FMO DATABASE

FMODB ID: 3JG4L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-589977.413534
FMO2-HF: Nuclear repulsion	545564.726399
FMO2-HF: Total energy	-44412.687135
FMO2-MP2: Total energy	-44543.637121

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.
14.74	18.164	0.143	-1.176	-2.39	-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 : 0.989 / q_NPA : 0.972

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	-0.061	-0.053	2.682	1.743	3.954	0.077	-0.908	-1.380	0.000
4	D	1794	GLN	0	-0.050	-0.012	3.159	1.799	2.739	0.067	-0.247	-0.759	-0.001
5	D	1795	HIS	0	0.079	0.030	4.645	5.652	5.925	-0.001	-0.021	-0.251	0.000
6	D	1796	ARG	1	0.961	0.990	6.969	25.545	25.545	0.000	0.000	0.000	0.000
7	D	1797	LEU	0	-0.019	-0.003	7.814	2.461	2.461	0.000	0.000	0.000	0.000
8	D	1798	ASP	-1	-0.801	-0.894	8.714	-25.506	-25.506	0.000	0.000	0.000	0.000
9	D	1799	GLU	-1	-0.964	-0.977	10.968	-18.080	-18.080	0.000	0.000	0.000	0.000
10	D	1800	ALA	0	-0.041	-0.034	12.424	1.670	1.670	0.000	0.000	0.000	0.000
11	D	1801	GLU	-1	-0.909	-0.956	12.864	-17.389	-17.389	0.000	0.000	0.000	0.000
12	D	1802	GLN	0	-0.017	-0.016	15.079	1.480	1.480	0.000	0.000	0.000	0.000
13	D	1803	ILE	0	-0.126	-0.069	16.303	1.143	1.143	0.000	0.000	0.000	0.000
14	D	1804	ALA	0	-0.011	-0.001	18.140	0.806	0.806	0.000	0.000	0.000	0.000
15	D	1805	LEU	0	-0.008	0.006	19.601	0.670	0.670	0.000	0.000	0.000	0.000
16	D	1806	MLY	1	0.897	0.964	18.880	14.835	14.835	0.000	0.000	0.000	0.000
17	D	1807	GLY	0	0.012	0.013	23.136	0.582	0.582	0.000	0.000	0.000	0.000
18	D	1808	GLY	0	0.017	0.011	23.805	-0.298	-0.298	0.000	0.000	0.000	0.000
19	D	1809	MLY	1	0.961	0.977	20.047	12.327	12.327	0.000	0.000	0.000	0.000
20	D	1810	MLY	1	0.978	0.980	26.144	10.597	10.597	0.000	0.000	0.000	0.000
21	D	1811	GLN	0	-0.012	-0.015	28.584	0.081	0.081	0.000	0.000	0.000	0.000
22	D	1812	LEU	0	0.038	0.017	28.773	0.232	0.232	0.000	0.000	0.000	0.000
23	D	1813	GLN	0	0.086	0.039	27.241	0.380	0.380	0.000	0.000	0.000	0.000
24	D	1814	MLY	1	0.963	0.983	32.002	8.687	8.687	0.000	0.000	0.000	0.000
25	D	1815	LEU	0	0.010	0.014	34.342	0.268	0.268	0.000	0.000	0.000	0.000
26	D	1816	GLU	-1	-0.866	-0.930	32.241	-8.955	-8.955	0.000	0.000	0.000	0.000
27	D	1817	ALA	0	-0.069	-0.018	36.232	0.106	0.106	0.000	0.000	0.000	0.000
28	D	1818	ARG	1	0.847	0.898	38.121	7.143	7.143	0.000	0.000	0.000	0.000
29	D	1819	VAL	0	-0.015	-0.005	39.549	0.181	0.181	0.000	0.000	0.000	0.000
30	D	1820	ARG	1	0.964	0.983	35.308	8.301	8.301	0.000	0.000	0.000	0.000
31	D	1821	GLU	-1	-0.884	-0.929	41.892	-6.862	-6.862	0.000	0.000	0.000	0.000
32	D	1822	LEU	0	0.015	0.010	43.828	0.159	0.159	0.000	0.000	0.000	0.000
33	D	1823	GLU	-1	-0.868	-0.947	43.106	-6.805	-6.805	0.000	0.000	0.000	0.000
