FMO DATABASE

FMODB ID: N91RQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-776610.978745
FMO2-HF: Nuclear repulsion	736363.488052
FMO2-HF: Total energy	-40247.490694
FMO2-MP2: Total energy	-40362.971056

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.
4.448	-1.326	11.361	-2	-3.587	0.004

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 : -0.002 / q_NPA : -0.012

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	-0.811	-0.906	3.828	-1.750	-0.490	-0.007	-0.513	-0.739	0.002
4	P	4	GLU	-1	-0.704	-0.854	5.572	0.236	0.236	0.000	0.000	0.000	0.000
5	P	5	ALA	0	-0.007	0.015	8.241	0.276	0.276	0.000	0.000	0.000	0.000
6	P	6	ASP	-1	-0.711	-0.838	8.354	-0.738	-0.738	0.000	0.000	0.000	0.000
7	P	7	ARG	1	0.817	0.904	4.267	-1.120	-0.941	0.000	-0.050	-0.128	0.000
8	P	8	ARG	1	0.792	0.872	9.829	0.556	0.556	0.000	0.000	0.000	0.000
9	P	9	LEU	0	-0.007	0.007	12.845	0.092	0.092	0.000	0.000	0.000	0.000
10	P	10	LEU	0	0.073	0.025	10.488	0.068	0.068	0.000	0.000	0.000	0.000
11	P	11	ARG	1	0.782	0.897	10.459	0.312	0.312	0.000	0.000	0.000	0.000
12	P	12	ARG	1	0.896	0.937	15.900	0.204	0.204	0.000	0.000	0.000	0.000
13	P	13	CYS	0	-0.012	0.013	17.816	0.020	0.020	0.000	0.000	0.000	0.000
14	P	14	ARG	1	0.953	0.984	15.866	0.036	0.036	0.000	0.000	0.000	0.000
15	P	15	LEU	0	0.006	-0.012	19.678	0.014	0.014	0.000	0.000	0.000	0.000
16	P	16	ARG	1	0.920	0.964	22.321	0.099	0.099	0.000	0.000	0.000	0.000
17	P	17	LEU	0	0.031	0.015	16.729	0.008	0.008	0.000	0.000	0.000	0.000
18	P	18	VAL	0	-0.053	-0.026	20.320	0.014	0.014	0.000	0.000	0.000	0.000
19	P	19	GLU	-1	-0.836	-0.907	22.342	-0.025	-0.025	0.000	0.000	0.000	0.000
20	P	20	GLU	-1	-0.840	-0.912	23.933	-0.059	-0.059	0.000	0.000	0.000	0.000
21	P	21	LEU	0	-0.047	-0.007	18.039	0.004	0.004	0.000	0.000	0.000	0.000
22	P	22	GLN	0	-0.040	-0.016	22.721	0.013	0.013	0.000	0.000	0.000	0.000
23	P	23	VAL	0	0.023	-0.018	20.406	-0.001	-0.001	0.000	0.000	0.000	0.000
24	P	24	ASP	-1	-0.902	-0.930	22.786	0.051	0.051	0.000	0.000	0.000	0.000
25	P	25	GLN	0	0.002	-0.009	25.178	0.006	0.006	0.000	0.000	0.000	0.000
26	P	26	LEU	0	0.016	0.013	18.489	0.001	0.001	0.000	0.000	0.000	0.000
27	P	27	TRP	0	-0.006	0.000	18.978	0.019	0.019	0.000	0.000	0.000	0.000
28	P	28	ASP	-1	-0.830	-0.928	19.735	0.117	0.117	0.000	0.000	0.000	0.000
29	P	29	VAL	0	-0.016	0.006	19.111	0.014	0.014	0.000	0.000	0.000	0.000
30	P	30	LEU	0	-0.040	-0.035	14.817	0.015	0.015	0.000	0.000	0.000	0.000
