FMO DATABASE

FMODB ID: 4LNMN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-509099.945239
FMO2-HF: Nuclear repulsion	476540.434294
FMO2-HF: Total energy	-32559.510944
FMO2-MP2: Total energy	-32648.421862

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.
113.409	117.541	1.64	-2.489	-3.283	0.014

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 : -0.950 / q_NPA : -0.995

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	4	TYR	0	-0.016	-0.042	3.870	-2.984	-1.499	-0.010	-0.648	-0.827	0.001
4	A	5	CYS	0	-0.090	-0.015	2.286	-2.041	0.328	1.647	-1.781	-2.235	0.013
5	A	6	GLU	-1	-0.901	-0.951	3.810	31.992	32.270	0.003	-0.060	-0.221	0.000
6	A	7	VAL	0	0.034	0.018	5.597	-5.195	-5.195	0.000	0.000	0.000	0.000
7	A	8	CYS	0	0.034	0.009	7.521	-4.415	-4.415	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.796	-0.907	6.801	27.420	27.420	0.000	0.000	0.000	0.000
9	A	10	PHE	0	-0.065	-0.031	9.242	-2.980	-2.980	0.000	0.000	0.000	0.000
10	A	11	LEU	0	0.003	-0.008	11.515	-2.132	-2.132	0.000	0.000	0.000	0.000
11	A	12	VAL	0	0.031	0.006	12.446	-1.808	-1.808	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.823	0.909	10.645	-28.420	-28.420	0.000	0.000	0.000	0.000
13	A	14	GLU	-1	-0.832	-0.897	15.380	15.269	15.269	0.000	0.000	0.000	0.000
14	A	15	VAL	0	0.013	0.001	17.048	-1.149	-1.149	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.004	-0.005	17.873	-0.868	-0.868	0.000	0.000	0.000	0.000
16	A	17	LYS	1	0.886	0.952	19.541	-13.665	-13.665	0.000	0.000	0.000	0.000
17	A	18	LEU	0	-0.043	-0.025	21.230	-0.883	-0.883	0.000	0.000	0.000	0.000
18	A	19	ILE	0	0.059	0.032	21.708	-0.698	-0.698	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.847	-0.911	22.455	12.837	12.837	0.000	0.000	0.000	0.000
20	A	21	ASN	0	-0.158	-0.085	25.576	-0.292	-0.292	0.000	0.000	0.000	0.000
21	A	22	ASN	0	-0.026	-0.010	27.656	-0.325	-0.325	0.000	0.000	0.000	0.000
22	A	23	LYS	1	0.723	0.864	26.087	-10.814	-10.814	0.000	0.000	0.000	0.000
23	A	24	THR	0	0.013	-0.036	27.461	0.195	0.195	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.849	-0.935	25.647	11.431	11.431	0.000	0.000	0.000	0.000
25	A	26	LYS	1	0.827	0.886	26.358	-9.865	-9.865	0.000	0.000	0.000	0.000
26	A	27	GLU	-1	-0.770	-0.850	27.875	10.237	10.237	0.000	0.000	0.000	0.000
27	A	28	ILE	0	-0.014	-0.008	21.836	0.242	0.242	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.034	-0.018	22.794	0.459	0.459	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.829	-0.881	23.897	10.712	10.712	0.000	0.000	0.000	0.000
30	A	31	ALA	0	-0.039	-0.017	23.716	0.216	0.216	0.000	0.000	0.000	0.000
31	A	32	PHE	0	0.068	0.007	17.186	0.552	0.552	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.864	-0.895	19.732	12.933	12.933	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.861	0.906	20.971	-13.116	-13.116	0.000	0.000	0.000	0.000
34	A	35	MET	0	-0.106	-0.026	16.780	0.025	0.025	0.000	0.000	0.000	0.000
35	A	36	CYS	0	0.011	0.000	11.408	0.993	0.993	0.000	0.000	0.000	0.000
