FMO DATABASE

FMODB ID: KGQZ3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1103511.097464
FMO2-HF: Nuclear repulsion	1032678.902143
FMO2-HF: Total energy	-70832.195321
FMO2-MP2: Total energy	-71040.037822

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.
-14.992	-6.37	6.955	-5.207	-10.369	-0.032

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 : -0.026 / q_NPA : -0.031

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	0.934	0.967	3.865	0.530	1.691	-0.013	-0.523	-0.625	0.003
4	A	5	PRO	0	-0.015	-0.014	6.657	0.418	0.418	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.854	-0.949	8.799	-0.654	-0.654	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.838	-0.917	7.173	-0.494	-0.494	0.000	0.000	0.000	0.000
7	A	8	HIS	0	-0.065	-0.043	6.695	0.265	0.265	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.870	-0.924	9.458	0.041	0.041	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.859	-0.934	12.723	0.168	0.168	0.000	0.000	0.000	0.000
10	A	11	ILE	0	-0.011	-0.021	8.907	0.062	0.062	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.028	-0.009	12.627	0.030	0.030	0.000	0.000	0.000	0.000
12	A	13	ASN	0	-0.061	-0.051	15.023	-0.003	-0.003	0.000	0.000	0.000	0.000
13	A	14	MLY	1	0.842	0.945	12.805	-0.290	-0.290	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.049	-0.034	14.513	0.036	0.036	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.054	-0.010	18.442	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.839	-0.905	21.281	0.097	0.097	0.000	0.000	0.000	0.000
17	A	18	PRO	0	-0.031	-0.017	23.603	0.015	0.015	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-0.992	-1.011	26.368	0.095	0.095	0.000	0.000	0.000	0.000
19	A	20	LEU	0	-0.030	0.003	19.715	0.004	0.004	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.036	0.028	23.351	0.003	0.003	0.000	0.000	0.000	0.000
21	A	22	GLN	0	0.042	0.007	22.269	0.014	0.014	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.058	-0.018	21.027	0.006	0.006	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.775	-0.885	18.396	0.257	0.257	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.863	0.933	17.219	-0.140	-0.140	0.000	0.000	0.000	0.000
25	A	26	THR	0	-0.101	-0.069	17.212	0.026	0.026	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.912	-0.962	15.281	0.456	0.456	0.000	0.000	0.000	0.000
27	A	28	ALA	0	0.055	0.033	12.870	0.122	0.122	0.000	0.000	0.000	0.000
28	A	29	LEU	0	0.003	-0.003	11.977	0.079	0.079	0.000	0.000	0.000	0.000
