FMO DATABASE

FMODB ID: P32LX

Calculation Name: 2ZPM-A-Xray13

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 2ZPM

Chain ID: A

ChEMBL ID:

UniProt ID: P0AEH1

Base Structure: X-ray

Registration Date: 2017-11-22

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	No
Procedure	Auto-FMO protocol ver. 1.20171117

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	87
LigandCharge	MLY=1
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-547512.315741
FMO2-HF: Nuclear repulsion	515588.287993
FMO2-HF: Total energy	-31924.027748
FMO2-MP2: Total energy	-32019.122483

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:223:ACE)

Summations of interaction energy for fragment #1(A:223: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.
-0.455	1.153	0.367	-0.803	-1.172	-0.001

Interaction energy analysis for fragmet #1(A:223:ACE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : -0.012

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	A	225	VAL	0	-0.027	-0.021	2.835	1.619	2.548	0.195	-0.436	-0.688	0.000
4	A	226	LEU	0	-0.014	-0.011	5.166	-0.081	-0.037	-0.001	-0.009	-0.033	0.000
5	A	227	GLU	-1	-0.860	-0.922	8.666	-0.449	-0.449	0.000	0.000	0.000	0.000
6	A	228	ASN	0	-0.016	-0.020	10.264	0.165	0.165	0.000	0.000	0.000	0.000
7	A	229	VAL	0	-0.015	0.003	13.548	-0.070	-0.070	0.000	0.000	0.000	0.000
8	A	230	GLN	0	-0.015	-0.004	15.917	0.057	0.057	0.000	0.000	0.000	0.000
9	A	231	PRO	0	0.066	0.042	19.324	0.000	0.000	0.000	0.000	0.000	0.000
10	A	232	ASN	0	-0.034	-0.033	22.351	0.003	0.003	0.000	0.000	0.000	0.000
11	A	233	SER	0	0.009	0.005	19.605	-0.002	-0.002	0.000	0.000	0.000	0.000
12	A	234	ALA	0	0.047	0.017	19.775	0.005	0.005	0.000	0.000	0.000	0.000
13	A	235	ALA	0	0.020	0.001	15.752	0.003	0.003	0.000	0.000	0.000	0.000
14	A	236	SER	0	-0.042	-0.009	17.687	0.013	0.013	0.000	0.000	0.000	0.000
15	A	237	MLY	1	0.834	0.892	19.928	0.179	0.179	0.000	0.000	0.000	0.000
16	A	238	ALA	0	-0.022	-0.002	17.902	0.016	0.016	0.000	0.000	0.000	0.000
17	A	239	GLY	0	0.002	0.010	19.024	0.007	0.007	0.000	0.000	0.000	0.000
18	A	240	LEU	0	-0.038	-0.012	12.487	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	241	GLN	0	-0.043	-0.029	13.796	0.037	0.037	0.000	0.000	0.000	0.000
20	A	242	ALA	0	0.046	0.010	12.155	-0.086	-0.086	0.000	0.000	0.000	0.000
21	A	243	GLY	0	-0.015	-0.004	9.159	0.088	0.088	0.000	0.000	0.000	0.000
22	A	244	ASP	-1	-0.771	-0.847	8.730	-0.322	-0.322	0.000	0.000	0.000	0.000
23	A	245	ARG	1	0.952	0.979	2.827	-2.791	-2.311	0.167	-0.314	-0.333	-0.001
24	A	246	ILE	0	0.004	-0.008	6.710	0.296	0.296	0.000	0.000	0.000	0.000
25	A	247	VAL	0	-0.002	0.004	7.284	-0.063	-0.063	0.000	0.000	0.000	0.000
26	A	248	MLY	1	0.894	0.943	9.329	0.078	0.078	0.000	0.000	0.000	0.000
27	A	249	VAL	0	0.005	0.003	11.653	-0.064	-0.064	0.000	0.000	0.000	0.000
28	A	250	ASP	-1	-0.821	-0.919	14.240	-0.145	-0.145	0.000	0.000	0.000	0.000
29	A	251	GLY	0	-0.025	-0.007	17.031	0.021	0.021	0.000	0.000	0.000	0.000
30	A	252	GLN	0	-0.013	-0.004	15.067	0.023	0.023	0.000	0.000	0.000	0.000
31	A	253	PRO	0	-0.042	-0.034	11.387	-0.046	-0.046	0.000	0.000	0.000	0.000
32	A	254	LEU	0	0.012	0.016	7.224	-0.016	-0.016	0.000	0.000	0.000	0.000
33	A	255	THR	0	-0.025	-0.024	7.198	0.013	0.013	0.000	0.000	0.000	0.000
34	A	256	GLN	0	-0.007	-0.002	7.056	0.059	0.059	0.000	0.000	0.000	0.000
35	A	257	TRP	0	0.074	0.032	5.466	-0.240	-0.240	0.000	0.000	0.000	0.000
36	A	258	VAL	0	0.050	0.014	7.208	0.068	0.068	0.000	0.000	0.000	0.000
37	A	259	THR	0	0.033	0.012	10.491	0.052	0.052	0.000	0.000	0.000	0.000
38	A	260	PHE	0	0.040	0.028	9.850	0.053	0.053	0.000	0.000	0.000	0.000
39	A	261	VAL	0	-0.019	-0.001	10.760	0.078	0.078	0.000	0.000	0.000	0.000
