FMO DATABASE

FMODB ID: N9Y4Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1205318.75227
FMO2-HF: Nuclear repulsion	1150824.534542
FMO2-HF: Total energy	-54494.217728
FMO2-MP2: Total energy	-54651.315837

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.
1.77	3.985	-0.018	-0.886	-1.311	0.003

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 : -0.001 / q_NPA : -0.001

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	-0.022	-0.019	3.863	0.451	2.540	-0.017	-0.882	-1.190	0.003
4	A	34	ALA	0	-0.049	-0.023	5.235	0.553	0.679	-0.001	-0.004	-0.121	0.000
5	A	35	GLU	-1	-0.890	-0.934	5.137	0.513	0.513	0.000	0.000	0.000	0.000
6	A	36	LYS	1	0.842	0.915	7.279	0.483	0.483	0.000	0.000	0.000	0.000
7	A	37	TYR	0	0.011	0.005	10.008	0.124	0.124	0.000	0.000	0.000	0.000
8	A	38	LYS	1	0.831	0.894	11.886	-0.186	-0.186	0.000	0.000	0.000	0.000
9	A	39	MET	0	-0.053	-0.025	14.326	0.016	0.016	0.000	0.000	0.000	0.000
10	A	40	ASP	-1	-0.798	-0.886	16.778	0.048	0.048	0.000	0.000	0.000	0.000
11	A	41	HIS	0	-0.075	-0.031	16.221	0.044	0.044	0.000	0.000	0.000	0.000
12	A	42	ARG	1	0.921	0.958	21.279	-0.073	-0.073	0.000	0.000	0.000	0.000
13	A	43	ARG	1	0.789	0.857	23.906	-0.076	-0.076	0.000	0.000	0.000	0.000
14	A	44	ARG	1	0.906	0.964	21.183	0.034	0.034	0.000	0.000	0.000	0.000
15	A	45	GLY	0	0.063	0.019	21.663	0.012	0.012	0.000	0.000	0.000	0.000
16	A	46	ILE	0	-0.052	-0.017	23.781	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	47	ALA	0	0.010	0.001	24.916	0.001	0.001	0.000	0.000	0.000	0.000
18	A	48	LEU	0	-0.015	0.000	26.892	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	49	ILE	0	-0.012	-0.016	28.313	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	50	PHE	0	0.019	0.013	29.974	0.001	0.001	0.000	0.000	0.000	0.000
21	A	51	ASN	0	-0.003	-0.011	32.936	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	52	HIS	0	0.022	0.012	34.828	0.001	0.001	0.000	0.000	0.000	0.000
23	A	53	GLU	-1	-0.771	-0.873	38.258	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	54	ARG	1	0.750	0.858	41.009	0.001	0.001	0.000	0.000	0.000	0.000
25	A	55	PHE	0	-0.008	-0.012	38.507	0.001	0.001	0.000	0.000	0.000	0.000
26	A	56	PHE	0	0.020	0.010	43.795	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	57	TRP	0	0.015	0.004	46.358	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	58	HIS	0	0.011	-0.001	48.897	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	59	LEU	0	-0.029	-0.006	42.032	0.000	0.000	0.000	0.000	0.000	0.000
30	A	60	THR	0	-0.046	-0.022	45.195	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	61	LEU	0	-0.008	0.017	40.423	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	62	PRO	0	0.005	0.008	43.234	0.000	0.000	0.000	0.000	0.000	0.000
33	A	63	GLU	-1	-0.761	-0.867	43.042	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	64	ARG	1	0.805	0.908	34.506	0.009	0.009	0.000	0.000	0.000	0.000
35	A	65	ARG	1	0.787	0.845	40.529	0.011	0.011	0.000	0.000	0.000	0.000
36	A	66	GLY	0	0.036	0.033	40.067	0.000	0.000	0.000	0.000	0.000	0.000
37	A	67	THR	0	0.017	0.006	36.281	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	68	CYS	0	-0.031	-0.004	36.645	0.001	0.001	0.000	0.000	0.000	0.000
39	A	69	ALA	0	0.047	0.036	38.110	0.000	0.000	0.000	0.000	0.000	0.000
40	A	70	ASP	-1	-0.859	-0.927	33.140	-0.035	-0.035	0.000	0.000	0.000	0.000
41	A	71	ARG	1	0.830	0.890	33.290	0.007	0.007	0.000	0.000	0.000	0.000
42	A	72	ASP	-1	-0.819	-0.881	33.866	-0.015	-0.015	0.000	0.000	0.000	0.000
