FMO DATABASE

FMODB ID: LZ579

Calculation Name: 4NXJ-A-Xray372

Preferred Name:
Warning: Undefined array key "pref_name" in /home/FMODBwui_src/fmodbwui/detail.php on line 446

Target Type:
Warning: Undefined array key "target_type" in /home/FMODBwui_src/fmodbwui/detail.php on line 447

Ligand Name:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 448

ligand 3-letter code:
Warning: Undefined variable $Ligand in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

Warning: Trying to access array offset on value of type null in /home/FMODBwui_src/fmodbwui/detail.php on line 449

PDB ID: 4NXJ

Chain ID: A

ChEMBL ID:
Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

Warning: Undefined array key "chembl_id" in /home/FMODBwui_src/fmodbwui/detail.php on line 452

UniProt ID: Q8IK82

Base Structure: X-ray

Registration Date: 2023-09-20

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	OptH
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	118
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1079150.336333
FMO2-HF: Nuclear repulsion	1029342.417942
FMO2-HF: Total energy	-49807.918391
FMO2-MP2: Total energy	-49954.098098

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:1:GLY)

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

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.
-16.092	-11.455	7.267	-6.177	-5.727	-0.057

Interaction energy analysis for fragmet #1(A:1:GLY)

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 : 0.008

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	3	ASP	-1	-0.832	-0.917	3.736	-3.764	-1.984	0.000	-0.839	-0.941	0.003
4	A	4	GLU	-1	-0.880	-0.934	2.014	-18.313	-15.811	7.268	-5.221	-4.548	-0.060
5	A	5	ILE	0	-0.042	-0.026	3.716	2.603	2.958	-0.001	-0.117	-0.238	0.000
6	A	6	GLU	-1	-0.823	-0.913	5.466	-0.506	-0.506	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.792	-0.881	7.593	-1.054	-1.054	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.009	-0.015	6.448	0.615	0.615	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.851	0.914	9.366	1.731	1.731	0.000	0.000	0.000	0.000
10	A	10	SER	0	-0.016	0.001	11.599	0.283	0.283	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.870	0.934	11.558	1.271	1.271	0.000	0.000	0.000	0.000
12	A	12	ASN	0	0.001	-0.021	13.638	0.132	0.132	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.922	-0.934	15.419	-0.380	-0.380	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.006	0.006	17.543	0.085	0.085	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.030	-0.014	16.927	0.064	0.064	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.013	-0.015	18.722	0.070	0.070	0.000	0.000	0.000	0.000
17	A	17	ASN	0	-0.050	-0.027	21.189	0.064	0.064	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.061	-0.014	23.109	0.033	0.033	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.031	0.012	23.167	0.027	0.027	0.000	0.000	0.000	0.000
20	A	20	ASN	0	0.026	-0.003	24.494	0.039	0.039	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.923	0.969	26.845	0.275	0.275	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.022	0.000	27.304	0.016	0.016	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.020	0.009	27.215	0.014	0.014	0.000	0.000	0.000	0.000
24	A	24	ALA	0	-0.016	-0.002	31.059	0.011	0.011	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.040	-0.015	33.094	0.010	0.010	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.731	-0.841	34.147	-0.097	-0.097	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.855	0.915	35.871	0.118	0.118	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.911	0.952	38.572	0.083	0.083	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.908	0.966	35.525	0.094	0.094	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.026	-0.017	36.677	0.005	0.005	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.029	0.001	32.872	0.004	0.004	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.023	-0.008	30.295	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	33	TYR	0	0.024	0.020	31.052	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	34	PRO	0	0.010	0.020	31.332	0.000	0.000	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.029	0.021	33.790	0.003	0.003	0.000	0.000	0.000	0.000
36	A	36	ASN	0	0.017	0.005	37.377	0.007	0.007	0.000	0.000	0.000	0.000
37	A	37	VAL	0	0.066	0.022	39.027	0.000	0.000	0.000	0.000	0.000	0.000
38	A	38	GLN	0	-0.053	-0.029	41.032	0.004	0.004	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.048	-0.017	43.051	0.001	0.001	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.028	-0.002	41.416	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.031	0.002	42.956	0.000	0.000	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.842	-0.895	43.961	-0.032	-0.032	0.000	0.000	0.000	0.000
43	A	43	TYR	0	0.063	0.031	36.072	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.020	-0.002	35.969	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.022	-0.005	39.255	0.003	0.003	0.000	0.000	0.000	0.000
46	A	46	VAL	0	0.007	0.019	41.194	0.001	0.001	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.052	-0.019	35.128	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.816	0.907	34.877	0.034	0.034	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.915	-0.961	27.716	-0.072	-0.072	0.000	0.000	0.000	0.000
