FMO DATABASE

FMODB ID: LNR69

Calculation Name: 4XA6-D-Xray372

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 4XA6

Chain ID: D

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	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	105
LigandCharge	MLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-590066.036727
FMO2-HF: Nuclear repulsion	545652.576137
FMO2-HF: Total energy	-44413.46059
FMO2-MP2: Total energy	-44544.252038

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(D:1791:MLY)

Summations of interaction energy for fragment #1(D:1791:MLY)

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.
20.224	23.481	0.042	-1.294	-2.005	0

Interaction energy analysis for fragmet #1(D:1791:MLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.004 / q_NPA : 0.981

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].
3	D	1793	LEU	0	-0.043	-0.040	2.870	3.443	5.904	0.034	-1.049	-1.446
4	D	1794	GLN	0	-0.051	-0.015	3.692	2.262	3.058	0.008	-0.245	-0.559
5	D	1795	HIS	0	0.074	0.030	4.815	5.858	5.858	0.000	0.000	0.000
6	D	1796	ARG	1	0.972	0.992	7.303	26.619	26.619	0.000	0.000	0.000
7	D	1797	LEU	0	-0.012	0.004	8.195	2.366	2.366	0.000	0.000	0.000
8	D	1798	ASP	-1	-0.814	-0.904	8.763	-25.220	-25.220	0.000	0.000	0.000
9	D	1799	GLU	-1	-0.974	-0.988	11.281	-18.120	-18.120	0.000	0.000	0.000
10	D	1800	ALA	0	-0.035	-0.025	12.682	1.631	1.631	0.000	0.000	0.000
11	D	1801	GLU	-1	-0.904	-0.954	13.347	-16.922	-16.922	0.000	0.000	0.000
12	D	1802	GLN	0	-0.002	-0.010	14.550	1.638	1.638	0.000	0.000	0.000
13	D	1803	ILE	0	-0.122	-0.067	16.306	1.099	1.099	0.000	0.000	0.000
14	D	1804	ALA	0	-0.002	0.008	18.612	0.749	0.749	0.000	0.000	0.000
15	D	1805	LEU	0	-0.005	0.001	19.783	0.667	0.667	0.000	0.000	0.000
16	D	1806	MLY	1	0.885	0.957	18.354	15.266	15.266	0.000	0.000	0.000
17	D	1807	GLY	0	-0.004	0.005	23.369	0.524	0.524	0.000	0.000	0.000
18	D	1808	GLY	0	0.034	0.017	24.341	-0.289	-0.289	0.000	0.000	0.000
19	D	1809	MLY	1	0.993	0.986	19.746	12.714	12.714	0.000	0.000	0.000
20	D	1810	MLY	1	0.963	0.966	26.131	10.821	10.821	0.000	0.000	0.000
21	D	1811	GLN	0	-0.019	-0.012	28.680	0.064	0.064	0.000	0.000	0.000
22	D	1812	LEU	0	0.026	0.019	29.144	0.273	0.273	0.000	0.000	0.000
23	D	1813	GLN	0	0.079	0.044	27.449	0.350	0.350	0.000	0.000	0.000
24	D	1814	MLY	1	0.946	0.977	32.217	8.739	8.739	0.000	0.000	0.000
25	D	1815	LEU	0	-0.003	0.001	34.137	0.270	0.270	0.000	0.000	0.000
26	D	1816	GLU	-1	-0.844	-0.929	31.948	-9.105	-9.105	0.000	0.000	0.000
27	D	1817	ALA	0	-0.079	-0.019	36.241	0.155	0.155	0.000	0.000	0.000
28	D	1818	ARG	1	0.852	0.902	38.144	7.151	7.151	0.000	0.000	0.000
