FMO DATABASE

FMODB ID: 98Q22

Calculation Name: 4XA6-C-Xray372

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 4XA6

Chain ID: C

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	116
LigandResidueName
LigandFragmentNumber	0
LigandCharge	MLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-674052.012379
FMO2-HF: Nuclear repulsion	624257.031216
FMO2-HF: Total energy	-49794.981164
FMO2-MP2: Total energy	-49939.984119

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(C:1781:ARG)

Summations of interaction energy for fragment #1(C:1781:ARG)

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.
71.388	73.377	9.434	-2.901	-8.523	-0.007

Interaction energy analysis for fragmet #1(C:1781:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 1.020 / q_NPA : 0.984

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	C	1783	MLY	1	0.951	0.968	2.400	31.329	33.796	0.704	-0.914	-2.257	-0.002
4	C	1784	MLY	1	0.932	0.949	1.836	50.772	49.947	8.729	-1.943	-5.962	-0.005
5	C	1785	ASN	0	-0.049	-0.003	4.054	4.567	4.914	0.001	-0.044	-0.304	0.000
6	C	1786	MET	0	0.076	0.044	6.190	2.328	2.328	0.000	0.000	0.000	0.000
7	C	1787	GLU	-1	-0.893	-0.955	5.943	-38.573	-38.573	0.000	0.000	0.000	0.000
8	C	1788	GLN	0	-0.018	-0.015	9.110	2.439	2.439	0.000	0.000	0.000	0.000
9	C	1789	THR	0	0.046	0.018	10.731	1.173	1.173	0.000	0.000	0.000	0.000
10	C	1790	ILE	0	-0.036	-0.007	11.464	1.072	1.072	0.000	0.000	0.000	0.000
11	C	1791	MLY	1	0.962	0.977	10.200	25.149	25.149	0.000	0.000	0.000	0.000
12	C	1792	ASP	-1	-0.919	-0.941	14.783	-14.776	-14.776	0.000	0.000	0.000	0.000
13	C	1793	LEU	0	0.008	-0.008	16.788	1.030	1.030	0.000	0.000	0.000	0.000
14	C	1794	GLN	0	0.004	-0.001	15.180	0.300	0.300	0.000	0.000	0.000	0.000
15	C	1795	HIS	0	0.004	0.017	17.356	0.897	0.897	0.000	0.000	0.000	0.000
16	C	1796	ARG	1	0.928	0.960	20.777	13.887	13.887	0.000	0.000	0.000	0.000
17	C	1797	LEU	0	-0.034	-0.015	22.225	0.526	0.526	0.000	0.000	0.000	0.000
18	C	1798	ASP	-1	-0.864	-0.922	23.328	-11.409	-11.409	0.000	0.000	0.000	0.000
19	C	1799	GLU	-1	-0.919	-0.959	25.169	-10.156	-10.156	0.000	0.000	0.000	0.000
20	C	1800	ALA	0	-0.020	-0.021	26.920	0.552	0.552	0.000	0.000	0.000	0.000
21	C	1801	GLU	-1	-0.934	-0.979	26.445	-11.078	-11.078	0.000	0.000	0.000	0.000
22	C	1802	GLN	0	-0.032	-0.013	29.006	0.778	0.778	0.000	0.000	0.000	0.000
23	C	1803	ILE	0	-0.039	-0.019	30.927	0.504	0.504	0.000	0.000	0.000	0.000
24	C	1804	ALA	0	-0.043	-0.028	32.592	0.405	0.405	0.000	0.000	0.000	0.000
25	C	1805	LEU	0	-0.029	-0.016	33.191	0.340	0.340	0.000	0.000	0.000	0.000
26	C	1806	MLY	1	0.892	0.954	36.182	8.403	8.403	0.000	0.000	0.000	0.000
27	C	1807	GLY	0	0.016	0.021	37.270	0.179	0.179	0.000	0.000	0.000	0.000
28	C	1808	GLY	0	0.026	-0.002	38.689	0.221	0.221	0.000	0.000	0.000	0.000
29	C	1809	MLY	1	0.945	0.969	33.460	9.127	9.127	0.000	0.000	0.000	0.000
30	C	1810	MLY	1	1.008	1.005	39.250	7.822	7.822	0.000	0.000	0.000	0.000
31	C	1811	GLN	0	-0.029	-0.006	42.452	0.073	0.073	0.000	0.000	0.000	0.000
32	C	1812	LEU	0	0.077	0.033	42.849	0.144	0.144	0.000	0.000	0.000	0.000
33	C	1813	GLN	0	0.087	0.038	45.414	0.082	0.082	0.000	0.000	0.000	0.000
