FMO DATABASE

FMODB ID: YVRN2

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:

Apendix: None

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	102
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-676886.338241
FMO2-HF: Nuclear repulsion	635768.030781
FMO2-HF: Total energy	-41118.30746
FMO2-MP2: Total energy	-41241.153739

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.
120.237	121.525	-0.02	-0.599	-0.668	0

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 : 0.967 / q_NPA : 0.975

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].
3	A	8	LYS	1	0.974	0.981	3.859	28.280	29.568	-0.020	-0.599	-0.668
4	A	9	VAL	0	0.011	0.015	6.928	2.067	2.067	0.000	0.000	0.000
5	A	10	THR	0	-0.031	-0.049	9.494	0.318	0.318	0.000	0.000	0.000
6	A	11	LYS	1	0.848	0.893	13.067	14.357	14.357	0.000	0.000	0.000
7	A	12	SER	0	0.018	0.004	16.192	1.135	1.135	0.000	0.000	0.000
8	A	13	ASP	-1	-0.793	-0.858	12.686	-19.373	-19.373	0.000	0.000	0.000
9	A	14	ILE	0	0.012	0.005	12.140	0.750	0.750	0.000	0.000	0.000
10	A	15	VAL	0	-0.001	-0.001	15.437	0.803	0.803	0.000	0.000	0.000
11	A	16	ASP	-1	-0.816	-0.894	17.326	-12.800	-12.800	0.000	0.000	0.000
12	A	17	GLN	0	-0.012	-0.012	12.200	-0.058	-0.058	0.000	0.000	0.000
13	A	18	ILE	0	0.005	0.004	17.234	0.507	0.507	0.000	0.000	0.000
14	A	19	ALA	0	0.003	-0.003	20.076	0.602	0.602	0.000	0.000	0.000
15	A	20	LEU	0	-0.056	-0.024	17.481	0.467	0.467	0.000	0.000	0.000
16	A	21	ASN	0	0.008	0.010	19.350	0.687	0.687	0.000	0.000	0.000
17	A	22	ILE	0	0.025	0.003	21.179	0.402	0.402	0.000	0.000	0.000
18	A	23	LYS	1	0.930	0.967	24.244	10.801	10.801	0.000	0.000	0.000
19	A	24	ASN	0	-0.091	-0.049	21.280	-0.035	-0.035	0.000	0.000	0.000
20	A	25	ASN	0	-0.029	-0.004	24.157	0.317	0.317	0.000	0.000	0.000
21	A	26	ASN	0	-0.004	0.003	27.541	0.041	0.041	0.000	0.000	0.000
22	A	27	LEU	0	0.046	0.038	28.658	0.258	0.258	0.000	0.000	0.000
23	A	28	LYS	1	0.928	0.942	28.753	8.185	8.185	0.000	0.000	0.000
24	A	29	LEU	0	0.058	0.036	26.950	0.185	0.185	0.000	0.000	0.000
25	A	30	GLU	-1	-0.846	-0.913	27.416	-9.256	-9.256	0.000	0.000	0.000
26	A	31	LYS	1	0.865	0.895	21.044	12.460	12.460	0.000	0.000	0.000
27	A	32	LYS	1	0.884	0.958	25.366	8.525	8.525	0.000	0.000	0.000
28	A	33	TYR	0	0.059	0.004	27.605	-0.104	-0.104	0.000	0.000	0.000
29	A	34	ILE	0	0.006	0.025	22.193	-0.062	-0.062	0.000	0.000	0.000
30	A	35	ARG	1	0.954	0.963	22.000	12.072	12.072	0.000	0.000	0.000
