FMO DATABASE

FMODB ID: 6GN7Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-506621.024204
FMO2-HF: Nuclear repulsion	473672.194034
FMO2-HF: Total energy	-32948.83017
FMO2-MP2: Total energy	-33037.878011

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.
-9.746	-5.52	0.328	-2.433	-2.118	-0.007

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 : 0.021 / 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

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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	0.048	0.018	3.795	-1.065	0.349	0.000	-0.823	-0.591	0.005
4	A	3	PRO	0	0.046	0.001	6.503	0.419	0.419	0.000	0.000	0.000	0.000
5	A	4	CYS	0	-0.118	-0.027	3.274	0.565	0.938	0.043	-0.101	-0.314	0.000
6	A	5	ASP	-1	-0.902	-0.971	2.975	-9.622	-7.521	0.285	-1.414	-0.972	-0.012
7	A	6	ILE	0	-0.023	-0.016	5.394	0.727	0.761	-0.001	0.000	-0.033	0.000
8	A	7	CYS	0	0.004	0.010	8.319	0.302	0.302	0.000	0.000	0.000	0.000
9	A	8	LYS	1	0.963	0.961	4.471	-1.641	-1.601	-0.001	-0.004	-0.034	0.000
10	A	9	ASP	-1	-0.955	-0.955	9.239	-0.334	-0.334	0.000	0.000	0.000	0.000
11	A	10	VAL	0	0.070	0.024	11.552	0.115	0.115	0.000	0.000	0.000	0.000
12	A	11	VAL	0	-0.023	-0.016	12.765	0.077	0.077	0.000	0.000	0.000	0.000
13	A	12	THR	0	-0.049	-0.034	12.436	0.095	0.095	0.000	0.000	0.000	0.000
14	A	13	ALA	0	0.016	0.020	15.088	0.029	0.029	0.000	0.000	0.000	0.000
15	A	14	ALA	0	0.023	0.008	17.126	0.025	0.025	0.000	0.000	0.000	0.000
16	A	15	GLY	0	-0.014	-0.015	18.055	0.023	0.023	0.000	0.000	0.000	0.000
17	A	16	ASP	-1	-0.941	-0.982	18.732	0.030	0.030	0.000	0.000	0.000	0.000
18	A	17	MET	0	-0.016	0.003	21.067	-0.005	-0.005	0.000	0.000	0.000	0.000
19	A	18	LEU	0	-0.011	-0.003	22.182	0.008	0.008	0.000	0.000	0.000	0.000
20	A	19	LYS	1	0.850	0.936	21.009	-0.034	-0.034	0.000	0.000	0.000	0.000
21	A	20	ASP	-1	-0.931	-0.943	25.551	-0.011	-0.011	0.000	0.000	0.000	0.000
22	A	21	ASN	0	-0.149	-0.084	27.474	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	22	ALA	0	0.006	0.015	25.683	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	23	THR	0	-0.016	-0.012	27.646	0.000	0.000	0.000	0.000	0.000	0.000
25	A	24	GLU	-1	-0.854	-0.952	25.383	-0.100	-0.100	0.000	0.000	0.000	0.000
26	A	25	GLU	-1	-0.919	-0.962	25.217	-0.129	-0.129	0.000	0.000	0.000	0.000
27	A	26	GLU	-1	-0.909	-0.960	26.402	-0.110	-0.110	0.000	0.000	0.000	0.000
28	A	27	ILE	0	-0.003	-0.011	20.871	-0.018	-0.018	0.000	0.000	0.000	0.000
29	A	28	LEU	0	0.000	0.006	21.727	-0.029	-0.029	0.000	0.000	0.000	0.000
30	A	29	VAL	0	0.014	0.012	22.356	-0.028	-0.028	0.000	0.000	0.000	0.000
31	A	30	TYR	0	-0.062	-0.042	21.138	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	31	LEU	0	-0.007	-0.003	16.220	-0.033	-0.033	0.000	0.000	0.000	0.000
33	A	32	GLU	-1	-0.891	-0.953	18.429	-0.328	-0.328	0.000	0.000	0.000	0.000
34	A	33	LYS	1	0.942	0.985	20.774	0.210	0.210	0.000	0.000	0.000	0.000
35	A	34	THR	0	-0.009	-0.013	15.104	0.000	0.000	0.000	0.000	0.000	0.000
36	A	35	CYS	0	-0.064	-0.018	13.509	-0.048	-0.048	0.000	0.000	0.000	0.000
37	A	36	ASP	-1	-0.844	-0.917	17.502	-0.408	-0.408	0.000	0.000	0.000	0.000
38	A	37	TRP	0	-0.077	-0.039	18.892	0.035	0.035	0.000	0.000	0.000	0.000
