FMO DATABASE

FMODB ID: 764ZK

Calculation Name: 4XA6-C-Xray372

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 4XA6

Chain ID: C

ChEMBL ID:

UniProt ID: Q15691

Base Structure: X-ray

Registration Date: 2023-09-23

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	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	116
LigandResidueName
LigandFragmentNumber	0
LigandCharge	MLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-674358.026802
FMO2-HF: Nuclear repulsion	624561.300123
FMO2-HF: Total energy	-49796.726678
FMO2-MP2: Total energy	-49941.541828

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(C:1781:ARG)

Summations of interaction energy for fragment #1(C:1781:ARG)

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.
64.446	68.808	0.339	-1.399	-3.301	0.001

Interaction energy analysis for fragmet #1(C:1781:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.031 / q_NPA : 0.993

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

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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	C	1783	MLY	1	0.954	0.975	3.049	29.449	31.436	0.062	-0.788	-1.261	0.000
4	C	1784	MLY	1	0.868	0.907	2.849	42.141	44.304	0.278	-0.599	-1.842	0.001
5	C	1785	ASN	0	-0.034	-0.002	4.878	3.706	3.918	-0.001	-0.012	-0.198	0.000
6	C	1786	MET	0	0.075	0.032	6.749	2.010	2.010	0.000	0.000	0.000	0.000
7	C	1787	GLU	-1	-0.789	-0.875	6.950	-33.698	-33.698	0.000	0.000	0.000	0.000
8	C	1788	GLN	0	0.034	0.018	9.720	0.976	0.976	0.000	0.000	0.000	0.000
9	C	1789	THR	0	0.031	0.014	11.489	0.946	0.946	0.000	0.000	0.000	0.000
10	C	1790	ILE	0	-0.017	-0.013	12.937	1.063	1.063	0.000	0.000	0.000	0.000
11	C	1791	MLY	1	0.871	0.946	10.063	24.463	24.463	0.000	0.000	0.000	0.000
12	C	1792	ASP	-1	-0.818	-0.876	15.483	-13.937	-13.937	0.000	0.000	0.000	0.000
13	C	1793	LEU	0	-0.012	-0.012	17.319	0.898	0.898	0.000	0.000	0.000	0.000
14	C	1794	GLN	0	-0.015	-0.009	16.681	0.122	0.122	0.000	0.000	0.000	0.000
15	C	1795	HIS	0	0.014	0.009	17.797	0.915	0.915	0.000	0.000	0.000	0.000
16	C	1796	ARG	1	0.822	0.869	19.701	14.149	14.149	0.000	0.000	0.000	0.000
17	C	1797	LEU	0	-0.036	0.002	22.955	0.471	0.471	0.000	0.000	0.000	0.000
18	C	1798	ASP	-1	-0.816	-0.899	24.387	-10.900	-10.900	0.000	0.000	0.000	0.000
19	C	1799	GLU	-1	-0.919	-0.956	25.977	-9.909	-9.909	0.000	0.000	0.000	0.000
20	C	1800	ALA	0	-0.012	-0.009	27.451	0.493	0.493	0.000	0.000	0.000	0.000
21	C	1801	GLU	-1	-0.925	-0.967	27.553	-10.559	-10.559	0.000	0.000	0.000	0.000
22	C	1802	GLN	0	-0.057	-0.058	29.454	0.843	0.843	0.000	0.000	0.000	0.000
23	C	1803	ILE	0	-0.035	-0.011	31.000	0.464	0.464	0.000	0.000	0.000	0.000
24	C	1804	ALA	0	-0.033	-0.018	33.194	0.393	0.393	0.000	0.000	0.000	0.000
25	C	1805	LEU	0	0.011	-0.001	34.145	0.335	0.335	0.000	0.000	0.000	0.000
26	C	1806	MLY	1	0.883	0.956	36.822	8.333	8.333	0.000	0.000	0.000	0.000
27	C	1807	GLY	0	0.015	0.017	38.033	0.169	0.169	0.000	0.000	0.000	0.000
28	C	1808	GLY	0	0.004	-0.022	39.535	0.176	0.176	0.000	0.000	0.000	0.000
29	C	1809	MLY	1	0.917	0.954	33.610	9.122	9.122	0.000	0.000	0.000	0.000
30	C	1810	MLY	1	0.994	1.005	39.713	7.693	7.693	0.000	0.000	0.000	0.000