29	A	30	GLN	0	0.002	0.008	12.117	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	31	GLN	0	0.016	0.003	8.233	0.065	0.065	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.007	0.007	7.441	0.354	0.354	0.000	0.000	0.000	0.000
32	A	33	ARG	1	0.888	0.939	7.906	-0.457	-0.457	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.025	-0.017	6.446	-0.001	-0.001	0.000	0.000	0.000	0.000
34	A	35	ASN	0	0.048	0.030	2.543	-0.231	0.965	1.460	-1.125	-1.530	-0.011
35	A	36	TYR	0	0.009	0.007	3.879	-0.017	0.422	0.004	-0.122	-0.320	-0.001
36	A	37	GLY	0	0.003	-0.002	6.059	-0.191	-0.191	0.000	0.000	0.000	0.000
37	A	38	SER	0	0.027	0.016	2.360	-1.399	-0.031	1.063	-0.813	-1.618	0.001
38	A	39	PHE	0	0.022	0.022	2.249	-3.323	-1.606	2.690	-1.285	-3.123	0.002
39	A	40	VAL	0	0.002	-0.001	3.316	-0.474	-1.006	0.061	0.696	-0.226	0.000
40	A	41	SER	0	-0.098	-0.055	5.279	-0.218	-0.218	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.870	-0.945	2.633	-10.973	-7.704	1.691	-2.032	-2.927	-0.026
42	A	43	TYR	0	0.015	0.009	5.302	-0.002	0.002	-0.001	-0.003	0.000	0.000
43	A	44	ASN	0	-0.015	-0.006	7.288	0.027	0.027	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.864	-0.938	8.757	-0.187	-0.187	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.025	-0.007	8.574	0.058	0.058	0.000	0.000	0.000	0.000
46	A	47	THR	0	-0.023	-0.023	10.380	0.089	0.089	0.000	0.000	0.000	0.000
47	A	48	MLY	1	0.879	0.943	12.936	0.184	0.184	0.000	0.000	0.000	0.000
48	A	49	SER	0	-0.035	-0.015	13.409	0.061	0.061	0.000	0.000	0.000	0.000
49	A	50	HIS	0	-0.022	-0.022	14.473	0.023	0.023	0.000	0.000	0.000	0.000
50	A	1777	ALA	0	0.053	0.021	16.308	0.033	0.033	0.000	0.000	0.000	0.000
51	A	1778	HIS	0	-0.027	-0.024	18.168	0.039	0.039	0.000	0.000	0.000	0.000
52	A	1779	LEU	0	0.029	0.005	17.428	0.024	0.024	0.000	0.000	0.000	0.000
53	A	1780	GLU	-1	-0.868	-0.928	19.598	-0.197	-0.197	0.000	0.000	0.000	0.000
54	A	1781	ARG	1	0.874	0.951	19.511	0.166	0.166	0.000	0.000	0.000	0.000
55	A	1782	MET	0	-0.016	0.002	21.482	0.011	0.011	0.000	0.000	0.000	0.000
56	A	1783	MLY	1	0.958	0.988	24.745	0.185	0.185	0.000	0.000	0.000	0.000
57	A	1784	MLY	1	0.849	0.909	26.471	0.137	0.137	0.000	0.000	0.000	0.000
58	A	1785	ASN	0	0.015	0.007	28.342	0.013	0.013	0.000	0.000	0.000	0.000
59	A	1786	MET	0	0.013	0.018	26.324	0.009	0.009	0.000	0.000	0.000	0.000
60	A	1787	GLU	-1	-0.791	-0.893	29.126	-0.124	-0.124	0.000	0.000	0.000	0.000
61	A	1788	GLN	0	0.011	0.004	32.302	0.002	0.002	0.000	0.000	0.000	0.000
62	A	1789	THR	0	0.010	-0.013	33.695	0.007	0.007	0.000	0.000	0.000	0.000
63	A	1790	ILE	0	0.006	0.005	32.818	0.005	0.005	0.000	0.000	0.000	0.000
64	A	1791	MLY	1	0.875	0.949	33.402	0.097	0.097	0.000	0.000	0.000	0.000
