FMO DATABASE

FMODB ID: R9K28

Calculation Name: 5E2C-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5E2C

Chain ID: A

ChEMBL ID:

UniProt ID: A5U5N4

Base Structure: X-ray

Registration Date: 2023-06-26

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	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	130
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1030792.386315
FMO2-HF: Nuclear repulsion	983722.470216
FMO2-HF: Total energy	-47069.916099
FMO2-MP2: Total energy	-47209.629431

3D Structure Molmil

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:4:ASN)

Summations of interaction energy for fragment #1(A:4:ASN)

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.
-42.839	-39.157	18.629	-8.688	-13.625	0.048

Interaction energy analysis for fragmet #1(A:4:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.087 / q_NPA : 0.026

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	6	ARG	1	0.853	0.931	2.237	-10.495	-8.615	4.410	-2.492	-3.798	0.029
4	A	7	ARG	1	0.885	0.914	1.864	-9.176	-10.642	14.162	-4.822	-7.875	0.024
5	A	8	ASP	-1	-0.850	-0.914	3.615	-7.596	-6.025	0.031	-0.736	-0.866	-0.001
6	A	9	LYS	1	0.889	0.937	5.335	-3.471	-3.366	-0.001	-0.005	-0.098	0.000
7	A	10	LEU	0	0.009	-0.002	6.557	-0.719	-0.719	0.000	0.000	0.000	0.000
8	A	11	LYS	1	0.852	0.936	5.891	0.746	0.746	0.000	0.000	0.000	0.000
9	A	12	ALA	0	0.008	0.012	9.627	-0.224	-0.224	0.000	0.000	0.000	0.000
10	A	13	GLN	0	-0.006	-0.007	11.436	-0.297	-0.297	0.000	0.000	0.000	0.000
11	A	14	ILE	0	-0.022	-0.011	10.329	-0.133	-0.133	0.000	0.000	0.000	0.000
12	A	15	ALA	0	0.026	0.012	13.771	-0.110	-0.110	0.000	0.000	0.000	0.000
13	A	16	ALA	0	-0.060	-0.023	15.657	-0.073	-0.073	0.000	0.000	0.000	0.000
14	A	17	SER	0	-0.053	-0.016	16.772	-0.049	-0.049	0.000	0.000	0.000	0.000
15	A	18	GLY	0	-0.057	-0.023	18.746	-0.045	-0.045	0.000	0.000	0.000	0.000
16	A	19	LEU	0	-0.063	-0.032	16.260	-0.044	-0.044	0.000	0.000	0.000	0.000
17	A	20	ASP	-1	-0.809	-0.906	16.411	0.112	0.112	0.000	0.000	0.000	0.000
18	A	21	ALA	0	-0.021	-0.013	13.282	-0.072	-0.072	0.000	0.000	0.000	0.000
19	A	22	MET	0	-0.030	-0.003	12.214	0.129	0.129	0.000	0.000	0.000	0.000
20	A	23	LEU	0	-0.005	0.007	12.543	-0.031	-0.031	0.000	0.000	0.000	0.000
21	A	24	ILE	0	-0.068	-0.044	9.783	0.097	0.097	0.000	0.000	0.000	0.000
22	A	25	SER	0	-0.015	-0.041	13.285	-0.170	-0.170	0.000	0.000	0.000	0.000
23	A	26	ASP	-1	-0.823	-0.884	14.878	0.383	0.383	0.000	0.000	0.000	0.000
24	A	27	LEU	0	0.059	0.010	13.555	0.085	0.085	0.000	0.000	0.000	0.000
25	A	28	ILE	0	-0.064	-0.020	12.355	-0.041	-0.041	0.000	0.000	0.000	0.000
