FMO DATABASE

FMODB ID: QV54Y

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1102111.366838
FMO2-HF: Nuclear repulsion	1031280.296396
FMO2-HF: Total energy	-70831.070443
FMO2-MP2: Total energy	-71039.099167

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.
-12.803	-4.77	3.962	-4.044	-7.949	-0.033

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 : -0.039 / q_NPA : -0.034

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	0.953	0.976	3.808	-0.283	1.051	-0.022	-0.550	-0.761	0.003
4	A	5	PRO	0	-0.005	-0.016	6.688	0.367	0.367	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.864	-0.942	9.163	-0.254	-0.254	0.000	0.000	0.000	0.000
6	A	7	GLU	-1	-0.833	-0.914	7.106	0.292	0.292	0.000	0.000	0.000	0.000
7	A	8	HIS	0	-0.060	-0.037	6.813	0.232	0.232	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.898	-0.944	9.172	0.187	0.187	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.903	-0.958	12.811	0.395	0.395	0.000	0.000	0.000	0.000
10	A	11	ILE	0	-0.018	-0.023	9.021	0.045	0.045	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.048	-0.019	12.431	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	13	ASN	0	-0.071	-0.037	14.705	-0.048	-0.048	0.000	0.000	0.000	0.000
13	A	14	MLY	1	0.892	0.964	13.501	-0.531	-0.531	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.023	-0.030	14.798	0.023	0.023	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.041	-0.011	18.820	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	17	ASP	-1	-0.889	-0.939	21.602	0.161	0.161	0.000	0.000	0.000	0.000
17	A	18	PRO	0	-0.029	-0.025	23.847	0.012	0.012	0.000	0.000	0.000	0.000
18	A	19	GLU	-1	-1.002	-1.001	26.634	0.131	0.131	0.000	0.000	0.000	0.000
19	A	20	LEU	0	0.006	0.030	19.945	0.000	0.000	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.049	0.023	23.657	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	22	GLN	0	0.054	0.014	22.542	0.027	0.027	0.000	0.000	0.000	0.000
22	A	23	SER	0	0.006	0.002	21.683	0.011	0.011	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.811	-0.913	19.073	0.350	0.350	0.000	0.000	0.000	0.000
24	A	25	ARG	1	0.870	0.948	17.675	-0.197	-0.197	0.000	0.000	0.000	0.000
25	A	26	THR	0	-0.076	-0.050	17.274	0.029	0.029	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.967	-0.979	15.763	0.566	0.566	0.000	0.000	0.000	0.000
27	A	28	ALA	0	0.047	0.034	13.391	0.138	0.138	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.006	-0.013	12.316	0.116	0.116	0.000	0.000	0.000	0.000
29	A	30	GLN	0	0.007	0.011	12.544	0.005	0.005	0.000	0.000	0.000	0.000
30	A	31	GLN	0	0.017	0.007	8.619	-0.010	-0.010	0.000	0.000	0.000	0.000
