FMO DATABASE

FMODB ID: 4933N

Calculation Name: 2PSP-A-Xray372

Preferred Name:

Target Type:

Ligand Name: pyroglutamic acid

ligand 3-letter code: PCA

PDB ID: 2PSP

Chain ID: A

ChEMBL ID:

UniProt ID: P01359

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-760819.091524
FMO2-HF: Nuclear repulsion	715863.300112
FMO2-HF: Total energy	-44955.791412
FMO2-MP2: Total energy	-45073.533223

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:1:PCA)

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

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.
-15.757	-11.386	6.5	-5.105	-5.768	-0.045

Interaction energy analysis for fragmet #1(A:1:PCA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / q_NPA : -0.030

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	3	PRO	0	-0.015	0.008	3.867	-0.899	0.828	-0.010	-0.749	-0.968	0.004
4	A	4	ALA	0	0.013	0.033	6.214	0.206	0.206	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.076	0.032	8.569	0.124	0.124	0.000	0.000	0.000	0.000
6	A	6	CYS	0	-0.072	0.006	11.897	0.103	0.103	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.835	0.910	5.884	1.053	1.053	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.043	-0.008	7.083	-0.837	-0.837	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.053	0.035	13.357	0.084	0.084	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.766	0.862	16.586	0.562	0.562	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.092	-0.064	13.565	0.164	0.164	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.828	-0.906	18.503	-0.225	-0.225	0.000	0.000	0.000	0.000
13	A	13	PRO	0	-0.003	-0.022	20.145	0.008	0.008	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.854	0.918	20.936	0.172	0.172	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.021	-0.006	20.925	0.051	0.051	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.785	0.889	16.665	0.477	0.477	0.000	0.000	0.000	0.000
17	A	17	VAL	0	0.015	0.011	15.195	0.041	0.041	0.000	0.000	0.000	0.000
18	A	18	ASN	0	0.010	-0.003	14.605	-0.106	-0.106	0.000	0.000	0.000	0.000
19	A	19	CYS	0	-0.147	-0.085	3.669	0.691	0.963	0.034	0.038	-0.345	0.001
20	A	20	GLY	0	0.071	0.027	10.932	-0.130	-0.130	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.018	0.001	11.171	0.073	0.073	0.000	0.000	0.000	0.000
22	A	22	PRO	0	0.018	-0.019	14.800	-0.089	-0.089	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.025	0.013	17.222	0.029	0.029	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.089	-0.008	8.987	-0.018	-0.018	0.000	0.000	0.000	0.000
25	A	25	THR	0	0.029	0.002	12.127	-0.077	-0.077	0.000	0.000	0.000	0.000
26	A	26	SER	0	0.049	0.001	10.980	-0.047	-0.047	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.858	-0.917	8.638	-1.468	-1.468	0.000	0.000	0.000	0.000
28	A	28	GLN	0	0.045	0.033	7.256	-0.545	-0.545	0.000	0.000	0.000	0.000
29	A	29	CYS	0	-0.041	0.032	6.598	-0.312	-0.312	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.050	0.003	5.626	-0.110	-0.110	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.025	-0.034	3.207	-4.288	-3.093	0.088	-0.675	-0.608	-0.004
32	A	32	SER	0	-0.059	-0.041	1.924	-9.885	-9.906	6.100	-3.199	-2.881	-0.044
33	A	33	GLY	0	0.002	0.029	2.715	2.095	3.293	0.288	-0.520	-0.966	-0.002
34	A	36	PHE	0	0.063	0.006	9.968	0.257	0.257	0.000	0.000	0.000	0.000
35	A	37	ASP	-1	-0.794	-0.875	12.030	-0.664	-0.664	0.000	0.000	0.000	0.000
36	A	38	SER	0	0.019	0.007	15.760	0.051	0.051	0.000	0.000	0.000	0.000
37	A	39	GLN	0	-0.061	-0.030	18.566	0.076	0.076	0.000	0.000	0.000	0.000
38	A	40	VAL	0	0.020	0.017	21.025	0.039	0.039	0.000	0.000	0.000	0.000
39	A	41	PRO	0	0.023	0.019	22.128	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	42	GLY	0	0.004	-0.010	24.484	0.009	0.009	0.000	0.000	0.000	0.000
41	A	43	VAL	0	-0.024	-0.014	19.794	0.024	0.024	0.000	0.000	0.000	0.000
42	A	44	PRO	0	0.012	0.011	16.468	-0.021	-0.021	0.000	0.000	0.000	0.000
43	A	45	TRP	0	0.006	0.015	16.321	-0.055	-0.055	0.000	0.000	0.000	0.000
44	A	47	PHE	0	0.000	-0.016	11.749	0.150	0.150	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.952	0.966	10.370	-0.304	-0.304	0.000	0.000	0.000	0.000
