FMO DATABASE

FMODB ID: MNZ2Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-674273.252655
FMO2-HF: Nuclear repulsion	624477.17569
FMO2-HF: Total energy	-49796.076964
FMO2-MP2: Total energy	-49941.025461

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.
64.511	69.932	2.761	-2.029	-6.153	-0.004

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 : 1.018 / 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

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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	0.943	0.971	2.491	29.485	31.643	0.593	-0.781	-1.970	-0.001
4	C	1784	MLY	1	0.861	0.897	2.325	43.170	46.146	2.169	-1.220	-3.925	-0.003
5	C	1785	ASN	0	-0.040	-0.003	4.328	4.150	4.437	-0.001	-0.028	-0.258	0.000
6	C	1786	MET	0	0.075	0.042	6.376	2.192	2.192	0.000	0.000	0.000	0.000
7	C	1787	GLU	-1	-0.829	-0.903	6.345	-35.728	-35.728	0.000	0.000	0.000	0.000
8	C	1788	GLN	0	0.029	0.004	9.191	1.250	1.250	0.000	0.000	0.000	0.000
9	C	1789	THR	0	0.030	0.013	10.851	1.047	1.047	0.000	0.000	0.000	0.000
10	C	1790	ILE	0	-0.027	-0.016	12.237	1.026	1.026	0.000	0.000	0.000	0.000
11	C	1791	MLY	1	0.893	0.964	9.534	25.224	25.224	0.000	0.000	0.000	0.000
12	C	1792	ASP	-1	-0.805	-0.884	14.875	-14.147	-14.147	0.000	0.000	0.000	0.000
13	C	1793	LEU	0	-0.009	-0.007	16.896	0.940	0.940	0.000	0.000	0.000	0.000
14	C	1794	GLN	0	-0.001	-0.006	15.931	0.203	0.203	0.000	0.000	0.000	0.000
15	C	1795	HIS	0	0.008	0.020	17.231	0.873	0.873	0.000	0.000	0.000	0.000
16	C	1796	ARG	1	0.841	0.896	19.480	14.346	14.346	0.000	0.000	0.000	0.000
17	C	1797	LEU	0	-0.040	-0.015	22.496	0.499	0.499	0.000	0.000	0.000	0.000
18	C	1798	ASP	-1	-0.818	-0.896	23.695	-11.168	-11.168	0.000	0.000	0.000	0.000
19	C	1799	GLU	-1	-0.916	-0.958	25.331	-10.026	-10.026	0.000	0.000	0.000	0.000
20	C	1800	ALA	0	-0.014	-0.018	27.105	0.521	0.521	0.000	0.000	0.000	0.000
21	C	1801	GLU	-1	-0.940	-0.980	26.669	-10.881	-10.881	0.000	0.000	0.000	0.000
22	C	1802	GLN	0	-0.072	-0.040	28.706	0.820	0.820	0.000	0.000	0.000	0.000
23	C	1803	ILE	0	-0.043	-0.020	30.763	0.496	0.496	0.000	0.000	0.000	0.000
24	C	1804	ALA	0	-0.039	-0.024	32.911	0.403	0.403	0.000	0.000	0.000	0.000
25	C	1805	LEU	0	-0.007	-0.010	33.823	0.320	0.320	0.000	0.000	0.000	0.000
26	C	1806	MLY	1	0.880	0.950	36.602	8.379	8.379	0.000	0.000	0.000	0.000
27	C	1807	GLY	0	0.011	0.016	37.541	0.177	0.177	0.000	0.000	0.000	0.000
28	C	1808	GLY	0	0.020	-0.002	38.945	0.217	0.217	0.000	0.000	0.000	0.000
29	C	1809	MLY	1	0.944	0.972	33.392	9.109	9.109	0.000	0.000	0.000	0.000
30	C	1810	MLY	1	1.009	1.004	39.420	7.738	7.738	0.000	0.000	0.000	0.000
31	C	1811	GLN	0	-0.035	-0.009	43.138	0.108	0.108	0.000	0.000	0.000	0.000
32	C	1812	LEU	0	0.064	0.033	43.070	0.141	0.141	0.000	0.000	0.000	0.000
33	C	1813	GLN	0	0.101	0.049	45.910	0.126	0.126	0.000	0.000	0.000	0.000
34	C	1814	MLY	1	0.898	0.943	47.274	6.592	6.592	0.000	0.000	0.000	0.000
35	C	1815	LEU	0	-0.037	-0.035	48.095	0.149	0.149	0.000	0.000	0.000	0.000
36	C	1816	GLU	-1	-0.898	-0.939	48.548	-6.467	-6.467	0.000	0.000	0.000	0.000