31	A	32	LEU	0	0.018	0.011	7.991	0.424	0.424	0.000	0.000	0.000	0.000
32	A	33	ARG	1	0.891	0.941	8.188	-0.488	-0.488	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.028	-0.017	7.062	-0.080	-0.080	0.000	0.000	0.000	0.000
34	A	35	ASN	0	0.045	0.024	2.694	0.514	1.616	0.651	-0.663	-1.090	-0.007
35	A	36	TYR	0	0.006	0.004	4.208	-0.308	-0.044	0.000	-0.040	-0.223	0.000
36	A	37	GLY	0	0.007	0.001	6.389	-0.302	-0.302	0.000	0.000	0.000	0.000
37	A	38	SER	0	-0.013	-0.001	2.569	-2.147	-0.907	1.234	-0.811	-1.663	-0.009
38	A	39	PHE	0	0.067	0.032	2.229	-3.123	-1.527	1.351	-0.740	-2.207	-0.002
39	A	40	VAL	0	-0.004	-0.004	3.505	-0.566	-0.567	0.015	0.136	-0.150	0.000
40	A	41	SER	0	-0.098	-0.043	5.338	-0.133	-0.133	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.864	-0.945	2.665	-9.303	-6.806	0.734	-1.373	-1.858	-0.018
42	A	43	TYR	0	0.014	0.011	5.391	0.106	0.107	-0.001	-0.003	0.003	0.000
43	A	44	ASN	0	-0.022	-0.014	7.543	0.099	0.099	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.896	-0.943	8.227	-0.516	-0.516	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.042	-0.018	8.593	0.116	0.116	0.000	0.000	0.000	0.000
46	A	47	THR	0	-0.005	-0.014	10.399	0.119	0.119	0.000	0.000	0.000	0.000
47	A	48	MLY	1	0.924	0.964	12.888	0.353	0.353	0.000	0.000	0.000	0.000
48	A	49	SER	0	-0.048	-0.031	13.272	0.079	0.079	0.000	0.000	0.000	0.000
49	A	50	HIS	0	-0.025	-0.019	14.385	0.034	0.034	0.000	0.000	0.000	0.000
50	A	1777	ALA	0	0.035	0.017	16.116	0.039	0.039	0.000	0.000	0.000	0.000
51	A	1778	HIS	0	-0.026	-0.025	18.026	0.043	0.043	0.000	0.000	0.000	0.000
52	A	1779	LEU	0	0.027	0.004	17.782	0.032	0.032	0.000	0.000	0.000	0.000
53	A	1780	GLU	-1	-0.863	-0.928	19.537	-0.215	-0.215	0.000	0.000	0.000	0.000
54	A	1781	ARG	1	0.883	0.959	19.609	0.228	0.228	0.000	0.000	0.000	0.000
55	A	1782	MET	0	-0.031	-0.006	21.661	0.014	0.014	0.000	0.000	0.000	0.000
56	A	1783	MLY	1	0.962	0.988	24.806	0.193	0.193	0.000	0.000	0.000	0.000
57	A	1784	MLY	1	0.860	0.909	26.514	0.150	0.150	0.000	0.000	0.000	0.000
58	A	1785	ASN	0	-0.002	0.005	28.076	0.016	0.016	0.000	0.000	0.000	0.000
59	A	1786	MET	0	0.021	0.016	26.039	0.010	0.010	0.000	0.000	0.000	0.000
60	A	1787	GLU	-1	-0.797	-0.894	29.516	-0.130	-0.130	0.000	0.000	0.000	0.000
61	A	1788	GLN	0	-0.010	-0.013	32.401	0.004	0.004	0.000	0.000	0.000	0.000
62	A	1789	THR	0	0.011	0.000	33.628	0.007	0.007	0.000	0.000	0.000	0.000
63	A	1790	ILE	0	0.003	0.014	32.997	0.006	0.006	0.000	0.000	0.000	0.000
64	A	1791	MLY	1	0.912	0.966	33.777	0.108	0.108	0.000	0.000	0.000	0.000
