FMO DATABASE

FMODB ID: 6Y5RZ

Calculation Name: 4XA6-B-Xray372

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 4XA6

Chain ID: B

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:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
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	166
LigandCharge	MLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1080024.286305
FMO2-HF: Nuclear repulsion	1009762.732148
FMO2-HF: Total energy	-70261.554157
FMO2-MP2: Total energy	-70467.800753

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(B:3:LEU)

Summations of interaction energy for fragment #1(B:3:LEU)

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.
-15.636	-11.431	21.32	-9.301	-16.224	-0.05

Interaction energy analysis for fragmet #1(B:3:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.030

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	B	5	PRO	0	0.000	-0.019	3.273	-2.225	-0.430	0.044	-0.904	-0.935	0.001
4	B	6	GLU	-1	-0.913	-0.952	5.983	-0.729	-0.729	0.000	0.000	0.000	0.000
5	B	7	GLU	-1	-0.853	-0.934	2.346	-4.840	-1.830	1.932	-1.789	-3.153	-0.017
6	B	8	HIS	0	-0.037	-0.011	3.413	-1.418	0.180	0.069	-0.594	-1.074	-0.004
7	B	9	GLU	-1	-0.853	-0.923	4.213	-0.386	-0.233	0.002	-0.021	-0.134	0.000
8	B	10	ASP	-1	-0.900	-0.952	6.846	-0.573	-0.573	0.000	0.000	0.000	0.000
9	B	11	ILE	0	-0.093	-0.059	2.631	-0.137	0.279	0.501	-0.150	-0.767	-0.001
10	B	12	LEU	0	-0.028	-0.018	6.621	0.218	0.218	0.000	0.000	0.000	0.000
11	B	13	ASN	0	-0.065	-0.022	9.023	0.134	0.134	0.000	0.000	0.000	0.000
12	B	14	MLY	1	0.963	0.974	7.064	0.417	0.417	0.000	0.000	0.000	0.000
13	B	15	LEU	0	-0.059	-0.029	9.537	0.063	0.063	0.000	0.000	0.000	0.000
14	B	16	LEU	0	-0.037	-0.012	13.024	0.024	0.024	0.000	0.000	0.000	0.000
15	B	17	ASP	-1	-0.840	-0.907	15.516	-0.131	-0.131	0.000	0.000	0.000	0.000
16	B	18	PRO	0	-0.042	-0.031	17.249	0.007	0.007	0.000	0.000	0.000	0.000
17	B	19	GLU	-1	-0.985	-0.996	19.723	-0.078	-0.078	0.000	0.000	0.000	0.000
18	B	20	LEU	0	-0.039	0.002	13.263	0.012	0.012	0.000	0.000	0.000	0.000
19	B	21	ALA	0	0.049	0.024	17.755	0.012	0.012	0.000	0.000	0.000	0.000
20	B	22	GLN	0	0.034	-0.003	16.572	-0.009	-0.009	0.000	0.000	0.000	0.000
21	B	23	SER	0	0.020	0.012	16.232	0.002	0.002	0.000	0.000	0.000	0.000
22	B	24	GLU	-1	-0.809	-0.908	13.181	-0.074	-0.074	0.000	0.000	0.000	0.000
23	B	25	ARG	1	0.889	0.957	11.672	0.106	0.106	0.000	0.000	0.000	0.000
24	B	26	THR	0	-0.100	-0.060	11.681	0.010	0.010	0.000	0.000	0.000	0.000
25	B	27	GLU	-1	-0.959	-0.981	10.218	0.071	0.071	0.000	0.000	0.000	0.000
26	B	28	ALA	0	0.065	0.042	7.480	0.070	0.070	0.000	0.000	0.000	0.000
