FMO DATABASE

FMODB ID: K9333

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-759138.928977
FMO2-HF: Nuclear repulsion	714183.331885
FMO2-HF: Total energy	-44955.597091
FMO2-MP2: Total energy	-45073.309195

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.
-15.928	-10.993	6.419	-5.506	-5.85	-0.044

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 : -0.061 / q_NPA : -0.029

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	-0.011	0.006	3.622	-1.964	0.313	0.001	-1.028	-1.250	0.006
4	A	4	ALA	0	0.017	0.033	5.686	0.263	0.263	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.083	0.027	8.141	0.158	0.158	0.000	0.000	0.000	0.000
6	A	6	CYS	0	-0.072	0.003	11.353	0.102	0.102	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.833	0.904	5.621	1.055	1.055	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.055	-0.015	7.093	-0.907	-0.907	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.069	0.028	12.932	0.103	0.103	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.755	0.866	15.821	0.565	0.565	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.080	-0.058	13.370	0.151	0.151	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.847	-0.915	18.257	-0.229	-0.229	0.000	0.000	0.000	0.000
13	A	13	PRO	0	0.019	-0.011	19.879	0.013	0.013	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.903	0.945	20.886	0.173	0.173	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.034	-0.018	20.759	0.050	0.050	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.810	0.910	16.691	0.469	0.469	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.005	0.007	15.589	0.050	0.050	0.000	0.000	0.000	0.000
18	A	18	ASN	0	0.009	-0.009	14.643	-0.102	-0.102	0.000	0.000	0.000	0.000
19	A	19	CYS	0	-0.144	-0.087	3.821	0.720	1.047	0.022	-0.020	-0.330	0.001
20	A	20	GLY	0	0.060	0.029	11.418	-0.121	-0.121	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.018	-0.001	11.357	0.002	0.002	0.000	0.000	0.000	0.000
22	A	22	PRO	0	0.042	-0.010	14.869	-0.085	-0.085	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.003	-0.003	17.168	0.024	0.024	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.059	0.013	9.081	-0.024	-0.024	0.000	0.000	0.000	0.000
25	A	25	THR	0	0.021	-0.005	12.136	-0.084	-0.084	0.000	0.000	0.000	0.000
26	A	26	SER	0	0.066	0.023	11.024	-0.039	-0.039	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.898	-0.957	8.947	-1.424	-1.424	0.000	0.000	0.000	0.000
28	A	28	GLN	0	0.040	0.028	7.223	-0.571	-0.571	0.000	0.000	0.000	0.000
29	A	29	CYS	0	-0.041	0.041	6.651	-0.263	-0.263	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.042	0.001	5.627	-0.116	-0.116	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.022	-0.029	3.204	-3.989	-2.960	0.055	-0.556	-0.528	-0.003
32	A	32	SER	0	-0.044	-0.033	1.923	-9.764	-9.560	6.190	-3.455	-2.940	-0.047
33	A	33	GLY	0	-0.008	0.027	2.995	2.444	3.542	0.151	-0.447	-0.802	-0.001
34	A	36	PHE	0	0.076	0.009	9.842	0.281	0.281	0.000	0.000	0.000	0.000
35	A	37	ASP	-1	-0.810	-0.902	11.946	-0.622	-0.622	0.000	0.000	0.000	0.000
36	A	38	SER	0	-0.009	-0.009	15.638	0.046	0.046	0.000	0.000	0.000	0.000
37	A	39	GLN	0	-0.062	-0.025	18.402	0.079	0.079	0.000	0.000	0.000	0.000
38	A	40	VAL	0	0.009	0.025	20.531	0.043	0.043	0.000	0.000	0.000	0.000
39	A	41	PRO	0	0.012	0.004	21.748	0.001	0.001	0.000	0.000	0.000	0.000
40	A	42	GLY	0	-0.015	-0.024	24.095	0.009	0.009	0.000	0.000	0.000	0.000
41	A	43	VAL	0	-0.037	-0.004	19.881	0.029	0.029	0.000	0.000	0.000	0.000
42	A	44	PRO	0	0.008	0.000	16.653	-0.022	-0.022	0.000	0.000	0.000	0.000
43	A	45	TRP	0	0.030	0.025	16.049	-0.048	-0.048	0.000	0.000	0.000	0.000
44	A	47	PHE	0	-0.017	-0.027	11.855	0.160	0.160	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.967	0.972	10.547	-0.352	-0.352	0.000	0.000	0.000	0.000
46	A	49	PRO	0	0.036	0.034	7.090	-0.025	-0.025	0.000	0.000	0.000	0.000
47	A	50	LEU	0	-0.017	-0.005	10.428	0.289	0.289	0.000	0.000	0.000	0.000
