FMO DATABASE

FMODB ID: 76QZK

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	OptH
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	-557755.397646
FMO2-HF: Nuclear repulsion	520657.908613
FMO2-HF: Total energy	-37097.489033
FMO2-MP2: Total energy	-37191.061529

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.
-27.271	-18.846	7.142	-6.002	-9.566	0.024

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 : -0.005 / q_NPA : -0.015

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	-0.035	-0.002	3.126	-3.586	0.167	0.061	-2.007	-1.808	-0.002
4	A	4	GLY	0	0.026	0.013	5.563	0.335	0.335	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.019	-0.009	9.294	-0.211	-0.211	0.000	0.000	0.000	0.000
6	A	6	GLN	0	-0.009	-0.013	9.618	0.033	0.033	0.000	0.000	0.000	0.000
7	A	7	GLY	0	-0.062	-0.016	6.629	-0.178	-0.178	0.000	0.000	0.000	0.000
8	A	8	GLY	0	-0.019	-0.009	7.088	-0.264	-0.264	0.000	0.000	0.000	0.000
9	A	9	GLY	0	-0.009	-0.004	9.200	0.248	0.248	0.000	0.000	0.000	0.000
10	A	10	ALA	0	-0.008	0.016	5.297	0.277	0.277	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.016	0.002	7.221	0.090	0.090	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.059	-0.034	2.622	-3.523	-1.184	2.539	-1.589	-3.289	0.008
13	A	13	PRO	0	0.055	0.014	2.196	-0.592	-0.679	2.846	-0.919	-1.840	0.001
14	A	14	GLY	0	0.007	-0.001	4.854	1.965	2.059	-0.001	-0.008	-0.084	0.000
15	A	15	LEU	0	-0.029	-0.009	7.634	-0.217	-0.217	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.895	0.966	2.239	-18.251	-17.154	1.634	-1.102	-1.629	0.018
17	A	17	CYS	0	-0.072	-0.025	7.573	-0.589	-0.589	0.000	0.000	0.000	0.000
18	A	19	SER	0	0.065	0.024	8.244	0.006	0.006	0.000	0.000	0.000	0.000
19	A	20	ILE	0	0.037	0.015	10.284	-0.298	-0.298	0.000	0.000	0.000	0.000
20	A	21	TRP	0	0.011	0.002	10.334	-0.078	-0.078	0.000	0.000	0.000	0.000
21	A	22	GLY	0	0.003	-0.003	8.205	-0.232	-0.232	0.000	0.000	0.000	0.000
22	A	23	TRP	0	-0.007	-0.003	3.194	-3.157	-2.240	0.064	-0.340	-0.642	-0.001
23	A	25	GLY	0	-0.031	-0.025	4.423	0.257	0.569	-0.001	-0.037	-0.274	0.000
24	A	26	ASP	-1	-0.825	-0.928	6.639	3.619	3.619	0.000	0.000	0.000	0.000
25	A	27	SER	0	0.037	0.027	9.750	-0.268	-0.268	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.813	-0.927	12.581	0.149	0.149	0.000	0.000	0.000	0.000
27	A	29	PRO	0	0.020	0.003	11.966	-0.050	-0.050	0.000	0.000	0.000	0.000
28	A	30	TYR	0	-0.027	0.000	6.135	-0.199	-0.199	0.000	0.000	0.000	0.000
29	A	32	GLY	0	0.023	0.021	13.139	-0.025	-0.025	0.000	0.000	0.000	0.000
30	A	33	ARG	1	0.967	0.984	16.668	0.057	0.057	0.000	0.000	0.000	0.000
31	A	34	THR	0	-0.048	-0.040	14.080	-0.029	-0.029	0.000	0.000	0.000	0.000
32	A	35	CYS	0	0.007	0.055	12.266	0.097	0.097	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.823	-0.906	11.938	-1.074	-1.074	0.000	0.000	0.000	0.000
34	A	37	ASN	0	-0.037	-0.043	9.717	0.232	0.232	0.000	0.000	0.000	0.000
35	A	38	LYS	1	0.911	0.948	10.070	-0.195	-0.195	0.000	0.000	0.000	0.000
36	A	40	TRP	0	0.045	0.012	14.090	-0.062	-0.062	0.000	0.000	0.000	0.000
37	A	41	SER	0	-0.033	-0.024	16.762	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	42	GLY	0	0.014	0.011	17.949	-0.045	-0.045	0.000	0.000	0.000	0.000
