FMO DATABASE

FMODB ID: 2NG5R

Calculation Name: 4XA6-B-Xray372

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 4XA6

Chain ID: B

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	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	166
LigandCharge	MLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1080590.01223
FMO2-HF: Nuclear repulsion	1010329.837432
FMO2-HF: Total energy	-70260.174798
FMO2-MP2: Total energy	-70466.479172

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(B:3:LEU)

Summations of interaction energy for fragment #1(B:3:LEU)

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.
-14.961	-12.115	22.125	-9.385	-15.587	-0.059

Interaction energy analysis for fragmet #1(B:3:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.034

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	B	5	PRO	0	0.003	-0.017	3.217	-2.387	-0.455	0.057	-0.978	-1.011	0.000
4	B	6	GLU	-1	-0.912	-0.947	5.900	-0.752	-0.752	0.000	0.000	0.000	0.000
5	B	7	GLU	-1	-0.876	-0.952	2.483	-4.096	-1.372	1.433	-1.474	-2.684	-0.015
6	B	8	HIS	0	-0.040	-0.006	3.175	-1.839	0.165	0.151	-0.815	-1.339	-0.006
7	B	9	GLU	-1	-0.856	-0.927	3.930	-0.380	-0.235	0.005	-0.012	-0.138	0.000
8	B	10	ASP	-1	-0.909	-0.955	6.356	-0.675	-0.675	0.000	0.000	0.000	0.000
9	B	11	ILE	0	-0.090	-0.059	2.833	-0.071	0.309	0.591	-0.143	-0.828	-0.001
10	B	12	LEU	0	-0.009	-0.016	6.538	0.217	0.217	0.000	0.000	0.000	0.000
11	B	13	ASN	0	-0.056	-0.019	8.903	0.128	0.128	0.000	0.000	0.000	0.000
12	B	14	MLY	1	0.958	0.974	7.459	0.355	0.355	0.000	0.000	0.000	0.000
13	B	15	LEU	0	-0.058	-0.031	9.715	0.065	0.065	0.000	0.000	0.000	0.000
14	B	16	LEU	0	-0.028	-0.008	13.009	0.021	0.021	0.000	0.000	0.000	0.000
15	B	17	ASP	-1	-0.847	-0.913	15.433	-0.123	-0.123	0.000	0.000	0.000	0.000
16	B	18	PRO	0	-0.054	-0.038	17.247	0.009	0.009	0.000	0.000	0.000	0.000
17	B	19	GLU	-1	-0.993	-0.991	19.723	-0.073	-0.073	0.000	0.000	0.000	0.000
18	B	20	LEU	0	-0.047	-0.003	13.011	0.013	0.013	0.000	0.000	0.000	0.000
19	B	21	ALA	0	0.047	0.018	17.634	0.011	0.011	0.000	0.000	0.000	0.000
20	B	22	GLN	0	0.033	-0.001	16.487	-0.006	-0.006	0.000	0.000	0.000	0.000
21	B	23	SER	0	-0.003	0.012	16.218	0.003	0.003	0.000	0.000	0.000	0.000
22	B	24	GLU	-1	-0.837	-0.918	13.131	-0.036	-0.036	0.000	0.000	0.000	0.000
23	B	25	ARG	1	0.962	0.996	11.607	0.101	0.101	0.000	0.000	0.000	0.000
24	B	26	THR	0	-0.082	-0.075	11.648	0.015	0.015	0.000	0.000	0.000	0.000
25	B	27	GLU	-1	-0.949	-0.970	9.942	0.126	0.126	0.000	0.000	0.000	0.000
26	B	28	ALA	0	0.071	0.046	7.445	0.082	0.082	0.000	0.000	0.000	0.000
27	B	29	LEU	0	-0.015	-0.026	6.865	0.087	0.087	0.000	0.000	0.000	0.000
