FMO DATABASE

FMODB ID: VQYK1

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	OptAll
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	-676882.5113
FMO2-HF: Nuclear repulsion	635763.723287
FMO2-HF: Total energy	-41118.788013
FMO2-MP2: Total energy	-41241.58906

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.
120.749	121.774	-0.012	-0.426	-0.587	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 : 0.973 / 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	0.958	0.971	3.916	29.246	30.271	-0.012	-0.426	-0.587	0.001
4	A	9	VAL	0	0.025	0.019	6.492	2.545	2.545	0.000	0.000	0.000	0.000
5	A	10	THR	0	-0.039	-0.045	9.157	-0.078	-0.078	0.000	0.000	0.000	0.000
6	A	11	LYS	1	0.862	0.892	12.749	14.594	14.594	0.000	0.000	0.000	0.000
7	A	12	SER	0	0.018	0.001	16.163	1.122	1.122	0.000	0.000	0.000	0.000
8	A	13	ASP	-1	-0.813	-0.870	12.661	-19.436	-19.436	0.000	0.000	0.000	0.000
9	A	14	ILE	0	0.028	0.014	12.243	0.698	0.698	0.000	0.000	0.000	0.000
10	A	15	VAL	0	-0.021	-0.008	15.400	0.807	0.807	0.000	0.000	0.000	0.000
11	A	16	ASP	-1	-0.799	-0.891	17.221	-12.884	-12.884	0.000	0.000	0.000	0.000
12	A	17	GLN	0	0.006	-0.003	11.749	0.007	0.007	0.000	0.000	0.000	0.000
13	A	18	ILE	0	0.015	0.014	17.035	0.517	0.517	0.000	0.000	0.000	0.000
14	A	19	ALA	0	-0.015	-0.017	19.925	0.586	0.586	0.000	0.000	0.000	0.000
15	A	20	LEU	0	-0.057	-0.024	17.587	0.513	0.513	0.000	0.000	0.000	0.000
16	A	21	ASN	0	0.014	0.009	19.665	0.640	0.640	0.000	0.000	0.000	0.000
17	A	22	ILE	0	0.016	0.003	21.593	0.403	0.403	0.000	0.000	0.000	0.000
18	A	23	LYS	1	0.945	0.976	24.663	10.988	10.988	0.000	0.000	0.000	0.000
19	A	24	ASN	0	-0.067	-0.034	21.209	-0.077	-0.077	0.000	0.000	0.000	0.000
20	A	25	ASN	0	-0.023	-0.005	24.478	0.311	0.311	0.000	0.000	0.000	0.000
21	A	26	ASN	0	-0.008	-0.005	27.735	0.098	0.098	0.000	0.000	0.000	0.000
22	A	27	LEU	0	0.015	0.030	28.533	0.250	0.250	0.000	0.000	0.000	0.000
23	A	28	LYS	1	0.929	0.938	28.999	8.239	8.239	0.000	0.000	0.000	0.000
24	A	29	LEU	0	0.056	0.030	26.957	0.167	0.167	0.000	0.000	0.000	0.000
25	A	30	GLU	-1	-0.824	-0.899	27.473	-9.369	-9.369	0.000	0.000	0.000	0.000
26	A	31	LYS	1	0.843	0.888	21.002	12.702	12.702	0.000	0.000	0.000	0.000
27	A	32	LYS	1	0.846	0.923	24.851	8.559	8.559	0.000	0.000	0.000	0.000
28	A	33	TYR	0	0.067	0.025	27.581	-0.065	-0.065	0.000	0.000	0.000	0.000
29	A	34	ILE	0	0.002	0.016	21.935	-0.102	-0.102	0.000	0.000	0.000	0.000
30	A	35	ARG	1	0.929	0.957	21.006	12.414	12.414	0.000	0.000	0.000	0.000
31	A	36	LEU	0	0.043	0.035	23.933	-0.195	-0.195	0.000	0.000	0.000	0.000
