FMO DATABASE

FMODB ID: JL389

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

Total energy (hartree)

FMO2-HF: Electronic energy	-776000.139382
FMO2-HF: Nuclear repulsion	735752.413788
FMO2-HF: Total energy	-40247.725595
FMO2-MP2: Total energy	-40363.120818

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.
-2.483	-0.472	2.735	-1.827	-2.919	0.005

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 : 0.037 / q_NPA : -0.004

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	-0.789	-0.889	3.238	-2.376	-0.786	0.043	-0.766	-0.867	-0.002
4	P	4	GLU	-1	-0.723	-0.864	5.596	0.328	0.328	0.000	0.000	0.000	0.000
5	P	5	ALA	0	-0.019	0.009	7.974	0.209	0.209	0.000	0.000	0.000	0.000
6	P	6	ASP	-1	-0.717	-0.849	8.607	-0.588	-0.588	0.000	0.000	0.000	0.000
7	P	7	ARG	1	0.779	0.882	3.082	-4.295	-3.248	0.119	-0.551	-0.615	0.005
8	P	8	ARG	1	0.818	0.893	9.286	0.356	0.356	0.000	0.000	0.000	0.000
9	P	9	LEU	0	0.013	0.019	12.406	0.060	0.060	0.000	0.000	0.000	0.000
10	P	10	LEU	0	0.067	0.019	10.343	0.045	0.045	0.000	0.000	0.000	0.000
11	P	11	ARG	1	0.763	0.862	9.609	0.092	0.092	0.000	0.000	0.000	0.000
12	P	12	ARG	1	0.904	0.945	15.017	0.122	0.122	0.000	0.000	0.000	0.000
13	P	13	CYS	0	-0.028	-0.001	17.193	0.009	0.009	0.000	0.000	0.000	0.000
14	P	14	ARG	1	0.889	0.965	14.852	-0.018	-0.018	0.000	0.000	0.000	0.000
15	P	15	LEU	0	0.024	0.005	19.424	0.008	0.008	0.000	0.000	0.000	0.000
16	P	16	ARG	1	0.913	0.940	22.358	0.081	0.081	0.000	0.000	0.000	0.000
17	P	17	LEU	0	0.005	0.008	16.532	0.002	0.002	0.000	0.000	0.000	0.000
18	P	18	VAL	0	-0.026	-0.017	20.418	0.007	0.007	0.000	0.000	0.000	0.000
19	P	19	GLU	-1	-0.835	-0.894	22.408	-0.020	-0.020	0.000	0.000	0.000	0.000
20	P	20	GLU	-1	-0.802	-0.895	23.964	-0.059	-0.059	0.000	0.000	0.000	0.000
21	P	21	LEU	0	-0.036	0.005	18.086	0.001	0.001	0.000	0.000	0.000	0.000
22	P	22	GLN	0	-0.037	-0.021	22.704	0.012	0.012	0.000	0.000	0.000	0.000
23	P	23	VAL	0	0.024	-0.003	20.449	-0.003	-0.003	0.000	0.000	0.000	0.000
24	P	24	ASP	-1	-0.903	-0.951	22.580	0.011	0.011	0.000	0.000	0.000	0.000
25	P	25	GLN	0	0.017	0.005	25.038	0.004	0.004	0.000	0.000	0.000	0.000
26	P	26	LEU	0	-0.011	0.004	18.613	-0.001	-0.001	0.000	0.000	0.000	0.000
27	P	27	TRP	0	-0.007	0.000	18.953	0.006	0.006	0.000	0.000	0.000	0.000
28	P	28	ASP	-1	-0.845	-0.927	19.970	0.034	0.034	0.000	0.000	0.000	0.000
29	P	29	VAL	0	-0.017	0.004	18.595	0.005	0.005	0.000	0.000	0.000	0.000
30	P	30	LEU	0	-0.033	-0.041	14.828	-0.002	-0.002	0.000	0.000	0.000	0.000
