FMO DATABASE

FMODB ID: X16VZ

Calculation Name: 2XUV-A-Xray32

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 2XUV

Chain ID: A

ChEMBL ID:

UniProt ID: P0AET2

Base Structure: X-ray

Registration Date: 2018-09-07

Reference:

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water	Apo structure with with a 3 angstrom solvent shell.
Procedure	Auto-FMO protocol ver. 1.20180227

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	125
LigandCharge	MLY=1,SO4=-2
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-560982.654828
FMO2-HF: Nuclear repulsion	526398.327165
FMO2-HF: Total energy	-34584.327663
FMO2-MP2: Total energy	-34680.000759

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(A:31:ACE)

Summations of interaction energy for fragment #1(A:31:ACE)

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.
-1.331	1.41	0.776	-1.864	-1.653	-0.014

Interaction energy analysis for fragmet #1(A:31:ACE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.062 / q_NPA : -0.038

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	A	33	SER	0	-0.027	-0.002	3.619	1.524	2.330	-0.006	-0.371	-0.430	0.000
4	A	34	ALA	0	0.063	0.022	5.566	-0.186	-0.186	0.000	0.000	0.000	0.000
5	A	35	MLY	1	0.905	0.962	5.960	-0.331	-0.331	0.000	0.000	0.000	0.000
6	A	36	ASP	-1	-0.784	-0.887	2.815	-2.039	-0.606	0.563	-1.072	-0.923	-0.011
7	A	37	MET	0	-0.012	0.033	5.831	0.002	0.002	0.000	0.000	0.000	0.000
8	A	38	THR	0	0.029	0.018	8.959	0.243	0.243	0.000	0.000	0.000	0.000
9	A	87	CYS	0	-0.035	-0.028	11.740	-0.007	-0.007	0.000	0.000	0.000	0.000
10	A	40	GLN	0	0.018	0.021	14.950	-0.022	-0.022	0.000	0.000	0.000	0.000
11	A	41	GLU	-1	-0.802	-0.887	9.773	-0.978	-0.978	0.000	0.000	0.000	0.000
12	A	42	PHE	0	0.031	-0.003	14.023	0.021	0.021	0.000	0.000	0.000	0.000
13	A	43	ILE	0	-0.057	-0.030	15.397	0.026	0.026	0.000	0.000	0.000	0.000
14	A	44	ASP	-1	-0.685	-0.800	17.008	-0.243	-0.243	0.000	0.000	0.000	0.000
15	A	45	LEU	0	-0.055	-0.004	13.713	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	46	ASN	0	0.053	0.021	17.603	0.060	0.060	0.000	0.000	0.000	0.000
17	A	47	PRO	0	0.072	0.026	20.081	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	48	MLY	1	0.906	0.958	22.546	0.160	0.160	0.000	0.000	0.000	0.000
19	A	49	ALA	0	0.005	0.010	16.944	0.006	0.006	0.000	0.000	0.000	0.000
20	A	50	MET	0	-0.023	0.001	17.926	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	51	THR	0	0.046	0.021	19.032	0.002	0.002	0.000	0.000	0.000	0.000
22	A	52	PRO	0	0.044	0.024	17.904	0.009	0.009	0.000	0.000	0.000	0.000
23	A	53	VAL	0	0.043	0.032	13.301	0.012	0.012	0.000	0.000	0.000	0.000
24	A	54	ALA	0	0.036	0.012	15.513	0.009	0.009	0.000	0.000	0.000	0.000
25	A	55	TRP	0	-0.047	-0.019	17.840	0.017	0.017	0.000	0.000	0.000	0.000
26	A	56	TRP	0	-0.010	-0.007	11.842	0.018	0.018	0.000	0.000	0.000	0.000
27	A	57	MET	0	-0.064	-0.001	14.042	0.039	0.039	0.000	0.000	0.000	0.000
28	A	58	LEU	0	-0.017	-0.016	15.130	0.031	0.031	0.000	0.000	0.000	0.000
29	A	59	HIS	1	0.773	0.865	18.286	0.066	0.066	0.000	0.000	0.000	0.000
30	A	60	GLU	-1	-0.807	-0.806	12.898	0.089	0.089	0.000	0.000	0.000	0.000
31	A	61	GLU	-1	-0.931	-0.966	13.532	0.188	0.188	0.000	0.000	0.000	0.000
32	A	62	THR	0	-0.093	-0.037	17.627	0.006	0.006	0.000	0.000	0.000	0.000
33	A	63	VAL	0	0.006	-0.008	20.923	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	64	TYR	0	-0.011	0.005	24.295	-0.008	-0.008	0.000	0.000	0.000	0.000
