FMO DATABASE

FMODB ID: 8521Y

Calculation Name: 3YGS-P-Xray372

Preferred Name: Apoptotic protease-activating factor 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3YGS

Chain ID: P

ChEMBL ID: CHEMBL1795093

UniProt ID: O14727

Base Structure: X-ray

Registration Date: 2023-06-21

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	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-777140.131268
FMO2-HF: Nuclear repulsion	736893.398378
FMO2-HF: Total energy	-40246.73289
FMO2-MP2: Total energy	-40362.272308

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(P:1:SER)

Summations of interaction energy for fragment #1(P:1:SER)

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.
10.118	-3.294	18.745	-1.037	-4.297	0

Interaction energy analysis for fragmet #1(P:1:SER)

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 : 0.003

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	P	3	ASP	-1	-0.794	-0.905	3.828	-1.708	-0.488	-0.006	-0.493	-0.721	0.002
4	P	4	GLU	-1	-0.822	-0.952	5.584	0.178	0.178	0.000	0.000	0.000	0.000
5	P	5	ALA	0	-0.002	0.016	8.256	0.267	0.267	0.000	0.000	0.000	0.000
6	P	6	ASP	-1	-0.712	-0.849	8.339	-0.764	-0.764	0.000	0.000	0.000	0.000
7	P	7	ARG	1	0.898	0.949	4.358	-0.830	-0.669	-0.001	-0.037	-0.123	0.000
8	P	8	ARG	1	0.895	0.940	9.849	0.593	0.593	0.000	0.000	0.000	0.000
9	P	9	LEU	0	-0.015	0.002	12.862	0.092	0.092	0.000	0.000	0.000	0.000
10	P	10	LEU	0	0.072	0.025	10.319	0.065	0.065	0.000	0.000	0.000	0.000
11	P	11	ARG	1	0.837	0.946	10.984	0.325	0.325	0.000	0.000	0.000	0.000
12	P	12	ARG	1	0.868	0.921	15.921	0.204	0.204	0.000	0.000	0.000	0.000
13	P	13	CYS	0	-0.008	0.020	17.739	0.019	0.019	0.000	0.000	0.000	0.000
14	P	14	ARG	1	0.952	0.992	15.871	0.020	0.020	0.000	0.000	0.000	0.000
15	P	15	LEU	0	-0.004	-0.023	19.476	0.016	0.016	0.000	0.000	0.000	0.000
16	P	16	ARG	1	1.024	1.029	22.122	0.081	0.081	0.000	0.000	0.000	0.000
17	P	17	LEU	0	0.043	0.022	16.584	0.010	0.010	0.000	0.000	0.000	0.000
18	P	18	VAL	0	-0.054	-0.026	20.184	0.015	0.015	0.000	0.000	0.000	0.000
19	P	19	GLU	-1	-0.989	-1.006	22.156	-0.019	-0.019	0.000	0.000	0.000	0.000
20	P	20	GLU	-1	-0.925	-0.966	23.895	-0.033	-0.033	0.000	0.000	0.000	0.000
21	P	21	LEU	0	-0.040	-0.003	18.078	0.006	0.006	0.000	0.000	0.000	0.000
22	P	22	GLN	0	-0.050	-0.014	22.570	0.009	0.009	0.000	0.000	0.000	0.000
23	P	23	VAL	0	0.022	-0.020	20.257	0.002	0.002	0.000	0.000	0.000	0.000
24	P	24	ASP	-1	-0.890	-0.924	22.664	0.078	0.078	0.000	0.000	0.000	0.000
25	P	25	GLN	0	-0.023	-0.022	25.097	0.005	0.005	0.000	0.000	0.000	0.000
26	P	26	LEU	0	0.015	0.014	18.042	0.005	0.005	0.000	0.000	0.000	0.000
