FMO DATABASE

FMODB ID: RY9M8

Calculation Name: 4UEX-A-Xray372

Preferred Name: Prosaposin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4UEX

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	78
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-508784.811768
FMO2-HF: Nuclear repulsion	475835.491595
FMO2-HF: Total energy	-32949.320173
FMO2-MP2: Total energy	-33038.400356

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:0:GLY)

Summations of interaction energy for fragment #1(A:0: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.
-25.006	-27.732	21.322	-10.56	-8.035	-0.048

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.015 / 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	2	LEU	0	-0.004	-0.013	3.825	-0.798	0.543	0.003	-0.774	-0.570	0.003
4	A	3	PRO	0	0.053	0.006	6.163	0.496	0.496	0.000	0.000	0.000	0.000
5	A	4	CYS	0	-0.058	0.018	2.572	1.483	2.265	0.897	-0.686	-0.993	0.000
6	A	5	ASP	-1	-0.775	-0.903	1.795	-8.930	-13.441	12.713	-5.125	-3.077	-0.065
7	A	6	ILE	0	0.006	0.007	4.756	0.597	0.664	-0.001	-0.014	-0.052	0.000
8	A	7	CYS	0	0.014	0.010	7.685	0.211	0.211	0.000	0.000	0.000	0.000
9	A	8	LYS	1	0.806	0.872	2.040	-16.456	-18.810	7.392	-2.725	-2.313	0.024
10	A	9	ASP	-1	-0.932	-0.944	8.399	-0.019	-0.019	0.000	0.000	0.000	0.000
11	A	10	VAL	0	0.035	0.013	10.771	0.066	0.066	0.000	0.000	0.000	0.000
12	A	11	VAL	0	-0.004	-0.016	12.154	0.021	0.021	0.000	0.000	0.000	0.000
13	A	12	THR	0	-0.042	-0.034	11.594	0.062	0.062	0.000	0.000	0.000	0.000
14	A	13	ALA	0	0.006	0.006	14.313	-0.032	-0.032	0.000	0.000	0.000	0.000
15	A	14	ALA	0	0.034	0.011	16.553	-0.016	-0.016	0.000	0.000	0.000	0.000
16	A	15	GLY	0	0.038	0.012	17.264	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	16	ASP	-1	-0.901	-0.931	18.043	0.367	0.367	0.000	0.000	0.000	0.000
18	A	17	MET	0	-0.001	0.007	20.341	-0.027	-0.027	0.000	0.000	0.000	0.000
19	A	18	LEU	0	0.018	0.007	21.626	-0.016	-0.016	0.000	0.000	0.000	0.000
20	A	19	LYS	1	0.731	0.852	19.757	-0.343	-0.343	0.000	0.000	0.000	0.000
21	A	20	ASP	-1	-0.941	-0.964	24.683	0.137	0.137	0.000	0.000	0.000	0.000
22	A	21	ASN	0	-0.147	-0.073	26.626	-0.015	-0.015	0.000	0.000	0.000	0.000
23	A	22	ALA	0	-0.008	0.011	25.212	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	23	THR	0	-0.036	-0.053	26.878	0.003	0.003	0.000	0.000	0.000	0.000
25	A	24	GLU	-1	-0.792	-0.905	24.726	0.064	0.064	0.000	0.000	0.000	0.000
26	A	25	GLU	-1	-0.907	-0.958	24.452	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	26	GLU	-1	-0.868	-0.905	25.668	0.008	0.008	0.000	0.000	0.000	0.000
28	A	27	ILE	0	0.001	0.000	20.052	-0.013	-0.013	0.000	0.000	0.000	0.000
29	A	28	LEU	0	0.015	0.011	20.825	-0.016	-0.016	0.000	0.000	0.000	0.000
30	A	29	VAL	0	0.004	0.003	21.488	-0.029	-0.029	0.000	0.000	0.000	0.000
31	A	30	TYR	0	-0.045	-0.032	20.296	-0.020	-0.020	0.000	0.000	0.000	0.000
32	A	31	LEU	0	0.013	0.014	15.361	-0.027	-0.027	0.000	0.000	0.000	0.000
33	A	32	GLU	-1	-0.860	-0.921	17.566	-0.237	-0.237	0.000	0.000	0.000	0.000
34	A	33	LYS	1	0.889	0.958	19.691	0.102	0.102	0.000	0.000	0.000	0.000
35	A	34	THR	0	-0.034	-0.021	14.150	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	35	CYS	0	-0.052	-0.014	12.972	-0.029	-0.029	0.000	0.000	0.000	0.000
37	A	36	ASP	-1	-0.829	-0.904	16.531	-0.342	-0.342	0.000	0.000	0.000	0.000