35	A	65	MLY	1	0.909	0.937	25.414	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	66	GLY	0	0.063	0.038	27.799	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	67	GLY	0	0.035	0.025	29.158	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	68	ASP	-1	-0.923	-0.961	30.504	-0.012	-0.012	0.000	0.000	0.000	0.000
39	A	69	THR	0	0.006	0.018	30.157	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	70	VAL	0	0.016	0.000	23.737	0.001	0.001	0.000	0.000	0.000	0.000
41	A	71	THR	0	-0.024	-0.006	27.064	-0.007	-0.007	0.000	0.000	0.000	0.000
42	A	72	LEU	0	-0.046	-0.015	24.184	0.000	0.000	0.000	0.000	0.000	0.000
43	A	73	ASN	0	-0.011	0.000	27.323	0.005	0.005	0.000	0.000	0.000	0.000
44	A	74	GLU	-1	-0.808	-0.890	28.842	-0.039	-0.039	0.000	0.000	0.000	0.000
45	A	75	THR	0	-0.023	-0.021	25.930	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	76	ASP	-1	-0.778	-0.866	24.117	-0.065	-0.065	0.000	0.000	0.000	0.000
47	A	77	LEU	0	-0.014	0.011	25.905	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	78	THR	0	-0.018	-0.010	28.650	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	79	GLN	0	0.088	0.050	23.366	-0.005	-0.005	0.000	0.000	0.000	0.000
50	A	80	ILE	0	0.016	0.007	21.748	-0.008	-0.008	0.000	0.000	0.000	0.000
51	A	81	PRO	0	0.007	0.005	23.104	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	82	MLY	1	0.980	1.005	24.773	0.040	0.040	0.000	0.000	0.000	0.000
53	A	83	VAL	0	0.023	0.025	18.331	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	84	ILE	0	-0.010	-0.003	20.551	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	85	GLU	-1	-0.901	-0.947	22.071	-0.089	-0.089	0.000	0.000	0.000	0.000
56	A	86	TYR	0	-0.049	-0.046	17.452	0.009	0.009	0.000	0.000	0.000	0.000
57	A	88	MLY	1	0.949	0.983	19.565	0.122	0.122	0.000	0.000	0.000	0.000
58	A	89	MLY	1	0.909	0.971	22.441	0.065	0.065	0.000	0.000	0.000	0.000
59	A	90	ASN	0	-0.097	-0.063	19.393	0.020	0.020	0.000	0.000	0.000	0.000
60	A	91	PRO	0	0.061	0.034	17.985	-0.012	-0.012	0.000	0.000	0.000	0.000
61	A	92	GLN	0	0.072	0.031	15.863	-0.046	-0.046	0.000	0.000	0.000	0.000
62	A	93	MLY	1	0.858	0.956	14.518	0.049	0.049	0.000	0.000	0.000	0.000
63	A	94	ASN	0	0.062	0.030	8.847	-0.113	-0.113	0.000	0.000	0.000	0.000
64	A	95	LEU	0	0.043	0.027	12.012	0.064	0.064	0.000	0.000	0.000	0.000
65	A	96	TYR	0	0.063	0.005	11.372	0.020	0.020	0.000	0.000	0.000	0.000
66	A	97	THR	0	-0.069	-0.031	13.346	0.043	0.043	0.000	0.000	0.000	0.000
67	A	98	PHE	0	0.018	0.007	15.689	0.014	0.014	0.000	0.000	0.000	0.000
68	A	99	MLY	1	0.903	0.956	14.755	-0.010	-0.010	0.000	0.000	0.000	0.000
69	A	100	ASN	0	-0.050	-0.009	16.081	0.020	0.020	0.000	0.000	0.000	0.000
70	A	101	NME	0	-0.031	0.005	19.891	0.005	0.005	0.000	0.000	0.000	0.000
71	A	1101	SO4	-2	-1.674	-1.817	30.252	-0.056	-0.056	0.000	0.000	0.000	0.000
72	A	2001	HOH	0	-0.040	-0.025	6.509	0.196	0.196	0.000	0.000	0.000	0.000
73	A	2003	HOH	0	-0.032	-0.029	8.744	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	2005	HOH	0	-0.055	-0.035	2.741	-0.368	0.134	0.219	-0.421	-0.300	-0.003
75	A	2006	HOH	0	-0.012	-0.013	9.336	0.043	0.043	0.000	0.000	0.000	0.000
76	A	2007	HOH	0	-0.037	-0.041	13.219	0.009	0.009	0.000	0.000	0.000	0.000
77	A	2009	HOH	0	-0.013	-0.018	7.429	0.094	0.094	0.000	0.000	0.000	0.000
78	A	2010	HOH	0	-0.062	-0.053	20.945	0.008	0.008	0.000	0.000	0.000	0.000
79	A	2011	HOH	0	-0.025	-0.019	21.933	0.007	0.007	0.000	0.000	0.000	0.000
80	A	2013	HOH	0	-0.025	-0.021	20.040	0.006	0.006	0.000	0.000	0.000	0.000
81	A	2014	HOH	0	-0.040	-0.024	21.639	0.009	0.009	0.000	0.000	0.000	0.000