37	C	1817	ALA	0	-0.069	-0.028	51.871	0.114	0.114	0.000	0.000	0.000	0.000
38	C	1818	ARG	1	0.980	0.987	53.503	5.858	5.858	0.000	0.000	0.000	0.000
39	C	1819	VAL	0	0.031	0.017	54.228	0.104	0.104	0.000	0.000	0.000	0.000
40	C	1820	ARG	1	0.970	1.003	53.651	5.887	5.887	0.000	0.000	0.000	0.000
41	C	1821	GLU	-1	-0.918	-0.952	57.955	-5.429	-5.429	0.000	0.000	0.000	0.000
42	C	1822	LEU	0	-0.030	-0.017	57.569	0.088	0.088	0.000	0.000	0.000	0.000
43	C	1823	GLU	-1	-0.915	-0.958	59.612	-5.316	-5.316	0.000	0.000	0.000	0.000
44	C	1824	ASN	0	-0.082	-0.059	62.081	0.144	0.144	0.000	0.000	0.000	0.000
45	C	1825	GLU	-1	-0.799	-0.892	64.133	-4.648	-4.648	0.000	0.000	0.000	0.000
46	C	1826	LEU	0	-0.031	-0.003	64.508	0.088	0.088	0.000	0.000	0.000	0.000
47	C	1827	GLU	-1	-0.834	-0.918	66.652	-4.585	-4.585	0.000	0.000	0.000	0.000
48	C	1828	ALA	0	-0.018	-0.008	68.415	0.096	0.096	0.000	0.000	0.000	0.000
49	C	1829	GLU	-1	-0.815	-0.895	69.619	-4.384	-4.384	0.000	0.000	0.000	0.000
50	C	1830	GLN	0	-0.052	-0.032	68.640	0.087	0.087	0.000	0.000	0.000	0.000
51	C	1831	MLY	1	0.809	0.894	71.044	4.601	4.601	0.000	0.000	0.000	0.000
52	C	1832	ARG	1	0.825	0.897	69.905	4.586	4.586	0.000	0.000	0.000	0.000
53	C	1833	ASN	0	-0.008	0.006	75.077	0.105	0.105	0.000	0.000	0.000	0.000
54	C	1834	ALA	0	-0.016	-0.008	76.771	0.070	0.070	0.000	0.000	0.000	0.000
55	C	1835	GLU	-1	-0.959	-0.978	78.618	-3.996	-3.996	0.000	0.000	0.000	0.000
56	C	1836	SER	0	-0.034	-0.020	79.467	0.069	0.069	0.000	0.000	0.000	0.000
57	C	1837	VAL	0	-0.010	-0.017	80.231	0.067	0.067	0.000	0.000	0.000	0.000
58	C	1838	MLY	1	0.942	0.986	82.828	3.779	3.779	0.000	0.000	0.000	0.000
59	C	1839	GLY	0	-0.002	-0.022	84.873	0.060	0.060	0.000	0.000	0.000	0.000
60	C	1840	MET	0	0.020	0.019	82.745	0.051	0.051	0.000	0.000	0.000	0.000
61	C	1841	ARG	1	0.994	1.006	86.828	3.690	3.690	0.000	0.000	0.000	0.000
62	C	1842	MLY	1	0.921	0.952	88.551	3.579	3.579	0.000	0.000	0.000	0.000
63	C	1843	SER	0	0.015	0.002	90.041	0.038	0.038	0.000	0.000	0.000	0.000
64	C	1844	GLU	-1	-0.860	-0.925	90.416	-3.517	-3.517	0.000	0.000	0.000	0.000
65	C	1845	ARG	1	0.906	0.941	92.111	3.483	3.483	0.000	0.000	0.000	0.000
66	C	1846	ARG	1	0.862	0.921	94.702	3.286	3.286	0.000	0.000	0.000	0.000
67	C	1847	ILE	0	0.015	0.012	93.675	0.038	0.038	0.000	0.000	0.000	0.000
68	C	1848	MLY	1	0.937	0.989	94.532	3.388	3.388	0.000	0.000	0.000	0.000
69	C	1849	GLU	-1	-0.871	-0.905	98.701	-3.242	-3.242	0.000	0.000	0.000	0.000
70	C	1850	LEU	0	0.001	-0.026	99.485	0.030	0.030	0.000	0.000	0.000	0.000
71	C	1851	THR	0	-0.010	-0.007	100.320	0.030	0.030	0.000	0.000	0.000	0.000
72	C	1852	TYR	0	0.023	0.024	101.856	0.011	0.011	0.000	0.000	0.000	0.000
73	C	1853	GLN	0	0.010	0.006	104.658	0.002	0.002	0.000	0.000	0.000	0.000
74	C	1854	THR	0	-0.069	-0.040	105.436	0.023	0.023	0.000	0.000	0.000	0.000
75	C	1855	GLU	-1	-0.883	-0.959	105.220	-3.042	-3.042	0.000	0.000	0.000	0.000
76	C	209	ASP	-1	-0.933	-0.957	109.067	-2.935	-2.935	0.000	0.000	0.000	0.000
77	C	210	LEU	0	-0.039	-0.026	109.727	0.033	0.033	0.000	0.000	0.000	0.000
