FMO DATABASE

FMODB ID: 5J5RZ

Calculation Name: 2NP2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NP2

Chain ID: A

ChEMBL ID:

UniProt ID: Q57267

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	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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-676961.03812
FMO2-HF: Nuclear repulsion	635843.703995
FMO2-HF: Total energy	-41117.334126
FMO2-MP2: Total energy	-41240.282513

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:6:ARG)

Summations of interaction energy for fragment #1(A:6:ARG)

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.
120.724	122.053	-0.022	-0.603	-0.704	0.001

Interaction energy analysis for fragmet #1(A:6:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.961 / q_NPA : 0.977

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	8	LYS	1	0.970	0.982	3.859	28.833	30.162	-0.022	-0.603	-0.704	0.001
4	A	9	VAL	0	0.041	0.032	6.702	2.017	2.017	0.000	0.000	0.000	0.000
5	A	10	THR	0	-0.030	-0.017	9.510	0.427	0.427	0.000	0.000	0.000	0.000
6	A	11	LYS	1	0.930	0.959	13.078	14.930	14.930	0.000	0.000	0.000	0.000
7	A	12	SER	0	0.002	-0.008	16.189	1.075	1.075	0.000	0.000	0.000	0.000
8	A	13	ASP	-1	-0.758	-0.866	12.016	-19.864	-19.864	0.000	0.000	0.000	0.000
9	A	14	ILE	0	-0.010	-0.008	12.168	0.735	0.735	0.000	0.000	0.000	0.000
10	A	15	VAL	0	0.003	0.000	15.466	0.784	0.784	0.000	0.000	0.000	0.000
11	A	16	ASP	-1	-0.890	-0.952	17.038	-13.396	-13.396	0.000	0.000	0.000	0.000
12	A	17	GLN	0	-0.037	-0.031	12.470	-0.185	-0.185	0.000	0.000	0.000	0.000
13	A	18	ILE	0	-0.002	0.002	17.234	0.505	0.505	0.000	0.000	0.000	0.000
14	A	19	ALA	0	-0.013	-0.010	20.089	0.607	0.607	0.000	0.000	0.000	0.000
15	A	20	LEU	0	-0.056	-0.026	17.492	0.478	0.478	0.000	0.000	0.000	0.000
16	A	21	ASN	0	-0.011	0.008	19.379	0.798	0.798	0.000	0.000	0.000	0.000
17	A	22	ILE	0	0.033	0.009	21.179	0.381	0.381	0.000	0.000	0.000	0.000
18	A	23	LYS	1	0.911	0.951	24.231	10.695	10.695	0.000	0.000	0.000	0.000
19	A	24	ASN	0	-0.095	-0.044	21.267	-0.104	-0.104	0.000	0.000	0.000	0.000
20	A	25	ASN	0	0.035	0.024	24.860	0.060	0.060	0.000	0.000	0.000	0.000
21	A	26	ASN	0	-0.009	-0.001	27.541	0.084	0.084	0.000	0.000	0.000	0.000
22	A	27	LEU	0	0.015	0.027	28.261	0.262	0.262	0.000	0.000	0.000	0.000
23	A	28	LYS	1	0.939	0.940	28.753	8.259	8.259	0.000	0.000	0.000	0.000
24	A	29	LEU	0	0.067	0.042	27.133	0.195	0.195	0.000	0.000	0.000	0.000
25	A	30	GLU	-1	-0.892	-0.952	27.416	-9.274	-9.274	0.000	0.000	0.000	0.000
26	A	31	LYS	1	0.963	0.969	21.803	11.856	11.856	0.000	0.000	0.000	0.000
27	A	32	LYS	1	0.924	0.981	25.392	8.587	8.587	0.000	0.000	0.000	0.000
28	A	33	TYR	0	0.060	0.012	27.628	-0.111	-0.111	0.000	0.000	0.000	0.000
