FMO DATABASE

FMODB ID: N955Q

Calculation Name: 2NPS-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NPS

Chain ID: D

ChEMBL ID:

UniProt ID: G3V7P1

Base Structure: X-ray

Registration Date: 2023-09-20

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	63
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-254234.205315
FMO2-HF: Nuclear repulsion	228604.432373
FMO2-HF: Total energy	-25629.772943
FMO2-MP2: Total energy	-25701.67126

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(D:170:ASP)

Summations of interaction energy for fragment #1(D:170:ASP)

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.
-1.801	1.772	0.111	-1.729	-1.955	0.004

Interaction energy analysis for fragmet #1(D:170:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.923 / q_NPA : -0.966

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	D	172	GLN	0	-0.057	-0.037	3.008	-5.317	-1.927	0.111	-1.704	-1.797	0.004
4	D	173	LEU	0	0.019	0.001	4.453	-5.025	-4.842	0.000	-0.025	-0.158	0.000
5	D	174	GLU	-1	-0.819	-0.910	7.136	19.694	19.694	0.000	0.000	0.000	0.000
6	D	175	LEU	0	-0.039	-0.020	6.820	-2.389	-2.389	0.000	0.000	0.000	0.000
7	D	176	VAL	0	-0.034	-0.016	9.134	-2.290	-2.290	0.000	0.000	0.000	0.000
8	D	177	SER	0	-0.040	-0.004	11.149	-2.430	-2.430	0.000	0.000	0.000	0.000
9	D	178	GLY	0	0.064	0.026	12.511	-1.462	-1.462	0.000	0.000	0.000	0.000
10	D	179	SER	0	-0.051	-0.020	13.570	-1.768	-1.768	0.000	0.000	0.000	0.000
11	D	180	ILE	0	0.017	-0.006	15.257	-1.218	-1.218	0.000	0.000	0.000	0.000
12	D	181	GLY	0	0.032	0.022	16.795	-0.994	-0.994	0.000	0.000	0.000	0.000
13	D	182	VAL	0	-0.023	-0.016	18.304	-0.985	-0.985	0.000	0.000	0.000	0.000
14	D	183	LEU	0	0.032	0.018	18.730	-0.813	-0.813	0.000	0.000	0.000	0.000
15	D	184	LYS	1	0.925	0.978	21.142	-12.817	-12.817	0.000	0.000	0.000	0.000
16	D	185	ASN	0	-0.013	-0.001	22.715	-0.721	-0.721	0.000	0.000	0.000	0.000
17	D	186	MET	0	-0.016	-0.017	23.227	-0.462	-0.462	0.000	0.000	0.000	0.000
18	D	187	SER	0	0.003	-0.012	24.913	-0.464	-0.464	0.000	0.000	0.000	0.000
19	D	188	GLN	0	0.017	0.010	26.843	0.010	0.010	0.000	0.000	0.000	0.000
20	D	189	ARG	1	0.885	0.941	26.244	-11.085	-11.085	0.000	0.000	0.000	0.000
21	D	190	ILE	0	0.007	0.010	28.489	-0.255	-0.255	0.000	0.000	0.000	0.000
22	D	191	GLY	0	0.002	0.002	31.421	-0.255	-0.255	0.000	0.000	0.000	0.000
23	D	192	GLY	0	0.005	0.002	33.253	-0.242	-0.242	0.000	0.000	0.000	0.000
24	D	193	GLU	-1	-0.862	-0.916	34.680	7.941	7.941	0.000	0.000	0.000	0.000
25	D	194	LEU	0	-0.030	-0.026	34.425	-0.203	-0.203	0.000	0.000	0.000	0.000
26	D	195	GLU	-1	-0.942	-0.956	37.609	7.412	7.412	0.000	0.000	0.000	0.000
27	D	196	GLU	-1	-0.943	-0.976	39.192	7.502	7.502	0.000	0.000	0.000	0.000
