FMO DATABASE

FMODB ID: 824KY

Calculation Name: 1PFP-A-Xray372

Preferred Name:

Target Type:

Ligand Name: selenocysteine

ligand 3-letter code: SEC

PDB ID: 1PFP

Chain ID: A

ChEMBL ID:

UniProt ID: P32196

Base Structure: X-ray

Registration Date: 2023-06-19

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	96
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-704410.478177
FMO2-HF: Nuclear repulsion	665281.765808
FMO2-HF: Total energy	-39128.712369
FMO2-MP2: Total energy	-39241.407081

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:31:ALA)

Summations of interaction energy for fragment #1(A:31:ALA)

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.
-8.873	-4.299	1.066	-2.291	-3.349	0.002

Interaction energy analysis for fragmet #1(A:31:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.073 / q_NPA : 0.029

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	33	SER	0	0.092	0.038	3.630	-3.585	-1.227	0.021	-1.202	-1.177	0.004
4	A	34	TYR	0	-0.030	-0.027	2.562	-2.795	-1.815	0.992	-0.656	-1.315	-0.001
5	A	35	ARG	1	0.972	0.982	2.951	0.064	0.716	0.050	-0.190	-0.512	0.001
6	A	36	GLU	-1	-0.876	-0.948	6.176	1.431	1.431	0.000	0.000	0.000	0.000
7	A	37	ALA	0	-0.025	-0.006	7.614	-0.043	-0.043	0.000	0.000	0.000	0.000
8	A	38	VAL	0	0.008	0.009	8.056	-0.040	-0.040	0.000	0.000	0.000	0.000
9	A	39	LEU	0	-0.024	-0.017	10.180	0.017	0.017	0.000	0.000	0.000	0.000
10	A	40	ARG	1	0.938	0.981	10.263	-0.425	-0.425	0.000	0.000	0.000	0.000
11	A	41	ALA	0	0.006	0.001	12.999	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	42	VAL	0	-0.029	-0.012	14.316	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	43	ASP	-1	-0.900	-0.950	16.370	0.094	0.094	0.000	0.000	0.000	0.000
14	A	44	ARG	1	0.815	0.896	16.460	-0.060	-0.060	0.000	0.000	0.000	0.000
15	A	45	LEU	0	-0.028	-0.016	17.249	-0.005	-0.005	0.000	0.000	0.000	0.000
16	A	46	ASN	0	0.004	-0.019	20.577	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	47	GLU	-1	-0.934	-0.956	22.174	0.053	0.053	0.000	0.000	0.000	0.000
18	A	48	GLN	0	-0.107	-0.050	22.393	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	49	SER	0	0.017	0.035	24.893	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	50	SER	0	-0.032	-0.043	26.478	0.006	0.006	0.000	0.000	0.000	0.000
21	A	51	GLU	-1	-0.859	-0.907	27.433	-0.036	-0.036	0.000	0.000	0.000	0.000
22	A	52	ALA	0	-0.001	-0.011	29.500	0.004	0.004	0.000	0.000	0.000	0.000
23	A	53	ASN	0	-0.046	-0.006	27.785	0.009	0.009	0.000	0.000	0.000	0.000
24	A	54	LEU	0	-0.025	0.010	23.083	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	55	TYR	0	-0.042	-0.058	20.823	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	56	ARG	1	0.929	0.963	18.305	0.016	0.016	0.000	0.000	0.000	0.000