28	B	30	GLN	0	-0.023	-0.013	8.601	-0.029	-0.029	0.000	0.000	0.000	0.000
29	B	31	GLN	0	-0.002	-0.006	3.567	-0.320	-0.036	0.005	-0.052	-0.237	0.000
30	B	32	LEU	0	0.023	0.011	4.023	0.052	0.301	0.000	-0.030	-0.219	0.000
31	B	33	ARG	1	0.897	0.969	5.260	-0.312	-0.289	-0.001	0.000	-0.023	0.000
32	B	34	VAL	0	-0.030	-0.026	5.674	-0.072	-0.072	0.000	0.000	0.000	0.000
33	B	35	ASN	0	0.057	0.041	1.838	-3.291	-9.541	18.004	-4.844	-6.910	-0.033
34	B	36	TYR	0	-0.004	0.008	4.379	-0.597	-0.423	-0.001	-0.020	-0.153	0.000
35	B	37	GLY	0	-0.002	-0.005	6.647	0.036	0.036	0.000	0.000	0.000	0.000
36	B	38	SER	0	-0.026	-0.014	4.430	-0.194	-0.130	-0.001	-0.003	-0.060	0.000
37	B	39	PHE	0	0.105	0.032	3.013	-2.276	-1.159	1.882	-1.014	-1.985	-0.004
38	B	40	VAL	0	-0.032	0.004	6.204	-0.021	-0.021	0.000	0.000	0.000	0.000
39	B	41	SER	0	-0.069	-0.041	9.538	0.006	0.006	0.000	0.000	0.000	0.000
40	B	42	GLU	-1	-0.909	-0.947	6.225	1.542	1.542	0.000	0.000	0.000	0.000
41	B	43	TYR	0	0.006	0.007	9.273	-0.077	-0.077	0.000	0.000	0.000	0.000
42	B	44	ASN	0	-0.005	-0.021	10.770	-0.045	-0.045	0.000	0.000	0.000	0.000
43	B	45	ASP	-1	-0.895	-0.935	12.863	0.354	0.354	0.000	0.000	0.000	0.000
44	B	46	LEU	0	-0.019	-0.005	11.747	-0.033	-0.033	0.000	0.000	0.000	0.000
45	B	47	THR	0	-0.057	-0.039	14.380	-0.043	-0.043	0.000	0.000	0.000	0.000
46	B	48	MLY	1	0.925	0.963	16.485	-0.205	-0.205	0.000	0.000	0.000	0.000
47	B	49	SER	0	-0.017	-0.004	17.030	-0.025	-0.025	0.000	0.000	0.000	0.000
48	B	50	HIS	0	0.016	0.001	17.963	-0.010	-0.010	0.000	0.000	0.000	0.000
49	B	1777	ALA	0	0.040	0.020	19.711	-0.015	-0.015	0.000	0.000	0.000	0.000
50	B	1778	HIS	0	-0.046	-0.030	21.994	-0.018	-0.018	0.000	0.000	0.000	0.000
51	B	1779	LEU	0	0.026	0.005	21.073	-0.010	-0.010	0.000	0.000	0.000	0.000
52	B	1780	GLU	-1	-0.826	-0.890	23.961	0.020	0.020	0.000	0.000	0.000	0.000
53	B	1781	ARG	1	0.929	0.970	25.792	-0.098	-0.098	0.000	0.000	0.000	0.000
54	B	1782	MET	0	-0.068	-0.043	26.306	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	1783	MLY	1	0.891	0.946	27.777	-0.028	-0.028	0.000	0.000	0.000	0.000
56	B	1784	MLY	1	0.966	0.983	29.709	-0.034	-0.034	0.000	0.000	0.000	0.000
57	B	1785	ASN	0	-0.031	-0.020	31.958	-0.007	-0.007	0.000	0.000	0.000	0.000
58	B	1786	MET	0	-0.002	0.001	29.063	0.000	0.000	0.000	0.000	0.000	0.000
59	B	1787	GLU	-1	-0.895	-0.947	32.938	0.019	0.019	0.000	0.000	0.000	0.000
60	B	1788	GLN	0	-0.050	-0.033	35.694	-0.005	-0.005	0.000	0.000	0.000	0.000
61	B	1789	THR	0	-0.005	0.012	37.040	0.000	0.000	0.000	0.000	0.000	0.000
62	B	1790	ILE	0	0.005	0.002	35.635	-0.002	-0.002	0.000	0.000	0.000	0.000
