FMO DATABASE

FMODB ID: ZV9GN

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	OptAll
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	-1081655.160892
FMO2-HF: Nuclear repulsion	1011392.341221
FMO2-HF: Total energy	-70262.819671
FMO2-MP2: Total energy	-70468.852579

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.
-17.735	-8.543	16.145	-8.665	-16.674	-0.055

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 : -0.031 / q_NPA : -0.019

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	-0.002	-0.022	3.169	-2.155	-0.384	0.094	-0.875	-0.990	-0.001
4	B	6	GLU	-1	-0.914	-0.947	5.835	-0.761	-0.761	0.000	0.000	0.000	0.000
5	B	7	GLU	-1	-0.840	-0.921	2.347	-5.917	-2.827	3.501	-2.571	-4.019	-0.026
6	B	8	HIS	0	-0.028	-0.014	2.937	-2.228	0.195	0.407	-0.947	-1.883	-0.006
7	B	9	GLU	-1	-0.865	-0.937	3.752	-0.368	-0.198	0.018	0.023	-0.212	0.000
8	B	10	ASP	-1	-0.866	-0.915	6.571	-0.547	-0.547	0.000	0.000	0.000	0.000
9	B	11	ILE	0	-0.112	-0.058	2.503	0.186	0.011	1.629	-0.230	-1.224	-0.001
10	B	12	LEU	0	-0.015	-0.014	6.353	0.196	0.196	0.000	0.000	0.000	0.000
11	B	13	ASN	0	-0.044	-0.043	8.857	0.150	0.150	0.000	0.000	0.000	0.000
12	B	14	MLY	1	0.927	0.974	6.889	0.479	0.479	0.000	0.000	0.000	0.000
13	B	15	LEU	0	-0.054	-0.031	8.933	0.063	0.063	0.000	0.000	0.000	0.000
14	B	16	LEU	0	-0.053	-0.010	12.367	0.029	0.029	0.000	0.000	0.000	0.000
15	B	17	ASP	-1	-0.838	-0.902	14.978	-0.135	-0.135	0.000	0.000	0.000	0.000
16	B	18	PRO	0	-0.041	-0.030	16.950	0.010	0.010	0.000	0.000	0.000	0.000
17	B	19	GLU	-1	-0.977	-1.001	19.633	-0.079	-0.079	0.000	0.000	0.000	0.000
18	B	20	LEU	0	-0.045	0.002	12.954	0.013	0.013	0.000	0.000	0.000	0.000
19	B	21	ALA	0	0.044	0.026	17.488	0.012	0.012	0.000	0.000	0.000	0.000
20	B	22	GLN	0	0.030	-0.002	16.245	-0.011	-0.011	0.000	0.000	0.000	0.000
21	B	23	SER	0	-0.008	0.006	15.867	0.001	0.001	0.000	0.000	0.000	0.000
22	B	24	GLU	-1	-0.775	-0.892	12.752	-0.082	-0.082	0.000	0.000	0.000	0.000
23	B	25	ARG	1	0.856	0.936	11.376	0.108	0.108	0.000	0.000	0.000	0.000
24	B	26	THR	0	-0.095	-0.062	11.560	0.009	0.009	0.000	0.000	0.000	0.000
25	B	27	GLU	-1	-0.949	-0.980	10.174	0.068	0.068	0.000	0.000	0.000	0.000
26	B	28	ALA	0	0.061	0.038	7.134	0.068	0.068	0.000	0.000	0.000	0.000
27	B	29	LEU	0	-0.001	-0.018	6.654	0.074	0.074	0.000	0.000	0.000	0.000
28	B	30	GLN	0	-0.003	0.005	8.421	-0.018	-0.018	0.000	0.000	0.000	0.000
29	B	31	GLN	0	0.009	-0.001	3.167	-0.497	-0.059	0.027	-0.083	-0.383	0.000
30	B	32	LEU	0	0.013	0.011	3.620	-0.184	0.270	0.010	-0.112	-0.351	0.000