27	B	29	LEU	0	-0.003	-0.021	6.869	0.087	0.087	0.000	0.000	0.000	0.000
28	B	30	GLN	0	-0.007	0.008	8.510	-0.009	-0.009	0.000	0.000	0.000	0.000
29	B	31	GLN	0	0.004	-0.002	3.458	-0.353	-0.038	0.009	-0.059	-0.264	0.000
30	B	32	LEU	0	0.019	0.011	3.760	-0.004	0.314	0.003	-0.053	-0.268	0.000
31	B	33	ARG	1	0.888	0.949	5.174	-0.275	-0.250	-0.001	0.000	-0.024	0.000
32	B	34	VAL	0	-0.021	-0.021	5.643	-0.060	-0.060	0.000	0.000	0.000	0.000
33	B	35	ASN	0	0.063	0.046	1.923	-4.744	-8.054	14.249	-4.134	-6.804	-0.029
34	B	36	TYR	0	0.002	0.005	4.377	-0.565	-0.393	-0.001	-0.019	-0.153	0.000
35	B	37	GLY	0	0.008	-0.001	6.719	0.052	0.052	0.000	0.000	0.000	0.000
36	B	38	SER	0	0.014	0.004	4.818	0.073	0.073	0.000	0.000	0.000	0.000
37	B	39	PHE	0	0.043	0.013	2.682	-1.746	-2.033	4.513	-1.578	-2.648	0.000
38	B	40	VAL	0	-0.016	0.008	6.182	-0.007	-0.007	0.000	0.000	0.000	0.000
39	B	41	SER	0	-0.055	-0.026	9.571	0.002	0.002	0.000	0.000	0.000	0.000
40	B	42	GLU	-1	-0.909	-0.950	6.799	1.718	1.718	0.000	0.000	0.000	0.000
41	B	43	TYR	0	0.014	0.011	9.286	-0.081	-0.081	0.000	0.000	0.000	0.000
42	B	44	ASN	0	-0.063	-0.056	10.793	-0.042	-0.042	0.000	0.000	0.000	0.000
43	B	45	ASP	-1	-0.867	-0.927	12.919	0.356	0.356	0.000	0.000	0.000	0.000
44	B	46	LEU	0	-0.019	-0.005	11.818	-0.039	-0.039	0.000	0.000	0.000	0.000
45	B	47	THR	0	-0.049	-0.032	14.436	-0.048	-0.048	0.000	0.000	0.000	0.000
46	B	48	MLY	1	0.908	0.959	15.973	-0.225	-0.225	0.000	0.000	0.000	0.000
47	B	49	SER	0	-0.028	-0.016	17.187	-0.028	-0.028	0.000	0.000	0.000	0.000
48	B	50	HIS	0	0.008	0.001	18.065	-0.015	-0.015	0.000	0.000	0.000	0.000
49	B	1777	ALA	0	0.037	0.018	19.777	-0.017	-0.017	0.000	0.000	0.000	0.000
50	B	1778	HIS	0	-0.001	0.005	21.801	-0.025	-0.025	0.000	0.000	0.000	0.000
51	B	1779	LEU	0	0.023	0.005	20.768	-0.012	-0.012	0.000	0.000	0.000	0.000
52	B	1780	GLU	-1	-0.801	-0.874	24.042	0.039	0.039	0.000	0.000	0.000	0.000
53	B	1781	ARG	1	0.883	0.940	25.859	-0.113	-0.113	0.000	0.000	0.000	0.000
54	B	1782	MET	0	-0.050	-0.034	26.373	-0.003	-0.003	0.000	0.000	0.000	0.000
55	B	1783	MLY	1	0.853	0.918	27.848	-0.047	-0.047	0.000	0.000	0.000	0.000
56	B	1784	MLY	1	0.965	0.985	29.788	-0.046	-0.046	0.000	0.000	0.000	0.000
57	B	1785	ASN	0	-0.028	-0.018	32.036	-0.007	-0.007	0.000	0.000	0.000	0.000
58	B	1786	MET	0	0.006	0.007	29.154	-0.001	-0.001	0.000	0.000	0.000	0.000
59	B	1787	GLU	-1	-0.833	-0.914	33.228	0.031	0.031	0.000	0.000	0.000	0.000
60	B	1788	GLN	0	-0.067	-0.040	35.776	-0.005	-0.005	0.000	0.000	0.000	0.000
61	B	1789	THR	0	-0.016	-0.001	37.053	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	1790	ILE	0	-0.001	-0.001	35.542	-0.002	-0.002	0.000	0.000	0.000	0.000
