FMO DATABASE

FMODB ID: XYNL2

Calculation Name: 4NL9-C-Xray40

Preferred Name:

Target Type:

Ligand Name: magnesium ion

ligand 3-letter code: MG

PDB ID: 4NL9

Chain ID: C

ChEMBL ID:

UniProt ID: Q6ZW76

Base Structure: X-ray

Registration Date: 2019-02-15

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	106
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-397178.930813
FMO2-HF: Nuclear repulsion	370504.436967
FMO2-HF: Total energy	-26674.493845
FMO2-MP2: Total energy	-26751.738121

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(C:7:ACE)

Summations of interaction energy for fragment #1(C:7: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.
-1.133	-0.218	-0.016	-0.398	-0.5	0

Interaction energy analysis for fragmet #1(C:7:ACE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.043 / q_NPA : -0.033

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].
3	C	9	LEU	0	0.078	0.046	3.808	1.223	2.058	-0.014	-0.387	-0.434
4	C	10	THR	0	0.047	0.019	6.896	0.444	0.444	0.000	0.000	0.000
5	C	11	GLY	0	0.029	0.007	4.487	0.302	0.352	-0.001	-0.007	-0.042
6	C	12	ILE	0	0.004	0.004	4.859	0.443	0.443	0.000	0.000	0.000
7	C	13	LEU	0	0.008	0.004	6.762	0.135	0.135	0.000	0.000	0.000
8	C	14	LYS	1	0.887	0.952	8.359	-0.033	-0.033	0.000	0.000	0.000
9	C	15	LYS	1	0.954	0.979	4.717	-2.205	-2.175	-0.001	-0.004	-0.024
10	C	16	LEU	0	0.000	0.021	9.842	-0.022	-0.022	0.000	0.000	0.000
11	C	17	SER	0	-0.034	0.002	12.490	-0.035	-0.035	0.000	0.000	0.000
12	C	18	LEU	0	-0.077	-0.039	13.357	-0.034	-0.034	0.000	0.000	0.000
13	C	19	GLU	-1	-0.782	-0.902	12.644	0.051	0.051	0.000	0.000	0.000
14	C	20	LYS	1	0.894	0.967	14.011	-0.016	-0.016	0.000	0.000	0.000
15	C	21	TYR	0	0.055	0.002	15.712	0.005	0.005	0.000	0.000	0.000
16	C	22	GLN	0	-0.025	0.000	11.904	-0.088	-0.088	0.000	0.000	0.000
17	C	23	PRO	0	0.022	0.009	14.412	-0.033	-0.033	0.000	0.000	0.000
18	C	24	ILE	0	0.000	0.017	17.490	-0.002	-0.002	0.000	0.000	0.000
19	C	25	PHE	0	-0.002	-0.025	13.824	0.004	0.004	0.000	0.000	0.000
20	C	26	GLU	-1	-0.895	-0.934	14.726	-0.297	-0.297	0.000	0.000	0.000
21	C	27	GLU	-1	-0.832	-0.904	15.793	-0.144	-0.144	0.000	0.000	0.000
22	C	28	GLN	0	-0.048	-0.023	18.770	0.012	0.012	0.000	0.000	0.000
23	C	29	GLU	-1	-0.905	-0.926	16.712	-0.263	-0.263	0.000	0.000	0.000
24	C	30	VAL	0	-0.027	-0.007	13.685	-0.010	-0.010	0.000	0.000	0.000
25	C	31	ASP	-1	-0.759	-0.859	11.811	-0.658	-0.658	0.000	0.000	0.000
26	C	32	MET	0	-0.042	-0.040	6.684	0.035	0.035	0.000	0.000	0.000
27	C	33	GLU	-1	-0.893	-0.943	10.231	-0.295	-0.295	0.000	0.000	0.000
28	C	34	ALA	0	0.081	0.059	13.396	0.077	0.077	0.000	0.000	0.000
