FMO DATABASE

FMODB ID: 2NYLR

Calculation Name: 2CXC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2CXC

Chain ID: A

ChEMBL ID:

UniProt ID: Q9YAU4

Base Structure: X-ray

Registration Date: 2023-09-24

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	138
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1214530.632418
FMO2-HF: Nuclear repulsion	1162011.482999
FMO2-HF: Total energy	-52519.149418
FMO2-MP2: Total energy	-52676.344002

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:ILE)

Summations of interaction energy for fragment #1(A:7: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.
-10.74	-8.43	11.883	-6.707	-7.491	-0.043

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : 0.006

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	LEU	0	0.079	0.020	3.740	-2.658	-0.418	-0.009	-1.264	-0.968	0.006
4	A	10	GLU	-1	-0.863	-0.898	6.348	-0.547	-0.547	0.000	0.000	0.000	0.000
5	A	11	GLU	-1	-0.719	-0.824	1.866	-6.825	-9.343	11.258	-4.671	-4.069	-0.047
6	A	12	LEU	0	0.014	0.012	3.984	0.513	0.793	-0.001	-0.042	-0.238	0.000
7	A	13	ARG	1	0.969	0.989	5.014	1.280	1.334	-0.001	-0.002	-0.051	0.000
8	A	14	TYR	0	-0.042	-0.072	7.770	0.328	0.328	0.000	0.000	0.000	0.000
9	A	15	ILE	0	-0.010	-0.004	4.372	0.129	0.220	-0.001	-0.005	-0.086	0.000
10	A	16	SER	0	0.012	0.008	8.304	0.170	0.170	0.000	0.000	0.000	0.000
11	A	17	VAL	0	-0.028	-0.017	10.576	0.087	0.087	0.000	0.000	0.000	0.000
12	A	18	PHE	0	0.024	-0.007	11.384	0.071	0.071	0.000	0.000	0.000	0.000
13	A	19	HIS	0	0.006	0.021	12.350	0.015	0.015	0.000	0.000	0.000	0.000
14	A	20	SER	0	-0.005	-0.005	14.122	0.018	0.018	0.000	0.000	0.000	0.000
15	A	21	ILE	0	-0.049	-0.011	16.308	0.009	0.009	0.000	0.000	0.000	0.000
16	A	22	THR	0	-0.038	-0.039	15.937	0.028	0.028	0.000	0.000	0.000	0.000
17	A	23	GLY	0	0.022	0.017	17.706	0.017	0.017	0.000	0.000	0.000	0.000
18	A	24	VAL	0	-0.062	-0.015	14.875	0.027	0.027	0.000	0.000	0.000	0.000
19	A	25	THR	0	0.002	-0.014	11.022	-0.060	-0.060	0.000	0.000	0.000	0.000
20	A	26	ALA	0	-0.043	-0.005	9.312	0.048	0.048	0.000	0.000	0.000	0.000
21	A	27	TYR	0	-0.014	-0.002	7.196	0.158	0.158	0.000	0.000	0.000	0.000
22	A	28	ARG	1	0.807	0.872	2.806	-3.277	-1.210	0.638	-0.721	-1.985	-0.002
23	A	29	CYS	0	-0.036	-0.021	5.173	-0.258	-0.258	0.000	0.000	0.000	0.000
24	A	30	ILE	0	-0.010	0.006	6.069	-0.358	-0.358	0.000	0.000	0.000	0.000
25	A	31	VAL	0	0.053	0.022	7.199	0.057	0.057	0.000	0.000	0.000	0.000
26	A	32	ASP	-1	-0.746	-0.869	9.604	0.014	0.014	0.000	0.000	0.000	0.000
27	A	33	GLU	-1	-0.748	-0.866	12.986	-0.342	-0.342	0.000	0.000	0.000	0.000
28	A	34	GLU	-1	-0.867	-0.900	15.297	-0.022	-0.022	0.000	0.000	0.000	0.000
29	A	35	ASN	0	-0.099	-0.066	17.244	0.023	0.023	0.000	0.000	0.000	0.000
