FMO DATABASE

FMODB ID: Q89JY

Calculation Name: 1PFP-A-Xray315

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	98
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-707507.488714
FMO2-HF: Nuclear repulsion	668206.53472
FMO2-HF: Total energy	-39300.953994
FMO2-MP2: Total energy	-39414.155074

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:30:ACE )

Summations of interaction energy for fragment #1(A:30:ACE )

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.
1.16	3.068	0.072	-0.833	-1.149	-0.002

Interaction energy analysis for fragmet #1(A:30:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.055 / q_NPA : 0.021

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	32	LEU	0	-0.022	-0.014	3.848	0.247	1.407	-0.006	-0.597	-0.558	-0.001
4	A	33	SER	0	0.093	0.040	3.136	0.012	0.290	0.040	-0.086	-0.232	0.000
5	A	34	TYR	0	-0.047	-0.036	4.174	-0.130	-0.018	0.000	-0.033	-0.079	0.000
6	A	35	ARG	1	0.981	0.985	5.752	1.052	1.052	0.000	0.000	0.000	0.000
7	A	36	GLU	-1	-0.866	-0.942	8.199	0.228	0.228	0.000	0.000	0.000	0.000
8	A	37	ALA	0	-0.034	-0.010	8.304	0.074	0.074	0.000	0.000	0.000	0.000
9	A	38	VAL	0	0.004	0.006	9.997	0.028	0.028	0.000	0.000	0.000	0.000
10	A	39	LEU	0	-0.016	-0.012	12.056	0.038	0.038	0.000	0.000	0.000	0.000
11	A	40	ARG	1	0.942	0.979	9.627	-0.134	-0.134	0.000	0.000	0.000	0.000
12	A	41	ALA	0	-0.001	-0.003	14.091	0.019	0.019	0.000	0.000	0.000	0.000
13	A	42	VAL	0	-0.030	-0.011	15.841	0.008	0.008	0.000	0.000	0.000	0.000
14	A	43	ASP	-1	-0.892	-0.946	17.769	-0.024	-0.024	0.000	0.000	0.000	0.000
15	A	44	ARG	1	0.835	0.909	16.233	-0.024	-0.024	0.000	0.000	0.000	0.000
16	A	45	LEU	0	-0.031	-0.017	18.963	0.003	0.003	0.000	0.000	0.000	0.000
17	A	46	ASN	0	0.008	-0.016	21.880	0.002	0.002	0.000	0.000	0.000	0.000
18	A	47	GLU	-1	-0.933	-0.955	22.792	0.007	0.007	0.000	0.000	0.000	0.000
19	A	48	GLN	0	-0.103	-0.049	23.290	-0.006	-0.006	0.000	0.000	0.000	0.000
20	A	49	SER	0	0.013	0.033	25.895	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	50	SER	0	-0.026	-0.040	27.789	0.006	0.006	0.000	0.000	0.000	0.000
22	A	51	GLU	-1	-0.859	-0.907	29.351	-0.051	-0.051	0.000	0.000	0.000	0.000
23	A	52	ALA	0	0.005	-0.007	31.299	0.002	0.002	0.000	0.000	0.000	0.000
24	A	53	ASN	0	-0.046	-0.004	30.267	0.006	0.006	0.000	0.000	0.000	0.000
25	A	54	LEU	0	-0.028	0.009	24.988	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	55	TYR	0	-0.038	-0.057	23.429	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	56	ARG	1	0.929	0.963	21.288	0.096	0.096	0.000	0.000	0.000	0.000
28	A	57	LEU	0	-0.008	-0.007	15.154	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	58	LEU	0	-0.075	-0.028	19.198	0.010	0.010	0.000	0.000	0.000	0.000
