FMO DATABASE

FMODB ID: 1647Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-434519.825457
FMO2-HF: Nuclear repulsion	401960.409901
FMO2-HF: Total energy	-32559.415556
FMO2-MP2: Total energy	-32648.229892

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.
-12.405	-6.24	5.696	-4.439	-7.422	-0.002

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 : 0.009 / 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	0.038	0.019	3.450	-1.797	0.601	0.044	-1.122	-1.321	0.005
4	A	4	TYR	0	-0.040	-0.029	2.443	-9.084	-5.726	5.651	-3.177	-5.831	-0.007
5	A	78	CYS	0	-0.023	0.018	4.212	-0.734	-0.325	0.001	-0.140	-0.270	0.000
6	A	6	GLU	-1	-0.905	-0.956	6.273	0.479	0.479	0.000	0.000	0.000	0.000
7	A	7	VAL	0	0.003	-0.008	7.087	0.183	0.183	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.026	-0.027	8.129	0.291	0.291	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.764	-0.885	9.854	-0.535	-0.535	0.000	0.000	0.000	0.000
10	A	10	PHE	0	-0.050	-0.029	11.552	0.149	0.149	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.010	0.000	11.146	0.104	0.104	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.020	0.009	13.531	0.089	0.089	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.831	0.917	14.924	0.712	0.712	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.836	-0.899	17.379	-0.245	-0.245	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.007	-0.019	18.081	0.044	0.044	0.000	0.000	0.000	0.000
16	A	16	THR	0	-0.005	-0.007	19.755	0.038	0.038	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.844	0.902	21.558	0.301	0.301	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.072	-0.020	23.012	0.028	0.028	0.000	0.000	0.000	0.000
19	A	19	ILE	0	-0.016	-0.033	24.115	0.024	0.024	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.889	-0.939	26.276	-0.191	-0.191	0.000	0.000	0.000	0.000
21	A	21	ASN	0	-0.044	0.005	27.193	0.018	0.018	0.000	0.000	0.000	0.000
22	A	22	ASN	0	0.053	-0.001	30.386	0.003	0.003	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.786	0.895	28.137	0.196	0.196	0.000	0.000	0.000	0.000
24	A	24	THR	0	0.021	0.017	28.210	0.008	0.008	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.783	-0.859	31.542	-0.149	-0.149	0.000	0.000	0.000	0.000
26	A	26	LYS	1	0.819	0.889	33.733	0.110	0.110	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.934	-0.972	31.609	-0.158	-0.158	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.017	-0.009	29.504	0.003	0.003	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.003	-0.010	34.125	0.003	0.003	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.820	-0.882	37.555	-0.100	-0.100	0.000	0.000	0.000	0.000
31	A	31	ALA	0	-0.020	0.006	35.520	0.006	0.006	0.000	0.000	0.000	0.000
32	A	32	PHE	0	0.023	0.006	36.114	0.004	0.004	0.000	0.000	0.000	0.000
33	A	33	ASP	-1	-0.759	-0.879	39.076	-0.097	-0.097	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.778	0.862	41.004	0.107	0.107	0.000	0.000	0.000	0.000
35	A	35	MET	0	-0.035	-0.006	38.064	0.003	0.003	0.000	0.000	0.000	0.000
36	A	36	CYS	0	-0.090	-0.012	41.423	-0.003	-0.003	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.055	-0.045	44.544	0.005	0.005	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.913	0.967	41.940	0.093	0.093	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.033	-0.019	44.390	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	PRO	0	-0.080	-0.040	48.280	0.003	0.003	0.000	0.000	0.000	0.000
41	A	41	LYS	1	1.024	1.018	50.806	0.053	0.053	0.000	0.000	0.000	0.000
42	A	42	SER	0	0.052	0.016	52.276	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.040	0.010	48.426	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.026	-0.003	47.634	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.908	-0.947	48.052	-0.071	-0.071	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.910	-0.973	49.050	-0.073	-0.073	0.000	0.000	0.000	0.000
47	A	48	GLN	0	0.031	-0.004	44.242	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.912	-0.936	45.004	-0.080	-0.080	0.000	0.000	0.000	0.000
49	A	50	VAL	0	-0.062	-0.021	41.747	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	51	VAL	0	-0.031	-0.021	39.700	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	52	ASP	-1	-0.910	-0.964	40.773	-0.101	-0.101	0.000	0.000	0.000	0.000
52	A	53	THR	0	-0.086	-0.043	42.698	0.000	0.000	0.000	0.000	0.000	0.000
53	A	54	TYR	0	-0.050	-0.031	39.178	0.000	0.000	0.000	0.000	0.000	0.000
54	A	55	GLY	0	0.014	0.015	37.174	-0.008	-0.008	0.000	0.000	0.000	0.000
55	A	56	SER	0	-0.031	-0.032	35.486	-0.008	-0.008	0.000	0.000	0.000	0.000
56	A	57	SER	0	0.007	0.007	34.578	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	58	ILE	0	-0.029	-0.012	32.929	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	59	LEU	0	-0.026	-0.012	29.793	-0.012	-0.012	0.000	0.000	0.000	0.000
59	A	60	SER	0	0.032	-0.006	29.744	-0.013	-0.013	0.000	0.000	0.000	0.000
60	A	61	ILE	0	0.032	0.020	29.173	-0.014	-0.014	0.000	0.000	0.000	0.000
61	A	62	LEU	0	-0.027	-0.012	26.697	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.067	-0.033	24.808	-0.028	-0.028	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.968	-0.985	24.017	-0.226	-0.226	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.983	-0.986	24.296	-0.245	-0.245	0.000	0.000	0.000	0.000
65	A	66	VAL	0	-0.060	-0.011	18.883	-0.032	-0.032	0.000	0.000	0.000	0.000
66	A	67	SER	0	0.027	0.010	17.079	-0.031	-0.031	0.000	0.000	0.000	0.000
67	A	68	PRO	0	-0.015	-0.027	14.748	-0.046	-0.046	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.899	-0.938	11.538	-0.897	-0.897	0.000	0.000	0.000	0.000
69	A	70	LEU	0	0.004	0.008	11.730	-0.126	-0.126	0.000	0.000	0.000	0.000
70	A	71	VAL	0	0.017	0.004	13.454	-0.031	-0.031	0.000	0.000	0.000	0.000
71	A	73	SER	0	-0.013	0.008	8.813	-0.270	-0.270	0.000	0.000	0.000	0.000
72	A	74	MET	0	-0.075	-0.038	10.123	0.088	0.088	0.000	0.000	0.000	0.000
73	A	75	LEU	0	-0.046	-0.020	10.388	0.108	0.108	0.000	0.000	0.000	0.000
74	A	76	HIS	0	-0.071	-0.033	7.820	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	77	LEU	0	-0.020	-0.003	4.936	-0.193	-0.193	0.000	0.000	0.000	0.000

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