39	A	38	LEU	0	-0.067	-0.011	12.907	-0.042	-0.042	0.000	0.000	0.000	0.000
40	A	39	PRO	0	0.011	0.006	14.204	0.032	0.032	0.000	0.000	0.000	0.000
41	A	40	LYS	1	0.918	0.950	13.624	0.993	0.993	0.000	0.000	0.000	0.000
42	A	41	PRO	0	0.075	0.029	16.580	-0.051	-0.051	0.000	0.000	0.000	0.000
43	A	42	ASN	0	0.026	0.003	12.540	0.099	0.099	0.000	0.000	0.000	0.000
44	A	43	MET	0	-0.027	-0.005	10.384	-0.024	-0.024	0.000	0.000	0.000	0.000
45	A	44	SER	0	0.046	0.023	13.788	-0.018	-0.018	0.000	0.000	0.000	0.000
46	A	45	ALA	0	-0.024	-0.010	16.882	0.028	0.028	0.000	0.000	0.000	0.000
47	A	46	SER	0	0.027	0.008	12.158	-0.013	-0.013	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.906	0.929	14.357	0.466	0.466	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.932	-0.945	16.136	-0.566	-0.566	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.037	-0.018	10.632	0.029	0.029	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.003	-0.011	14.953	0.068	0.068	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.892	-0.955	17.343	-0.296	-0.296	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.101	-0.042	17.276	0.050	0.050	0.000	0.000	0.000	0.000
54	A	54	TYR	0	-0.026	-0.032	14.570	0.018	0.018	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.001	0.020	17.533	0.037	0.037	0.000	0.000	0.000	0.000
56	A	56	PRO	0	0.035	0.009	18.845	0.035	0.035	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.057	0.030	18.475	0.021	0.021	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.029	-0.015	14.492	0.030	0.030	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.004	-0.003	18.538	0.034	0.034	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.901	-0.948	21.676	-0.057	-0.057	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.063	-0.031	17.980	0.023	0.023	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.046	-0.020	17.772	0.030	0.030	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.874	0.942	21.298	0.069	0.069	0.000	0.000	0.000	0.000
64	A	64	GLY	0	-0.032	0.001	23.979	0.006	0.006	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-1.002	-0.996	24.131	0.078	0.078	0.000	0.000	0.000	0.000
66	A	66	MET	0	-0.052	-0.013	18.205	0.025	0.025	0.000	0.000	0.000	0.000
67	A	67	SER	0	0.028	-0.011	17.909	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.932	0.973	14.663	-0.320	-0.320	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.081	0.045	10.859	0.029	0.029	0.000	0.000	0.000	0.000
70	A	70	GLY	0	-0.010	-0.014	8.998	-0.018	-0.018	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.940	-0.969	9.985	0.316	0.316	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.052	0.021	12.991	-0.029	-0.029	0.000	0.000	0.000	0.000
73	A	74	SER	0	-0.041	-0.020	9.628	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	75	ALA	0	-0.030	0.002	10.702	-0.046	-0.046	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.056	-0.025	13.013	-0.027	-0.027	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.048	-0.023	11.471	-0.034	-0.034	0.000	0.000	0.000	0.000
77	A	78	LEU	0	0.002	0.007	8.915	-0.129	-0.129	0.000	0.000	0.000	0.000
78	A	80	GLU	-1	-0.908	-0.952	4.085	0.729	0.993	0.002	-0.091	-0.174	0.000

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