30	A	59	GLU	-1	-0.926	-0.962	18.497	-0.209	-0.209	0.000	0.000	0.000	0.000
31	A	60	LEU	0	-0.035	-0.018	10.814	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	61	ASP	-1	-0.822	-0.912	15.102	-0.279	-0.279	0.000	0.000	0.000	0.000
33	A	62	GLN	0	-0.005	-0.001	12.765	-0.030	-0.030	0.000	0.000	0.000	0.000
34	A	63	PRO	0	0.044	0.017	8.867	0.070	0.070	0.000	0.000	0.000	0.000
35	A	64	PRO	0	-0.062	-0.034	11.832	0.022	0.022	0.000	0.000	0.000	0.000
36	A	65	LYS	1	0.833	0.902	13.300	0.334	0.334	0.000	0.000	0.000	0.000
37	A	66	ALA	0	0.044	0.037	11.400	0.049	0.049	0.000	0.000	0.000	0.000
38	A	67	ASP	-1	-0.918	-0.961	11.627	-0.183	-0.183	0.000	0.000	0.000	0.000
39	A	68	GLU	-1	-0.896	-0.952	11.011	0.042	0.042	0.000	0.000	0.000	0.000
40	A	69	ASP	-1	-0.976	-1.021	4.935	-0.207	-0.107	0.000	-0.008	-0.093	0.000
41	A	70	PRO	0	0.003	0.007	7.425	0.193	0.193	0.000	0.000	0.000	0.000
42	A	71	GLY	0	-0.012	-0.005	8.202	0.123	0.123	0.000	0.000	0.000	0.000
43	A	72	THR	0	-0.075	-0.018	9.142	-0.035	-0.035	0.000	0.000	0.000	0.000
44	A	73	PRO	0	0.031	0.004	9.472	0.002	0.002	0.000	0.000	0.000	0.000
45	A	74	LYS	1	0.849	0.941	5.721	-0.096	-0.096	0.000	0.000	0.000	0.000
46	A	75	PRO	0	0.042	0.021	9.613	0.013	0.013	0.000	0.000	0.000	0.000
47	A	76	VAL	0	-0.023	0.017	10.847	-0.120	-0.120	0.000	0.000	0.000	0.000
48	A	77	SER	0	-0.018	-0.014	12.981	0.055	0.055	0.000	0.000	0.000	0.000
49	A	78	PHE	0	0.013	0.008	14.828	-0.039	-0.039	0.000	0.000	0.000	0.000
50	A	79	THR	0	0.057	0.030	17.198	0.036	0.036	0.000	0.000	0.000	0.000
51	A	80	VAL	0	-0.005	-0.002	19.754	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	81	LYS	1	0.924	0.970	22.005	0.089	0.089	0.000	0.000	0.000	0.000
53	A	82	GLU	-1	-0.856	-0.921	25.355	-0.048	-0.048	0.000	0.000	0.000	0.000
54	A	83	THR	0	-0.019	-0.019	25.738	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	84	VAL	0	-0.023	-0.027	28.707	0.004	0.004	0.000	0.000	0.000	0.000
56	A	96	CYS	0	-0.084	-0.013	25.331	0.011	0.011	0.000	0.000	0.000	0.000
57	A	86	PRO	0	0.068	0.030	30.225	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	87	ARG	1	0.894	0.945	28.095	0.019	0.019	0.000	0.000	0.000	0.000
59	A	88	PRO	0	-0.041	-0.012	28.658	0.002	0.002	0.000	0.000	0.000	0.000
60	A	89	THR	0	0.002	-0.009	28.071	0.002	0.002	0.000	0.000	0.000	0.000
61	A	90	ARG	1	0.937	0.960	26.706	-0.016	-0.016	0.000	0.000	0.000	0.000
62	A	91	GLN	0	-0.007	0.010	26.129	0.006	0.006	0.000	0.000	0.000	0.000
63	A	92	PRO	0	0.076	0.029	21.110	-0.002	-0.002	0.000	0.000	0.000	0.000
64	A	93	PRO	0	0.071	0.021	20.661	-0.003	-0.003	0.000	0.000	0.000	0.000
