FMO DATABASE

FMODB ID: ZN6LN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-506900.042157
FMO2-HF: Nuclear repulsion	473950.831074
FMO2-HF: Total energy	-32949.211083
FMO2-MP2: Total energy	-33038.290185

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.
-6.488	-2.153	0.216	-2.34	-2.212	-0.006

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 : 0.029 / q_NPA : 0.013

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	0.022	0.002	3.795	-1.023	0.416	0.001	-0.842	-0.598	0.005
4	A	3	PRO	0	0.061	0.011	6.509	0.385	0.385	0.000	0.000	0.000	0.000
5	A	4	CYS	0	-0.073	0.004	3.296	0.526	0.924	0.049	-0.114	-0.334	0.000
6	A	5	ASP	-1	-0.844	-0.935	3.167	-6.153	-4.197	0.134	-1.193	-0.897	-0.010
7	A	6	ILE	0	-0.014	-0.008	5.401	0.639	0.639	0.000	0.000	0.000	0.000
8	A	7	CYS	0	-0.003	0.005	8.329	0.257	0.257	0.000	0.000	0.000	0.000
9	A	8	LYS	1	0.877	0.913	3.013	-1.449	-1.217	0.028	-0.076	-0.184	0.000
10	A	9	ASP	-1	-0.944	-0.950	9.242	-0.273	-0.273	0.000	0.000	0.000	0.000
11	A	10	VAL	0	0.051	0.017	11.557	0.098	0.098	0.000	0.000	0.000	0.000
12	A	11	VAL	0	-0.007	-0.008	12.768	0.063	0.063	0.000	0.000	0.000	0.000
13	A	12	THR	0	-0.046	-0.042	12.409	0.084	0.084	0.000	0.000	0.000	0.000
14	A	13	ALA	0	0.002	0.011	15.091	0.021	0.021	0.000	0.000	0.000	0.000
15	A	14	ALA	0	0.024	0.009	17.129	0.019	0.019	0.000	0.000	0.000	0.000
16	A	15	GLY	0	0.038	0.013	18.057	0.017	0.017	0.000	0.000	0.000	0.000
17	A	16	ASP	-1	-0.911	-0.956	18.785	0.082	0.082	0.000	0.000	0.000	0.000
18	A	17	MET	0	-0.005	0.011	21.070	-0.007	-0.007	0.000	0.000	0.000	0.000
19	A	18	LEU	0	0.009	0.008	22.164	0.004	0.004	0.000	0.000	0.000	0.000
20	A	19	LYS	1	0.768	0.879	20.014	-0.066	-0.066	0.000	0.000	0.000	0.000
21	A	20	ASP	-1	-0.948	-0.956	25.556	0.009	0.009	0.000	0.000	0.000	0.000
22	A	21	ASN	0	-0.161	-0.091	27.478	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	22	ALA	0	-0.002	0.014	25.681	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	23	THR	0	-0.035	-0.050	27.650	0.001	0.001	0.000	0.000	0.000	0.000
25	A	24	GLU	-1	-0.773	-0.897	25.273	-0.069	-0.069	0.000	0.000	0.000	0.000
26	A	25	GLU	-1	-0.916	-0.960	25.222	-0.107	-0.107	0.000	0.000	0.000	0.000
27	A	26	GLU	-1	-0.858	-0.905	26.407	-0.090	-0.090	0.000	0.000	0.000	0.000
28	A	27	ILE	0	-0.001	-0.007	20.859	-0.017	-0.017	0.000	0.000	0.000	0.000
29	A	28	LEU	0	0.010	0.009	21.732	-0.026	-0.026	0.000	0.000	0.000	0.000
30	A	29	VAL	0	0.002	-0.001	22.362	-0.027	-0.027	0.000	0.000	0.000	0.000
31	A	30	TYR	0	-0.042	-0.030	21.193	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	31	LEU	0	-0.005	0.002	16.250	-0.031	-0.031	0.000	0.000	0.000	0.000
33	A	32	GLU	-1	-0.851	-0.925	18.436	-0.321	-0.321	0.000	0.000	0.000	0.000
34	A	33	LYS	1	0.916	0.977	20.781	0.188	0.188	0.000	0.000	0.000	0.000
35	A	34	THR	0	-0.014	-0.014	15.165	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	35	CYS	0	-0.079	-0.028	13.519	-0.038	-0.038	0.000	0.000	0.000	0.000
37	A	36	ASP	-1	-0.826	-0.917	17.510	-0.387	-0.387	0.000	0.000	0.000	0.000
38	A	37	TRP	0	-0.070	-0.042	18.958	0.036	0.036	0.000	0.000	0.000	0.000
