FMO DATABASE

FMODB ID: JLL49

Calculation Name: 4NPX-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4NPX

Chain ID: A

ChEMBL ID:

UniProt ID: Q0PAX7

Base Structure: X-ray

Registration Date: 2023-06-21

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	80
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-484212.730163
FMO2-HF: Nuclear repulsion	452099.84124
FMO2-HF: Total energy	-32112.888923
FMO2-MP2: Total energy	-32207.166969

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:8:PHE)

Summations of interaction energy for fragment #1(A:8:PHE)

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.
-7.753	-3.021	0.744	-2.598	-2.876	-0.003

Interaction energy analysis for fragmet #1(A:8:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / q_NPA : -0.016

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	10	LYS	1	0.844	0.890	2.395	-4.751	-1.554	0.579	-1.705	-2.069	0.006
4	A	11	THR	0	0.023	0.027	2.916	-4.036	-2.501	0.165	-0.893	-0.807	-0.009
5	A	12	PRO	0	0.051	0.010	5.574	0.701	0.701	0.000	0.000	0.000	0.000
6	A	13	LYS	1	0.996	1.014	7.382	0.322	0.322	0.000	0.000	0.000	0.000
7	A	14	GLU	-1	-0.868	-0.945	7.129	0.432	0.432	0.000	0.000	0.000	0.000
8	A	15	LYS	1	0.976	0.984	5.149	-1.038	-1.038	0.000	0.000	0.000	0.000
9	A	16	PHE	0	0.015	0.006	7.998	-0.052	-0.052	0.000	0.000	0.000	0.000
10	A	17	ILE	0	-0.001	-0.004	11.415	-0.026	-0.026	0.000	0.000	0.000	0.000
11	A	18	GLU	-1	-0.832	-0.883	9.145	1.614	1.614	0.000	0.000	0.000	0.000
12	A	19	ILE	0	-0.070	-0.021	10.158	-0.023	-0.023	0.000	0.000	0.000	0.000
13	A	20	ILE	0	0.031	0.020	13.496	-0.052	-0.052	0.000	0.000	0.000	0.000
14	A	21	GLN	0	-0.057	-0.038	14.921	0.037	0.037	0.000	0.000	0.000	0.000
15	A	22	ASN	0	-0.109	-0.057	14.320	-0.057	-0.057	0.000	0.000	0.000	0.000
16	A	23	GLY	0	0.005	0.030	17.303	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	24	ASN	0	-0.008	-0.011	18.942	-0.006	-0.006	0.000	0.000	0.000	0.000
18	A	25	LEU	0	0.029	-0.006	22.373	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	26	GLY	0	0.018	0.018	25.291	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	27	ALA	0	0.008	0.008	20.618	-0.012	-0.012	0.000	0.000	0.000	0.000
21	A	28	LEU	0	-0.005	-0.015	18.914	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	29	GLU	-1	-0.951	-0.972	22.331	0.111	0.111	0.000	0.000	0.000	0.000
23	A	30	LYS	1	0.884	0.947	24.412	-0.136	-0.136	0.000	0.000	0.000	0.000
24	A	31	VAL	0	-0.028	-0.022	19.524	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	32	PHE	0	-0.044	-0.031	19.173	-0.010	-0.010	0.000	0.000	0.000	0.000
26	A	33	GLU	-1	-0.945	-0.964	24.263	0.079	0.079	0.000	0.000	0.000	0.000
27	A	34	GLU	-1	-0.933	-0.968	25.643	0.044	0.044	0.000	0.000	0.000	0.000
28	A	35	PHE	0	-0.013	0.004	21.374	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	36	PHE	0	-0.020	-0.032	24.254	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	37	ALA	0	0.008	0.014	27.627	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	38	ASP	-1	-0.887	-0.945	26.807	0.011	0.011	0.000	0.000	0.000	0.000
32	A	39	HIS	0	-0.053	-0.027	26.174	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	40	ILE	0	-0.016	-0.015	28.775	-0.005	-0.005	0.000	0.000	0.000	0.000
34	A	41	ALA	0	-0.002	0.003	32.060	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	42	MET	0	-0.023	-0.016	26.371	-0.008	-0.008	0.000	0.000	0.000	0.000
36	A	43	VAL	0	0.014	0.014	31.653	-0.005	-0.005	0.000	0.000	0.000	0.000
