FMO DATABASE

FMODB ID: VKR51

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	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	75
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-433808.423694
FMO2-HF: Nuclear repulsion	401249.307932
FMO2-HF: Total energy	-32559.115762
FMO2-MP2: Total energy	-32647.963419

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.
-12.71	-6.18	3.214	-4.006	-5.739	0

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 : -0.011 / q_NPA : -0.005

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	0.037	0.020	3.238	-2.813	0.219	0.065	-1.413	-1.685	0.007
4	A	4	TYR	0	-0.022	-0.020	2.310	-7.652	-4.513	3.150	-2.482	-3.808	-0.007
5	A	78	CYS	0	-0.015	0.025	4.108	-1.331	-0.972	-0.001	-0.111	-0.246	0.000
6	A	6	GLU	-1	-0.884	-0.948	6.229	0.520	0.520	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.003	-0.009	7.505	0.123	0.123	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.036	-0.021	8.290	0.219	0.219	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.762	-0.885	9.961	-0.594	-0.594	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.072	-0.040	11.959	0.127	0.127	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.023	-0.009	11.539	0.084	0.084	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.012	0.005	13.825	0.077	0.077	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.849	0.913	15.144	0.618	0.618	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.823	-0.892	17.657	-0.198	-0.198	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.024	-0.014	18.375	0.038	0.038	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.020	-0.014	20.156	0.031	0.031	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.866	0.914	22.122	0.247	0.247	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.088	-0.028	23.565	0.025	0.025	0.000	0.000	0.000	0.000
19	A	19	ILE	0	-0.026	-0.041	24.488	0.019	0.019	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.876	-0.932	26.778	-0.167	-0.167	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.046	0.006	27.897	0.016	0.016	0.000	0.000	0.000	0.000
22	A	22	ASN	0	0.050	0.006	30.803	0.003	0.003	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.814	0.900	28.730	0.164	0.164	0.000	0.000	0.000	0.000
24	A	24	THR	0	0.010	0.005	28.724	0.007	0.007	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.833	-0.905	32.023	-0.133	-0.133	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.838	0.901	33.864	0.096	0.096	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.939	-0.959	32.326	-0.134	-0.134	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.021	-0.016	30.045	0.003	0.003	0.000	0.000	0.000	0.000
29	A	29	LEU	0	0.002	-0.002	34.639	0.002	0.002	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.800	-0.884	37.870	-0.088	-0.088	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.057	-0.007	36.238	0.006	0.006	0.000	0.000	0.000	0.000
32	A	32	PHE	0	0.001	0.001	36.816	0.003	0.003	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.714	-0.862	39.269	-0.088	-0.088	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.775	0.854	41.242	0.094	0.094	0.000	0.000	0.000	0.000
35	A	35	MET	0	-0.035	-0.011	38.224	0.003	0.003	0.000	0.000	0.000	0.000
36	A	36	CYS	0	-0.108	-0.038	41.606	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.033	-0.022	44.669	0.004	0.004	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.880	0.957	42.298	0.084	0.084	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.018	-0.020	44.831	0.001	0.001	0.000	0.000	0.000	0.000
40	A	40	PRO	0	-0.117	-0.046	48.537	0.003	0.003	0.000	0.000	0.000	0.000
41	A	41	LYS	1	1.022	1.014	51.161	0.049	0.049	0.000	0.000	0.000	0.000
42	A	42	SER	0	0.082	0.024	53.658	0.000	0.000	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.025	0.000	48.493	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.021	-0.025	47.937	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.907	-0.946	49.042	-0.063	-0.063	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.946	-0.967	48.869	-0.065	-0.065	0.000	0.000	0.000	0.000
47	A	48	GLN	0	0.039	0.009	44.154	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.885	-0.922	45.147	-0.072	-0.072	0.000	0.000	0.000	0.000
49	A	50	VAL	0	-0.035	-0.010	41.823	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	51	VAL	0	-0.031	-0.018	39.722	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.884	-0.946	40.791	-0.089	-0.089	0.000	0.000	0.000	0.000
52	A	53	THR	0	-0.134	-0.063	42.672	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	54	TYR	0	-0.047	-0.039	39.213	0.000	0.000	0.000	0.000	0.000	0.000
54	A	55	GLY	0	0.020	0.023	37.288	-0.007	-0.007	0.000	0.000	0.000	0.000
55	A	56	SER	0	-0.010	-0.004	35.820	-0.007	-0.007	0.000	0.000	0.000	0.000
56	A	57	SER	0	0.014	-0.005	35.075	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.025	-0.015	32.846	-0.007	-0.007	0.000	0.000	0.000	0.000
58	A	59	LEU	0	-0.015	-0.002	30.049	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	60	SER	0	0.060	0.018	29.928	-0.012	-0.012	0.000	0.000	0.000	0.000
60	A	61	ILE	0	0.013	0.012	29.423	-0.009	-0.009	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.039	-0.013	26.350	-0.013	-0.013	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.053	-0.031	24.951	-0.026	-0.026	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.963	-0.982	24.015	-0.207	-0.207	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.980	-0.977	24.240	-0.229	-0.229	0.000	0.000	0.000	0.000
65	A	66	VAL	0	-0.058	-0.012	18.892	-0.032	-0.032	0.000	0.000	0.000	0.000
66	A	67	SER	0	0.034	0.015	16.837	-0.032	-0.032	0.000	0.000	0.000	0.000
67	A	68	PRO	0	-0.035	-0.036	14.698	-0.044	-0.044	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.898	-0.949	11.571	-0.865	-0.865	0.000	0.000	0.000	0.000
69	A	70	LEU	0	-0.024	-0.006	11.924	-0.108	-0.108	0.000	0.000	0.000	0.000
70	A	71	VAL	0	0.020	-0.003	13.513	-0.038	-0.038	0.000	0.000	0.000	0.000
71	A	73	SER	0	0.010	0.020	8.943	-0.283	-0.283	0.000	0.000	0.000	0.000
72	A	74	MET	0	-0.082	-0.038	10.185	0.068	0.068	0.000	0.000	0.000	0.000
73	A	75	LEU	0	-0.029	-0.005	10.327	0.114	0.114	0.000	0.000	0.000	0.000
74	A	76	HIS	0	-0.072	-0.032	7.727	0.037	0.037	0.000	0.000	0.000	0.000
75	A	77	LEU	0	-0.026	-0.010	5.059	-0.152	-0.152	0.000	0.000	0.000	0.000

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