63	B	1791	MLY	1	0.955	0.987	37.549	-0.020	-0.020	0.000	0.000	0.000	0.000
64	B	1792	ASP	-1	-0.871	-0.929	41.780	0.028	0.028	0.000	0.000	0.000	0.000
65	B	1793	LEU	0	-0.085	-0.047	40.697	-0.001	-0.001	0.000	0.000	0.000	0.000
66	B	1794	GLN	0	0.035	0.006	41.603	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	1795	HIS	0	0.048	0.039	45.336	-0.001	-0.001	0.000	0.000	0.000	0.000
68	B	1796	ARG	1	0.929	0.942	45.103	-0.033	-0.033	0.000	0.000	0.000	0.000
69	B	1797	LEU	0	-0.061	-0.020	46.477	0.001	0.001	0.000	0.000	0.000	0.000
70	B	1798	ASP	-1	-0.850	-0.930	49.152	0.016	0.016	0.000	0.000	0.000	0.000
71	B	1799	GLU	-1	-0.997	-1.001	51.304	0.020	0.020	0.000	0.000	0.000	0.000
72	B	1800	ALA	0	-0.015	-0.010	52.004	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	1801	GLU	-1	-0.948	-0.969	50.728	0.018	0.018	0.000	0.000	0.000	0.000
74	B	1802	GLN	0	-0.028	-0.021	54.645	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	1803	ILE	0	-0.062	-0.037	56.567	-0.001	-0.001	0.000	0.000	0.000	0.000
76	B	1804	ALA	0	-0.027	-0.008	57.502	0.000	0.000	0.000	0.000	0.000	0.000
77	B	1805	LEU	0	0.010	0.016	59.262	0.000	0.000	0.000	0.000	0.000	0.000
78	B	1806	MLY	1	0.881	0.946	61.254	-0.015	-0.015	0.000	0.000	0.000	0.000
79	B	1807	GLY	0	-0.041	-0.023	64.173	0.000	0.000	0.000	0.000	0.000	0.000
80	B	1808	GLY	0	0.050	0.026	65.409	0.001	0.001	0.000	0.000	0.000	0.000
81	B	1809	MLY	1	0.971	0.972	66.406	-0.016	-0.016	0.000	0.000	0.000	0.000
82	B	1810	MLY	1	0.989	0.994	69.511	-0.010	-0.010	0.000	0.000	0.000	0.000
83	B	1811	GLN	0	-0.012	-0.014	67.561	-0.001	-0.001	0.000	0.000	0.000	0.000
84	B	1812	LEU	0	0.036	0.027	67.923	0.000	0.000	0.000	0.000	0.000	0.000
85	B	1813	GLN	0	0.040	0.008	70.499	0.000	0.000	0.000	0.000	0.000	0.000
86	B	1814	MLY	1	0.968	0.998	71.363	-0.010	-0.010	0.000	0.000	0.000	0.000
87	B	1815	LEU	0	-0.004	-0.015	69.771	-0.001	-0.001	0.000	0.000	0.000	0.000
88	B	1816	GLU	-1	-0.881	-0.936	74.177	0.013	0.013	0.000	0.000	0.000	0.000
89	B	1817	ALA	0	-0.031	-0.013	76.676	0.000	0.000	0.000	0.000	0.000	0.000
90	B	1818	ARG	1	0.932	0.980	75.853	-0.009	-0.009	0.000	0.000	0.000	0.000
91	B	1819	VAL	0	0.004	-0.010	75.261	0.000	0.000	0.000	0.000	0.000	0.000
92	B	1820	ARG	1	0.969	0.979	78.120	-0.010	-0.010	0.000	0.000	0.000	0.000
93	B	1821	GLU	-1	-0.943	-0.952	81.127	0.008	0.008	0.000	0.000	0.000	0.000
94	B	1822	LEU	0	-0.044	-0.036	77.965	0.000	0.000	0.000	0.000	0.000	0.000
95	B	1823	GLU	-1	-0.932	-0.975	80.407	0.011	0.011	0.000	0.000	0.000	0.000
96	B	1824	ASN	0	0.008	0.019	83.305	0.000	0.000	0.000	0.000	0.000	0.000
97	B	1825	GLU	-1	-0.894	-0.965	84.694	0.007	0.007	0.000	0.000	0.000	0.000