29	C	35	PHE	0	-0.009	-0.012	9.724	0.068	0.068	0.000	0.000	0.000
30	C	36	LEU	0	-0.006	-0.004	9.827	0.067	0.067	0.000	0.000	0.000
31	C	37	THR	0	-0.067	-0.030	13.320	0.080	0.080	0.000	0.000	0.000
32	C	38	LEU	0	-0.011	0.029	14.728	0.043	0.043	0.000	0.000	0.000
33	C	39	THR	0	0.018	0.019	17.681	0.023	0.023	0.000	0.000	0.000
34	C	40	ASP	-1	-0.721	-0.853	20.501	-0.069	-0.069	0.000	0.000	0.000
35	C	41	GLY	0	0.003	0.006	22.179	0.002	0.002	0.000	0.000	0.000
36	C	42	ASP	-1	-0.635	-0.807	20.358	-0.160	-0.160	0.000	0.000	0.000
37	C	43	LEU	0	-0.015	-0.001	16.572	-0.001	-0.001	0.000	0.000	0.000
38	C	44	LYS	1	0.866	0.937	20.628	0.066	0.066	0.000	0.000	0.000
39	C	45	GLU	-1	-0.838	-0.867	24.216	-0.120	-0.120	0.000	0.000	0.000
40	C	46	LEU	0	0.005	0.007	18.175	0.002	0.002	0.000	0.000	0.000
41	C	47	GLY	0	-0.007	0.015	22.285	0.000	0.000	0.000	0.000	0.000
42	C	48	ILE	0	-0.036	-0.007	17.666	0.017	0.017	0.000	0.000	0.000
43	C	49	LYS	1	1.035	1.010	21.977	0.053	0.053	0.000	0.000	0.000
44	C	50	THR	0	-0.065	-0.038	22.685	0.010	0.010	0.000	0.000	0.000
45	C	51	ASP	-1	-0.800	-0.893	22.604	-0.033	-0.033	0.000	0.000	0.000
46	C	52	GLY	0	0.018	0.005	22.199	-0.002	-0.002	0.000	0.000	0.000
47	C	53	SER	0	0.004	0.028	18.718	0.008	0.008	0.000	0.000	0.000
48	C	54	ARG	1	0.766	0.865	17.688	0.055	0.055	0.000	0.000	0.000
49	C	55	GLN	0	-0.009	0.013	18.355	-0.002	-0.002	0.000	0.000	0.000
50	C	56	GLN	0	0.067	0.037	15.447	-0.012	-0.012	0.000	0.000	0.000
51	C	57	ILE	0	0.024	0.010	13.282	0.013	0.013	0.000	0.000	0.000
52	C	58	LEU	0	-0.002	0.000	13.776	-0.020	-0.020	0.000	0.000	0.000
53	C	59	ALA	0	-0.003	0.006	15.694	-0.005	-0.005	0.000	0.000	0.000
54	C	60	ALA	0	-0.016	-0.013	10.112	0.019	0.019	0.000	0.000	0.000
55	C	61	ILE	0	-0.018	-0.001	11.130	-0.003	-0.003	0.000	0.000	0.000
56	C	62	SER	0	-0.022	-0.010	12.608	-0.008	-0.008	0.000	0.000	0.000
57	C	63	GLU	-1	-0.970	-0.985	11.196	0.230	0.230	0.000	0.000	0.000
58	C	64	LEU	0	-0.073	-0.041	6.700	0.006	0.006	0.000	0.000	0.000
59	C	65	ASN	0	-0.018	-0.012	10.716	-0.055	-0.055	0.000	0.000	0.000
60	C	66	ALA	0	-0.048	-0.002	14.002	0.011	0.011	0.000	0.000	0.000
61	C	67	GLY	0	-0.034	-0.015	15.368	0.012	0.012	0.000	0.000	0.000
62	C	68	NME	0	-0.009	0.001	17.491	-0.017	-0.017	0.000	0.000	0.000
63	A	152	HOH	0	-0.042	-0.020	19.649	0.013	0.013	0.000	0.000	0.000
64	B	105	HOH	0	0.016	-0.001	22.098	0.001	0.001	0.000	0.000	0.000
65	B	106	HOH	0	-0.038	-0.027	25.532	0.004	0.004	0.000	0.000	0.000
66	B	110	HOH	0	-0.029	-0.018	20.337	0.004	0.004	0.000	0.000	0.000
67	B	113	HOH	0	-0.031	-0.022	19.707	-0.002	-0.002	0.000	0.000	0.000
68	B	116	HOH	0	-0.010	-0.002	22.160	-0.001	-0.001	0.000	0.000	0.000