63	B	1791	MLY	1	0.910	0.961	37.288	-0.031	-0.031	0.000	0.000	0.000	0.000
64	B	1792	ASP	-1	-0.859	-0.924	41.864	0.033	0.033	0.000	0.000	0.000	0.000
65	B	1793	LEU	0	-0.079	-0.042	40.668	-0.001	-0.001	0.000	0.000	0.000	0.000
66	B	1794	GLN	0	0.024	0.002	42.230	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	1795	HIS	0	0.053	0.042	45.428	-0.002	-0.002	0.000	0.000	0.000	0.000
68	B	1796	ARG	1	0.926	0.941	44.800	-0.038	-0.038	0.000	0.000	0.000	0.000
69	B	1797	LEU	0	-0.070	-0.021	46.771	0.000	0.000	0.000	0.000	0.000	0.000
70	B	1798	ASP	-1	-0.863	-0.937	49.247	0.021	0.021	0.000	0.000	0.000	0.000
71	B	1799	GLU	-1	-0.967	-0.991	51.397	0.024	0.024	0.000	0.000	0.000	0.000
72	B	1800	ALA	0	-0.024	-0.014	52.077	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	1801	GLU	-1	-0.933	-0.963	50.926	0.023	0.023	0.000	0.000	0.000	0.000
74	B	1802	GLN	0	-0.052	-0.027	54.744	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	1803	ILE	0	-0.060	-0.040	56.145	-0.001	-0.001	0.000	0.000	0.000	0.000
76	B	1804	ALA	0	-0.019	-0.003	57.547	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	1805	LEU	0	0.014	0.017	59.362	-0.001	-0.001	0.000	0.000	0.000	0.000
78	B	1806	MLY	1	0.893	0.950	61.355	-0.018	-0.018	0.000	0.000	0.000	0.000
79	B	1807	GLY	0	-0.061	-0.033	64.272	0.000	0.000	0.000	0.000	0.000	0.000
80	B	1808	GLY	0	0.064	0.033	65.515	0.001	0.001	0.000	0.000	0.000	0.000
81	B	1809	MLY	1	0.971	0.972	66.512	-0.018	-0.018	0.000	0.000	0.000	0.000
82	B	1810	MLY	1	0.992	0.992	69.616	-0.012	-0.012	0.000	0.000	0.000	0.000
83	B	1811	GLN	0	-0.005	-0.008	67.409	-0.001	-0.001	0.000	0.000	0.000	0.000
84	B	1812	LEU	0	0.033	0.024	67.975	0.000	0.000	0.000	0.000	0.000	0.000
85	B	1813	GLN	0	0.013	-0.012	70.599	-0.001	-0.001	0.000	0.000	0.000	0.000
86	B	1814	MLY	1	0.949	0.991	71.382	-0.013	-0.013	0.000	0.000	0.000	0.000
87	B	1815	LEU	0	-0.008	-0.015	69.667	-0.001	-0.001	0.000	0.000	0.000	0.000
88	B	1816	GLU	-1	-0.847	-0.909	74.273	0.015	0.015	0.000	0.000	0.000	0.000
89	B	1817	ALA	0	-0.030	-0.009	76.771	0.000	0.000	0.000	0.000	0.000	0.000
90	B	1818	ARG	1	0.838	0.912	76.148	-0.011	-0.011	0.000	0.000	0.000	0.000
91	B	1819	VAL	0	0.021	-0.008	75.282	0.000	0.000	0.000	0.000	0.000	0.000
92	B	1820	ARG	1	0.927	0.970	78.210	-0.012	-0.012	0.000	0.000	0.000	0.000
93	B	1821	GLU	-1	-0.864	-0.899	80.972	0.010	0.010	0.000	0.000	0.000	0.000
94	B	1822	LEU	0	-0.041	-0.032	77.932	0.000	0.000	0.000	0.000	0.000	0.000
95	B	1823	GLU	-1	-0.883	-0.959	80.416	0.012	0.012	0.000	0.000	0.000	0.000
96	B	1824	ASN	0	-0.011	0.011	83.391	0.000	0.000	0.000	0.000	0.000	0.000