31	P	31	LEU	0	-0.026	-0.008	15.377	0.045	0.045	0.000	0.000	0.000	0.000
32	P	32	SER	0	-0.014	-0.002	17.335	0.018	0.018	0.000	0.000	0.000	0.000
33	P	33	ARG	1	0.786	0.877	14.766	-0.047	-0.047	0.000	0.000	0.000	0.000
34	P	34	GLU	-1	-0.968	-0.975	13.138	0.403	0.403	0.000	0.000	0.000	0.000
35	P	35	LEU	0	-0.030	0.014	9.539	0.077	0.077	0.000	0.000	0.000	0.000
36	P	36	PHE	0	-0.017	-0.017	10.245	0.120	0.120	0.000	0.000	0.000	0.000
37	P	37	ARG	1	1.003	0.999	9.719	-0.785	-0.785	0.000	0.000	0.000	0.000
38	P	38	PRO	0	0.089	0.020	14.427	-0.015	-0.015	0.000	0.000	0.000	0.000
39	P	39	HIS	1	0.810	0.897	17.043	-0.242	-0.242	0.000	0.000	0.000	0.000
40	P	40	MET	0	0.000	0.010	10.516	0.010	0.010	0.000	0.000	0.000	0.000
41	P	41	ILE	0	0.034	0.019	15.743	-0.024	-0.024	0.000	0.000	0.000	0.000
42	P	42	GLU	-1	-0.779	-0.868	17.729	0.150	0.150	0.000	0.000	0.000	0.000
43	P	43	ASP	-1	-0.830	-0.900	17.394	0.196	0.196	0.000	0.000	0.000	0.000
44	P	44	ILE	0	-0.057	-0.023	14.359	-0.022	-0.022	0.000	0.000	0.000	0.000
45	P	45	GLN	0	-0.019	-0.011	18.850	-0.016	-0.016	0.000	0.000	0.000	0.000
46	P	46	ARG	1	0.788	0.874	21.515	-0.161	-0.161	0.000	0.000	0.000	0.000
47	P	47	ALA	0	0.005	0.023	20.283	-0.004	-0.004	0.000	0.000	0.000	0.000
48	P	48	GLY	0	-0.023	-0.011	22.348	-0.012	-0.012	0.000	0.000	0.000	0.000
49	P	49	SER	0	-0.055	-0.046	25.183	0.000	0.000	0.000	0.000	0.000	0.000
50	P	50	GLY	0	0.039	0.021	25.460	-0.002	-0.002	0.000	0.000	0.000	0.000
51	P	51	SER	0	-0.041	-0.013	26.514	-0.004	-0.004	0.000	0.000	0.000	0.000
52	P	52	ARG	1	0.929	0.942	24.883	-0.001	-0.001	0.000	0.000	0.000	0.000
53	P	53	ARG	1	0.827	0.903	23.763	0.013	0.013	0.000	0.000	0.000	0.000
54	P	54	ASP	-1	-0.752	-0.849	22.639	0.041	0.041	0.000	0.000	0.000	0.000
55	P	55	GLN	0	-0.016	-0.004	21.096	0.005	0.005	0.000	0.000	0.000	0.000
56	P	56	ALA	0	0.017	0.006	19.283	0.012	0.012	0.000	0.000	0.000	0.000
57	P	57	ARG	1	0.799	0.874	18.231	-0.041	-0.041	0.000	0.000	0.000	0.000
58	P	58	GLN	0	-0.038	-0.027	15.135	-0.024	-0.024	0.000	0.000	0.000	0.000
59	P	59	LEU	0	0.022	0.023	14.169	0.029	0.029	0.000	0.000	0.000	0.000
60	P	60	ILE	0	-0.007	-0.025	13.352	0.019	0.019	0.000	0.000	0.000	0.000
61	P	61	ILE	0	-0.074	-0.024	12.536	-0.023	-0.023	0.000	0.000	0.000	0.000
62	P	62	ASP	-1	-0.792	-0.896	10.961	0.328	0.328	0.000	0.000	0.000	0.000
63	P	63	LEU	0	-0.017	0.004	9.042	0.145	0.145	0.000	0.000	0.000	0.000
64	P	64	GLU	-1	-0.802	-0.922	7.409	0.114	0.114	0.000	0.000	0.000	0.000