27	P	27	TRP	0	0.006	0.002	18.910	0.028	0.028	0.000	0.000	0.000	0.000
28	P	28	ASP	-1	-0.829	-0.929	19.687	0.163	0.163	0.000	0.000	0.000	0.000
29	P	29	VAL	0	-0.022	0.008	18.451	0.018	0.018	0.000	0.000	0.000	0.000
30	P	30	LEU	0	-0.041	-0.035	14.710	0.026	0.026	0.000	0.000	0.000	0.000
31	P	31	LEU	0	-0.024	-0.009	15.312	0.059	0.059	0.000	0.000	0.000	0.000
32	P	32	SER	0	-0.024	-0.005	17.250	0.022	0.022	0.000	0.000	0.000	0.000
33	P	33	ARG	1	0.844	0.925	14.491	-0.139	-0.139	0.000	0.000	0.000	0.000
34	P	34	GLU	-1	-0.975	-0.979	12.964	0.546	0.546	0.000	0.000	0.000	0.000
35	P	35	LEU	0	-0.038	0.006	9.548	0.116	0.116	0.000	0.000	0.000	0.000
36	P	36	PHE	0	-0.033	-0.026	10.215	0.146	0.146	0.000	0.000	0.000	0.000
37	P	37	ARG	1	0.985	0.984	9.017	-0.926	-0.926	0.000	0.000	0.000	0.000
38	P	38	PRO	0	0.097	0.026	14.419	-0.021	-0.021	0.000	0.000	0.000	0.000
39	P	39	HIS	1	0.867	0.945	17.170	-0.260	-0.260	0.000	0.000	0.000	0.000
40	P	40	MET	0	0.024	0.025	10.534	0.010	0.010	0.000	0.000	0.000	0.000
41	P	41	ILE	0	0.017	0.009	15.639	-0.027	-0.027	0.000	0.000	0.000	0.000
42	P	42	GLU	-1	-0.797	-0.896	17.650	0.168	0.168	0.000	0.000	0.000	0.000
43	P	43	ASP	-1	-0.914	-0.964	17.189	0.215	0.215	0.000	0.000	0.000	0.000
44	P	44	ILE	0	-0.050	-0.024	14.381	-0.025	-0.025	0.000	0.000	0.000	0.000
45	P	45	GLN	0	-0.040	-0.023	18.719	-0.025	-0.025	0.000	0.000	0.000	0.000
46	P	46	ARG	1	0.846	0.928	21.934	-0.173	-0.173	0.000	0.000	0.000	0.000
47	P	47	ALA	0	0.011	0.023	20.139	-0.007	-0.007	0.000	0.000	0.000	0.000
48	P	48	GLY	0	-0.025	-0.007	22.194	-0.011	-0.011	0.000	0.000	0.000	0.000
49	P	49	SER	0	-0.064	-0.048	25.015	0.000	0.000	0.000	0.000	0.000	0.000
50	P	50	GLY	0	0.039	0.021	25.311	-0.002	-0.002	0.000	0.000	0.000	0.000
51	P	51	SER	0	-0.035	-0.003	26.363	-0.002	-0.002	0.000	0.000	0.000	0.000
52	P	52	ARG	1	0.964	0.968	24.300	-0.021	-0.021	0.000	0.000	0.000	0.000
53	P	53	ARG	1	0.916	0.960	23.601	-0.001	-0.001	0.000	0.000	0.000	0.000
54	P	54	ASP	-1	-0.774	-0.877	22.458	0.050	0.050	0.000	0.000	0.000	0.000
55	P	55	GLN	0	-0.001	0.004	20.931	0.006	0.006	0.000	0.000	0.000	0.000
56	P	56	ALA	0	0.016	0.005	19.123	0.015	0.015	0.000	0.000	0.000	0.000
57	P	57	ARG	1	0.845	0.903	18.057	-0.042	-0.042	0.000	0.000	0.000	0.000
58	P	58	GLN	0	-0.027	-0.010	15.142	-0.031	-0.031	0.000	0.000	0.000	0.000
59	P	59	LEU	0	0.029	0.026	14.135	0.029	0.029	0.000	0.000	0.000	0.000
60	P	60	ILE	0	-0.015	-0.032	13.189	0.025	0.025	0.000	0.000	0.000	0.000
61	P	61	ILE	0	-0.069	-0.022	12.343	-0.026	-0.026	0.000	0.000	0.000	0.000
62	P	62	ASP	-1	-0.803	-0.907	10.776	0.339	0.339	0.000	0.000	0.000	0.000