26	A	29	ASN	0	0.005	-0.009	10.603	0.245	0.245	0.000	0.000	0.000	0.000
27	A	30	VAL	0	0.026	0.024	8.947	0.408	0.408	0.000	0.000	0.000	0.000
28	A	31	ARG	1	0.966	1.001	7.915	-0.195	-0.195	0.000	0.000	0.000	0.000
29	A	32	TYR	0	-0.074	-0.038	6.776	-0.189	-0.189	0.000	0.000	0.000	0.000
30	A	33	LEU	0	0.035	0.017	4.431	0.520	0.739	-0.001	-0.019	-0.200	0.000
31	A	34	SER	0	-0.021	-0.012	3.766	-0.114	0.344	0.018	-0.205	-0.271	-0.001
32	A	35	GLY	0	0.019	0.023	5.201	-1.210	-1.124	-0.001	-0.001	-0.084	0.000
33	A	36	PHE	0	-0.024	-0.009	6.576	0.306	0.306	0.000	0.000	0.000	0.000
34	A	37	SER	0	-0.019	-0.024	9.821	0.246	0.246	0.000	0.000	0.000	0.000
35	A	38	GLY	0	-0.009	0.009	12.723	0.090	0.090	0.000	0.000	0.000	0.000
36	A	39	SER	0	-0.011	-0.008	15.498	0.039	0.039	0.000	0.000	0.000	0.000
37	A	40	ASN	0	-0.050	-0.039	17.660	0.083	0.083	0.000	0.000	0.000	0.000
38	A	41	GLY	0	0.016	0.016	14.569	-0.097	-0.097	0.000	0.000	0.000	0.000
39	A	42	ALA	0	-0.012	0.014	14.214	0.102	0.102	0.000	0.000	0.000	0.000
40	A	43	LEU	0	-0.003	-0.003	6.964	-0.132	-0.132	0.000	0.000	0.000	0.000
41	A	44	LEU	0	-0.010	0.016	11.156	0.208	0.208	0.000	0.000	0.000	0.000
42	A	45	VAL	0	0.008	-0.007	7.107	-0.199	-0.199	0.000	0.000	0.000	0.000
43	A	46	PHE	0	0.009	-0.002	9.343	0.184	0.184	0.000	0.000	0.000	0.000
44	A	47	ALA	0	0.032	0.004	9.854	0.032	0.032	0.000	0.000	0.000	0.000
45	A	48	ASP	-1	-0.843	-0.907	11.086	-0.336	-0.336	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.907	-0.970	8.511	-0.841	-0.841	0.000	0.000	0.000	0.000
47	A	50	ARG	1	0.812	0.920	8.942	0.068	0.068	0.000	0.000	0.000	0.000
48	A	51	ASP	-1	-0.882	-0.937	6.786	-2.429	-2.429	0.000	0.000	0.000	0.000
49	A	52	ALA	0	-0.072	-0.047	6.189	0.456	0.456	0.000	0.000	0.000	0.000
50	A	53	VAL	0	0.021	0.020	7.928	-0.231	-0.231	0.000	0.000	0.000	0.000
51	A	54	LEU	0	-0.024	-0.004	9.843	0.255	0.255	0.000	0.000	0.000	0.000
52	A	55	ALA	0	0.026	0.022	11.707	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	56	THR	0	-0.008	-0.036	15.357	0.066	0.066	0.000	0.000	0.000	0.000
54	A	57	ASP	-1	-0.708	-0.823	17.207	-0.242	-0.242	0.000	0.000	0.000	0.000
55	A	58	GLY	0	0.000	-0.027	19.797	-0.041	-0.041	0.000	0.000	0.000	0.000
56	A	59	ARG	1	0.810	0.887	21.648	0.186	0.186	0.000	0.000	0.000	0.000
57	A	60	TYR	0	-0.004	-0.014	16.634	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	61	ARG	1	0.986	1.009	16.559	0.375	0.375	0.000	0.000	0.000	0.000
59	A	62	THR	0	0.029	0.003	16.593	-0.076	-0.076	0.000	0.000	0.000	0.000
60	A	63	GLN	0	0.010	0.005	14.159	-0.065	-0.065	0.000	0.000	0.000	0.000