43	A	73	ASN	0	-0.035	-0.022	33.156	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	74	LEU	0	0.019	0.008	27.906	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	75	THR	0	0.003	-0.023	30.126	0.002	0.002	0.000	0.000	0.000	0.000
46	A	76	ARG	1	0.899	0.967	31.978	0.036	0.036	0.000	0.000	0.000	0.000
47	A	77	ARG	1	0.899	0.940	28.366	0.059	0.059	0.000	0.000	0.000	0.000
48	A	78	PHE	0	0.014	0.001	23.555	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	79	SER	0	-0.003	-0.019	27.764	0.005	0.005	0.000	0.000	0.000	0.000
50	A	80	ASP	-1	-0.864	-0.916	29.330	-0.050	-0.050	0.000	0.000	0.000	0.000
51	A	81	LEU	0	-0.049	-0.016	23.364	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	82	GLY	0	0.001	0.004	25.051	0.002	0.002	0.000	0.000	0.000	0.000
53	A	83	PHE	0	-0.051	-0.041	21.334	0.009	0.009	0.000	0.000	0.000	0.000
54	A	84	GLU	-1	-0.800	-0.886	27.040	0.039	0.039	0.000	0.000	0.000	0.000
55	A	85	VAL	0	-0.019	-0.022	29.342	0.005	0.005	0.000	0.000	0.000	0.000
56	A	86	LYS	1	0.831	0.917	30.702	-0.036	-0.036	0.000	0.000	0.000	0.000
57	A	87	CYS	0	-0.001	0.012	32.285	0.001	0.001	0.000	0.000	0.000	0.000
58	A	88	PHE	0	0.021	0.000	32.942	0.003	0.003	0.000	0.000	0.000	0.000
59	A	89	ASN	0	0.041	0.010	36.332	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	90	ASP	-1	-0.781	-0.891	39.096	0.004	0.004	0.000	0.000	0.000	0.000
61	A	91	LEU	0	-0.044	0.006	35.871	0.001	0.001	0.000	0.000	0.000	0.000
62	A	92	LYS	1	0.927	0.930	39.118	-0.020	-0.020	0.000	0.000	0.000	0.000
63	A	93	ALA	0	-0.004	-0.015	37.637	0.002	0.002	0.000	0.000	0.000	0.000
64	A	94	GLU	-1	-0.903	-0.951	37.058	0.037	0.037	0.000	0.000	0.000	0.000
65	A	95	GLU	-1	-0.794	-0.880	37.577	0.024	0.024	0.000	0.000	0.000	0.000
66	A	96	LEU	0	-0.025	-0.011	32.336	0.002	0.002	0.000	0.000	0.000	0.000
67	A	97	LEU	0	0.026	0.002	32.298	0.003	0.003	0.000	0.000	0.000	0.000
68	A	98	LEU	0	-0.007	0.002	32.801	0.005	0.005	0.000	0.000	0.000	0.000
69	A	99	LYS	1	0.798	0.893	32.935	-0.035	-0.035	0.000	0.000	0.000	0.000
70	A	100	ILE	0	-0.007	-0.015	26.887	0.002	0.002	0.000	0.000	0.000	0.000
71	A	101	HIS	0	0.048	0.031	28.639	0.006	0.006	0.000	0.000	0.000	0.000
72	A	102	GLU	-1	-0.806	-0.859	29.443	0.053	0.053	0.000	0.000	0.000	0.000
73	A	103	VAL	0	-0.004	-0.009	27.208	0.006	0.006	0.000	0.000	0.000	0.000
74	A	104	SER	0	-0.076	-0.034	25.055	0.007	0.007	0.000	0.000	0.000	0.000
75	A	105	THR	0	-0.008	-0.008	25.077	0.011	0.011	0.000	0.000	0.000	0.000
76	A	106	VAL	0	-0.025	0.002	27.588	0.005	0.005	0.000	0.000	0.000	0.000
77	A	107	SER	0	-0.023	-0.013	24.881	0.010	0.010	0.000	0.000	0.000	0.000
78	A	108	HIS	1	0.919	0.936	21.195	-0.109	-0.109	0.000	0.000	0.000	0.000
79	A	109	ALA	0	0.022	0.016	20.650	0.006	0.006	0.000	0.000	0.000	0.000
80	A	110	ASP	-1	-0.842	-0.892	20.709	0.099	0.099	0.000	0.000	0.000	0.000
81	A	111	ALA	0	0.022	0.000	21.706	-0.016	-0.016	0.000	0.000	0.000	0.000
82	A	112	ASP	-1	-0.704	-0.834	17.984	0.060	0.060	0.000	0.000	0.000	0.000
83	A	113	CYS	0	-0.095	-0.044	17.099	0.012	0.012	0.000	0.000	0.000	0.000
84	A	114	PHE	0	-0.029	-0.018	18.933	0.002	0.002	0.000	0.000	0.000	0.000
85	A	115	VAL	0	0.021	0.028	20.401	-0.006	-0.006	0.000	0.000	0.000	0.000
86	A	116	CYS	0	-0.039	-0.003	23.038	0.006	0.006	0.000	0.000	0.000	0.000
87	A	117	VAL	0	-0.012	-0.004	24.913	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	118	PHE	0	0.020	-0.001	26.358	0.005	0.005	0.000	0.000	0.000	0.000