28	D	197	GLN	0	-0.104	-0.076	38.736	-0.267	-0.267	0.000	0.000	0.000	0.000
29	D	198	ALA	0	-0.022	-0.006	41.653	-0.185	-0.185	0.000	0.000	0.000	0.000
30	D	199	VAL	0	0.001	0.001	43.478	-0.180	-0.180	0.000	0.000	0.000	0.000
31	D	200	MET	0	0.004	0.009	43.755	-0.172	-0.172	0.000	0.000	0.000	0.000
32	D	201	LEU	0	-0.041	-0.028	44.013	-0.158	-0.158	0.000	0.000	0.000	0.000
33	D	202	GLU	-1	-0.887	-0.923	47.635	6.004	6.004	0.000	0.000	0.000	0.000
34	D	203	ASP	-1	-0.907	-0.955	49.336	6.084	6.084	0.000	0.000	0.000	0.000
35	D	204	PHE	0	-0.026	-0.019	50.275	-0.159	-0.159	0.000	0.000	0.000	0.000
36	D	205	SER	0	-0.028	-0.021	51.892	-0.099	-0.099	0.000	0.000	0.000	0.000
37	D	206	HIS	0	-0.009	-0.018	53.341	-0.255	-0.255	0.000	0.000	0.000	0.000
38	D	207	GLU	-1	-0.952	-0.976	53.704	5.670	5.670	0.000	0.000	0.000	0.000
39	D	208	LEU	0	-0.022	0.007	53.802	-0.168	-0.168	0.000	0.000	0.000	0.000
40	D	209	GLU	-1	-0.869	-0.917	56.376	5.388	5.388	0.000	0.000	0.000	0.000
41	D	210	SER	0	0.017	0.023	59.571	-0.163	-0.163	0.000	0.000	0.000	0.000
42	D	211	THR	0	-0.082	-0.060	59.501	-0.136	-0.136	0.000	0.000	0.000	0.000
43	D	212	GLN	0	0.013	-0.001	61.117	-0.118	-0.118	0.000	0.000	0.000	0.000
44	D	213	SER	0	-0.015	-0.015	63.407	-0.119	-0.119	0.000	0.000	0.000	0.000
45	D	214	ARG	1	0.839	0.915	62.419	-5.112	-5.112	0.000	0.000	0.000	0.000
46	D	215	LEU	0	0.026	0.009	64.300	-0.103	-0.103	0.000	0.000	0.000	0.000
47	D	216	ASP	-1	-0.767	-0.876	67.376	4.478	4.478	0.000	0.000	0.000	0.000
48	D	217	ASN	0	-0.008	-0.010	69.244	-0.147	-0.147	0.000	0.000	0.000	0.000
49	D	218	VAL	0	-0.043	-0.018	70.044	-0.093	-0.093	0.000	0.000	0.000	0.000
50	D	219	MET	0	0.009	0.011	68.780	-0.079	-0.079	0.000	0.000	0.000	0.000
51	D	220	LYS	1	0.816	0.898	70.822	-4.532	-4.532	0.000	0.000	0.000	0.000
52	D	221	LYS	1	0.910	0.954	74.400	-4.263	-4.263	0.000	0.000	0.000	0.000
53	D	222	LEU	0	0.009	0.015	74.754	-0.068	-0.068	0.000	0.000	0.000	0.000
54	D	223	ALA	0	0.065	0.029	77.237	-0.061	-0.061	0.000	0.000	0.000	0.000
55	D	224	LYS	1	0.967	0.991	79.086	-3.907	-3.907	0.000	0.000	0.000	0.000
56	D	225	VAL	0	-0.027	-0.021	80.472	-0.064	-0.064	0.000	0.000	0.000	0.000
57	D	226	SER	0	0.030	0.018	81.243	-0.043	-0.043	0.000	0.000	0.000	0.000
58	D	227	HIS	0	-0.033	-0.011	82.108	-0.048	-0.048	0.000	0.000	0.000	0.000
59	D	228	MET	0	-0.093	-0.059	84.734	-0.060	-0.060	0.000	0.000	0.000	0.000
60	D	229	THR	0	-0.064	-0.042	85.592	-0.042	-0.042	0.000	0.000	0.000	0.000
61	D	230	SER	0	-0.005	-0.009	86.495	-0.042	-0.042	0.000	0.000	0.000	0.000
62	D	231	ASP	-1	-0.883	-0.928	87.971	3.599	3.599	0.000	0.000	0.000	0.000
63	D	232	ARG	1	0.860	0.953	89.913	-3.545	-3.545	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(D:170:ASP)