34	C	1814	MLY	1	0.918	0.960	47.274	6.648	6.648	0.000	0.000	0.000	0.000
35	C	1815	LEU	0	-0.050	-0.046	47.844	0.143	0.143	0.000	0.000	0.000	0.000
36	C	1816	GLU	-1	-0.939	-0.951	48.756	-6.471	-6.471	0.000	0.000	0.000	0.000
37	C	1817	ALA	0	-0.068	-0.025	51.540	0.112	0.112	0.000	0.000	0.000	0.000
38	C	1818	ARG	1	0.996	0.994	52.970	5.939	5.939	0.000	0.000	0.000	0.000
39	C	1819	VAL	0	0.024	0.016	53.649	0.103	0.103	0.000	0.000	0.000	0.000
40	C	1820	ARG	1	1.001	1.009	54.160	5.864	5.864	0.000	0.000	0.000	0.000
41	C	1821	GLU	-1	-0.962	-0.982	58.086	-5.447	-5.447	0.000	0.000	0.000	0.000
42	C	1822	LEU	0	-0.015	-0.013	57.385	0.082	0.082	0.000	0.000	0.000	0.000
43	C	1823	GLU	-1	-0.938	-0.963	58.937	-5.340	-5.340	0.000	0.000	0.000	0.000
44	C	1824	ASN	0	-0.024	-0.022	61.755	0.142	0.142	0.000	0.000	0.000	0.000
45	C	1825	GLU	-1	-0.894	-0.951	63.785	-4.698	-4.698	0.000	0.000	0.000	0.000
46	C	1826	LEU	0	-0.020	0.002	64.120	0.089	0.089	0.000	0.000	0.000	0.000
47	C	1827	GLU	-1	-0.912	-0.964	66.263	-4.668	-4.668	0.000	0.000	0.000	0.000
48	C	1828	ALA	0	-0.036	-0.020	68.061	0.100	0.100	0.000	0.000	0.000	0.000
49	C	1829	GLU	-1	-0.828	-0.907	69.178	-4.438	-4.438	0.000	0.000	0.000	0.000
50	C	1830	GLN	0	-0.022	-0.021	68.048	0.091	0.091	0.000	0.000	0.000	0.000
51	C	1831	MLY	1	0.884	0.942	70.577	4.589	4.589	0.000	0.000	0.000	0.000
52	C	1832	ARG	1	0.896	0.954	70.139	4.589	4.589	0.000	0.000	0.000	0.000
53	C	1833	ASN	0	0.013	0.018	74.675	0.104	0.104	0.000	0.000	0.000	0.000
54	C	1834	ALA	0	-0.016	0.023	76.376	0.073	0.073	0.000	0.000	0.000	0.000
55	C	1835	GLU	-1	-0.945	-0.979	78.240	-4.009	-4.009	0.000	0.000	0.000	0.000
56	C	1836	SER	0	-0.083	-0.065	79.078	0.061	0.061	0.000	0.000	0.000	0.000
57	C	1837	VAL	0	-0.001	-0.015	79.491	0.068	0.068	0.000	0.000	0.000	0.000
58	C	1838	MLY	1	0.952	0.990	82.407	3.787	3.787	0.000	0.000	0.000	0.000
59	C	1839	GLY	0	-0.020	-0.030	84.479	0.061	0.061	0.000	0.000	0.000	0.000
60	C	1840	MET	0	0.033	0.026	82.180	0.054	0.054	0.000	0.000	0.000	0.000
61	C	1841	ARG	1	1.016	1.012	86.408	3.706	3.706	0.000	0.000	0.000	0.000
62	C	1842	MLY	1	0.895	0.940	88.120	3.611	3.611	0.000	0.000	0.000	0.000
63	C	1843	SER	0	0.051	0.013	90.001	0.029	0.029	0.000	0.000	0.000	0.000
64	C	1844	GLU	-1	-0.882	-0.926	89.537	-3.561	-3.561	0.000	0.000	0.000	0.000
65	C	1845	ARG	1	0.882	0.933	91.441	3.505	3.505	0.000	0.000	0.000	0.000
66	C	1846	ARG	1	0.949	0.983	94.267	3.308	3.308	0.000	0.000	0.000	0.000
67	C	1847	ILE	0	0.008	0.002	93.403	0.038	0.038	0.000	0.000	0.000	0.000
68	C	1848	MLY	1	0.934	0.988	94.426	3.392	3.392	0.000	0.000	0.000	0.000
69	C	1849	GLU	-1	-0.919	-0.941	98.281	-3.259	-3.259	0.000	0.000	0.000	0.000
70	C	1850	LEU	0	-0.025	-0.039	99.581	0.031	0.031	0.000	0.000	0.000	0.000
71	C	1851	THR	0	0.001	-0.010	99.947	0.028	0.028	0.000	0.000	0.000	0.000
72	C	1852	TYR	0	0.037	0.038	101.608	0.015	0.015	0.000	0.000	0.000	0.000
73	C	1853	GLN	0	0.013	0.010	104.040	-0.003	-0.003	0.000	0.000	0.000	0.000
74	C	1854	THR	0	-0.102	-0.062	104.514	0.028	0.028	0.000	0.000	0.000	0.000
75	C	1855	GLU	-1	-0.871	-0.950	104.901	-3.057	-3.057	0.000	0.000	0.000	0.000
