FMO DATABASE

FMODB ID: N1J6Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-705857.019783
FMO2-HF: Nuclear repulsion	666727.576303
FMO2-HF: Total energy	-39129.44348
FMO2-MP2: Total energy	-39242.092718

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.
-6.025	-1.521	1.113	-2.218	-3.4	-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 : 0.064 / q_NPA : 0.019

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	0.093	0.037	3.387	-2.803	-0.642	0.014	-1.029	-1.146	0.002
4	A	34	TYR	0	-0.033	-0.022	2.500	-1.405	-0.399	1.067	-0.711	-1.362	-0.002
5	A	35	ARG	1	0.971	0.978	3.320	0.609	1.230	0.021	-0.170	-0.473	0.000
6	A	36	GLU	-1	-0.877	-0.949	6.200	0.956	0.956	0.000	0.000	0.000	0.000
7	A	37	ALA	0	-0.009	0.001	7.419	0.145	0.145	0.000	0.000	0.000	0.000
8	A	38	VAL	0	0.009	0.007	8.017	0.100	0.100	0.000	0.000	0.000	0.000
9	A	39	LEU	0	-0.016	-0.014	10.202	0.096	0.096	0.000	0.000	0.000	0.000
10	A	40	ARG	1	0.890	0.955	9.894	0.168	0.168	0.000	0.000	0.000	0.000
11	A	41	ALA	0	0.013	0.003	13.015	0.040	0.040	0.000	0.000	0.000	0.000
12	A	42	VAL	0	-0.027	-0.010	14.272	0.032	0.032	0.000	0.000	0.000	0.000
13	A	43	ASP	-1	-0.899	-0.951	16.384	-0.066	-0.066	0.000	0.000	0.000	0.000
14	A	44	ARG	1	0.814	0.893	16.217	0.147	0.147	0.000	0.000	0.000	0.000
15	A	45	LEU	0	-0.027	-0.012	17.330	0.015	0.015	0.000	0.000	0.000	0.000
16	A	46	ASN	0	0.016	-0.001	20.372	0.013	0.013	0.000	0.000	0.000	0.000
17	A	47	GLU	-1	-0.945	-0.955	22.196	-0.038	-0.038	0.000	0.000	0.000	0.000
18	A	48	GLN	0	-0.097	-0.047	22.359	0.001	0.001	0.000	0.000	0.000	0.000
19	A	49	SER	0	0.014	0.029	24.911	0.003	0.003	0.000	0.000	0.000	0.000
20	A	50	SER	0	-0.011	-0.028	26.496	0.009	0.009	0.000	0.000	0.000	0.000
21	A	51	GLU	-1	-0.827	-0.884	26.774	-0.093	-0.093	0.000	0.000	0.000	0.000
22	A	52	ALA	0	-0.002	-0.010	29.521	0.002	0.002	0.000	0.000	0.000	0.000
23	A	53	ASN	0	-0.044	-0.017	27.937	0.010	0.010	0.000	0.000	0.000	0.000
24	A	54	LEU	0	-0.009	0.014	23.283	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	55	TYR	0	-0.057	-0.051	20.958	0.000	0.000	0.000	0.000	0.000	0.000
26	A	56	ARG	1	0.898	0.946	18.382	0.080	0.080	0.000	0.000	0.000	0.000
27	A	57	LEU	0	-0.008	-0.010	11.530	0.000	0.000	0.000	0.000	0.000	0.000
28	A	58	LEU	0	-0.083	-0.033	16.048	0.028	0.028	0.000	0.000	0.000	0.000
29	A	59	GLU	-1	-0.943	-0.972	14.405	-0.209	-0.209	0.000	0.000	0.000	0.000
30	A	60	LEU	0	-0.031	-0.014	6.948	-0.034	-0.034	0.000	0.000	0.000	0.000