29	D	1819	VAL	0	-0.013	-0.002	39.597	0.188	0.188	0.000	0.000	0.000
30	D	1820	ARG	1	0.968	0.974	35.386	8.340	8.340	0.000	0.000	0.000
31	D	1821	GLU	-1	-0.889	-0.926	42.266	-6.869	-6.869	0.000	0.000	0.000
32	D	1822	LEU	0	0.005	0.008	44.086	0.157	0.157	0.000	0.000	0.000
33	D	1823	GLU	-1	-0.890	-0.960	43.356	-6.818	-6.818	0.000	0.000	0.000
34	D	1824	ASN	0	-0.067	-0.042	46.112	0.045	0.045	0.000	0.000	0.000
35	D	1825	GLU	-1	-0.804	-0.866	48.080	-5.765	-5.765	0.000	0.000	0.000
36	D	1826	LEU	0	0.004	0.003	49.440	0.149	0.149	0.000	0.000	0.000
37	D	1827	GLU	-1	-0.855	-0.917	50.885	-5.766	-5.766	0.000	0.000	0.000
38	D	1828	ALA	0	0.042	0.018	52.597	0.139	0.139	0.000	0.000	0.000
39	D	1829	GLU	-1	-0.829	-0.910	54.553	-5.281	-5.281	0.000	0.000	0.000
40	D	1830	GLN	0	-0.037	-0.028	53.042	0.177	0.177	0.000	0.000	0.000
41	D	1831	MLY	1	0.814	0.910	53.718	5.841	5.841	0.000	0.000	0.000
42	D	1832	ARG	1	0.767	0.848	54.914	5.689	5.689	0.000	0.000	0.000
43	D	1833	ASN	0	-0.048	-0.032	59.972	0.174	0.174	0.000	0.000	0.000
44	D	1834	ALA	0	-0.001	0.009	61.587	0.103	0.103	0.000	0.000	0.000
45	D	1835	GLU	-1	-0.813	-0.897	63.350	-4.751	-4.751	0.000	0.000	0.000
46	D	1836	SER	0	0.025	0.024	65.097	0.092	0.092	0.000	0.000	0.000
47	D	1837	VAL	0	-0.019	-0.004	66.173	0.096	0.096	0.000	0.000	0.000
48	D	1838	MLY	1	0.812	0.886	64.848	4.874	4.874	0.000	0.000	0.000
49	D	1839	GLY	0	0.012	0.004	69.560	0.076	0.076	0.000	0.000	0.000
50	D	1840	MET	0	0.024	0.024	71.008	0.066	0.066	0.000	0.000	0.000
51	D	1841	ARG	1	0.912	0.939	72.552	4.289	4.289	0.000	0.000	0.000
52	D	1842	MLY	1	0.981	1.004	73.946	4.294	4.294	0.000	0.000	0.000
53	D	1843	SER	0	-0.048	-0.042	75.500	0.069	0.069	0.000	0.000	0.000
54	D	1844	GLU	-1	-0.784	-0.877	77.174	-4.002	-4.002	0.000	0.000	0.000
55	D	1845	ARG	1	0.825	0.899	77.423	4.102	4.102	0.000	0.000	0.000
56	D	1846	ARG	1	0.911	0.954	80.605	3.803	3.803	0.000	0.000	0.000
57	D	1847	ILE	0	0.013	0.000	79.520	0.044	0.044	0.000	0.000	0.000
58	D	1848	MLY	1	0.934	0.966	81.189	3.871	3.871	0.000	0.000	0.000
59	D	1849	GLU	-1	-0.864	-0.917	84.037	-3.737	-3.737	0.000	0.000	0.000
60	D	1850	LEU	0	-0.034	-0.014	84.321	0.042	0.042	0.000	0.000	0.000
61	D	1851	THR	0	0.026	0.013	87.319	0.029	0.029	0.000	0.000	0.000
62	D	1852	TYR	0	-0.029	-0.018	89.134	0.028	0.028	0.000	0.000	0.000
63	D	1853	GLN	0	-0.009	-0.018	89.093	0.026	0.026	0.000	0.000	0.000
64	D	1854	THR	0	-0.025	-0.020	91.494	0.023	0.023	0.000	0.000	0.000
65	D	1855	GLU	-1	-0.908	-0.950	92.556	-3.411	-3.411	0.000	0.000	0.000
66	D	209	ASP	-1	-0.833	-0.917	95.369	-3.236	-3.236	0.000	0.000	0.000
67	D	210	LEU	0	-0.018	-0.007	94.890	0.038	0.038	0.000	0.000	0.000
