FMO DATABASE

FMODB ID: R84K8

Calculation Name: 4XA6-A-Xray372

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 4XA6

Chain ID: A

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	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	168
LigandResidueName
LigandFragmentNumber	0
LigandCharge	MLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1101799.159177
FMO2-HF: Nuclear repulsion	1030969.411145
FMO2-HF: Total energy	-70829.748031
FMO2-MP2: Total energy	-71037.805908

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:2:PRO)

Summations of interaction energy for fragment #1(A:2: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.
-15.211	-8.413	6.088	-4.726	-8.159	-0.031

Interaction energy analysis for fragmet #1(A:2:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.027

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	4	MLY	1	0.956	0.980	3.808	0.771	2.192	-0.021	-0.583	-0.817	0.003
4	A	5	PRO	0	0.007	-0.014	6.688	0.384	0.384	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.870	-0.936	9.146	-0.550	-0.550	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.883	-0.946	6.942	-0.449	-0.449	0.000	0.000	0.000	0.000
7	A	8	HIS	0	-0.047	-0.023	7.162	0.329	0.329	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.949	-0.971	9.186	0.121	0.121	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.887	-0.951	12.686	0.156	0.156	0.000	0.000	0.000	0.000
10	A	11	ILE	0	-0.031	-0.029	9.116	0.075	0.075	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.051	-0.022	12.409	0.024	0.024	0.000	0.000	0.000	0.000
12	A	13	ASN	0	-0.003	-0.008	14.721	-0.028	-0.028	0.000	0.000	0.000	0.000
13	A	14	MLY	1	0.892	0.962	14.094	-0.366	-0.366	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.023	-0.032	14.884	0.035	0.035	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.045	-0.008	18.847	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.912	-0.952	21.620	0.126	0.126	0.000	0.000	0.000	0.000
17	A	18	PRO	0	-0.030	-0.022	23.877	0.016	0.016	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.988	-0.994	26.660	0.125	0.125	0.000	0.000	0.000	0.000
19	A	20	LEU	0	-0.025	0.009	19.845	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.051	0.026	23.652	0.001	0.001	0.000	0.000	0.000	0.000
21	A	22	GLN	0	0.052	0.009	22.594	0.019	0.019	0.000	0.000	0.000	0.000
22	A	23	SER	0	0.016	-0.002	21.733	0.018	0.018	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.797	-0.901	19.134	0.299	0.299	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.915	0.987	17.729	-0.200	-0.200	0.000	0.000	0.000	0.000
25	A	26	THR	0	-0.137	-0.082	17.316	0.051	0.051	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.932	-0.968	15.845	0.554	0.554	0.000	0.000	0.000	0.000