97	B	1825	GLU	-1	-0.890	-0.963	84.812	0.009	0.009	0.000	0.000	0.000	0.000
98	B	1826	LEU	0	-0.046	-0.007	81.657	0.000	0.000	0.000	0.000	0.000	0.000
99	B	1827	GLU	-1	-0.811	-0.891	85.189	0.010	0.010	0.000	0.000	0.000	0.000
100	B	1828	ALA	0	0.063	0.023	88.441	0.000	0.000	0.000	0.000	0.000	0.000
101	B	1829	GLU	-1	-0.875	-0.925	87.420	0.008	0.008	0.000	0.000	0.000	0.000
102	B	1830	GLN	0	-0.062	-0.039	85.804	0.000	0.000	0.000	0.000	0.000	0.000
103	B	1831	MLY	1	0.801	0.892	90.164	-0.009	-0.009	0.000	0.000	0.000	0.000
104	B	1832	ARG	1	0.871	0.917	90.979	-0.008	-0.008	0.000	0.000	0.000	0.000
105	B	1833	ASN	0	-0.013	0.013	90.694	0.000	0.000	0.000	0.000	0.000	0.000
106	B	1834	ALA	0	0.035	0.009	93.431	0.000	0.000	0.000	0.000	0.000	0.000
107	B	1835	GLU	-1	-0.904	-0.963	94.990	0.007	0.007	0.000	0.000	0.000	0.000
108	B	1836	SER	0	0.042	0.028	96.319	0.000	0.000	0.000	0.000	0.000	0.000
109	B	1837	VAL	0	-0.039	-0.045	95.601	0.000	0.000	0.000	0.000	0.000	0.000
110	B	1838	MLY	1	0.876	0.949	96.585	-0.008	-0.008	0.000	0.000	0.000	0.000
111	B	1839	GLY	0	0.051	0.024	100.908	0.000	0.000	0.000	0.000	0.000	0.000
112	B	1840	MET	0	0.021	0.043	99.089	0.000	0.000	0.000	0.000	0.000	0.000
113	B	1841	ARG	1	0.830	0.888	101.153	-0.006	-0.006	0.000	0.000	0.000	0.000
114	B	1842	MLY	1	0.937	0.985	104.004	-0.006	-0.006	0.000	0.000	0.000	0.000
115	B	1843	SER	0	-0.009	-0.024	104.046	0.000	0.000	0.000	0.000	0.000	0.000
116	B	1844	GLU	-1	-0.810	-0.904	105.067	0.006	0.006	0.000	0.000	0.000	0.000
117	B	1845	ARG	1	0.881	0.927	106.296	-0.007	-0.007	0.000	0.000	0.000	0.000
118	B	1846	ARG	1	0.879	0.913	109.750	-0.005	-0.005	0.000	0.000	0.000	0.000
119	B	1847	ILE	0	0.031	0.028	107.337	0.000	0.000	0.000	0.000	0.000	0.000
120	B	1848	MLY	1	0.949	0.976	108.297	-0.006	-0.006	0.000	0.000	0.000	0.000
121	B	1849	GLU	-1	-0.833	-0.863	111.669	0.005	0.005	0.000	0.000	0.000	0.000
122	B	1850	LEU	0	-0.027	-0.036	114.038	0.000	0.000	0.000	0.000	0.000	0.000
123	B	1851	THR	0	-0.024	-0.010	112.676	0.000	0.000	0.000	0.000	0.000	0.000
124	B	1852	TYR	0	-0.039	-0.029	113.539	0.000	0.000	0.000	0.000	0.000	0.000
125	B	1853	GLN	0	0.027	0.031	117.984	0.000	0.000	0.000	0.000	0.000	0.000
126	B	1854	THR	0	-0.034	-0.019	116.670	0.000	0.000	0.000	0.000	0.000	0.000
127	B	1855	GLU	-1	-0.954	-0.960	118.919	0.004	0.004	0.000	0.000	0.000	0.000
128	B	209	ASP	-1	-0.875	-0.954	121.154	0.004	0.004	0.000	0.000	0.000	0.000
129	B	210	LEU	0	0.030	0.020	123.532	0.000	0.000	0.000	0.000	0.000	0.000
130	B	211	GLU	-1	-0.865	-0.927	121.881	0.003	0.003	0.000	0.000	0.000	0.000
131	B	212	MLY	1	0.974	0.991	125.100	-0.004	-0.004	0.000	0.000	0.000	0.000
