FMO DATABASE

FMODB ID: Z69NN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1043600.728647
FMO2-HF: Nuclear repulsion	995343.718681
FMO2-HF: Total energy	-48257.009966
FMO2-MP2: Total energy	-48397.282686

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.
0.954	3.261	0.012	-0.836	-1.482	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 : 0.001 / 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	-0.032	-0.021	3.192	-0.204	1.925	0.013	-0.780	-1.362	0.003
4	A	4	LEU	0	-0.015	-0.006	5.700	0.475	0.475	0.000	0.000	0.000	0.000
5	A	5	GLN	0	0.012	-0.003	9.488	0.024	0.024	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.764	-0.871	12.352	-0.878	-0.878	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.028	-0.018	16.026	0.057	0.057	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.033	0.001	18.995	-0.004	-0.004	0.000	0.000	0.000	0.000
9	A	9	GLY	0	-0.004	0.018	22.157	0.025	0.025	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.031	0.005	24.041	0.016	0.016	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.036	-0.010	27.462	-0.008	-0.008	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.003	-0.006	30.672	0.008	0.008	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.014	0.011	32.889	0.002	0.002	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.034	0.000	35.969	-0.007	-0.007	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.027	-0.011	36.854	0.010	0.010	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.022	-0.004	35.300	0.004	0.004	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.025	-0.041	31.873	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.018	-0.006	26.530	0.007	0.007	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.884	0.949	24.149	0.259	0.259	0.000	0.000	0.000	0.000
20	A	20	LEU	0	0.000	0.018	21.091	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.002	-0.015	18.632	0.022	0.022	0.000	0.000	0.000	0.000
22	A	22	CYS	0	-0.091	-0.016	14.188	-0.051	-0.051	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.033	0.022	13.185	0.027	0.027	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.028	0.010	9.082	-0.231	-0.231	0.000	0.000	0.000	0.000
25	A	25	SER	0	0.024	0.023	4.318	0.663	0.841	-0.001	-0.056	-0.120	0.000
26	A	26	GLY	0	0.038	0.017	6.807	-0.227	-0.227	0.000	0.000	0.000	0.000
27	A	27	ARG	1	0.975	0.974	7.629	0.390	0.390	0.000	0.000	0.000	0.000
28	A	28	THR	0	0.053	0.026	6.749	-0.162	-0.162	0.000	0.000	0.000	0.000
29	A	29	PHE	0	0.024	-0.007	8.689	0.126	0.126	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.085	-0.041	11.643	0.222	0.222	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.031	-0.020	9.627	0.109	0.109	0.000	0.000	0.000	0.000
32	A	32	TYR	0	-0.039	0.000	7.086	-0.086	-0.086	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.090	-0.031	12.149	0.096	0.096	0.000	0.000	0.000	0.000
34	A	34	VAL	0	0.053	0.012	13.911	-0.126	-0.126	0.000	0.000	0.000	0.000
35	A	35	GLY	0	-0.009	0.007	15.857	0.119	0.119	0.000	0.000	0.000	0.000
36	A	36	TRP	0	-0.017	-0.010	17.403	-0.085	-0.085	0.000	0.000	0.000	0.000