38	A	37	TRP	0	-0.032	-0.032	18.159	0.044	0.044	0.000	0.000	0.000	0.000
39	A	38	LEU	0	-0.038	0.005	12.262	-0.050	-0.050	0.000	0.000	0.000	0.000
40	A	39	PRO	0	-0.012	-0.010	13.768	0.015	0.015	0.000	0.000	0.000	0.000
41	A	40	LYS	1	0.914	0.947	13.200	1.073	1.073	0.000	0.000	0.000	0.000
42	A	41	PRO	0	0.073	0.034	16.260	-0.051	-0.051	0.000	0.000	0.000	0.000
43	A	42	ASN	0	0.030	0.006	12.708	0.073	0.073	0.000	0.000	0.000	0.000
44	A	43	MET	0	-0.045	-0.003	10.198	-0.059	-0.059	0.000	0.000	0.000	0.000
45	A	44	SER	0	0.046	0.017	13.410	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	45	ALA	0	-0.035	-0.005	16.310	0.043	0.043	0.000	0.000	0.000	0.000
47	A	46	SER	0	0.033	0.001	11.888	-0.022	-0.022	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.827	0.889	13.885	0.337	0.337	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.913	-0.951	15.719	-0.515	-0.515	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.039	-0.006	10.076	0.031	0.031	0.000	0.000	0.000	0.000
51	A	51	VAL	0	0.003	-0.008	14.378	0.088	0.088	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.891	-0.956	16.870	-0.170	-0.170	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.105	-0.057	16.414	0.035	0.035	0.000	0.000	0.000	0.000
54	A	54	TYR	0	-0.040	-0.035	13.343	0.010	0.010	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.007	0.016	16.817	0.055	0.055	0.000	0.000	0.000	0.000
56	A	56	PRO	0	0.037	0.011	18.301	0.038	0.038	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.045	0.023	17.362	0.023	0.023	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.021	-0.010	13.572	0.047	0.047	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.011	0.004	17.544	0.043	0.043	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.868	-0.931	20.854	0.100	0.100	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.060	-0.034	17.015	0.018	0.018	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.039	-0.010	17.457	0.031	0.031	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.739	0.858	20.736	-0.086	-0.086	0.000	0.000	0.000	0.000
64	A	64	GLY	0	-0.047	-0.005	23.117	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.988	-0.991	23.373	0.243	0.243	0.000	0.000	0.000	0.000
66	A	66	MET	0	-0.060	-0.014	17.162	0.049	0.049	0.000	0.000	0.000	0.000
67	A	67	SER	0	0.060	0.004	16.864	-0.028	-0.028	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.808	0.879	14.101	-0.650	-0.650	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.059	0.025	10.315	0.085	0.085	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.035	0.011	8.073	0.021	0.021	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.853	-0.875	8.989	0.704	0.704	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.066	0.028	12.058	-0.084	-0.084	0.000	0.000	0.000	0.000
73	A	74	SER	0	-0.045	-0.028	8.633	-0.058	-0.058	0.000	0.000	0.000	0.000
74	A	75	ALA	0	-0.029	-0.007	9.690	-0.169	-0.169	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.035	-0.013	11.923	-0.094	-0.094	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.079	-0.042	10.361	-0.047	-0.047	0.000	0.000	0.000	0.000
77	A	78	LEU	0	0.008	0.014	8.237	-0.193	-0.193	0.000	0.000	0.000	0.000
78	A	80	GLU	-1	-0.847	-0.908	3.015	-2.126	-0.177	0.318	-1.236	-1.030	-0.010

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)