FMO DATABASE

FMODB ID: K9YN3

Calculation Name: 2NPS-B-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 2NPS

Chain ID: B

ChEMBL ID:
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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	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	68
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-285091.996044
FMO2-HF: Nuclear repulsion	257407.675489
FMO2-HF: Total energy	-27684.320555
FMO2-MP2: Total energy	-27763.489614

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.
-0.309	2.022	0.021	-0.894	-1.457	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 : 0.003 / q_NPA : -0.009

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	0.011	0.003	3.252	-0.322	1.420	0.018	-0.771	-0.988	0.002
4	B	184	ARG	1	0.950	0.964	3.668	1.568	2.001	0.004	-0.111	-0.327	0.000
5	B	185	GLU	-1	-0.937	-0.974	5.302	-1.880	-1.724	-0.001	-0.012	-0.142	0.000
6	B	186	THR	0	0.019	0.012	7.487	0.283	0.283	0.000	0.000	0.000	0.000
7	B	187	ALA	0	0.011	0.022	8.248	0.016	0.016	0.000	0.000	0.000	0.000
8	B	188	ILE	0	-0.018	-0.012	8.928	-0.011	-0.011	0.000	0.000	0.000	0.000
9	B	189	GLN	0	0.028	0.017	11.293	-0.021	-0.021	0.000	0.000	0.000	0.000
10	B	190	GLN	0	-0.014	-0.017	12.212	0.079	0.079	0.000	0.000	0.000	0.000
11	B	191	LEU	0	0.013	0.021	13.715	-0.006	-0.006	0.000	0.000	0.000	0.000
12	B	192	GLU	-1	-0.933	-0.967	15.412	-0.158	-0.158	0.000	0.000	0.000	0.000
13	B	193	ALA	0	-0.010	-0.008	17.223	0.007	0.007	0.000	0.000	0.000	0.000
14	B	194	ASP	-1	-0.881	-0.956	18.011	0.096	0.096	0.000	0.000	0.000	0.000
15	B	195	ILE	0	-0.103	-0.056	18.276	0.000	0.000	0.000	0.000	0.000	0.000
16	B	196	LEU	0	-0.037	-0.029	21.321	-0.002	-0.002	0.000	0.000	0.000	0.000
17	B	197	ASP	-1	-0.877	-0.925	22.981	0.027	0.027	0.000	0.000	0.000	0.000
18	B	198	VAL	0	-0.029	0.000	23.709	0.000	0.000	0.000	0.000	0.000	0.000
19	B	199	ASN	0	-0.048	-0.020	25.700	-0.003	-0.003	0.000	0.000	0.000	0.000
20	B	200	GLN	0	-0.018	-0.014	27.384	-0.007	-0.007	0.000	0.000	0.000	0.000
21	B	201	ILE	0	0.038	0.012	27.150	0.001	0.001	0.000	0.000	0.000	0.000
22	B	202	PHE	0	-0.060	-0.038	28.771	0.000	0.000	0.000	0.000	0.000	0.000
23	B	203	LYS	1	0.890	0.961	30.868	0.025	0.025	0.000	0.000	0.000	0.000
24	B	204	ASP	-1	-0.822	-0.911	32.793	0.005	0.005	0.000	0.000	0.000	0.000
25	B	205	LEU	0	-0.049	-0.028	34.370	0.001	0.001	0.000	0.000	0.000	0.000
26	B	206	ALA	0	-0.012	-0.013	35.916	0.000	0.000	0.000	0.000	0.000	0.000
27	B	207	MET	0	-0.012	-0.002	37.640	-0.001	-0.001	0.000	0.000	0.000	0.000
28	B	208	MET	0	-0.020	-0.009	36.813	0.001	0.001	0.000	0.000	0.000	0.000
29	B	209	ILE	0	-0.036	-0.023	39.036	0.000	0.000	0.000	0.000	0.000	0.000
30	B	210	HIS	0	-0.091	-0.054	41.927	-0.001	-0.001	0.000	0.000	0.000	0.000
