FMO DATABASE

FMODB ID: QN89Y

Calculation Name: 2GTG-A-Xray372

Preferred Name: Prosaposin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2GTG

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

Total energy (hartree)

FMO2-HF: Electronic energy	-508598.241793
FMO2-HF: Nuclear repulsion	476039.924535
FMO2-HF: Total energy	-32558.317258
FMO2-MP2: Total energy	-32647.315429

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:2:ASP)

Summations of interaction energy for fragment #1(A:2:ASP)

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.
114.614	117.81	3.43	-2.604	-4.023	0.018

Interaction energy analysis for fragmet #1(A:2:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.964 / q_NPA : -1.000

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

Sort

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	4	TYR	0	-0.016	-0.028	3.869	-3.273	-1.864	-0.005	-0.557	-0.848	0.001
4	A	5	CYS	0	-0.108	-0.022	2.434	-0.889	0.305	3.428	-1.910	-2.712	0.016
5	A	6	GLU	-1	-0.884	-0.949	3.633	34.072	34.525	0.009	-0.131	-0.332	0.001
6	A	7	VAL	0	0.044	0.024	5.168	-5.522	-5.445	-0.001	-0.002	-0.073	0.000
7	A	8	CYS	0	0.049	0.015	7.408	-4.632	-4.632	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.890	-0.967	6.309	29.981	29.981	0.000	0.000	0.000	0.000
9	A	10	PHE	0	-0.113	-0.058	9.095	-3.135	-3.135	0.000	0.000	0.000	0.000
10	A	11	LEU	0	0.030	-0.006	11.159	-2.054	-2.054	0.000	0.000	0.000	0.000
11	A	12	VAL	0	0.042	0.035	12.382	-1.816	-1.816	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.965	0.969	10.760	-26.924	-26.924	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.953	-0.977	15.295	15.505	15.505	0.000	0.000	0.000	0.000
14	A	15	VAL	0	0.022	0.003	17.014	-1.161	-1.161	0.000	0.000	0.000	0.000
15	A	16	THR	0	0.012	0.015	17.119	-0.704	-0.704	0.000	0.000	0.000	0.000
16	A	17	LYS	1	0.945	0.987	19.488	-13.677	-13.677	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.074	-0.043	21.188	-0.904	-0.904	0.000	0.000	0.000	0.000
18	A	19	ILE	0	0.036	0.028	21.328	-0.596	-0.596	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.883	-0.941	23.192	12.500	12.500	0.000	0.000	0.000	0.000
20	A	21	ASN	0	-0.205	-0.111	25.200	-0.653	-0.653	0.000	0.000	0.000	0.000
21	A	22	ASN	0	-0.063	-0.038	27.557	-0.290	-0.290	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.913	0.977	25.826	-11.094	-11.094	0.000	0.000	0.000	0.000
23	A	24	THR	0	0.014	-0.002	27.913	0.137	0.137	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.837	-0.935	25.665	11.283	11.283	0.000	0.000	0.000	0.000
25	A	26	LYS	1	0.865	0.936	26.351	-9.780	-9.780	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.870	-0.942	27.675	10.141	10.141	0.000	0.000	0.000	0.000
27	A	28	ILE	0	-0.037	-0.005	21.704	0.265	0.265	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.025	-0.021	22.537	0.493	0.493	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.865	-0.933	23.556	10.840	10.840	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.063	-0.020	23.145	0.147	0.147	0.000	0.000	0.000	0.000
31	A	32	PHE	0	0.031	-0.002	17.525	0.663	0.663	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.872	-0.924	19.758	12.885	12.885	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.900	0.953	21.375	-13.598	-13.598	0.000	0.000	0.000	0.000