32	A	37	VAL	0	0.020	0.008	25.149	0.028	0.028	0.000	0.000	0.000	0.000
33	A	38	ILE	0	-0.009	-0.004	19.564	-0.140	-0.140	0.000	0.000	0.000	0.000
34	A	39	ASP	-1	-0.790	-0.881	22.816	-13.420	-13.420	0.000	0.000	0.000	0.000
35	A	40	ALA	0	0.023	0.018	24.259	0.021	0.021	0.000	0.000	0.000	0.000
36	A	41	PHE	0	-0.027	0.001	20.644	0.106	0.106	0.000	0.000	0.000	0.000
37	A	42	PHE	0	-0.015	-0.027	17.357	-0.272	-0.272	0.000	0.000	0.000	0.000
38	A	43	GLU	-1	-0.837	-0.889	23.330	-11.533	-11.533	0.000	0.000	0.000	0.000
39	A	44	GLU	-1	-0.808	-0.894	26.773	-9.588	-9.588	0.000	0.000	0.000	0.000
40	A	45	LEU	0	-0.057	-0.009	21.627	0.103	0.103	0.000	0.000	0.000	0.000
41	A	46	LYS	1	0.785	0.867	22.874	12.124	12.124	0.000	0.000	0.000	0.000
42	A	47	SER	0	0.042	0.011	26.310	0.076	0.076	0.000	0.000	0.000	0.000
43	A	48	ASN	0	0.024	0.015	28.769	0.450	0.450	0.000	0.000	0.000	0.000
44	A	49	LEU	0	-0.037	-0.023	23.521	0.067	0.067	0.000	0.000	0.000	0.000
45	A	50	CYS	0	-0.067	-0.045	27.743	0.035	0.035	0.000	0.000	0.000	0.000
46	A	51	SER	0	-0.034	-0.012	29.659	0.342	0.342	0.000	0.000	0.000	0.000
47	A	52	ASN	0	-0.123	-0.069	30.138	0.136	0.136	0.000	0.000	0.000	0.000
48	A	53	ASN	0	0.020	0.017	31.186	0.289	0.289	0.000	0.000	0.000	0.000
49	A	54	VAL	0	-0.057	-0.037	28.131	-0.420	-0.420	0.000	0.000	0.000	0.000
50	A	55	ILE	0	0.005	0.005	25.834	0.255	0.255	0.000	0.000	0.000	0.000
51	A	56	GLU	-1	-0.804	-0.871	25.526	-10.842	-10.842	0.000	0.000	0.000	0.000
52	A	57	PHE	0	0.027	0.020	22.558	0.293	0.293	0.000	0.000	0.000	0.000
53	A	58	ARG	1	0.916	0.921	23.364	9.251	9.251	0.000	0.000	0.000	0.000
54	A	59	SER	0	0.001	0.001	22.705	-0.051	-0.051	0.000	0.000	0.000	0.000
55	A	60	PHE	0	0.029	0.019	15.667	-0.456	-0.456	0.000	0.000	0.000	0.000
56	A	61	GLY	0	0.028	-0.008	19.202	-0.723	-0.723	0.000	0.000	0.000	0.000
57	A	62	THR	0	-0.086	-0.048	21.444	0.200	0.200	0.000	0.000	0.000	0.000
58	A	63	PHE	0	0.015	0.010	18.646	-0.526	-0.526	0.000	0.000	0.000	0.000
59	A	64	GLU	-1	-0.694	-0.816	23.721	-11.268	-11.268	0.000	0.000	0.000	0.000
60	A	65	VAL	0	0.035	0.025	24.590	-0.593	-0.593	0.000	0.000	0.000	0.000
61	A	66	ARG	1	0.777	0.880	23.822	12.431	12.431	0.000	0.000	0.000	0.000
62	A	67	LYS	1	0.969	0.970	26.010	9.366	9.366	0.000	0.000	0.000	0.000
63	A	68	ARG	1	0.877	0.937	21.298	12.740	12.740	0.000	0.000	0.000	0.000
64	A	69	LYS	1	0.905	0.949	26.628	9.557	9.557	0.000	0.000	0.000	0.000
65	A	70	GLY	0	0.010	0.017	27.031	-0.438	-0.438	0.000	0.000	0.000	0.000
66	A	71	ARG	1	0.887	0.925	23.101	12.484	12.484	0.000	0.000	0.000	0.000
67	A	72	LEU	0	0.060	0.017	28.731	0.009	0.009	0.000	0.000	0.000	0.000
