FMO DATABASE

FMODB ID: J37K9

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	OptAll
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	-706449.059737
FMO2-HF: Nuclear repulsion	667319.378796
FMO2-HF: Total energy	-39129.68094
FMO2-MP2: Total energy	-39242.357406

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.
-5.1	-0.76	0.683	-1.837	-3.189	0.001

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 : 0.060 / 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	0.046	-0.010	3.696	-2.469	-0.840	0.007	-0.744	-0.892	0.002
4	A	34	TYR	0	-0.042	-0.027	2.705	-1.589	-0.265	0.433	-0.560	-1.198	-0.003
5	A	35	ARG	1	0.962	0.983	4.206	1.068	1.442	0.000	-0.071	-0.303	0.000
6	A	36	GLU	-1	-0.858	-0.921	6.548	0.996	0.996	0.000	0.000	0.000	0.000
7	A	37	ALA	0	0.021	0.013	7.176	0.109	0.109	0.000	0.000	0.000	0.000
8	A	38	VAL	0	0.020	0.013	8.442	0.095	0.095	0.000	0.000	0.000	0.000
9	A	39	LEU	0	-0.016	-0.008	10.440	0.095	0.095	0.000	0.000	0.000	0.000
10	A	40	ARG	1	0.820	0.899	9.537	0.161	0.161	0.000	0.000	0.000	0.000
11	A	41	ALA	0	0.012	0.003	12.727	0.041	0.041	0.000	0.000	0.000	0.000
12	A	42	VAL	0	-0.019	-0.006	14.482	0.034	0.034	0.000	0.000	0.000	0.000
13	A	43	ASP	-1	-0.851	-0.937	16.429	-0.073	-0.073	0.000	0.000	0.000	0.000
14	A	44	ARG	1	0.795	0.889	16.082	0.131	0.131	0.000	0.000	0.000	0.000
15	A	45	LEU	0	0.001	-0.002	17.417	0.014	0.014	0.000	0.000	0.000	0.000
16	A	46	ASN	0	-0.022	-0.015	20.368	0.016	0.016	0.000	0.000	0.000	0.000
17	A	47	GLU	-1	-0.937	-0.960	22.017	-0.037	-0.037	0.000	0.000	0.000	0.000
18	A	48	GLN	0	-0.052	-0.025	22.384	0.001	0.001	0.000	0.000	0.000	0.000
19	A	49	SER	0	0.004	0.025	24.696	0.005	0.005	0.000	0.000	0.000	0.000
20	A	50	SER	0	-0.043	-0.042	26.380	0.010	0.010	0.000	0.000	0.000	0.000
21	A	51	GLU	-1	-0.800	-0.859	26.692	-0.096	-0.096	0.000	0.000	0.000	0.000
22	A	52	ALA	0	0.002	-0.011	30.017	0.002	0.002	0.000	0.000	0.000	0.000
23	A	53	ASN	0	-0.056	-0.026	28.257	0.010	0.010	0.000	0.000	0.000	0.000
24	A	54	LEU	0	0.004	0.014	23.747	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	55	TYR	0	-0.056	-0.046	21.317	0.001	0.001	0.000	0.000	0.000	0.000
26	A	56	ARG	1	0.866	0.937	18.995	0.097	0.097	0.000	0.000	0.000	0.000
27	A	57	LEU	0	0.010	0.001	11.780	0.000	0.000	0.000	0.000	0.000	0.000
28	A	58	LEU	0	-0.089	-0.037	16.346	0.032	0.032	0.000	0.000	0.000	0.000
29	A	59	GLU	-1	-0.931	-0.962	14.596	-0.229	-0.229	0.000	0.000	0.000	0.000
