FMO DATABASE

FMODB ID: YNYZ2

Calculation Name: 2QYP-A-Xray372

Preferred Name: Prosaposin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2QYP

Chain ID: A

ChEMBL ID: CHEMBL3580523

UniProt ID: P07602

Base Structure: X-ray

Registration Date: 2023-09-26

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	75
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-433538.673356
FMO2-HF: Nuclear repulsion	400980.340286
FMO2-HF: Total energy	-32558.333069
FMO2-MP2: Total energy	-32647.187745

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:1:SER)

Summations of interaction energy for fragment #1(A:1:SER)

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.
-13.66	-7.262	3.86	-4.313	-5.946	0.007

Interaction energy analysis for fragmet #1(A:1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.007

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	3	VAL	0	0.028	0.020	3.027	-3.276	-0.031	0.145	-1.535	-1.855	0.008
4	A	4	TYR	0	-0.031	-0.023	2.156	-7.550	-4.760	3.715	-2.656	-3.850	-0.001
5	A	78	CYS	0	-0.009	0.027	4.105	-1.598	-1.235	0.000	-0.122	-0.241	0.000
6	A	6	GLU	-1	-0.856	-0.935	6.224	0.560	0.560	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.021	-0.014	7.455	0.042	0.042	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.032	-0.025	8.419	0.164	0.164	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.863	-0.946	10.088	-0.736	-0.736	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.071	-0.041	12.025	0.111	0.111	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.035	-0.017	11.979	0.066	0.066	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.009	0.010	13.913	0.065	0.065	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.941	0.959	16.263	0.400	0.400	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.933	-0.962	17.760	-0.177	-0.177	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.027	-0.013	18.141	0.031	0.031	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.013	-0.002	20.440	0.028	0.028	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.991	0.990	22.508	0.185	0.185	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.072	-0.020	23.528	0.022	0.022	0.000	0.000	0.000	0.000
19	A	19	ILE	0	-0.043	-0.046	24.461	0.016	0.016	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.860	-0.932	26.903	-0.143	-0.143	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.096	-0.025	28.191	0.012	0.012	0.000	0.000	0.000	0.000
22	A	22	ASN	0	0.108	0.033	30.898	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.867	0.934	28.946	0.137	0.137	0.000	0.000	0.000	0.000
24	A	24	THR	0	0.008	0.007	29.010	0.006	0.006	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.876	-0.927	32.143	-0.121	-0.121	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.936	0.962	33.989	0.083	0.083	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.949	-0.954	32.628	-0.115	-0.115	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.025	-0.017	30.288	0.002	0.002	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.027	-0.022	34.758	0.002	0.002	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.879	-0.935	37.992	-0.079	-0.079	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.095	-0.045	36.350	0.004	0.004	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.006	-0.004	37.170	0.002	0.002	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.728	-0.865	39.384	-0.077	-0.077	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.837	0.892	41.330	0.082	0.082	0.000	0.000	0.000	0.000
35	A	35	MET	0	-0.057	-0.034	38.367	0.002	0.002	0.000	0.000	0.000	0.000
36	A	36	CYS	0	-0.133	-0.039	41.713	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.014	0.005	44.713	0.004	0.004	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.883	0.959	42.245	0.074	0.074	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.017	-0.023	45.256	0.001	0.001	0.000	0.000	0.000	0.000
40	A	40	PRO	0	-0.125	-0.053	48.535	0.002	0.002	0.000	0.000	0.000	0.000
41	A	41	LYS	1	1.026	1.019	51.198	0.043	0.043	0.000	0.000	0.000	0.000
42	A	42	SER	0	0.062	0.011	53.656	0.000	0.000	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.035	0.008	48.385	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.019	-0.024	47.935	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.924	-0.960	49.040	-0.054	-0.054	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.925	-0.951	48.691	-0.056	-0.056	0.000	0.000	0.000	0.000
47	A	48	GLN	0	0.045	0.010	44.151	-0.003	-0.003	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.862	-0.914	45.144	-0.062	-0.062	0.000	0.000	0.000	0.000
49	A	50	VAL	0	-0.026	0.024	41.932	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	51	VAL	0	-0.018	-0.011	39.719	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.894	-0.947	40.788	-0.077	-0.077	0.000	0.000	0.000	0.000
52	A	53	THR	0	-0.133	-0.101	42.669	0.000	0.000	0.000	0.000	0.000	0.000
53	A	54	TYR	0	-0.060	-0.043	39.219	0.000	0.000	0.000	0.000	0.000	0.000
54	A	55	GLY	0	0.020	0.024	37.285	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	56	SER	0	0.001	-0.001	35.817	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	57	SER	0	0.009	-0.009	35.072	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.017	-0.011	32.707	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	59	LEU	0	-0.018	-0.010	30.067	-0.010	-0.010	0.000	0.000	0.000	0.000
59	A	60	SER	0	0.059	0.025	29.925	-0.011	-0.011	0.000	0.000	0.000	0.000
60	A	61	ILE	0	0.002	0.008	29.419	-0.008	-0.008	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.024	-0.008	26.186	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.051	-0.028	24.952	-0.023	-0.023	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.967	-0.984	24.011	-0.177	-0.177	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.989	-0.982	24.237	-0.200	-0.200	0.000	0.000	0.000	0.000
65	A	66	VAL	0	-0.056	-0.007	18.838	-0.029	-0.029	0.000	0.000	0.000	0.000
66	A	67	SER	0	0.018	0.005	16.990	-0.023	-0.023	0.000	0.000	0.000	0.000
67	A	68	PRO	0	-0.031	-0.041	14.654	-0.036	-0.036	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.862	-0.928	11.461	-0.770	-0.770	0.000	0.000	0.000	0.000
69	A	70	LEU	0	-0.044	-0.019	11.922	-0.099	-0.099	0.000	0.000	0.000	0.000
70	A	71	VAL	0	0.007	-0.004	13.512	-0.033	-0.033	0.000	0.000	0.000	0.000
71	A	73	SER	0	0.008	0.022	8.942	-0.257	-0.257	0.000	0.000	0.000	0.000
72	A	74	MET	0	-0.069	-0.038	10.185	0.061	0.061	0.000	0.000	0.000	0.000
73	A	75	LEU	0	-0.024	-0.003	10.477	0.106	0.106	0.000	0.000	0.000	0.000
74	A	76	HIS	0	-0.079	-0.033	7.663	0.017	0.017	0.000	0.000	0.000	0.000
75	A	77	LEU	0	-0.035	-0.014	5.065	-0.135	-0.135	0.000	0.000	0.000	0.000

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