FMO DATABASE

FMODB ID: QYRQY

Calculation Name: 2NPS-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2NPS

Chain ID: B

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	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	68
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-285645.637496
FMO2-HF: Nuclear repulsion	257961.738575
FMO2-HF: Total energy	-27683.898921
FMO2-MP2: Total energy	-27763.159586

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(B:181:GLY)

Summations of interaction energy for fragment #1(B:181:GLY)

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.
0.041	2.348	0.02	-0.881	-1.446	0.002

Interaction energy analysis for fragmet #1(B:181:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.008

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

Sort

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	B	183	MET	0	0.018	0.009	3.250	-0.188	1.537	0.018	-0.762	-0.981	0.002
4	B	184	ARG	1	0.950	0.963	3.642	1.626	2.049	0.003	-0.108	-0.319	0.000
5	B	185	GLU	-1	-0.946	-0.974	5.278	-1.724	-1.565	-0.001	-0.011	-0.146	0.000
6	B	186	THR	0	0.019	0.005	7.488	0.296	0.296	0.000	0.000	0.000	0.000
7	B	187	ALA	0	-0.002	0.016	8.219	0.022	0.022	0.000	0.000	0.000	0.000
8	B	188	ILE	0	-0.007	-0.005	9.227	-0.009	-0.009	0.000	0.000	0.000	0.000
9	B	189	GLN	0	0.027	0.014	11.270	-0.031	-0.031	0.000	0.000	0.000	0.000
10	B	190	GLN	0	-0.013	-0.017	12.496	0.074	0.074	0.000	0.000	0.000	0.000
11	B	191	LEU	0	0.004	0.017	13.715	-0.004	-0.004	0.000	0.000	0.000	0.000
12	B	192	GLU	-1	-0.934	-0.969	15.388	-0.152	-0.152	0.000	0.000	0.000	0.000
13	B	193	ALA	0	-0.012	-0.006	17.200	0.007	0.007	0.000	0.000	0.000	0.000
14	B	194	ASP	-1	-0.852	-0.940	18.283	0.085	0.085	0.000	0.000	0.000	0.000
15	B	195	ILE	0	-0.111	-0.056	18.539	0.001	0.001	0.000	0.000	0.000	0.000
16	B	196	LEU	0	-0.020	-0.029	21.298	-0.001	-0.001	0.000	0.000	0.000	0.000
17	B	197	ASP	-1	-0.874	-0.918	22.960	0.024	0.024	0.000	0.000	0.000	0.000
18	B	198	VAL	0	-0.040	-0.011	23.346	0.001	0.001	0.000	0.000	0.000	0.000
19	B	199	ASN	0	-0.042	-0.017	25.676	-0.001	-0.001	0.000	0.000	0.000	0.000
20	B	200	GLN	0	0.005	0.008	27.358	-0.006	-0.006	0.000	0.000	0.000	0.000
21	B	201	ILE	0	0.017	-0.001	27.195	0.001	0.001	0.000	0.000	0.000	0.000
22	B	202	PHE	0	-0.055	-0.035	28.601	0.000	0.000	0.000	0.000	0.000	0.000
23	B	203	LYS	1	0.875	0.950	31.048	0.027	0.027	0.000	0.000	0.000	0.000
24	B	204	ASP	-1	-0.835	-0.921	33.157	0.003	0.003	0.000	0.000	0.000	0.000
25	B	205	LEU	0	-0.041	-0.030	34.344	0.001	0.001	0.000	0.000	0.000	0.000
26	B	206	ALA	0	-0.017	-0.013	35.893	0.000	0.000	0.000	0.000	0.000	0.000
27	B	207	MET	0	-0.016	-0.006	37.616	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	208	MET	0	-0.025	-0.009	36.786	0.001	0.001	0.000	0.000	0.000	0.000
29	B	209	ILE	0	-0.035	-0.020	39.204	0.000	0.000	0.000	0.000	0.000	0.000