27	A	57	LEU	0	0.000	-0.003	11.860	-0.008	-0.008	0.000	0.000	0.000	0.000
28	A	58	LEU	0	-0.083	-0.035	16.025	0.019	0.019	0.000	0.000	0.000	0.000
29	A	59	GLU	-1	-0.931	-0.965	14.329	-0.186	-0.186	0.000	0.000	0.000	0.000
30	A	60	LEU	0	-0.040	-0.021	7.114	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	61	ASP	-1	-0.842	-0.924	10.997	-0.298	-0.298	0.000	0.000	0.000	0.000
32	A	62	GLN	0	-0.054	-0.029	9.424	-0.114	-0.114	0.000	0.000	0.000	0.000
33	A	63	PRO	0	-0.026	-0.001	6.342	0.083	0.083	0.000	0.000	0.000	0.000
34	A	64	PRO	0	-0.030	-0.027	9.681	0.035	0.035	0.000	0.000	0.000	0.000
35	A	65	LYN	0	-0.019	-0.016	3.866	-1.233	-0.735	0.004	-0.233	-0.270	-0.002
36	A	66	ALA	0	-0.047	-0.030	7.141	-0.208	-0.208	0.000	0.000	0.000	0.000
37	A	67	ASP	-1	-0.945	-0.965	8.850	-0.543	-0.543	0.000	0.000	0.000	0.000
38	A	68	GLU	-1	-0.829	-0.924	9.608	-0.641	-0.641	0.000	0.000	0.000	0.000
39	A	69	ASP	-1	-0.945	-0.995	6.800	-1.069	-1.069	0.000	0.000	0.000	0.000
40	A	70	PRO	0	-0.055	-0.022	9.878	0.056	0.056	0.000	0.000	0.000	0.000
41	A	71	GLY	0	0.017	0.013	9.856	0.088	0.088	0.000	0.000	0.000	0.000
42	A	72	THR	0	-0.093	-0.037	10.800	0.068	0.068	0.000	0.000	0.000	0.000
43	A	73	PRO	0	0.008	-0.007	10.370	-0.064	-0.064	0.000	0.000	0.000	0.000
44	A	74	LYN	0	0.008	0.012	6.253	-0.049	-0.049	0.000	0.000	0.000	0.000
45	A	75	PRO	0	0.021	0.015	9.558	0.086	0.086	0.000	0.000	0.000	0.000
46	A	76	VAL	0	-0.031	0.016	8.738	-0.133	-0.133	0.000	0.000	0.000	0.000
47	A	77	SER	0	-0.003	-0.007	10.944	0.073	0.073	0.000	0.000	0.000	0.000
48	A	78	PHE	0	0.019	0.011	12.013	-0.035	-0.035	0.000	0.000	0.000	0.000
49	A	79	THR	0	0.048	0.025	13.982	0.042	0.042	0.000	0.000	0.000	0.000
50	A	80	VAL	0	-0.007	-0.002	16.419	0.002	0.002	0.000	0.000	0.000	0.000
51	A	81	LYS	1	0.919	0.967	18.900	0.049	0.049	0.000	0.000	0.000	0.000
52	A	82	GLU	-1	-0.857	-0.922	22.160	-0.016	-0.016	0.000	0.000	0.000	0.000
53	A	83	THR	0	-0.016	-0.017	22.979	0.001	0.001	0.000	0.000	0.000	0.000
54	A	84	VAL	0	-0.026	-0.029	25.810	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	85	CYS	0	-0.091	-0.016	22.724	0.003	0.003	0.000	0.000	0.000	0.000
56	A	86	PRO	0	0.066	0.030	27.969	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	87	ARG	1	0.894	0.945	26.475	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	88	PRO	0	-0.043	-0.014	27.186	0.005	0.005	0.000	0.000	0.000	0.000
59	A	89	THR	0	0.002	-0.009	26.334	0.002	0.002	0.000	0.000	0.000	0.000
60	A	90	ARG	1	0.934	0.960	25.663	-0.074	-0.074	0.000	0.000	0.000	0.000
61	A	91	GLN	0	-0.009	0.009	24.718	0.018	0.018	0.000	0.000	0.000	0.000