50	A	50	PRO	0	0.001	0.015	31.800	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	51	MET	0	-0.025	-0.014	25.909	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.728	-0.807	28.783	-0.096	-0.096	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.039	-0.018	27.407	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	54	THR	0	-0.054	-0.038	26.329	-0.020	-0.020	0.000	0.000	0.000	0.000
55	A	55	THR	0	-0.050	-0.082	25.016	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	56	MET	0	-0.017	-0.004	23.139	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.894	0.953	21.634	0.191	0.191	0.000	0.000	0.000	0.000
58	A	58	GLN	0	0.020	0.005	20.978	-0.018	-0.018	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.801	0.895	19.291	0.147	0.147	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.013	-0.003	17.150	-0.021	-0.021	0.000	0.000	0.000	0.000
61	A	61	GLN	0	-0.028	0.011	15.993	-0.058	-0.058	0.000	0.000	0.000	0.000
62	A	62	ASN	0	-0.014	-0.002	15.461	0.004	0.004	0.000	0.000	0.000	0.000
63	A	63	PHE	0	0.000	0.005	11.451	-0.010	-0.010	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.937	0.963	12.944	0.071	0.071	0.000	0.000	0.000	0.000
65	A	65	TYR	0	-0.061	-0.057	15.642	0.021	0.021	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.893	0.932	9.594	0.325	0.325	0.000	0.000	0.000	0.000
67	A	67	SER	0	0.012	0.007	13.712	-0.043	-0.043	0.000	0.000	0.000	0.000
68	A	68	PHE	0	0.015	0.003	16.520	0.023	0.023	0.000	0.000	0.000	0.000
69	A	69	GLN	0	0.007	-0.016	19.487	0.042	0.042	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.880	-0.922	16.842	-0.228	-0.228	0.000	0.000	0.000	0.000
71	A	71	PHE	0	0.004	-0.001	19.928	0.021	0.021	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.795	-0.900	21.581	-0.191	-0.191	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.967	0.985	24.133	0.125	0.125	0.000	0.000	0.000	0.000
74	A	74	ASP	-1	-0.725	-0.821	23.414	-0.143	-0.143	0.000	0.000	0.000	0.000
75	A	75	VAL	0	-0.004	-0.007	25.626	0.012	0.012	0.000	0.000	0.000	0.000
76	A	76	LEU	0	0.012	-0.011	28.052	0.012	0.012	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.037	0.015	28.296	0.010	0.010	0.000	0.000	0.000	0.000
78	A	78	ILE	0	-0.023	-0.008	28.514	0.009	0.009	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.031	-0.013	32.078	0.007	0.007	0.000	0.000	0.000	0.000
80	A	80	ASN	0	0.046	0.007	33.170	0.009	0.009	0.000	0.000	0.000	0.000
81	A	81	ASN	0	-0.033	-0.009	32.728	0.010	0.010	0.000	0.000	0.000	0.000
82	A	82	CYS	0	-0.077	-0.025	36.225	0.006	0.006	0.000	0.000	0.000	0.000
83	A	83	TYR	0	-0.039	-0.057	37.679	0.005	0.005	0.000	0.000	0.000	0.000
84	A	84	THR	0	-0.055	-0.039	38.305	0.005	0.005	0.000	0.000	0.000	0.000
85	A	85	TYR	0	-0.078	-0.066	40.312	0.003	0.003	0.000	0.000	0.000	0.000
86	A	86	ASN	0	-0.041	-0.016	41.504	0.000	0.000	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.774	-0.889	44.119	-0.046	-0.046	0.000	0.000	0.000	0.000
88	A	88	PRO	0	-0.009	-0.014	46.270	-0.003	-0.003	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.027	-0.006	47.303	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	90	THR	0	-0.055	-0.027	45.847	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	91	ILE	0	0.031	-0.001	44.668	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	92	TYR	0	-0.016	-0.010	40.951	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	93	TYR	0	0.089	0.062	41.109	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.961	0.992	41.901	0.077	0.077	0.000	0.000	0.000	0.000
95	A	95	PHE	0	-0.040	-0.044	39.400	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.024	0.017	37.373	-0.008	-0.008	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.835	-0.919	37.432	-0.087	-0.087	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.931	-0.961	39.020	-0.101	-0.101	0.000	0.000	0.000	0.000
99	A	99	ILE	0	-0.073	-0.042	32.426	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.833	-0.881	34.037	-0.126	-0.126	0.000	0.000	0.000	0.000
101	A	101	THR	0	-0.039	-0.025	34.775	-0.008	-0.008	0.000	0.000	0.000	0.000
102	A	102	TYR	0	-0.091	-0.052	31.861	-0.011	-0.011	0.000	0.000	0.000	0.000
103	A	103	TYR	0	-0.013	-0.048	26.446	-0.017	-0.017	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.973	0.989	30.754	0.112	0.112	0.000	0.000	0.000	0.000
105	A	105	LYS	1	0.919	0.984	32.862	0.135	0.135	0.000	0.000	0.000	0.000
106	A	106	LEU	0	-0.070	-0.035	28.792	-0.009	-0.009	0.000	0.000	0.000	0.000
107	A	107	ASN	0	0.050	0.011	26.992	-0.010	-0.010	0.000	0.000	0.000	0.000
108	A	108	ILE	0	0.038	0.037	26.161	-0.024	-0.024	0.000	0.000	0.000	0.000
109	A	109	LYS	1	0.903	0.943	26.320	0.188	0.188	0.000	0.000	0.000	0.000
110	A	110	ILE	0	-0.045	-0.036	22.363	-0.025	-0.025	0.000	0.000	0.000	0.000
111	A	111	GLN	0	0.027	0.021	21.985	-0.039	-0.039	0.000	0.000	0.000	0.000
112	A	112	THR	0	0.020	0.011	21.205	-0.031	-0.031	0.000	0.000	0.000	0.000
113	A	113	LYS	1	0.911	0.952	20.763	0.344	0.344	0.000	0.000	0.000	0.000
114	A	114	TYR	0	0.029	0.014	14.840	-0.068	-0.068	0.000	0.000	0.000	0.000
115	A	115	MET	0	-0.017	-0.018	16.430	-0.077	-0.077	0.000	0.000	0.000	0.000
116	A	116	ASN	0	-0.028	-0.018	16.702	-0.025	-0.025	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.057	-0.006	12.377	-0.016	-0.016	0.000	0.000	0.000	0.000
118	A	118	HIS	0	-0.062	-0.023	9.618	0.152	0.152	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

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