30	A	36	ASN	0	-0.006	-0.003	16.758	-0.024	-0.024	0.000	0.000	0.000	0.000
31	A	37	ARG	1	0.703	0.839	14.510	0.035	0.035	0.000	0.000	0.000	0.000
32	A	38	LEU	0	0.026	0.027	10.009	-0.046	-0.046	0.000	0.000	0.000	0.000
33	A	39	ILE	0	-0.047	-0.032	11.041	0.055	0.055	0.000	0.000	0.000	0.000
34	A	40	PHE	0	0.021	0.008	10.004	0.022	0.022	0.000	0.000	0.000	0.000
35	A	41	LEU	0	-0.019	-0.007	8.747	0.019	0.019	0.000	0.000	0.000	0.000
36	A	42	VAL	0	0.022	0.008	10.785	0.076	0.076	0.000	0.000	0.000	0.000
37	A	43	SER	0	0.047	0.008	13.596	0.055	0.055	0.000	0.000	0.000	0.000
38	A	44	GLU	-1	-0.794	-0.871	16.029	0.177	0.177	0.000	0.000	0.000	0.000
39	A	45	GLY	0	-0.015	-0.007	19.267	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	46	GLU	-1	-0.815	-0.903	17.409	0.121	0.121	0.000	0.000	0.000	0.000
41	A	47	ALA	0	-0.019	-0.014	18.511	-0.023	-0.023	0.000	0.000	0.000	0.000
42	A	48	GLY	0	-0.010	-0.005	19.385	-0.023	-0.023	0.000	0.000	0.000	0.000
43	A	49	ARG	1	0.808	0.874	19.194	-0.105	-0.105	0.000	0.000	0.000	0.000
44	A	50	ALA	0	-0.005	0.006	17.187	-0.018	-0.018	0.000	0.000	0.000	0.000
45	A	51	ILE	0	-0.009	0.001	19.002	-0.026	-0.026	0.000	0.000	0.000	0.000
46	A	52	GLY	0	0.065	0.028	21.678	-0.015	-0.015	0.000	0.000	0.000	0.000
47	A	53	ARG	1	0.938	0.950	24.472	-0.012	-0.012	0.000	0.000	0.000	0.000
48	A	54	GLY	0	0.028	0.006	28.082	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	55	GLY	0	0.035	0.025	24.289	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	56	ARG	1	0.929	0.961	23.983	0.021	0.021	0.000	0.000	0.000	0.000
51	A	57	LEU	0	0.013	0.022	20.361	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	58	ILE	0	0.035	0.026	18.653	-0.017	-0.017	0.000	0.000	0.000	0.000
53	A	59	LYS	1	0.747	0.861	20.500	0.063	0.063	0.000	0.000	0.000	0.000
54	A	60	LEU	0	0.025	0.003	21.449	-0.011	-0.011	0.000	0.000	0.000	0.000
55	A	61	LEU	0	0.010	0.013	15.057	-0.022	-0.022	0.000	0.000	0.000	0.000
56	A	62	ARG	1	0.906	0.950	17.474	0.057	0.057	0.000	0.000	0.000	0.000
57	A	63	GLU	-1	-0.858	-0.906	19.352	-0.115	-0.115	0.000	0.000	0.000	0.000
58	A	64	ALA	0	0.006	0.009	17.777	-0.009	-0.009	0.000	0.000	0.000	0.000
59	A	65	LEU	0	-0.061	-0.032	13.096	-0.049	-0.049	0.000	0.000	0.000	0.000
60	A	66	GLY	0	0.015	0.026	16.289	-0.030	-0.030	0.000	0.000	0.000	0.000
61	A	67	LYS	1	0.790	0.883	13.091	0.377	0.377	0.000	0.000	0.000	0.000
62	A	68	ASN	0	-0.001	-0.013	17.218	0.028	0.028	0.000	0.000	0.000	0.000
63	A	69	ILE	0	0.005	0.009	15.055	-0.020	-0.020	0.000	0.000	0.000	0.000
64	A	70	GLU	-1	-0.815	-0.888	15.128	0.038	0.038	0.000	0.000	0.000	0.000
65	A	71	VAL	0	0.010	0.003	14.472	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	72	VAL	0	-0.032	-0.015	14.454	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	73	GLU	-1	-0.787	-0.877	14.485	0.222	0.222	0.000	0.000	0.000	0.000