65	A	1792	ASP	-1	-0.869	-0.913	38.741	-0.059	-0.059	0.000	0.000	0.000	0.000
66	A	1793	LEU	0	0.015	0.000	37.517	0.004	0.004	0.000	0.000	0.000	0.000
67	A	1794	GLN	0	0.006	0.002	38.786	0.004	0.004	0.000	0.000	0.000	0.000
68	A	1795	HIS	1	0.899	0.948	42.166	0.068	0.068	0.000	0.000	0.000	0.000
69	A	1796	ARG	1	0.894	0.936	42.685	0.060	0.060	0.000	0.000	0.000	0.000
70	A	1797	LEU	0	0.004	0.011	44.373	0.002	0.002	0.000	0.000	0.000	0.000
71	A	1798	ASP	-1	-0.860	-0.926	46.571	-0.052	-0.052	0.000	0.000	0.000	0.000
72	A	1799	GLU	-1	-0.829	-0.934	48.648	-0.041	-0.041	0.000	0.000	0.000	0.000
73	A	1800	ALA	0	-0.004	0.004	49.584	0.002	0.002	0.000	0.000	0.000	0.000
74	A	1801	GLU	-1	-0.908	-0.977	49.583	-0.054	-0.054	0.000	0.000	0.000	0.000
75	A	1802	GLN	0	-0.054	-0.032	52.050	0.004	0.004	0.000	0.000	0.000	0.000
76	A	1803	ILE	0	-0.022	-0.005	53.628	0.002	0.002	0.000	0.000	0.000	0.000
77	A	1804	ALA	0	0.001	0.003	55.327	0.002	0.002	0.000	0.000	0.000	0.000
78	A	1805	LEU	0	-0.056	-0.039	56.551	0.001	0.001	0.000	0.000	0.000	0.000
79	A	1806	MLY	1	0.882	0.942	54.890	0.042	0.042	0.000	0.000	0.000	0.000
80	A	1807	GLY	0	0.002	0.018	59.898	0.002	0.002	0.000	0.000	0.000	0.000
81	A	1808	GLY	0	0.026	0.017	61.729	0.001	0.001	0.000	0.000	0.000	0.000
82	A	1809	MLY	1	0.849	0.946	52.795	0.050	0.050	0.000	0.000	0.000	0.000
83	A	1810	MLY	1	0.944	0.966	57.189	0.045	0.045	0.000	0.000	0.000	0.000
84	A	1811	GLN	0	0.013	0.010	61.634	0.000	0.000	0.000	0.000	0.000	0.000
85	A	1812	LEU	0	0.035	0.021	61.332	0.001	0.001	0.000	0.000	0.000	0.000
86	A	1813	GLN	0	0.050	0.016	56.752	0.000	0.000	0.000	0.000	0.000	0.000
87	A	1814	MLY	1	0.899	0.961	62.481	0.035	0.035	0.000	0.000	0.000	0.000
88	A	1815	LEU	0	0.003	-0.003	65.388	0.001	0.001	0.000	0.000	0.000	0.000
89	A	1816	GLU	-1	-0.852	-0.937	61.550	-0.037	-0.037	0.000	0.000	0.000	0.000
90	A	1817	ALA	0	-0.102	-0.056	64.016	0.000	0.000	0.000	0.000	0.000	0.000
91	A	1818	ARG	1	0.912	0.938	65.533	0.029	0.029	0.000	0.000	0.000	0.000
92	A	1819	VAL	0	0.003	0.015	68.083	0.001	0.001	0.000	0.000	0.000	0.000
93	A	1820	ARG	1	1.028	1.018	62.156	0.038	0.038	0.000	0.000	0.000	0.000
94	A	1821	GLU	-1	-0.938	-0.946	67.846	-0.031	-0.031	0.000	0.000	0.000	0.000
95	A	1822	LEU	0	0.004	-0.003	69.640	0.001	0.001	0.000	0.000	0.000	0.000
96	A	1823	GLU	-1	-0.910	-0.963	68.739	-0.029	-0.029	0.000	0.000	0.000	0.000
97	A	1824	ASN	0	-0.081	-0.046	67.253	0.000	0.000	0.000	0.000	0.000	0.000
98	A	1825	GLU	-1	-0.913	-0.953	71.134	-0.027	-0.027	0.000	0.000	0.000	0.000
99	A	1826	LEU	0	-0.005	0.003	74.426	0.001	0.001	0.000	0.000	0.000	0.000