68	A	73	ASN	0	0.040	0.021	27.668	0.165	0.165	0.000	0.000	0.000	0.000
69	A	74	ALA	0	-0.034	0.003	23.743	-0.437	-0.437	0.000	0.000	0.000	0.000
70	A	75	ARG	1	0.940	0.978	21.832	13.257	13.257	0.000	0.000	0.000	0.000
71	A	76	ASN	0	0.031	0.022	21.685	-1.341	-1.341	0.000	0.000	0.000	0.000
72	A	77	PRO	0	-0.034	-0.035	17.064	0.164	0.164	0.000	0.000	0.000	0.000
73	A	78	GLN	0	-0.027	-0.006	18.546	0.007	0.007	0.000	0.000	0.000	0.000
74	A	79	THR	0	-0.028	-0.040	20.315	0.062	0.062	0.000	0.000	0.000	0.000
75	A	80	GLY	0	-0.029	-0.019	23.085	0.363	0.363	0.000	0.000	0.000	0.000
76	A	81	GLU	-1	-0.799	-0.869	24.455	-11.029	-11.029	0.000	0.000	0.000	0.000
77	A	82	TYR	0	-0.010	-0.011	25.985	-0.523	-0.523	0.000	0.000	0.000	0.000
78	A	83	VAL	0	0.012	0.011	24.589	0.238	0.238	0.000	0.000	0.000	0.000
79	A	84	LYS	1	0.932	0.975	27.601	8.976	8.976	0.000	0.000	0.000	0.000
80	A	85	VAL	0	0.003	0.002	24.375	-0.219	-0.219	0.000	0.000	0.000	0.000
81	A	86	LEU	0	0.028	0.012	27.632	0.322	0.322	0.000	0.000	0.000	0.000
82	A	87	ASP	-1	-0.765	-0.878	28.255	-10.069	-10.069	0.000	0.000	0.000	0.000
83	A	88	HIS	0	-0.059	-0.034	23.973	-0.296	-0.296	0.000	0.000	0.000	0.000
84	A	89	HIS	0	0.042	0.020	26.819	0.328	0.328	0.000	0.000	0.000	0.000
85	A	90	VAL	0	-0.004	0.003	20.242	-0.264	-0.264	0.000	0.000	0.000	0.000
86	A	91	ALA	0	0.053	0.037	21.129	0.345	0.345	0.000	0.000	0.000	0.000
87	A	92	TYR	0	-0.037	-0.035	19.478	-0.543	-0.543	0.000	0.000	0.000	0.000
88	A	93	PHE	0	0.025	0.011	16.423	0.313	0.313	0.000	0.000	0.000	0.000
89	A	94	ARG	1	0.849	0.919	19.472	11.259	11.259	0.000	0.000	0.000	0.000
90	A	95	PRO	0	0.006	0.000	16.754	0.507	0.507	0.000	0.000	0.000	0.000
91	A	96	GLY	0	0.017	0.014	19.196	0.574	0.574	0.000	0.000	0.000	0.000
92	A	97	LYS	1	0.879	0.943	20.179	10.396	10.396	0.000	0.000	0.000	0.000
93	A	98	ASP	-1	-0.814	-0.889	18.897	-13.686	-13.686	0.000	0.000	0.000	0.000
94	A	99	LEU	0	0.021	0.016	13.699	-0.494	-0.494	0.000	0.000	0.000	0.000
95	A	100	LYS	1	0.931	0.965	15.677	12.321	12.321	0.000	0.000	0.000	0.000
96	A	101	GLU	-1	-0.874	-0.961	16.899	-12.555	-12.555	0.000	0.000	0.000	0.000
97	A	102	ARG	1	0.842	0.910	15.169	14.256	14.256	0.000	0.000	0.000	0.000
98	A	103	VAL	0	-0.018	-0.011	11.463	-0.785	-0.785	0.000	0.000	0.000	0.000
99	A	104	TRP	0	-0.029	-0.019	13.052	-0.982	-0.982	0.000	0.000	0.000	0.000
100	A	105	GLY	0	0.014	0.016	14.998	0.034	0.034	0.000	0.000	0.000	0.000
101	A	106	ILE	0	-0.061	-0.013	8.342	-0.018	-0.018	0.000	0.000	0.000	0.000
102	A	107	LYS	1	0.981	0.997	7.272	16.810	16.810	0.000	0.000	0.000	0.000

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