89	A	119	LEU	0	0.002	0.013	30.082	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	120	SER	0	-0.015	-0.045	32.844	0.002	0.002	0.000	0.000	0.000	0.000
91	A	121	HIS	1	0.802	0.835	34.658	0.002	0.002	0.000	0.000	0.000	0.000
92	A	122	GLY	0	0.014	-0.028	33.209	0.003	0.003	0.000	0.000	0.000	0.000
93	A	123	GLU	-1	-0.788	-0.883	33.252	0.011	0.011	0.000	0.000	0.000	0.000
94	A	124	GLY	0	0.032	0.027	32.080	0.004	0.004	0.000	0.000	0.000	0.000
95	A	125	ASN	0	-0.017	-0.005	28.380	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	126	HIS	0	-0.007	-0.015	29.664	0.010	0.010	0.000	0.000	0.000	0.000
97	A	127	ILE	0	-0.026	-0.002	30.168	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	128	TYR	0	-0.028	-0.032	32.800	0.004	0.004	0.000	0.000	0.000	0.000
99	A	129	ALA	0	-0.002	0.034	35.774	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	130	TYR	0	0.002	-0.006	37.667	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	131	ASP	-1	-0.767	-0.908	41.395	0.019	0.019	0.000	0.000	0.000	0.000
102	A	132	ALA	0	-0.015	-0.003	39.708	0.000	0.000	0.000	0.000	0.000	0.000
103	A	133	LYS	1	0.837	0.925	35.989	-0.018	-0.018	0.000	0.000	0.000	0.000
104	A	134	ILE	0	0.001	-0.012	31.790	0.004	0.004	0.000	0.000	0.000	0.000
105	A	135	GLU	-1	-0.844	-0.900	29.593	0.045	0.045	0.000	0.000	0.000	0.000
106	A	136	ILE	0	0.027	0.004	24.836	0.004	0.004	0.000	0.000	0.000	0.000
107	A	137	GLN	0	-0.045	-0.027	24.807	0.001	0.001	0.000	0.000	0.000	0.000
108	A	138	THR	0	0.011	0.004	25.326	0.010	0.010	0.000	0.000	0.000	0.000
109	A	139	LEU	0	-0.012	0.003	27.174	0.006	0.006	0.000	0.000	0.000	0.000
110	A	140	THR	0	-0.009	-0.021	21.590	0.006	0.006	0.000	0.000	0.000	0.000
111	A	141	GLY	0	0.008	0.002	22.119	0.012	0.012	0.000	0.000	0.000	0.000
112	A	142	LEU	0	-0.007	-0.009	22.780	0.016	0.016	0.000	0.000	0.000	0.000
113	A	143	PHE	0	0.005	-0.007	20.511	0.008	0.008	0.000	0.000	0.000	0.000
114	A	144	LYS	1	0.850	0.919	17.829	-0.137	-0.137	0.000	0.000	0.000	0.000
115	A	145	GLY	0	0.053	0.014	16.488	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	146	ASP	-1	-0.805	-0.872	17.391	0.176	0.176	0.000	0.000	0.000	0.000
117	A	147	LYS	1	0.769	0.869	20.499	-0.163	-0.163	0.000	0.000	0.000	0.000
118	A	148	CYS	0	0.021	0.021	20.648	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	149	HIS	0	0.068	0.029	18.776	0.005	0.005	0.000	0.000	0.000	0.000
120	A	150	SER	0	-0.033	-0.011	18.048	0.016	0.016	0.000	0.000	0.000	0.000
121	A	151	LEU	0	0.038	0.009	17.452	-0.009	-0.009	0.000	0.000	0.000	0.000
122	A	152	VAL	0	0.012	0.014	12.971	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	153	GLY	0	-0.011	-0.001	10.566	0.015	0.015	0.000	0.000	0.000	0.000
124	A	154	LYS	1	0.813	0.931	11.527	-0.182	-0.182	0.000	0.000	0.000	0.000
125	A	155	PRO	0	0.000	0.000	13.699	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	156	LYS	1	0.832	0.903	14.493	-0.158	-0.158	0.000	0.000	0.000	0.000
127	A	157	ILE	0	0.000	0.014	17.693	-0.006	-0.006	0.000	0.000	0.000	0.000
128	A	158	PHE	0	0.023	0.004	19.348	0.008	0.008	0.000	0.000	0.000	0.000
129	A	159	ILE	0	-0.005	0.001	21.847	-0.011	-0.011	0.000	0.000	0.000	0.000
130	A	160	ILE	0	-0.003	-0.010	24.599	0.008	0.008	0.000	0.000	0.000	0.000
131	A	161	GLN	0	-0.060	-0.019	27.463	-0.006	-0.006	0.000	0.000	0.000	0.000
132	A	162	ALA	0	0.044	0.011	30.577	0.004	0.004	0.000	0.000	0.000	0.000
133	A	163	CYM	-1	-0.819	-0.809	32.160	-0.012	-0.012	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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