65	P	65	THR	0	-0.131	-0.078	5.260	0.492	0.492	0.000	0.000	0.000	0.000
66	P	66	ARG	1	0.805	0.885	5.026	-0.670	-0.551	-0.001	-0.007	-0.111	0.000
67	P	67	GLY	0	0.018	-0.001	1.957	1.536	-1.873	11.161	-5.996	-1.756	0.007
68	P	68	SER	0	0.016	-0.018	2.507	3.203	-0.873	0.208	4.610	-0.743	-0.005
69	P	69	GLN	0	0.015	0.021	4.308	-0.002	0.151	0.000	-0.044	-0.110	0.000
70	P	70	ALA	0	0.038	0.029	6.236	0.199	0.199	0.000	0.000	0.000	0.000
71	P	71	LEU	0	0.038	0.015	8.014	0.118	0.118	0.000	0.000	0.000	0.000
72	P	72	PRO	0	0.015	0.010	9.355	0.085	0.085	0.000	0.000	0.000	0.000
73	P	73	LEU	0	0.023	0.030	10.383	0.052	0.052	0.000	0.000	0.000	0.000
74	P	74	PHE	0	0.032	0.002	12.052	0.041	0.041	0.000	0.000	0.000	0.000
75	P	75	ILE	0	-0.039	-0.025	13.891	0.015	0.015	0.000	0.000	0.000	0.000
76	P	76	SER	0	-0.021	-0.009	15.425	0.019	0.019	0.000	0.000	0.000	0.000
77	P	77	CYS	0	-0.065	-0.014	15.345	0.026	0.026	0.000	0.000	0.000	0.000
78	P	78	LEU	0	-0.014	-0.001	17.751	0.005	0.005	0.000	0.000	0.000	0.000
79	P	79	GLU	-1	-0.759	-0.857	19.943	-0.087	-0.087	0.000	0.000	0.000	0.000
80	P	80	ASP	-1	-0.795	-0.876	20.548	0.038	0.038	0.000	0.000	0.000	0.000
81	P	81	THR	0	-0.035	-0.026	21.887	0.012	0.012	0.000	0.000	0.000	0.000
82	P	82	GLY	0	0.006	0.007	24.327	0.001	0.001	0.000	0.000	0.000	0.000
83	P	83	GLN	0	-0.027	-0.010	22.151	-0.009	-0.009	0.000	0.000	0.000	0.000
84	P	84	ASP	-1	-0.847	-0.937	23.432	-0.051	-0.051	0.000	0.000	0.000	0.000
85	P	85	MET	0	-0.026	-0.017	24.697	-0.013	-0.013	0.000	0.000	0.000	0.000
86	P	86	LEU	0	0.018	0.007	20.008	-0.016	-0.016	0.000	0.000	0.000	0.000
87	P	87	ALA	0	0.048	0.022	19.869	-0.021	-0.021	0.000	0.000	0.000	0.000
88	P	88	SER	0	0.027	0.013	20.295	-0.026	-0.026	0.000	0.000	0.000	0.000
89	P	89	PHE	0	-0.011	-0.005	21.133	-0.020	-0.020	0.000	0.000	0.000	0.000
90	P	90	LEU	0	0.011	0.006	16.385	-0.025	-0.025	0.000	0.000	0.000	0.000
91	P	91	ARG	1	0.833	0.886	17.684	0.090	0.090	0.000	0.000	0.000	0.000
92	P	92	THR	0	-0.037	-0.028	18.968	-0.022	-0.022	0.000	0.000	0.000	0.000
93	P	93	ASN	0	-0.086	-0.057	18.038	-0.018	-0.018	0.000	0.000	0.000	0.000
94	P	94	ARG	1	0.813	0.870	10.013	0.739	0.739	0.000	0.000	0.000	0.000
95	P	95	GLN	0	-0.029	-0.024	16.177	-0.027	-0.027	0.000	0.000	0.000	0.000
96	P	96	ALA	0	-0.041	0.028	18.862	0.018	0.018	0.000	0.000	0.000	0.000
97	P	97	GLY	0	-0.035	-0.029	17.888	-0.018	-0.018	0.000	0.000	0.000	0.000

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