FMO DATABASE

FMODB ID: 6N5GZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1042842.239561
FMO2-HF: Nuclear repulsion	994585.659609
FMO2-HF: Total energy	-48256.579952
FMO2-MP2: Total energy	-48396.875221

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.
0.789	3.601	0.238	-1.104	-1.946	0.004

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 : -0.001 / q_NPA : -0.017

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	-0.001	-0.003	2.432	-0.605	2.041	0.239	-1.057	-1.828	0.004
4	A	4	LEU	0	-0.024	-0.011	5.556	0.502	0.502	0.000	0.000	0.000	0.000
5	A	5	GLN	0	0.008	-0.005	9.337	0.022	0.022	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.760	-0.876	12.228	-0.867	-0.867	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.042	-0.014	15.891	0.059	0.059	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.043	0.004	18.883	-0.005	-0.005	0.000	0.000	0.000	0.000
9	A	9	GLY	0	-0.007	0.017	22.029	0.025	0.025	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.028	0.002	23.912	0.016	0.016	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.031	-0.011	27.339	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.013	-0.004	30.676	0.008	0.008	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.010	0.006	32.753	0.002	0.002	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.031	-0.001	35.823	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.027	-0.012	36.702	0.010	0.010	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.019	-0.002	35.160	0.004	0.004	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.020	-0.036	31.760	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.011	0.004	26.243	0.007	0.007	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.896	0.958	23.968	0.255	0.255	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.006	0.015	20.878	0.000	0.000	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.005	-0.016	18.398	0.021	0.021	0.000	0.000	0.000	0.000
22	A	22	CYS	0	-0.083	-0.011	14.007	-0.045	-0.045	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.034	0.023	13.064	0.026	0.026	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.035	0.013	9.094	-0.231	-0.231	0.000	0.000	0.000	0.000
25	A	25	SER	0	0.032	0.022	4.548	0.629	0.795	-0.001	-0.047	-0.118	0.000
26	A	26	GLY	0	0.029	0.017	6.855	-0.238	-0.238	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.981	0.984	7.652	0.427	0.427	0.000	0.000	0.000	0.000
28	A	28	THR	0	0.049	0.019	6.833	-0.167	-0.167	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.045	0.000	8.720	0.123	0.123	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.071	-0.043	11.668	0.208	0.208	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.101	-0.045	9.862	0.086	0.086	0.000	0.000	0.000	0.000
32	A	32	TYR	0	0.005	0.021	6.400	0.057	0.057	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.095	-0.038	12.159	0.094	0.094	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.045	0.009	13.910	-0.127	-0.127	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.010	0.004	15.864	0.118	0.118	0.000	0.000	0.000	0.000
36	A	36	TRP	0	-0.014	-0.005	17.406	-0.085	-0.085	0.000	0.000	0.000	0.000