132	B	213	GLU	-1	-0.916	-0.956	127.023	0.004	0.004	0.000	0.000	0.000	0.000
133	B	214	ARG	1	0.759	0.860	124.289	-0.003	-0.003	0.000	0.000	0.000	0.000
134	B	215	ASP	-1	-0.821	-0.898	126.945	0.003	0.003	0.000	0.000	0.000	0.000
135	B	216	PHE	0	-0.051	-0.025	130.072	0.000	0.000	0.000	0.000	0.000	0.000
136	B	217	TYR	0	-0.061	-0.052	132.557	0.000	0.000	0.000	0.000	0.000	0.000
137	B	218	PHE	0	0.031	0.026	131.341	0.000	0.000	0.000	0.000	0.000	0.000
138	B	219	GLY	0	0.018	0.014	134.143	0.000	0.000	0.000	0.000	0.000	0.000
139	B	220	MLY	1	0.870	0.922	135.610	-0.003	-0.003	0.000	0.000	0.000	0.000
140	B	221	LEU	0	0.020	0.017	135.996	0.000	0.000	0.000	0.000	0.000	0.000
141	B	222	ARG	1	0.923	0.947	135.630	-0.002	-0.002	0.000	0.000	0.000	0.000
142	B	223	ASN	0	-0.081	-0.028	138.835	0.000	0.000	0.000	0.000	0.000	0.000
143	B	224	ILE	0	0.038	0.001	141.228	0.000	0.000	0.000	0.000	0.000	0.000
144	B	225	GLU	-1	-0.775	-0.835	138.970	0.002	0.002	0.000	0.000	0.000	0.000
145	B	226	LEU	0	-0.066	-0.042	139.485	0.000	0.000	0.000	0.000	0.000	0.000
146	B	227	ILE	0	-0.072	-0.026	143.210	0.000	0.000	0.000	0.000	0.000	0.000
147	B	228	CYS	0	-0.073	-0.029	145.448	0.000	0.000	0.000	0.000	0.000	0.000
148	B	229	GLN	0	0.046	0.034	142.079	0.000	0.000	0.000	0.000	0.000	0.000
149	B	230	GLU	-1	-0.926	-0.946	146.889	0.002	0.002	0.000	0.000	0.000	0.000
150	B	231	ASN	0	-0.133	-0.087	149.660	0.000	0.000	0.000	0.000	0.000	0.000
151	B	232	GLU	-1	-0.920	-0.962	146.617	0.002	0.002	0.000	0.000	0.000	0.000
152	B	233	GLY	0	0.041	0.020	151.115	0.000	0.000	0.000	0.000	0.000	0.000
153	B	234	GLU	-1	-1.034	-1.026	154.559	0.002	0.002	0.000	0.000	0.000	0.000
154	B	235	ASN	0	-0.027	0.008	152.653	0.000	0.000	0.000	0.000	0.000	0.000
155	B	236	ASP	-1	-0.840	-0.921	154.803	0.002	0.002	0.000	0.000	0.000	0.000
156	B	237	PRO	0	0.026	0.006	154.214	0.000	0.000	0.000	0.000	0.000	0.000
157	B	238	VAL	0	-0.047	-0.034	152.767	0.000	0.000	0.000	0.000	0.000	0.000
158	B	239	LEU	0	0.019	-0.002	150.294	0.000	0.000	0.000	0.000	0.000	0.000
159	B	240	GLN	0	-0.022	0.002	148.929	0.000	0.000	0.000	0.000	0.000	0.000
160	B	241	ARG	1	0.935	0.968	149.249	-0.002	-0.002	0.000	0.000	0.000	0.000
161	B	242	ILE	0	-0.041	-0.028	146.307	0.000	0.000	0.000	0.000	0.000	0.000
162	B	243	VAL	0	0.050	0.021	145.418	0.000	0.000	0.000	0.000	0.000	0.000
163	B	244	ASP	-1	-0.895	-0.951	144.399	0.002	0.002	0.000	0.000	0.000	0.000
164	B	245	ILE	0	-0.135	-0.067	142.682	0.000	0.000	0.000	0.000	0.000	0.000
165	B	246	LEU	0	-0.073	-0.026	141.097	0.000	0.000	0.000	0.000	0.000	0.000
166	B	247	TYR	0	-0.096	-0.056	138.844	0.000	0.000	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(B:3:LEU)