FMO DATABASE

FMODB ID: 85YLY

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1202773.742105
FMO2-HF: Nuclear repulsion	1148279.956427
FMO2-HF: Total energy	-54493.785678
FMO2-MP2: Total energy	-54650.765154

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.
1.151	3.763	-0.035	-1.087	-1.489	0

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 : -0.008 / q_NPA : -0.006

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].
3	A	33	PRO	0	0.011	0.006	3.779	-0.409	2.203	-0.035	-1.087	-1.489
4	A	34	ALA	0	-0.049	-0.018	5.450	0.648	0.648	0.000	0.000	0.000
5	A	35	GLU	-1	-0.968	-0.986	5.619	0.493	0.493	0.000	0.000	0.000
6	A	36	LYS	1	0.892	0.954	7.749	0.499	0.499	0.000	0.000	0.000
7	A	37	TYR	0	0.032	0.008	10.192	0.105	0.105	0.000	0.000	0.000
8	A	38	LYS	1	0.821	0.891	11.875	-0.114	-0.114	0.000	0.000	0.000
9	A	39	MET	0	-0.071	-0.035	14.193	0.011	0.011	0.000	0.000	0.000
10	A	40	ASP	-1	-0.811	-0.887	17.161	0.019	0.019	0.000	0.000	0.000
11	A	41	HIS	0	-0.042	-0.015	16.312	0.043	0.043	0.000	0.000	0.000
12	A	42	ARG	1	0.932	0.957	21.370	-0.045	-0.045	0.000	0.000	0.000
13	A	43	ARG	1	0.818	0.889	24.132	-0.040	-0.040	0.000	0.000	0.000
14	A	44	ARG	1	0.910	0.955	21.477	0.070	0.070	0.000	0.000	0.000
15	A	45	GLY	0	0.043	0.002	22.122	0.006	0.006	0.000	0.000	0.000
16	A	46	ILE	0	-0.061	-0.023	24.245	-0.005	-0.005	0.000	0.000	0.000
17	A	47	ALA	0	0.016	0.008	24.975	-0.003	-0.003	0.000	0.000	0.000
18	A	48	LEU	0	-0.031	-0.012	26.980	0.002	0.002	0.000	0.000	0.000
19	A	49	ILE	0	0.011	0.004	28.567	-0.005	-0.005	0.000	0.000	0.000
20	A	50	PHE	0	-0.004	-0.008	29.816	0.004	0.004	0.000	0.000	0.000
21	A	51	ASN	0	0.004	-0.014	33.306	-0.007	-0.007	0.000	0.000	0.000
22	A	52	HIS	0	0.030	0.024	34.907	0.003	0.003	0.000	0.000	0.000
23	A	53	GLU	-1	-0.775	-0.865	38.309	-0.026	-0.026	0.000	0.000	0.000
24	A	54	ARG	1	0.811	0.892	41.321	0.016	0.016	0.000	0.000	0.000
25	A	55	PHE	0	-0.028	-0.024	38.789	0.000	0.000	0.000	0.000	0.000
26	A	56	PHE	0	0.019	0.004	44.160	0.000	0.000	0.000	0.000	0.000
27	A	57	TRP	0	0.034	0.006	46.349	-0.001	-0.001	0.000	0.000	0.000
28	A	58	HIS	0	-0.003	-0.005	49.043	-0.002	-0.002	0.000	0.000	0.000
29	A	59	LEU	0	-0.037	-0.001	42.140	0.000	0.000	0.000	0.000	0.000
30	A	60	THR	0	-0.057	-0.018	45.418	-0.001	-0.001	0.000	0.000	0.000