100	A	1827	GLU	-1	-0.796	-0.884	72.428	-0.026	-0.026	0.000	0.000	0.000	0.000
101	A	1828	ALA	0	0.012	0.004	73.990	0.001	0.001	0.000	0.000	0.000	0.000
102	A	1829	GLU	-1	-0.784	-0.860	75.667	-0.023	-0.023	0.000	0.000	0.000	0.000
103	A	1830	GLN	0	-0.031	-0.018	77.379	0.001	0.001	0.000	0.000	0.000	0.000
104	A	1831	MLY	1	0.792	0.889	71.168	0.027	0.027	0.000	0.000	0.000	0.000
105	A	1832	ARG	1	0.819	0.867	78.428	0.024	0.024	0.000	0.000	0.000	0.000
106	A	1833	ASN	0	0.011	0.024	81.045	0.001	0.001	0.000	0.000	0.000	0.000
107	A	1834	ALA	0	-0.011	-0.008	80.867	0.001	0.001	0.000	0.000	0.000	0.000
108	A	1835	GLU	-1	-0.863	-0.942	81.491	-0.019	-0.019	0.000	0.000	0.000	0.000
109	A	1836	SER	0	0.044	0.019	83.404	0.001	0.001	0.000	0.000	0.000	0.000
110	A	1837	VAL	0	0.032	0.016	86.090	0.001	0.001	0.000	0.000	0.000	0.000
111	A	1838	MLY	1	0.811	0.935	83.625	0.020	0.020	0.000	0.000	0.000	0.000
112	A	1839	GLY	0	-0.016	-0.040	87.179	0.001	0.001	0.000	0.000	0.000	0.000
113	A	1840	MET	0	0.044	0.021	88.643	0.000	0.000	0.000	0.000	0.000	0.000
114	A	1841	ARG	1	0.909	0.956	87.939	0.017	0.017	0.000	0.000	0.000	0.000
115	A	1842	MLY	1	0.887	0.960	90.238	0.016	0.016	0.000	0.000	0.000	0.000
116	A	1843	SER	0	0.010	0.003	92.655	0.000	0.000	0.000	0.000	0.000	0.000
117	A	1844	GLU	-1	-0.797	-0.907	94.714	-0.015	-0.015	0.000	0.000	0.000	0.000
118	A	1845	ARG	1	0.823	0.899	93.938	0.015	0.015	0.000	0.000	0.000	0.000
119	A	1846	ARG	1	0.848	0.893	98.361	0.014	0.014	0.000	0.000	0.000	0.000
120	A	1847	ILE	0	0.078	0.047	100.031	0.000	0.000	0.000	0.000	0.000	0.000
121	A	1848	MLY	1	0.918	0.973	100.377	0.013	0.013	0.000	0.000	0.000	0.000
122	A	1849	GLU	-1	-0.808	-0.867	101.336	-0.013	-0.013	0.000	0.000	0.000	0.000
123	A	1850	LEU	0	0.001	0.000	104.148	0.000	0.000	0.000	0.000	0.000	0.000
124	A	1851	THR	0	0.003	-0.017	105.979	0.000	0.000	0.000	0.000	0.000	0.000
125	A	1852	TYR	0	-0.048	-0.027	107.712	0.000	0.000	0.000	0.000	0.000	0.000
126	A	1853	GLN	0	-0.050	-0.035	105.124	0.000	0.000	0.000	0.000	0.000	0.000
127	A	1854	THR	0	-0.087	-0.047	110.044	0.000	0.000	0.000	0.000	0.000	0.000
128	A	1855	GLU	-1	-0.940	-0.973	111.999	-0.011	-0.011	0.000	0.000	0.000	0.000
129	A	209	ASP	-1	-0.820	-0.898	112.798	-0.010	-0.010	0.000	0.000	0.000	0.000
130	A	210	LEU	0	0.011	-0.005	112.444	0.000	0.000	0.000	0.000	0.000	0.000
131	A	211	GLU	-1	-0.831	-0.865	116.106	-0.010	-0.010	0.000	0.000	0.000	0.000
132	A	212	MLY	1	0.922	0.966	117.933	0.009	0.009	0.000	0.000	0.000	0.000
133	A	213	GLU	-1	-0.924	-0.945	117.484	-0.009	-0.009	0.000	0.000	0.000	0.000
134	A	214	ARG	1	0.717	0.812	119.628	0.010	0.010	0.000	0.000	0.000	0.000