82	A	2015	HOH	0	-0.030	-0.017	20.361	0.005	0.005	0.000	0.000	0.000	0.000
83	A	2016	HOH	0	-0.075	-0.049	20.824	0.008	0.008	0.000	0.000	0.000	0.000
84	A	2020	HOH	0	-0.051	-0.033	23.514	0.005	0.005	0.000	0.000	0.000	0.000
85	A	2022	HOH	0	0.010	-0.002	23.276	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	2023	HOH	0	-0.015	-0.013	16.999	0.010	0.010	0.000	0.000	0.000	0.000
87	A	2025	HOH	0	-0.009	-0.012	12.667	-0.030	-0.030	0.000	0.000	0.000	0.000
88	A	2027	HOH	0	0.024	0.009	17.995	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	2028	HOH	0	-0.051	-0.030	20.647	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	2031	HOH	0	-0.114	-0.135	12.756	-0.014	-0.014	0.000	0.000	0.000	0.000
91	A	2032	HOH	0	-0.037	-0.022	18.681	-0.001	-0.001	0.000	0.000	0.000	0.000
92	A	2036	HOH	0	0.049	0.023	22.379	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	2038	HOH	0	-0.033	-0.028	23.964	0.001	0.001	0.000	0.000	0.000	0.000
94	A	2039	HOH	0	-0.034	-0.024	29.449	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	2041	HOH	0	0.037	0.026	24.792	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	2043	HOH	0	-0.014	-0.013	29.853	0.001	0.001	0.000	0.000	0.000	0.000
97	A	2044	HOH	0	-0.026	-0.019	31.027	0.001	0.001	0.000	0.000	0.000	0.000
98	A	2045	HOH	0	0.015	0.000	29.513	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	2046	HOH	0	-0.011	0.001	28.199	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	2048	HOH	0	-0.047	-0.032	34.181	0.000	0.000	0.000	0.000	0.000	0.000
101	A	2049	HOH	0	-0.050	-0.030	36.458	0.000	0.000	0.000	0.000	0.000	0.000
102	A	2050	HOH	0	0.018	0.024	24.535	0.001	0.001	0.000	0.000	0.000	0.000
103	A	2051	HOH	0	-0.025	-0.024	27.335	0.000	0.000	0.000	0.000	0.000	0.000
104	A	2052	HOH	0	0.004	-0.015	24.059	0.001	0.001	0.000	0.000	0.000	0.000
105	A	2053	HOH	0	-0.021	-0.027	25.654	0.002	0.002	0.000	0.000	0.000	0.000
106	A	2054	HOH	0	-0.011	-0.009	30.287	0.000	0.000	0.000	0.000	0.000	0.000
107	A	2055	HOH	0	-0.043	-0.028	28.751	0.001	0.001	0.000	0.000	0.000	0.000
108	A	2057	HOH	0	-0.050	-0.041	24.174	0.003	0.003	0.000	0.000	0.000	0.000
109	A	2058	HOH	0	-0.062	-0.045	26.150	0.001	0.001	0.000	0.000	0.000	0.000
110	A	2059	HOH	0	-0.033	-0.024	24.334	0.004	0.004	0.000	0.000	0.000	0.000
111	A	2060	HOH	0	0.024	0.012	26.779	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	2062	HOH	0	-0.023	-0.012	23.547	0.001	0.001	0.000	0.000	0.000	0.000
113	A	2064	HOH	0	0.031	0.022	24.223	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	2066	HOH	0	-0.030	-0.024	13.071	0.014	0.014	0.000	0.000	0.000	0.000
115	A	2068	HOH	0	0.032	0.021	13.221	-0.012	-0.012	0.000	0.000	0.000	0.000
116	A	2069	HOH	0	-0.042	-0.021	7.845	0.064	0.064	0.000	0.000	0.000	0.000
117	A	2070	HOH	0	-0.032	-0.030	15.591	0.009	0.009	0.000	0.000	0.000	0.000
118	A	2072	HOH	0	-0.051	-0.047	32.726	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	2073	HOH	0	-0.015	-0.011	31.046	0.000	0.000	0.000	0.000	0.000	0.000
120	B	2003	HOH	0	-0.004	-0.011	24.090	0.006	0.006	0.000	0.000	0.000	0.000
121	B	2015	HOH	0	0.030	0.022	19.519	0.008	0.008	0.000	0.000	0.000	0.000
122	B	2043	HOH	0	-0.045	-0.027	31.136	0.002	0.002	0.000	0.000	0.000	0.000
123	B	2049	HOH	0	0.027	0.016	23.473	-0.002	-0.002	0.000	0.000	0.000	0.000
124	D	2009	HOH	0	-0.039	-0.021	17.350	-0.020	-0.020	0.000	0.000	0.000	0.000
125	D	2014	HOH	0	-0.026	-0.017	14.783	-0.028	-0.028	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:31:ACE)