27	A	28	ALA	0	0.052	0.039	13.451	0.140	0.140	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.027	-0.022	12.358	0.131	0.131	0.000	0.000	0.000	0.000
29	A	30	GLN	0	-0.017	-0.009	12.553	0.040	0.040	0.000	0.000	0.000	0.000
30	A	31	GLN	0	0.025	0.001	9.130	0.116	0.116	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.001	0.010	8.036	0.516	0.516	0.000	0.000	0.000	0.000
32	A	33	ARG	1	0.921	0.968	8.196	-0.544	-0.544	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.021	-0.013	6.968	0.019	0.019	0.000	0.000	0.000	0.000
34	A	35	ASN	0	0.043	0.019	2.786	0.698	1.824	0.429	-0.580	-0.975	-0.006
35	A	36	TYR	0	-0.002	0.003	4.191	0.302	0.517	-0.001	-0.033	-0.181	0.000
36	A	37	GLY	0	0.003	-0.001	6.745	-0.273	-0.273	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.014	-0.006	2.515	-5.495	-3.703	0.562	-0.888	-1.466	-0.003
38	A	39	PHE	0	0.049	0.016	1.938	-2.280	-2.109	2.923	-0.926	-2.167	-0.001
39	A	40	VAL	0	-0.009	-0.005	4.083	-0.941	-0.833	0.001	-0.007	-0.102	0.000
40	A	41	SER	0	-0.065	-0.024	5.698	-0.315	-0.315	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.845	-0.926	2.389	-9.200	-7.235	2.195	-1.709	-2.451	-0.024
42	A	43	TYR	0	-0.003	-0.002	5.783	-0.152	-0.152	0.000	0.000	0.000	0.000
43	A	44	ASN	0	-0.027	-0.025	7.989	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.919	-0.951	8.516	-0.241	-0.241	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.030	-0.018	8.674	0.051	0.051	0.000	0.000	0.000	0.000
46	A	47	THR	0	0.005	0.006	10.566	0.069	0.069	0.000	0.000	0.000	0.000
47	A	48	MLY	1	0.933	0.967	13.264	0.158	0.158	0.000	0.000	0.000	0.000
48	A	49	SER	0	-0.059	-0.036	13.211	0.051	0.051	0.000	0.000	0.000	0.000
49	A	50	HIS	0	0.005	0.003	14.506	0.013	0.013	0.000	0.000	0.000	0.000
50	A	1777	ALA	0	0.038	0.017	16.195	0.028	0.028	0.000	0.000	0.000	0.000
51	A	1778	HIS	0	-0.036	-0.031	18.199	0.037	0.037	0.000	0.000	0.000	0.000
52	A	1779	LEU	0	0.025	0.000	18.085	0.024	0.024	0.000	0.000	0.000	0.000
53	A	1780	GLU	-1	-0.892	-0.947	19.940	-0.154	-0.154	0.000	0.000	0.000	0.000
54	A	1781	ARG	1	0.890	0.962	20.313	0.138	0.138	0.000	0.000	0.000	0.000
55	A	1782	MET	0	-0.025	-0.002	21.763	0.009	0.009	0.000	0.000	0.000	0.000
56	A	1783	MLY	1	0.972	0.996	24.804	0.164	0.164	0.000	0.000	0.000	0.000
57	A	1784	MLY	1	0.942	0.961	26.482	0.119	0.119	0.000	0.000	0.000	0.000
58	A	1785	ASN	0	-0.002	0.005	28.071	0.014	0.014	0.000	0.000	0.000	0.000
59	A	1786	MET	0	0.012	0.012	25.840	0.007	0.007	0.000	0.000	0.000	0.000
60	A	1787	GLU	-1	-0.894	-0.957	29.901	-0.113	-0.113	0.000	0.000	0.000	0.000
61	A	1788	GLN	0	-0.034	-0.020	32.343	0.003	0.003	0.000	0.000	0.000	0.000
