FMO DATABASE

FMODB ID: G6311

Calculation Name: 3P45-A-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3P45

Chain ID: A

ChEMBL ID: CHEMBL3308

UniProt ID: P55212

Base Structure: X-ray

Registration Date: 2023-09-20

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	133
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1201971.118265
FMO2-HF: Nuclear repulsion	1147478.444333
FMO2-HF: Total energy	-54492.673932
FMO2-MP2: Total energy	-54649.615796

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:PHE)

Summations of interaction energy for fragment #1(A:31:PHE)

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.
0.724	3.126	-0.033	-0.808	-1.562	-0.002

Interaction energy analysis for fragmet #1(A:31:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.043 / q_NPA : -0.040

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	PRO	0	0.003	0.002	3.706	-1.065	1.190	-0.032	-0.801	-1.422	-0.002
4	A	34	ALA	0	-0.044	-0.023	5.158	0.192	0.339	-0.001	-0.007	-0.140	0.000
5	A	35	GLU	-1	-1.000	-0.999	5.402	2.121	2.121	0.000	0.000	0.000	0.000
6	A	36	LYS	1	0.910	0.962	7.750	-0.376	-0.376	0.000	0.000	0.000	0.000
7	A	37	TYR	0	0.036	0.010	10.501	0.104	0.104	0.000	0.000	0.000	0.000
8	A	38	LYS	1	0.839	0.909	12.034	-0.444	-0.444	0.000	0.000	0.000	0.000
9	A	39	MET	0	-0.085	-0.045	14.264	-0.047	-0.047	0.000	0.000	0.000	0.000
10	A	40	ASP	-1	-0.827	-0.903	17.623	0.303	0.303	0.000	0.000	0.000	0.000
11	A	41	HIS	0	-0.018	0.008	16.463	0.017	0.017	0.000	0.000	0.000	0.000
12	A	42	ARG	1	0.953	0.969	21.633	-0.125	-0.125	0.000	0.000	0.000	0.000
13	A	43	ARG	1	0.943	0.977	24.367	-0.101	-0.101	0.000	0.000	0.000	0.000
14	A	44	ARG	1	0.924	0.962	21.408	-0.081	-0.081	0.000	0.000	0.000	0.000
15	A	45	GLY	0	0.026	-0.006	22.320	0.005	0.005	0.000	0.000	0.000	0.000
16	A	46	ILE	0	-0.060	-0.022	24.452	-0.005	-0.005	0.000	0.000	0.000	0.000
17	A	47	ALA	0	0.008	0.009	25.184	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	48	LEU	0	-0.027	-0.012	27.180	0.000	0.000	0.000	0.000	0.000	0.000
19	A	49	ILE	0	0.007	0.004	28.752	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	50	PHE	0	-0.011	-0.011	29.902	0.002	0.002	0.000	0.000	0.000	0.000
21	A	51	ASN	0	-0.001	-0.015	33.489	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	52	HIS	0	0.006	0.015	35.309	0.001	0.001	0.000	0.000	0.000	0.000
23	A	53	GLU	-1	-0.764	-0.858	38.460	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	54	ARG	1	0.804	0.883	41.450	0.001	0.001	0.000	0.000	0.000	0.000
25	A	55	PHE	0	-0.026	-0.024	38.835	0.000	0.000	0.000	0.000	0.000	0.000
26	A	56	PHE	0	0.017	0.005	44.321	0.000	0.000	0.000	0.000	0.000	0.000