69	B	117	HOH	0	-0.040	-0.022	26.529	0.004	0.004	0.000	0.000	0.000
70	C	101	HOH	0	-0.059	-0.032	25.131	0.005	0.005	0.000	0.000	0.000
71	C	102	HOH	0	0.000	-0.002	16.907	-0.012	-0.012	0.000	0.000	0.000
72	C	103	HOH	0	0.033	0.019	21.383	-0.003	-0.003	0.000	0.000	0.000
73	C	104	HOH	0	-0.014	-0.011	22.937	-0.004	-0.004	0.000	0.000	0.000
74	C	105	HOH	0	0.025	0.015	25.600	-0.001	-0.001	0.000	0.000	0.000
75	C	106	HOH	0	-0.022	-0.021	26.254	0.001	0.001	0.000	0.000	0.000
76	C	107	HOH	0	-0.050	-0.037	16.611	0.008	0.008	0.000	0.000	0.000
77	C	108	HOH	0	-0.024	-0.021	17.786	0.012	0.012	0.000	0.000	0.000
78	C	109	HOH	0	-0.022	-0.019	25.642	0.001	0.001	0.000	0.000	0.000
79	C	111	HOH	0	-0.034	-0.023	23.978	0.006	0.006	0.000	0.000	0.000
80	C	112	HOH	0	-0.014	-0.008	24.633	0.005	0.005	0.000	0.000	0.000
81	C	113	HOH	0	-0.044	-0.036	16.480	0.002	0.002	0.000	0.000	0.000
82	C	114	HOH	0	-0.037	-0.029	19.147	-0.003	-0.003	0.000	0.000	0.000
83	C	115	HOH	0	-0.022	-0.018	18.873	0.003	0.003	0.000	0.000	0.000
84	C	116	HOH	0	-0.044	-0.045	22.358	0.001	0.001	0.000	0.000	0.000
85	C	117	HOH	0	-0.021	-0.016	13.740	0.011	0.011	0.000	0.000	0.000
86	C	119	HOH	0	-0.005	0.004	16.649	0.012	0.012	0.000	0.000	0.000
87	C	120	HOH	0	-0.039	-0.029	23.593	0.007	0.007	0.000	0.000	0.000
88	C	123	HOH	0	-0.064	-0.039	17.106	-0.012	-0.012	0.000	0.000	0.000
89	C	124	HOH	0	-0.042	-0.039	20.247	0.005	0.005	0.000	0.000	0.000
90	C	128	HOH	0	-0.046	-0.023	21.947	0.008	0.008	0.000	0.000	0.000
91	C	129	HOH	0	-0.054	-0.045	24.088	-0.001	-0.001	0.000	0.000	0.000
92	C	130	HOH	0	-0.026	-0.014	27.309	-0.002	-0.002	0.000	0.000	0.000
93	C	131	HOH	0	-0.027	-0.023	25.653	0.002	0.002	0.000	0.000	0.000
94	C	132	HOH	0	-0.045	-0.041	14.948	0.002	0.002	0.000	0.000	0.000
95	C	134	HOH	0	-0.026	-0.024	19.653	-0.012	-0.012	0.000	0.000	0.000
96	C	138	HOH	0	-0.069	-0.061	26.345	0.004	0.004	0.000	0.000	0.000
97	C	139	HOH	0	0.016	0.011	11.904	-0.066	-0.066	0.000	0.000	0.000
98	C	141	HOH	0	-0.048	-0.032	23.784	0.005	0.005	0.000	0.000	0.000
99	C	143	HOH	0	-0.061	-0.086	20.403	0.001	0.001	0.000	0.000	0.000
100	C	145	HOH	0	-0.046	-0.036	13.303	0.016	0.016	0.000	0.000	0.000
101	C	147	HOH	0	-0.058	-0.041	26.117	0.004	0.004	0.000	0.000	0.000
102	C	148	HOH	0	-0.013	-0.012	9.975	0.018	0.018	0.000	0.000	0.000
103	C	149	HOH	0	0.000	0.012	23.290	-0.003	-0.003	0.000	0.000	0.000
104	C	151	HOH	0	-0.066	-0.050	13.644	-0.041	-0.041	0.000	0.000	0.000
105	C	153	HOH	0	0.033	0.046	19.088	-0.007	-0.007	0.000	0.000	0.000
106	D	248	HOH	0	0.021	0.014	26.066	-0.002	-0.002	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:7:ACE)