FMO DATABASE

FMODB ID: QYQ3Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1138572.493832
FMO2-HF: Nuclear repulsion	1083893.990981
FMO2-HF: Total energy	-54678.50285
FMO2-MP2: Total energy	-54840.406814

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.
5.374	-0.398	-0.11	6.813	-0.929	-0.006

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 : -0.028 / q_NPA : -0.023

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	-0.031	-0.058	2.745	7.529	1.772	-0.109	6.827	-0.960	-0.006
4	A	10	ALA	0	-0.020	-0.013	4.924	-1.011	-1.026	-0.001	-0.014	0.031	0.000
5	A	11	GLU	-1	-0.972	-0.973	7.615	-0.149	-0.149	0.000	0.000	0.000	0.000
6	A	12	GLU	-1	-0.912	-0.938	8.178	0.009	0.009	0.000	0.000	0.000	0.000
7	A	13	SER	0	-0.013	-0.034	11.878	0.064	0.064	0.000	0.000	0.000	0.000
8	A	14	VAL	0	0.066	0.011	15.694	0.017	0.017	0.000	0.000	0.000	0.000
9	A	15	ASP	-1	-0.843	-0.875	18.213	-0.091	-0.091	0.000	0.000	0.000	0.000
10	A	16	VAL	0	0.049	0.018	13.994	0.014	0.014	0.000	0.000	0.000	0.000
11	A	17	ILE	0	0.003	0.011	13.400	0.024	0.024	0.000	0.000	0.000	0.000
12	A	18	THR	0	-0.030	-0.029	16.214	0.038	0.038	0.000	0.000	0.000	0.000
13	A	19	ASP	-1	-0.891	-0.943	18.599	-0.077	-0.077	0.000	0.000	0.000	0.000
14	A	20	ALA	0	-0.027	-0.002	15.368	0.010	0.010	0.000	0.000	0.000	0.000
15	A	21	LEU	0	0.006	0.000	17.328	0.025	0.025	0.000	0.000	0.000	0.000
16	A	22	LEU	0	-0.011	0.008	19.544	0.007	0.007	0.000	0.000	0.000	0.000
17	A	23	THR	0	-0.033	-0.025	19.434	0.000	0.000	0.000	0.000	0.000	0.000
18	A	24	ALA	0	0.014	0.005	18.661	0.004	0.004	0.000	0.000	0.000	0.000
19	A	25	SER	0	-0.060	-0.040	20.725	0.003	0.003	0.000	0.000	0.000	0.000
20	A	26	ARG	1	0.968	0.974	24.156	0.006	0.006	0.000	0.000	0.000	0.000
21	A	27	LEU	0	0.031	0.030	21.128	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	28	LEU	0	0.028	0.008	22.157	0.001	0.001	0.000	0.000	0.000	0.000
23	A	29	VAL	0	-0.016	0.009	25.663	0.000	0.000	0.000	0.000	0.000	0.000
24	A	30	ALA	0	0.010	0.010	27.731	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	31	ILE	0	0.029	0.018	24.448	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	32	SER	0	-0.058	-0.038	28.959	0.004	0.004	0.000	0.000	0.000	0.000
27	A	33	ALA	0	-0.002	0.004	31.375	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	34	HIS	0	0.031	0.016	31.004	-0.007	-0.007	0.000	0.000	0.000	0.000
29	A	35	SER	0	-0.021	-0.032	31.812	0.001	0.001	0.000	0.000	0.000	0.000
30	A	36	ILE	0	-0.045	-0.023	34.493	0.000	0.000	0.000	0.000	0.000	0.000
31	A	37	ALA	0	0.044	0.020	37.220	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	38	GLN	0	-0.052	-0.019	36.443	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	39	VAL	0	-0.136	-0.057	38.760	0.001	0.001	0.000	0.000	0.000	0.000
34	A	40	ASP	-1	-0.865	-0.957	41.212	0.036	0.036	0.000	0.000	0.000	0.000
