FMO DATABASE

FMODB ID: 6YKRZ

Calculation Name: 1EHD-A-Xray372

Preferred Name:

Target Type:

Ligand Name: pyroglutamic acid

ligand 3-letter code: PCA

PDB ID: 1EHD

Chain ID: A

ChEMBL ID:

UniProt ID: Q9S7B3

Base Structure: X-ray

Registration Date: 2023-09-23

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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-557417.034437
FMO2-HF: Nuclear repulsion	520319.014052
FMO2-HF: Total energy	-37098.020386
FMO2-MP2: Total energy	-37191.595713

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.
-31.228	-30.42	17.25	-7.701	-10.358	0.043

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 : 0.023 / q_NPA : 0.014

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	3	CYS	0	-0.025	-0.002	2.924	-4.002	-0.829	0.227	-1.764	-1.637	-0.007
4	A	4	GLY	0	0.074	0.036	5.677	0.392	0.392	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.043	-0.044	9.338	-0.285	-0.285	0.000	0.000	0.000	0.000
6	A	6	GLN	0	-0.035	-0.022	10.432	-0.048	-0.048	0.000	0.000	0.000	0.000
7	A	7	GLY	0	-0.041	-0.023	6.808	-0.389	-0.389	0.000	0.000	0.000	0.000
8	A	8	GLY	0	-0.019	0.000	7.285	-0.266	-0.266	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.003	0.001	9.684	0.225	0.225	0.000	0.000	0.000	0.000
10	A	10	ALA	0	-0.026	0.003	5.451	0.305	0.305	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.022	-0.002	6.638	0.006	0.006	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.028	0.003	2.668	-3.599	-1.310	2.517	-1.457	-3.350	0.008
13	A	13	PRO	0	0.055	0.013	2.389	-0.889	-0.318	1.938	-0.814	-1.695	0.001
14	A	14	GLY	0	0.018	0.006	5.184	2.163	2.231	-0.001	-0.002	-0.065	0.000
15	A	15	LEU	0	-0.035	-0.016	7.774	-0.326	-0.326	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.842	0.916	1.758	-22.492	-28.723	12.557	-3.436	-2.890	0.041
17	A	17	CYS	0	-0.083	-0.011	7.180	-0.561	-0.561	0.000	0.000	0.000	0.000
18	A	19	SER	0	0.040	0.006	7.942	-0.132	-0.132	0.000	0.000	0.000	0.000
19	A	20	ILE	0	0.022	0.003	10.192	-0.390	-0.390	0.000	0.000	0.000	0.000
20	A	21	TRP	0	0.009	0.006	10.475	-0.110	-0.110	0.000	0.000	0.000	0.000
21	A	22	GLY	0	0.013	0.024	8.393	-0.248	-0.248	0.000	0.000	0.000	0.000
22	A	23	TRP	0	-0.004	-0.002	3.529	-2.605	-2.009	0.013	-0.155	-0.453	0.000
23	A	25	GLY	0	-0.002	-0.016	4.111	0.281	0.623	-0.001	-0.073	-0.268	0.000
24	A	26	ASP	-1	-0.813	-0.903	6.854	5.102	5.102	0.000	0.000	0.000	0.000
25	A	27	SER	0	0.055	0.019	9.736	-0.326	-0.326	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.796	-0.898	12.652	0.230	0.230	0.000	0.000	0.000	0.000
27	A	29	PRO	0	0.028	0.010	12.165	-0.033	-0.033	0.000	0.000	0.000	0.000
28	A	30	TYR	0	-0.030	-0.004	6.580	0.035	0.035	0.000	0.000	0.000	0.000
29	A	32	GLY	0	0.040	0.023	13.191	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	33	ARG	1	0.951	0.968	16.727	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	34	THR	0	-0.052	-0.036	14.010	-0.057	-0.057	0.000	0.000	0.000	0.000
32	A	35	CYS	0	-0.013	0.034	11.989	0.176	0.176	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.795	-0.857	11.423	-1.073	-1.073	0.000	0.000	0.000	0.000
34	A	37	ASN	0	-0.049	-0.054	8.705	0.349	0.349	0.000	0.000	0.000	0.000
35	A	38	LYS	1	0.908	0.939	9.532	-0.441	-0.441	0.000	0.000	0.000	0.000
36	A	40	TRP	0	0.029	0.002	13.912	-0.048	-0.048	0.000	0.000	0.000	0.000