65	A	1792	ASP	-1	-0.863	-0.907	38.411	-0.072	-0.072	0.000	0.000	0.000	0.000
66	A	1793	LEU	0	0.007	-0.011	37.661	0.004	0.004	0.000	0.000	0.000	0.000
67	A	1794	GLN	0	0.005	-0.006	39.075	0.005	0.005	0.000	0.000	0.000	0.000
68	A	1795	HIS	1	0.902	0.961	42.308	0.078	0.078	0.000	0.000	0.000	0.000
69	A	1796	ARG	1	0.921	0.952	42.644	0.073	0.073	0.000	0.000	0.000	0.000
70	A	1797	LEU	0	-0.016	-0.003	44.409	0.003	0.003	0.000	0.000	0.000	0.000
71	A	1798	ASP	-1	-0.857	-0.927	46.511	-0.056	-0.056	0.000	0.000	0.000	0.000
72	A	1799	GLU	-1	-0.878	-0.946	48.636	-0.048	-0.048	0.000	0.000	0.000	0.000
73	A	1800	ALA	0	-0.005	-0.002	49.742	0.003	0.003	0.000	0.000	0.000	0.000
74	A	1801	GLU	-1	-0.918	-0.976	49.179	-0.060	-0.060	0.000	0.000	0.000	0.000
75	A	1802	GLN	0	-0.063	-0.039	52.214	0.005	0.005	0.000	0.000	0.000	0.000
76	A	1803	ILE	0	-0.036	-0.015	53.560	0.003	0.003	0.000	0.000	0.000	0.000
77	A	1804	ALA	0	-0.020	-0.016	55.243	0.002	0.002	0.000	0.000	0.000	0.000
78	A	1805	LEU	0	-0.058	-0.032	56.183	0.002	0.002	0.000	0.000	0.000	0.000
79	A	1806	MLY	1	0.929	0.960	55.538	0.047	0.047	0.000	0.000	0.000	0.000
80	A	1807	GLY	0	-0.012	0.014	60.019	0.002	0.002	0.000	0.000	0.000	0.000
81	A	1808	GLY	0	0.000	0.011	61.933	0.001	0.001	0.000	0.000	0.000	0.000
82	A	1809	MLY	1	0.907	0.968	52.590	0.054	0.054	0.000	0.000	0.000	0.000
83	A	1810	MLY	1	0.938	0.949	56.649	0.049	0.049	0.000	0.000	0.000	0.000
84	A	1811	GLN	0	0.018	0.002	61.570	0.000	0.000	0.000	0.000	0.000	0.000
85	A	1812	LEU	0	0.064	0.039	61.424	0.001	0.001	0.000	0.000	0.000	0.000
86	A	1813	GLN	0	0.050	0.020	56.740	0.000	0.000	0.000	0.000	0.000	0.000
87	A	1814	MLY	1	0.906	0.963	62.443	0.038	0.038	0.000	0.000	0.000	0.000
88	A	1815	LEU	0	0.017	0.003	65.082	0.001	0.001	0.000	0.000	0.000	0.000
89	A	1816	GLU	-1	-0.866	-0.925	61.629	-0.041	-0.041	0.000	0.000	0.000	0.000
90	A	1817	ALA	0	-0.111	-0.062	63.995	0.000	0.000	0.000	0.000	0.000	0.000
91	A	1818	ARG	1	0.957	0.982	65.463	0.032	0.032	0.000	0.000	0.000	0.000
92	A	1819	VAL	0	-0.016	-0.008	68.042	0.001	0.001	0.000	0.000	0.000	0.000
93	A	1820	ARG	1	1.031	1.025	62.202	0.042	0.042	0.000	0.000	0.000	0.000
94	A	1821	GLU	-1	-0.952	-0.968	67.831	-0.034	-0.034	0.000	0.000	0.000	0.000
95	A	1822	LEU	0	-0.003	-0.012	69.608	0.001	0.001	0.000	0.000	0.000	0.000
96	A	1823	GLU	-1	-0.898	-0.958	68.776	-0.033	-0.033	0.000	0.000	0.000	0.000
97	A	1824	ASN	0	-0.078	-0.040	67.334	0.000	0.000	0.000	0.000	0.000	0.000
98	A	1825	GLU	-1	-0.914	-0.957	71.218	-0.029	-0.029	0.000	0.000	0.000	0.000
99	A	1826	LEU	0	-0.017	-0.005	74.376	0.001	0.001	0.000	0.000	0.000	0.000
