FMO DATABASE

FMODB ID: ZV62N

Calculation Name: 2NX2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NX2

Chain ID: A

ChEMBL ID:

UniProt ID: P50838

Base Structure: X-ray

Registration Date: 2023-09-21

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	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	178
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-2037092.843917
FMO2-HF: Nuclear repulsion	1965591.967429
FMO2-HF: Total energy	-71500.876488
FMO2-MP2: Total energy	-71714.392015

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:0:SER)

Summations of interaction energy for fragment #1(A:0:SER)

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.
3.842	6.339	0.064	-0.915	-1.646	0

Interaction energy analysis for fragmet #1(A:0:SER)

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 : -0.037

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].
3	A	2	LYS	1	1.007	1.019	3.105	2.602	4.826	0.061	-0.841	-1.444
4	A	3	VAL	0	0.006	0.017	5.617	0.430	0.430	0.000	0.000	0.000
5	A	4	LEU	0	0.026	0.013	8.739	-0.006	-0.006	0.000	0.000	0.000
6	A	5	ALA	0	-0.012	-0.004	10.542	-0.014	-0.014	0.000	0.000	0.000
7	A	6	ILE	0	0.027	0.014	13.853	0.085	0.085	0.000	0.000	0.000
8	A	7	THR	0	-0.049	-0.077	16.541	-0.033	-0.033	0.000	0.000	0.000
9	A	8	GLY	0	0.035	-0.004	19.874	0.034	0.034	0.000	0.000	0.000
10	A	9	TYR	0	-0.076	-0.030	22.682	-0.014	-0.014	0.000	0.000	0.000
11	A	10	LYS	1	0.976	0.996	26.458	-0.037	-0.037	0.000	0.000	0.000
12	A	11	PRO	0	0.038	0.009	29.040	0.006	0.006	0.000	0.000	0.000
13	A	12	PHE	0	-0.007	-0.015	31.478	0.004	0.004	0.000	0.000	0.000
14	A	13	GLU	-1	-0.814	-0.850	29.108	0.073	0.073	0.000	0.000	0.000
15	A	14	LEU	0	0.022	0.005	27.270	0.007	0.007	0.000	0.000	0.000
16	A	15	GLY	0	-0.013	0.013	31.928	0.001	0.001	0.000	0.000	0.000
17	A	16	ILE	0	-0.007	0.017	30.230	-0.002	-0.002	0.000	0.000	0.000
18	A	17	PHE	0	-0.025	-0.036	33.895	-0.004	-0.004	0.000	0.000	0.000
19	A	18	LYS	1	0.923	0.964	35.670	-0.042	-0.042	0.000	0.000	0.000
20	A	19	GLN	0	0.045	0.014	29.344	0.008	0.008	0.000	0.000	0.000
21	A	20	ASP	-1	-0.943	-0.958	33.313	0.043	0.043	0.000	0.000	0.000
22	A	21	ASP	-1	-0.866	-0.968	33.030	0.058	0.058	0.000	0.000	0.000
23	A	22	LYS	1	0.914	0.963	32.509	-0.050	-0.050	0.000	0.000	0.000
24	A	23	ALA	0	0.081	0.033	30.587	0.005	0.005	0.000	0.000	0.000
25	A	24	LEU	0	0.026	0.027	27.528	0.010	0.010	0.000	0.000	0.000
26	A	25	TYR	0	0.007	0.018	27.657	0.008	0.008	0.000	0.000	0.000
27	A	26	TYR	0	0.036	0.008	26.920	0.003	0.003	0.000	0.000	0.000
