0.000	0.000	0.000
137	A	143	LEU	0	0.007	-0.006	14.355	-0.038	-0.038	0.000	0.000	0.000	0.000
138	A	144	THR	0	-0.029	-0.016	17.472	-0.031	-0.031	0.000	0.000	0.000	0.000
139	A	145	ALA	0	0.003	0.008	15.595	-0.010	-0.010	0.000	0.000	0.000	0.000
140	A	146	PHE	0	-0.044	-0.023	17.688	-0.030	-0.030	0.000	0.000	0.000	0.000
141	A	147	THR	0	-0.080	-0.063	19.724	-0.026	-0.026	0.000	0.000	0.000	0.000
142	A	148	GLU	-1	-0.948	-0.960	20.317	0.245	0.245	0.000	0.000	0.000	0.000
143	A	149	ALA	0	-0.047	-0.013	20.065	-0.012	-0.012	0.000	0.000	0.000	0.000
144	A	150	GLY	0	0.012	0.018	22.076	-0.013	-0.013	0.000	0.000	0.000	0.000
145	A	151	GLY	0	-0.048	-0.043	24.851	0.007	0.007	0.000	0.000	0.000	0.000
146	A	152	GLU	-1	-0.995	-0.979	25.887	0.141	0.141	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:PRO)