31	A	36	LEU	0	0.019	0.015	24.078	-0.175	-0.175	0.000	0.000	0.000
32	A	37	VAL	0	0.025	0.020	25.215	-0.016	-0.016	0.000	0.000	0.000
33	A	38	ILE	0	-0.003	-0.012	19.852	-0.148	-0.148	0.000	0.000	0.000
34	A	39	ASP	-1	-0.797	-0.884	23.009	-13.137	-13.137	0.000	0.000	0.000
35	A	40	ALA	0	0.024	0.020	24.680	0.003	0.003	0.000	0.000	0.000
36	A	41	PHE	0	-0.033	-0.004	20.731	0.076	0.076	0.000	0.000	0.000
37	A	42	PHE	0	-0.005	-0.018	17.634	-0.230	-0.230	0.000	0.000	0.000
38	A	43	GLU	-1	-0.896	-0.934	23.564	-11.153	-11.153	0.000	0.000	0.000
39	A	44	GLU	-1	-0.866	-0.950	26.961	-9.521	-9.521	0.000	0.000	0.000
40	A	45	LEU	0	-0.041	0.001	21.856	0.116	0.116	0.000	0.000	0.000
41	A	46	LYS	1	0.842	0.914	23.678	12.151	12.151	0.000	0.000	0.000
42	A	47	SER	0	0.086	0.053	26.456	0.057	0.057	0.000	0.000	0.000
43	A	48	ASN	0	0.017	0.004	28.678	0.433	0.433	0.000	0.000	0.000
44	A	49	LEU	0	-0.033	-0.025	23.757	0.057	0.057	0.000	0.000	0.000
45	A	50	CYS	0	-0.057	-0.028	28.325	0.062	0.062	0.000	0.000	0.000
46	A	51	SER	0	-0.061	-0.018	30.289	0.298	0.298	0.000	0.000	0.000
47	A	52	ASN	0	-0.112	-0.072	30.804	0.042	0.042	0.000	0.000	0.000
48	A	53	ASN	0	0.009	0.020	31.090	0.377	0.377	0.000	0.000	0.000
49	A	54	VAL	0	-0.034	-0.035	28.161	-0.377	-0.377	0.000	0.000	0.000
50	A	55	ILE	0	-0.004	0.016	25.759	0.217	0.217	0.000	0.000	0.000
51	A	56	GLU	-1	-0.823	-0.909	25.887	-10.505	-10.505	0.000	0.000	0.000
52	A	57	PHE	0	0.017	0.015	22.835	0.233	0.233	0.000	0.000	0.000
53	A	58	ARG	1	0.888	0.909	23.564	9.174	9.174	0.000	0.000	0.000
54	A	59	SER	0	-0.017	-0.015	22.795	-0.022	-0.022	0.000	0.000	0.000
55	A	60	PHE	0	0.039	0.020	15.868	-0.470	-0.470	0.000	0.000	0.000
56	A	61	GLY	0	0.028	0.003	19.012	-0.744	-0.744	0.000	0.000	0.000
57	A	62	THR	0	-0.047	-0.010	21.106	0.324	0.324	0.000	0.000	0.000
58	A	63	PHE	0	0.011	0.021	18.897	-0.669	-0.669	0.000	0.000	0.000
59	A	64	GLU	-1	-0.704	-0.838	23.686	-11.292	-11.292	0.000	0.000	0.000
60	A	65	VAL	0	0.038	0.030	25.101	-0.610	-0.610	0.000	0.000	0.000
61	A	66	ARG	1	0.766	0.877	23.987	12.245	12.245	0.000	0.000	0.000
62	A	67	LYS	1	0.962	0.972	26.591	9.377	9.377	0.000	0.000	0.000
63	A	68	ARG	1	0.891	0.940	21.934	12.597	12.597	0.000	0.000	0.000
64	A	69	LYS	1	0.906	0.952	26.822	9.440	9.440	0.000	0.000	0.000
65	A	70	GLY	0	0.027	0.015	27.275	-0.438	-0.438	0.000	0.000	0.000
66	A	71	ARG	1	0.866	0.920	23.226	12.378	12.378	0.000	0.000	0.000
67	A	72	LEU	0	0.063	0.016	28.958	0.089	0.089	0.000	0.000	0.000