30	B	210	HIS	0	-0.072	-0.037	41.904	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	211	ASP	-1	-0.859	-0.933	43.368	-0.003	-0.003	0.000	0.000	0.000	0.000
32	B	212	GLN	0	-0.067	-0.028	43.732	0.001	0.001	0.000	0.000	0.000	0.000
33	B	213	GLY	0	0.004	0.004	47.004	0.001	0.001	0.000	0.000	0.000	0.000
34	B	214	ASP	-1	-0.817	-0.902	48.825	-0.003	-0.003	0.000	0.000	0.000	0.000
35	B	215	LEU	0	-0.082	-0.045	48.912	0.001	0.001	0.000	0.000	0.000	0.000
36	B	216	ILE	0	-0.036	-0.030	48.752	0.000	0.000	0.000	0.000	0.000	0.000
37	B	217	ASP	-1	-0.823	-0.898	52.722	-0.003	-0.003	0.000	0.000	0.000	0.000
38	B	218	SER	0	-0.102	-0.054	54.979	0.000	0.000	0.000	0.000	0.000	0.000
39	B	219	ILE	0	-0.030	-0.011	53.342	0.000	0.000	0.000	0.000	0.000	0.000
40	B	220	GLU	-1	-0.952	-0.963	55.692	0.000	0.000	0.000	0.000	0.000	0.000
41	B	221	ALA	0	0.030	0.014	58.171	0.000	0.000	0.000	0.000	0.000	0.000
42	B	222	ASN	0	-0.083	-0.053	59.944	0.000	0.000	0.000	0.000	0.000	0.000
43	B	223	VAL	0	0.018	0.004	60.186	0.000	0.000	0.000	0.000	0.000	0.000
44	B	224	GLU	-1	-0.877	-0.916	62.357	0.000	0.000	0.000	0.000	0.000	0.000
45	B	225	SER	0	-0.025	-0.021	64.189	0.000	0.000	0.000	0.000	0.000	0.000
46	B	226	SER	0	-0.049	-0.033	65.333	0.000	0.000	0.000	0.000	0.000	0.000
47	B	227	GLH	0	-0.047	-0.037	66.104	0.000	0.000	0.000	0.000	0.000	0.000
48	B	228	VAL	0	0.068	0.030	68.094	0.000	0.000	0.000	0.000	0.000	0.000
49	B	229	HIS	0	-0.096	-0.065	69.904	0.000	0.000	0.000	0.000	0.000	0.000
50	B	230	VAL	0	-0.018	-0.002	70.324	0.000	0.000	0.000	0.000	0.000	0.000
51	B	231	GLU	-1	-0.871	-0.905	71.666	0.001	0.001	0.000	0.000	0.000	0.000
52	B	232	ARG	1	0.953	0.986	72.789	0.000	0.000	0.000	0.000	0.000	0.000
53	B	233	ALA	0	-0.027	-0.032	75.707	0.000	0.000	0.000	0.000	0.000	0.000
54	B	234	SER	0	-0.028	-0.016	76.642	0.000	0.000	0.000	0.000	0.000	0.000
55	B	235	ASP	-1	-0.842	-0.931	78.438	0.001	0.001	0.000	0.000	0.000	0.000
56	B	236	GLN	0	-0.096	-0.051	80.274	0.000	0.000	0.000	0.000	0.000	0.000
57	B	237	LEU	0	0.013	0.007	79.521	0.000	0.000	0.000	0.000	0.000	0.000
58	B	238	GLN	0	0.016	0.024	80.771	0.000	0.000	0.000	0.000	0.000	0.000
59	B	239	ARG	1	0.906	0.960	82.504	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	240	ALA	0	0.000	0.005	85.955	0.000	0.000	0.000	0.000	0.000	0.000
61	B	241	ALA	0	0.025	0.008	86.807	0.000	0.000	0.000	0.000	0.000	0.000
62	B	242	TYR	0	-0.026	-0.017	88.574	0.000	0.000	0.000	0.000	0.000	0.000
63	B	243	TYR	0	0.001	-0.018	89.548	0.000	0.000	0.000	0.000	0.000	0.000
64	B	244	GLN	0	0.007	0.019	90.724	0.000	0.000	0.000	0.000	0.000	0.000
65	B	245	LYS	1	0.963	0.976	92.301	-0.002	-0.002	0.000	0.000	0.000	0.000
66	B	246	LYS	1	0.860	0.950	94.683	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	247	SER	0	-0.022	-0.009	96.487	0.000	0.000	0.000	0.000	0.000	0.000
68	B	248	ARG	1	0.954	0.987	98.112	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:181:GLY)