FMO DATABASE

FMODB ID: K2R13

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

Total energy (hartree)

FMO2-HF: Electronic energy	-508463.43379
FMO2-HF: Nuclear repulsion	475904.241448
FMO2-HF: Total energy	-32559.192342
FMO2-MP2: Total energy	-32648.139424

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.
110.806	114.293	3.335	-2.736	-4.086	0.02

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 : -0.955 / q_NPA : -0.996

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	-0.034	-0.038	3.869	-3.106	-1.707	-0.005	-0.561	-0.834	0.001
4	A	5	CYS	0	-0.114	-0.032	2.374	-1.548	-0.045	3.332	-2.029	-2.806	0.018
5	A	6	GLU	-1	-0.906	-0.955	3.631	33.388	33.834	0.010	-0.140	-0.316	0.001
6	A	7	VAL	0	0.039	0.023	5.166	-5.566	-5.493	-0.001	-0.002	-0.069	0.000
7	A	8	CYS	0	0.048	0.015	7.394	-4.498	-4.498	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.803	-0.913	6.647	27.533	27.533	0.000	0.000	0.000	0.000
9	A	10	PHE	0	-0.080	-0.040	9.085	-3.046	-3.046	0.000	0.000	0.000	0.000
10	A	11	LEU	0	0.024	-0.005	11.153	-2.072	-2.072	0.000	0.000	0.000	0.000
11	A	12	VAL	0	0.039	0.024	12.301	-1.824	-1.824	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.843	0.909	10.127	-29.130	-29.130	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.826	-0.900	15.286	15.577	15.577	0.000	0.000	0.000	0.000
14	A	15	VAL	0	0.016	0.006	16.999	-1.182	-1.182	0.000	0.000	0.000	0.000
15	A	16	THR	0	0.054	0.018	17.377	-0.847	-0.847	0.000	0.000	0.000	0.000
16	A	17	LYS	1	0.874	0.951	19.479	-13.559	-13.559	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.062	-0.041	21.134	-0.894	-0.894	0.000	0.000	0.000	0.000
18	A	19	ILE	0	0.025	0.018	21.277	-0.647	-0.647	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.874	-0.927	23.012	12.631	12.631	0.000	0.000	0.000	0.000
20	A	21	ASN	0	-0.164	-0.084	25.540	-0.336	-0.336	0.000	0.000	0.000	0.000
21	A	22	ASN	0	-0.050	-0.026	27.546	-0.348	-0.348	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.779	0.904	25.777	-10.928	-10.928	0.000	0.000	0.000	0.000
23	A	24	THR	0	0.002	-0.039	27.893	0.135	0.135	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.845	-0.936	25.629	11.391	11.391	0.000	0.000	0.000	0.000
25	A	26	LYS	1	0.816	0.881	26.351	-9.919	-9.919	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.771	-0.858	27.675	10.293	10.293	0.000	0.000	0.000	0.000
27	A	28	ILE	0	-0.019	-0.001	21.858	0.242	0.242	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.009	-0.013	22.696	0.504	0.504	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.820	-0.885	23.556	10.840	10.840	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.045	-0.012	23.111	0.122	0.122	0.000	0.000	0.000	0.000
31	A	32	PHE	0	0.067	0.016	17.198	0.618	0.618	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.902	-0.934	19.747	12.814	12.814	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.885	0.944	21.490	-13.398	-13.398	0.000	0.000	0.000	0.000
34	A	35	MET	0	-0.114	-0.030	16.537	0.163	0.163	0.000	0.000	0.000	0.000
35	A	36	CYS	0	-0.028	-0.038	11.554	0.643	0.643	0.000	0.000	0.000	0.000