35	A	41	GLU	-1	-0.936	-0.954	41.711	0.027	0.027	0.000	0.000	0.000	0.000
36	A	42	ASN	0	-0.062	-0.031	42.995	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	43	ILE	0	-0.096	-0.022	40.679	0.000	0.000	0.000	0.000	0.000	0.000
38	A	44	THR	0	0.018	-0.018	41.265	0.002	0.002	0.000	0.000	0.000	0.000
39	A	45	ILE	0	0.066	0.020	36.006	0.003	0.003	0.000	0.000	0.000	0.000
40	A	46	PRO	0	-0.004	-0.005	38.978	0.005	0.005	0.000	0.000	0.000	0.000
41	A	47	GLN	0	0.094	0.068	41.151	0.001	0.001	0.000	0.000	0.000	0.000
42	A	48	PHE	0	0.069	0.030	35.013	0.003	0.003	0.000	0.000	0.000	0.000
43	A	49	ARG	1	0.873	0.931	36.167	-0.061	-0.061	0.000	0.000	0.000	0.000
44	A	50	THR	0	-0.018	-0.023	38.801	0.003	0.003	0.000	0.000	0.000	0.000
45	A	51	LEU	0	0.033	0.007	40.929	0.002	0.002	0.000	0.000	0.000	0.000
46	A	52	VAL	0	0.004	0.000	34.975	0.003	0.003	0.000	0.000	0.000	0.000
47	A	53	ILE	0	-0.025	-0.009	38.317	0.004	0.004	0.000	0.000	0.000	0.000
48	A	54	LEU	0	0.015	-0.001	39.679	0.002	0.002	0.000	0.000	0.000	0.000
49	A	55	SER	0	-0.056	-0.028	37.842	0.000	0.000	0.000	0.000	0.000	0.000
50	A	56	ASN	0	-0.061	-0.026	34.620	0.001	0.001	0.000	0.000	0.000	0.000
51	A	57	HIS	0	0.012	0.015	36.998	0.002	0.002	0.000	0.000	0.000	0.000
52	A	58	GLY	0	0.006	0.023	40.806	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	59	PRO	0	-0.039	-0.041	43.983	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	60	ILE	0	0.035	0.041	43.373	0.000	0.000	0.000	0.000	0.000	0.000
55	A	61	ASN	0	-0.017	-0.007	47.523	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	62	LEU	0	0.052	0.007	48.083	0.002	0.002	0.000	0.000	0.000	0.000
57	A	63	ALA	0	-0.009	0.010	48.167	0.000	0.000	0.000	0.000	0.000	0.000
58	A	64	THR	0	0.035	0.014	43.772	0.001	0.001	0.000	0.000	0.000	0.000
59	A	65	LEU	0	0.020	0.005	43.144	0.002	0.002	0.000	0.000	0.000	0.000
60	A	66	ALA	0	-0.002	-0.002	43.313	0.001	0.001	0.000	0.000	0.000	0.000
61	A	67	THR	0	-0.026	-0.022	41.579	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	68	LEU	0	0.002	0.000	37.880	0.002	0.002	0.000	0.000	0.000	0.000
63	A	69	LEU	0	-0.049	-0.024	38.643	0.003	0.003	0.000	0.000	0.000	0.000
64	A	70	GLY	0	0.019	0.036	39.690	0.000	0.000	0.000	0.000	0.000	0.000
65	A	71	VAL	0	-0.050	-0.025	40.843	-0.004	-0.004	0.000	0.000	0.000	0.000
66	A	72	GLN	0	0.075	0.028	44.120	0.001	0.001	0.000	0.000	0.000	0.000
67	A	73	PRO	0	0.054	0.015	47.827	0.000	0.000	0.000	0.000	0.000	0.000
68	A	74	SER	0	-0.012	0.007	49.841	0.000	0.000	0.000	0.000	0.000	0.000
69	A	75	ALA	0	0.023	0.007	48.331	0.000	0.000	0.000	0.000	0.000	0.000
70	A	76	THR	0	0.016	0.004	46.588	0.001	0.001	0.000	0.000	0.000	0.000
71	A	77	GLY	0	0.014	0.007	48.366	0.001	0.001	0.000	0.000	0.000	0.000
72	A	78	ARG	1	0.960	0.978	51.864	-0.024	-0.024	0.000	0.000	0.000	0.000