31	A	61	LEU	0	-0.004	0.007	40.701	-0.002	-0.002	0.000	0.000	0.000
32	A	62	PRO	0	-0.004	0.007	43.147	0.000	0.000	0.000	0.000	0.000
33	A	63	GLU	-1	-0.765	-0.872	43.248	-0.021	-0.021	0.000	0.000	0.000
34	A	64	ARG	1	0.826	0.926	35.038	0.031	0.031	0.000	0.000	0.000
35	A	65	ARG	1	0.814	0.869	41.385	0.026	0.026	0.000	0.000	0.000
36	A	66	GLY	0	0.013	0.000	40.085	0.000	0.000	0.000	0.000	0.000
37	A	67	THR	0	0.024	0.011	36.890	-0.003	-0.003	0.000	0.000	0.000
38	A	68	CYS	0	-0.011	-0.003	37.216	0.000	0.000	0.000	0.000	0.000
39	A	69	ALA	0	0.023	0.032	38.574	0.000	0.000	0.000	0.000	0.000
40	A	70	ASP	-1	-0.868	-0.938	33.916	-0.057	-0.057	0.000	0.000	0.000
41	A	71	ARG	1	0.788	0.866	33.981	0.024	0.024	0.000	0.000	0.000
42	A	72	ASP	-1	-0.826	-0.896	34.334	-0.033	-0.033	0.000	0.000	0.000
43	A	73	ASN	0	-0.030	-0.014	33.778	-0.002	-0.002	0.000	0.000	0.000
44	A	74	LEU	0	0.015	0.010	28.419	-0.005	-0.005	0.000	0.000	0.000
45	A	75	THR	0	0.014	-0.015	30.550	0.000	0.000	0.000	0.000	0.000
46	A	76	ARG	1	0.909	0.967	32.340	0.053	0.053	0.000	0.000	0.000
47	A	77	ARG	1	0.906	0.952	28.790	0.078	0.078	0.000	0.000	0.000
48	A	78	PHE	0	0.019	0.007	23.661	-0.005	-0.005	0.000	0.000	0.000
49	A	79	SER	0	-0.003	-0.012	27.856	0.004	0.004	0.000	0.000	0.000
50	A	80	ASP	-1	-0.877	-0.914	29.737	-0.068	-0.068	0.000	0.000	0.000
51	A	81	LEU	0	-0.065	-0.026	23.983	-0.006	-0.006	0.000	0.000	0.000
52	A	82	GLY	0	-0.002	-0.012	25.268	-0.001	-0.001	0.000	0.000	0.000
53	A	83	PHE	0	-0.042	-0.032	21.451	0.007	0.007	0.000	0.000	0.000
54	A	84	GLU	-1	-0.820	-0.897	27.236	0.009	0.009	0.000	0.000	0.000
55	A	85	VAL	0	-0.012	-0.020	29.406	0.003	0.003	0.000	0.000	0.000
56	A	86	LYS	1	0.850	0.935	30.999	-0.008	-0.008	0.000	0.000	0.000
57	A	87	CYS	0	0.006	0.011	32.319	-0.002	-0.002	0.000	0.000	0.000
58	A	88	PHE	0	0.011	-0.009	33.117	0.004	0.004	0.000	0.000	0.000
59	A	89	ASN	0	0.031	0.006	36.597	-0.005	-0.005	0.000	0.000	0.000
60	A	90	ASP	-1	-0.784	-0.887	39.042	-0.013	-0.013	0.000	0.000	0.000
61	A	91	LEU	0	-0.079	-0.009	35.821	0.002	0.002	0.000	0.000	0.000
62	A	92	LYS	1	0.950	0.949	39.232	-0.005	-0.005	0.000	0.000	0.000
63	A	93	ALA	0	-0.030	-0.027	37.545	0.001	0.001	0.000	0.000	0.000
64	A	94	GLU	-1	-0.876	-0.947	37.181	0.019	0.019	0.000	0.000	0.000
65	A	95	GLU	-1	-0.815	-0.889	37.997	0.007	0.007	0.000	0.000	0.000