27	A	57	TRP	0	0.047	0.011	46.532	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	58	HIS	0	-0.008	-0.005	49.214	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	59	LEU	0	-0.059	-0.011	42.586	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	60	THR	0	-0.045	-0.009	45.561	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	61	LEU	0	-0.013	0.002	40.935	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	62	PRO	0	0.011	0.007	42.930	0.001	0.001	0.000	0.000	0.000	0.000
33	A	63	GLU	-1	-0.792	-0.890	43.352	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	64	ARG	1	0.849	0.936	35.372	0.014	0.014	0.000	0.000	0.000	0.000
35	A	65	ARG	1	0.840	0.891	41.470	0.008	0.008	0.000	0.000	0.000	0.000
36	A	66	GLY	0	0.016	0.000	40.126	0.001	0.001	0.000	0.000	0.000	0.000
37	A	67	THR	0	0.036	0.014	36.927	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	68	CYS	0	-0.005	-0.002	37.306	0.001	0.001	0.000	0.000	0.000	0.000
39	A	69	ALA	0	0.013	0.033	38.663	0.002	0.002	0.000	0.000	0.000	0.000
40	A	70	ASP	-1	-0.880	-0.947	33.941	-0.017	-0.017	0.000	0.000	0.000	0.000
41	A	71	ARG	1	0.799	0.880	34.053	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	72	ASP	-1	-0.824	-0.903	34.438	0.007	0.007	0.000	0.000	0.000	0.000
43	A	73	ASN	0	-0.057	-0.027	33.928	0.004	0.004	0.000	0.000	0.000	0.000
44	A	74	LEU	0	0.017	0.010	28.422	0.001	0.001	0.000	0.000	0.000	0.000
45	A	75	THR	0	0.028	0.001	30.637	0.004	0.004	0.000	0.000	0.000	0.000
46	A	76	ARG	1	0.953	1.004	32.443	0.003	0.003	0.000	0.000	0.000	0.000
47	A	77	ARG	1	0.936	0.972	28.629	0.005	0.005	0.000	0.000	0.000	0.000
48	A	78	PHE	0	0.011	0.006	23.837	0.002	0.002	0.000	0.000	0.000	0.000
49	A	79	SER	0	0.002	-0.033	27.967	0.007	0.007	0.000	0.000	0.000	0.000
50	A	80	ASP	-1	-0.919	-0.937	30.095	0.025	0.025	0.000	0.000	0.000	0.000
51	A	81	LEU	0	-0.081	-0.033	24.139	0.004	0.004	0.000	0.000	0.000	0.000
52	A	82	GLY	0	0.006	-0.006	25.367	0.010	0.010	0.000	0.000	0.000	0.000
53	A	83	PHE	0	-0.054	-0.037	21.767	0.005	0.005	0.000	0.000	0.000	0.000
54	A	84	GLU	-1	-0.906	-0.941	27.393	0.052	0.052	0.000	0.000	0.000	0.000
55	A	85	VAL	0	-0.006	-0.018	29.607	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	86	LYS	1	0.919	0.967	31.196	-0.042	-0.042	0.000	0.000	0.000	0.000
57	A	87	CYS	0	-0.002	0.009	32.520	-0.003	-0.003	0.000	0.000	0.000	0.000
58	A	88	PHE	0	-0.001	-0.015	33.201	0.002	0.002	0.000	0.000	0.000	0.000
59	A	89	ASN	0	0.059	0.014	36.786	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	90	ASP	-1	-0.806	-0.907	39.251	0.001	0.001	0.000	0.000	0.000	0.000
61	A	91	LEU	0	-0.076	-0.006	36.288	0.001	0.001	0.000	0.000	0.000	0.000
