FMO DATABASE

FMODB ID: 765VK

Calculation Name: 3NX6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NX6

Chain ID: A

ChEMBL ID:

UniProt ID: Q5GUT0

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptHSide
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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-420717.097077
FMO2-HF: Nuclear repulsion	393559.602552
FMO2-HF: Total energy	-27157.494525
FMO2-MP2: Total energy	-27239.085931

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:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-4.11	-2.183	-0.005	-0.854	-1.071	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.004

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	4	LYS	1	1.021	1.013	3.878	-0.918	0.454	-0.006	-0.695	-0.671	0.001
4	A	5	PRO	0	-0.042	0.000	6.410	-0.214	-0.214	0.000	0.000	0.000	0.000
5	A	6	LEU	0	0.029	-0.011	9.822	-0.138	-0.138	0.000	0.000	0.000	0.000
6	A	7	HIS	0	-0.006	-0.009	12.938	0.060	0.060	0.000	0.000	0.000	0.000
7	A	8	ASP	-1	-0.740	-0.839	16.040	0.413	0.413	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.899	0.962	12.874	-0.490	-0.490	0.000	0.000	0.000	0.000
9	A	10	VAL	0	0.037	0.011	12.337	0.050	0.050	0.000	0.000	0.000	0.000
10	A	11	VAL	0	-0.026	-0.010	6.607	-0.068	-0.068	0.000	0.000	0.000	0.000
11	A	12	VAL	0	0.040	0.022	9.874	0.025	0.025	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.960	0.992	10.037	-0.564	-0.564	0.000	0.000	0.000	0.000
13	A	14	PRO	0	0.020	0.013	11.647	-0.091	-0.091	0.000	0.000	0.000	0.000
14	A	15	ILE	0	-0.060	-0.016	14.825	-0.029	-0.029	0.000	0.000	0.000	0.000
15	A	35	SER	0	0.002	-0.022	23.463	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	36	THR	0	-0.079	-0.046	19.948	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	37	LYS	1	1.004	0.997	20.166	-0.241	-0.241	0.000	0.000	0.000	0.000
18	A	38	GLY	0	0.020	-0.005	16.092	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	39	GLU	-1	-0.981	-0.981	13.703	0.599	0.599	0.000	0.000	0.000	0.000
20	A	40	VAL	0	-0.010	-0.004	12.605	0.139	0.139	0.000	0.000	0.000	0.000
21	A	41	VAL	0	0.018	0.007	6.723	-0.034	-0.034	0.000	0.000	0.000	0.000
22	A	42	ALA	0	-0.011	-0.014	6.941	0.332	0.332	0.000	0.000	0.000	0.000
23	A	43	ILE	0	0.022	0.010	9.103	-0.170	-0.170	0.000	0.000	0.000	0.000
24	A	44	GLY	0	-0.027	0.002	11.526	0.032	0.032	0.000	0.000	0.000	0.000
25	A	45	ALA	0	-0.021	-0.027	13.223	-0.034	-0.034	0.000	0.000	0.000	0.000
26	A	46	GLY	0	0.089	0.048	15.320	-0.037	-0.037	0.000	0.000	0.000	0.000
27	A	47	LYS	1	0.898	0.950	18.330	-0.240	-0.240	0.000	0.000	0.000	0.000
28	A	48	PRO	0	0.003	-0.003	19.608	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	49	LEU	0	-0.026	-0.010	22.580	0.002	0.002	0.000	0.000	0.000	0.000
30	A	50	ASP	-1	-0.885	-0.952	26.256	0.125	0.125	0.000	0.000	0.000	0.000
31	A	51	ASN	0	-0.069	-0.021	29.165	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	52	GLY	0	0.015	0.013	27.215	-0.005	-0.005	0.000	0.000	0.000	0.000
33	A	53	SER	0	-0.041	-0.017	25.258	0.003	0.003	0.000	0.000	0.000	0.000
34	A	54	LEU	0	-0.023	-0.017	18.700	0.000	0.000	0.000	0.000	0.000	0.000