31	A	61	ASP	-1	-0.795	-0.873	11.075	-0.337	-0.337	0.000	0.000	0.000	0.000
32	A	62	GLN	0	-0.039	-0.022	9.431	-0.099	-0.099	0.000	0.000	0.000	0.000
33	A	63	PRO	0	-0.028	0.001	6.375	0.069	0.069	0.000	0.000	0.000	0.000
34	A	64	PRO	0	-0.040	-0.031	9.718	0.058	0.058	0.000	0.000	0.000	0.000
35	A	65	LYN	0	-0.010	-0.014	3.677	-1.185	-0.564	0.012	-0.294	-0.339	-0.002
36	A	66	ALA	0	-0.036	-0.018	6.940	-0.174	-0.174	0.000	0.000	0.000	0.000
37	A	67	ASP	-1	-0.950	-0.968	8.833	-0.443	-0.443	0.000	0.000	0.000	0.000
38	A	68	GLU	-1	-0.839	-0.936	9.764	-0.712	-0.712	0.000	0.000	0.000	0.000
39	A	69	ASP	-1	-0.903	-0.952	6.928	-1.067	-1.067	0.000	0.000	0.000	0.000
40	A	70	PRO	0	-0.063	-0.026	9.988	0.058	0.058	0.000	0.000	0.000	0.000
41	A	71	GLY	0	0.036	0.020	9.908	0.090	0.090	0.000	0.000	0.000	0.000
42	A	72	THR	0	-0.088	-0.032	10.882	0.039	0.039	0.000	0.000	0.000	0.000
43	A	73	PRO	0	-0.011	-0.022	10.491	-0.088	-0.088	0.000	0.000	0.000	0.000
44	A	74	LYN	0	-0.009	-0.011	6.365	0.020	0.020	0.000	0.000	0.000	0.000
45	A	75	PRO	0	0.023	0.016	9.693	0.051	0.051	0.000	0.000	0.000	0.000
46	A	76	VAL	0	-0.044	0.000	8.697	-0.144	-0.144	0.000	0.000	0.000	0.000
47	A	77	SER	0	-0.009	-0.026	10.950	0.106	0.106	0.000	0.000	0.000	0.000
48	A	78	PHE	0	0.018	0.010	12.050	-0.045	-0.045	0.000	0.000	0.000	0.000
49	A	79	THR	0	0.048	0.023	13.997	0.047	0.047	0.000	0.000	0.000	0.000
50	A	80	VAL	0	-0.003	-0.005	16.439	-0.010	-0.010	0.000	0.000	0.000	0.000
51	A	81	LYS	1	0.884	0.953	18.921	0.099	0.099	0.000	0.000	0.000	0.000
52	A	82	GLU	-1	-0.767	-0.853	22.182	-0.069	-0.069	0.000	0.000	0.000	0.000
53	A	83	THR	0	-0.009	-0.023	22.982	0.005	0.005	0.000	0.000	0.000	0.000
54	A	84	VAL	0	-0.019	-0.028	25.834	0.001	0.001	0.000	0.000	0.000	0.000
55	A	85	CYS	0	-0.088	-0.009	22.764	0.014	0.014	0.000	0.000	0.000	0.000
56	A	86	PRO	0	0.070	0.032	28.024	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	87	ARG	1	0.896	0.948	26.313	0.065	0.065	0.000	0.000	0.000	0.000
58	A	88	PRO	0	-0.053	-0.020	27.208	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	89	THR	0	-0.010	-0.023	26.634	0.009	0.009	0.000	0.000	0.000	0.000
60	A	90	ARG	1	0.927	0.955	25.665	0.001	0.001	0.000	0.000	0.000	0.000
61	A	91	GLN	0	0.005	0.015	24.497	0.013	0.013	0.000	0.000	0.000	0.000
62	A	92	PRO	0	0.070	0.027	19.353	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	93	PRO	0	0.075	0.026	18.951	0.006	0.006	0.000	0.000	0.000	0.000
64	A	94	GLU	-1	-0.963	-0.981	16.224	-0.025	-0.025	0.000	0.000	0.000	0.000