37	A	41	SER	0	-0.022	-0.018	16.463	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	42	GLY	0	0.021	0.017	17.656	-0.069	-0.069	0.000	0.000	0.000	0.000
39	A	43	GLU	-1	-0.776	-0.831	18.578	0.624	0.624	0.000	0.000	0.000	0.000
40	A	44	ARG	1	0.853	0.905	19.708	-0.370	-0.370	0.000	0.000	0.000	0.000
41	A	45	SER	0	0.044	0.018	22.636	0.024	0.024	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.799	-0.871	24.941	0.321	0.321	0.000	0.000	0.000	0.000
43	A	47	HIS	1	0.857	0.908	22.943	-0.385	-0.385	0.000	0.000	0.000	0.000
44	A	48	ARG	1	0.912	0.986	22.671	-0.350	-0.350	0.000	0.000	0.000	0.000
45	A	49	CYS	0	-0.049	-0.035	15.690	-0.174	-0.174	0.000	0.000	0.000	0.000
46	A	50	GLY	0	0.087	0.039	17.297	-0.050	-0.050	0.000	0.000	0.000	0.000
47	A	51	ALA	0	0.016	-0.006	17.391	-0.057	-0.057	0.000	0.000	0.000	0.000
48	A	52	ALA	0	-0.007	-0.003	18.295	-0.051	-0.051	0.000	0.000	0.000	0.000
49	A	53	VAL	0	-0.025	0.001	19.782	-0.041	-0.041	0.000	0.000	0.000	0.000
50	A	54	GLY	0	0.033	0.017	17.812	-0.007	-0.007	0.000	0.000	0.000	0.000
51	A	55	ASN	0	-0.059	-0.027	13.381	0.059	0.059	0.000	0.000	0.000	0.000
52	A	56	PRO	0	0.004	0.033	13.846	0.079	0.079	0.000	0.000	0.000	0.000
53	A	57	PRO	0	0.021	0.027	13.314	0.154	0.154	0.000	0.000	0.000	0.000
54	A	58	CYS	0	0.010	0.012	14.712	-0.057	-0.057	0.000	0.000	0.000	0.000
55	A	59	GLY	0	0.058	0.007	15.671	0.090	0.090	0.000	0.000	0.000	0.000
56	A	60	GLN	0	-0.047	-0.043	16.837	0.074	0.074	0.000	0.000	0.000	0.000
57	A	61	ASP	-1	-0.888	-0.932	17.111	0.728	0.728	0.000	0.000	0.000	0.000
58	A	62	ARG	1	0.760	0.859	17.304	-0.654	-0.654	0.000	0.000	0.000	0.000
59	A	63	CYS	0	-0.065	-0.002	15.783	0.235	0.235	0.000	0.000	0.000	0.000
60	A	65	SER	0	0.067	0.014	17.405	0.051	0.051	0.000	0.000	0.000	0.000
61	A	66	VAL	0	0.019	0.004	19.542	-0.007	-0.007	0.000	0.000	0.000	0.000
62	A	67	HIS	0	-0.006	0.003	20.864	-0.030	-0.030	0.000	0.000	0.000	0.000
63	A	68	GLY	0	0.011	0.006	20.691	-0.052	-0.052	0.000	0.000	0.000	0.000
64	A	69	TRP	0	-0.006	-0.011	21.772	-0.055	-0.055	0.000	0.000	0.000	0.000
65	A	71	GLY	0	0.010	-0.011	20.361	-0.091	-0.091	0.000	0.000	0.000	0.000
66	A	72	GLY	0	0.050	0.021	20.400	0.086	0.086	0.000	0.000	0.000	0.000
67	A	73	GLY	0	0.063	0.036	21.780	-0.061	-0.061	0.000	0.000	0.000	0.000
68	A	74	ASN	0	0.061	0.011	22.151	0.058	0.058	0.000	0.000	0.000	0.000
69	A	75	ASP	-1	-0.845	-0.924	22.573	0.539	0.539	0.000	0.000	0.000	0.000
70	A	76	TYR	0	-0.051	-0.015	20.286	-0.016	-0.016	0.000	0.000	0.000	0.000
71	A	78	SER	0	0.060	0.034	17.716	0.081	0.081	0.000	0.000	0.000	0.000
72	A	79	GLY	0	0.026	0.016	18.926	0.052	0.052	0.000	0.000	0.000	0.000
73	A	80	GLY	0	-0.011	-0.003	19.479	-0.078	-0.078	0.000	0.000	0.000	0.000
74	A	81	LYS	1	0.812	0.903	21.200	-0.572	-0.572	0.000	0.000	0.000	0.000
75	A	82	CYS	0	-0.055	0.014	11.836	-0.187	-0.187	0.000	0.000	0.000	0.000
76	A	83	GLN	0	-0.075	-0.053	15.917	-0.016	-0.016	0.000	0.000	0.000	0.000
77	A	84	TYR	0	-0.016	-0.049	11.270	0.143	0.143	0.000	0.000	0.000	0.000
78	A	85	ARG	1	0.814	0.878	10.539	-1.904	-1.904	0.000	0.000	0.000	0.000
79	A	87	SER	0	0.075	0.029	13.557	-0.066	-0.066	0.000	0.000	0.000	0.000
80	A	88	SER	0	0.011	0.005	14.591	-0.258	-0.258	0.000	0.000	0.000	0.000
81	A	89	SER	0	-0.093	-0.027	13.759	0.141	0.141	0.000	0.000	0.000	0.000

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