28	A	27	ILE	0	-0.011	0.002	23.996	0.016	0.016	0.000	0.000	0.000
29	A	28	LYS	1	0.867	0.920	22.980	-0.034	-0.034	0.000	0.000	0.000
30	A	29	LYS	1	0.912	0.972	22.098	-0.123	-0.123	0.000	0.000	0.000
31	A	30	ALA	0	0.035	0.023	21.136	0.018	0.018	0.000	0.000	0.000
32	A	31	ILE	0	-0.017	-0.019	17.829	0.034	0.034	0.000	0.000	0.000
33	A	32	LYS	1	0.849	0.921	17.264	-0.055	-0.055	0.000	0.000	0.000
34	A	33	ASN	0	0.033	0.011	17.035	0.007	0.007	0.000	0.000	0.000
35	A	34	ARG	1	0.886	0.960	12.439	-0.523	-0.523	0.000	0.000	0.000
36	A	35	LEU	0	-0.002	-0.006	12.939	0.084	0.084	0.000	0.000	0.000
37	A	36	ILE	0	0.024	0.018	12.187	0.045	0.045	0.000	0.000	0.000
38	A	37	ALA	0	0.019	0.019	12.126	0.014	0.014	0.000	0.000	0.000
39	A	38	PHE	0	0.006	-0.012	7.859	0.026	0.026	0.000	0.000	0.000
40	A	39	LEU	0	-0.040	-0.021	7.567	0.246	0.246	0.000	0.000	0.000
41	A	40	ASP	-1	-0.925	-0.952	8.546	0.234	0.234	0.000	0.000	0.000
42	A	41	GLU	-1	-1.042	-1.016	5.661	1.734	1.734	0.000	0.000	0.000
43	A	42	GLY	0	-0.050	-0.024	3.836	1.906	2.147	0.004	-0.071	-0.174
44	A	43	LEU	0	-0.065	-0.030	4.888	-0.451	-0.419	-0.001	-0.003	-0.028
45	A	44	GLU	-1	-0.977	-0.988	6.841	-1.677	-1.677	0.000	0.000	0.000
46	A	45	TRP	0	-0.012	-0.017	9.052	0.080	0.080	0.000	0.000	0.000
47	A	46	ILE	0	0.026	0.025	10.944	0.038	0.038	0.000	0.000	0.000
48	A	47	LEU	0	-0.017	-0.009	13.704	-0.045	-0.045	0.000	0.000	0.000
49	A	48	ILE	0	-0.018	-0.002	15.812	0.045	0.045	0.000	0.000	0.000
50	A	49	SER	0	-0.075	-0.073	19.187	-0.024	-0.024	0.000	0.000	0.000
51	A	50	GLY	0	0.075	0.034	22.231	-0.004	-0.004	0.000	0.000	0.000
52	A	51	GLN	0	-0.047	-0.015	24.362	-0.002	-0.002	0.000	0.000	0.000
53	A	52	LEU	0	0.039	0.006	25.938	0.005	0.005	0.000	0.000	0.000
54	A	53	GLY	0	-0.016	-0.017	27.439	0.006	0.006	0.000	0.000	0.000
55	A	54	VAL	0	0.013	0.013	21.271	-0.004	-0.004	0.000	0.000	0.000
56	A	55	GLU	-1	-0.744	-0.814	21.063	0.005	0.005	0.000	0.000	0.000
57	A	56	LEU	0	0.024	0.016	21.983	-0.007	-0.007	0.000	0.000	0.000
58	A	57	TRP	0	-0.015	-0.013	23.993	0.002	0.002	0.000	0.000	0.000
59	A	58	ALA	0	0.020	0.004	18.660	0.008	0.008	0.000	0.000	0.000
60	A	59	ALA	0	0.002	0.012	19.466	0.002	0.002	0.000	0.000	0.000
61	A	60	GLU	-1	-0.748	-0.867	20.773	0.021	0.021	0.000	0.000	0.000
62	A	61	ALA	0	-0.049	-0.027	20.053	0.001	0.001	0.000	0.000	0.000
63	A	62	ALA	0	0.053	0.016	16.965	0.009	0.009	0.000	0.000	0.000
64	A	63	TYR	0	-0.018	-0.035	18.426	-0.011	-0.011	0.000	0.000	0.000
65	A	64	ASP	-1	-0.891	-0.929	21.256	0.030	0.030	0.000	0.000	0.000
66	A	65	LEU	0	-0.072	-0.036	16.318	0.014	0.014	0.000	0.000	0.000