61	A	64	ALA	0	0.048	0.015	12.221	-0.125	-0.125	0.000	0.000	0.000	0.000
62	A	65	ALA	0	-0.009	0.007	11.386	-0.234	-0.234	0.000	0.000	0.000	0.000
63	A	66	SER	0	-0.066	-0.031	12.189	-0.098	-0.098	0.000	0.000	0.000	0.000
64	A	67	GLN	0	-0.010	-0.023	9.738	-0.063	-0.063	0.000	0.000	0.000	0.000
65	A	68	ALA	0	0.007	0.011	6.930	-0.476	-0.476	0.000	0.000	0.000	0.000
66	A	69	PRO	0	-0.019	-0.008	7.752	0.125	0.125	0.000	0.000	0.000	0.000
67	A	70	ASP	-1	-0.874	-0.928	3.559	-10.271	-9.442	0.011	-0.408	-0.433	-0.003
68	A	71	LEU	0	-0.051	-0.011	5.435	0.033	0.033	0.000	0.000	0.000	0.000
69	A	72	GLU	-1	-0.782	-0.865	8.167	-0.471	-0.471	0.000	0.000	0.000	0.000
70	A	73	VAL	0	-0.029	-0.029	11.499	0.038	0.038	0.000	0.000	0.000	0.000
71	A	74	ALA	0	0.009	0.017	13.702	0.075	0.075	0.000	0.000	0.000	0.000
72	A	75	ILE	0	-0.087	-0.059	16.995	0.016	0.016	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.889	-0.956	19.749	-0.253	-0.253	0.000	0.000	0.000	0.000
74	A	77	ARG	1	0.918	0.955	21.892	0.163	0.163	0.000	0.000	0.000	0.000
75	A	78	ALA	0	0.004	0.000	23.371	0.018	0.018	0.000	0.000	0.000	0.000
76	A	79	VAL	0	0.024	0.019	17.699	0.003	0.003	0.000	0.000	0.000	0.000
77	A	80	GLY	0	0.067	0.036	18.326	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	81	ARG	1	0.977	0.982	19.387	0.102	0.102	0.000	0.000	0.000	0.000
79	A	82	TYR	0	0.015	0.023	17.012	-0.021	-0.021	0.000	0.000	0.000	0.000
80	A	83	LEU	0	0.023	0.006	13.803	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	84	ALA	0	0.030	0.014	17.434	0.002	0.002	0.000	0.000	0.000	0.000
82	A	85	GLY	0	0.019	0.008	19.645	0.003	0.003	0.000	0.000	0.000	0.000
83	A	86	ARG	1	0.798	0.873	15.108	0.531	0.531	0.000	0.000	0.000	0.000
84	A	87	ALA	0	0.013	0.005	16.954	-0.016	-0.016	0.000	0.000	0.000	0.000
85	A	88	GLY	0	0.035	0.012	18.074	0.005	0.005	0.000	0.000	0.000	0.000
86	A	89	GLU	-1	-1.028	-1.017	20.933	-0.225	-0.225	0.000	0.000	0.000	0.000
87	A	90	ALA	0	-0.061	-0.018	17.253	-0.013	-0.013	0.000	0.000	0.000	0.000
88	A	91	GLY	0	-0.010	-0.001	19.247	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	92	VAL	0	-0.041	-0.010	16.552	0.020	0.020	0.000	0.000	0.000	0.000
90	A	93	GLY	0	0.074	0.052	19.506	0.006	0.006	0.000	0.000	0.000	0.000
91	A	94	LYS	1	0.906	0.963	20.426	-0.160	-0.160	0.000	0.000	0.000	0.000
92	A	95	LEU	0	0.021	0.014	16.204	0.015	0.015	0.000	0.000	0.000	0.000
93	A	96	GLY	0	0.022	0.009	16.997	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	97	PHE	0	0.017	-0.002	17.110	-0.018	-0.018	0.000	0.000	0.000	0.000
95	A	98	GLU	-1	-0.708	-0.857	14.457	0.715	0.715	0.000	0.000	0.000	0.000
96	A	99	SER	0	0.016	-0.002	18.531	-0.040	-0.040	0.000	0.000	0.000	0.000