30	A	60	LEU	0	-0.038	-0.029	7.217	-0.028	-0.028	0.000	0.000	0.000	0.000
31	A	61	ASP	-1	-0.792	-0.855	11.045	-0.360	-0.360	0.000	0.000	0.000	0.000
32	A	62	GLN	0	-0.047	-0.024	9.197	-0.095	-0.095	0.000	0.000	0.000	0.000
33	A	63	PRO	0	-0.020	0.005	6.072	0.082	0.082	0.000	0.000	0.000	0.000
34	A	64	PRO	0	-0.054	-0.035	9.376	0.046	0.046	0.000	0.000	0.000	0.000
35	A	65	LYN	0	-0.007	-0.015	2.577	-1.006	-0.132	0.243	-0.431	-0.688	0.002
36	A	66	ALA	0	-0.030	-0.011	6.557	-0.200	-0.200	0.000	0.000	0.000	0.000
37	A	67	ASP	-1	-0.939	-0.963	8.505	-0.371	-0.371	0.000	0.000	0.000	0.000
38	A	68	GLU	-1	-0.832	-0.938	9.509	-0.663	-0.663	0.000	0.000	0.000	0.000
39	A	69	ASP	-1	-0.895	-0.941	6.521	-0.947	-0.947	0.000	0.000	0.000	0.000
40	A	70	PRO	0	-0.078	-0.040	9.401	0.054	0.054	0.000	0.000	0.000	0.000
41	A	71	GLY	0	0.025	0.009	9.167	0.088	0.088	0.000	0.000	0.000	0.000
42	A	72	THR	0	-0.060	-0.020	10.214	0.064	0.064	0.000	0.000	0.000	0.000
43	A	73	PRO	0	-0.038	-0.041	10.266	-0.075	-0.075	0.000	0.000	0.000	0.000
44	A	74	LYN	0	0.018	0.023	6.296	0.077	0.077	0.000	0.000	0.000	0.000
45	A	75	PRO	0	-0.003	-0.004	9.492	0.031	0.031	0.000	0.000	0.000	0.000
46	A	76	VAL	0	-0.021	0.005	8.902	-0.157	-0.157	0.000	0.000	0.000	0.000
47	A	77	SER	0	-0.011	-0.034	11.120	0.108	0.108	0.000	0.000	0.000	0.000
48	A	78	PHE	0	0.020	0.015	12.135	-0.055	-0.055	0.000	0.000	0.000	0.000
49	A	79	THR	0	0.032	0.016	14.067	0.048	0.048	0.000	0.000	0.000	0.000
50	A	80	VAL	0	0.016	0.001	16.628	-0.011	-0.011	0.000	0.000	0.000	0.000
51	A	81	LYS	1	0.852	0.928	19.158	0.104	0.104	0.000	0.000	0.000	0.000
52	A	82	GLU	-1	-0.745	-0.842	22.593	-0.074	-0.074	0.000	0.000	0.000	0.000
53	A	83	THR	0	-0.019	-0.024	23.365	0.004	0.004	0.000	0.000	0.000	0.000
54	A	84	VAL	0	-0.023	-0.025	26.247	0.003	0.003	0.000	0.000	0.000	0.000
55	A	85	CYS	0	-0.083	-0.006	23.011	0.017	0.017	0.000	0.000	0.000	0.000
56	A	86	PRO	0	0.082	0.044	28.445	-0.006	-0.006	0.000	0.000	0.000	0.000
57	A	87	ARG	1	0.873	0.935	26.437	0.066	0.066	0.000	0.000	0.000	0.000
58	A	88	PRO	0	-0.052	-0.014	27.658	0.000	0.000	0.000	0.000	0.000	0.000
59	A	89	THR	0	-0.028	-0.032	26.933	0.009	0.009	0.000	0.000	0.000	0.000
60	A	90	ARG	1	0.946	0.953	25.565	0.008	0.008	0.000	0.000	0.000	0.000
61	A	91	GLN	0	0.012	0.015	24.755	0.010	0.010	0.000	0.000	0.000	0.000
62	A	92	PRO	0	0.070	0.031	19.624	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	93	PRO	0	0.057	0.025	19.521	0.003	0.003	0.000	0.000	0.000	0.000
