FMO DATABASE

FMODB ID: LZK89

Calculation Name: 3P45-J-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3P45

Chain ID: J

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	70
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-409504.733947
FMO2-HF: Nuclear repulsion	380581.408456
FMO2-HF: Total energy	-28923.325492
FMO2-MP2: Total energy	-29004.008914

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(J:201:PRO)

Summations of interaction energy for fragment #1(J:201:PRO)

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.
-3.273	-2.438	6.301	-1.523	-5.612	-0.006

Interaction energy analysis for fragmet #1(J:201:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.044

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

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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	J	203	GLY	0	0.044	0.036	3.843	-1.997	0.758	-0.022	-1.293	-1.440	-0.005
4	J	204	ALA	0	-0.019	-0.023	6.664	0.195	0.195	0.000	0.000	0.000	0.000
5	J	205	ASP	-1	-0.840	-0.908	9.027	-0.223	-0.223	0.000	0.000	0.000	0.000
6	J	206	PHE	0	-0.030	0.002	4.565	0.203	0.294	-0.001	-0.009	-0.080	0.000
7	J	207	LEU	0	0.001	-0.003	6.283	-0.132	-0.132	0.000	0.000	0.000	0.000
8	J	208	MET	0	-0.028	-0.011	2.250	-1.462	-0.698	1.244	-0.858	-1.150	-0.003
9	J	209	CYS	0	-0.007	-0.006	5.548	-0.449	-0.449	0.000	0.000	0.000	0.000
10	J	210	TYR	0	0.034	0.016	3.796	0.271	0.668	0.004	-0.086	-0.315	0.000
11	J	211	SER	0	0.047	0.003	9.878	-0.163	-0.163	0.000	0.000	0.000	0.000
12	J	212	VAL	0	-0.035	0.001	11.390	-0.084	-0.084	0.000	0.000	0.000	0.000
13	J	222	THR	0	0.003	-0.011	25.776	-0.003	-0.003	0.000	0.000	0.000	0.000
14	J	223	VAL	0	0.034	0.000	27.246	0.017	0.017	0.000	0.000	0.000	0.000
15	J	224	ASN	0	0.022	0.029	28.807	0.009	0.009	0.000	0.000	0.000	0.000
16	J	225	GLY	0	0.026	0.023	24.937	0.005	0.005	0.000	0.000	0.000	0.000
17	J	226	SER	0	0.000	-0.004	19.706	-0.017	-0.017	0.000	0.000	0.000	0.000
18	J	227	TRP	0	0.055	0.014	21.011	0.008	0.008	0.000	0.000	0.000	0.000
19	J	228	TYR	0	0.076	0.040	12.764	0.012	0.012	0.000	0.000	0.000	0.000
20	J	229	ILE	0	0.044	0.022	16.469	0.001	0.001	0.000	0.000	0.000	0.000
21	J	230	GLN	0	-0.018	-0.014	19.519	-0.030	-0.030	0.000	0.000	0.000	0.000
22	J	231	ASP	-1	-0.798	-0.920	20.612	0.232	0.232	0.000	0.000	0.000	0.000
23	J	232	LEU	0	-0.044	-0.025	15.290	-0.016	-0.016	0.000	0.000	0.000	0.000
24	J	233	CYS	0	-0.015	-0.026	19.087	-0.018	-0.018	0.000	0.000	0.000	0.000
25	J	234	GLU	-1	-0.861	-0.925	21.735	0.152	0.152	0.000	0.000	0.000	0.000
26	J	235	MET	0	-0.047	-0.024	20.547	-0.033	-0.033	0.000	0.000	0.000	0.000
27	J	236	LEU	0	0.007	-0.005	17.803	-0.016	-0.016	0.000	0.000	0.000	0.000
28	J	237	GLY	0	-0.001	0.015	21.668	-0.019	-0.019	0.000	0.000	0.000	0.000
29	J	238	LYS	1	0.849	0.934	25.440	-0.156	-0.156	0.000	0.000	0.000	0.000
30	J	239	TYR	0	0.010	-0.013	23.107	-0.013	-0.013	0.000	0.000	0.000	0.000