39	A	38	LEU	0	-0.060	-0.007	12.889	-0.042	-0.042	0.000	0.000	0.000	0.000
40	A	39	PRO	0	0.008	0.003	14.242	0.024	0.024	0.000	0.000	0.000	0.000
41	A	40	LYS	1	0.914	0.952	13.102	1.021	1.021	0.000	0.000	0.000	0.000
42	A	41	PRO	0	0.084	0.032	16.570	-0.048	-0.048	0.000	0.000	0.000	0.000
43	A	42	ASN	0	0.028	0.005	12.480	0.081	0.081	0.000	0.000	0.000	0.000
44	A	43	MET	0	-0.036	-0.002	10.455	-0.042	-0.042	0.000	0.000	0.000	0.000
45	A	44	SER	0	0.066	0.039	13.783	-0.023	-0.023	0.000	0.000	0.000	0.000
46	A	45	ALA	0	-0.020	-0.008	16.889	0.028	0.028	0.000	0.000	0.000	0.000
47	A	46	SER	0	0.020	-0.003	12.188	-0.018	-0.018	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.850	0.903	14.363	0.407	0.407	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.924	-0.942	16.102	-0.544	-0.544	0.000	0.000	0.000	0.000
50	A	50	ILE	0	-0.040	-0.011	10.622	0.031	0.031	0.000	0.000	0.000	0.000
51	A	51	VAL	0	-0.005	-0.013	14.957	0.069	0.069	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.894	-0.952	17.347	-0.260	-0.260	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.112	-0.059	17.244	0.044	0.044	0.000	0.000	0.000	0.000
54	A	54	TYR	0	-0.029	-0.035	14.687	0.016	0.016	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.004	0.020	17.535	0.037	0.037	0.000	0.000	0.000	0.000
56	A	56	PRO	0	0.027	0.007	18.848	0.033	0.033	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.054	0.026	18.519	0.020	0.020	0.000	0.000	0.000	0.000
58	A	58	ILE	0	-0.025	-0.013	14.401	0.030	0.030	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.001	-0.002	18.539	0.032	0.032	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.917	-0.954	21.678	-0.032	-0.032	0.000	0.000	0.000	0.000
61	A	61	ILE	0	-0.067	-0.034	18.049	0.021	0.021	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.036	-0.016	17.714	0.026	0.026	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.800	0.893	21.299	0.052	0.052	0.000	0.000	0.000	0.000
64	A	64	GLY	0	-0.043	-0.008	23.964	0.004	0.004	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-1.001	-0.994	24.080	0.093	0.093	0.000	0.000	0.000	0.000
66	A	66	MET	0	-0.061	-0.019	18.207	0.026	0.026	0.000	0.000	0.000	0.000
67	A	67	SER	0	0.064	0.006	17.888	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.808	0.898	14.636	-0.339	-0.339	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.067	0.037	10.892	0.030	0.030	0.000	0.000	0.000	0.000
70	A	70	GLY	0	0.015	0.004	8.996	-0.015	-0.015	0.000	0.000	0.000	0.000
71	A	71	GLU	-1	-0.862	-0.909	9.983	0.357	0.357	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.064	0.026	12.988	-0.033	-0.033	0.000	0.000	0.000	0.000
73	A	74	SER	0	-0.038	-0.030	9.691	-0.005	-0.005	0.000	0.000	0.000	0.000
74	A	75	ALA	0	-0.036	-0.001	10.698	-0.058	-0.058	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.046	-0.019	12.964	-0.035	-0.035	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.066	-0.034	11.424	-0.019	-0.019	0.000	0.000	0.000	0.000
77	A	78	LEU	0	0.003	0.009	8.929	-0.130	-0.130	0.000	0.000	0.000	0.000
78	A	80	GLU	-1	-0.881	-0.937	4.000	0.374	0.684	0.004	-0.115	-0.199	-0.001

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