FMO DATABASE

FMODB ID: XVK71

Calculation Name: 4NL9-A-Xray40

Preferred Name:

Target Type:

Ligand Name: magnesium ion

ligand 3-letter code: MG

PDB ID: 4NL9

Chain ID: A

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	109
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-449397.102472
FMO2-HF: Nuclear repulsion	420599.141475
FMO2-HF: Total energy	-28797.960997
FMO2-MP2: Total energy	-28881.013493

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:2:ACE)

Summations of interaction energy for fragment #1(A:2: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.
2.018	2.787	-0.013	-0.332	-0.423	0

Interaction energy analysis for fragmet #1(A:2:ACE)

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 : 0.002

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].
3	A	4	PRO	0	-0.008	0.010	3.819	1.032	1.801	-0.013	-0.332	-0.423
4	A	5	TYR	0	-0.040	-0.056	6.900	-0.013	-0.013	0.000	0.000	0.000
5	A	6	SER	0	-0.006	0.021	4.998	0.253	0.253	0.000	0.000	0.000
6	A	7	GLY	0	0.044	0.035	7.629	0.125	0.125	0.000	0.000	0.000
7	A	8	PRO	0	-0.024	0.002	7.544	0.059	0.059	0.000	0.000	0.000
8	A	9	GLN	0	0.023	-0.006	5.820	-0.109	-0.109	0.000	0.000	0.000
9	A	10	ASP	-1	-0.866	-0.937	8.448	0.430	0.430	0.000	0.000	0.000
10	A	11	LEU	0	0.010	0.001	12.102	-0.011	-0.011	0.000	0.000	0.000
11	A	12	ALA	0	0.022	0.010	14.214	-0.023	-0.023	0.000	0.000	0.000
12	A	13	ALA	0	0.028	0.023	10.027	-0.020	-0.020	0.000	0.000	0.000
13	A	14	LEU	0	-0.012	0.001	12.086	-0.047	-0.047	0.000	0.000	0.000
14	A	15	LEU	0	-0.009	-0.027	14.063	-0.034	-0.034	0.000	0.000	0.000
15	A	16	GLU	-1	-0.954	-0.967	12.854	0.344	0.344	0.000	0.000	0.000
16	A	17	GLN	0	-0.018	0.008	12.160	-0.005	-0.005	0.000	0.000	0.000
17	A	18	ILE	0	-0.071	-0.035	14.998	-0.037	-0.037	0.000	0.000	0.000
18	A	19	GLY	0	0.006	0.004	18.273	-0.017	-0.017	0.000	0.000	0.000
19	A	20	CYS	0	-0.137	-0.082	19.671	-0.019	-0.019	0.000	0.000	0.000
20	A	21	LEU	0	0.127	0.061	16.696	-0.010	-0.010	0.000	0.000	0.000
21	A	22	LYS	1	0.900	0.966	20.628	-0.075	-0.075	0.000	0.000	0.000
22	A	23	TYR	0	-0.017	-0.036	23.181	-0.011	-0.011	0.000	0.000	0.000
23	A	24	LEU	0	0.027	0.030	18.262	-0.006	-0.006	0.000	0.000	0.000
24	A	25	GLN	0	0.038	0.016	21.699	-0.009	-0.009	0.000	0.000	0.000
25	A	26	VAL	0	-0.026	0.004	24.457	-0.006	-0.006	0.000	0.000	0.000
26	A	27	PHE	0	0.014	-0.016	22.073	-0.008	-0.008	0.000	0.000	0.000
27	A	28	GLU	-1	-0.847	-0.909	19.924	0.186	0.186	0.000	0.000	0.000
28	A	29	GLU	-1	-0.947	-0.959	23.486	0.085	0.085	0.000	0.000	0.000
29	A	30	GLN	0	-0.042	-0.009	26.356	-0.006	-0.006	0.000	0.000	0.000
30	A	31	ASP	-1	-0.890	-0.931	24.238	0.088	0.088	0.000	0.000	0.000