65	A	95	LEU	0	-0.037	-0.010	19.479	0.007	0.007	0.000	0.000	0.000	0.000
66	A	97	ASP	-1	-0.876	-0.922	23.562	-0.041	-0.041	0.000	0.000	0.000	0.000
67	A	98	PHE	0	0.005	-0.022	19.237	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	99	LYS	1	0.806	0.906	25.251	0.071	0.071	0.000	0.000	0.000	0.000
69	A	100	GLU	-1	-0.874	-0.949	28.118	-0.063	-0.063	0.000	0.000	0.000	0.000
70	A	101	ASN	0	-0.057	-0.033	30.235	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	102	GLY	0	-0.047	-0.008	27.610	0.002	0.002	0.000	0.000	0.000	0.000
72	A	103	ARG	1	0.826	0.879	25.888	0.085	0.085	0.000	0.000	0.000	0.000
73	A	104	VAL	0	0.030	0.002	21.689	-0.003	-0.003	0.000	0.000	0.000	0.000
74	A	105	LYS	1	0.807	0.901	21.538	0.132	0.132	0.000	0.000	0.000	0.000
75	A	106	GLN	0	0.033	0.018	16.615	-0.023	-0.023	0.000	0.000	0.000	0.000
76	A	107	CYS	0	-0.089	-0.042	16.341	0.014	0.014	0.000	0.000	0.000	0.000
77	A	108	VAL	0	0.075	0.029	15.454	-0.040	-0.040	0.000	0.000	0.000	0.000
78	A	109	GLY	0	0.004	-0.006	14.996	0.043	0.043	0.000	0.000	0.000	0.000
79	A	110	THR	0	-0.093	-0.057	12.462	-0.042	-0.042	0.000	0.000	0.000	0.000
80	A	111	VAL	0	0.014	0.015	8.269	0.049	0.049	0.000	0.000	0.000	0.000
81	A	112	THR	0	0.032	0.021	9.981	-0.079	-0.079	0.000	0.000	0.000	0.000
82	A	113	LEU	0	0.012	-0.005	4.158	-0.110	-0.015	-0.001	-0.014	-0.080	0.000
83	A	114	ASP	-1	-0.894	-0.939	7.633	0.258	0.258	0.000	0.000	0.000	0.000
84	A	115	GLN	0	-0.043	-0.031	9.199	-0.102	-0.102	0.000	0.000	0.000	0.000
85	A	116	ILE	0	-0.018	-0.007	12.890	0.038	0.038	0.000	0.000	0.000	0.000
86	A	117	LYS	1	0.869	0.919	15.838	0.061	0.061	0.000	0.000	0.000	0.000
87	A	118	ASP	-1	-0.747	-0.849	14.225	-0.122	-0.122	0.000	0.000	0.000	0.000
88	A	119	PRO	0	-0.018	0.012	16.297	0.028	0.028	0.000	0.000	0.000	0.000
89	A	120	LEU	0	-0.026	-0.029	16.521	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	121	ASP	-1	-0.841	-0.923	16.025	-0.256	-0.256	0.000	0.000	0.000	0.000
91	A	122	ILE	0	0.003	0.017	13.866	-0.032	-0.032	0.000	0.000	0.000	0.000
92	A	123	THR	0	-0.049	-0.010	17.968	0.034	0.034	0.000	0.000	0.000	0.000
93	A	125	ASN	0	-0.012	-0.006	21.301	0.028	0.028	0.000	0.000	0.000	0.000
94	A	126	GLU	-1	-0.816	-0.886	23.396	-0.103	-0.103	0.000	0.000	0.000	0.000
95	A	127	VAL	0	-0.005	0.003	22.483	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	128	GLN	0	-0.029	-0.010	25.560	0.014	0.014	0.000	0.000	0.000	0.000

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