31	B	33	ARG	1	0.886	0.947	5.081	-0.268	-0.242	-0.001	0.000	-0.024	0.000
32	B	34	VAL	0	-0.025	-0.022	5.610	-0.044	-0.044	0.000	0.000	0.000	0.000
33	B	35	ASN	0	0.048	0.032	2.236	-4.771	-4.051	7.222	-2.454	-5.489	-0.022
34	B	36	TYR	0	0.013	0.009	4.285	-0.254	-0.118	-0.001	-0.018	-0.118	0.000
35	B	37	GLY	0	0.014	0.006	7.353	0.055	0.055	0.000	0.000	0.000	0.000
36	B	38	SER	0	0.021	0.020	5.261	0.071	0.071	0.000	0.000	0.000	0.000
37	B	39	PHE	0	0.023	0.007	2.454	-2.086	-1.947	3.239	-1.398	-1.981	0.001
38	B	40	VAL	0	-0.019	-0.001	6.617	0.004	0.004	0.000	0.000	0.000	0.000
39	B	41	SER	0	-0.042	-0.028	10.042	-0.011	-0.011	0.000	0.000	0.000	0.000
40	B	42	GLU	-1	-0.910	-0.953	7.592	1.401	1.401	0.000	0.000	0.000	0.000
41	B	43	TYR	0	0.020	0.012	9.909	-0.072	-0.072	0.000	0.000	0.000	0.000
42	B	44	ASN	0	-0.069	-0.038	11.589	-0.042	-0.042	0.000	0.000	0.000	0.000
43	B	45	ASP	-1	-0.862	-0.937	13.549	0.332	0.332	0.000	0.000	0.000	0.000
44	B	46	LEU	0	-0.021	-0.004	12.069	-0.033	-0.033	0.000	0.000	0.000	0.000
45	B	47	THR	0	-0.021	-0.027	14.784	-0.035	-0.035	0.000	0.000	0.000	0.000
46	B	48	MLY	1	0.890	0.953	16.311	-0.211	-0.211	0.000	0.000	0.000	0.000
47	B	49	SER	0	-0.027	-0.011	17.565	-0.026	-0.026	0.000	0.000	0.000	0.000
48	B	50	HIS	0	0.014	0.003	18.715	-0.015	-0.015	0.000	0.000	0.000	0.000
49	B	1777	ALA	0	0.034	0.016	20.402	-0.014	-0.014	0.000	0.000	0.000	0.000
50	B	1778	HIS	0	0.010	0.005	22.066	-0.022	-0.022	0.000	0.000	0.000	0.000
51	B	1779	LEU	0	0.033	0.016	20.810	-0.009	-0.009	0.000	0.000	0.000	0.000
52	B	1780	GLU	-1	-0.809	-0.880	24.526	0.036	0.036	0.000	0.000	0.000	0.000
53	B	1781	ARG	1	0.859	0.925	26.432	-0.108	-0.108	0.000	0.000	0.000	0.000
54	B	1782	MET	0	-0.047	-0.031	27.040	-0.002	-0.002	0.000	0.000	0.000	0.000
55	B	1783	MLY	1	0.845	0.916	28.296	-0.045	-0.045	0.000	0.000	0.000	0.000
56	B	1784	MLY	1	0.970	0.984	30.139	-0.045	-0.045	0.000	0.000	0.000	0.000
57	B	1785	ASN	0	-0.024	-0.013	32.384	-0.007	-0.007	0.000	0.000	0.000	0.000
58	B	1786	MET	0	0.000	0.004	29.454	-0.002	-0.002	0.000	0.000	0.000	0.000
59	B	1787	GLU	-1	-0.807	-0.903	33.843	0.029	0.029	0.000	0.000	0.000	0.000
60	B	1788	GLN	0	-0.067	-0.037	36.125	-0.004	-0.004	0.000	0.000	0.000	0.000
61	B	1789	THR	0	-0.020	-0.009	37.158	-0.001	-0.001	0.000	0.000	0.000	0.000
62	B	1790	ILE	0	-0.010	-0.007	35.797	-0.001	-0.001	0.000	0.000	0.000	0.000
63	B	1791	MLY	1	0.876	0.937	37.797	-0.030	-0.030	0.000	0.000	0.000	0.000
64	B	1792	ASP	-1	-0.842	-0.931	42.148	0.032	0.032	0.000	0.000	0.000	0.000
65	B	1793	LEU	0	-0.093	-0.047	40.978	0.000	0.000	0.000	0.000	0.000	0.000