100	A	1827	GLU	-1	-0.869	-0.946	71.697	-0.031	-0.031	0.000	0.000	0.000	0.000
101	A	1828	ALA	0	-0.015	-0.015	74.402	0.001	0.001	0.000	0.000	0.000	0.000
102	A	1829	GLU	-1	-0.824	-0.907	75.936	-0.025	-0.025	0.000	0.000	0.000	0.000
103	A	1830	GLN	0	-0.016	-0.009	77.328	0.001	0.001	0.000	0.000	0.000	0.000
104	A	1831	MLY	1	0.867	0.953	71.683	0.031	0.031	0.000	0.000	0.000	0.000
105	A	1832	ARG	1	0.850	0.905	78.822	0.026	0.026	0.000	0.000	0.000	0.000
106	A	1833	ASN	0	-0.024	-0.003	81.287	0.001	0.001	0.000	0.000	0.000	0.000
107	A	1834	ALA	0	0.002	-0.008	81.191	0.001	0.001	0.000	0.000	0.000	0.000
108	A	1835	GLU	-1	-0.912	-0.960	81.929	-0.022	-0.022	0.000	0.000	0.000	0.000
109	A	1836	SER	0	0.004	0.009	83.874	0.001	0.001	0.000	0.000	0.000	0.000
110	A	1837	VAL	0	0.064	0.037	86.236	0.001	0.001	0.000	0.000	0.000	0.000
111	A	1838	MLY	1	0.858	0.950	84.546	0.022	0.022	0.000	0.000	0.000	0.000
112	A	1839	GLY	0	-0.064	-0.060	87.474	0.001	0.001	0.000	0.000	0.000	0.000
113	A	1840	MET	0	0.074	0.039	89.151	0.000	0.000	0.000	0.000	0.000	0.000
114	A	1841	ARG	1	0.954	0.980	88.566	0.020	0.020	0.000	0.000	0.000	0.000
115	A	1842	MLY	1	0.886	0.956	90.790	0.019	0.019	0.000	0.000	0.000	0.000
116	A	1843	SER	0	-0.033	-0.030	93.149	0.000	0.000	0.000	0.000	0.000	0.000
117	A	1844	GLU	-1	-0.801	-0.883	95.206	-0.017	-0.017	0.000	0.000	0.000	0.000
118	A	1845	ARG	1	0.822	0.887	94.204	0.018	0.018	0.000	0.000	0.000	0.000
119	A	1846	ARG	1	0.884	0.926	98.973	0.016	0.016	0.000	0.000	0.000	0.000
120	A	1847	ILE	0	0.123	0.071	100.691	0.000	0.000	0.000	0.000	0.000	0.000
121	A	1848	MLY	1	0.912	0.977	100.580	0.016	0.016	0.000	0.000	0.000	0.000
122	A	1849	GLU	-1	-0.810	-0.870	101.784	-0.015	-0.015	0.000	0.000	0.000	0.000
123	A	1850	LEU	0	-0.043	-0.026	104.253	0.000	0.000	0.000	0.000	0.000	0.000
124	A	1851	THR	0	-0.010	-0.043	106.330	0.000	0.000	0.000	0.000	0.000	0.000
125	A	1852	TYR	0	-0.056	-0.024	107.907	0.000	0.000	0.000	0.000	0.000	0.000
126	A	1853	GLN	0	0.018	-0.002	105.496	0.000	0.000	0.000	0.000	0.000	0.000
127	A	1854	THR	0	-0.086	-0.043	110.272	0.000	0.000	0.000	0.000	0.000	0.000
128	A	1855	GLU	-1	-0.941	-0.980	112.438	-0.013	-0.013	0.000	0.000	0.000	0.000
129	A	209	ASP	-1	-0.851	-0.910	113.059	-0.012	-0.012	0.000	0.000	0.000	0.000
130	A	210	LEU	0	-0.002	-0.001	112.638	0.000	0.000	0.000	0.000	0.000	0.000
131	A	211	GLU	-1	-0.862	-0.900	116.265	-0.011	-0.011	0.000	0.000	0.000	0.000
132	A	212	MLY	1	0.972	0.999	118.172	0.011	0.011	0.000	0.000	0.000	0.000
133	A	213	GLU	-1	-0.869	-0.920	117.524	-0.011	-0.011	0.000	0.000	0.000	0.000
134	A	214	ARG	1	0.748	0.847	119.934	0.011	0.011	0.000	0.000	0.000	0.000