31	C	1811	GLN	0	-0.057	-0.019	43.259	0.098	0.098	0.000	0.000	0.000	0.000
32	C	1812	LEU	0	0.032	0.024	43.684	0.147	0.147	0.000	0.000	0.000	0.000
33	C	1813	GLN	0	0.079	0.045	46.158	0.139	0.139	0.000	0.000	0.000	0.000
34	C	1814	MLY	1	0.946	0.977	47.843	6.518	6.518	0.000	0.000	0.000	0.000
35	C	1815	LEU	0	-0.017	-0.019	48.724	0.152	0.152	0.000	0.000	0.000	0.000
36	C	1816	GLU	-1	-0.855	-0.932	48.791	-6.401	-6.401	0.000	0.000	0.000	0.000
37	C	1817	ALA	0	-0.063	-0.010	52.630	0.112	0.112	0.000	0.000	0.000	0.000
38	C	1818	ARG	1	0.958	0.969	54.131	5.799	5.799	0.000	0.000	0.000	0.000
39	C	1819	VAL	0	-0.007	-0.004	54.841	0.096	0.096	0.000	0.000	0.000	0.000
40	C	1820	ARG	1	0.958	0.984	53.812	5.883	5.883	0.000	0.000	0.000	0.000
41	C	1821	GLU	-1	-0.919	-0.954	58.097	-5.415	-5.415	0.000	0.000	0.000	0.000
42	C	1822	LEU	0	-0.033	-0.017	58.275	0.095	0.095	0.000	0.000	0.000	0.000
43	C	1823	GLU	-1	-0.902	-0.961	59.975	-5.281	-5.281	0.000	0.000	0.000	0.000
44	C	1824	ASN	0	-0.076	-0.045	62.671	0.143	0.143	0.000	0.000	0.000	0.000
45	C	1825	GLU	-1	-0.772	-0.872	64.819	-4.602	-4.602	0.000	0.000	0.000	0.000
46	C	1826	LEU	0	-0.036	-0.002	64.956	0.084	0.084	0.000	0.000	0.000	0.000
47	C	1827	GLU	-1	-0.823	-0.899	67.282	-4.521	-4.521	0.000	0.000	0.000	0.000
48	C	1828	ALA	0	0.018	0.010	69.113	0.093	0.093	0.000	0.000	0.000	0.000
49	C	1829	GLU	-1	-0.822	-0.889	70.210	-4.364	-4.364	0.000	0.000	0.000	0.000
50	C	1830	GLN	0	-0.044	-0.028	68.892	0.094	0.094	0.000	0.000	0.000	0.000
51	C	1831	MLY	1	0.795	0.883	71.526	4.584	4.584	0.000	0.000	0.000	0.000
52	C	1832	ARG	1	0.804	0.862	70.362	4.571	4.571	0.000	0.000	0.000	0.000
53	C	1833	ASN	0	-0.007	0.003	75.506	0.106	0.106	0.000	0.000	0.000	0.000
54	C	1834	ALA	0	0.002	0.008	77.243	0.072	0.072	0.000	0.000	0.000	0.000
55	C	1835	GLU	-1	-0.958	-0.977	79.216	-3.970	-3.970	0.000	0.000	0.000	0.000
56	C	1836	SER	0	-0.033	-0.029	80.039	0.069	0.069	0.000	0.000	0.000	0.000
57	C	1837	VAL	0	0.015	0.001	80.643	0.071	0.071	0.000	0.000	0.000	0.000
58	C	1838	MLY	1	0.909	0.964	83.234	3.780	3.780	0.000	0.000	0.000	0.000
59	C	1839	GLY	0	-0.003	-0.004	85.206	0.060	0.060	0.000	0.000	0.000	0.000
60	C	1840	MET	0	0.013	0.003	83.550	0.056	0.056	0.000	0.000	0.000	0.000
61	C	1841	ARG	1	0.975	0.986	87.199	3.685	3.685	0.000	0.000	0.000	0.000
62	C	1842	MLY	1	0.915	0.957	89.002	3.552	3.552	0.000	0.000	0.000	0.000
63	C	1843	SER	0	0.014	0.000	89.971	0.042	0.042	0.000	0.000	0.000	0.000
64	C	1844	GLU	-1	-0.884	-0.946	90.798	-3.460	-3.460	0.000	0.000	0.000	0.000
65	C	1845	ARG	1	0.971	0.975	92.622	3.462	3.462	0.000	0.000	0.000	0.000
66	C	1846	ARG	1	0.856	0.930	95.043	3.288	3.288	0.000	0.000	0.000	0.000
67	C	1847	ILE	0	0.023	0.005	94.379	0.037	0.037	0.000	0.000	0.000	0.000
68	C	1848	MLY	1	0.895	0.977	94.612	3.393	3.393	0.000	0.000	0.000	0.000
69	C	1849	GLU	-1	-0.840	-0.911	98.986	-3.213	-3.213	0.000	0.000	0.000	0.000
70	C	1850	LEU	0	-0.023	-0.026	99.612	0.031	0.031	0.000	0.000	0.000	0.000
71	C	1851	THR	0	-0.015	0.001	100.846	0.026	0.026	0.000	0.000	0.000	0.000
72	C	1852	TYR	0	0.032	0.025	101.650	0.009	0.009	0.000	0.000	0.000	0.000
73	C	1853	GLN	0	-0.017	-0.006	105.027	0.007	0.007	0.000	0.000	0.000	0.000
74	C	1854	THR	0	-0.051	-0.036	105.946	0.022	0.022	0.000	0.000	0.000	0.000