62	A	92	LYS	1	1.047	1.006	39.448	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	93	ALA	0	-0.021	-0.011	37.789	0.001	0.001	0.000	0.000	0.000	0.000
64	A	94	GLU	-1	-0.875	-0.948	37.446	0.012	0.012	0.000	0.000	0.000	0.000
65	A	95	GLU	-1	-0.862	-0.925	38.247	0.012	0.012	0.000	0.000	0.000	0.000
66	A	96	LEU	0	-0.028	-0.017	32.379	0.002	0.002	0.000	0.000	0.000	0.000
67	A	97	LEU	0	0.029	-0.005	32.506	0.002	0.002	0.000	0.000	0.000	0.000
68	A	98	LEU	0	0.012	0.016	33.369	0.003	0.003	0.000	0.000	0.000	0.000
69	A	99	LYS	1	0.849	0.941	33.268	-0.024	-0.024	0.000	0.000	0.000	0.000
70	A	100	ILE	0	-0.011	-0.023	27.261	0.004	0.004	0.000	0.000	0.000	0.000
71	A	101	HIS	0	0.069	0.041	29.170	0.002	0.002	0.000	0.000	0.000	0.000
72	A	102	GLU	-1	-0.863	-0.889	30.043	0.039	0.039	0.000	0.000	0.000	0.000
73	A	103	VAL	0	-0.046	-0.025	26.974	0.005	0.005	0.000	0.000	0.000	0.000
74	A	104	SER	0	-0.096	-0.051	25.629	0.007	0.007	0.000	0.000	0.000	0.000
75	A	105	THR	0	0.010	-0.017	25.558	0.006	0.006	0.000	0.000	0.000	0.000
76	A	106	VAL	0	-0.034	0.014	27.805	0.004	0.004	0.000	0.000	0.000	0.000
77	A	107	SER	0	0.009	0.002	25.078	0.005	0.005	0.000	0.000	0.000	0.000
78	A	108	HIS	1	0.876	0.901	21.719	-0.075	-0.075	0.000	0.000	0.000	0.000
79	A	109	ALA	0	-0.003	-0.017	21.154	0.010	0.010	0.000	0.000	0.000	0.000
80	A	110	ASP	-1	-0.908	-0.938	21.140	0.144	0.144	0.000	0.000	0.000	0.000
81	A	111	ALA	0	-0.079	-0.047	21.850	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	112	ASP	-1	-0.696	-0.850	18.665	0.167	0.167	0.000	0.000	0.000	0.000
83	A	113	CYS	0	-0.071	-0.033	17.488	0.002	0.002	0.000	0.000	0.000	0.000
84	A	114	PHE	0	-0.035	-0.014	19.309	0.001	0.001	0.000	0.000	0.000	0.000
85	A	115	VAL	0	0.025	0.033	20.848	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	116	CYS	0	-0.015	-0.002	23.297	0.005	0.005	0.000	0.000	0.000	0.000
87	A	117	VAL	0	-0.013	-0.007	25.334	-0.007	-0.007	0.000	0.000	0.000	0.000
88	A	118	PHE	0	-0.015	-0.013	26.805	0.004	0.004	0.000	0.000	0.000	0.000
89	A	119	LEU	0	-0.012	0.008	30.377	-0.004	-0.004	0.000	0.000	0.000	0.000
90	A	120	SER	0	-0.010	-0.049	33.215	0.002	0.002	0.000	0.000	0.000	0.000
91	A	121	HIS	1	0.841	0.887	34.999	0.014	0.014	0.000	0.000	0.000	0.000
92	A	122	GLY	0	-0.002	-0.035	33.451	0.002	0.002	0.000	0.000	0.000	0.000
93	A	123	GLU	-1	-0.867	-0.947	33.634	-0.021	-0.021	0.000	0.000	0.000	0.000
94	A	124	GLY	0	0.006	0.030	32.952	0.002	0.002	0.000	0.000	0.000	0.000
95	A	125	ASN	0	-0.023	-0.014	28.429	0.001	0.001	0.000	0.000	0.000	0.000
96	A	126	HIS	0	-0.014	-0.016	29.962	0.004	0.004	0.000	0.000	0.000	0.000
97	A	127	ILE	0	-0.021	-0.001	30.838	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	128	TYR	0	0.010	-0.003	33.287	0.002	0.002	0.000	0.000	0.000	0.000