73	A	79	MET	0	-0.034	-0.006	44.107	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	80	VAL	0	0.030	0.003	47.962	0.001	0.001	0.000	0.000	0.000	0.000
75	A	81	ASP	-1	-0.858	-0.903	49.926	0.030	0.030	0.000	0.000	0.000	0.000
76	A	82	ARG	1	0.962	0.971	50.717	-0.027	-0.027	0.000	0.000	0.000	0.000
77	A	83	LEU	0	-0.003	0.008	45.516	0.000	0.000	0.000	0.000	0.000	0.000
78	A	84	VAL	0	-0.030	-0.009	49.736	0.001	0.001	0.000	0.000	0.000	0.000
79	A	85	GLY	0	-0.034	-0.017	52.795	0.000	0.000	0.000	0.000	0.000	0.000
80	A	86	ALA	0	-0.021	-0.003	49.970	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	87	GLU	-1	-0.936	-0.958	50.677	0.035	0.035	0.000	0.000	0.000	0.000
82	A	88	LEU	0	-0.031	-0.028	45.313	0.003	0.003	0.000	0.000	0.000	0.000
83	A	89	ILE	0	-0.063	-0.038	46.114	0.004	0.004	0.000	0.000	0.000	0.000
84	A	90	ASP	-1	-0.795	-0.869	49.564	0.041	0.041	0.000	0.000	0.000	0.000
85	A	91	ARG	1	0.802	0.853	51.656	-0.033	-0.033	0.000	0.000	0.000	0.000
86	A	92	LEU	0	0.014	0.015	52.068	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	93	PRO	0	0.008	0.005	55.577	0.000	0.000	0.000	0.000	0.000	0.000
88	A	94	HIS	0	0.030	0.019	53.370	0.001	0.001	0.000	0.000	0.000	0.000
89	A	95	PRO	0	-0.009	0.008	53.966	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	96	THR	0	0.010	-0.017	56.758	0.001	0.001	0.000	0.000	0.000	0.000
91	A	97	SER	0	-0.046	-0.030	56.852	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	98	ARG	1	0.939	0.960	58.855	-0.030	-0.030	0.000	0.000	0.000	0.000
93	A	99	ARG	1	0.901	0.954	58.351	-0.034	-0.034	0.000	0.000	0.000	0.000
94	A	100	GLU	-1	-0.803	-0.857	53.389	0.042	0.042	0.000	0.000	0.000	0.000
95	A	101	LEU	0	-0.013	-0.011	54.146	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	102	LEU	0	0.035	-0.008	50.655	0.001	0.001	0.000	0.000	0.000	0.000
97	A	103	ALA	0	0.001	0.001	48.884	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	104	ALA	0	0.031	0.008	47.316	0.003	0.003	0.000	0.000	0.000	0.000
99	A	105	LEU	0	0.000	0.016	42.215	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	106	THR	0	0.040	0.017	46.909	0.001	0.001	0.000	0.000	0.000	0.000
101	A	107	LYS	1	0.770	0.866	46.646	-0.051	-0.051	0.000	0.000	0.000	0.000
102	A	108	ARG	1	1.005	0.999	44.213	-0.045	-0.045	0.000	0.000	0.000	0.000
103	A	109	GLY	0	0.094	0.045	45.314	0.001	0.001	0.000	0.000	0.000	0.000
104	A	110	ARG	1	0.863	0.922	42.940	-0.056	-0.056	0.000	0.000	0.000	0.000
105	A	111	ASP	-1	-0.820	-0.886	41.850	0.059	0.059	0.000	0.000	0.000	0.000
106	A	112	VAL	0	0.027	0.021	40.907	0.003	0.003	0.000	0.000	0.000	0.000
107	A	113	VAL	0	0.022	0.008	37.426	0.003	0.003	0.000	0.000	0.000	0.000
108	A	114	ARG	1	0.888	0.953	37.078	-0.086	-0.086	0.000	0.000	0.000	0.000
109	A	115	GLN	0	0.084	0.035	36.864	0.003	0.003	0.000	0.000	0.000	0.000