62	A	1789	THR	0	0.023	0.008	33.641	0.006	0.006	0.000	0.000	0.000	0.000
63	A	1790	ILE	0	0.001	0.013	32.870	0.005	0.005	0.000	0.000	0.000	0.000
64	A	1791	MLY	1	0.940	0.969	34.448	0.087	0.087	0.000	0.000	0.000	0.000
65	A	1792	ASP	-1	-0.892	-0.936	38.362	-0.059	-0.059	0.000	0.000	0.000	0.000
66	A	1793	LEU	0	0.003	-0.015	37.496	0.003	0.003	0.000	0.000	0.000	0.000
67	A	1794	GLN	0	0.008	-0.006	38.653	0.005	0.005	0.000	0.000	0.000	0.000
68	A	1795	HIS	1	0.883	0.954	42.261	0.066	0.066	0.000	0.000	0.000	0.000
69	A	1796	ARG	1	0.963	0.990	42.980	0.058	0.058	0.000	0.000	0.000	0.000
70	A	1797	LEU	0	-0.028	-0.004	44.017	0.002	0.002	0.000	0.000	0.000	0.000
71	A	1798	ASP	-1	-0.888	-0.944	46.331	-0.050	-0.050	0.000	0.000	0.000	0.000
72	A	1799	GLU	-1	-0.872	-0.947	48.515	-0.040	-0.040	0.000	0.000	0.000	0.000
73	A	1800	ALA	0	-0.011	-0.006	49.593	0.002	0.002	0.000	0.000	0.000	0.000
74	A	1801	GLU	-1	-0.986	-1.006	48.694	-0.058	-0.058	0.000	0.000	0.000	0.000
75	A	1802	GLN	0	-0.028	-0.016	52.079	0.004	0.004	0.000	0.000	0.000	0.000
76	A	1803	ILE	0	-0.036	-0.013	53.959	0.002	0.002	0.000	0.000	0.000	0.000
77	A	1804	ALA	0	-0.020	-0.016	55.063	0.002	0.002	0.000	0.000	0.000	0.000
78	A	1805	LEU	0	-0.061	-0.035	55.571	0.001	0.001	0.000	0.000	0.000	0.000
79	A	1806	MLY	1	0.932	0.958	56.594	0.039	0.039	0.000	0.000	0.000	0.000
80	A	1807	GLY	0	-0.010	0.017	59.831	0.002	0.002	0.000	0.000	0.000	0.000
81	A	1808	GLY	0	0.003	0.014	61.743	0.001	0.001	0.000	0.000	0.000	0.000
82	A	1809	MLY	1	0.988	1.001	52.657	0.050	0.050	0.000	0.000	0.000	0.000
83	A	1810	MLY	1	0.942	0.951	56.001	0.047	0.047	0.000	0.000	0.000	0.000
84	A	1811	GLN	0	0.014	0.001	61.255	0.000	0.000	0.000	0.000	0.000	0.000
85	A	1812	LEU	0	0.088	0.048	60.922	0.000	0.000	0.000	0.000	0.000	0.000
86	A	1813	GLN	0	0.057	0.015	56.434	0.000	0.000	0.000	0.000	0.000	0.000
87	A	1814	MLY	1	0.914	0.970	62.090	0.037	0.037	0.000	0.000	0.000	0.000
88	A	1815	LEU	0	0.004	-0.003	64.709	0.001	0.001	0.000	0.000	0.000	0.000
89	A	1816	GLU	-1	-0.899	-0.937	61.454	-0.038	-0.038	0.000	0.000	0.000	0.000
90	A	1817	ALA	0	-0.095	-0.049	63.645	0.000	0.000	0.000	0.000	0.000	0.000
91	A	1818	ARG	1	0.968	0.981	65.040	0.030	0.030	0.000	0.000	0.000	0.000
92	A	1819	VAL	0	-0.010	-0.003	67.559	0.001	0.001	0.000	0.000	0.000	0.000
93	A	1820	ARG	1	1.022	1.020	60.946	0.042	0.042	0.000	0.000	0.000	0.000
94	A	1821	GLU	-1	-0.967	-0.971	67.387	-0.034	-0.034	0.000	0.000	0.000	0.000
95	A	1822	LEU	0	-0.005	-0.015	69.136	0.001	0.001	0.000	0.000	0.000	0.000
96	A	1823	GLU	-1	-0.899	-0.960	68.435	-0.032	-0.032	0.000	0.000	0.000	0.000
97	A	1824	ASN	0	-0.066	-0.031	66.729	0.000	0.000	0.000	0.000	0.000	0.000