99	A	129	ALA	0	-0.007	0.037	36.455	0.000	0.000	0.000	0.000	0.000	0.000
100	A	130	TYR	0	0.010	-0.019	37.900	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	131	ASP	-1	-0.802	-0.916	41.175	0.002	0.002	0.000	0.000	0.000	0.000
102	A	132	ALA	0	-0.003	-0.002	40.068	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	133	LYS	1	0.932	0.990	36.384	0.015	0.015	0.000	0.000	0.000	0.000
104	A	134	ILE	0	0.012	-0.004	31.754	0.002	0.002	0.000	0.000	0.000	0.000
105	A	135	GLU	-1	-0.942	-0.960	30.362	-0.012	-0.012	0.000	0.000	0.000	0.000
106	A	136	ILE	0	0.051	0.006	25.436	0.003	0.003	0.000	0.000	0.000	0.000
107	A	137	GLN	0	0.010	-0.006	24.998	0.000	0.000	0.000	0.000	0.000	0.000
108	A	138	THR	0	-0.010	0.008	25.729	0.005	0.005	0.000	0.000	0.000	0.000
109	A	139	LEU	0	0.018	0.011	27.490	0.005	0.005	0.000	0.000	0.000	0.000
110	A	140	THR	0	-0.024	-0.013	21.914	0.006	0.006	0.000	0.000	0.000	0.000
111	A	141	GLY	0	-0.007	-0.012	22.615	0.005	0.005	0.000	0.000	0.000	0.000
112	A	142	LEU	0	-0.005	-0.006	23.394	0.005	0.005	0.000	0.000	0.000	0.000
113	A	143	PHE	0	0.004	-0.011	20.978	0.008	0.008	0.000	0.000	0.000	0.000
114	A	144	LYS	1	0.943	0.976	18.430	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	145	GLY	0	0.033	0.009	16.933	0.007	0.007	0.000	0.000	0.000	0.000
116	A	146	ASP	-1	-0.929	-0.969	17.829	0.042	0.042	0.000	0.000	0.000	0.000
117	A	147	LYS	1	0.913	0.953	20.663	-0.031	-0.031	0.000	0.000	0.000	0.000
118	A	148	CYS	0	0.010	0.021	21.077	0.003	0.003	0.000	0.000	0.000	0.000
119	A	149	HIS	0	0.049	0.028	19.130	0.010	0.010	0.000	0.000	0.000	0.000
120	A	150	SER	0	-0.035	0.000	18.459	0.012	0.012	0.000	0.000	0.000	0.000
121	A	151	LEU	0	0.047	-0.004	18.042	0.011	0.011	0.000	0.000	0.000	0.000
122	A	152	VAL	0	-0.020	0.012	13.200	-0.009	-0.009	0.000	0.000	0.000	0.000
123	A	153	GLY	0	-0.004	0.000	11.167	0.024	0.024	0.000	0.000	0.000	0.000
124	A	154	LYS	1	0.832	0.948	12.095	-0.144	-0.144	0.000	0.000	0.000	0.000
125	A	155	PRO	0	-0.008	-0.001	13.933	-0.028	-0.028	0.000	0.000	0.000	0.000
126	A	156	LYS	1	0.851	0.919	14.737	-0.050	-0.050	0.000	0.000	0.000	0.000
127	A	157	ILE	0	0.014	0.001	17.801	-0.014	-0.014	0.000	0.000	0.000	0.000
128	A	158	PHE	0	0.007	-0.006	19.725	0.008	0.008	0.000	0.000	0.000	0.000
129	A	159	ILE	0	-0.012	0.007	22.450	-0.009	-0.009	0.000	0.000	0.000	0.000
130	A	160	ILE	0	0.003	-0.011	24.899	0.006	0.006	0.000	0.000	0.000	0.000
131	A	161	GLN	0	-0.043	-0.006	27.434	-0.006	-0.006	0.000	0.000	0.000	0.000
132	A	162	ALA	0	0.021	-0.009	30.495	0.004	0.004	0.000	0.000	0.000	0.000
133	A	163	CYM	-1	-0.827	-0.841	32.487	-0.026	-0.026	0.000	0.000	0.000	0.000

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