66	A	96	LEU	0	-0.023	-0.019	32.422	0.001	0.001	0.000	0.000	0.000
67	A	97	LEU	0	0.025	-0.002	32.355	0.001	0.001	0.000	0.000	0.000
68	A	98	LEU	0	0.001	0.010	33.191	0.004	0.004	0.000	0.000	0.000
69	A	99	LYS	1	0.792	0.890	33.176	-0.014	-0.014	0.000	0.000	0.000
70	A	100	ILE	0	-0.003	-0.018	27.119	0.002	0.002	0.000	0.000	0.000
71	A	101	HIS	0	0.056	0.037	28.976	0.003	0.003	0.000	0.000	0.000
72	A	102	GLU	-1	-0.799	-0.852	29.816	0.029	0.029	0.000	0.000	0.000
73	A	103	VAL	0	-0.038	-0.024	27.103	0.004	0.004	0.000	0.000	0.000
74	A	104	SER	0	-0.085	-0.040	25.410	0.006	0.006	0.000	0.000	0.000
75	A	105	THR	0	-0.010	-0.018	25.310	0.009	0.009	0.000	0.000	0.000
76	A	106	VAL	0	-0.033	0.013	27.776	0.004	0.004	0.000	0.000	0.000
77	A	107	SER	0	-0.005	-0.008	24.799	0.007	0.007	0.000	0.000	0.000
78	A	108	HIS	1	0.916	0.929	21.403	-0.060	-0.060	0.000	0.000	0.000
79	A	109	ALA	0	0.014	0.001	20.836	0.002	0.002	0.000	0.000	0.000
80	A	110	ASP	-1	-0.848	-0.891	20.828	0.058	0.058	0.000	0.000	0.000
81	A	111	ALA	0	-0.003	-0.002	21.613	-0.012	-0.012	0.000	0.000	0.000
82	A	112	ASP	-1	-0.699	-0.837	18.433	0.001	0.001	0.000	0.000	0.000
83	A	113	CYS	0	-0.082	-0.034	17.273	0.001	0.001	0.000	0.000	0.000
84	A	114	PHE	0	-0.032	-0.014	19.119	0.006	0.006	0.000	0.000	0.000
85	A	115	VAL	0	0.025	0.032	20.642	-0.008	-0.008	0.000	0.000	0.000
86	A	116	CYS	0	-0.025	-0.003	23.112	0.011	0.011	0.000	0.000	0.000
87	A	117	VAL	0	-0.008	-0.010	25.170	-0.007	-0.007	0.000	0.000	0.000
88	A	118	PHE	0	-0.005	-0.007	26.737	0.007	0.007	0.000	0.000	0.000
89	A	119	LEU	0	-0.016	0.004	30.226	-0.006	-0.006	0.000	0.000	0.000
90	A	120	SER	0	-0.002	-0.043	33.095	0.003	0.003	0.000	0.000	0.000
91	A	121	HIS	1	0.826	0.845	34.893	0.021	0.021	0.000	0.000	0.000
92	A	122	GLY	0	0.019	-0.022	33.342	0.003	0.003	0.000	0.000	0.000
93	A	123	GLU	-1	-0.759	-0.870	33.481	-0.009	-0.009	0.000	0.000	0.000
94	A	124	GLY	0	0.019	0.039	32.840	0.004	0.004	0.000	0.000	0.000
95	A	125	ASN	0	-0.009	-0.003	28.109	-0.005	-0.005	0.000	0.000	0.000
96	A	126	HIS	0	-0.031	-0.028	29.786	0.008	0.008	0.000	0.000	0.000
97	A	127	ILE	0	-0.034	-0.009	30.503	-0.005	-0.005	0.000	0.000	0.000
98	A	128	TYR	0	-0.030	-0.033	33.121	0.005	0.005	0.000	0.000	0.000
99	A	129	ALA	0	-0.004	0.030	36.280	-0.002	-0.002	0.000	0.000	0.000
100	A	130	TYR	0	0.018	-0.007	37.700	-0.001	-0.001	0.000	0.000	0.000