37	A	37	PHE	0	0.017	-0.006	18.315	0.054	0.054	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.810	0.896	21.334	0.301	0.301	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.018	-0.009	23.174	-0.024	-0.024	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.026	0.024	24.900	0.003	0.003	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.035	-0.009	28.348	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.001	0.009	29.487	0.013	0.013	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.865	0.944	29.410	0.289	0.289	0.000	0.000	0.000	0.000
44	A	44	GLU	-1	-0.904	-0.950	26.401	-0.331	-0.331	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.851	0.942	16.497	0.702	0.702	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.794	-0.878	24.028	-0.306	-0.306	0.000	0.000	0.000	0.000
47	A	47	PHE	0	0.015	-0.010	21.824	-0.016	-0.016	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.028	-0.001	23.304	0.033	0.033	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.033	-0.003	22.933	0.042	0.042	0.000	0.000	0.000	0.000
50	A	50	TYR	0	-0.028	-0.007	17.650	-0.022	-0.022	0.000	0.000	0.000	0.000
51	A	51	PHE	0	0.063	0.018	17.965	0.065	0.065	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.030	-0.008	18.564	-0.059	-0.059	0.000	0.000	0.000	0.000
53	A	52	THR	0	0.048	0.004	15.242	0.068	0.068	0.000	0.000	0.000	0.000
54	A	53	ARG	1	0.859	0.935	18.345	0.303	0.303	0.000	0.000	0.000	0.000
55	A	54	GLY	0	-0.001	-0.012	20.450	0.029	0.029	0.000	0.000	0.000	0.000
56	A	55	GLY	0	0.035	0.036	22.154	0.022	0.022	0.000	0.000	0.000	0.000
57	A	56	ARG	1	0.926	0.982	21.553	0.346	0.346	0.000	0.000	0.000	0.000
58	A	57	THR	0	0.021	0.007	23.275	-0.030	-0.030	0.000	0.000	0.000	0.000
59	A	58	TYR	0	-0.039	-0.014	24.032	0.026	0.026	0.000	0.000	0.000	0.000
60	A	59	TYR	0	0.041	0.008	25.407	-0.033	-0.033	0.000	0.000	0.000	0.000
61	A	60	ALA	0	0.022	0.027	27.524	0.019	0.019	0.000	0.000	0.000	0.000
62	A	61	ASP	-1	-0.820	-0.930	29.126	-0.227	-0.227	0.000	0.000	0.000	0.000
63	A	62	SER	0	-0.025	0.003	30.256	0.009	0.009	0.000	0.000	0.000	0.000
64	A	63	VAL	0	0.003	-0.010	27.927	0.008	0.008	0.000	0.000	0.000	0.000
65	A	64	LYS	1	0.866	0.939	31.224	0.223	0.223	0.000	0.000	0.000	0.000
66	A	65	GLY	0	0.007	0.012	32.087	0.014	0.014	0.000	0.000	0.000	0.000
67	A	66	ARG	1	0.766	0.863	32.487	0.239	0.239	0.000	0.000	0.000	0.000
68	A	67	PHE	0	-0.004	-0.017	26.946	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	68	THR	0	-0.011	-0.007	27.413	0.006	0.006	0.000	0.000	0.000	0.000
70	A	69	ILE	0	-0.016	-0.005	20.915	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	70	ALA	0	-0.021	-0.001	22.446	0.029	0.029	0.000	0.000	0.000	0.000
72	A	71	ILE	0	-0.015	-0.003	15.963	-0.050	-0.050	0.000	0.000	0.000	0.000
73	A	72	ASP	-1	-0.737	-0.850	17.539	-0.403	-0.403	0.000	0.000	0.000	0.000
74	A	73	ASN	0	-0.008	-0.027	19.499	-0.020	-0.020	0.000	0.000	0.000	0.000
75	A	74	ALA	0	-0.005	0.001	16.553	0.016	0.016	0.000	0.000	0.000	0.000
76	A	75	LYS	1	0.901	0.960	15.474	0.306	0.306	0.000	0.000	0.000	0.000
77	A	76	ASN	0	-0.026	-0.011	11.484	0.007	0.007	0.000	0.000	0.000	0.000
78	A	77	THR	0	-0.031	-0.038	13.464	-0.146	-0.146	0.000	0.000	0.000	0.000
79	A	78	VAL	0	-0.025	-0.002	16.043	0.079	0.079	0.000	0.000	0.000	0.000
80	A	79	TYR	0	-0.018	-0.025	17.894	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	80	LEU	0	0.026	0.013	21.102	0.001	0.001	0.000	0.000	0.000	0.000