34	A	35	MET	0	-0.114	-0.045	16.211	0.125	0.125	0.000	0.000	0.000	0.000
35	A	36	CYS	0	-0.024	-0.027	11.579	0.510	0.510	0.000	0.000	0.000	0.000
36	A	37	SER	0	-0.002	-0.001	16.950	0.200	0.200	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.847	0.943	16.509	-17.939	-17.939	0.000	0.000	0.000	0.000
38	A	39	LEU	0	-0.034	-0.002	11.880	0.291	0.291	0.000	0.000	0.000	0.000
39	A	40	PRO	0	0.010	0.010	13.584	-1.239	-1.239	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.985	0.952	15.099	-13.726	-13.726	0.000	0.000	0.000	0.000
41	A	42	SER	0	-0.043	-0.020	12.335	-0.849	-0.849	0.000	0.000	0.000	0.000
42	A	43	LEU	0	0.083	0.055	8.487	-0.149	-0.149	0.000	0.000	0.000	0.000
43	A	44	SER	0	-0.056	-0.014	11.984	-0.345	-0.345	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.931	-0.952	14.440	17.217	17.217	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.840	-0.922	8.905	23.719	23.719	0.000	0.000	0.000	0.000
46	A	48	GLN	0	-0.041	-0.036	12.630	-0.557	-0.557	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.829	-0.878	11.583	20.583	20.583	0.000	0.000	0.000	0.000
48	A	50	VAL	0	-0.012	-0.022	9.246	-0.436	-0.436	0.000	0.000	0.000	0.000
49	A	51	VAL	0	-0.010	-0.018	12.601	-0.764	-0.764	0.000	0.000	0.000	0.000
50	A	52	ASP	-1	-0.926	-0.971	16.012	13.810	13.810	0.000	0.000	0.000	0.000
51	A	53	THR	0	-0.079	-0.016	14.731	-0.981	-0.981	0.000	0.000	0.000	0.000
52	A	54	TYR	0	-0.012	-0.030	11.914	-0.136	-0.136	0.000	0.000	0.000	0.000
53	A	55	GLY	0	0.015	0.042	15.290	-0.125	-0.125	0.000	0.000	0.000	0.000
54	A	56	SER	0	0.015	-0.009	17.248	0.099	0.099	0.000	0.000	0.000	0.000
55	A	57	SER	0	0.007	-0.001	17.144	-0.649	-0.649	0.000	0.000	0.000	0.000
56	A	58	ILE	0	-0.021	-0.019	12.692	0.032	0.032	0.000	0.000	0.000	0.000
57	A	59	LEU	0	-0.025	-0.011	16.743	-0.204	-0.204	0.000	0.000	0.000	0.000
58	A	60	SER	0	0.021	0.007	20.179	-0.490	-0.490	0.000	0.000	0.000	0.000
59	A	61	ILE	0	0.024	0.015	16.645	-0.301	-0.301	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.046	-0.028	16.754	-0.113	-0.113	0.000	0.000	0.000	0.000
61	A	63	LEU	0	-0.052	-0.029	20.239	-0.350	-0.350	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.980	-0.972	22.776	10.855	10.855	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.986	-0.992	23.468	10.986	10.986	0.000	0.000	0.000	0.000
64	A	66	VAL	0	-0.062	-0.020	17.823	0.142	0.142	0.000	0.000	0.000	0.000
65	A	67	SER	0	-0.023	-0.020	18.063	0.388	0.388	0.000	0.000	0.000	0.000
66	A	68	PRO	0	0.087	0.021	15.871	0.789	0.789	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.978	-0.994	13.223	19.576	19.576	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.024	-0.011	12.469	1.132	1.132	0.000	0.000	0.000	0.000
69	A	71	VAL	0	0.011	0.023	13.334	0.205	0.205	0.000	0.000	0.000	0.000
70	A	73	SER	0	-0.040	-0.007	8.928	0.250	0.250	0.000	0.000	0.000	0.000
71	A	74	MET	0	-0.023	0.008	9.827	-0.999	-0.999	0.000	0.000	0.000	0.000
72	A	75	LEU	0	-0.032	-0.017	11.548	-1.032	-1.032	0.000	0.000	0.000	0.000
73	A	76	HIS	0	-0.076	-0.035	9.192	0.901	0.901	0.000	0.000	0.000	0.000
74	A	77	LEU	0	0.029	0.018	6.930	0.976	0.976	0.000	0.000	0.000	0.000
75	A	79	SER	0	0.015	0.003	4.327	-4.998	-4.935	-0.001	-0.004	-0.058	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:2:ASP)