101	A	131	ASP	-1	-0.752	-0.887	40.976	0.004	0.004	0.000	0.000	0.000
102	A	132	ALA	0	-0.009	-0.004	39.866	0.000	0.000	0.000	0.000	0.000
103	A	133	LYS	1	0.838	0.928	36.157	0.003	0.003	0.000	0.000	0.000
104	A	134	ILE	0	-0.004	-0.012	31.754	0.004	0.004	0.000	0.000	0.000
105	A	135	GLU	-1	-0.906	-0.936	29.793	0.016	0.016	0.000	0.000	0.000
106	A	136	ILE	0	0.047	0.000	25.195	0.003	0.003	0.000	0.000	0.000
107	A	137	GLN	0	-0.003	-0.013	24.751	-0.004	-0.004	0.000	0.000	0.000
108	A	138	THR	0	-0.006	0.002	25.463	0.008	0.008	0.000	0.000	0.000
109	A	139	LEU	0	0.022	0.017	27.261	0.005	0.005	0.000	0.000	0.000
110	A	140	THR	0	-0.018	-0.011	21.622	0.006	0.006	0.000	0.000	0.000
111	A	141	GLY	0	0.002	-0.007	22.366	0.008	0.008	0.000	0.000	0.000
112	A	142	LEU	0	-0.017	-0.007	23.227	0.012	0.012	0.000	0.000	0.000
113	A	143	PHE	0	0.004	-0.011	20.860	0.006	0.006	0.000	0.000	0.000
114	A	144	LYS	1	0.878	0.932	18.257	-0.094	-0.094	0.000	0.000	0.000
115	A	145	GLY	0	0.056	0.017	16.694	0.003	0.003	0.000	0.000	0.000
116	A	146	ASP	-1	-0.834	-0.900	17.593	0.124	0.124	0.000	0.000	0.000
117	A	147	LYS	1	0.847	0.909	20.422	-0.106	-0.106	0.000	0.000	0.000
118	A	148	CYS	0	0.009	0.016	20.774	-0.010	-0.010	0.000	0.000	0.000
119	A	149	HIS	0	0.039	0.018	18.829	0.001	0.001	0.000	0.000	0.000
120	A	150	SER	0	-0.018	0.008	18.149	0.008	0.008	0.000	0.000	0.000
121	A	151	LEU	0	0.037	0.002	17.786	-0.006	-0.006	0.000	0.000	0.000
122	A	152	VAL	0	-0.020	0.015	12.915	-0.011	-0.011	0.000	0.000	0.000
123	A	153	GLY	0	0.012	0.005	10.913	0.018	0.018	0.000	0.000	0.000
124	A	154	LYS	1	0.819	0.932	11.828	-0.118	-0.118	0.000	0.000	0.000
125	A	155	PRO	0	-0.005	-0.004	13.676	0.001	0.001	0.000	0.000	0.000
126	A	156	LYS	1	0.833	0.914	14.876	-0.061	-0.061	0.000	0.000	0.000
127	A	157	ILE	0	0.008	-0.001	17.646	-0.008	-0.008	0.000	0.000	0.000
128	A	158	PHE	0	0.013	0.002	19.561	0.010	0.010	0.000	0.000	0.000
129	A	159	ILE	0	-0.003	0.009	22.335	-0.010	-0.010	0.000	0.000	0.000
130	A	160	ILE	0	-0.007	-0.015	24.794	0.009	0.009	0.000	0.000	0.000
131	A	161	GLN	0	-0.030	0.002	27.328	-0.006	-0.006	0.000	0.000	0.000
132	A	162	ALA	0	0.034	-0.001	30.420	0.005	0.005	0.000	0.000	0.000
133	A	163	CYM	-1	-0.840	-0.821	32.528	-0.033	-0.033	0.000	0.000	0.000

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