68	A	74	TYR	0	0.019	-0.005	10.622	0.024	0.024	0.000	0.000	0.000	0.000
69	A	75	SER	0	-0.014	-0.025	13.886	-0.046	-0.046	0.000	0.000	0.000	0.000
70	A	76	SER	0	0.042	0.019	13.287	0.034	0.034	0.000	0.000	0.000	0.000
71	A	77	ASP	-1	-0.830	-0.903	14.295	0.233	0.233	0.000	0.000	0.000	0.000
72	A	78	LEU	0	0.025	0.015	14.906	0.008	0.008	0.000	0.000	0.000	0.000
73	A	79	GLU	-1	-0.859	-0.923	16.931	0.141	0.141	0.000	0.000	0.000	0.000
74	A	80	ARG	1	0.849	0.898	19.238	-0.218	-0.218	0.000	0.000	0.000	0.000
75	A	81	ILE	0	-0.002	0.009	12.693	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	82	VAL	0	-0.026	-0.019	16.954	-0.020	-0.020	0.000	0.000	0.000	0.000
77	A	83	LYS	1	0.872	0.899	18.769	-0.157	-0.157	0.000	0.000	0.000	0.000
78	A	84	ASN	0	-0.027	-0.016	17.975	-0.038	-0.038	0.000	0.000	0.000	0.000
79	A	85	LEU	0	-0.035	-0.009	14.672	-0.017	-0.017	0.000	0.000	0.000	0.000
80	A	86	PHE	0	-0.078	-0.029	18.965	-0.022	-0.022	0.000	0.000	0.000	0.000
81	A	87	PRO	0	0.052	0.024	21.846	-0.005	-0.005	0.000	0.000	0.000	0.000
82	A	88	GLY	0	-0.025	0.002	24.574	-0.005	-0.005	0.000	0.000	0.000	0.000
83	A	89	VAL	0	-0.041	-0.024	26.079	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	90	LYS	1	0.886	0.941	27.666	-0.057	-0.057	0.000	0.000	0.000	0.000
85	A	91	ILE	0	-0.061	-0.035	23.122	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	92	GLU	-1	-0.800	-0.855	27.292	0.075	0.075	0.000	0.000	0.000	0.000
87	A	93	SER	0	0.030	0.008	27.144	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	94	ILE	0	0.004	0.012	20.407	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	95	ASN	0	-0.029	-0.019	23.514	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	96	VAL	0	0.061	0.022	18.317	0.005	0.005	0.000	0.000	0.000	0.000
91	A	97	ARG	1	0.892	0.953	21.140	-0.121	-0.121	0.000	0.000	0.000	0.000
92	A	98	GLU	-1	-0.812	-0.919	17.066	0.247	0.247	0.000	0.000	0.000	0.000
93	A	99	ARG	1	0.950	0.972	20.702	-0.100	-0.100	0.000	0.000	0.000	0.000
94	A	100	ASN	0	-0.015	-0.018	21.183	0.001	0.001	0.000	0.000	0.000	0.000
95	A	101	GLY	0	0.077	0.059	17.312	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	102	VAL	0	-0.035	-0.016	16.189	0.023	0.023	0.000	0.000	0.000	0.000
97	A	103	LYS	1	0.898	0.970	12.964	-0.366	-0.366	0.000	0.000	0.000	0.000
98	A	104	GLN	0	-0.065	-0.047	17.306	-0.010	-0.010	0.000	0.000	0.000	0.000
99	A	105	VAL	0	0.026	0.019	17.114	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	106	VAL	0	-0.071	-0.046	19.950	-0.015	-0.015	0.000	0.000	0.000	0.000
101	A	107	ILE	0	0.041	0.017	20.125	0.005	0.005	0.000	0.000	0.000	0.000
102	A	108	LYS	1	0.895	0.944	24.255	-0.086	-0.086	0.000	0.000	0.000	0.000