97	A	100	HIS	0	-0.059	-0.008	16.859	-0.051	-0.051	0.000	0.000	0.000	0.000
98	A	101	VAL	0	-0.023	-0.012	18.402	-0.020	-0.020	0.000	0.000	0.000	0.000
99	A	102	VAL	0	-0.041	-0.005	20.126	-0.041	-0.041	0.000	0.000	0.000	0.000
100	A	103	THR	0	0.016	0.011	22.676	0.003	0.003	0.000	0.000	0.000	0.000
101	A	104	VAL	0	0.037	0.004	26.447	0.001	0.001	0.000	0.000	0.000	0.000
102	A	105	ASP	-1	-0.846	-0.915	29.186	0.021	0.021	0.000	0.000	0.000	0.000
103	A	106	GLY	0	-0.048	-0.029	25.411	-0.013	-0.013	0.000	0.000	0.000	0.000
104	A	107	LEU	0	-0.007	-0.016	24.408	-0.007	-0.007	0.000	0.000	0.000	0.000
105	A	108	ASP	-1	-0.861	-0.920	26.067	0.034	0.034	0.000	0.000	0.000	0.000
106	A	109	ALA	0	-0.070	-0.036	26.039	-0.015	-0.015	0.000	0.000	0.000	0.000
107	A	110	LEU	0	-0.069	-0.043	21.040	-0.020	-0.020	0.000	0.000	0.000	0.000
108	A	111	ALA	0	0.027	0.006	24.217	-0.012	-0.012	0.000	0.000	0.000	0.000
109	A	112	GLY	0	0.022	0.016	26.855	-0.008	-0.008	0.000	0.000	0.000	0.000
110	A	113	ALA	0	-0.107	-0.055	23.899	-0.013	-0.013	0.000	0.000	0.000	0.000
111	A	114	LEU	0	-0.021	-0.011	21.768	-0.017	-0.017	0.000	0.000	0.000	0.000
112	A	115	GLU	-1	-0.931	-0.950	25.792	-0.024	-0.024	0.000	0.000	0.000	0.000
113	A	116	GLY	0	-0.040	-0.021	29.454	-0.013	-0.013	0.000	0.000	0.000	0.000
114	A	117	LYS	1	0.894	0.957	24.937	0.096	0.096	0.000	0.000	0.000	0.000
115	A	118	ASN	0	-0.037	-0.021	26.596	0.018	0.018	0.000	0.000	0.000	0.000
116	A	119	THR	0	0.007	-0.010	21.198	-0.007	-0.007	0.000	0.000	0.000	0.000
117	A	120	GLU	-1	-0.956	-0.974	23.722	0.135	0.135	0.000	0.000	0.000	0.000
118	A	121	LEU	0	-0.028	-0.011	21.117	0.017	0.017	0.000	0.000	0.000	0.000
119	A	122	VAL	0	0.005	-0.004	21.005	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	123	ARG	1	0.923	0.953	20.591	-0.161	-0.161	0.000	0.000	0.000	0.000
121	A	124	ALA	0	0.061	0.034	16.935	0.004	0.004	0.000	0.000	0.000	0.000
122	A	125	SER	0	-0.021	-0.042	16.866	0.087	0.087	0.000	0.000	0.000	0.000
123	A	126	GLY	0	0.026	0.023	16.582	-0.047	-0.047	0.000	0.000	0.000	0.000
124	A	127	THR	0	0.002	-0.003	12.480	0.081	0.081	0.000	0.000	0.000	0.000
125	A	128	VAL	0	0.003	0.013	9.011	0.235	0.235	0.000	0.000	0.000	0.000
126	A	129	GLU	-1	-0.873	-0.949	11.083	1.168	1.168	0.000	0.000	0.000	0.000
127	A	130	SER	0	-0.071	-0.049	13.050	0.040	0.040	0.000	0.000	0.000	0.000
128	A	131	LEU	0	-0.035	-0.022	7.216	0.147	0.147	0.000	0.000	0.000	0.000
129	A	132	ARG	1	0.785	0.897	10.480	-1.249	-1.249	0.000	0.000	0.000	0.000
130	A	133	GLU	-1	-0.939	-0.961	12.621	1.173	1.173	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ASN)