34	D	1824	ASN	0	-0.107	-0.058	45.759	0.053	0.053	0.000	0.000	0.000	0.000
35	D	1825	GLU	-1	-0.814	-0.891	47.744	-5.790	-5.790	0.000	0.000	0.000	0.000
36	D	1826	LEU	0	-0.021	-0.007	49.683	0.151	0.151	0.000	0.000	0.000	0.000
37	D	1827	GLU	-1	-0.847	-0.934	50.666	-5.815	-5.815	0.000	0.000	0.000	0.000
38	D	1828	ALA	0	0.023	0.006	52.349	0.140	0.140	0.000	0.000	0.000	0.000
39	D	1829	GLU	-1	-0.840	-0.914	54.229	-5.321	-5.321	0.000	0.000	0.000	0.000
40	D	1830	GLN	0	-0.017	-0.006	53.273	0.128	0.128	0.000	0.000	0.000	0.000
41	D	1831	MLY	1	0.815	0.914	53.383	5.836	5.836	0.000	0.000	0.000	0.000
42	D	1832	ARG	1	0.793	0.886	55.097	5.639	5.639	0.000	0.000	0.000	0.000
43	D	1833	ASN	0	-0.061	-0.051	59.655	0.167	0.167	0.000	0.000	0.000	0.000
44	D	1834	ALA	0	-0.014	0.015	61.167	0.089	0.089	0.000	0.000	0.000	0.000
45	D	1835	GLU	-1	-0.826	-0.931	62.992	-4.816	-4.816	0.000	0.000	0.000	0.000
46	D	1836	SER	0	-0.023	0.007	64.938	0.081	0.081	0.000	0.000	0.000	0.000
47	D	1837	VAL	0	-0.008	-0.002	66.306	0.075	0.075	0.000	0.000	0.000	0.000
48	D	1838	MLY	1	0.858	0.904	65.093	4.838	4.838	0.000	0.000	0.000	0.000
49	D	1839	GLY	0	0.002	0.006	69.474	0.070	0.070	0.000	0.000	0.000	0.000
50	D	1840	MET	0	0.023	0.032	71.162	0.033	0.033	0.000	0.000	0.000	0.000
51	D	1841	ARG	1	0.884	0.938	72.748	4.268	4.268	0.000	0.000	0.000	0.000
52	D	1842	MLY	1	1.018	1.014	73.572	4.266	4.266	0.000	0.000	0.000	0.000
53	D	1843	SER	0	-0.023	-0.032	75.640	0.061	0.061	0.000	0.000	0.000	0.000
54	D	1844	GLU	-1	-0.752	-0.870	77.244	-3.984	-3.984	0.000	0.000	0.000	0.000
55	D	1845	ARG	1	0.845	0.917	77.292	4.088	4.088	0.000	0.000	0.000	0.000
56	D	1846	ARG	1	0.932	0.958	80.152	3.823	3.823	0.000	0.000	0.000	0.000
57	D	1847	ILE	0	-0.020	-0.008	79.379	0.037	0.037	0.000	0.000	0.000	0.000
58	D	1848	MLY	1	0.944	0.966	81.574	3.845	3.845	0.000	0.000	0.000	0.000
59	D	1849	GLU	-1	-0.844	-0.913	83.606	-3.748	-3.748	0.000	0.000	0.000	0.000
60	D	1850	LEU	0	-0.014	-0.002	84.488	0.045	0.045	0.000	0.000	0.000	0.000
61	D	1851	THR	0	-0.035	-0.011	87.015	0.027	0.027	0.000	0.000	0.000	0.000
62	D	1852	TYR	0	-0.026	-0.005	88.886	0.018	0.018	0.000	0.000	0.000	0.000
63	D	1853	GLN	0	0.012	0.005	89.466	0.040	0.040	0.000	0.000	0.000	0.000
64	D	1854	THR	0	0.014	-0.002	90.992	0.026	0.026	0.000	0.000	0.000	0.000
65	D	1855	GLU	-1	-0.942	-0.963	92.964	-3.406	-3.406	0.000	0.000	0.000	0.000
66	D	209	ASP	-1	-0.886	-0.962	94.987	-3.242	-3.242	0.000	0.000	0.000	0.000
67	D	210	LEU	0	-0.065	-0.033	94.668	0.035	0.035	0.000	0.000	0.000	0.000
68	D	211	GLU	-1	-0.864	-0.916	97.249	-3.234	-3.234	0.000	0.000	0.000	0.000
69	D	212	MLY	1	0.975	1.008	99.435	3.210	3.210	0.000	0.000	0.000	0.000
70	D	213	GLU	-1	-0.865	-0.921	101.005	-3.112	-3.112	0.000	0.000	0.000	0.000
