FMO DATABASE

FMODB ID: 2N95R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-557652.433703
FMO2-HF: Nuclear repulsion	520554.570146
FMO2-HF: Total energy	-37097.863557
FMO2-MP2: Total energy	-37191.436154

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.
-28.447	-26.139	15.228	-6.819	-10.719	0.032

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 : -0.006 / q_NPA : -0.007

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	CYS	0	-0.017	0.008	3.248	-2.939	0.448	0.027	-1.764	-1.650	-0.001
4	A	4	GLY	0	0.054	0.026	5.725	0.324	0.324	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.048	-0.035	9.452	-0.232	-0.232	0.000	0.000	0.000	0.000
6	A	6	GLN	0	-0.027	-0.023	9.914	-0.032	-0.032	0.000	0.000	0.000	0.000
7	A	7	GLY	0	-0.038	-0.009	6.703	-0.202	-0.202	0.000	0.000	0.000	0.000
8	A	8	GLY	0	-0.024	-0.011	7.128	-0.297	-0.297	0.000	0.000	0.000	0.000
9	A	9	GLY	0	-0.009	-0.003	9.274	0.248	0.248	0.000	0.000	0.000	0.000
10	A	10	ALA	0	-0.015	0.009	5.449	0.273	0.273	0.000	0.000	0.000	0.000
11	A	11	THR	0	0.024	0.009	7.078	0.138	0.138	0.000	0.000	0.000	0.000
12	A	12	CYS	0	-0.036	-0.016	2.517	-4.118	-2.387	3.951	-1.759	-3.923	0.006
13	A	13	PRO	0	0.058	0.011	2.156	0.211	-0.472	3.427	-0.864	-1.881	-0.003
14	A	14	GLY	0	0.003	-0.001	5.023	2.162	2.247	-0.001	-0.004	-0.081	0.000
15	A	15	LEU	0	-0.033	-0.013	7.640	-0.168	-0.168	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.871	0.934	1.857	-21.431	-24.689	7.799	-2.178	-2.363	0.030
17	A	17	CYS	0	-0.083	-0.021	7.514	-0.658	-0.658	0.000	0.000	0.000	0.000
18	A	19	SER	0	0.047	0.018	8.055	-0.095	-0.095	0.000	0.000	0.000	0.000
19	A	20	ILE	0	0.022	0.001	10.336	-0.324	-0.324	0.000	0.000	0.000	0.000
20	A	21	TRP	0	0.010	0.002	10.351	-0.084	-0.084	0.000	0.000	0.000	0.000
21	A	22	GLY	0	0.004	0.007	8.205	-0.252	-0.252	0.000	0.000	0.000	0.000
22	A	23	TRP	0	-0.002	-0.003	3.384	-2.844	-2.103	0.026	-0.214	-0.553	0.000
23	A	25	GLY	0	-0.026	-0.025	4.467	0.319	0.624	-0.001	-0.036	-0.268	0.000
24	A	26	ASP	-1	-0.812	-0.914	6.549	4.428	4.428	0.000	0.000	0.000	0.000
25	A	27	SER	0	0.053	0.034	9.667	-0.329	-0.329	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.791	-0.908	12.509	0.261	0.261	0.000	0.000	0.000	0.000
27	A	29	PRO	0	0.016	0.005	11.935	-0.048	-0.048	0.000	0.000	0.000	0.000
28	A	30	TYR	0	-0.033	-0.009	6.082	0.090	0.090	0.000	0.000	0.000	0.000
29	A	32	GLY	0	0.015	0.011	13.050	-0.047	-0.047	0.000	0.000	0.000	0.000
30	A	33	ARG	1	0.969	0.982	16.626	-0.016	-0.016	0.000	0.000	0.000	0.000
31	A	34	THR	0	-0.060	-0.039	14.089	-0.049	-0.049	0.000	0.000	0.000	0.000
32	A	35	CYS	0	-0.002	0.051	12.084	0.147	0.147	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.783	-0.868	11.486	-1.062	-1.062	0.000	0.000	0.000	0.000
34	A	37	ASN	0	-0.066	-0.065	9.218	0.240	0.240	0.000	0.000	0.000	0.000
35	A	38	LYS	1	0.909	0.936	9.787	-0.219	-0.219	0.000	0.000	0.000	0.000
36	A	40	TRP	0	0.051	0.016	13.944	-0.070	-0.070	0.000	0.000	0.000	0.000
37	A	41	SER	0	-0.021	-0.018	16.684	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	42	GLY	0	0.005	0.006	17.611	-0.054	-0.054	0.000	0.000	0.000	0.000
39	A	43	GLU	-1	-0.784	-0.832	18.569	0.528	0.528	0.000	0.000	0.000	0.000