37	A	37	PHE	0	0.012	-0.009	18.287	0.052	0.052	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.837	0.919	21.141	0.301	0.301	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.022	-0.009	23.170	-0.016	-0.016	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.011	0.008	24.708	0.004	0.004	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.021	-0.012	28.161	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.006	0.009	29.305	0.013	0.013	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.942	0.989	29.397	0.270	0.270	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.895	-0.945	26.475	-0.332	-0.332	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.857	0.944	16.781	0.695	0.695	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.866	-0.935	24.015	-0.313	-0.313	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.000	-0.015	21.858	-0.017	-0.017	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.023	0.006	23.304	0.032	0.032	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.025	-0.011	22.937	0.042	0.042	0.000	0.000	0.000	0.000
50	A	50	TYR	0	-0.023	-0.006	17.731	-0.024	-0.024	0.000	0.000	0.000	0.000
51	A	51	PHE	0	0.046	0.016	18.106	0.066	0.066	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.030	-0.011	18.573	-0.058	-0.058	0.000	0.000	0.000	0.000
53	A	52	THR	0	0.053	0.010	15.293	0.066	0.066	0.000	0.000	0.000	0.000
54	A	53	ARG	1	0.875	0.942	18.357	0.313	0.313	0.000	0.000	0.000	0.000
55	A	54	GLY	0	0.003	-0.021	20.464	0.028	0.028	0.000	0.000	0.000	0.000
56	A	55	GLY	0	0.039	0.037	22.158	0.023	0.023	0.000	0.000	0.000	0.000
57	A	56	ARG	1	0.905	0.992	21.063	0.358	0.358	0.000	0.000	0.000	0.000
58	A	57	THR	0	0.023	-0.001	23.418	-0.029	-0.029	0.000	0.000	0.000	0.000
59	A	58	TYR	0	-0.047	-0.018	24.269	0.027	0.027	0.000	0.000	0.000	0.000
60	A	59	TYR	0	0.030	0.012	25.413	-0.033	-0.033	0.000	0.000	0.000	0.000
61	A	60	ALA	0	0.033	0.031	27.580	0.018	0.018	0.000	0.000	0.000	0.000
62	A	61	ASP	-1	-0.871	-0.954	29.129	-0.223	-0.223	0.000	0.000	0.000	0.000
63	A	62	SER	0	-0.046	-0.011	30.052	0.009	0.009	0.000	0.000	0.000	0.000
64	A	63	VAL	0	0.005	-0.004	27.896	0.009	0.009	0.000	0.000	0.000	0.000
65	A	64	LYS	1	0.963	0.989	31.221	0.227	0.227	0.000	0.000	0.000	0.000
66	A	65	GLY	0	-0.010	0.004	32.084	0.014	0.014	0.000	0.000	0.000	0.000
67	A	66	ARG	1	0.757	0.863	32.380	0.239	0.239	0.000	0.000	0.000	0.000
68	A	67	PHE	0	0.001	-0.009	26.743	-0.004	-0.004	0.000	0.000	0.000	0.000
69	A	68	THR	0	-0.021	-0.015	27.413	0.006	0.006	0.000	0.000	0.000	0.000
70	A	69	ILE	0	-0.006	-0.002	20.889	-0.013	-0.013	0.000	0.000	0.000	0.000
71	A	70	ALA	0	-0.018	0.000	22.441	0.029	0.029	0.000	0.000	0.000	0.000
72	A	71	ILE	0	-0.028	-0.008	16.023	-0.052	-0.052	0.000	0.000	0.000	0.000
73	A	72	ASP	-1	-0.757	-0.878	17.762	-0.396	-0.396	0.000	0.000	0.000	0.000
74	A	73	ASN	0	-0.003	-0.025	19.562	-0.022	-0.022	0.000	0.000	0.000	0.000
75	A	74	ALA	0	-0.008	0.001	16.571	0.016	0.016	0.000	0.000	0.000	0.000
76	A	75	LYS	1	0.912	0.962	15.418	0.318	0.318	0.000	0.000	0.000	0.000
77	A	76	ASN	0	-0.035	-0.016	11.287	0.038	0.038	0.000	0.000	0.000	0.000
78	A	77	THR	0	-0.017	-0.008	13.554	-0.149	-0.149	0.000	0.000	0.000	0.000
79	A	78	VAL	0	-0.019	0.001	15.810	0.077	0.077	0.000	0.000	0.000	0.000
80	A	79	TYR	0	-0.017	-0.024	17.894	-0.009	-0.009	0.000	0.000	0.000	0.000