71	D	214	ARG	1	0.732	0.831	99.262	3.218	3.218	0.000	0.000	0.000	0.000
72	D	215	ASP	-1	-0.830	-0.905	102.751	-3.082	-3.082	0.000	0.000	0.000	0.000
73	D	216	PHE	0	-0.047	-0.017	105.301	0.044	0.044	0.000	0.000	0.000	0.000
74	D	217	TYR	0	-0.094	-0.078	104.042	0.059	0.059	0.000	0.000	0.000	0.000
75	D	218	PHE	0	0.039	0.015	107.296	0.034	0.034	0.000	0.000	0.000	0.000
76	D	219	GLY	0	0.053	0.032	109.203	0.026	0.026	0.000	0.000	0.000	0.000
77	D	220	MLY	1	0.861	0.933	109.389	2.932	2.932	0.000	0.000	0.000	0.000
78	D	221	LEU	0	-0.011	-0.016	110.035	0.027	0.027	0.000	0.000	0.000	0.000
79	D	222	ARG	1	0.848	0.920	111.601	2.857	2.857	0.000	0.000	0.000	0.000
80	D	223	ASN	0	-0.036	-0.001	115.034	0.024	0.024	0.000	0.000	0.000	0.000
81	D	224	ILE	0	0.012	-0.005	116.055	0.024	0.024	0.000	0.000	0.000	0.000
82	D	225	GLU	-1	-0.748	-0.836	117.170	-2.720	-2.720	0.000	0.000	0.000	0.000
83	D	226	LEU	0	-0.007	0.006	118.938	0.016	0.016	0.000	0.000	0.000	0.000
84	D	227	ILE	0	0.012	-0.003	121.293	0.023	0.023	0.000	0.000	0.000	0.000
85	D	228	CYS	0	-0.085	-0.054	121.755	0.021	0.021	0.000	0.000	0.000	0.000
86	D	229	GLN	0	0.004	0.014	122.224	-0.016	-0.016	0.000	0.000	0.000	0.000
87	D	230	GLU	-1	-1.021	-1.001	125.023	-2.559	-2.559	0.000	0.000	0.000	0.000
88	D	231	ASN	0	-0.086	-0.041	127.182	0.012	0.012	0.000	0.000	0.000	0.000
89	D	232	GLU	-1	-0.868	-0.948	126.694	-2.523	-2.523	0.000	0.000	0.000	0.000
90	D	233	GLY	0	0.014	0.007	129.317	-0.004	-0.004	0.000	0.000	0.000	0.000
91	D	234	GLU	-1	-0.983	-0.998	132.325	-2.407	-2.407	0.000	0.000	0.000	0.000
92	D	235	ASN	0	-0.081	-0.031	130.179	0.008	0.008	0.000	0.000	0.000	0.000
93	D	236	ASP	-1	-0.795	-0.890	129.679	-2.493	-2.493	0.000	0.000	0.000	0.000
94	D	237	PRO	0	0.028	0.003	128.452	-0.024	-0.024	0.000	0.000	0.000	0.000
95	D	238	VAL	0	-0.097	-0.049	125.686	-0.029	-0.029	0.000	0.000	0.000	0.000
96	D	239	LEU	0	0.046	0.017	124.741	-0.031	-0.031	0.000	0.000	0.000	0.000
97	D	240	GLN	0	-0.033	-0.006	123.962	-0.001	-0.001	0.000	0.000	0.000	0.000
98	D	241	ARG	1	0.926	0.962	122.213	2.571	2.571	0.000	0.000	0.000	0.000
99	D	242	ILE	0	-0.043	-0.025	119.681	-0.029	-0.029	0.000	0.000	0.000	0.000
100	D	243	VAL	0	0.052	0.021	119.292	-0.032	-0.032	0.000	0.000	0.000	0.000
101	D	244	ASP	-1	-0.885	-0.943	119.211	-2.671	-2.671	0.000	0.000	0.000	0.000
102	D	245	ILE	0	-0.114	-0.051	115.064	-0.030	-0.030	0.000	0.000	0.000	0.000
103	D	246	LEU	0	-0.092	-0.027	115.032	-0.035	-0.035	0.000	0.000	0.000	0.000
104	D	247	TYR	0	-0.083	-0.062	114.473	-0.033	-0.033	0.000	0.000	0.000	0.000
105	D	248	ALA	0	-0.043	-0.012	111.057	-0.011	-0.011	0.000	0.000	0.000	0.000

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