36	A	37	SER	0	-0.026	-0.013	16.949	0.125	0.125	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.740	0.860	16.798	-17.001	-17.001	0.000	0.000	0.000	0.000
38	A	39	LEU	0	-0.027	0.010	11.724	0.225	0.225	0.000	0.000	0.000	0.000
39	A	40	PRO	0	-0.007	-0.005	13.684	-1.239	-1.239	0.000	0.000	0.000	0.000
40	A	41	LYS	1	0.993	0.962	15.117	-13.449	-13.449	0.000	0.000	0.000	0.000
41	A	42	SER	0	-0.060	-0.020	12.394	-0.651	-0.651	0.000	0.000	0.000	0.000
42	A	43	LEU	0	0.089	0.052	8.675	0.057	0.057	0.000	0.000	0.000	0.000
43	A	44	SER	0	-0.027	-0.008	11.984	0.080	0.080	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.941	-0.958	14.475	16.584	16.584	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.818	-0.910	8.835	24.040	24.040	0.000	0.000	0.000	0.000
46	A	48	GLN	0	-0.007	-0.019	12.630	-0.069	-0.069	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.834	-0.877	11.883	20.250	20.250	0.000	0.000	0.000	0.000
48	A	50	VAL	0	-0.027	-0.025	9.261	-0.306	-0.306	0.000	0.000	0.000	0.000
49	A	51	VAL	0	-0.020	-0.019	12.601	-0.807	-0.807	0.000	0.000	0.000	0.000
50	A	52	ASP	-1	-0.919	-0.965	16.012	13.821	13.821	0.000	0.000	0.000	0.000
51	A	53	THR	0	-0.088	-0.017	14.709	-0.932	-0.932	0.000	0.000	0.000	0.000
52	A	54	TYR	0	-0.009	-0.036	11.616	-0.269	-0.269	0.000	0.000	0.000	0.000
53	A	55	GLY	0	0.019	0.043	15.290	-0.079	-0.079	0.000	0.000	0.000	0.000
54	A	56	SER	0	0.026	-0.003	17.248	0.134	0.134	0.000	0.000	0.000	0.000
55	A	57	SER	0	-0.005	0.003	17.015	-0.765	-0.765	0.000	0.000	0.000	0.000
56	A	58	ILE	0	-0.007	-0.015	12.546	0.060	0.060	0.000	0.000	0.000	0.000
57	A	59	LEU	0	-0.032	-0.010	16.767	-0.213	-0.213	0.000	0.000	0.000	0.000
58	A	60	SER	0	0.004	-0.011	20.203	-0.507	-0.507	0.000	0.000	0.000	0.000
59	A	61	ILE	0	0.035	0.016	16.842	-0.322	-0.322	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.024	-0.013	16.840	-0.124	-0.124	0.000	0.000	0.000	0.000
61	A	63	LEU	0	-0.045	-0.024	20.263	-0.407	-0.407	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-1.018	-0.998	22.818	10.822	10.822	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.998	-0.993	23.405	10.897	10.897	0.000	0.000	0.000	0.000
64	A	66	VAL	0	-0.045	-0.012	17.747	0.125	0.125	0.000	0.000	0.000	0.000
65	A	67	SER	0	-0.053	-0.052	17.966	0.270	0.270	0.000	0.000	0.000	0.000
66	A	68	PRO	0	0.077	0.017	16.134	0.894	0.894	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.927	-0.949	13.211	19.387	19.387	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.032	-0.017	12.489	1.320	1.320	0.000	0.000	0.000	0.000
69	A	71	VAL	0	0.013	0.022	13.354	0.234	0.234	0.000	0.000	0.000	0.000
70	A	73	SER	0	-0.030	-0.001	8.927	0.437	0.437	0.000	0.000	0.000	0.000
71	A	74	MET	0	-0.028	0.000	9.844	-0.968	-0.968	0.000	0.000	0.000	0.000
72	A	75	LEU	0	-0.025	-0.012	11.600	-1.107	-1.107	0.000	0.000	0.000	0.000
73	A	76	HIS	0	-0.082	-0.041	9.184	0.767	0.767	0.000	0.000	0.000	0.000
74	A	77	LEU	0	0.022	0.018	6.958	0.922	0.922	0.000	0.000	0.000	0.000
75	A	79	SER	0	0.026	0.013	4.301	-5.476	-5.410	-0.001	-0.004	-0.061	0.000

Top

Graph

Manual

About

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