98	A	1825	GLU	-1	-0.922	-0.962	70.719	-0.030	-0.030	0.000	0.000	0.000	0.000
99	A	1826	LEU	0	-0.014	-0.002	73.863	0.001	0.001	0.000	0.000	0.000	0.000
100	A	1827	GLU	-1	-0.939	-0.968	70.674	-0.031	-0.031	0.000	0.000	0.000	0.000
101	A	1828	ALA	0	-0.033	-0.023	73.996	0.001	0.001	0.000	0.000	0.000	0.000
102	A	1829	GLU	-1	-0.909	-0.978	75.396	-0.026	-0.026	0.000	0.000	0.000	0.000
103	A	1830	GLN	0	-0.030	-0.012	76.524	0.001	0.001	0.000	0.000	0.000	0.000
104	A	1831	MLY	1	0.945	0.975	71.988	0.030	0.030	0.000	0.000	0.000	0.000
105	A	1832	ARG	1	0.956	0.982	78.276	0.026	0.026	0.000	0.000	0.000	0.000
106	A	1833	ASN	0	-0.029	-0.003	80.720	0.001	0.001	0.000	0.000	0.000	0.000
107	A	1834	ALA	0	0.007	-0.007	80.647	0.001	0.001	0.000	0.000	0.000	0.000
108	A	1835	GLU	-1	-0.939	-0.974	81.382	-0.023	-0.023	0.000	0.000	0.000	0.000
109	A	1836	SER	0	0.018	0.022	83.299	0.001	0.001	0.000	0.000	0.000	0.000
110	A	1837	VAL	0	0.058	0.038	85.605	0.001	0.001	0.000	0.000	0.000	0.000
111	A	1838	MLY	1	0.887	0.949	84.591	0.023	0.023	0.000	0.000	0.000	0.000
112	A	1839	GLY	0	-0.110	-0.086	86.898	0.001	0.001	0.000	0.000	0.000	0.000
113	A	1840	MET	0	0.123	0.064	88.556	0.000	0.000	0.000	0.000	0.000	0.000
114	A	1841	ARG	1	0.966	0.996	87.909	0.020	0.020	0.000	0.000	0.000	0.000
115	A	1842	MLY	1	0.875	0.935	89.761	0.019	0.019	0.000	0.000	0.000	0.000
116	A	1843	SER	0	-0.005	0.009	92.562	0.000	0.000	0.000	0.000	0.000	0.000
117	A	1844	GLU	-1	-0.821	-0.922	94.604	-0.018	-0.018	0.000	0.000	0.000	0.000
118	A	1845	ARG	1	0.811	0.884	92.967	0.019	0.019	0.000	0.000	0.000	0.000
119	A	1846	ARG	1	0.998	1.008	98.442	0.017	0.017	0.000	0.000	0.000	0.000
120	A	1847	ILE	0	0.110	0.077	99.788	0.000	0.000	0.000	0.000	0.000	0.000
121	A	1848	MLY	1	0.906	0.963	99.609	0.016	0.016	0.000	0.000	0.000	0.000
122	A	1849	GLU	-1	-0.906	-0.938	101.472	-0.016	-0.016	0.000	0.000	0.000	0.000
123	A	1850	LEU	0	-0.053	-0.034	103.223	0.000	0.000	0.000	0.000	0.000	0.000
124	A	1851	THR	0	-0.031	-0.040	105.757	0.000	0.000	0.000	0.000	0.000	0.000
125	A	1852	TYR	0	0.003	0.016	107.361	0.000	0.000	0.000	0.000	0.000	0.000
126	A	1853	GLN	0	0.036	0.005	106.101	0.000	0.000	0.000	0.000	0.000	0.000
127	A	1854	THR	0	-0.112	-0.055	109.636	0.000	0.000	0.000	0.000	0.000	0.000
128	A	1855	GLU	-1	-0.912	-0.962	111.769	-0.013	-0.013	0.000	0.000	0.000	0.000
129	A	209	ASP	-1	-0.902	-0.951	112.495	-0.013	-0.013	0.000	0.000	0.000	0.000
130	A	210	LEU	0	0.002	0.001	112.335	0.000	0.000	0.000	0.000	0.000	0.000
131	A	211	GLU	-1	-0.964	-0.964	115.751	-0.012	-0.012	0.000	0.000	0.000	0.000
132	A	212	MLY	1	0.994	1.007	117.634	0.011	0.011	0.000	0.000	0.000	0.000
133	A	213	GLU	-1	-0.925	-0.972	116.762	-0.012	-0.012	0.000	0.000	0.000	0.000
