FMO DATABASE

FMODB ID: R94Y8

Calculation Name: 1U0Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name: pyroglutamic acid

ligand 3-letter code: PCA

PDB ID: 1U0Q

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1045053.989352
FMO2-HF: Nuclear repulsion	996796.780492
FMO2-HF: Total energy	-48257.20886
FMO2-MP2: Total energy	-48397.521524

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.
1.114	3.9	0.019	-1.117	-1.687	0.003

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 : 0.018 / q_NPA : -0.008

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	GLN	0	-0.029	-0.020	3.290	-0.174	1.866	0.021	-0.805	-1.255	0.002
4	A	4	LEU	0	-0.006	-0.008	5.644	0.348	0.348	0.000	0.000	0.000	0.000
5	A	5	GLN	0	-0.009	-0.011	9.488	0.034	0.034	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.769	-0.866	12.464	-0.818	-0.818	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.017	-0.010	16.150	0.065	0.065	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.041	0.006	19.128	-0.014	-0.014	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.017	0.019	22.242	0.015	0.015	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.003	-0.010	24.020	0.019	0.019	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.035	-0.009	27.461	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.000	-0.002	30.683	0.006	0.006	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.017	0.007	33.013	0.003	0.003	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.024	-0.003	35.812	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.028	-0.014	37.141	0.009	0.009	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.007	0.004	35.606	0.002	0.002	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.031	-0.047	32.036	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.016	0.001	26.644	0.009	0.009	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.869	0.931	24.099	0.261	0.261	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.016	0.033	21.055	0.001	0.001	0.000	0.000	0.000	0.000
21	A	21	SER	0	-0.011	-0.025	19.144	0.013	0.013	0.000	0.000	0.000	0.000
22	A	22	CYS	0	-0.106	-0.037	14.070	-0.024	-0.024	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.043	0.031	13.071	0.000	0.000	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.027	0.000	9.025	-0.169	-0.169	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.011	-0.005	4.110	0.669	1.237	-0.001	-0.302	-0.265	0.001
26	A	26	GLY	0	0.032	0.010	6.732	-0.307	-0.307	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.964	0.976	7.574	0.724	0.724	0.000	0.000	0.000	0.000
28	A	28	THR	0	0.066	0.031	7.030	-0.115	-0.115	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.008	-0.010	8.805	0.175	0.175	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.074	-0.045	11.702	0.262	0.262	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.033	-0.009	9.238	0.111	0.111	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.014	0.015	7.003	-0.128	-0.128	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.066	-0.009	12.149	0.101	0.101	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.038	0.012	13.886	-0.133	-0.133	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.014	-0.007	15.862	0.121	0.121	0.000	0.000	0.000	0.000
36	A	36	TRP	0	-0.013	-0.003	17.313	-0.084	-0.084	0.000	0.000	0.000	0.000