66	B	1794	GLN	0	-0.010	-0.005	42.434	0.000	0.000	0.000	0.000	0.000	0.000
67	B	1795	HIS	0	0.057	0.037	45.799	-0.002	-0.002	0.000	0.000	0.000	0.000
68	B	1796	ARG	1	0.919	0.951	45.189	-0.036	-0.036	0.000	0.000	0.000	0.000
69	B	1797	LEU	0	-0.044	-0.002	47.360	0.001	0.001	0.000	0.000	0.000	0.000
70	B	1798	ASP	-1	-0.874	-0.940	49.664	0.020	0.020	0.000	0.000	0.000	0.000
71	B	1799	GLU	-1	-0.959	-0.987	51.999	0.024	0.024	0.000	0.000	0.000	0.000
72	B	1800	ALA	0	-0.007	-0.001	52.544	-0.001	-0.001	0.000	0.000	0.000	0.000
73	B	1801	GLU	-1	-0.911	-0.958	51.656	0.021	0.021	0.000	0.000	0.000	0.000
74	B	1802	GLN	0	-0.017	-0.019	55.442	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	1803	ILE	0	-0.054	-0.027	56.570	-0.001	-0.001	0.000	0.000	0.000	0.000
76	B	1804	ALA	0	-0.005	-0.004	57.755	-0.001	-0.001	0.000	0.000	0.000	0.000
77	B	1805	LEU	0	-0.024	-0.004	59.627	-0.001	-0.001	0.000	0.000	0.000	0.000
78	B	1806	MLY	1	0.911	0.967	61.551	-0.017	-0.017	0.000	0.000	0.000	0.000
79	B	1807	GLY	0	0.003	0.021	64.146	-0.001	-0.001	0.000	0.000	0.000	0.000
80	B	1808	GLY	0	0.044	0.022	65.635	0.001	0.001	0.000	0.000	0.000	0.000
81	B	1809	MLY	1	0.969	0.961	66.575	-0.019	-0.019	0.000	0.000	0.000	0.000
82	B	1810	MLY	1	0.983	0.998	70.081	-0.012	-0.012	0.000	0.000	0.000	0.000
83	B	1811	GLN	0	-0.082	-0.062	67.848	-0.001	-0.001	0.000	0.000	0.000	0.000
84	B	1812	LEU	0	0.049	0.026	68.298	0.000	0.000	0.000	0.000	0.000	0.000
85	B	1813	GLN	0	0.013	0.004	70.962	-0.001	-0.001	0.000	0.000	0.000	0.000
86	B	1814	MLY	1	0.925	0.976	71.615	-0.012	-0.012	0.000	0.000	0.000	0.000
87	B	1815	LEU	0	-0.012	-0.014	69.736	0.000	0.000	0.000	0.000	0.000	0.000
88	B	1816	GLU	-1	-0.841	-0.919	74.407	0.015	0.015	0.000	0.000	0.000	0.000
89	B	1817	ALA	0	0.002	-0.003	76.806	0.000	0.000	0.000	0.000	0.000	0.000
90	B	1818	ARG	1	0.851	0.926	76.461	-0.010	-0.010	0.000	0.000	0.000	0.000
91	B	1819	VAL	0	0.003	-0.010	75.590	0.000	0.000	0.000	0.000	0.000	0.000
92	B	1820	ARG	1	0.903	0.935	78.566	-0.012	-0.012	0.000	0.000	0.000	0.000
93	B	1821	GLU	-1	-0.867	-0.910	81.354	0.009	0.009	0.000	0.000	0.000	0.000
94	B	1822	LEU	0	-0.026	-0.027	78.226	0.000	0.000	0.000	0.000	0.000	0.000
95	B	1823	GLU	-1	-0.872	-0.927	80.970	0.012	0.012	0.000	0.000	0.000	0.000
96	B	1824	ASN	0	-0.030	0.002	83.849	0.000	0.000	0.000	0.000	0.000	0.000
97	B	1825	GLU	-1	-0.861	-0.945	85.515	0.008	0.008	0.000	0.000	0.000	0.000
98	B	1826	LEU	0	-0.027	0.006	81.894	0.000	0.000	0.000	0.000	0.000	0.000
99	B	1827	GLU	-1	-0.814	-0.883	85.557	0.009	0.009	0.000	0.000	0.000	0.000