98	B	1826	LEU	0	-0.053	-0.009	81.639	0.000	0.000	0.000	0.000	0.000	0.000
99	B	1827	GLU	-1	-0.874	-0.946	85.108	0.009	0.009	0.000	0.000	0.000	0.000
100	B	1828	ALA	0	0.050	0.020	88.360	0.000	0.000	0.000	0.000	0.000	0.000
101	B	1829	GLU	-1	-0.965	-0.989	87.524	0.006	0.006	0.000	0.000	0.000	0.000
102	B	1830	GLN	0	-0.035	-0.018	86.125	0.000	0.000	0.000	0.000	0.000	0.000
103	B	1831	MLY	1	0.875	0.939	90.088	-0.008	-0.008	0.000	0.000	0.000	0.000
104	B	1832	ARG	1	0.925	0.962	91.176	-0.006	-0.006	0.000	0.000	0.000	0.000
105	B	1833	ASN	0	-0.003	0.019	90.566	0.000	0.000	0.000	0.000	0.000	0.000
106	B	1834	ALA	0	0.042	0.011	93.397	0.000	0.000	0.000	0.000	0.000	0.000
107	B	1835	GLU	-1	-0.913	-0.970	94.918	0.006	0.006	0.000	0.000	0.000	0.000
108	B	1836	SER	0	0.028	0.028	96.176	0.000	0.000	0.000	0.000	0.000	0.000
109	B	1837	VAL	0	-0.008	-0.024	95.226	0.000	0.000	0.000	0.000	0.000	0.000
110	B	1838	MLY	1	0.865	0.938	96.928	-0.007	-0.007	0.000	0.000	0.000	0.000
111	B	1839	GLY	0	0.045	0.019	100.845	0.000	0.000	0.000	0.000	0.000	0.000
112	B	1840	MET	0	0.034	0.038	99.220	0.000	0.000	0.000	0.000	0.000	0.000
113	B	1841	ARG	1	0.889	0.935	101.625	-0.005	-0.005	0.000	0.000	0.000	0.000
114	B	1842	MLY	1	0.925	0.981	103.939	-0.005	-0.005	0.000	0.000	0.000	0.000
115	B	1843	SER	0	-0.044	-0.028	104.200	0.000	0.000	0.000	0.000	0.000	0.000
116	B	1844	GLU	-1	-0.805	-0.944	105.169	0.005	0.005	0.000	0.000	0.000	0.000
117	B	1845	ARG	1	0.858	0.922	106.205	-0.006	-0.006	0.000	0.000	0.000	0.000
118	B	1846	ARG	1	1.016	1.006	109.686	-0.004	-0.004	0.000	0.000	0.000	0.000
119	B	1847	ILE	0	-0.016	0.028	107.302	0.000	0.000	0.000	0.000	0.000	0.000
120	B	1848	MLY	1	0.976	0.993	108.249	-0.005	-0.005	0.000	0.000	0.000	0.000
121	B	1849	GLU	-1	-0.953	-0.963	111.610	0.004	0.004	0.000	0.000	0.000	0.000
122	B	1850	LEU	0	-0.019	-0.029	113.975	0.000	0.000	0.000	0.000	0.000	0.000
123	B	1851	THR	0	-0.010	0.001	112.544	0.000	0.000	0.000	0.000	0.000	0.000
124	B	1852	TYR	0	-0.057	-0.040	113.810	0.000	0.000	0.000	0.000	0.000	0.000
125	B	1853	GLN	0	0.039	0.037	117.926	0.000	0.000	0.000	0.000	0.000	0.000
126	B	1854	THR	0	-0.049	-0.021	116.647	0.000	0.000	0.000	0.000	0.000	0.000
127	B	1855	GLU	-1	-0.929	-0.955	118.905	0.003	0.003	0.000	0.000	0.000	0.000
128	B	209	ASP	-1	-0.883	-0.942	121.099	0.003	0.003	0.000	0.000	0.000	0.000
129	B	210	LEU	0	0.041	0.011	123.526	0.000	0.000	0.000	0.000	0.000	0.000
130	B	211	GLU	-1	-0.964	-0.978	122.070	0.003	0.003	0.000	0.000	0.000	0.000
131	B	212	MLY	1	0.980	1.005	125.054	-0.003	-0.003	0.000	0.000	0.000	0.000