31	A	32	VAL	0	-0.032	0.006	21.393	-0.001	-0.001	0.000	0.000	0.000
32	A	33	ASP	-1	-0.764	-0.834	17.632	0.140	0.140	0.000	0.000	0.000
33	A	34	LEU	0	-0.019	-0.020	12.421	-0.019	-0.019	0.000	0.000	0.000
34	A	35	ARG	1	0.945	0.970	16.524	-0.081	-0.081	0.000	0.000	0.000
35	A	36	GLU	-1	-0.757	-0.854	18.046	0.054	0.054	0.000	0.000	0.000
36	A	37	PHE	0	0.037	0.011	18.314	-0.012	-0.012	0.000	0.000	0.000
37	A	38	LEU	0	-0.084	-0.049	15.096	-0.011	-0.011	0.000	0.000	0.000
38	A	39	THR	0	-0.094	-0.044	19.785	-0.015	-0.015	0.000	0.000	0.000
39	A	40	LEU	0	-0.003	0.025	23.175	-0.005	-0.005	0.000	0.000	0.000
40	A	41	THR	0	0.004	0.003	25.129	-0.006	-0.006	0.000	0.000	0.000
41	A	42	GLU	-1	-0.763	-0.887	27.870	0.020	0.020	0.000	0.000	0.000
42	A	43	SER	0	0.007	-0.005	29.263	0.003	0.003	0.000	0.000	0.000
43	A	44	ASP	-1	-0.716	-0.825	28.031	0.032	0.032	0.000	0.000	0.000
44	A	45	LEU	0	0.022	0.006	24.036	0.005	0.005	0.000	0.000	0.000
45	A	46	LYS	1	0.807	0.888	28.133	-0.021	-0.021	0.000	0.000	0.000
46	A	47	GLU	-1	-0.872	-0.886	31.594	0.037	0.037	0.000	0.000	0.000
47	A	48	ILE	0	0.037	0.057	26.360	0.001	0.001	0.000	0.000	0.000
48	A	49	GLY	0	0.053	0.038	30.170	0.004	0.004	0.000	0.000	0.000
49	A	50	ILE	0	-0.083	-0.028	25.974	0.002	0.002	0.000	0.000	0.000
50	A	51	THR	0	0.011	0.002	29.226	-0.005	-0.005	0.000	0.000	0.000
51	A	52	LEU	0	0.029	0.007	30.667	-0.006	-0.006	0.000	0.000	0.000
52	A	53	PHE	0	0.037	0.008	30.291	0.002	0.002	0.000	0.000	0.000
53	A	54	GLY	0	0.006	0.002	28.869	-0.001	-0.001	0.000	0.000	0.000
54	A	55	PRO	0	0.023	-0.001	25.330	-0.001	-0.001	0.000	0.000	0.000
55	A	56	LYS	1	0.957	0.989	24.900	-0.027	-0.027	0.000	0.000	0.000
56	A	57	ARG	1	0.870	0.943	26.029	-0.011	-0.011	0.000	0.000	0.000
57	A	58	LYS	1	0.859	0.933	21.935	-0.069	-0.069	0.000	0.000	0.000
58	A	59	MET	0	0.070	0.046	21.270	-0.003	-0.003	0.000	0.000	0.000
59	A	60	THR	0	0.054	0.048	21.687	-0.006	-0.006	0.000	0.000	0.000
60	A	61	SER	0	-0.031	-0.013	22.089	-0.010	-0.010	0.000	0.000	0.000
61	A	62	ALA	0	0.001	-0.005	17.439	-0.013	-0.013	0.000	0.000	0.000
62	A	63	ILE	0	0.010	0.019	17.959	-0.009	-0.009	0.000	0.000	0.000
63	A	64	ALA	0	-0.041	-0.024	19.764	-0.009	-0.009	0.000	0.000	0.000
64	A	65	ARG	1	0.841	0.921	15.786	-0.001	-0.001	0.000	0.000	0.000
65	A	66	TRP	0	-0.028	-0.014	11.485	-0.022	-0.022	0.000	0.000	0.000
66	A	67	NME	0	0.020	0.035	16.084	0.002	0.002	0.000	0.000	0.000
67	A	101	HOH	0	0.002	0.000	28.122	0.001	0.001	0.000	0.000	0.000
68	A	102	HOH	0	-0.061	-0.048	30.193	-0.002	-0.002	0.000	0.000	0.000
69	A	103	HOH	0	0.007	0.007	29.620	0.000	0.000	0.000	0.000	0.000
70	A	104	HOH	0	-0.001	-0.016	15.220	0.002	0.002	0.000	0.000	0.000