37	A	44	GLU	-1	-0.924	-0.956	33.943	0.005	0.005	0.000	0.000	0.000	0.000
38	A	45	LEU	0	-0.067	-0.042	34.406	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	46	LEU	0	0.004	0.016	31.944	-0.003	-0.003	0.000	0.000	0.000	0.000
40	A	47	GLU	-1	-0.859	-0.928	36.354	-0.004	-0.004	0.000	0.000	0.000	0.000
41	A	48	LYS	1	0.826	0.925	39.300	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	49	GLN	0	-0.095	-0.066	38.339	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	50	GLY	0	-0.064	-0.019	40.818	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	51	LEU	0	-0.033	-0.004	35.682	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	52	THR	0	-0.020	-0.011	37.313	0.004	0.004	0.000	0.000	0.000	0.000
46	A	53	GLU	-1	-0.811	-0.931	30.903	-0.019	-0.019	0.000	0.000	0.000	0.000
47	A	54	MET	0	-0.079	-0.049	33.189	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	55	ASP	-1	-0.828	-0.919	34.097	-0.038	-0.038	0.000	0.000	0.000	0.000
49	A	56	VAL	0	-0.002	0.010	28.998	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	57	LYS	1	0.918	0.946	27.079	0.019	0.019	0.000	0.000	0.000	0.000
51	A	58	ASN	0	0.035	0.004	29.499	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	59	PHE	0	0.041	0.046	25.575	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	60	ILE	0	-0.049	-0.036	24.268	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	61	LEU	0	-0.087	-0.042	25.726	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	62	GLU	-1	-0.964	-0.966	28.020	-0.080	-0.080	0.000	0.000	0.000	0.000
56	A	63	ASN	0	-0.092	-0.039	25.527	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	64	GLY	0	0.026	-0.001	22.806	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	65	ASP	-1	-0.852	-0.924	19.941	-0.243	-0.243	0.000	0.000	0.000	0.000
59	A	66	PHE	0	-0.046	-0.020	19.449	-0.018	-0.018	0.000	0.000	0.000	0.000
60	A	67	ILE	0	-0.030	-0.026	19.927	0.000	0.000	0.000	0.000	0.000	0.000
61	A	68	GLU	-1	-0.947	-0.965	14.949	-0.362	-0.362	0.000	0.000	0.000	0.000
62	A	69	GLU	-1	-0.951	-0.979	15.257	-0.412	-0.412	0.000	0.000	0.000	0.000
63	A	70	ARG	1	0.954	0.970	15.422	0.129	0.129	0.000	0.000	0.000	0.000
64	A	71	GLN	0	-0.038	-0.016	15.586	0.006	0.006	0.000	0.000	0.000	0.000
65	A	72	ASN	0	0.004	-0.011	11.095	0.048	0.048	0.000	0.000	0.000	0.000
66	A	73	ASP	-1	-0.871	-0.925	12.187	-0.222	-0.222	0.000	0.000	0.000	0.000
67	A	74	ILE	0	-0.005	0.000	14.456	0.044	0.044	0.000	0.000	0.000	0.000
68	A	75	TYR	0	-0.052	-0.027	11.225	0.050	0.050	0.000	0.000	0.000	0.000
69	A	76	ILE	0	-0.048	-0.030	9.503	0.083	0.083	0.000	0.000	0.000	0.000
70	A	77	GLU	-1	-0.850	-0.907	11.892	0.091	0.091	0.000	0.000	0.000	0.000
71	A	78	LEU	0	0.030	0.003	15.458	0.039	0.039	0.000	0.000	0.000	0.000
72	A	79	GLY	0	0.014	0.006	12.565	0.041	0.041	0.000	0.000	0.000	0.000
73	A	80	ALA	0	-0.036	-0.019	13.106	0.058	0.058	0.000	0.000	0.000	0.000
74	A	81	LYS	1	0.882	0.933	14.148	-0.048	-0.048	0.000	0.000	0.000	0.000
75	A	82	ILE	0	0.002	0.010	16.050	0.009	0.009	0.000	0.000	0.000	0.000
76	A	83	LEU	0	-0.052	-0.045	11.084	0.030	0.030	0.000	0.000	0.000	0.000
77	A	84	GLY	0	-0.013	0.009	15.599	0.004	0.004	0.000	0.000	0.000	0.000
78	A	85	HIS	0	-0.058	-0.032	18.093	-0.044	-0.044	0.000	0.000	0.000	0.000
79	A	86	GLU	-1	-0.932	-0.945	19.794	0.091	0.091	0.000	0.000	0.000	0.000
80	A	87	GLY	0	0.033	0.018	22.081	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:PHE)