76	C	209	ASP	-1	-0.940	-0.960	108.683	-2.961	-2.961	0.000	0.000	0.000	0.000
77	C	210	LEU	0	-0.030	-0.021	109.835	0.033	0.033	0.000	0.000	0.000	0.000
78	C	211	GLU	-1	-0.977	-0.989	109.644	-2.929	-2.929	0.000	0.000	0.000	0.000
79	C	212	MLY	1	0.995	1.005	112.776	2.875	2.875	0.000	0.000	0.000	0.000
80	C	213	GLU	-1	-0.984	-1.004	114.319	-2.799	-2.799	0.000	0.000	0.000	0.000
81	C	214	ARG	1	0.877	0.944	113.921	2.857	2.857	0.000	0.000	0.000	0.000
82	C	215	ASP	-1	-0.845	-0.932	115.634	-2.784	-2.784	0.000	0.000	0.000	0.000
83	C	216	PHE	0	-0.039	-0.016	118.592	0.036	0.036	0.000	0.000	0.000	0.000
84	C	217	TYR	0	-0.025	-0.026	119.847	0.037	0.037	0.000	0.000	0.000	0.000
85	C	218	PHE	0	0.016	0.017	120.878	0.026	0.026	0.000	0.000	0.000	0.000
86	C	219	GLY	0	0.032	0.021	122.572	0.020	0.020	0.000	0.000	0.000	0.000
87	C	220	MLY	1	0.877	0.935	124.336	2.617	2.617	0.000	0.000	0.000	0.000
88	C	221	LEU	0	0.024	0.010	124.429	0.022	0.022	0.000	0.000	0.000	0.000
89	C	222	ARG	1	1.019	1.020	123.270	2.629	2.629	0.000	0.000	0.000	0.000
90	C	223	ASN	0	-0.029	-0.017	127.460	0.020	0.020	0.000	0.000	0.000	0.000
91	C	224	ILE	0	-0.020	-0.008	130.319	0.021	0.021	0.000	0.000	0.000	0.000
92	C	225	GLU	-1	-0.902	-0.967	129.048	-2.507	-2.507	0.000	0.000	0.000	0.000
93	C	226	LEU	0	-0.043	-0.009	131.965	0.012	0.012	0.000	0.000	0.000	0.000
94	C	227	ILE	0	0.003	-0.018	133.585	0.016	0.016	0.000	0.000	0.000	0.000
95	C	228	CYS	0	-0.069	-0.028	135.426	0.020	0.020	0.000	0.000	0.000	0.000
96	C	229	GLN	0	-0.039	-0.009	132.924	0.000	0.000	0.000	0.000	0.000	0.000
97	C	230	GLU	-1	-0.972	-0.975	137.144	-2.363	-2.363	0.000	0.000	0.000	0.000
98	C	231	ASN	0	-0.067	-0.034	139.525	0.003	0.003	0.000	0.000	0.000	0.000
99	C	232	GLU	-1	-0.897	-0.942	139.083	-2.344	-2.344	0.000	0.000	0.000	0.000
100	C	233	GLY	0	-0.042	-0.019	141.925	0.005	0.005	0.000	0.000	0.000	0.000
101	C	234	GLU	-1	-0.943	-0.985	145.028	-2.218	-2.218	0.000	0.000	0.000	0.000
102	C	235	ASN	0	-0.100	-0.056	146.559	-0.001	-0.001	0.000	0.000	0.000	0.000
103	C	236	ASP	-1	-0.803	-0.907	143.687	-2.255	-2.255	0.000	0.000	0.000	0.000
104	C	237	PRO	0	-0.011	-0.007	143.517	-0.018	-0.018	0.000	0.000	0.000	0.000
105	C	238	VAL	0	-0.032	-0.018	140.165	-0.020	-0.020	0.000	0.000	0.000	0.000
106	C	239	LEU	0	0.063	0.023	139.046	-0.023	-0.023	0.000	0.000	0.000	0.000
107	C	240	GLN	0	0.006	0.022	138.549	-0.007	-0.007	0.000	0.000	0.000	0.000
108	C	241	ARG	1	0.931	0.962	137.594	2.339	2.339	0.000	0.000	0.000	0.000
109	C	242	ILE	0	-0.033	-0.017	134.120	-0.022	-0.022	0.000	0.000	0.000	0.000
110	C	243	VAL	0	0.055	0.031	133.835	-0.026	-0.026	0.000	0.000	0.000	0.000
111	C	244	ASP	-1	-0.914	-0.967	133.693	-2.394	-2.394	0.000	0.000	0.000	0.000
112	C	245	ILE	0	-0.112	-0.058	130.348	-0.021	-0.021	0.000	0.000	0.000	0.000
113	C	246	LEU	0	-0.070	-0.038	129.770	-0.025	-0.025	0.000	0.000	0.000	0.000
114	C	247	TYR	0	-0.047	-0.006	128.752	-0.016	-0.016	0.000	0.000	0.000	0.000
115	C	248	ALA	0	-0.030	0.009	128.864	-0.005	-0.005	0.000	0.000	0.000	0.000
116	C	249	THR	0	-0.053	-0.028	123.578	-0.008	-0.008	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(C:1781:ARG)