103	A	109	VAL	0	-0.007	0.005	26.442	0.002	0.002	0.000	0.000	0.000	0.000
104	A	110	SER	0	0.031	0.001	28.992	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	111	GLU	-1	-0.939	-0.967	32.404	0.043	0.043	0.000	0.000	0.000	0.000
106	A	112	ASP	-1	-0.849	-0.936	33.538	0.035	0.035	0.000	0.000	0.000	0.000
107	A	113	ASP	-1	-0.815	-0.902	29.635	0.062	0.062	0.000	0.000	0.000	0.000
108	A	114	LYS	1	0.828	0.901	28.447	-0.053	-0.053	0.000	0.000	0.000	0.000
109	A	115	GLY	0	0.051	0.035	28.049	0.000	0.000	0.000	0.000	0.000	0.000
110	A	116	ALA	0	-0.006	-0.005	27.819	-0.003	-0.003	0.000	0.000	0.000	0.000
111	A	117	ALA	0	-0.006	-0.004	24.641	0.003	0.003	0.000	0.000	0.000	0.000
112	A	118	ILE	0	0.019	0.004	23.234	0.007	0.007	0.000	0.000	0.000	0.000
113	A	119	GLY	0	0.058	0.034	23.391	-0.002	-0.002	0.000	0.000	0.000	0.000
114	A	120	LYS	1	0.976	0.968	25.378	0.017	0.017	0.000	0.000	0.000	0.000
115	A	121	GLY	0	0.037	0.014	24.874	-0.004	-0.004	0.000	0.000	0.000	0.000
116	A	122	GLY	0	0.024	0.023	23.080	-0.003	-0.003	0.000	0.000	0.000	0.000
117	A	123	LYS	1	0.889	0.953	19.680	0.029	0.029	0.000	0.000	0.000	0.000
118	A	124	ASN	0	-0.039	-0.023	19.248	0.001	0.001	0.000	0.000	0.000	0.000
119	A	125	VAL	0	0.058	0.023	18.939	0.019	0.019	0.000	0.000	0.000	0.000
120	A	126	LYS	1	0.762	0.864	14.788	0.071	0.071	0.000	0.000	0.000	0.000
121	A	127	ARG	1	0.850	0.926	14.949	-0.077	-0.077	0.000	0.000	0.000	0.000
122	A	128	ALA	0	0.037	0.019	14.038	0.038	0.038	0.000	0.000	0.000	0.000
123	A	129	ARG	1	0.830	0.913	14.104	-0.060	-0.060	0.000	0.000	0.000	0.000
124	A	130	LEU	0	-0.004	0.002	10.683	0.048	0.048	0.000	0.000	0.000	0.000
125	A	131	VAL	0	0.027	0.012	9.445	0.090	0.090	0.000	0.000	0.000	0.000
126	A	132	LEU	0	0.023	0.007	9.805	0.109	0.109	0.000	0.000	0.000	0.000
127	A	133	SER	0	-0.042	-0.034	9.564	0.075	0.075	0.000	0.000	0.000	0.000
128	A	134	LYS	1	0.843	0.902	5.279	-0.286	-0.286	0.000	0.000	0.000	0.000
129	A	135	LEU	0	-0.025	-0.007	5.197	0.311	0.407	-0.001	-0.002	-0.094	0.000
130	A	136	PHE	0	-0.003	0.007	7.501	-0.019	-0.019	0.000	0.000	0.000	0.000
131	A	137	GLY	0	0.012	0.013	9.347	-0.066	-0.066	0.000	0.000	0.000	0.000
132	A	138	VAL	0	-0.032	-0.023	10.725	-0.073	-0.073	0.000	0.000	0.000	0.000
133	A	139	GLU	-1	-0.784	-0.855	11.198	0.299	0.299	0.000	0.000	0.000	0.000
134	A	140	LYS	1	0.889	0.953	14.116	-0.129	-0.129	0.000	0.000	0.000	0.000
135	A	141	VAL	0	0.059	0.029	16.429	0.012	0.012	0.000	0.000	0.000	0.000
136	A	142	VAL	0	-0.044	-0.028	19.247	-0.020	-0.020	0.000	0.000	0.000	0.000
137	A	143	ILE	0	0.047	0.042	22.484	0.008	0.008	0.000	0.000	0.000	0.000
138	A	144	ARG	1	0.946	0.963	25.349	-0.092	-0.092	0.000	0.000	0.000	0.000

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