64	A	94	GLU	-1	-0.947	-0.971	16.859	-0.052	-0.052	0.000	0.000	0.000	0.000
65	A	95	LEU	0	-0.046	-0.021	19.611	0.005	0.005	0.000	0.000	0.000	0.000
66	A	97	ASP	-1	-0.870	-0.924	23.906	-0.055	-0.055	0.000	0.000	0.000	0.000
67	A	98	PHE	0	0.015	-0.011	19.561	0.000	0.000	0.000	0.000	0.000	0.000
68	A	99	LYS	1	0.808	0.911	25.433	0.074	0.074	0.000	0.000	0.000	0.000
69	A	100	GLU	-1	-0.831	-0.916	28.370	-0.075	-0.075	0.000	0.000	0.000	0.000
70	A	101	ASN	0	-0.100	-0.068	30.677	0.001	0.001	0.000	0.000	0.000	0.000
71	A	102	GLY	0	-0.047	-0.016	28.305	0.001	0.001	0.000	0.000	0.000	0.000
72	A	103	ARG	1	0.804	0.861	26.109	0.086	0.086	0.000	0.000	0.000	0.000
73	A	104	VAL	0	0.035	0.006	22.181	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	105	LYS	1	0.811	0.900	21.794	0.136	0.136	0.000	0.000	0.000	0.000
75	A	106	GLN	0	0.022	0.002	16.415	-0.022	-0.022	0.000	0.000	0.000	0.000
76	A	107	CYS	0	-0.112	-0.041	16.581	0.019	0.019	0.000	0.000	0.000	0.000
77	A	108	VAL	0	0.071	0.032	15.548	-0.039	-0.039	0.000	0.000	0.000	0.000
78	A	109	GLY	0	0.009	-0.006	14.979	0.045	0.045	0.000	0.000	0.000	0.000
79	A	110	THR	0	-0.075	-0.045	12.447	-0.041	-0.041	0.000	0.000	0.000	0.000
80	A	111	VAL	0	0.019	0.010	8.255	0.040	0.040	0.000	0.000	0.000	0.000
81	A	112	THR	0	-0.007	-0.007	9.807	-0.075	-0.075	0.000	0.000	0.000	0.000
82	A	113	LEU	0	0.038	0.014	3.841	-0.177	-0.038	0.000	-0.031	-0.108	0.000
83	A	114	ASP	-1	-0.914	-0.948	7.243	0.294	0.294	0.000	0.000	0.000	0.000
84	A	115	GLN	0	-0.013	0.007	9.082	-0.152	-0.152	0.000	0.000	0.000	0.000
85	A	116	ILE	0	-0.016	-0.013	12.970	0.033	0.033	0.000	0.000	0.000	0.000
86	A	117	LYS	1	0.863	0.919	15.928	0.041	0.041	0.000	0.000	0.000	0.000
87	A	118	ASP	-1	-0.719	-0.841	14.166	-0.091	-0.091	0.000	0.000	0.000	0.000
88	A	119	PRO	0	-0.034	0.003	16.267	0.023	0.023	0.000	0.000	0.000	0.000
89	A	120	LEU	0	-0.005	-0.023	16.239	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	121	ASP	-1	-0.856	-0.900	15.477	-0.236	-0.236	0.000	0.000	0.000	0.000
91	A	122	ILE	0	0.007	0.009	13.999	-0.028	-0.028	0.000	0.000	0.000	0.000
92	A	123	THR	0	-0.051	-0.015	17.936	0.031	0.031	0.000	0.000	0.000	0.000
93	A	125	ASN	0	-0.008	-0.014	21.481	0.029	0.029	0.000	0.000	0.000	0.000
94	A	126	GLU	-1	-0.810	-0.875	23.471	-0.104	-0.104	0.000	0.000	0.000	0.000
95	A	127	VAL	0	-0.020	-0.004	22.376	0.001	0.001	0.000	0.000	0.000	0.000
96	A	128	GLN	0	-0.035	-0.012	25.530	0.013	0.013	0.000	0.000	0.000	0.000

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