31	J	240	GLY	0	0.044	0.026	21.224	-0.004	-0.004	0.000	0.000	0.000	0.000
32	J	241	SER	0	-0.061	-0.022	21.738	-0.001	-0.001	0.000	0.000	0.000	0.000
33	J	242	SER	0	0.009	-0.008	24.131	-0.013	-0.013	0.000	0.000	0.000	0.000
34	J	243	LEU	0	-0.049	-0.023	21.235	-0.012	-0.012	0.000	0.000	0.000	0.000
35	J	244	GLU	-1	-0.725	-0.786	15.936	0.121	0.121	0.000	0.000	0.000	0.000
36	J	245	PHE	0	0.043	0.009	12.481	0.020	0.020	0.000	0.000	0.000	0.000
37	J	246	THR	0	-0.057	-0.103	11.764	0.032	0.032	0.000	0.000	0.000	0.000
38	J	247	GLU	-1	-0.911	-0.956	14.251	0.090	0.090	0.000	0.000	0.000	0.000
39	J	248	LEU	0	-0.025	0.001	17.437	0.008	0.008	0.000	0.000	0.000	0.000
40	J	249	LEU	0	-0.006	-0.014	11.446	0.020	0.020	0.000	0.000	0.000	0.000
41	J	250	THR	0	-0.016	-0.011	15.075	0.014	0.014	0.000	0.000	0.000	0.000
42	J	251	LEU	0	-0.042	-0.024	16.371	-0.011	-0.011	0.000	0.000	0.000	0.000
43	J	252	VAL	0	-0.015	0.007	16.380	-0.010	-0.010	0.000	0.000	0.000	0.000
44	J	253	ASN	0	0.023	0.002	12.759	0.046	0.046	0.000	0.000	0.000	0.000
45	J	254	ARG	1	0.937	0.978	16.810	-0.146	-0.146	0.000	0.000	0.000	0.000
46	J	255	LYS	1	0.876	0.940	20.420	-0.189	-0.189	0.000	0.000	0.000	0.000
47	J	256	VAL	0	0.029	0.007	18.390	-0.006	-0.006	0.000	0.000	0.000	0.000
48	J	257	SER	0	-0.094	-0.033	19.858	-0.015	-0.015	0.000	0.000	0.000	0.000
49	J	258	GLN	0	-0.073	-0.032	21.356	-0.012	-0.012	0.000	0.000	0.000	0.000
50	J	259	ARG	1	0.866	0.968	23.539	-0.233	-0.233	0.000	0.000	0.000	0.000
51	J	273	LYS	1	1.024	1.018	20.654	-0.156	-0.156	0.000	0.000	0.000	0.000
52	J	274	GLN	0	-0.030	-0.047	17.482	0.042	0.042	0.000	0.000	0.000	0.000
53	J	275	VAL	0	-0.041	-0.024	15.153	-0.026	-0.026	0.000	0.000	0.000	0.000
54	J	276	PRO	0	-0.017	0.024	13.320	0.026	0.026	0.000	0.000	0.000	0.000
55	J	277	CYS	0	0.003	-0.003	8.356	-0.080	-0.080	0.000	0.000	0.000	0.000
56	J	278	PHE	0	0.002	-0.008	7.785	0.154	0.154	0.000	0.000	0.000	0.000
57	J	279	ALA	0	0.027	0.019	3.227	-0.574	-0.268	0.049	-0.089	-0.267	0.000
58	J	280	SER	0	-0.014	-0.009	5.062	0.245	0.317	-0.001	-0.003	-0.068	0.000
59	J	281	MET	0	-0.032	0.007	2.012	1.087	-2.463	5.028	0.815	-2.292	0.002
60	J	282	LEU	0	-0.011	0.007	6.547	-0.027	-0.027	0.000	0.000	0.000	0.000
61	J	283	THR	0	-0.033	-0.031	10.216	-0.022	-0.022	0.000	0.000	0.000	0.000
62	J	284	LYS	1	0.922	0.956	12.961	0.153	0.153	0.000	0.000	0.000	0.000
63	J	285	LYS	1	0.936	0.979	14.930	0.014	0.014	0.000	0.000	0.000	0.000
64	J	286	LEU	0	0.002	0.014	13.875	-0.010	-0.010	0.000	0.000	0.000	0.000
65	J	287	HIS	0	0.012	-0.010	17.208	0.005	0.005	0.000	0.000	0.000	0.000
66	J	288	PHE	0	-0.005	-0.006	15.781	-0.006	-0.006	0.000	0.000	0.000	0.000
67	J	289	PHE	0	0.011	0.011	21.510	0.005	0.005	0.000	0.000	0.000	0.000
68	J	290	PRO	0	0.013	0.001	25.213	0.004	0.004	0.000	0.000	0.000	0.000
69	J	291	LYS	1	0.912	0.966	24.259	-0.082	-0.082	0.000	0.000	0.000	0.000
70	J	292	SER	0	0.053	0.035	28.003	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(J:201:PRO)