67	A	66	GLN	0	-0.001	-0.012	17.327	0.014	0.014	0.000	0.000	0.000
68	A	67	GLU	-1	-0.909	-0.902	18.675	-0.028	-0.028	0.000	0.000	0.000
69	A	68	GLH	0	-0.116	-0.097	18.595	-0.005	-0.005	0.000	0.000	0.000
70	A	69	TYR	0	-0.029	-0.009	13.105	-0.002	-0.002	0.000	0.000	0.000
71	A	70	PRO	0	0.026	0.015	15.412	-0.011	-0.011	0.000	0.000	0.000
72	A	71	ASP	-1	-0.917	-0.947	11.877	-0.363	-0.363	0.000	0.000	0.000
73	A	72	LEU	0	-0.055	-0.001	12.484	-0.057	-0.057	0.000	0.000	0.000
74	A	73	LYS	1	0.860	0.922	11.490	0.442	0.442	0.000	0.000	0.000
75	A	74	VAL	0	-0.001	-0.010	14.577	0.011	0.011	0.000	0.000	0.000
76	A	75	ALA	0	-0.016	-0.007	16.305	-0.017	-0.017	0.000	0.000	0.000
77	A	76	VAL	0	0.001	-0.012	18.006	0.025	0.025	0.000	0.000	0.000
78	A	77	ILE	0	-0.037	-0.011	17.805	-0.011	-0.011	0.000	0.000	0.000
79	A	78	THR	0	0.032	0.012	21.592	0.011	0.011	0.000	0.000	0.000
80	A	79	PRO	0	-0.017	-0.018	24.724	-0.012	-0.012	0.000	0.000	0.000
81	A	80	PHE	0	-0.042	-0.021	25.774	0.001	0.001	0.000	0.000	0.000
82	A	81	TYR	0	0.015	0.000	29.114	0.000	0.000	0.000	0.000	0.000
83	A	82	GLU	-1	-0.906	-0.964	31.691	-0.037	-0.037	0.000	0.000	0.000
84	A	83	GLN	0	-0.072	-0.050	26.320	0.013	0.013	0.000	0.000	0.000
85	A	84	GLU	-1	-0.825	-0.923	31.879	-0.033	-0.033	0.000	0.000	0.000
86	A	85	LYS	1	0.915	0.969	33.472	0.033	0.033	0.000	0.000	0.000
87	A	86	ASN	0	-0.023	-0.029	36.817	-0.001	-0.001	0.000	0.000	0.000
88	A	87	TRP	0	-0.053	-0.001	29.253	0.006	0.006	0.000	0.000	0.000
89	A	88	LYS	1	0.926	0.963	36.505	-0.017	-0.017	0.000	0.000	0.000
90	A	89	GLU	-1	-0.833	-0.929	37.375	-0.015	-0.015	0.000	0.000	0.000
91	A	90	PRO	0	0.006	-0.008	37.174	0.000	0.000	0.000	0.000	0.000
92	A	91	ASN	0	-0.016	-0.018	33.647	0.002	0.002	0.000	0.000	0.000
93	A	92	LYS	1	0.888	0.967	32.770	0.018	0.018	0.000	0.000	0.000
94	A	93	GLU	-1	-0.854	-0.915	33.227	-0.014	-0.014	0.000	0.000	0.000
95	A	94	GLN	0	-0.114	-0.069	28.112	-0.003	-0.003	0.000	0.000	0.000
96	A	95	TYR	0	-0.010	-0.023	27.601	-0.004	-0.004	0.000	0.000	0.000
97	A	96	GLU	-1	-0.904	-0.964	28.594	-0.038	-0.038	0.000	0.000	0.000
98	A	97	ALA	0	-0.012	0.007	29.501	-0.008	-0.008	0.000	0.000	0.000
99	A	98	VAL	0	-0.012	-0.009	23.438	-0.006	-0.006	0.000	0.000	0.000
100	A	99	LEU	0	-0.003	-0.006	24.785	-0.012	-0.012	0.000	0.000	0.000
101	A	100	ALA	0	-0.050	0.018	26.159	-0.015	-0.015	0.000	0.000	0.000
102	A	101	GLN	0	-0.021	-0.009	23.304	-0.005	-0.005	0.000	0.000	0.000
103	A	102	ALA	0	-0.019	0.016	21.283	-0.007	-0.007	0.000	0.000	0.000
104	A	103	ASP	-1	-0.807	-0.894	18.070	-0.193	-0.193	0.000	0.000	0.000