100	B	1828	ALA	0	0.027	0.009	88.686	0.000	0.000	0.000	0.000	0.000	0.000
101	B	1829	GLU	-1	-0.828	-0.898	87.402	0.008	0.008	0.000	0.000	0.000	0.000
102	B	1830	GLN	0	-0.071	-0.039	86.231	0.000	0.000	0.000	0.000	0.000	0.000
103	B	1831	MLY	1	0.815	0.890	90.385	-0.009	-0.009	0.000	0.000	0.000	0.000
104	B	1832	ARG	1	0.862	0.906	91.077	-0.008	-0.008	0.000	0.000	0.000	0.000
105	B	1833	ASN	0	-0.026	0.001	91.704	0.000	0.000	0.000	0.000	0.000	0.000
106	B	1834	ALA	0	0.027	0.001	93.960	0.000	0.000	0.000	0.000	0.000	0.000
107	B	1835	GLU	-1	-0.899	-0.964	95.480	0.007	0.007	0.000	0.000	0.000	0.000
108	B	1836	SER	0	0.013	0.014	96.596	0.000	0.000	0.000	0.000	0.000	0.000
109	B	1837	VAL	0	-0.041	-0.030	95.612	0.000	0.000	0.000	0.000	0.000	0.000
110	B	1838	MLY	1	0.885	0.970	96.978	-0.008	-0.008	0.000	0.000	0.000	0.000
111	B	1839	GLY	0	0.068	0.028	101.504	0.000	0.000	0.000	0.000	0.000	0.000
112	B	1840	MET	0	0.011	0.025	99.248	0.000	0.000	0.000	0.000	0.000	0.000
113	B	1841	ARG	1	0.845	0.892	101.206	-0.006	-0.006	0.000	0.000	0.000	0.000
114	B	1842	MLY	1	0.928	0.976	104.239	-0.006	-0.006	0.000	0.000	0.000	0.000
115	B	1843	SER	0	0.008	-0.015	104.743	0.000	0.000	0.000	0.000	0.000	0.000
116	B	1844	GLU	-1	-0.805	-0.876	105.523	0.006	0.006	0.000	0.000	0.000	0.000
117	B	1845	ARG	1	0.925	0.943	106.928	-0.007	-0.007	0.000	0.000	0.000	0.000
118	B	1846	ARG	1	0.842	0.907	110.374	-0.005	-0.005	0.000	0.000	0.000	0.000
119	B	1847	ILE	0	0.022	0.010	108.044	0.000	0.000	0.000	0.000	0.000	0.000
120	B	1848	MLY	1	0.892	0.941	107.611	-0.006	-0.006	0.000	0.000	0.000	0.000
121	B	1849	GLU	-1	-0.812	-0.858	112.513	0.005	0.005	0.000	0.000	0.000	0.000
122	B	1850	LEU	0	0.008	-0.019	114.653	0.000	0.000	0.000	0.000	0.000	0.000
123	B	1851	THR	0	-0.036	-0.021	113.130	0.000	0.000	0.000	0.000	0.000	0.000
124	B	1852	TYR	0	-0.022	-0.017	113.804	0.000	0.000	0.000	0.000	0.000	0.000
125	B	1853	GLN	0	0.005	0.004	118.476	0.000	0.000	0.000	0.000	0.000	0.000
126	B	1854	THR	0	-0.010	-0.003	117.606	0.000	0.000	0.000	0.000	0.000	0.000
127	B	1855	GLU	-1	-0.973	-0.970	119.823	0.004	0.004	0.000	0.000	0.000	0.000
128	B	209	ASP	-1	-0.898	-0.956	121.754	0.004	0.004	0.000	0.000	0.000	0.000
129	B	210	LEU	0	0.037	0.017	123.911	0.000	0.000	0.000	0.000	0.000	0.000
130	B	211	GLU	-1	-0.860	-0.911	122.153	0.003	0.003	0.000	0.000	0.000	0.000
131	B	212	MLY	1	0.966	0.974	125.096	-0.004	-0.004	0.000	0.000	0.000	0.000
132	B	213	GLU	-1	-0.905	-0.938	127.514	0.004	0.004	0.000	0.000	0.000	0.000
