FMO DATABASE

FMODB ID: JQKR9

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:

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	105
LigandResidueName
LigandFragmentNumber	0
LigandCharge	MLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-589348.656769
FMO2-HF: Nuclear repulsion	544937.188066
FMO2-HF: Total energy	-44411.468703
FMO2-MP2: Total energy	-44542.416928

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.
11.55	15.043	0.161	-1.213	-2.44	-0.001

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 : 0.990 / q_NPA : 0.974

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	D	1793	LEU	0	-0.070	-0.058	2.793	1.127	3.327	0.058	-0.912	-1.346	0.000
4	D	1794	GLN	0	-0.050	-0.006	3.014	1.291	2.309	0.104	-0.277	-0.844	-0.001
5	D	1795	HIS	0	0.085	0.028	4.437	5.965	6.240	-0.001	-0.024	-0.250	0.000
6	D	1796	ARG	1	0.969	0.997	6.942	24.806	24.806	0.000	0.000	0.000	0.000
7	D	1797	LEU	0	-0.033	-0.012	7.790	2.441	2.441	0.000	0.000	0.000	0.000
8	D	1798	ASP	-1	-0.809	-0.893	8.710	-25.128	-25.128	0.000	0.000	0.000	0.000
9	D	1799	GLU	-1	-0.948	-0.967	10.942	-17.838	-17.838	0.000	0.000	0.000	0.000
10	D	1800	ALA	0	-0.042	-0.038	12.396	1.686	1.686	0.000	0.000	0.000	0.000
11	D	1801	GLU	-1	-0.908	-0.958	12.467	-17.933	-17.933	0.000	0.000	0.000	0.000
12	D	1802	GLN	0	-0.012	-0.016	15.198	0.864	0.864	0.000	0.000	0.000	0.000
13	D	1803	ILE	0	-0.136	-0.071	16.786	1.171	1.171	0.000	0.000	0.000	0.000
14	D	1804	ALA	0	-0.009	0.000	18.115	0.818	0.818	0.000	0.000	0.000	0.000
15	D	1805	LEU	0	-0.004	0.006	19.567	0.648	0.648	0.000	0.000	0.000	0.000
16	D	1806	MLY	1	0.889	0.959	18.855	14.575	14.575	0.000	0.000	0.000	0.000
17	D	1807	GLY	0	0.020	0.021	23.111	0.573	0.573	0.000	0.000	0.000	0.000
18	D	1808	GLY	0	0.020	0.012	23.780	-0.297	-0.297	0.000	0.000	0.000	0.000
19	D	1809	MLY	1	0.948	0.970	20.548	12.142	12.142	0.000	0.000	0.000	0.000
20	D	1810	MLY	1	1.008	0.993	26.138	10.516	10.516	0.000	0.000	0.000	0.000
21	D	1811	GLN	0	-0.003	-0.006	28.665	0.097	0.097	0.000	0.000	0.000	0.000
22	D	1812	LEU	0	0.049	0.012	28.826	0.225	0.225	0.000	0.000	0.000	0.000
23	D	1813	GLN	0	0.062	0.023	27.152	0.430	0.430	0.000	0.000	0.000	0.000
24	D	1814	MLY	1	0.972	0.989	31.975	8.628	8.628	0.000	0.000	0.000	0.000
25	D	1815	LEU	0	-0.004	0.006	34.467	0.261	0.261	0.000	0.000	0.000	0.000
26	D	1816	GLU	-1	-0.912	-0.948	32.589	-8.789	-8.789	0.000	0.000	0.000	0.000
27	D	1817	ALA	0	-0.071	-0.029	36.206	0.095	0.095	0.000	0.000	0.000	0.000
28	D	1818	ARG	1	0.900	0.944	38.095	7.113	7.113	0.000	0.000	0.000	0.000
29	D	1819	VAL	0	0.002	0.004	39.592	0.182	0.182	0.000	0.000	0.000	0.000
30	D	1820	ARG	1	1.005	1.013	35.950	8.169	8.169	0.000	0.000	0.000	0.000
31	D	1821	GLU	-1	-0.928	-0.971	41.873	-6.928	-6.928	0.000	0.000	0.000	0.000