36	A	37	SER	0	-0.040	-0.022	17.119	0.172	0.172	0.000	0.000	0.000	0.000
37	A	38	LYS	1	0.735	0.855	17.007	-16.818	-16.818	0.000	0.000	0.000	0.000
38	A	39	LEU	0	-0.001	0.020	11.894	0.435	0.435	0.000	0.000	0.000	0.000
39	A	40	PRO	0	-0.007	-0.002	13.764	-1.305	-1.305	0.000	0.000	0.000	0.000
40	A	41	LYS	1	1.010	0.963	15.016	-13.246	-13.246	0.000	0.000	0.000	0.000
41	A	42	SER	0	-0.060	-0.022	12.665	-0.843	-0.843	0.000	0.000	0.000	0.000
42	A	43	LEU	0	0.049	0.044	8.534	1.181	1.181	0.000	0.000	0.000	0.000
43	A	44	SER	0	-0.039	-0.022	11.993	0.024	0.024	0.000	0.000	0.000	0.000
44	A	45	GLU	-1	-0.954	-0.959	14.443	16.280	16.280	0.000	0.000	0.000	0.000
45	A	46	GLU	-1	-0.823	-0.923	8.963	23.954	23.954	0.000	0.000	0.000	0.000
46	A	48	GLN	0	-0.034	-0.030	12.752	-0.326	-0.326	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.839	-0.890	11.667	20.727	20.727	0.000	0.000	0.000	0.000
48	A	50	VAL	0	-0.006	-0.009	9.321	-0.358	-0.358	0.000	0.000	0.000	0.000
49	A	51	VAL	0	-0.023	-0.020	12.716	-0.682	-0.682	0.000	0.000	0.000	0.000
50	A	52	ASP	-1	-0.883	-0.936	16.186	13.975	13.975	0.000	0.000	0.000	0.000
51	A	53	THR	0	-0.093	-0.037	14.314	-0.902	-0.902	0.000	0.000	0.000	0.000
52	A	54	TYR	0	-0.027	-0.029	11.364	-0.251	-0.251	0.000	0.000	0.000	0.000
53	A	55	GLY	0	0.026	0.035	15.500	0.004	0.004	0.000	0.000	0.000	0.000
54	A	56	SER	0	0.025	0.000	17.280	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	57	SER	0	0.014	0.020	16.772	-0.691	-0.691	0.000	0.000	0.000	0.000
56	A	58	ILE	0	0.005	-0.004	12.710	-0.047	-0.047	0.000	0.000	0.000	0.000
57	A	59	LEU	0	-0.020	-0.005	16.816	-0.224	-0.224	0.000	0.000	0.000	0.000
58	A	60	SER	0	-0.013	-0.025	20.358	-0.578	-0.578	0.000	0.000	0.000	0.000
59	A	61	ILE	0	-0.011	-0.014	16.600	-0.351	-0.351	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.014	-0.012	16.959	-0.085	-0.085	0.000	0.000	0.000	0.000
61	A	63	LEU	0	-0.046	-0.020	20.601	-0.455	-0.455	0.000	0.000	0.000	0.000
62	A	64	GLU	-1	-0.999	-0.983	22.867	10.892	10.892	0.000	0.000	0.000	0.000
63	A	65	GLU	-1	-0.997	-1.000	23.733	11.087	11.087	0.000	0.000	0.000	0.000
64	A	66	VAL	0	-0.054	-0.013	18.069	0.207	0.207	0.000	0.000	0.000	0.000
65	A	67	SER	0	-0.031	-0.055	18.127	0.358	0.358	0.000	0.000	0.000	0.000
66	A	68	PRO	0	0.064	0.003	15.661	0.832	0.832	0.000	0.000	0.000	0.000
67	A	69	GLU	-1	-0.932	-0.925	13.178	19.352	19.352	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.034	-0.019	12.573	1.433	1.433	0.000	0.000	0.000	0.000
69	A	71	VAL	0	0.012	0.024	13.499	0.252	0.252	0.000	0.000	0.000	0.000
70	A	73	SER	0	-0.011	0.007	9.029	0.744	0.744	0.000	0.000	0.000	0.000
71	A	74	MET	0	-0.020	-0.004	10.032	-0.798	-0.798	0.000	0.000	0.000	0.000
72	A	75	LEU	0	-0.031	-0.015	11.524	-1.116	-1.116	0.000	0.000	0.000	0.000
73	A	76	HIS	0	-0.065	-0.036	9.068	0.775	0.775	0.000	0.000	0.000	0.000
74	A	77	LEU	0	0.013	0.021	6.731	1.441	1.441	0.000	0.000	0.000	0.000
75	A	79	SER	0	0.001	0.007	4.990	-5.501	-5.501	0.000	0.000	0.000	0.000

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