FMO DATABASE

FMODB ID: QY11Y

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

Total energy (hartree)

FMO2-HF: Electronic energy	-758210.187893
FMO2-HF: Nuclear repulsion	713254.979307
FMO2-HF: Total energy	-44955.208586
FMO2-MP2: Total energy	-45072.924067

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.
-16.708	-11.252	6.42	-5.773	-6.105	-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 : -0.069 / q_NPA : -0.031

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	-0.001	0.011	3.670	-2.065	0.220	-0.001	-1.040	-1.244	0.006
4	A	4	ALA	0	0.035	0.030	5.737	0.254	0.254	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.084	0.029	8.192	0.192	0.192	0.000	0.000	0.000	0.000
6	A	6	CYS	0	-0.052	0.004	11.403	0.109	0.109	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.851	0.915	5.369	0.692	0.692	0.000	0.000	0.000	0.000
8	A	8	CYS	0	-0.046	-0.017	7.070	-1.007	-1.007	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.024	0.010	12.912	0.165	0.165	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.780	0.893	15.847	0.500	0.500	0.000	0.000	0.000	0.000
11	A	11	GLN	0	-0.077	-0.057	13.312	0.150	0.150	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.866	-0.930	18.183	-0.165	-0.165	0.000	0.000	0.000	0.000
13	A	13	PRO	0	0.020	-0.009	19.856	0.025	0.025	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.915	0.948	20.863	0.117	0.117	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.036	-0.014	20.609	0.047	0.047	0.000	0.000	0.000	0.000
16	A	16	ARG	1	0.826	0.909	16.441	0.394	0.394	0.000	0.000	0.000	0.000
17	A	17	VAL	0	-0.004	0.011	15.015	0.043	0.043	0.000	0.000	0.000	0.000
18	A	18	ASN	0	0.010	-0.014	14.586	-0.082	-0.082	0.000	0.000	0.000	0.000
19	A	19	CYS	0	-0.142	-0.083	3.801	0.417	0.807	0.033	-0.032	-0.391	0.001
20	A	20	GLY	0	0.055	0.028	11.408	-0.140	-0.140	0.000	0.000	0.000	0.000
21	A	21	PHE	0	-0.024	-0.004	11.390	-0.012	-0.012	0.000	0.000	0.000	0.000
22	A	22	PRO	0	0.037	-0.011	14.860	-0.085	-0.085	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.005	-0.003	17.159	0.017	0.017	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.055	0.018	9.022	-0.032	-0.032	0.000	0.000	0.000	0.000
25	A	25	THR	0	0.034	0.005	12.034	-0.087	-0.087	0.000	0.000	0.000	0.000
26	A	26	SER	0	0.082	0.027	11.013	-0.022	-0.022	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.913	-0.958	8.960	-1.504	-1.504	0.000	0.000	0.000	0.000
28	A	28	GLN	0	0.012	0.000	7.217	-0.575	-0.575	0.000	0.000	0.000	0.000
29	A	29	CYS	0	-0.049	0.022	6.644	-0.192	-0.192	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.035	0.000	5.612	-0.036	-0.036	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.026	-0.015	3.208	-4.176	-3.133	0.053	-0.578	-0.519	-0.003
32	A	32	SER	0	-0.046	-0.027	1.927	-9.976	-9.662	6.122	-3.486	-2.951	-0.048
33	A	33	GLY	0	-0.002	0.032	2.973	3.064	4.488	0.213	-0.637	-1.000	0.000
34	A	36	PHE	0	0.070	0.010	9.819	0.290	0.290	0.000	0.000	0.000	0.000
35	A	37	ASP	-1	-0.835	-0.901	11.926	-0.594	-0.594	0.000	0.000	0.000	0.000
36	A	38	SER	0	-0.015	-0.009	15.617	0.053	0.053	0.000	0.000	0.000	0.000
37	A	39	GLN	0	-0.053	-0.028	18.382	0.084	0.084	0.000	0.000	0.000	0.000
38	A	40	VAL	0	0.002	0.023	20.515	0.038	0.038	0.000	0.000	0.000	0.000
39	A	41	PRO	0	0.003	-0.002	21.727	0.005	0.005	0.000	0.000	0.000	0.000
40	A	42	GLY	0	-0.013	-0.022	24.091	0.009	0.009	0.000	0.000	0.000	0.000
41	A	43	VAL	0	-0.031	0.002	19.931	0.029	0.029	0.000	0.000	0.000	0.000
42	A	44	PRO	0	0.003	-0.005	16.610	-0.027	-0.027	0.000	0.000	0.000	0.000
43	A	45	TRP	0	0.046	0.032	16.000	-0.050	-0.050	0.000	0.000	0.000	0.000
44	A	47	PHE	0	-0.015	-0.027	11.836	0.163	0.163	0.000	0.000	0.000	0.000
45	A	48	LYS	1	0.988	0.989	10.151	-0.736	-0.736	0.000	0.000	0.000	0.000
46	A	49	PRO	0	0.019	0.022	7.071	-0.082	-0.082	0.000	0.000	0.000	0.000
47	A	50	LEU	0	-0.008	-0.001	10.372	0.288	0.288	0.000	0.000	0.000	0.000