65	A	94	GLU	-1	-0.984	-0.996	18.420	-0.085	-0.085	0.000	0.000	0.000	0.000
66	A	95	LEU	0	-0.035	-0.001	22.088	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	97	ASP	-1	-0.878	-0.927	26.425	-0.061	-0.061	0.000	0.000	0.000	0.000
68	A	98	PHE	0	-0.020	-0.032	22.762	0.003	0.003	0.000	0.000	0.000	0.000
69	A	99	LYS	1	0.916	0.965	28.557	0.051	0.051	0.000	0.000	0.000	0.000
70	A	100	GLU	-1	-0.901	-0.954	31.533	-0.062	-0.062	0.000	0.000	0.000	0.000
71	A	101	ASN	0	-0.033	-0.027	33.876	0.000	0.000	0.000	0.000	0.000	0.000
72	A	102	GLY	0	-0.051	-0.009	30.840	0.004	0.004	0.000	0.000	0.000	0.000
73	A	103	ARG	1	0.983	0.990	28.902	0.049	0.049	0.000	0.000	0.000	0.000
74	A	104	VAL	0	0.024	0.003	25.272	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	105	LYS	1	0.852	0.945	24.007	0.070	0.070	0.000	0.000	0.000	0.000
76	A	106	GLN	0	0.058	0.047	19.985	-0.022	-0.022	0.000	0.000	0.000	0.000
77	A	124	CYS	0	-0.083	-0.036	18.802	0.009	0.009	0.000	0.000	0.000	0.000
78	A	108	VAL	0	0.063	0.020	17.497	-0.029	-0.029	0.000	0.000	0.000	0.000
79	A	109	GLY	0	0.026	0.005	16.531	0.027	0.027	0.000	0.000	0.000	0.000
80	A	110	THR	0	-0.076	-0.043	12.622	-0.023	-0.023	0.000	0.000	0.000	0.000
81	A	111	VAL	0	0.026	0.027	8.465	0.019	0.019	0.000	0.000	0.000	0.000
82	A	112	THR	0	-0.018	-0.029	9.587	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	113	LEU	0	0.011	-0.008	3.251	-0.299	-0.041	0.038	-0.109	-0.187	-0.001
84	A	114	ASP	-1	-0.844	-0.906	6.984	0.677	0.677	0.000	0.000	0.000	0.000
85	A	115	GLN	0	-0.030	-0.006	9.881	-0.117	-0.117	0.000	0.000	0.000	0.000
86	A	116	ILE	0	-0.006	-0.033	12.751	-0.038	-0.038	0.000	0.000	0.000	0.000
87	A	117	LYS	1	0.839	0.933	12.284	-0.345	-0.345	0.000	0.000	0.000	0.000
88	A	118	ASP	-1	-0.787	-0.862	13.768	0.167	0.167	0.000	0.000	0.000	0.000
89	A	119	PRO	0	0.027	0.005	16.816	-0.009	-0.009	0.000	0.000	0.000	0.000
90	A	120	LEU	0	-0.045	-0.017	17.324	0.002	0.002	0.000	0.000	0.000	0.000
91	A	121	ASP	-1	-0.884	-0.957	16.418	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	122	ILE	0	-0.021	0.002	15.074	-0.022	-0.022	0.000	0.000	0.000	0.000
93	A	123	THR	0	-0.038	-0.015	19.064	0.016	0.016	0.000	0.000	0.000	0.000
94	A	125	ASN	0	-0.016	-0.010	23.411	0.017	0.017	0.000	0.000	0.000	0.000
95	A	126	GLU	-1	-0.952	-0.983	26.121	-0.069	-0.069	0.000	0.000	0.000	0.000
96	A	127	VAL	0	-0.031	-0.009	26.005	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	128	GLN	0	0.018	0.007	28.768	0.007	0.007	0.000	0.000	0.000	0.000
98	A	129	NME	0	-0.009	-0.001	32.223	-0.003	-0.003	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:30:ACE )