40	A	44	ARG	1	0.862	0.898	19.914	-0.288	-0.288	0.000	0.000	0.000	0.000
41	A	45	SER	0	0.030	0.008	22.727	0.026	0.026	0.000	0.000	0.000	0.000
42	A	46	ASP	-1	-0.791	-0.867	25.108	0.263	0.263	0.000	0.000	0.000	0.000
43	A	47	HIS	1	0.854	0.910	23.165	-0.331	-0.331	0.000	0.000	0.000	0.000
44	A	48	ARG	1	0.946	1.007	22.942	-0.279	-0.279	0.000	0.000	0.000	0.000
45	A	49	CYS	0	-0.002	-0.024	16.052	-0.167	-0.167	0.000	0.000	0.000	0.000
46	A	50	GLY	0	0.051	0.013	17.428	-0.038	-0.038	0.000	0.000	0.000	0.000
47	A	51	ALA	0	0.028	0.005	17.688	-0.053	-0.053	0.000	0.000	0.000	0.000
48	A	52	ALA	0	0.005	0.005	18.595	-0.048	-0.048	0.000	0.000	0.000	0.000
49	A	53	VAL	0	-0.047	-0.012	19.907	-0.038	-0.038	0.000	0.000	0.000	0.000
50	A	54	GLY	0	0.025	0.016	17.919	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	55	ASN	0	-0.055	-0.027	13.594	0.041	0.041	0.000	0.000	0.000	0.000
52	A	56	PRO	0	0.015	0.046	14.101	0.050	0.050	0.000	0.000	0.000	0.000
53	A	57	PRO	0	0.010	0.016	13.634	0.123	0.123	0.000	0.000	0.000	0.000
54	A	58	CYS	0	0.019	0.028	15.108	-0.037	-0.037	0.000	0.000	0.000	0.000
55	A	59	GLY	0	0.036	-0.005	16.025	0.069	0.069	0.000	0.000	0.000	0.000
56	A	60	GLN	0	-0.054	-0.048	16.925	0.055	0.055	0.000	0.000	0.000	0.000
57	A	61	ASP	-1	-0.896	-0.931	16.930	0.731	0.731	0.000	0.000	0.000	0.000
58	A	62	ARG	1	0.765	0.864	17.526	-0.595	-0.595	0.000	0.000	0.000	0.000
59	A	63	CYS	0	-0.020	-0.009	16.072	0.191	0.191	0.000	0.000	0.000	0.000
60	A	65	SER	0	0.048	0.019	17.601	0.052	0.052	0.000	0.000	0.000	0.000
61	A	66	VAL	0	0.006	-0.003	19.745	-0.023	-0.023	0.000	0.000	0.000	0.000
62	A	67	HIS	0	0.017	0.021	21.149	-0.033	-0.033	0.000	0.000	0.000	0.000
63	A	68	GLY	0	-0.024	-0.004	21.231	-0.048	-0.048	0.000	0.000	0.000	0.000
64	A	69	TRP	0	0.005	-0.010	22.206	-0.049	-0.049	0.000	0.000	0.000	0.000
65	A	71	GLY	0	-0.013	-0.022	20.635	-0.081	-0.081	0.000	0.000	0.000	0.000
66	A	72	GLY	0	0.072	0.039	20.698	0.081	0.081	0.000	0.000	0.000	0.000
67	A	73	GLY	0	0.044	0.020	22.010	-0.049	-0.049	0.000	0.000	0.000	0.000
68	A	74	ASN	0	0.065	0.013	22.339	0.066	0.066	0.000	0.000	0.000	0.000
69	A	75	ASP	-1	-0.937	-0.969	23.083	0.474	0.474	0.000	0.000	0.000	0.000
70	A	76	TYR	0	-0.074	-0.033	20.663	-0.019	-0.019	0.000	0.000	0.000	0.000
71	A	78	SER	0	0.036	0.032	17.772	0.093	0.093	0.000	0.000	0.000	0.000
72	A	79	GLY	0	0.005	0.000	19.000	0.002	0.002	0.000	0.000	0.000	0.000
73	A	80	GLY	0	-0.008	0.011	19.519	-0.077	-0.077	0.000	0.000	0.000	0.000
74	A	81	LYS	1	0.879	0.929	21.216	-0.520	-0.520	0.000	0.000	0.000	0.000
75	A	82	CYS	0	-0.030	0.013	12.034	-0.235	-0.235	0.000	0.000	0.000	0.000
76	A	83	GLN	0	-0.080	-0.052	16.214	0.022	0.022	0.000	0.000	0.000	0.000
77	A	84	TYR	0	-0.009	-0.051	11.596	0.104	0.104	0.000	0.000	0.000	0.000
78	A	85	ARG	1	0.811	0.881	10.826	-1.605	-1.605	0.000	0.000	0.000	0.000
79	A	87	SER	0	0.069	0.043	13.524	-0.020	-0.020	0.000	0.000	0.000	0.000
80	A	88	SER	0	0.049	0.035	14.963	-0.249	-0.249	0.000	0.000	0.000	0.000
81	A	89	SER	0	-0.066	-0.020	13.417	0.206	0.206	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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