32	D	1822	LEU	0	-0.008	0.000	43.801	0.158	0.158	0.000	0.000	0.000	0.000
33	D	1823	GLU	-1	-0.894	-0.956	43.370	-6.763	-6.763	0.000	0.000	0.000	0.000
34	D	1824	ASN	0	-0.077	-0.053	45.881	0.037	0.037	0.000	0.000	0.000	0.000
35	D	1825	GLU	-1	-0.943	-0.956	47.719	-5.915	-5.915	0.000	0.000	0.000	0.000
36	D	1826	LEU	0	-0.017	-0.009	49.662	0.156	0.156	0.000	0.000	0.000	0.000
37	D	1827	GLU	-1	-0.865	-0.938	50.161	-5.942	-5.942	0.000	0.000	0.000	0.000
38	D	1828	ALA	0	-0.041	-0.028	52.327	0.142	0.142	0.000	0.000	0.000	0.000
39	D	1829	GLU	-1	-0.884	-0.954	54.208	-5.319	-5.319	0.000	0.000	0.000	0.000
40	D	1830	GLN	0	-0.008	-0.011	53.314	0.104	0.104	0.000	0.000	0.000	0.000
41	D	1831	MLY	1	0.852	0.928	53.623	5.788	5.788	0.000	0.000	0.000	0.000
42	D	1832	ARG	1	0.926	0.986	55.578	5.555	5.555	0.000	0.000	0.000	0.000
43	D	1833	ASN	0	0.000	-0.010	59.798	0.142	0.142	0.000	0.000	0.000	0.000
44	D	1834	ALA	0	-0.031	0.004	61.319	0.091	0.091	0.000	0.000	0.000	0.000
45	D	1835	GLU	-1	-0.902	-0.978	62.596	-4.920	-4.920	0.000	0.000	0.000	0.000
46	D	1836	SER	0	-0.019	0.003	64.899	0.083	0.083	0.000	0.000	0.000	0.000
47	D	1837	VAL	0	-0.010	0.001	66.226	0.077	0.077	0.000	0.000	0.000	0.000
48	D	1838	MLY	1	0.932	0.950	65.550	4.771	4.771	0.000	0.000	0.000	0.000
49	D	1839	GLY	0	0.001	0.005	69.441	0.069	0.069	0.000	0.000	0.000	0.000
50	D	1840	MET	0	0.034	0.042	71.150	0.030	0.030	0.000	0.000	0.000	0.000
51	D	1841	ARG	1	0.966	0.998	72.425	4.294	4.294	0.000	0.000	0.000	0.000
52	D	1842	MLY	1	1.013	1.013	73.600	4.262	4.262	0.000	0.000	0.000	0.000
53	D	1843	SER	0	-0.043	-0.055	75.614	0.061	0.061	0.000	0.000	0.000	0.000
54	D	1844	GLU	-1	-0.836	-0.928	77.218	-3.951	-3.951	0.000	0.000	0.000	0.000
55	D	1845	ARG	1	0.902	0.949	77.538	4.072	4.072	0.000	0.000	0.000	0.000
56	D	1846	ARG	1	0.987	1.000	80.125	3.839	3.839	0.000	0.000	0.000	0.000
57	D	1847	ILE	0	-0.016	-0.003	79.632	0.038	0.038	0.000	0.000	0.000	0.000
58	D	1848	MLY	1	0.927	0.948	82.254	3.821	3.821	0.000	0.000	0.000	0.000
59	D	1849	GLU	-1	-0.918	-0.962	83.966	-3.729	-3.729	0.000	0.000	0.000	0.000
60	D	1850	LEU	0	-0.011	-0.005	84.745	0.041	0.041	0.000	0.000	0.000	0.000
61	D	1851	THR	0	-0.036	-0.008	86.936	0.026	0.026	0.000	0.000	0.000	0.000
62	D	1852	TYR	0	0.043	0.038	88.861	0.024	0.024	0.000	0.000	0.000	0.000
63	D	1853	GLN	0	-0.001	0.002	89.577	0.049	0.049	0.000	0.000	0.000	0.000
64	D	1854	THR	0	0.002	-0.013	90.580	0.024	0.024	0.000	0.000	0.000	0.000
65	D	1855	GLU	-1	-0.943	-0.962	92.555	-3.406	-3.406	0.000	0.000	0.000	0.000
66	D	209	ASP	-1	-0.970	-0.994	94.963	-3.248	-3.248	0.000	0.000	0.000	0.000
67	D	210	LEU	0	-0.056	-0.034	95.078	0.035	0.035	0.000	0.000	0.000	0.000
68	D	211	GLU	-1	-0.952	-0.966	97.204	-3.233	-3.233	0.000	0.000	0.000	0.000
69	D	212	MLY	1	1.024	1.027	99.409	3.180	3.180	0.000	0.000	0.000	0.000