48	A	51	PRO	0	-0.022	-0.018	10.548	-0.048	-0.048	0.000	0.000	0.000	0.000
49	A	52	ALA	0	-0.016	-0.002	8.287	-0.149	-0.149	0.000	0.000	0.000	0.000
50	A	53	GLN	0	-0.037	-0.018	10.400	0.171	0.171	0.000	0.000	0.000	0.000
51	A	54	GLU	-1	-0.869	-0.934	12.726	-0.152	-0.152	0.000	0.000	0.000	0.000
52	A	55	SER	0	0.042	0.017	14.556	-0.042	-0.042	0.000	0.000	0.000	0.000
53	A	56	GLU	-1	-0.834	-0.944	11.714	-1.080	-1.080	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.858	-0.937	14.161	-0.437	-0.437	0.000	0.000	0.000	0.000
55	A	58	CYS	0	-0.009	0.026	16.913	0.035	0.035	0.000	0.000	0.000	0.000
56	A	59	VAL	0	-0.026	0.011	12.435	0.052	0.052	0.000	0.000	0.000	0.000
57	A	60	MET	0	0.005	0.007	15.675	-0.029	-0.029	0.000	0.000	0.000	0.000
58	A	61	GLN	0	0.036	0.039	17.922	0.053	0.053	0.000	0.000	0.000	0.000
59	A	62	VAL	0	0.039	0.016	19.595	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	63	SER	0	0.026	-0.001	21.796	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	64	ALA	0	-0.039	-0.007	22.316	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	65	ARG	1	0.859	0.943	19.544	-0.027	-0.027	0.000	0.000	0.000	0.000
63	A	66	LYS	1	0.933	0.985	24.640	0.166	0.166	0.000	0.000	0.000	0.000
64	A	67	ASN	0	0.028	-0.009	27.480	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	68	CYS	0	-0.109	-0.030	24.760	-0.021	-0.021	0.000	0.000	0.000	0.000
66	A	69	GLY	0	0.017	-0.006	29.602	0.000	0.000	0.000	0.000	0.000	0.000
67	A	70	TYR	0	-0.047	-0.020	31.317	-0.002	-0.002	0.000	0.000	0.000	0.000
68	A	71	PRO	0	-0.008	-0.023	32.400	0.005	0.005	0.000	0.000	0.000	0.000
69	A	72	GLY	0	0.034	0.015	32.156	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	73	ILE	0	-0.078	-0.009	28.966	0.001	0.001	0.000	0.000	0.000	0.000
71	A	74	SER	0	0.048	0.033	29.414	0.006	0.006	0.000	0.000	0.000	0.000
72	A	75	PRO	0	0.041	0.013	24.270	-0.014	-0.014	0.000	0.000	0.000	0.000
73	A	76	GLU	-1	-0.858	-0.945	26.118	0.025	0.025	0.000	0.000	0.000	0.000
74	A	77	ASP	-1	-0.879	-0.933	27.833	-0.016	-0.016	0.000	0.000	0.000	0.000
75	A	78	CYS	0	-0.113	-0.015	24.171	-0.021	-0.021	0.000	0.000	0.000	0.000
76	A	79	ALA	0	0.022	0.002	24.580	-0.017	-0.017	0.000	0.000	0.000	0.000
77	A	80	ALA	0	-0.018	0.006	25.902	-0.017	-0.017	0.000	0.000	0.000	0.000
78	A	81	ARG	1	0.833	0.909	29.341	0.031	0.031	0.000	0.000	0.000	0.000
79	A	82	ASN	0	-0.030	-0.012	25.750	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	85	PHE	0	0.053	0.004	21.006	0.012	0.012	0.000	0.000	0.000	0.000
81	A	86	SER	0	-0.057	-0.038	18.739	0.012	0.012	0.000	0.000	0.000	0.000
82	A	87	ASP	-1	-0.882	-0.942	21.022	0.133	0.133	0.000	0.000	0.000	0.000
83	A	88	THR	0	-0.012	-0.009	18.458	0.002	0.002	0.000	0.000	0.000	0.000
84	A	89	ILE	0	-0.055	-0.019	19.132	0.024	0.024	0.000	0.000	0.000	0.000
85	A	90	PRO	0	0.029	-0.004	23.003	-0.020	-0.020	0.000	0.000	0.000	0.000
86	A	91	GLU	-1	-0.951	-0.980	26.550	0.055	0.055	0.000	0.000	0.000	0.000
87	A	92	VAL	0	-0.028	0.017	23.603	-0.017	-0.017	0.000	0.000	0.000	0.000
88	A	93	PRO	0	-0.026	-0.030	26.749	0.010	0.010	0.000	0.000	0.000	0.000
89	A	94	TRP	0	0.048	0.031	24.608	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	96	PHE	0	-0.033	-0.036	19.338	0.002	0.002	0.000	0.000	0.000	0.000
91	A	97	PHE	0	0.044	0.009	24.172	-0.009	-0.009	0.000	0.000	0.000	0.000
92	A	98	PRO	0	0.056	0.024	21.404	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	99	MET	0	-0.089	-0.065	20.818	0.016	0.016	0.000	0.000	0.000	0.000
94	A	100	SER	0	-0.011	-0.016	19.968	-0.028	-0.028	0.000	0.000	0.000	0.000
95	A	101	VAL	0	0.061	-0.006	15.823	0.010	0.010	0.000	0.000	0.000	0.000
96	A	102	GLU	-1	-0.895	-0.924	17.983	-0.423	-0.423	0.000	0.000	0.000	0.000
97	A	103	ASP	-1	-0.819	-0.899	19.733	-0.457	-0.457	0.000	0.000	0.000	0.000
98	A	105	HIS	0	-0.001	-0.004	15.370	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	106	TYR	0	-0.051	-0.044	8.036	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)