37	A	37	PHE	0	0.020	0.001	18.383	0.048	0.048	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.782	0.876	21.259	0.293	0.293	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.020	-0.017	23.005	-0.028	-0.028	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.033	0.025	24.968	0.006	0.006	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.008	-0.013	28.456	-0.005	-0.005	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.014	0.016	29.764	0.010	0.010	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.816	0.915	29.022	0.276	0.276	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.877	-0.933	26.101	-0.320	-0.320	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.857	0.939	16.160	0.690	0.690	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.742	-0.836	23.634	-0.309	-0.309	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.015	-0.009	22.139	-0.018	-0.018	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.032	-0.008	23.389	0.034	0.034	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.029	-0.005	23.038	0.040	0.040	0.000	0.000	0.000	0.000
50	A	50	TYR	0	-0.015	-0.002	17.838	-0.023	-0.023	0.000	0.000	0.000	0.000
51	A	51	PHE	0	0.057	0.022	17.696	0.068	0.068	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.025	0.012	18.694	-0.066	-0.066	0.000	0.000	0.000	0.000
53	A	52	THR	0	0.007	-0.031	15.073	0.080	0.080	0.000	0.000	0.000	0.000
54	A	53	ARG	1	0.926	0.971	18.260	0.391	0.391	0.000	0.000	0.000	0.000
55	A	54	GLY	0	-0.017	-0.039	20.049	0.040	0.040	0.000	0.000	0.000	0.000
56	A	55	GLY	0	-0.005	0.024	21.850	0.028	0.028	0.000	0.000	0.000	0.000
57	A	56	ARG	1	0.908	0.978	22.445	0.384	0.384	0.000	0.000	0.000	0.000
58	A	57	THR	0	0.013	0.010	23.082	-0.032	-0.032	0.000	0.000	0.000	0.000
59	A	58	TYR	0	-0.025	-0.007	23.790	0.025	0.025	0.000	0.000	0.000	0.000
60	A	59	TYR	0	0.028	0.003	25.376	-0.030	-0.030	0.000	0.000	0.000	0.000
61	A	60	ALA	0	0.030	0.027	27.368	0.015	0.015	0.000	0.000	0.000	0.000
62	A	61	ASP	-1	-0.815	-0.926	29.022	-0.246	-0.246	0.000	0.000	0.000	0.000
63	A	62	SER	0	0.006	0.020	30.436	0.011	0.011	0.000	0.000	0.000	0.000
64	A	63	VAL	0	-0.010	-0.011	27.832	0.011	0.011	0.000	0.000	0.000	0.000
65	A	64	LYS	1	0.869	0.929	31.160	0.231	0.231	0.000	0.000	0.000	0.000
66	A	65	GLY	0	0.011	0.021	31.768	0.015	0.015	0.000	0.000	0.000	0.000
67	A	66	ARG	1	0.773	0.868	32.457	0.233	0.233	0.000	0.000	0.000	0.000
68	A	67	PHE	0	-0.013	-0.018	27.047	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	68	THR	0	-0.021	-0.017	27.589	0.006	0.006	0.000	0.000	0.000	0.000
70	A	69	ILE	0	-0.013	-0.002	21.160	-0.012	-0.012	0.000	0.000	0.000	0.000
71	A	70	ALA	0	-0.015	-0.001	22.280	0.026	0.026	0.000	0.000	0.000	0.000
72	A	71	ILE	0	-0.013	-0.004	16.095	-0.054	-0.054	0.000	0.000	0.000	0.000
73	A	72	ASP	-1	-0.734	-0.843	17.211	-0.450	-0.450	0.000	0.000	0.000	0.000
74	A	73	ASN	0	-0.011	-0.028	19.595	-0.021	-0.021	0.000	0.000	0.000	0.000
75	A	74	ALA	0	0.024	0.015	16.251	0.002	0.002	0.000	0.000	0.000	0.000
76	A	75	LYS	1	0.824	0.919	15.177	0.369	0.369	0.000	0.000	0.000	0.000
77	A	76	ASN	0	-0.016	-0.014	11.554	-0.007	-0.007	0.000	0.000	0.000	0.000
78	A	77	THR	0	-0.020	-0.021	13.165	-0.120	-0.120	0.000	0.000	0.000	0.000
79	A	78	VAL	0	-0.024	-0.005	15.923	0.067	0.067	0.000	0.000	0.000	0.000
80	A	79	TYR	0	-0.018	-0.019	17.688	0.001	0.001	0.000	0.000	0.000	0.000