70	D	213	GLU	-1	-0.941	-0.971	100.552	-3.134	-3.134	0.000	0.000	0.000	0.000
71	D	214	ARG	1	0.858	0.932	100.188	3.210	3.210	0.000	0.000	0.000	0.000
72	D	215	ASP	-1	-0.864	-0.957	102.592	-3.081	-3.081	0.000	0.000	0.000	0.000
73	D	216	PHE	0	-0.069	-0.028	105.275	0.045	0.045	0.000	0.000	0.000	0.000
74	D	217	TYR	0	-0.066	-0.039	104.637	0.051	0.051	0.000	0.000	0.000	0.000
75	D	218	PHE	0	0.046	0.017	107.274	0.035	0.035	0.000	0.000	0.000	0.000
76	D	219	GLY	0	0.049	0.029	109.176	0.026	0.026	0.000	0.000	0.000	0.000
77	D	220	MLY	1	0.917	0.952	110.397	2.921	2.921	0.000	0.000	0.000	0.000
78	D	221	LEU	0	-0.007	-0.023	110.204	0.026	0.026	0.000	0.000	0.000	0.000
79	D	222	ARG	1	0.932	0.971	110.736	2.876	2.876	0.000	0.000	0.000	0.000
80	D	223	ASN	0	-0.011	0.008	115.283	0.023	0.023	0.000	0.000	0.000	0.000
81	D	224	ILE	0	-0.001	-0.008	115.992	0.023	0.023	0.000	0.000	0.000	0.000
82	D	225	GLU	-1	-0.839	-0.867	117.282	-2.694	-2.694	0.000	0.000	0.000	0.000
83	D	226	LEU	0	-0.012	-0.003	118.541	0.016	0.016	0.000	0.000	0.000	0.000
84	D	227	ILE	0	-0.001	-0.005	121.267	0.022	0.022	0.000	0.000	0.000	0.000
85	D	228	CYS	0	-0.068	-0.046	121.680	0.020	0.020	0.000	0.000	0.000	0.000
86	D	229	GLN	0	0.045	0.048	122.556	-0.006	-0.006	0.000	0.000	0.000	0.000
87	D	230	GLU	-1	-1.036	-1.003	124.997	-2.546	-2.546	0.000	0.000	0.000	0.000
88	D	231	ASN	0	-0.091	-0.047	127.156	0.010	0.010	0.000	0.000	0.000	0.000
89	D	232	GLU	-1	-0.882	-0.947	126.619	-2.533	-2.533	0.000	0.000	0.000	0.000
90	D	233	GLY	0	-0.003	-0.001	129.290	-0.003	-0.003	0.000	0.000	0.000	0.000
91	D	234	GLU	-1	-0.999	-1.013	132.474	-2.387	-2.387	0.000	0.000	0.000	0.000
92	D	235	ASN	0	-0.058	-0.016	130.282	-0.006	-0.006	0.000	0.000	0.000	0.000
93	D	236	ASP	-1	-0.813	-0.911	129.392	-2.476	-2.476	0.000	0.000	0.000	0.000
94	D	237	PRO	0	0.025	0.010	128.419	-0.025	-0.025	0.000	0.000	0.000	0.000
95	D	238	VAL	0	-0.078	-0.036	125.544	-0.028	-0.028	0.000	0.000	0.000	0.000
96	D	239	LEU	0	0.053	0.017	124.708	-0.031	-0.031	0.000	0.000	0.000	0.000
97	D	240	GLN	0	0.017	0.028	124.166	-0.006	-0.006	0.000	0.000	0.000	0.000
98	D	241	ARG	1	0.920	0.957	122.085	2.577	2.577	0.000	0.000	0.000	0.000
99	D	242	ILE	0	-0.048	-0.027	119.659	-0.029	-0.029	0.000	0.000	0.000	0.000
100	D	243	VAL	0	0.068	0.025	119.265	-0.033	-0.033	0.000	0.000	0.000	0.000
101	D	244	ASP	-1	-0.908	-0.963	119.169	-2.673	-2.673	0.000	0.000	0.000	0.000
102	D	245	ILE	0	-0.117	-0.050	115.002	-0.030	-0.030	0.000	0.000	0.000	0.000
103	D	246	LEU	0	-0.112	-0.044	114.973	-0.037	-0.037	0.000	0.000	0.000	0.000
104	D	247	TYR	0	-0.143	-0.114	114.416	-0.025	-0.025	0.000	0.000	0.000	0.000
105	D	248	ALA	0	-0.012	0.007	110.952	-0.001	-0.001	0.000	0.000	0.000	0.000

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