135	A	215	ASP	-1	-0.799	-0.893	122.335	-0.011	-0.011	0.000	0.000	0.000	0.000
136	A	216	PHE	0	-0.112	-0.049	123.667	0.000	0.000	0.000	0.000	0.000	0.000
137	A	217	TYR	0	-0.101	-0.097	121.044	0.000	0.000	0.000	0.000	0.000	0.000
138	A	218	PHE	0	0.037	0.016	126.421	0.000	0.000	0.000	0.000	0.000	0.000
139	A	219	GLY	0	0.051	0.038	128.121	0.000	0.000	0.000	0.000	0.000	0.000
140	A	220	MLY	1	0.900	0.955	126.873	0.010	0.010	0.000	0.000	0.000	0.000
141	A	221	LEU	0	0.002	0.007	129.278	0.000	0.000	0.000	0.000	0.000	0.000
142	A	222	ARG	1	0.903	0.941	132.434	0.009	0.009	0.000	0.000	0.000	0.000
143	A	223	ASN	0	-0.042	-0.033	133.303	0.000	0.000	0.000	0.000	0.000	0.000
144	A	224	ILE	0	-0.007	-0.006	134.158	0.000	0.000	0.000	0.000	0.000	0.000
145	A	225	GLU	-1	-0.791	-0.877	136.608	-0.009	-0.009	0.000	0.000	0.000	0.000
146	A	226	LEU	0	-0.020	-0.012	137.799	0.000	0.000	0.000	0.000	0.000	0.000
147	A	227	ILE	0	0.020	0.009	139.188	0.000	0.000	0.000	0.000	0.000	0.000
148	A	228	CYS	0	-0.092	-0.046	140.672	0.000	0.000	0.000	0.000	0.000	0.000
149	A	229	GLN	0	-0.099	-0.051	140.414	0.000	0.000	0.000	0.000	0.000	0.000
150	A	230	GLU	-1	-1.027	-0.999	143.352	-0.008	-0.008	0.000	0.000	0.000	0.000
151	A	231	ASN	0	-0.050	-0.026	146.487	0.000	0.000	0.000	0.000	0.000	0.000
152	A	232	GLU	-1	-0.948	-0.975	148.533	-0.007	-0.007	0.000	0.000	0.000	0.000
153	A	233	GLY	0	-0.028	0.000	151.810	0.000	0.000	0.000	0.000	0.000	0.000
154	A	234	GLU	-1	-0.930	-0.975	150.747	-0.007	-0.007	0.000	0.000	0.000	0.000
155	A	235	ASN	0	-0.035	-0.019	146.181	0.000	0.000	0.000	0.000	0.000	0.000
156	A	236	ASP	-1	-0.830	-0.916	147.214	-0.007	-0.007	0.000	0.000	0.000	0.000
157	A	237	PRO	0	0.009	-0.014	146.400	0.000	0.000	0.000	0.000	0.000	0.000
158	A	238	VAL	0	-0.041	-0.006	141.651	0.000	0.000	0.000	0.000	0.000	0.000
159	A	239	LEU	0	0.055	0.014	142.159	0.000	0.000	0.000	0.000	0.000	0.000
160	A	240	GLN	0	-0.021	-0.001	142.901	0.000	0.000	0.000	0.000	0.000	0.000
161	A	241	ARG	1	0.909	0.963	135.900	0.008	0.008	0.000	0.000	0.000	0.000
162	A	242	ILE	0	-0.024	-0.033	137.632	0.000	0.000	0.000	0.000	0.000	0.000
163	A	243	VAL	0	0.062	0.021	138.189	0.000	0.000	0.000	0.000	0.000	0.000
164	A	244	ASP	-1	-0.893	-0.940	139.337	-0.008	-0.008	0.000	0.000	0.000	0.000
165	A	245	ILE	0	-0.137	-0.068	133.559	0.000	0.000	0.000	0.000	0.000	0.000
166	A	246	LEU	0	-0.050	0.009	134.465	0.000	0.000	0.000	0.000	0.000	0.000
167	A	247	TYR	0	-0.023	-0.022	135.043	0.000	0.000	0.000	0.000	0.000	0.000
168	A	248	ALA	0	-0.044	-0.012	130.015	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)