29	A	34	ILE	0	0.008	0.027	22.271	-0.049	-0.049	0.000	0.000	0.000	0.000
30	A	35	ARG	1	0.954	0.962	22.482	11.879	11.879	0.000	0.000	0.000	0.000
31	A	36	LEU	0	0.039	0.026	24.099	-0.157	-0.157	0.000	0.000	0.000	0.000
32	A	37	VAL	0	0.016	0.017	25.343	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	38	ILE	0	-0.010	-0.016	19.909	-0.145	-0.145	0.000	0.000	0.000	0.000
34	A	39	ASP	-1	-0.882	-0.947	23.024	-12.819	-12.819	0.000	0.000	0.000	0.000
35	A	40	ALA	0	0.022	0.013	24.692	0.006	0.006	0.000	0.000	0.000	0.000
36	A	41	PHE	0	-0.035	-0.004	20.550	0.062	0.062	0.000	0.000	0.000	0.000
37	A	42	PHE	0	-0.031	-0.034	17.796	-0.253	-0.253	0.000	0.000	0.000	0.000
38	A	43	GLU	-1	-0.979	-0.977	23.573	-10.907	-10.907	0.000	0.000	0.000	0.000
39	A	44	GLU	-1	-0.841	-0.942	26.966	-9.581	-9.581	0.000	0.000	0.000	0.000
40	A	45	LEU	0	-0.057	-0.007	21.988	0.110	0.110	0.000	0.000	0.000	0.000
41	A	46	LYS	1	0.941	0.964	23.140	12.652	12.652	0.000	0.000	0.000	0.000
42	A	47	SER	0	0.092	0.060	26.406	0.069	0.069	0.000	0.000	0.000	0.000
43	A	48	ASN	0	0.013	0.001	28.612	0.444	0.444	0.000	0.000	0.000	0.000
44	A	49	LEU	0	-0.038	-0.026	23.814	0.048	0.048	0.000	0.000	0.000	0.000
45	A	50	CYS	0	-0.066	-0.029	28.323	0.073	0.073	0.000	0.000	0.000	0.000
46	A	51	SER	0	-0.064	-0.017	30.571	0.301	0.301	0.000	0.000	0.000	0.000
47	A	52	ASN	0	-0.088	-0.054	31.107	-0.063	-0.063	0.000	0.000	0.000	0.000
48	A	53	ASN	0	0.000	0.008	31.061	0.373	0.373	0.000	0.000	0.000	0.000
49	A	54	VAL	0	-0.031	-0.032	28.195	-0.371	-0.371	0.000	0.000	0.000	0.000
50	A	55	ILE	0	-0.011	0.011	25.707	0.204	0.204	0.000	0.000	0.000	0.000
51	A	56	GLU	-1	-0.900	-0.957	25.898	-10.383	-10.383	0.000	0.000	0.000	0.000
52	A	57	PHE	0	0.007	0.009	22.807	0.221	0.221	0.000	0.000	0.000	0.000
53	A	58	ARG	1	0.971	0.962	23.588	9.027	9.027	0.000	0.000	0.000	0.000
54	A	59	SER	0	-0.019	-0.016	22.786	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	60	PHE	0	0.036	0.025	16.157	-0.469	-0.469	0.000	0.000	0.000	0.000
56	A	61	GLY	0	0.027	-0.009	19.032	-0.731	-0.731	0.000	0.000	0.000	0.000
57	A	62	THR	0	-0.019	0.004	21.122	0.501	0.501	0.000	0.000	0.000	0.000
58	A	63	PHE	0	-0.022	0.006	19.001	-0.701	-0.701	0.000	0.000	0.000	0.000
59	A	64	GLU	-1	-0.871	-0.945	23.691	-10.900	-10.900	0.000	0.000	0.000	0.000
60	A	65	VAL	0	0.045	0.040	25.347	-0.618	-0.618	0.000	0.000	0.000	0.000
61	A	66	ARG	1	0.834	0.924	24.134	12.261	12.261	0.000	0.000	0.000	0.000
62	A	67	LYS	1	0.990	0.993	26.926	9.286	9.286	0.000	0.000	0.000	0.000
63	A	68	ARG	1	0.884	0.932	22.424	12.421	12.421	0.000	0.000	0.000	0.000
64	A	69	LYS	1	0.973	0.996	27.132	9.421	9.421	0.000	0.000	0.000	0.000
65	A	70	GLY	0	0.037	0.037	27.548	-0.424	-0.424	0.000	0.000	0.000	0.000