135	A	215	ASP	-1	-0.780	-0.877	121.985	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	216	PHE	0	-0.052	-0.018	123.592	0.000	0.000	0.000	0.000	0.000	0.000
137	A	217	TYR	0	-0.075	-0.082	120.887	0.000	0.000	0.000	0.000	0.000	0.000
138	A	218	PHE	0	0.024	0.020	126.086	0.000	0.000	0.000	0.000	0.000	0.000
139	A	219	GLY	0	0.038	0.017	127.894	0.000	0.000	0.000	0.000	0.000	0.000
140	A	220	MLY	1	0.875	0.944	126.470	0.008	0.008	0.000	0.000	0.000	0.000
141	A	221	LEU	0	0.005	0.005	128.933	0.000	0.000	0.000	0.000	0.000	0.000
142	A	222	ARG	1	0.897	0.942	132.099	0.008	0.008	0.000	0.000	0.000	0.000
143	A	223	ASN	0	-0.010	-0.016	133.135	0.000	0.000	0.000	0.000	0.000	0.000
144	A	224	ILE	0	-0.016	-0.002	133.765	0.000	0.000	0.000	0.000	0.000	0.000
145	A	225	GLU	-1	-0.816	-0.883	136.170	-0.008	-0.008	0.000	0.000	0.000	0.000
146	A	226	LEU	0	-0.017	-0.012	137.198	0.000	0.000	0.000	0.000	0.000	0.000
147	A	227	ILE	0	0.047	0.028	138.689	0.000	0.000	0.000	0.000	0.000	0.000
148	A	228	CYS	0	-0.096	-0.058	140.279	0.000	0.000	0.000	0.000	0.000	0.000
149	A	229	GLN	0	-0.106	-0.060	140.016	0.000	0.000	0.000	0.000	0.000	0.000
150	A	230	GLU	-1	-0.987	-0.988	142.663	-0.007	-0.007	0.000	0.000	0.000	0.000
151	A	231	ASN	0	-0.079	-0.028	146.209	0.000	0.000	0.000	0.000	0.000	0.000
152	A	232	GLU	-1	-0.921	-0.961	148.035	-0.006	-0.006	0.000	0.000	0.000	0.000
153	A	233	GLY	0	-0.047	-0.016	151.702	0.000	0.000	0.000	0.000	0.000	0.000
154	A	234	GLU	-1	-0.920	-0.963	150.329	-0.006	-0.006	0.000	0.000	0.000	0.000
155	A	235	ASN	0	-0.038	-0.026	145.761	0.000	0.000	0.000	0.000	0.000	0.000
156	A	236	ASP	-1	-0.816	-0.911	146.483	-0.006	-0.006	0.000	0.000	0.000	0.000
157	A	237	PRO	0	-0.018	-0.017	146.040	0.000	0.000	0.000	0.000	0.000	0.000
158	A	238	VAL	0	-0.043	-0.019	141.221	0.000	0.000	0.000	0.000	0.000	0.000
159	A	239	LEU	0	0.028	0.013	141.770	0.000	0.000	0.000	0.000	0.000	0.000
160	A	240	GLN	0	-0.003	-0.004	142.405	0.000	0.000	0.000	0.000	0.000	0.000
161	A	241	ARG	1	0.807	0.898	136.064	0.008	0.008	0.000	0.000	0.000	0.000
162	A	242	ILE	0	0.004	-0.007	137.394	0.000	0.000	0.000	0.000	0.000	0.000
163	A	243	VAL	0	0.078	0.034	137.887	0.000	0.000	0.000	0.000	0.000	0.000
164	A	244	ASP	-1	-0.869	-0.923	138.809	-0.007	-0.007	0.000	0.000	0.000	0.000
165	A	245	ILE	0	-0.096	-0.049	133.037	0.000	0.000	0.000	0.000	0.000	0.000
166	A	246	LEU	0	-0.071	-0.017	133.875	0.000	0.000	0.000	0.000	0.000	0.000
167	A	247	TYR	0	-0.013	-0.001	134.717	0.000	0.000	0.000	0.000	0.000	0.000
168	A	248	ALA	0	-0.034	-0.010	129.511	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)