105	A	104	TYR	0	-0.060	-0.042	18.416	-0.021	-0.021	0.000	0.000	0.000
106	A	105	GLH	0	-0.020	-0.059	20.392	0.021	0.021	0.000	0.000	0.000
107	A	106	ALA	0	-0.039	-0.008	22.537	-0.006	-0.006	0.000	0.000	0.000
108	A	107	SER	0	-0.011	-0.009	24.276	0.011	0.011	0.000	0.000	0.000
109	A	108	LEU	0	-0.020	-0.009	20.772	-0.005	-0.005	0.000	0.000	0.000
110	A	109	THR	0	-0.033	-0.014	24.869	0.004	0.004	0.000	0.000	0.000
111	A	110	HIS	0	0.032	0.023	27.738	0.008	0.008	0.000	0.000	0.000
112	A	111	ARG	1	0.882	0.928	31.350	0.064	0.064	0.000	0.000	0.000
113	A	112	PRO	0	0.071	0.045	32.312	-0.001	-0.001	0.000	0.000	0.000
114	A	113	TYR	0	-0.042	-0.015	31.981	0.000	0.000	0.000	0.000	0.000
115	A	114	GLU	-1	-0.913	-0.950	33.308	-0.043	-0.043	0.000	0.000	0.000
116	A	115	SER	0	0.028	0.001	33.029	0.006	0.006	0.000	0.000	0.000
117	A	116	PRO	0	0.002	-0.013	31.078	-0.004	-0.004	0.000	0.000	0.000
118	A	117	LEU	0	-0.011	0.004	28.013	0.001	0.001	0.000	0.000	0.000
119	A	118	GLN	0	0.095	0.053	27.355	0.002	0.002	0.000	0.000	0.000
120	A	119	PHE	0	0.016	0.010	25.812	-0.007	-0.007	0.000	0.000	0.000
121	A	120	LYS	1	0.928	0.977	24.160	-0.001	-0.001	0.000	0.000	0.000
122	A	121	GLN	0	0.018	-0.009	22.939	-0.003	-0.003	0.000	0.000	0.000
123	A	122	LYS	1	0.954	0.996	20.998	0.013	0.013	0.000	0.000	0.000
124	A	123	ASN	0	-0.011	-0.020	19.786	-0.022	-0.022	0.000	0.000	0.000
125	A	124	GLN	0	-0.054	-0.019	17.188	0.020	0.020	0.000	0.000	0.000
126	A	125	PHE	0	0.015	0.011	16.952	-0.025	-0.025	0.000	0.000	0.000
127	A	126	PHE	0	0.031	-0.005	15.569	-0.048	-0.048	0.000	0.000	0.000
128	A	127	ILE	0	-0.029	0.016	13.571	-0.037	-0.037	0.000	0.000	0.000
129	A	128	ASP	-1	-0.873	-0.938	12.119	-0.168	-0.168	0.000	0.000	0.000
130	A	129	LYS	1	0.837	0.921	11.714	0.273	0.273	0.000	0.000	0.000
131	A	130	SER	0	-0.018	0.019	9.909	-0.044	-0.044	0.000	0.000	0.000
132	A	131	ASP	-1	-0.822	-0.924	4.808	-2.540	-2.540	0.000	0.000	0.000
133	A	132	GLY	0	0.032	-0.002	6.792	0.533	0.533	0.000	0.000	0.000
134	A	133	LEU	0	-0.051	-0.006	9.281	-0.146	-0.146	0.000	0.000	0.000
135	A	134	LEU	0	0.007	0.007	13.000	0.103	0.103	0.000	0.000	0.000
136	A	135	LEU	0	-0.041	-0.037	14.533	-0.071	-0.071	0.000	0.000	0.000
137	A	136	LEU	0	-0.009	0.018	18.299	0.023	0.023	0.000	0.000	0.000
138	A	137	TYR	0	-0.013	-0.041	21.245	-0.036	-0.036	0.000	0.000	0.000
139	A	138	ASP	-1	-0.789	-0.921	22.793	0.189	0.189	0.000	0.000	0.000
140	A	139	PRO	0	-0.027	-0.026	23.410	-0.015	-0.015	0.000	0.000	0.000
141	A	140	GLU	-1	-0.921	-0.940	26.094	0.119	0.119	0.000	0.000	0.000