48	A	51	PRO	0	-0.014	-0.010	10.626	-0.100	-0.100	0.000	0.000	0.000	0.000
49	A	52	ALA	0	-0.021	-0.004	8.349	-0.131	-0.131	0.000	0.000	0.000	0.000
50	A	53	GLN	0	-0.056	-0.039	10.493	0.176	0.176	0.000	0.000	0.000	0.000
51	A	54	GLU	-1	-0.827	-0.907	12.828	-0.220	-0.220	0.000	0.000	0.000	0.000
52	A	55	SER	0	-0.005	-0.034	14.480	-0.028	-0.028	0.000	0.000	0.000	0.000
53	A	56	GLU	-1	-0.824	-0.937	11.638	-1.190	-1.190	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.827	-0.899	14.116	-0.473	-0.473	0.000	0.000	0.000	0.000
55	A	58	CYS	0	0.009	0.040	17.011	0.038	0.038	0.000	0.000	0.000	0.000
56	A	59	VAL	0	-0.035	0.007	12.547	0.041	0.041	0.000	0.000	0.000	0.000
57	A	60	MET	0	0.010	0.003	15.782	-0.016	-0.016	0.000	0.000	0.000	0.000
58	A	61	GLN	0	0.013	0.021	18.012	0.059	0.059	0.000	0.000	0.000	0.000
59	A	62	VAL	0	0.037	0.013	19.678	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	63	SER	0	0.022	0.005	21.875	0.001	0.001	0.000	0.000	0.000	0.000
61	A	64	ALA	0	-0.024	-0.005	22.384	0.003	0.003	0.000	0.000	0.000	0.000
62	A	65	ARG	1	0.837	0.917	19.609	0.051	0.051	0.000	0.000	0.000	0.000
63	A	66	LYS	1	0.921	0.976	24.736	0.209	0.209	0.000	0.000	0.000	0.000
64	A	67	ASN	0	0.029	-0.008	27.582	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	68	CYS	0	-0.099	-0.025	24.847	-0.022	-0.022	0.000	0.000	0.000	0.000
66	A	69	GLY	0	0.037	0.008	29.705	0.002	0.002	0.000	0.000	0.000	0.000
67	A	70	TYR	0	-0.025	-0.010	31.414	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	71	PRO	0	0.003	-0.021	32.485	0.004	0.004	0.000	0.000	0.000	0.000
69	A	72	GLY	0	0.032	0.017	32.233	0.001	0.001	0.000	0.000	0.000	0.000
70	A	73	ILE	0	-0.095	-0.021	28.990	0.002	0.002	0.000	0.000	0.000	0.000
71	A	74	SER	0	0.008	-0.006	29.496	0.005	0.005	0.000	0.000	0.000	0.000
72	A	75	PRO	0	0.054	0.014	24.270	-0.013	-0.013	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.858	-0.939	26.201	0.003	0.003	0.000	0.000	0.000	0.000
74	A	77	ASP	-1	-0.842	-0.896	27.919	-0.027	-0.027	0.000	0.000	0.000	0.000
75	A	78	CYS	0	-0.102	-0.008	24.258	-0.022	-0.022	0.000	0.000	0.000	0.000
76	A	79	ALA	0	0.026	0.004	24.652	-0.017	-0.017	0.000	0.000	0.000	0.000
77	A	80	ALA	0	-0.019	0.002	26.002	-0.015	-0.015	0.000	0.000	0.000	0.000
78	A	81	ARG	1	0.774	0.884	29.442	0.054	0.054	0.000	0.000	0.000	0.000
79	A	82	ASN	0	-0.025	-0.010	25.821	-0.010	-0.010	0.000	0.000	0.000	0.000
80	A	85	PHE	0	0.046	-0.003	21.084	0.013	0.013	0.000	0.000	0.000	0.000
81	A	86	SER	0	-0.055	-0.026	19.010	0.000	0.000	0.000	0.000	0.000	0.000
82	A	87	ASP	-1	-0.860	-0.933	21.101	0.077	0.077	0.000	0.000	0.000	0.000
83	A	88	THR	0	-0.011	-0.005	18.468	0.004	0.004	0.000	0.000	0.000	0.000
84	A	89	ILE	0	-0.057	-0.021	19.221	0.019	0.019	0.000	0.000	0.000	0.000
85	A	90	PRO	0	0.042	0.003	23.059	-0.014	-0.014	0.000	0.000	0.000	0.000
86	A	91	GLU	-1	-0.964	-0.986	26.612	0.011	0.011	0.000	0.000	0.000	0.000
87	A	92	VAL	0	-0.015	0.022	23.606	-0.016	-0.016	0.000	0.000	0.000	0.000
88	A	93	PRO	0	-0.029	-0.028	26.616	0.011	0.011	0.000	0.000	0.000	0.000
89	A	94	TRP	0	0.025	0.021	24.684	-0.007	-0.007	0.000	0.000	0.000	0.000
90	A	96	PHE	0	-0.028	-0.035	19.354	0.004	0.004	0.000	0.000	0.000	0.000
91	A	97	PHE	0	0.041	0.006	24.278	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	98	PRO	0	0.061	0.033	21.462	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	99	MET	0	-0.111	-0.075	20.770	0.017	0.017	0.000	0.000	0.000	0.000
94	A	100	SER	0	-0.020	-0.035	19.920	-0.032	-0.032	0.000	0.000	0.000	0.000
95	A	101	VAL	0	0.072	0.002	15.561	0.008	0.008	0.000	0.000	0.000	0.000
96	A	102	GLU	-1	-0.876	-0.901	17.936	-0.451	-0.451	0.000	0.000	0.000	0.000
97	A	103	ASP	-1	-0.815	-0.886	19.558	-0.503	-0.503	0.000	0.000	0.000	0.000
98	A	105	HIS	0	0.034	0.013	15.312	0.024	0.024	0.000	0.000	0.000	0.000
99	A	106	TYR	0	-0.040	-0.046	7.888	0.040	0.040	0.000	0.000	0.000	0.000

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