39	A	43	GLU	-1	-0.782	-0.855	18.953	0.462	0.462	0.000	0.000	0.000	0.000
40	A	44	ARG	1	0.842	0.890	20.132	-0.257	-0.257	0.000	0.000	0.000	0.000
41	A	45	SER	0	0.027	0.009	23.008	0.025	0.025	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.772	-0.862	25.455	0.232	0.232	0.000	0.000	0.000	0.000
43	A	47	HIS	1	0.854	0.913	23.218	-0.296	-0.296	0.000	0.000	0.000	0.000
44	A	48	ARG	1	0.955	1.011	22.986	-0.258	-0.258	0.000	0.000	0.000	0.000
45	A	49	CYS	0	-0.010	-0.026	16.069	-0.158	-0.158	0.000	0.000	0.000	0.000
46	A	50	GLY	0	0.046	0.011	17.423	-0.034	-0.034	0.000	0.000	0.000	0.000
47	A	51	ALA	0	0.034	0.008	17.662	-0.055	-0.055	0.000	0.000	0.000	0.000
48	A	52	ALA	0	0.004	0.004	18.562	-0.048	-0.048	0.000	0.000	0.000	0.000
49	A	53	VAL	0	-0.047	-0.007	19.927	-0.038	-0.038	0.000	0.000	0.000	0.000
50	A	54	GLY	0	0.026	0.014	17.985	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	55	ASN	0	-0.054	-0.029	13.601	0.059	0.059	0.000	0.000	0.000	0.000
52	A	56	PRO	0	-0.012	0.023	14.266	0.044	0.044	0.000	0.000	0.000	0.000
53	A	57	PRO	0	0.022	0.011	13.923	0.117	0.117	0.000	0.000	0.000	0.000
54	A	58	CYS	0	-0.003	0.023	15.249	-0.020	-0.020	0.000	0.000	0.000	0.000
55	A	59	GLY	0	0.041	-0.007	16.092	0.055	0.055	0.000	0.000	0.000	0.000
56	A	60	GLN	0	-0.013	-0.017	17.004	0.050	0.050	0.000	0.000	0.000	0.000
57	A	61	ASP	-1	-0.928	-0.952	17.005	0.635	0.635	0.000	0.000	0.000	0.000
58	A	62	ARG	1	0.772	0.878	17.592	-0.525	-0.525	0.000	0.000	0.000	0.000
59	A	63	CYS	0	-0.029	-0.021	16.123	0.177	0.177	0.000	0.000	0.000	0.000
60	A	65	SER	0	0.073	0.035	17.624	0.068	0.068	0.000	0.000	0.000	0.000
61	A	66	VAL	0	0.005	-0.003	19.711	-0.023	-0.023	0.000	0.000	0.000	0.000
62	A	67	HIS	0	-0.022	-0.007	21.156	-0.033	-0.033	0.000	0.000	0.000	0.000
63	A	68	GLY	0	-0.043	-0.016	21.241	-0.045	-0.045	0.000	0.000	0.000	0.000
64	A	69	TRP	0	0.016	-0.001	22.205	-0.048	-0.048	0.000	0.000	0.000	0.000
65	A	71	GLY	0	-0.027	-0.021	20.688	-0.074	-0.074	0.000	0.000	0.000	0.000
66	A	72	GLY	0	0.070	0.037	20.748	0.075	0.075	0.000	0.000	0.000	0.000
67	A	73	GLY	0	0.045	0.021	22.057	-0.044	-0.044	0.000	0.000	0.000	0.000
68	A	74	ASN	0	0.065	0.013	22.377	0.069	0.069	0.000	0.000	0.000	0.000
69	A	75	ASP	-1	-0.937	-0.961	23.109	0.448	0.448	0.000	0.000	0.000	0.000
70	A	76	TYR	0	-0.065	-0.039	20.627	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	78	SER	0	0.051	0.039	17.797	0.090	0.090	0.000	0.000	0.000	0.000
72	A	79	GLY	0	0.006	0.001	19.001	0.004	0.004	0.000	0.000	0.000	0.000
73	A	80	GLY	0	-0.009	0.010	19.518	-0.077	-0.077	0.000	0.000	0.000	0.000
74	A	81	LYS	1	0.915	0.951	21.228	-0.506	-0.506	0.000	0.000	0.000	0.000
75	A	82	CYS	0	-0.029	0.014	12.076	-0.224	-0.224	0.000	0.000	0.000	0.000
76	A	83	GLN	0	-0.067	-0.042	16.181	0.042	0.042	0.000	0.000	0.000	0.000
77	A	84	TYR	0	-0.008	-0.038	11.655	0.122	0.122	0.000	0.000	0.000	0.000
78	A	85	ARG	1	0.801	0.877	10.975	-1.420	-1.420	0.000	0.000	0.000	0.000
79	A	87	SER	0	0.054	0.030	13.595	-0.016	-0.016	0.000	0.000	0.000	0.000
80	A	88	SER	0	0.048	0.034	15.000	-0.236	-0.236	0.000	0.000	0.000	0.000
81	A	89	SER	0	-0.055	-0.012	13.214	0.172	0.172	0.000	0.000	0.000	0.000

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