62	A	92	PRO	0	0.078	0.030	19.427	-0.007	-0.007	0.000	0.000	0.000	0.000
63	A	93	PRO	0	0.074	0.023	18.641	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	94	GLU	-1	-0.977	-0.994	16.061	0.100	0.100	0.000	0.000	0.000	0.000
65	A	95	LEU	0	-0.039	-0.003	19.454	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	97	ASP	-1	-0.883	-0.929	23.454	0.004	0.004	0.000	0.000	0.000	0.000
67	A	98	PHE	0	-0.014	-0.028	19.179	0.000	0.000	0.000	0.000	0.000	0.000
68	A	99	LYS	1	0.912	0.963	25.226	0.025	0.025	0.000	0.000	0.000	0.000
69	A	100	GLU	-1	-0.904	-0.955	28.095	-0.033	-0.033	0.000	0.000	0.000	0.000
70	A	101	ASN	0	-0.036	-0.029	30.250	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	102	GLY	0	-0.052	-0.010	27.582	0.002	0.002	0.000	0.000	0.000	0.000
72	A	103	ARG	1	0.979	0.989	26.012	0.038	0.038	0.000	0.000	0.000	0.000
73	A	104	VAL	0	0.028	0.004	21.802	0.002	0.002	0.000	0.000	0.000	0.000
74	A	105	LYS	1	0.845	0.942	21.300	0.054	0.054	0.000	0.000	0.000	0.000
75	A	106	GLN	0	0.059	0.048	16.990	-0.023	-0.023	0.000	0.000	0.000	0.000
76	A	107	CYS	0	-0.091	-0.039	16.246	0.011	0.011	0.000	0.000	0.000	0.000
77	A	108	VAL	0	0.076	0.028	15.453	-0.033	-0.033	0.000	0.000	0.000	0.000
78	A	109	GLY	0	0.013	-0.003	14.990	0.038	0.038	0.000	0.000	0.000	0.000
79	A	110	THR	0	-0.071	-0.036	12.462	-0.042	-0.042	0.000	0.000	0.000	0.000
80	A	111	VAL	0	0.034	0.029	8.379	0.057	0.057	0.000	0.000	0.000	0.000
81	A	112	THR	0	0.025	0.008	10.055	-0.090	-0.090	0.000	0.000	0.000	0.000
82	A	113	LEU	0	0.008	-0.003	4.091	0.020	0.106	-0.001	-0.010	-0.075	0.000
83	A	114	ASP	-1	-0.905	-0.938	7.920	0.604	0.604	0.000	0.000	0.000	0.000
84	A	115	GLN	0	-0.028	-0.024	9.786	-0.109	-0.109	0.000	0.000	0.000	0.000
85	A	116	ILE	0	-0.016	-0.006	13.547	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	117	LYS	1	0.856	0.913	16.287	-0.100	-0.100	0.000	0.000	0.000	0.000
87	A	118	ASP	-1	-0.769	-0.868	14.489	0.128	0.128	0.000	0.000	0.000	0.000
88	A	119	PRO	0	-0.018	0.018	16.599	0.012	0.012	0.000	0.000	0.000	0.000
89	A	120	LEU	0	-0.018	-0.025	16.891	0.012	0.012	0.000	0.000	0.000	0.000
90	A	121	ASP	-1	-0.881	-0.961	16.497	-0.076	-0.076	0.000	0.000	0.000	0.000
91	A	122	ILE	0	-0.013	0.010	13.906	-0.030	-0.030	0.000	0.000	0.000	0.000
92	A	123	THR	0	-0.043	-0.019	17.958	0.021	0.021	0.000	0.000	0.000	0.000
93	A	125	ASN	0	-0.020	-0.013	21.272	0.022	0.022	0.000	0.000	0.000	0.000
94	A	126	GLU	-1	-0.955	-0.985	23.381	-0.063	-0.063	0.000	0.000	0.000	0.000
95	A	127	VAL	0	-0.022	-0.005	22.572	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	128	GLN	0	0.003	0.004	25.545	0.010	0.010	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:31:ALA)