40	A	262	MET	0	-0.007	-0.008	13.246	0.051	0.051	0.000	0.000	0.000	0.000
41	A	263	LEU	0	0.007	0.014	13.859	0.034	0.034	0.000	0.000	0.000	0.000
42	A	264	VAL	0	0.013	0.003	14.894	0.040	0.040	0.000	0.000	0.000	0.000
43	A	265	ARG	1	0.883	0.953	16.140	0.339	0.339	0.000	0.000	0.000	0.000
44	A	266	ASP	-1	-0.858	-0.940	19.363	-0.166	-0.166	0.000	0.000	0.000	0.000
45	A	267	ASN	0	-0.103	-0.053	19.731	0.043	0.043	0.000	0.000	0.000	0.000
46	A	268	PRO	0	-0.003	0.000	22.290	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	269	GLY	0	-0.025	-0.014	23.926	0.015	0.015	0.000	0.000	0.000	0.000
48	A	270	MLY	1	0.930	0.979	21.843	0.155	0.155	0.000	0.000	0.000	0.000
49	A	271	SER	0	-0.017	-0.024	22.322	-0.016	-0.016	0.000	0.000	0.000	0.000
50	A	272	LEU	0	-0.041	-0.015	16.607	0.007	0.007	0.000	0.000	0.000	0.000
51	A	273	ALA	0	0.025	0.023	18.790	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	274	LEU	0	-0.031	-0.026	13.353	-0.023	-0.023	0.000	0.000	0.000	0.000
53	A	275	GLU	-1	-0.846	-0.897	13.468	-0.075	-0.075	0.000	0.000	0.000	0.000
54	A	276	ILE	0	-0.035	-0.032	10.769	-0.072	-0.072	0.000	0.000	0.000	0.000
55	A	277	GLU	-1	-0.940	-0.973	9.267	0.268	0.268	0.000	0.000	0.000	0.000
56	A	278	ARG	1	0.832	0.875	10.114	0.155	0.155	0.000	0.000	0.000	0.000
57	A	279	GLN	0	-0.021	-0.017	11.964	0.074	0.074	0.000	0.000	0.000	0.000
58	A	280	GLY	0	0.005	0.008	12.012	0.021	0.021	0.000	0.000	0.000	0.000
59	A	281	SER	0	0.004	0.000	13.370	0.022	0.022	0.000	0.000	0.000	0.000
60	A	282	PRO	0	-0.020	0.008	14.220	-0.034	-0.034	0.000	0.000	0.000	0.000
61	A	283	LEU	0	-0.020	-0.026	14.830	0.004	0.004	0.000	0.000	0.000	0.000
62	A	284	SER	0	0.014	0.001	15.514	-0.018	-0.018	0.000	0.000	0.000	0.000
63	A	285	LEU	0	-0.054	-0.015	14.947	0.003	0.003	0.000	0.000	0.000	0.000
64	A	286	THR	0	-0.017	-0.014	18.314	0.005	0.005	0.000	0.000	0.000	0.000
65	A	287	LEU	0	0.003	0.006	15.243	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	288	ILE	0	0.008	0.006	19.135	0.007	0.007	0.000	0.000	0.000	0.000
67	A	289	PRO	0	-0.042	-0.001	18.680	-0.004	-0.004	0.000	0.000	0.000	0.000
68	A	290	GLU	-1	-0.773	-0.867	21.025	-0.157	-0.157	0.000	0.000	0.000	0.000
69	A	291	SER	0	0.014	-0.012	23.107	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	292	MLY	1	0.901	0.962	22.171	0.204	0.204	0.000	0.000	0.000	0.000
71	A	293	PRO	0	0.069	0.022	26.061	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	294	GLY	0	-0.020	0.012	25.751	0.004	0.004	0.000	0.000	0.000	0.000
73	A	295	ASN	0	-0.018	-0.031	26.695	0.010	0.010	0.000	0.000	0.000	0.000
74	A	296	GLY	0	0.049	0.030	29.209	0.003	0.003	0.000	0.000	0.000	0.000
75	A	297	MLY	1	0.945	0.971	25.969	0.123	0.123	0.000	0.000	0.000	0.000
76	A	298	ALA	0	-0.012	0.008	27.128	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	299	ILE	0	-0.049	-0.026	21.223	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	300	GLY	0	0.034	0.022	21.256	0.008	0.008	0.000	0.000	0.000	0.000
79	A	301	PHE	0	-0.050	-0.049	19.245	-0.026	-0.026	0.000	0.000	0.000	0.000
80	A	302	VAL	0	0.064	0.006	15.027	0.024	0.024	0.000	0.000	0.000	0.000
81	A	303	GLY	0	0.021	0.021	17.883	0.005	0.005	0.000	0.000	0.000	0.000
82	A	304	ILE	0	-0.014	0.005	11.064	0.007	0.007	0.000	0.000	0.000	0.000
83	A	305	GLU	-1	-0.920	-0.949	13.028	-0.363	-0.363	0.000	0.000	0.000	0.000
84	A	306	PRO	0	-0.037	-0.051	8.986	-0.117	-0.117	0.000	0.000	0.000	0.000
85	A	307	MLY	1	0.958	0.998	3.550	0.576	0.731	0.006	-0.044	-0.118	0.000
86	A	308	VAL	0	-0.039	-0.018	7.291	0.083	0.083	0.000	0.000	0.000	0.000
87	A	309	ILE	-1	-0.971	-0.970	7.861	-0.181	-0.181	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:223:ACE)