66	A	71	ARG	1	0.870	0.922	23.224	12.269	12.269	0.000	0.000	0.000	0.000
67	A	72	LEU	0	0.070	0.018	29.184	0.070	0.070	0.000	0.000	0.000	0.000
68	A	73	ASN	0	0.045	0.006	27.478	0.071	0.071	0.000	0.000	0.000	0.000
69	A	74	ALA	0	-0.033	0.013	24.685	-0.385	-0.385	0.000	0.000	0.000	0.000
70	A	75	ARG	1	1.029	1.022	21.312	13.471	13.471	0.000	0.000	0.000	0.000
71	A	76	ASN	0	0.066	0.055	22.080	-1.150	-1.150	0.000	0.000	0.000	0.000
72	A	77	PRO	0	-0.047	-0.040	17.460	0.178	0.178	0.000	0.000	0.000	0.000
73	A	78	GLN	0	-0.018	-0.004	19.014	-0.305	-0.305	0.000	0.000	0.000	0.000
74	A	79	THR	0	0.038	0.023	20.684	0.040	0.040	0.000	0.000	0.000	0.000
75	A	80	GLY	0	-0.071	-0.038	23.679	0.326	0.326	0.000	0.000	0.000	0.000
76	A	81	GLU	-1	-0.910	-0.957	25.113	-10.562	-10.562	0.000	0.000	0.000	0.000
77	A	82	TYR	0	-0.030	-0.016	26.806	-0.350	-0.350	0.000	0.000	0.000	0.000
78	A	83	VAL	0	0.016	0.009	24.715	0.208	0.208	0.000	0.000	0.000	0.000
79	A	84	LYS	1	0.926	0.962	27.936	9.067	9.067	0.000	0.000	0.000	0.000
80	A	85	VAL	0	-0.021	-0.010	24.650	-0.196	-0.196	0.000	0.000	0.000	0.000
81	A	86	LEU	0	0.040	0.019	27.958	0.233	0.233	0.000	0.000	0.000	0.000
82	A	87	ASP	-1	-0.853	-0.939	28.671	-10.011	-10.011	0.000	0.000	0.000	0.000
83	A	88	HIS	0	-0.050	-0.021	24.445	-0.247	-0.247	0.000	0.000	0.000	0.000
84	A	89	HIS	0	0.010	-0.015	27.368	0.203	0.203	0.000	0.000	0.000	0.000
85	A	90	VAL	0	-0.020	-0.005	20.990	-0.290	-0.290	0.000	0.000	0.000	0.000
86	A	91	ALA	0	0.056	0.039	21.429	0.374	0.374	0.000	0.000	0.000	0.000
87	A	92	TYR	0	0.000	-0.013	20.667	-0.587	-0.587	0.000	0.000	0.000	0.000
88	A	93	PHE	0	0.048	0.035	16.229	0.359	0.359	0.000	0.000	0.000	0.000
89	A	94	ARG	1	0.940	0.951	19.268	11.192	11.192	0.000	0.000	0.000	0.000
90	A	95	PRO	0	-0.021	-0.012	16.927	0.584	0.584	0.000	0.000	0.000	0.000
91	A	96	GLY	0	0.022	0.019	19.164	0.562	0.562	0.000	0.000	0.000	0.000
92	A	97	LYS	1	0.906	0.963	20.029	10.103	10.103	0.000	0.000	0.000	0.000
93	A	98	ASP	-1	-0.821	-0.917	19.703	-13.220	-13.220	0.000	0.000	0.000	0.000
94	A	99	LEU	0	0.012	0.011	13.768	-0.442	-0.442	0.000	0.000	0.000	0.000
95	A	100	LYS	1	0.927	0.946	15.898	12.400	12.400	0.000	0.000	0.000	0.000
96	A	101	GLU	-1	-0.927	-0.982	17.250	-12.218	-12.218	0.000	0.000	0.000	0.000
97	A	102	ARG	1	0.886	0.958	14.285	14.501	14.501	0.000	0.000	0.000	0.000
98	A	103	VAL	0	-0.025	-0.016	11.164	-0.704	-0.704	0.000	0.000	0.000	0.000
99	A	104	TRP	0	-0.029	-0.003	12.854	-0.913	-0.913	0.000	0.000	0.000	0.000
100	A	105	GLY	0	0.010	0.011	14.426	-0.559	-0.559	0.000	0.000	0.000	0.000
101	A	106	ILE	0	-0.013	0.005	8.205	0.080	0.080	0.000	0.000	0.000	0.000
102	A	107	LYS	1	0.962	0.987	6.567	17.155	17.155	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:ARG)