68	D	211	GLU	-1	-0.878	-0.923	96.991	-3.249	-3.249	0.000	0.000	0.000
69	D	212	MLY	1	0.928	0.978	99.546	3.213	3.213	0.000	0.000	0.000
70	D	213	GLU	-1	-0.918	-0.948	101.230	-3.107	-3.107	0.000	0.000	0.000
71	D	214	ARG	1	0.723	0.822	99.399	3.224	3.224	0.000	0.000	0.000
72	D	215	ASP	-1	-0.786	-0.867	103.400	-3.077	-3.077	0.000	0.000	0.000
73	D	216	PHE	0	0.008	0.009	105.715	0.046	0.046	0.000	0.000	0.000
74	D	217	TYR	0	-0.071	-0.068	104.424	0.059	0.059	0.000	0.000	0.000
75	D	218	PHE	0	0.015	0.009	107.580	0.032	0.032	0.000	0.000	0.000
76	D	219	GLY	0	0.034	0.014	109.468	0.027	0.027	0.000	0.000	0.000
77	D	220	MLY	1	0.824	0.923	109.160	2.947	2.947	0.000	0.000	0.000
78	D	221	LEU	0	0.008	0.000	110.396	0.027	0.027	0.000	0.000	0.000
79	D	222	ARG	1	0.814	0.889	111.923	2.864	2.864	0.000	0.000	0.000
80	D	223	ASN	0	-0.004	0.002	115.304	0.024	0.024	0.000	0.000	0.000
81	D	224	ILE	0	-0.026	-0.013	116.350	0.024	0.024	0.000	0.000	0.000
82	D	225	GLU	-1	-0.772	-0.858	117.284	-2.723	-2.723	0.000	0.000	0.000
83	D	226	LEU	0	0.011	0.017	118.962	0.016	0.016	0.000	0.000	0.000
84	D	227	ILE	0	0.034	0.021	121.650	0.021	0.021	0.000	0.000	0.000
85	D	228	CYS	0	-0.097	-0.053	121.968	0.024	0.024	0.000	0.000	0.000
86	D	229	GLN	0	-0.019	-0.014	122.606	-0.017	-0.017	0.000	0.000	0.000
87	D	230	GLU	-1	-1.011	-0.984	125.163	-2.568	-2.568	0.000	0.000	0.000
88	D	231	ASN	0	-0.127	-0.079	127.763	0.018	0.018	0.000	0.000	0.000
89	D	232	GLU	-1	-0.830	-0.926	126.803	-2.526	-2.526	0.000	0.000	0.000
90	D	233	GLY	0	-0.010	-0.006	129.355	-0.006	-0.006	0.000	0.000	0.000
91	D	234	GLU	-1	-0.923	-0.955	132.264	-2.428	-2.428	0.000	0.000	0.000
92	D	235	ASN	0	-0.072	-0.032	130.405	0.011	0.011	0.000	0.000	0.000
93	D	236	ASP	-1	-0.763	-0.869	129.169	-2.503	-2.503	0.000	0.000	0.000
94	D	237	PRO	0	-0.016	-0.013	128.657	-0.023	-0.023	0.000	0.000	0.000
95	D	238	VAL	0	-0.122	-0.068	125.636	-0.026	-0.026	0.000	0.000	0.000
96	D	239	LEU	0	0.049	0.012	124.861	-0.029	-0.029	0.000	0.000	0.000
97	D	240	GLN	0	-0.018	-0.002	123.768	-0.006	-0.006	0.000	0.000	0.000
98	D	241	ARG	1	0.905	0.950	121.944	2.573	2.573	0.000	0.000	0.000
99	D	242	ILE	0	-0.044	-0.016	119.599	-0.031	-0.031	0.000	0.000	0.000
100	D	243	VAL	0	0.048	0.017	119.123	-0.032	-0.032	0.000	0.000	0.000
101	D	244	ASP	-1	-0.867	-0.940	118.952	-2.678	-2.678	0.000	0.000	0.000
102	D	245	ILE	0	-0.095	-0.040	114.678	-0.031	-0.031	0.000	0.000	0.000
103	D	246	LEU	0	-0.054	-0.015	114.667	-0.037	-0.037	0.000	0.000	0.000
104	D	247	TYR	0	-0.088	-0.050	114.720	-0.036	-0.036	0.000	0.000	0.000
105	D	248	ALA	0	-0.062	-0.022	111.664	-0.024	-0.024	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:1791:MLY)