71	A	105	HOH	0	0.067	0.032	14.962	-0.009	-0.009	0.000	0.000	0.000
72	A	106	HOH	0	-0.032	-0.028	33.829	-0.001	-0.001	0.000	0.000	0.000
73	A	107	HOH	0	-0.020	-0.021	32.222	0.000	0.000	0.000	0.000	0.000
74	A	108	HOH	0	0.014	0.010	28.520	-0.001	-0.001	0.000	0.000	0.000
75	A	109	HOH	0	-0.059	-0.039	31.760	0.000	0.000	0.000	0.000	0.000
76	A	110	HOH	0	-0.003	-0.003	24.028	0.002	0.002	0.000	0.000	0.000
77	A	111	HOH	0	-0.030	-0.024	31.362	-0.001	-0.001	0.000	0.000	0.000
78	A	112	HOH	0	-0.015	-0.018	26.535	-0.002	-0.002	0.000	0.000	0.000
79	A	113	HOH	0	-0.040	-0.044	15.736	0.000	0.000	0.000	0.000	0.000
80	A	114	HOH	0	-0.004	-0.011	24.983	0.000	0.000	0.000	0.000	0.000
81	A	115	HOH	0	-0.025	-0.019	33.298	0.001	0.001	0.000	0.000	0.000
82	A	116	HOH	0	0.015	0.019	33.480	0.000	0.000	0.000	0.000	0.000
83	A	117	HOH	0	-0.001	-0.017	19.938	0.010	0.010	0.000	0.000	0.000
84	A	118	HOH	0	-0.014	-0.007	27.328	0.001	0.001	0.000	0.000	0.000
85	A	119	HOH	0	-0.011	-0.021	34.620	-0.001	-0.001	0.000	0.000	0.000
86	A	120	HOH	0	-0.039	-0.028	30.895	0.002	0.002	0.000	0.000	0.000
87	A	122	HOH	0	0.008	0.000	26.019	0.002	0.002	0.000	0.000	0.000
88	A	123	HOH	0	-0.033	-0.024	19.600	-0.002	-0.002	0.000	0.000	0.000
89	A	125	HOH	0	-0.040	-0.044	19.204	-0.006	-0.006	0.000	0.000	0.000
90	A	126	HOH	0	0.039	0.022	36.078	0.001	0.001	0.000	0.000	0.000
91	A	128	HOH	0	0.033	0.040	13.376	-0.021	-0.021	0.000	0.000	0.000
92	A	129	HOH	0	-0.065	-0.065	36.212	-0.001	-0.001	0.000	0.000	0.000
93	A	130	HOH	0	-0.049	-0.044	30.082	0.002	0.002	0.000	0.000	0.000
94	A	131	HOH	0	0.007	0.009	35.424	0.000	0.000	0.000	0.000	0.000
95	A	132	HOH	0	-0.021	-0.020	31.609	-0.001	-0.001	0.000	0.000	0.000
96	A	133	HOH	0	-0.033	-0.020	21.249	-0.002	-0.002	0.000	0.000	0.000
97	A	134	HOH	0	-0.018	-0.017	28.603	0.000	0.000	0.000	0.000	0.000
98	A	135	HOH	0	-0.077	-0.064	25.699	-0.003	-0.003	0.000	0.000	0.000
99	A	139	HOH	0	-0.036	-0.017	32.188	-0.002	-0.002	0.000	0.000	0.000
100	A	142	HOH	0	-0.028	-0.013	25.614	-0.002	-0.002	0.000	0.000	0.000
101	A	146	HOH	0	-0.061	-0.031	26.872	-0.002	-0.002	0.000	0.000	0.000
102	A	147	HOH	0	-0.035	-0.014	18.052	0.013	0.013	0.000	0.000	0.000
103	A	152	HOH	0	-0.001	0.004	20.241	-0.004	-0.004	0.000	0.000	0.000
104	A	153	HOH	0	-0.074	-0.062	23.621	0.000	0.000	0.000	0.000	0.000
105	A	155	HOH	0	0.006	0.008	26.360	0.004	0.004	0.000	0.000	0.000
106	A	160	HOH	0	-0.055	-0.061	8.859	-0.032	-0.032	0.000	0.000	0.000
107	A	162	HOH	0	-0.030	-0.018	34.429	-0.001	-0.001	0.000	0.000	0.000
108	C	123	HOH	0	0.020	0.006	26.421	0.001	0.001	0.000	0.000	0.000
109	D	201	HOH	0	0.028	0.022	28.906	-0.002	-0.002	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:2:ACE)