31	P	31	LEU	0	-0.038	-0.006	15.298	0.013	0.013	0.000	0.000	0.000	0.000
32	P	32	SER	0	-0.024	-0.014	17.333	0.009	0.009	0.000	0.000	0.000	0.000
33	P	33	ARG	1	0.826	0.896	15.270	0.052	0.052	0.000	0.000	0.000	0.000
34	P	34	GLU	-1	-0.963	-0.977	13.070	0.134	0.134	0.000	0.000	0.000	0.000
35	P	35	LEU	0	-0.027	0.016	9.649	0.023	0.023	0.000	0.000	0.000	0.000
36	P	36	PHE	0	-0.007	-0.017	10.416	0.038	0.038	0.000	0.000	0.000	0.000
37	P	37	ARG	1	1.014	1.009	9.952	-0.349	-0.349	0.000	0.000	0.000	0.000
38	P	38	PRO	0	0.076	0.018	14.518	0.000	0.000	0.000	0.000	0.000	0.000
39	P	39	HIS	1	0.795	0.870	17.255	-0.124	-0.124	0.000	0.000	0.000	0.000
40	P	40	MET	0	-0.023	-0.007	10.373	-0.001	-0.001	0.000	0.000	0.000	0.000
41	P	41	ILE	0	0.025	0.024	15.670	-0.006	-0.006	0.000	0.000	0.000	0.000
42	P	42	GLU	-1	-0.737	-0.835	17.903	0.082	0.082	0.000	0.000	0.000	0.000
43	P	43	ASP	-1	-0.832	-0.890	17.682	0.109	0.109	0.000	0.000	0.000	0.000
44	P	44	ILE	0	-0.048	-0.019	14.104	-0.010	-0.010	0.000	0.000	0.000	0.000
45	P	45	GLN	0	-0.027	-0.022	18.681	-0.007	-0.007	0.000	0.000	0.000	0.000
46	P	46	ARG	1	0.786	0.868	21.779	-0.086	-0.086	0.000	0.000	0.000	0.000
47	P	47	ALA	0	0.013	0.028	20.275	0.000	0.000	0.000	0.000	0.000	0.000
48	P	48	GLY	0	-0.035	-0.020	22.296	-0.008	-0.008	0.000	0.000	0.000	0.000
49	P	49	SER	0	-0.049	-0.046	25.148	-0.001	-0.001	0.000	0.000	0.000	0.000
50	P	50	GLY	0	0.046	0.024	25.737	-0.002	-0.002	0.000	0.000	0.000	0.000
51	P	51	SER	0	-0.054	-0.035	26.753	-0.004	-0.004	0.000	0.000	0.000	0.000
52	P	52	ARG	1	0.914	0.930	25.260	0.012	0.012	0.000	0.000	0.000	0.000
53	P	53	ARG	1	0.828	0.899	23.888	0.008	0.008	0.000	0.000	0.000	0.000
54	P	54	ASP	-1	-0.774	-0.843	22.958	0.031	0.031	0.000	0.000	0.000	0.000
55	P	55	GLN	0	-0.001	-0.005	21.100	0.004	0.004	0.000	0.000	0.000	0.000
56	P	56	ALA	0	0.013	0.010	19.324	0.008	0.008	0.000	0.000	0.000	0.000
57	P	57	ARG	1	0.813	0.878	18.219	-0.033	-0.033	0.000	0.000	0.000	0.000
58	P	58	GLN	0	-0.041	-0.031	15.269	-0.008	-0.008	0.000	0.000	0.000	0.000
59	P	59	LEU	0	0.027	0.028	14.074	0.028	0.028	0.000	0.000	0.000	0.000
60	P	60	ILE	0	-0.009	-0.023	13.293	0.018	0.018	0.000	0.000	0.000	0.000
61	P	61	ILE	0	-0.083	-0.026	13.022	0.004	0.004	0.000	0.000	0.000	0.000
62	P	62	ASP	-1	-0.769	-0.883	11.095	0.297	0.297	0.000	0.000	0.000	0.000
63	P	63	LEU	0	-0.012	0.011	9.131	0.119	0.119	0.000	0.000	0.000	0.000
64	P	64	GLU	-1	-0.764	-0.881	7.388	0.443	0.443	0.000	0.000	0.000	0.000