35	A	55	HIS	0	-0.023	-0.011	21.732	-0.024	-0.024	0.000	0.000	0.000	0.000
36	A	56	ALA	0	-0.004	-0.003	20.814	0.030	0.030	0.000	0.000	0.000	0.000
37	A	57	PRO	0	0.006	0.002	16.737	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	58	VAL	0	-0.033	-0.008	19.550	-0.021	-0.021	0.000	0.000	0.000	0.000
39	A	59	VAL	0	-0.060	-0.026	16.229	0.000	0.000	0.000	0.000	0.000	0.000
40	A	60	LYS	1	0.876	0.910	15.980	-0.394	-0.394	0.000	0.000	0.000	0.000
41	A	61	VAL	0	-0.008	-0.015	10.939	0.015	0.015	0.000	0.000	0.000	0.000
42	A	62	GLY	0	0.031	0.020	13.602	-0.101	-0.101	0.000	0.000	0.000	0.000
43	A	63	ASP	-1	-0.855	-0.888	15.385	0.392	0.392	0.000	0.000	0.000	0.000
44	A	64	LYS	1	0.968	0.981	16.508	-0.297	-0.297	0.000	0.000	0.000	0.000
45	A	65	VAL	0	0.007	-0.004	16.597	-0.038	-0.038	0.000	0.000	0.000	0.000
46	A	66	ILE	0	-0.031	-0.015	19.610	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	67	TYR	0	0.084	0.038	16.622	0.036	0.036	0.000	0.000	0.000	0.000
48	A	68	GLY	0	0.082	0.043	20.890	-0.026	-0.026	0.000	0.000	0.000	0.000
49	A	69	GLN	0	0.037	0.036	20.330	0.058	0.058	0.000	0.000	0.000	0.000
50	A	70	TYR	0	-0.033	-0.039	19.942	0.023	0.023	0.000	0.000	0.000	0.000
51	A	71	ALA	0	0.032	0.044	19.309	-0.017	-0.017	0.000	0.000	0.000	0.000
52	A	72	GLY	0	0.060	0.020	16.392	0.040	0.040	0.000	0.000	0.000	0.000
53	A	73	SER	0	-0.056	-0.021	13.723	-0.058	-0.058	0.000	0.000	0.000	0.000
54	A	74	SER	0	-0.033	-0.031	12.639	0.120	0.120	0.000	0.000	0.000	0.000
55	A	75	TYR	0	-0.003	-0.015	3.556	-0.282	-0.054	0.000	-0.067	-0.162	0.000
56	A	76	LYS	1	0.887	0.919	8.704	0.010	0.010	0.000	0.000	0.000	0.000
57	A	77	SER	0	-0.043	-0.039	3.690	0.138	0.371	0.002	-0.085	-0.151	0.000
58	A	78	GLU	-1	-0.859	-0.905	4.509	-3.247	-3.153	-0.001	-0.007	-0.087	0.000
59	A	79	GLY	0	-0.017	-0.013	7.919	0.211	0.211	0.000	0.000	0.000	0.000
60	A	80	VAL	0	-0.047	-0.004	8.165	0.087	0.087	0.000	0.000	0.000	0.000
61	A	81	GLU	-1	-0.847	-0.897	9.026	0.406	0.406	0.000	0.000	0.000	0.000
62	A	82	TYR	0	-0.032	-0.022	6.124	0.221	0.221	0.000	0.000	0.000	0.000
63	A	83	LYS	1	0.888	0.943	9.777	-0.591	-0.591	0.000	0.000	0.000	0.000
64	A	84	VAL	0	-0.014	-0.005	9.280	0.168	0.168	0.000	0.000	0.000	0.000
65	A	85	LEU	0	-0.018	0.000	11.920	-0.142	-0.142	0.000	0.000	0.000	0.000
66	A	86	ARG	1	0.829	0.867	14.938	-0.288	-0.288	0.000	0.000	0.000	0.000
67	A	87	GLU	-1	-0.817	-0.920	17.680	0.406	0.406	0.000	0.000	0.000	0.000
68	A	88	ASP	-1	-0.933	-0.969	18.921	0.256	0.256	0.000	0.000	0.000	0.000
69	A	89	ASP	-1	-0.872	-0.927	18.706	0.393	0.393	0.000	0.000	0.000	0.000
70	A	90	ILE	0	-0.112	-0.061	16.543	0.002	0.002	0.000	0.000	0.000	0.000
71	A	91	LEU	0	0.000	0.003	20.720	-0.025	-0.025	0.000	0.000	0.000	0.000
72	A	92	ALA	0	0.005	-0.004	22.927	-0.022	-0.022	0.000	0.000	0.000	0.000
73	A	93	VAL	0	0.030	0.019	20.719	0.035	0.035	0.000	0.000	0.000	0.000
74	A	94	ILE	0	-0.078	-0.034	22.257	-0.033	-0.033	0.000	0.000	0.000	0.000
75	A	95	GLY	0	0.005	0.010	21.033	-0.011	-0.011	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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