63	P	63	LEU	0	-0.016	0.006	8.883	0.158	0.158	0.000	0.000	0.000	0.000
64	P	64	GLU	-1	-0.920	-0.978	7.244	0.098	0.098	0.000	0.000	0.000	0.000
65	P	65	THR	0	-0.141	-0.092	5.045	0.413	0.413	0.000	0.000	0.000	0.000
66	P	66	ARG	1	0.829	0.905	4.930	-0.744	-0.630	-0.001	-0.007	-0.107	0.000
67	P	67	GLY	0	0.020	-0.008	1.835	4.236	-2.985	18.180	-8.868	-2.091	0.009
68	P	68	SER	0	0.027	0.001	2.344	6.426	-1.495	0.570	8.452	-1.101	-0.011
69	P	69	GLN	0	0.011	0.005	4.073	-0.181	0.054	0.003	-0.084	-0.154	0.000
70	P	70	ALA	0	0.043	0.032	5.952	0.127	0.127	0.000	0.000	0.000	0.000
71	P	71	LEU	0	0.027	0.007	7.725	0.066	0.066	0.000	0.000	0.000	0.000
72	P	72	PRO	0	0.002	0.003	9.111	0.072	0.072	0.000	0.000	0.000	0.000
73	P	73	LEU	0	0.023	0.029	9.968	0.032	0.032	0.000	0.000	0.000	0.000
74	P	74	PHE	0	0.015	-0.005	11.769	0.018	0.018	0.000	0.000	0.000	0.000
75	P	75	ILE	0	-0.046	-0.028	13.606	0.001	0.001	0.000	0.000	0.000	0.000
76	P	76	SER	0	-0.009	0.003	15.277	0.010	0.010	0.000	0.000	0.000	0.000
77	P	77	CYS	0	-0.057	-0.005	15.205	0.021	0.021	0.000	0.000	0.000	0.000
78	P	78	LEU	0	-0.009	-0.002	17.607	-0.005	-0.005	0.000	0.000	0.000	0.000
79	P	79	GLU	-1	-0.789	-0.897	19.785	-0.029	-0.029	0.000	0.000	0.000	0.000
80	P	80	ASP	-1	-0.829	-0.916	20.197	0.098	0.098	0.000	0.000	0.000	0.000
81	P	81	THR	0	-0.028	-0.015	21.707	0.008	0.008	0.000	0.000	0.000	0.000
82	P	82	GLY	0	0.008	0.002	24.070	-0.002	-0.002	0.000	0.000	0.000	0.000
83	P	83	GLN	0	-0.024	-0.012	22.434	-0.016	-0.016	0.000	0.000	0.000	0.000
84	P	84	ASP	-1	-0.855	-0.941	23.122	-0.012	-0.012	0.000	0.000	0.000	0.000
85	P	85	MET	0	-0.025	-0.016	24.386	-0.012	-0.012	0.000	0.000	0.000	0.000
86	P	86	LEU	0	0.034	0.011	19.854	-0.016	-0.016	0.000	0.000	0.000	0.000
87	P	87	ALA	0	0.046	0.020	19.557	-0.019	-0.019	0.000	0.000	0.000	0.000
88	P	88	SER	0	0.000	0.004	19.982	-0.028	-0.028	0.000	0.000	0.000	0.000
89	P	89	PHE	0	-0.004	-0.009	20.898	-0.022	-0.022	0.000	0.000	0.000	0.000
90	P	90	LEU	0	0.000	-0.005	16.210	-0.027	-0.027	0.000	0.000	0.000	0.000
91	P	91	ARG	1	0.867	0.923	17.468	0.034	0.034	0.000	0.000	0.000	0.000
92	P	92	THR	0	-0.033	-0.024	18.667	-0.023	-0.023	0.000	0.000	0.000	0.000
93	P	93	ASN	0	-0.073	-0.044	18.058	-0.022	-0.022	0.000	0.000	0.000	0.000
94	P	94	ARG	1	0.807	0.888	10.030	0.606	0.606	0.000	0.000	0.000	0.000
95	P	95	GLN	0	-0.017	-0.020	16.177	-0.022	-0.022	0.000	0.000	0.000	0.000
96	P	96	ALA	0	-0.044	0.028	18.824	0.015	0.015	0.000	0.000	0.000	0.000
97	P	97	GLY	0	-0.037	-0.030	17.929	-0.019	-0.019	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(P:1:SER)