133	B	214	ARG	1	0.728	0.832	124.663	-0.003	-0.003	0.000	0.000	0.000	0.000
134	B	215	ASP	-1	-0.793	-0.878	127.572	0.003	0.003	0.000	0.000	0.000	0.000
135	B	216	PHE	0	-0.036	-0.010	130.804	0.000	0.000	0.000	0.000	0.000	0.000
136	B	217	TYR	0	-0.064	-0.066	133.034	0.000	0.000	0.000	0.000	0.000	0.000
137	B	218	PHE	0	0.009	0.017	131.560	0.000	0.000	0.000	0.000	0.000	0.000
138	B	219	GLY	0	0.018	0.008	134.482	0.000	0.000	0.000	0.000	0.000	0.000
139	B	220	MLY	1	0.857	0.925	136.076	-0.003	-0.003	0.000	0.000	0.000	0.000
140	B	221	LEU	0	0.016	0.015	136.346	0.000	0.000	0.000	0.000	0.000	0.000
141	B	222	ARG	1	0.848	0.902	136.596	-0.002	-0.002	0.000	0.000	0.000	0.000
142	B	223	ASN	0	-0.063	-0.029	139.057	0.000	0.000	0.000	0.000	0.000	0.000
143	B	224	ILE	0	0.043	0.009	141.729	0.000	0.000	0.000	0.000	0.000	0.000
144	B	225	GLU	-1	-0.747	-0.825	139.422	0.002	0.002	0.000	0.000	0.000	0.000
145	B	226	LEU	0	-0.066	-0.038	140.265	0.000	0.000	0.000	0.000	0.000	0.000
146	B	227	ILE	0	-0.053	-0.012	144.076	0.000	0.000	0.000	0.000	0.000	0.000
147	B	228	CYS	0	-0.056	-0.020	146.248	0.000	0.000	0.000	0.000	0.000	0.000
148	B	229	GLN	0	0.060	0.031	141.677	0.000	0.000	0.000	0.000	0.000	0.000
149	B	230	GLU	-1	-0.937	-0.956	147.251	0.002	0.002	0.000	0.000	0.000	0.000
150	B	231	ASN	0	-0.136	-0.096	150.193	0.000	0.000	0.000	0.000	0.000	0.000
151	B	232	GLU	-1	-0.874	-0.935	147.190	0.002	0.002	0.000	0.000	0.000	0.000
152	B	233	GLY	0	-0.037	-0.006	151.611	0.000	0.000	0.000	0.000	0.000	0.000
153	B	234	GLU	-1	-0.991	-1.013	154.907	0.002	0.002	0.000	0.000	0.000	0.000
154	B	235	ASN	0	-0.058	-0.015	152.739	0.000	0.000	0.000	0.000	0.000	0.000
155	B	236	ASP	-1	-0.789	-0.893	155.627	0.002	0.002	0.000	0.000	0.000	0.000
156	B	237	PRO	0	-0.020	-0.017	154.876	0.000	0.000	0.000	0.000	0.000	0.000
157	B	238	VAL	0	-0.076	-0.041	153.615	0.000	0.000	0.000	0.000	0.000	0.000
158	B	239	LEU	0	0.040	0.010	150.882	0.000	0.000	0.000	0.000	0.000	0.000
159	B	240	GLN	0	-0.013	0.002	149.672	0.000	0.000	0.000	0.000	0.000	0.000
160	B	241	ARG	1	0.919	0.961	149.529	-0.002	-0.002	0.000	0.000	0.000	0.000
161	B	242	ILE	0	-0.041	-0.017	146.600	0.000	0.000	0.000	0.000	0.000	0.000
162	B	243	VAL	0	0.050	0.020	145.727	0.000	0.000	0.000	0.000	0.000	0.000
163	B	244	ASP	-1	-0.875	-0.941	144.742	0.002	0.002	0.000	0.000	0.000	0.000
164	B	245	ILE	0	-0.125	-0.061	143.178	0.000	0.000	0.000	0.000	0.000	0.000
165	B	246	LEU	0	-0.063	-0.024	141.475	0.000	0.000	0.000	0.000	0.000	0.000
166	B	247	TYR	0	-0.104	-0.061	139.574	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)