75	C	1855	GLU	-1	-0.890	-0.954	106.022	-3.023	-3.023	0.000	0.000	0.000	0.000
76	C	209	ASP	-1	-0.926	-0.965	109.530	-2.909	-2.909	0.000	0.000	0.000	0.000
77	C	210	LEU	0	-0.038	-0.021	109.818	0.031	0.031	0.000	0.000	0.000	0.000
78	C	211	GLU	-1	-0.876	-0.909	110.805	-2.884	-2.884	0.000	0.000	0.000	0.000
79	C	212	MLY	1	0.977	0.988	113.547	2.867	2.867	0.000	0.000	0.000	0.000
80	C	213	GLU	-1	-0.903	-0.938	115.579	-2.762	-2.762	0.000	0.000	0.000	0.000
81	C	214	ARG	1	0.759	0.842	113.299	2.857	2.857	0.000	0.000	0.000	0.000
82	C	215	ASP	-1	-0.799	-0.882	116.868	-2.748	-2.748	0.000	0.000	0.000	0.000
83	C	216	PHE	0	-0.037	-0.014	119.553	0.036	0.036	0.000	0.000	0.000	0.000
84	C	217	TYR	0	-0.091	-0.086	119.511	0.046	0.046	0.000	0.000	0.000	0.000
85	C	218	PHE	0	0.015	0.011	120.919	0.026	0.026	0.000	0.000	0.000	0.000
86	C	219	GLY	0	0.028	0.013	123.345	0.021	0.021	0.000	0.000	0.000	0.000
87	C	220	MLY	1	0.851	0.936	124.362	2.614	2.614	0.000	0.000	0.000	0.000
88	C	221	LEU	0	0.018	0.008	125.097	0.022	0.022	0.000	0.000	0.000	0.000
89	C	222	ARG	1	0.874	0.914	125.366	2.582	2.582	0.000	0.000	0.000	0.000
90	C	223	ASN	0	-0.013	-0.011	128.636	0.018	0.018	0.000	0.000	0.000	0.000
91	C	224	ILE	0	-0.021	-0.009	130.902	0.021	0.021	0.000	0.000	0.000	0.000
92	C	225	GLU	-1	-0.755	-0.835	129.183	-2.506	-2.506	0.000	0.000	0.000	0.000
93	C	226	LEU	0	-0.029	-0.002	132.664	0.012	0.012	0.000	0.000	0.000	0.000
94	C	227	ILE	0	0.023	0.007	134.364	0.016	0.016	0.000	0.000	0.000	0.000
95	C	228	CYS	0	-0.085	-0.051	136.001	0.020	0.020	0.000	0.000	0.000	0.000
96	C	229	GLN	0	-0.015	-0.001	133.737	0.000	0.000	0.000	0.000	0.000	0.000
97	C	230	GLU	-1	-0.987	-0.988	137.946	-2.351	-2.351	0.000	0.000	0.000	0.000
98	C	231	ASN	0	-0.129	-0.076	140.218	0.008	0.008	0.000	0.000	0.000	0.000
99	C	232	GLU	-1	-0.924	-0.954	138.647	-2.335	-2.335	0.000	0.000	0.000	0.000
100	C	233	GLY	0	-0.011	0.002	142.244	0.005	0.005	0.000	0.000	0.000	0.000
101	C	234	GLU	-1	-0.909	-0.961	145.875	-2.223	-2.223	0.000	0.000	0.000	0.000
102	C	235	ASN	0	-0.087	-0.051	146.587	0.013	0.013	0.000	0.000	0.000	0.000
103	C	236	ASP	-1	-0.778	-0.868	144.340	-2.256	-2.256	0.000	0.000	0.000	0.000
104	C	237	PRO	0	0.007	-0.015	144.011	-0.017	-0.017	0.000	0.000	0.000	0.000
105	C	238	VAL	0	-0.078	-0.035	140.607	-0.018	-0.018	0.000	0.000	0.000	0.000
106	C	239	LEU	0	0.043	0.011	139.819	-0.023	-0.023	0.000	0.000	0.000	0.000
107	C	240	GLN	0	-0.042	-0.017	139.020	-0.006	-0.006	0.000	0.000	0.000	0.000
108	C	241	ARG	1	0.950	0.966	138.130	2.328	2.328	0.000	0.000	0.000	0.000
109	C	242	ILE	0	-0.045	-0.016	134.706	-0.022	-0.022	0.000	0.000	0.000	0.000
110	C	243	VAL	0	0.055	0.022	134.373	-0.025	-0.025	0.000	0.000	0.000	0.000
111	C	244	ASP	-1	-0.888	-0.939	134.013	-2.378	-2.378	0.000	0.000	0.000	0.000
112	C	245	ILE	0	-0.096	-0.058	131.051	-0.022	-0.022	0.000	0.000	0.000	0.000
113	C	246	LEU	0	-0.051	-0.023	130.135	-0.025	-0.025	0.000	0.000	0.000	0.000
114	C	247	TYR	0	-0.065	-0.041	129.137	-0.014	-0.014	0.000	0.000	0.000	0.000
115	C	248	ALA	0	-0.023	0.013	129.434	-0.006	-0.006	0.000	0.000	0.000	0.000
116	C	249	THR	0	-0.065	-0.032	124.359	-0.020	-0.020	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:1781:ARG)