134	A	214	ARG	1	0.899	0.960	119.971	0.012	0.012	0.000	0.000	0.000	0.000
135	A	215	ASP	-1	-0.871	-0.960	121.515	-0.011	-0.011	0.000	0.000	0.000	0.000
136	A	216	PHE	0	-0.079	-0.031	123.148	0.000	0.000	0.000	0.000	0.000	0.000
137	A	217	TYR	0	-0.066	-0.053	120.700	0.000	0.000	0.000	0.000	0.000	0.000
138	A	218	PHE	0	0.035	0.016	125.903	0.000	0.000	0.000	0.000	0.000	0.000
139	A	219	GLY	0	0.043	0.032	127.588	0.000	0.000	0.000	0.000	0.000	0.000
140	A	220	MLY	1	0.889	0.951	126.475	0.010	0.010	0.000	0.000	0.000	0.000
141	A	221	LEU	0	0.011	0.009	129.224	0.000	0.000	0.000	0.000	0.000	0.000
142	A	222	ARG	1	0.970	0.993	131.905	0.010	0.010	0.000	0.000	0.000	0.000
143	A	223	ASN	0	-0.040	-0.029	133.302	0.000	0.000	0.000	0.000	0.000	0.000
144	A	224	ILE	0	-0.019	-0.010	133.704	0.000	0.000	0.000	0.000	0.000	0.000
145	A	225	GLU	-1	-0.854	-0.945	135.922	-0.009	-0.009	0.000	0.000	0.000	0.000
146	A	226	LEU	0	-0.042	-0.027	137.129	0.000	0.000	0.000	0.000	0.000	0.000
147	A	227	ILE	0	0.020	0.012	139.099	0.000	0.000	0.000	0.000	0.000	0.000
148	A	228	CYS	0	-0.092	-0.047	140.220	0.000	0.000	0.000	0.000	0.000	0.000
149	A	229	GLN	0	-0.078	-0.032	139.841	0.000	0.000	0.000	0.000	0.000	0.000
150	A	230	GLU	-1	-1.032	-1.002	142.762	-0.008	-0.008	0.000	0.000	0.000	0.000
151	A	231	ASN	0	-0.010	-0.010	145.970	0.000	0.000	0.000	0.000	0.000	0.000
152	A	232	GLU	-1	-0.944	-0.970	148.046	-0.007	-0.007	0.000	0.000	0.000	0.000
153	A	233	GLY	0	-0.041	-0.006	151.310	0.000	0.000	0.000	0.000	0.000	0.000
154	A	234	GLU	-1	-0.948	-0.982	150.380	-0.008	-0.008	0.000	0.000	0.000	0.000
155	A	235	ASN	0	-0.043	-0.023	145.868	0.000	0.000	0.000	0.000	0.000	0.000
156	A	236	ASP	-1	-0.864	-0.932	147.297	-0.008	-0.008	0.000	0.000	0.000	0.000
157	A	237	PRO	0	0.029	-0.003	145.998	0.000	0.000	0.000	0.000	0.000	0.000
158	A	238	VAL	0	-0.024	0.002	141.287	0.000	0.000	0.000	0.000	0.000	0.000
159	A	239	LEU	0	0.048	0.011	141.764	0.000	0.000	0.000	0.000	0.000	0.000
160	A	240	GLN	0	-0.007	0.006	142.458	0.000	0.000	0.000	0.000	0.000	0.000
161	A	241	ARG	1	0.947	0.980	134.991	0.009	0.009	0.000	0.000	0.000	0.000
162	A	242	ILE	0	-0.035	-0.039	137.094	0.000	0.000	0.000	0.000	0.000	0.000
163	A	243	VAL	0	0.067	0.025	137.728	0.000	0.000	0.000	0.000	0.000	0.000
164	A	244	ASP	-1	-0.902	-0.955	138.835	-0.009	-0.009	0.000	0.000	0.000	0.000
165	A	245	ILE	0	-0.147	-0.066	133.212	0.000	0.000	0.000	0.000	0.000	0.000
166	A	246	LEU	0	-0.059	0.008	134.310	0.000	0.000	0.000	0.000	0.000	0.000
167	A	247	TYR	0	-0.022	-0.019	134.477	0.000	0.000	0.000	0.000	0.000	0.000
168	A	248	ALA	0	-0.057	-0.017	129.438	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:PRO)