81	A	80	LEU	0	0.025	0.015	21.102	0.001	0.001	0.000	0.000	0.000	0.000
82	A	81	GLN	0	-0.019	-0.010	23.187	0.010	0.010	0.000	0.000	0.000	0.000
83	A	82	MET	0	-0.013	0.005	25.528	0.003	0.003	0.000	0.000	0.000	0.000
84	A	82	ASN	0	0.061	0.022	29.130	0.015	0.015	0.000	0.000	0.000	0.000
85	A	82	SER	0	-0.009	-0.011	32.901	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	82	LEU	0	-0.026	-0.007	29.757	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	83	LYS	1	0.995	0.997	33.665	0.217	0.217	0.000	0.000	0.000	0.000
88	A	84	LEU	0	0.073	0.016	33.820	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	85	ASP	-1	-0.945	-0.967	33.615	-0.228	-0.228	0.000	0.000	0.000	0.000
90	A	86	ASP	-1	-0.736	-0.829	29.953	-0.266	-0.266	0.000	0.000	0.000	0.000
91	A	87	THR	0	-0.022	0.002	28.753	-0.022	-0.022	0.000	0.000	0.000	0.000
92	A	88	ALA	0	-0.016	-0.022	25.658	0.002	0.002	0.000	0.000	0.000	0.000
93	A	89	VAL	0	0.001	0.037	20.304	0.001	0.001	0.000	0.000	0.000	0.000
94	A	90	TYR	0	-0.037	-0.056	21.209	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	91	TYR	0	0.026	0.001	16.097	-0.017	-0.017	0.000	0.000	0.000	0.000
96	A	93	ALA	0	0.049	0.017	12.956	-0.105	-0.105	0.000	0.000	0.000	0.000
97	A	94	VAL	0	-0.021	-0.008	8.903	0.110	0.110	0.000	0.000	0.000	0.000
98	A	95	ARG	1	0.916	0.954	11.939	0.545	0.545	0.000	0.000	0.000	0.000
99	A	96	MET	0	0.017	0.022	11.042	0.033	0.033	0.000	0.000	0.000	0.000
100	A	97	PRO	0	-0.042	-0.033	13.488	0.087	0.087	0.000	0.000	0.000	0.000
101	A	98	TYR	0	-0.046	-0.023	16.937	0.019	0.019	0.000	0.000	0.000	0.000
102	A	99	SER	0	0.067	0.041	16.135	0.030	0.030	0.000	0.000	0.000	0.000
103	A	100	GLY	0	0.063	0.031	18.439	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	100	ASP	-1	-0.867	-0.938	21.360	-0.377	-0.377	0.000	0.000	0.000	0.000
105	A	100	TYR	0	-0.004	0.001	20.309	-0.024	-0.024	0.000	0.000	0.000	0.000
106	A	100	ARG	1	0.951	0.995	21.158	0.264	0.264	0.000	0.000	0.000	0.000
107	A	100	SER	0	0.025	0.028	22.043	-0.013	-0.013	0.000	0.000	0.000	0.000
108	A	100	SER	0	0.029	0.003	19.209	-0.040	-0.040	0.000	0.000	0.000	0.000
109	A	100	GLY	0	0.030	0.011	17.700	-0.071	-0.071	0.000	0.000	0.000	0.000
110	A	100	THR	0	-0.070	-0.030	17.438	-0.030	-0.030	0.000	0.000	0.000	0.000
111	A	100	TYR	0	-0.100	-0.078	14.027	-0.020	-0.020	0.000	0.000	0.000	0.000
112	A	101	ASP	-1	-0.821	-0.915	9.316	-1.139	-1.139	0.000	0.000	0.000	0.000
113	A	102	TYR	0	-0.049	-0.026	5.408	-0.478	-0.478	0.000	0.000	0.000	0.000
114	A	103	TRP	0	-0.029	-0.033	9.677	0.276	0.276	0.000	0.000	0.000	0.000
115	A	104	GLY	0	0.036	0.037	10.444	-0.190	-0.190	0.000	0.000	0.000	0.000
116	A	105	GLN	0	-0.019	-0.026	12.053	0.158	0.158	0.000	0.000	0.000	0.000
117	A	106	GLY	0	-0.007	0.001	14.232	0.091	0.091	0.000	0.000	0.000	0.000
118	A	107	THR	0	-0.042	-0.019	17.379	0.045	0.045	0.000	0.000	0.000	0.000
119	A	108	GLN	0	0.022	-0.003	20.175	0.001	0.001	0.000	0.000	0.000	0.000
120	A	109	VAL	0	0.008	0.019	23.827	0.011	0.011	0.000	0.000	0.000	0.000
121	A	110	THR	0	0.000	-0.011	26.610	0.001	0.001	0.000	0.000	0.000	0.000
122	A	111	VAL	0	0.007	0.019	30.118	0.010	0.010	0.000	0.000	0.000	0.000
123	A	112	SER	0	-0.016	-0.002	33.095	0.005	0.005	0.000	0.000	0.000	0.000
124	A	113	SER	0	0.029	0.015	36.426	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)