142	A	141	LYS	1	0.822	0.937	28.996	-0.105	-0.105	0.000	0.000	0.000
143	A	142	GLU	-1	-0.906	-0.955	27.476	0.102	0.102	0.000	0.000	0.000
144	A	143	GLY	0	0.026	0.009	28.281	-0.001	-0.001	0.000	0.000	0.000
145	A	144	SER	0	-0.116	-0.126	27.728	0.002	0.002	0.000	0.000	0.000
146	A	145	PRO	0	0.006	0.012	22.602	-0.008	-0.008	0.000	0.000	0.000
147	A	146	LYS	1	0.970	1.006	22.668	-0.129	-0.129	0.000	0.000	0.000
148	A	147	TYR	0	-0.042	-0.026	23.461	0.000	0.000	0.000	0.000	0.000
149	A	148	MET	0	0.016	0.001	17.101	0.001	0.001	0.000	0.000	0.000
150	A	149	LEU	0	0.057	0.041	18.293	-0.003	-0.003	0.000	0.000	0.000
151	A	150	GLY	0	0.009	0.011	18.986	0.020	0.020	0.000	0.000	0.000
152	A	151	THR	0	-0.086	-0.045	17.902	0.000	0.000	0.000	0.000	0.000
153	A	152	ALA	0	0.044	0.022	14.910	-0.011	-0.011	0.000	0.000	0.000
154	A	153	GLU	-1	-0.855	-0.940	15.211	0.362	0.362	0.000	0.000	0.000
155	A	154	LYS	1	0.896	0.954	17.369	-0.073	-0.073	0.000	0.000	0.000
156	A	155	ARG	1	0.828	0.913	8.102	0.212	0.212	0.000	0.000	0.000
157	A	156	ARG	1	0.899	0.967	12.801	-0.381	-0.381	0.000	0.000	0.000
158	A	157	GLU	-1	-1.032	-1.031	13.874	0.224	0.224	0.000	0.000	0.000
159	A	158	GLN	0	-0.076	-0.024	14.974	-0.010	-0.010	0.000	0.000	0.000
160	A	159	ASP	-1	-0.814	-0.916	10.257	0.186	0.186	0.000	0.000	0.000
161	A	160	GLY	0	-0.025	-0.004	9.818	0.155	0.155	0.000	0.000	0.000
162	A	161	TYR	0	-0.057	-0.049	8.704	0.302	0.302	0.000	0.000	0.000
163	A	162	PRO	0	-0.007	0.012	6.924	-0.110	-0.110	0.000	0.000	0.000
164	A	163	ILE	0	-0.008	-0.013	10.223	-0.169	-0.169	0.000	0.000	0.000
165	A	164	TYR	0	-0.011	-0.011	7.237	0.057	0.057	0.000	0.000	0.000
166	A	165	PHE	0	0.006	-0.007	14.027	-0.080	-0.080	0.000	0.000	0.000
167	A	166	ILE	0	-0.011	0.000	17.685	0.024	0.024	0.000	0.000	0.000
168	A	167	THR	0	-0.015	-0.013	20.080	-0.038	-0.038	0.000	0.000	0.000
169	A	168	MET	0	-0.036	-0.040	23.236	-0.006	-0.006	0.000	0.000	0.000
170	A	169	ASP	-1	-0.843	-0.910	25.151	0.201	0.201	0.000	0.000	0.000
171	A	170	ASP	-1	-0.777	-0.889	20.562	0.309	0.309	0.000	0.000	0.000
172	A	171	LEU	0	-0.042	-0.027	23.458	-0.007	-0.007	0.000	0.000	0.000
173	A	172	ARG	1	0.818	0.911	25.725	-0.191	-0.191	0.000	0.000	0.000
174	A	173	VAL	0	0.034	0.023	23.824	-0.011	-0.011	0.000	0.000	0.000
175	A	174	THR	0	-0.053	-0.036	23.571	-0.001	-0.001	0.000	0.000	0.000
176	A	175	VAL	0	-0.103	-0.053	25.488	-0.011	-0.011	0.000	0.000	0.000
177	A	176	GLU	-1	-0.985	-0.981	28.745	0.153	0.153	0.000	0.000	0.000
178	A	177	GLU	-1	-1.010	-0.993	24.041	0.223	0.223	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:SER)