132	B	213	GLU	-1	-0.983	-0.998	126.970	0.003	0.003	0.000	0.000	0.000	0.000
133	B	214	ARG	1	0.932	0.960	124.490	-0.003	-0.003	0.000	0.000	0.000	0.000
134	B	215	ASP	-1	-0.889	-0.947	126.734	0.002	0.002	0.000	0.000	0.000	0.000
135	B	216	PHE	0	-0.095	-0.039	130.019	0.000	0.000	0.000	0.000	0.000	0.000
136	B	217	TYR	0	-0.017	-0.028	132.716	0.000	0.000	0.000	0.000	0.000	0.000
137	B	218	PHE	0	0.026	0.026	131.333	0.000	0.000	0.000	0.000	0.000	0.000
138	B	219	GLY	0	0.014	0.012	134.084	0.000	0.000	0.000	0.000	0.000	0.000
139	B	220	MLY	1	0.890	0.922	135.560	-0.003	-0.003	0.000	0.000	0.000	0.000
140	B	221	LEU	0	0.029	0.018	136.195	0.000	0.000	0.000	0.000	0.000	0.000
141	B	222	ARG	1	1.044	1.012	135.447	-0.002	-0.002	0.000	0.000	0.000	0.000
142	B	223	ASN	0	-0.070	-0.026	138.785	0.000	0.000	0.000	0.000	0.000	0.000
143	B	224	ILE	0	0.017	-0.006	141.179	0.000	0.000	0.000	0.000	0.000	0.000
144	B	225	GLU	-1	-0.873	-0.917	138.876	0.002	0.002	0.000	0.000	0.000	0.000
145	B	226	LEU	0	-0.077	-0.047	139.564	0.000	0.000	0.000	0.000	0.000	0.000
146	B	227	ILE	0	-0.072	-0.027	143.162	0.000	0.000	0.000	0.000	0.000	0.000
147	B	228	CYS	0	-0.083	-0.035	145.401	0.000	0.000	0.000	0.000	0.000	0.000
148	B	229	GLN	0	0.031	0.026	141.888	0.000	0.000	0.000	0.000	0.000	0.000
149	B	230	GLU	-1	-0.924	-0.946	146.841	0.001	0.001	0.000	0.000	0.000	0.000
150	B	231	ASN	0	-0.101	-0.065	149.613	0.000	0.000	0.000	0.000	0.000	0.000
151	B	232	GLU	-1	-0.934	-0.974	146.761	0.001	0.001	0.000	0.000	0.000	0.000
152	B	233	GLY	0	0.040	0.023	151.065	0.000	0.000	0.000	0.000	0.000	0.000
153	B	234	GLU	-1	-1.038	-1.026	154.509	0.001	0.001	0.000	0.000	0.000	0.000
154	B	235	ASN	0	-0.027	0.006	153.023	0.000	0.000	0.000	0.000	0.000	0.000
155	B	236	ASP	-1	-0.881	-0.948	154.606	0.001	0.001	0.000	0.000	0.000	0.000
156	B	237	PRO	0	0.022	0.006	154.159	0.000	0.000	0.000	0.000	0.000	0.000
157	B	238	VAL	0	-0.026	-0.033	152.703	0.000	0.000	0.000	0.000	0.000	0.000
158	B	239	LEU	0	0.061	0.021	149.774	0.000	0.000	0.000	0.000	0.000	0.000
159	B	240	GLN	0	0.029	0.036	149.150	0.000	0.000	0.000	0.000	0.000	0.000
160	B	241	ARG	1	0.910	0.962	149.192	-0.002	-0.002	0.000	0.000	0.000	0.000
161	B	242	ILE	0	-0.046	-0.031	146.133	0.000	0.000	0.000	0.000	0.000	0.000
162	B	243	VAL	0	0.057	0.026	145.204	0.000	0.000	0.000	0.000	0.000	0.000
163	B	244	ASP	-1	-0.905	-0.965	144.343	0.001	0.001	0.000	0.000	0.000	0.000
164	B	245	ILE	0	-0.151	-0.072	142.446	0.000	0.000	0.000	0.000	0.000	0.000
165	B	246	LEU	0	-0.080	-0.032	141.037	0.000	0.000	0.000	0.000	0.000	0.000
166	B	247	TYR	0	-0.097	-0.024	138.989	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:3:LEU)