82	A	81	GLN	0	-0.005	-0.002	23.252	0.008	0.008	0.000	0.000	0.000	0.000
83	A	82	MET	0	-0.021	0.001	26.256	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	82	ASN	0	0.053	0.025	29.287	0.012	0.012	0.000	0.000	0.000	0.000
85	A	82	SER	0	0.013	0.003	33.056	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	82	LEU	0	-0.022	0.000	29.891	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	83	LYS	1	0.927	0.961	33.846	0.226	0.226	0.000	0.000	0.000	0.000
88	A	84	LEU	0	0.070	0.019	33.991	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	85	ASP	-1	-0.860	-0.923	33.790	-0.223	-0.223	0.000	0.000	0.000	0.000
90	A	86	ASP	-1	-0.765	-0.836	30.119	-0.267	-0.267	0.000	0.000	0.000	0.000
91	A	87	THR	0	-0.005	0.003	28.929	-0.023	-0.023	0.000	0.000	0.000	0.000
92	A	88	ALA	0	-0.019	-0.015	25.762	0.002	0.002	0.000	0.000	0.000	0.000
93	A	89	VAL	0	-0.003	0.028	20.459	0.000	0.000	0.000	0.000	0.000	0.000
94	A	90	TYR	0	-0.023	-0.046	21.386	-0.009	-0.009	0.000	0.000	0.000	0.000
95	A	91	TYR	0	0.023	-0.003	16.481	-0.020	-0.020	0.000	0.000	0.000	0.000
96	A	93	ALA	0	0.052	0.020	13.065	-0.106	-0.106	0.000	0.000	0.000	0.000
97	A	94	VAL	0	-0.025	-0.017	8.995	0.103	0.103	0.000	0.000	0.000	0.000
98	A	95	ARG	1	0.906	0.948	11.938	0.538	0.538	0.000	0.000	0.000	0.000
99	A	96	MET	0	0.006	0.021	11.189	0.038	0.038	0.000	0.000	0.000	0.000
100	A	97	PRO	0	-0.037	-0.018	13.482	0.083	0.083	0.000	0.000	0.000	0.000
101	A	98	TYR	0	-0.048	-0.023	16.929	0.021	0.021	0.000	0.000	0.000	0.000
102	A	99	SER	0	0.063	0.024	16.325	0.028	0.028	0.000	0.000	0.000	0.000
103	A	100	GLY	0	0.071	0.038	18.437	-0.008	-0.008	0.000	0.000	0.000	0.000
104	A	100	ASP	-1	-0.858	-0.930	21.358	-0.381	-0.381	0.000	0.000	0.000	0.000
105	A	100	TYR	0	-0.009	0.001	20.299	-0.024	-0.024	0.000	0.000	0.000	0.000
106	A	100	ARG	1	0.931	0.969	21.156	0.266	0.266	0.000	0.000	0.000	0.000
107	A	100	SER	0	0.016	0.022	22.013	-0.012	-0.012	0.000	0.000	0.000	0.000
108	A	100	SER	0	0.032	0.002	19.148	-0.037	-0.037	0.000	0.000	0.000	0.000
109	A	100	GLY	0	0.027	0.010	17.602	-0.070	-0.070	0.000	0.000	0.000	0.000
110	A	100	THR	0	-0.057	-0.016	17.370	-0.028	-0.028	0.000	0.000	0.000	0.000
111	A	100	TYR	0	-0.097	-0.069	14.031	-0.021	-0.021	0.000	0.000	0.000	0.000
112	A	101	ASP	-1	-0.805	-0.910	9.295	-1.161	-1.161	0.000	0.000	0.000	0.000
113	A	102	TYR	0	-0.036	-0.024	4.913	-0.519	-0.519	0.000	0.000	0.000	0.000
114	A	103	TRP	0	-0.036	-0.036	9.566	0.278	0.278	0.000	0.000	0.000	0.000
115	A	104	GLY	0	0.043	0.040	10.634	-0.191	-0.191	0.000	0.000	0.000	0.000
116	A	105	GLN	0	-0.020	-0.022	11.890	0.164	0.164	0.000	0.000	0.000	0.000
117	A	106	GLY	0	-0.014	-0.005	14.389	0.092	0.092	0.000	0.000	0.000	0.000
118	A	107	THR	0	-0.043	-0.025	17.541	0.045	0.045	0.000	0.000	0.000	0.000
119	A	108	GLN	0	0.019	0.002	20.322	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	109	VAL	0	0.009	0.016	23.976	0.011	0.011	0.000	0.000	0.000	0.000
121	A	110	THR	0	-0.012	-0.016	26.763	0.002	0.002	0.000	0.000	0.000	0.000
122	A	111	VAL	0	0.003	0.016	30.269	0.009	0.009	0.000	0.000	0.000	0.000
123	A	112	SER	0	-0.016	0.001	33.251	0.006	0.006	0.000	0.000	0.000	0.000
124	A	113	SER	0	0.035	0.016	36.576	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)