65	P	65	THR	0	-0.130	-0.084	5.397	1.241	1.241	0.000	0.000	0.000	0.000
66	P	66	ARG	1	0.809	0.897	5.019	-0.588	-0.477	-0.001	-0.005	-0.105	0.000
67	P	67	GLY	0	0.016	0.011	2.157	-0.395	-0.482	2.557	-1.562	-0.909	0.003
68	P	68	SER	0	0.011	-0.018	3.159	1.080	0.346	0.018	1.061	-0.345	-0.001
69	P	69	GLN	0	0.015	0.020	5.178	0.261	0.345	-0.001	-0.004	-0.078	0.000
70	P	70	ALA	0	0.023	0.019	6.723	0.230	0.230	0.000	0.000	0.000	0.000
71	P	71	LEU	0	0.049	0.029	8.455	0.141	0.141	0.000	0.000	0.000	0.000
72	P	72	PRO	0	0.000	-0.003	10.004	0.079	0.079	0.000	0.000	0.000	0.000
73	P	73	LEU	0	0.010	0.025	11.009	0.061	0.061	0.000	0.000	0.000	0.000
74	P	74	PHE	0	0.046	0.013	12.474	0.052	0.052	0.000	0.000	0.000	0.000
75	P	75	ILE	0	-0.033	-0.017	14.179	0.025	0.025	0.000	0.000	0.000	0.000
76	P	76	SER	0	-0.021	-0.021	16.012	0.025	0.025	0.000	0.000	0.000	0.000
77	P	77	CYS	0	-0.076	-0.024	15.615	0.024	0.024	0.000	0.000	0.000	0.000
78	P	78	LEU	0	-0.024	-0.011	17.587	0.014	0.014	0.000	0.000	0.000	0.000
79	P	79	GLU	-1	-0.794	-0.866	20.291	-0.121	-0.121	0.000	0.000	0.000	0.000
80	P	80	ASP	-1	-0.791	-0.879	21.051	-0.036	-0.036	0.000	0.000	0.000	0.000
81	P	81	THR	0	-0.031	-0.016	21.892	0.012	0.012	0.000	0.000	0.000	0.000
82	P	82	GLY	0	0.018	0.021	24.330	0.004	0.004	0.000	0.000	0.000	0.000
83	P	83	GLN	0	-0.030	-0.025	22.472	0.000	0.000	0.000	0.000	0.000	0.000
84	P	84	ASP	-1	-0.852	-0.931	23.666	-0.069	-0.069	0.000	0.000	0.000	0.000
85	P	85	MET	0	-0.018	-0.015	24.688	-0.010	-0.010	0.000	0.000	0.000	0.000
86	P	86	LEU	0	0.026	0.021	19.971	-0.011	-0.011	0.000	0.000	0.000	0.000
87	P	87	ALA	0	0.039	0.017	19.898	-0.016	-0.016	0.000	0.000	0.000	0.000
88	P	88	SER	0	0.050	0.022	20.451	-0.023	-0.023	0.000	0.000	0.000	0.000
89	P	89	PHE	0	-0.003	0.008	21.150	-0.013	-0.013	0.000	0.000	0.000	0.000
90	P	90	LEU	0	0.004	0.001	16.358	-0.016	-0.016	0.000	0.000	0.000	0.000
91	P	91	ARG	1	0.818	0.872	17.811	0.127	0.127	0.000	0.000	0.000	0.000
92	P	92	THR	0	-0.036	-0.033	19.390	-0.016	-0.016	0.000	0.000	0.000	0.000
93	P	93	ASN	0	-0.087	-0.058	17.637	-0.008	-0.008	0.000	0.000	0.000	0.000
94	P	94	ARG	1	0.825	0.876	10.191	0.659	0.659	0.000	0.000	0.000	0.000
95	P	95	GLN	0	-0.026	-0.013	16.316	-0.031	-0.031	0.000	0.000	0.000	0.000
96	P	96	ALA	0	-0.026	0.018	19.329	0.019	0.019	0.000	0.000	0.000	0.000
97	P	97	GLY	0	-0.044	-0.020	18.528	-0.007	-0.007	0.000	0.000	0.000	0.000

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