81	A	80	LEU	0	0.020	0.001	20.983	-0.012	-0.012	0.000	0.000	0.000	0.000
82	A	81	GLN	0	0.012	0.019	23.329	0.011	0.011	0.000	0.000	0.000	0.000
83	A	82	MET	0	-0.026	-0.007	26.274	-0.008	-0.008	0.000	0.000	0.000	0.000
84	A	82	ASN	0	0.073	0.038	29.186	0.014	0.014	0.000	0.000	0.000	0.000
85	A	82	SER	0	0.013	0.008	33.008	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	82	LEU	0	-0.029	0.000	29.805	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	83	LYS	1	0.904	0.940	33.955	0.220	0.220	0.000	0.000	0.000	0.000
88	A	84	LEU	0	0.063	0.021	34.036	-0.008	-0.008	0.000	0.000	0.000	0.000
89	A	85	ASP	-1	-0.843	-0.914	33.713	-0.211	-0.211	0.000	0.000	0.000	0.000
90	A	86	ASP	-1	-0.758	-0.835	30.152	-0.257	-0.257	0.000	0.000	0.000	0.000
91	A	87	THR	0	-0.021	-0.001	29.003	-0.020	-0.020	0.000	0.000	0.000	0.000
92	A	88	ALA	0	-0.018	-0.019	25.810	0.002	0.002	0.000	0.000	0.000	0.000
93	A	89	VAL	0	0.027	0.038	20.630	0.001	0.001	0.000	0.000	0.000	0.000
94	A	90	TYR	0	0.000	-0.027	21.440	-0.016	-0.016	0.000	0.000	0.000	0.000
95	A	91	TYR	0	0.022	-0.004	16.593	-0.014	-0.014	0.000	0.000	0.000	0.000
96	A	93	ALA	0	0.047	0.021	13.093	-0.092	-0.092	0.000	0.000	0.000	0.000
97	A	94	VAL	0	-0.044	-0.029	9.287	0.079	0.079	0.000	0.000	0.000	0.000
98	A	95	ARG	1	0.867	0.923	12.245	0.583	0.583	0.000	0.000	0.000	0.000
99	A	96	MET	0	0.016	0.022	11.132	0.069	0.069	0.000	0.000	0.000	0.000
100	A	97	PRO	0	-0.034	-0.025	13.353	0.094	0.094	0.000	0.000	0.000	0.000
101	A	98	TYR	0	-0.043	-0.026	16.849	0.011	0.011	0.000	0.000	0.000	0.000
102	A	99	SER	0	0.054	0.034	16.221	0.055	0.055	0.000	0.000	0.000	0.000
103	A	100	GLY	0	0.059	0.038	18.374	0.011	0.011	0.000	0.000	0.000	0.000
104	A	100	ASP	-1	-0.832	-0.923	21.749	-0.410	-0.410	0.000	0.000	0.000	0.000
105	A	100	TYR	0	-0.005	0.008	20.912	-0.026	-0.026	0.000	0.000	0.000	0.000
106	A	100	ARG	1	0.874	0.945	21.609	0.282	0.282	0.000	0.000	0.000	0.000
107	A	100	SER	0	0.024	0.009	22.283	-0.018	-0.018	0.000	0.000	0.000	0.000
108	A	100	SER	0	0.041	0.016	19.062	-0.040	-0.040	0.000	0.000	0.000	0.000
109	A	100	GLY	0	0.021	0.009	17.588	-0.070	-0.070	0.000	0.000	0.000	0.000
110	A	100	THR	0	-0.062	-0.017	17.417	-0.025	-0.025	0.000	0.000	0.000	0.000
111	A	100	TYR	0	-0.085	-0.067	14.154	-0.036	-0.036	0.000	0.000	0.000	0.000
112	A	101	ASP	-1	-0.786	-0.894	9.325	-1.263	-1.263	0.000	0.000	0.000	0.000
113	A	102	TYR	0	-0.020	-0.015	4.585	-0.741	-0.563	-0.001	-0.010	-0.167	0.000
114	A	103	TRP	0	-0.032	-0.034	9.548	0.284	0.284	0.000	0.000	0.000	0.000
115	A	104	GLY	0	0.031	0.032	10.196	-0.219	-0.219	0.000	0.000	0.000	0.000
116	A	105	GLN	0	-0.026	-0.015	11.941	0.142	0.142	0.000	0.000	0.000	0.000
117	A	106	GLY	0	-0.007	-0.007	14.384	0.077	0.077	0.000	0.000	0.000	0.000
118	A	107	THR	0	-0.052	-0.034	17.511	0.040	0.040	0.000	0.000	0.000	0.000
119	A	108	GLN	0	0.030	0.014	20.385	-0.009	-0.009	0.000	0.000	0.000	0.000
120	A	109	VAL	0	0.014	0.013	24.093	0.008	0.008	0.000	0.000	0.000	0.000
121	A	110	THR	0	-0.041	-0.029	26.930	0.003	0.003	0.000	0.000	0.000	0.000
122	A	111	VAL	0	0.013	0.017	30.542	0.009	0.009	0.000	0.000	0.000	0.000
123	A	112	SER	0	0.000	0.011	33.450	0.006	0.006	0.000	0.000	0.000	0.000
124	A	113	SER	0	0.028	0.014	36.694	0.002	0.002	0.000	0.000	0.000	0.000

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