31	B	211	ASP	-1	-0.830	-0.910	43.432	-0.002	-0.002	0.000	0.000	0.000	0.000
32	B	212	GLN	0	-0.064	-0.031	43.075	0.001	0.001	0.000	0.000	0.000	0.000
33	B	213	GLY	0	0.008	0.007	47.009	0.001	0.001	0.000	0.000	0.000	0.000
34	B	214	ASP	-1	-0.831	-0.905	48.849	-0.002	-0.002	0.000	0.000	0.000	0.000
35	B	215	LEU	0	-0.086	-0.057	48.866	0.001	0.001	0.000	0.000	0.000	0.000
36	B	216	ILE	0	-0.042	-0.033	48.657	0.000	0.000	0.000	0.000	0.000	0.000
37	B	217	ASP	-1	-0.852	-0.911	52.745	-0.002	-0.002	0.000	0.000	0.000	0.000
38	B	218	SER	0	-0.066	-0.027	55.002	0.000	0.000	0.000	0.000	0.000	0.000
39	B	219	ILE	0	-0.038	-0.019	53.401	0.000	0.000	0.000	0.000	0.000	0.000
40	B	220	GLU	-1	-0.943	-0.962	56.094	0.001	0.001	0.000	0.000	0.000	0.000
41	B	221	ALA	0	0.038	0.022	58.194	0.000	0.000	0.000	0.000	0.000	0.000
42	B	222	ASN	0	-0.090	-0.057	60.125	0.000	0.000	0.000	0.000	0.000	0.000
43	B	223	VAL	0	0.014	0.010	60.098	0.000	0.000	0.000	0.000	0.000	0.000
44	B	224	GLU	-1	-0.872	-0.914	62.384	0.001	0.001	0.000	0.000	0.000	0.000
45	B	225	SER	0	-0.012	-0.013	64.212	0.000	0.000	0.000	0.000	0.000	0.000
46	B	226	SER	0	-0.054	-0.039	65.264	0.000	0.000	0.000	0.000	0.000	0.000
47	B	227	GLH	0	-0.049	-0.047	66.150	0.000	0.000	0.000	0.000	0.000	0.000
48	B	228	VAL	0	0.067	0.027	68.117	0.000	0.000	0.000	0.000	0.000	0.000
49	B	229	HIS	0	-0.089	-0.064	69.649	0.000	0.000	0.000	0.000	0.000	0.000
50	B	230	VAL	0	-0.019	-0.006	70.376	0.000	0.000	0.000	0.000	0.000	0.000
51	B	231	GLU	-1	-0.864	-0.892	71.740	0.001	0.001	0.000	0.000	0.000	0.000
52	B	232	ARG	1	0.930	0.971	72.768	-0.001	-0.001	0.000	0.000	0.000	0.000
53	B	233	ALA	0	-0.025	-0.026	75.730	0.000	0.000	0.000	0.000	0.000	0.000
54	B	234	SER	0	-0.023	-0.012	76.662	0.000	0.000	0.000	0.000	0.000	0.000
55	B	235	ASP	-1	-0.766	-0.871	78.513	0.001	0.001	0.000	0.000	0.000	0.000
56	B	236	GLN	0	-0.059	-0.028	80.324	0.000	0.000	0.000	0.000	0.000	0.000
57	B	237	LEU	0	0.012	0.010	79.472	0.000	0.000	0.000	0.000	0.000	0.000
58	B	238	GLN	0	0.008	0.019	80.891	0.000	0.000	0.000	0.000	0.000	0.000
59	B	239	ARG	1	0.802	0.879	82.516	-0.001	-0.001	0.000	0.000	0.000	0.000
60	B	240	ALA	0	-0.007	0.001	85.971	0.000	0.000	0.000	0.000	0.000	0.000
61	B	241	ALA	0	0.027	0.010	86.797	0.000	0.000	0.000	0.000	0.000	0.000
62	B	242	TYR	0	-0.020	-0.016	88.596	0.000	0.000	0.000	0.000	0.000	0.000
63	B	243	TYR	0	0.007	-0.013	89.149	0.000	0.000	0.000	0.000	0.000	0.000
64	B	244	GLN	0	0.007	0.017	90.559	0.000	0.000	0.000	0.000	0.000	0.000
65	B	245	LYS	1	0.963	0.976	92.220	-0.002	-0.002	0.000	0.000	0.000	0.000
66	B	246	LYS	1	0.864	0.952	94.706	-0.001	-0.001	0.000	0.000	0.000	0.000
67	B	247	SER	0	0.005	0.012	96.519	0.000	0.000	0.000	0.000	0.000	0.000
68	B	248	ARG	1	0.915	0.961	98.135	-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)