68	A	73	ASN	0	0.039	0.000	27.444	0.103	0.103	0.000	0.000	0.000
69	A	74	ALA	0	-0.050	0.007	24.179	-0.376	-0.376	0.000	0.000	0.000
70	A	75	ARG	1	1.027	1.018	21.480	13.366	13.366	0.000	0.000	0.000
71	A	76	ASN	0	0.048	0.048	21.904	-1.234	-1.234	0.000	0.000	0.000
72	A	77	PRO	0	-0.048	-0.039	17.280	0.178	0.178	0.000	0.000	0.000
73	A	78	GLN	0	-0.026	-0.006	18.777	-0.023	-0.023	0.000	0.000	0.000
74	A	79	THR	0	0.011	-0.028	20.540	-0.017	-0.017	0.000	0.000	0.000
75	A	80	GLY	0	-0.064	-0.034	23.506	0.344	0.344	0.000	0.000	0.000
76	A	81	GLU	-1	-0.849	-0.894	24.938	-10.768	-10.768	0.000	0.000	0.000
77	A	82	TYR	0	-0.025	-0.020	26.592	-0.403	-0.403	0.000	0.000	0.000
78	A	83	VAL	0	0.008	0.003	24.402	0.207	0.207	0.000	0.000	0.000
79	A	84	LYS	1	0.944	0.979	27.791	9.079	9.079	0.000	0.000	0.000
80	A	85	VAL	0	-0.030	-0.013	24.423	-0.194	-0.194	0.000	0.000	0.000
81	A	86	LEU	0	0.055	0.026	27.738	0.232	0.232	0.000	0.000	0.000
82	A	87	ASP	-1	-0.783	-0.880	28.408	-10.056	-10.056	0.000	0.000	0.000
83	A	88	HIS	0	-0.061	-0.030	24.145	-0.226	-0.226	0.000	0.000	0.000
84	A	89	HIS	0	0.050	0.017	27.051	0.238	0.238	0.000	0.000	0.000
85	A	90	VAL	0	-0.012	-0.004	20.664	-0.299	-0.299	0.000	0.000	0.000
86	A	91	ALA	0	0.047	0.036	21.129	0.383	0.383	0.000	0.000	0.000
87	A	92	TYR	0	-0.042	-0.035	19.749	-0.568	-0.568	0.000	0.000	0.000
88	A	93	PHE	0	0.036	0.025	16.056	0.341	0.341	0.000	0.000	0.000
89	A	94	ARG	1	0.877	0.915	19.268	11.143	11.143	0.000	0.000	0.000
90	A	95	PRO	0	-0.003	-0.004	16.688	0.603	0.603	0.000	0.000	0.000
91	A	96	GLY	0	0.023	0.023	19.152	0.560	0.560	0.000	0.000	0.000
92	A	97	LYS	1	0.870	0.950	20.008	10.290	10.290	0.000	0.000	0.000
93	A	98	ASP	-1	-0.786	-0.885	19.181	-13.480	-13.480	0.000	0.000	0.000
94	A	99	LEU	0	0.025	0.015	13.658	-0.448	-0.448	0.000	0.000	0.000
95	A	100	LYS	1	0.928	0.948	15.873	12.473	12.473	0.000	0.000	0.000
96	A	101	GLU	-1	-0.881	-0.964	17.231	-12.272	-12.272	0.000	0.000	0.000
97	A	102	ARG	1	0.827	0.914	15.118	14.232	14.232	0.000	0.000	0.000
98	A	103	VAL	0	-0.033	-0.021	11.048	-0.738	-0.738	0.000	0.000	0.000
99	A	104	TRP	0	-0.029	-0.001	12.836	-0.954	-0.954	0.000	0.000	0.000
100	A	105	GLY	0	0.013	0.013	14.443	-0.577	-0.577	0.000	0.000	0.000
101	A	106	ILE	0	-0.024	-0.003	8.162	0.030	0.030	0.000	0.000	0.000
102	A	107	LYS	1	0.972	0.993	6.530	17.298	17.298	0.000	0.000	0.000

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