46	A	49	PRO	0	0.024	0.020	7.495	-0.045	-0.045	0.000	0.000	0.000	0.000
47	A	50	LEU	0	0.003	0.014	10.754	0.284	0.284	0.000	0.000	0.000	0.000
48	A	51	PRO	0	0.014	-0.003	10.784	-0.055	-0.055	0.000	0.000	0.000	0.000
49	A	52	ALA	0	-0.024	-0.003	8.860	-0.168	-0.168	0.000	0.000	0.000	0.000
50	A	53	GLN	0	-0.066	-0.048	10.931	0.165	0.165	0.000	0.000	0.000	0.000
51	A	54	GLU	-1	-0.784	-0.885	13.427	-0.211	-0.211	0.000	0.000	0.000	0.000
52	A	55	SER	0	-0.022	-0.037	14.979	-0.014	-0.014	0.000	0.000	0.000	0.000
53	A	56	GLU	-1	-0.815	-0.935	11.879	-1.192	-1.192	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.821	-0.895	14.547	-0.463	-0.463	0.000	0.000	0.000	0.000
55	A	58	CYS	0	0.006	0.034	17.326	0.043	0.043	0.000	0.000	0.000	0.000
56	A	59	VAL	0	-0.027	0.002	12.645	0.043	0.043	0.000	0.000	0.000	0.000
57	A	60	MET	0	-0.019	0.001	15.901	-0.023	-0.023	0.000	0.000	0.000	0.000
58	A	61	GLN	0	0.014	0.010	18.294	0.067	0.067	0.000	0.000	0.000	0.000
59	A	62	VAL	0	0.033	0.017	19.904	0.003	0.003	0.000	0.000	0.000	0.000
60	A	63	SER	0	0.011	-0.001	22.103	0.003	0.003	0.000	0.000	0.000	0.000
61	A	64	ALA	0	-0.008	0.002	22.488	0.000	0.000	0.000	0.000	0.000	0.000
62	A	65	ARG	1	0.835	0.902	19.868	0.029	0.029	0.000	0.000	0.000	0.000
63	A	66	LYS	1	0.862	0.932	25.035	0.218	0.218	0.000	0.000	0.000	0.000
64	A	67	ASN	0	0.023	0.002	27.658	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	68	CYS	0	-0.106	-0.033	24.949	-0.026	-0.026	0.000	0.000	0.000	0.000
66	A	69	GLY	0	0.036	0.006	29.960	0.003	0.003	0.000	0.000	0.000	0.000
67	A	70	TYR	0	-0.030	-0.001	31.410	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	71	PRO	0	0.015	-0.016	32.832	0.004	0.004	0.000	0.000	0.000	0.000
69	A	72	GLY	0	0.019	0.009	32.795	0.000	0.000	0.000	0.000	0.000	0.000
70	A	73	ILE	0	-0.099	-0.022	29.182	0.001	0.001	0.000	0.000	0.000	0.000
71	A	74	SER	0	0.005	-0.003	29.466	0.006	0.006	0.000	0.000	0.000	0.000
72	A	75	PRO	0	0.025	0.001	24.121	-0.014	-0.014	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.855	-0.934	26.033	0.009	0.009	0.000	0.000	0.000	0.000
74	A	77	ASP	-1	-0.817	-0.894	27.883	-0.022	-0.022	0.000	0.000	0.000	0.000
75	A	78	CYS	0	-0.093	-0.014	24.616	-0.020	-0.020	0.000	0.000	0.000	0.000
76	A	79	ALA	0	0.048	0.020	24.594	-0.018	-0.018	0.000	0.000	0.000	0.000
77	A	80	ALA	0	-0.024	-0.010	26.003	-0.016	-0.016	0.000	0.000	0.000	0.000
78	A	81	ARG	1	0.789	0.892	29.434	0.053	0.053	0.000	0.000	0.000	0.000
79	A	82	ASN	0	-0.054	-0.022	25.737	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	85	PHE	0	0.040	-0.006	21.055	0.015	0.015	0.000	0.000	0.000	0.000
81	A	86	SER	0	-0.046	-0.021	19.218	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	87	ASP	-1	-0.801	-0.906	21.300	0.100	0.100	0.000	0.000	0.000	0.000
83	A	88	THR	0	-0.055	-0.022	18.563	-0.007	-0.007	0.000	0.000	0.000	0.000
84	A	89	ILE	0	-0.039	-0.016	19.357	0.020	0.020	0.000	0.000	0.000	0.000
85	A	90	PRO	0	0.043	0.015	23.281	-0.015	-0.015	0.000	0.000	0.000	0.000
86	A	91	GLU	-1	-0.940	-0.972	26.716	0.023	0.023	0.000	0.000	0.000	0.000
87	A	92	VAL	0	-0.045	-0.002	24.026	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	93	PRO	0	-0.027	-0.026	26.989	0.012	0.012	0.000	0.000	0.000	0.000
89	A	94	TRP	0	0.007	0.017	24.959	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	96	PHE	0	-0.017	-0.025	19.680	0.001	0.001	0.000	0.000	0.000	0.000
91	A	97	PHE	0	0.050	0.013	24.554	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	98	PRO	0	0.053	0.016	21.599	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	99	MET	0	-0.079	-0.044	21.284	0.022	0.022	0.000	0.000	0.000	0.000
94	A	100	SER	0	-0.008	-0.017	20.368	-0.031	-0.031	0.000	0.000	0.000	0.000
95	A	101	VAL	0	0.059	0.005	16.053	0.006	0.006	0.000	0.000	0.000	0.000
96	A	102	GLU	-1	-0.840	-0.900	18.409	-0.452	-0.452	0.000	0.000	0.000	0.000
97	A	103	ASP	-1	-0.824	-0.892	19.403	-0.508	-0.508	0.000	0.000	0.000	0.000
98	A	105	HIS	0	0.018	-0.003	15.666	0.014	0.014	0.000	0.000	0.000	0.000
99	A	106	TYR	0	-0.081	-0.076	8.531	0.004	0.004	0.000	0.000	0.000	0.000

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