110	A	116	VAL	0	0.014	0.029	34.520	0.002	0.002	0.000	0.000	0.000	0.000
111	A	117	THR	0	-0.068	-0.059	32.266	0.006	0.006	0.000	0.000	0.000	0.000
112	A	118	GLU	-1	-0.822	-0.895	32.038	0.114	0.114	0.000	0.000	0.000	0.000
113	A	119	HIS	0	-0.009	-0.004	32.329	0.001	0.001	0.000	0.000	0.000	0.000
114	A	120	ARG	1	0.921	0.958	27.697	-0.110	-0.110	0.000	0.000	0.000	0.000
115	A	121	ARG	1	0.838	0.901	27.663	-0.119	-0.119	0.000	0.000	0.000	0.000
116	A	122	THR	0	-0.001	-0.001	27.546	0.008	0.008	0.000	0.000	0.000	0.000
117	A	123	GLU	-1	-0.791	-0.863	27.034	0.070	0.070	0.000	0.000	0.000	0.000
118	A	124	ILE	0	-0.025	-0.021	22.711	0.003	0.003	0.000	0.000	0.000	0.000
119	A	125	ALA	0	-0.017	0.001	23.129	0.015	0.015	0.000	0.000	0.000	0.000
120	A	126	ARG	1	0.889	0.912	23.521	-0.058	-0.058	0.000	0.000	0.000	0.000
121	A	127	ILE	0	-0.054	-0.021	20.337	-0.009	-0.009	0.000	0.000	0.000	0.000
122	A	128	VAL	0	0.004	-0.020	18.825	0.010	0.010	0.000	0.000	0.000	0.000
123	A	129	GLU	-1	-0.978	-1.001	18.963	0.149	0.149	0.000	0.000	0.000	0.000
124	A	130	GLN	0	-0.067	-0.031	19.943	-0.008	-0.008	0.000	0.000	0.000	0.000
125	A	131	MET	0	-0.019	0.020	14.495	-0.020	-0.020	0.000	0.000	0.000	0.000
126	A	132	ALA	0	0.060	0.031	11.743	0.010	0.010	0.000	0.000	0.000	0.000
127	A	133	PRO	0	-0.006	-0.030	13.018	0.076	0.076	0.000	0.000	0.000	0.000
128	A	134	ALA	0	0.019	0.008	8.162	0.024	0.024	0.000	0.000	0.000	0.000
129	A	135	GLU	-1	-0.838	-0.904	10.125	0.376	0.376	0.000	0.000	0.000	0.000
130	A	136	ARG	1	0.831	0.920	11.385	-0.298	-0.298	0.000	0.000	0.000	0.000
131	A	137	HIS	0	0.008	0.002	11.762	0.043	0.043	0.000	0.000	0.000	0.000
132	A	138	GLY	0	0.018	0.008	10.442	0.022	0.022	0.000	0.000	0.000	0.000
133	A	139	LEU	0	0.005	0.010	11.206	-0.083	-0.083	0.000	0.000	0.000	0.000
134	A	140	VAL	0	0.025	0.005	14.446	-0.055	-0.055	0.000	0.000	0.000	0.000
135	A	141	ARG	1	0.970	0.998	8.917	-1.149	-1.149	0.000	0.000	0.000	0.000
136	A	142	ALA	0	-0.004	0.004	13.193	-0.053	-0.053	0.000	0.000	0.000	0.000
137	A	143	LEU	0	0.005	-0.005	14.552	-0.066	-0.066	0.000	0.000	0.000	0.000
138	A	144	THR	0	-0.026	-0.011	17.162	-0.050	-0.050	0.000	0.000	0.000	0.000
139	A	145	ALA	0	0.006	0.000	14.888	-0.030	-0.030	0.000	0.000	0.000	0.000
140	A	146	PHE	0	-0.035	-0.019	16.954	-0.044	-0.044	0.000	0.000	0.000	0.000
141	A	147	THR	0	-0.058	-0.051	19.247	-0.034	-0.034	0.000	0.000	0.000	0.000
142	A	148	GLU	-1	-0.957	-0.973	19.613	0.259	0.259	0.000	0.000	0.000	0.000
143	A	149	ALA	0	-0.048	-0.018	19.332	-0.019	-0.019	0.000	0.000	0.000	0.000
144	A	150	GLY	0	0.005	-0.004	21.414	-0.024	-0.024	0.000	0.000	0.000	0.000
145	A	151	GLY	0	-0.085	-0.041	24.715	0.009	0.009	0.000	0.000	0.000	0.000
146	A	152	GLU	-1	-0.980	-0.967	25.436	0.134	0.134	0.000	0.000	0.000	0.000

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