78	C	211	GLU	-1	-0.870	-0.918	110.209	-2.900	-2.900	0.000	0.000	0.000	0.000
79	C	212	MLY	1	0.990	1.000	113.093	2.869	2.869	0.000	0.000	0.000	0.000
80	C	213	GLU	-1	-0.935	-0.965	115.195	-2.770	-2.770	0.000	0.000	0.000	0.000
81	C	214	ARG	1	0.767	0.866	112.805	2.862	2.862	0.000	0.000	0.000	0.000
82	C	215	ASP	-1	-0.830	-0.916	116.042	-2.768	-2.768	0.000	0.000	0.000	0.000
83	C	216	PHE	0	-0.036	-0.010	118.896	0.035	0.035	0.000	0.000	0.000	0.000
84	C	217	TYR	0	-0.067	-0.066	119.230	0.045	0.045	0.000	0.000	0.000	0.000
85	C	218	PHE	0	0.027	0.023	120.851	0.026	0.026	0.000	0.000	0.000	0.000
86	C	219	GLY	0	0.035	0.024	122.875	0.020	0.020	0.000	0.000	0.000	0.000
87	C	220	MLY	1	0.858	0.933	124.106	2.617	2.617	0.000	0.000	0.000	0.000
88	C	221	LEU	0	0.015	0.005	124.587	0.022	0.022	0.000	0.000	0.000	0.000
89	C	222	ARG	1	0.884	0.937	124.446	2.598	2.598	0.000	0.000	0.000	0.000
90	C	223	ASN	0	-0.027	-0.020	128.114	0.018	0.018	0.000	0.000	0.000	0.000
91	C	224	ILE	0	-0.021	-0.008	130.495	0.021	0.021	0.000	0.000	0.000	0.000
92	C	225	GLU	-1	-0.724	-0.837	128.618	-2.512	-2.512	0.000	0.000	0.000	0.000
93	C	226	LEU	0	-0.042	-0.008	132.161	0.012	0.012	0.000	0.000	0.000	0.000
94	C	227	ILE	0	0.005	-0.014	133.800	0.016	0.016	0.000	0.000	0.000	0.000
95	C	228	CYS	0	-0.084	-0.040	135.636	0.020	0.020	0.000	0.000	0.000	0.000
96	C	229	GLN	0	-0.040	-0.010	132.861	0.002	0.002	0.000	0.000	0.000	0.000
97	C	230	GLU	-1	-0.972	-0.978	137.415	-2.359	-2.359	0.000	0.000	0.000	0.000
98	C	231	ASN	0	-0.114	-0.060	139.717	0.008	0.008	0.000	0.000	0.000	0.000
99	C	232	GLU	-1	-0.909	-0.950	138.642	-2.340	-2.340	0.000	0.000	0.000	0.000
100	C	233	GLY	0	-0.022	-0.006	142.066	0.006	0.006	0.000	0.000	0.000	0.000
101	C	234	GLU	-1	-0.905	-0.962	145.161	-2.224	-2.224	0.000	0.000	0.000	0.000
102	C	235	ASN	0	-0.105	-0.069	146.654	0.005	0.005	0.000	0.000	0.000	0.000
103	C	236	ASP	-1	-0.761	-0.861	144.049	-2.258	-2.258	0.000	0.000	0.000	0.000
104	C	237	PRO	0	0.001	-0.015	143.696	-0.016	-0.016	0.000	0.000	0.000	0.000
105	C	238	VAL	0	-0.054	-0.027	140.473	-0.019	-0.019	0.000	0.000	0.000	0.000
106	C	239	LEU	0	0.038	0.010	139.375	-0.024	-0.024	0.000	0.000	0.000	0.000
107	C	240	GLN	0	-0.036	-0.010	138.731	-0.006	-0.006	0.000	0.000	0.000	0.000
108	C	241	ARG	1	0.941	0.966	137.704	2.334	2.334	0.000	0.000	0.000	0.000
109	C	242	ILE	0	-0.039	-0.020	134.358	-0.022	-0.022	0.000	0.000	0.000	0.000
110	C	243	VAL	0	0.055	0.030	134.021	-0.026	-0.026	0.000	0.000	0.000	0.000
111	C	244	ASP	-1	-0.886	-0.943	133.818	-2.382	-2.382	0.000	0.000	0.000	0.000
112	C	245	ILE	0	-0.118	-0.063	130.664	-0.021	-0.021	0.000	0.000	0.000	0.000
113	C	246	LEU	0	-0.056	-0.028	129.952	-0.025	-0.025	0.000	0.000	0.000	0.000
114	C	247	TYR	0	-0.080	-0.047	128.883	-0.015	-0.015	0.000	0.000	0.000	0.000
115	C	248	ALA	0	-0.033	0.008	128.956	-0.005	-0.005	0.000	0.000	0.000	0.000
116	C	249	THR	0	-0.047	-0.025	123.640	-0.008	-0.008	0.000	0.000	0.000	0.000

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