FMO DATABASE

FMODB ID: R97R8

Calculation Name: 3P45-F-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3P45

Chain ID: F

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	68
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-396954.991275
FMO2-HF: Nuclear repulsion	368604.629677
FMO2-HF: Total energy	-28350.361598
FMO2-MP2: Total energy	-28429.310985

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(F:202:ALA)

Summations of interaction energy for fragment #1(F:202:ALA)

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.
-5.614	-2.81	7.615	-4.251	-6.168	-0.017

Interaction energy analysis for fragmet #1(F:202:ALA)

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 : 0.007

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	F	204	ALA	0	-0.009	-0.022	3.900	-1.176	0.926	-0.015	-1.309	-0.779	0.004
4	F	205	ASP	-1	-0.772	-0.860	6.500	-0.683	-0.683	0.000	0.000	0.000	0.000
5	F	206	PHE	0	-0.021	0.009	2.746	-1.368	-0.369	3.329	-1.331	-2.997	-0.013
6	F	207	LEU	0	-0.003	-0.012	4.665	0.054	0.086	-0.001	-0.009	-0.021	0.000
7	F	208	MET	0	-0.001	0.018	4.549	-0.228	0.036	0.007	-0.046	-0.225	0.000
8	F	209	CYS	0	-0.023	-0.016	7.296	-0.218	-0.218	0.000	0.000	0.000	0.000
9	F	210	TYR	0	0.028	0.003	6.787	0.043	0.043	0.000	0.000	0.000	0.000
10	F	211	SER	0	0.005	-0.005	12.617	-0.063	-0.063	0.000	0.000	0.000	0.000
11	F	212	VAL	0	0.036	0.018	15.741	-0.044	-0.044	0.000	0.000	0.000	0.000
12	F	223	VAL	0	0.022	-0.009	29.162	0.002	0.002	0.000	0.000	0.000	0.000
13	F	224	ASN	0	-0.028	-0.010	29.848	0.001	0.001	0.000	0.000	0.000	0.000
14	F	225	GLY	0	0.067	0.046	26.035	-0.002	-0.002	0.000	0.000	0.000	0.000
15	F	226	SER	0	-0.024	-0.021	20.673	-0.005	-0.005	0.000	0.000	0.000	0.000
16	F	227	TRP	0	0.069	0.016	23.792	-0.003	-0.003	0.000	0.000	0.000	0.000
17	F	228	TYR	0	0.055	0.034	14.885	-0.001	-0.001	0.000	0.000	0.000	0.000
18	F	229	ILE	0	0.056	0.028	17.312	-0.003	-0.003	0.000	0.000	0.000	0.000
19	F	230	GLN	0	0.061	0.036	20.773	-0.014	-0.014	0.000	0.000	0.000	0.000
20	F	231	ASP	-1	-0.755	-0.855	22.841	0.161	0.161	0.000	0.000	0.000	0.000
21	F	232	LEU	0	0.005	0.004	16.424	-0.016	-0.016	0.000	0.000	0.000	0.000
22	F	233	CYS	0	-0.034	-0.029	20.515	-0.020	-0.020	0.000	0.000	0.000	0.000
23	F	234	GLU	-1	-0.815	-0.878	22.666	0.094	0.094	0.000	0.000	0.000	0.000
24	F	235	MET	0	-0.042	-0.035	21.839	-0.019	-0.019	0.000	0.000	0.000	0.000
25	F	236	LEU	0	0.003	-0.006	18.146	-0.016	-0.016	0.000	0.000	0.000	0.000
26	F	237	GLY	0	-0.004	0.002	22.252	-0.016	-0.016	0.000	0.000	0.000	0.000
27	F	238	LYS	1	0.799	0.904	25.739	-0.098	-0.098	0.000	0.000	0.000	0.000
28	F	239	TYR	0	0.025	-0.009	23.862	-0.005	-0.005	0.000	0.000	0.000	0.000
29	F	240	GLY	0	0.035	0.014	21.361	-0.006	-0.006	0.000	0.000	0.000	0.000
30	F	241	SER	0	-0.038	-0.008	21.709	-0.009	-0.009	0.000	0.000	0.000	0.000
31	F	242	SER	0	-0.025	-0.024	24.070	-0.010	-0.010	0.000	0.000	0.000	0.000
32	F	243	LEU	0	0.008	0.008	22.079	-0.010	-0.010	0.000	0.000	0.000	0.000
33	F	244	GLU	-1	-0.777	-0.835	16.138	-0.034	-0.034	0.000	0.000	0.000	0.000
34	F	245	PHE	0	0.039	0.004	12.335	0.029	0.029	0.000	0.000	0.000	0.000
35	F	246	THR	0	-0.003	-0.033	13.034	0.047	0.047	0.000	0.000	0.000	0.000
36	F	247	GLU	-1	-0.853	-0.919	15.738	0.036	0.036	0.000	0.000	0.000	0.000
37	F	248	LEU	0	0.003	0.004	18.495	0.021	0.021	0.000	0.000	0.000	0.000
38	F	249	LEU	0	0.002	-0.015	13.168	0.022	0.022	0.000	0.000	0.000	0.000
39	F	250	THR	0	-0.039	-0.023	17.303	0.035	0.035	0.000	0.000	0.000	0.000
40	F	251	LEU	0	-0.061	-0.032	18.982	0.001	0.001	0.000	0.000	0.000	0.000
41	F	252	VAL	0	-0.007	0.013	18.930	-0.002	-0.002	0.000	0.000	0.000	0.000
42	F	253	ASN	0	0.016	0.014	16.038	0.019	0.019	0.000	0.000	0.000	0.000
43	F	254	ARG	1	0.974	0.983	20.242	-0.118	-0.118	0.000	0.000	0.000	0.000
44	F	255	LYS	1	0.810	0.896	23.799	-0.142	-0.142	0.000	0.000	0.000	0.000
45	F	256	VAL	0	0.001	-0.014	21.232	-0.005	-0.005	0.000	0.000	0.000	0.000
46	F	257	SER	0	-0.034	-0.001	23.371	-0.006	-0.006	0.000	0.000	0.000	0.000
47	F	258	GLN	0	-0.030	-0.019	25.006	-0.009	-0.009	0.000	0.000	0.000	0.000
48	F	259	ARG	1	0.833	0.922	26.171	-0.184	-0.184	0.000	0.000	0.000	0.000
49	F	260	ARG	1	0.891	0.953	28.436	-0.141	-0.141	0.000	0.000	0.000	0.000
50	F	274	GLN	0	-0.035	-0.031	19.851	-0.027	-0.027	0.000	0.000	0.000	0.000
51	F	275	VAL	0	-0.012	-0.018	19.266	-0.028	-0.028	0.000	0.000	0.000	0.000
52	F	276	PRO	0	-0.015	0.024	17.007	0.033	0.033	0.000	0.000	0.000	0.000
53	F	277	CYS	0	-0.022	-0.016	12.855	-0.006	-0.006	0.000	0.000	0.000	0.000
54	F	278	PHE	0	-0.010	-0.015	10.921	0.040	0.040	0.000	0.000	0.000	0.000
55	F	279	ALA	0	0.046	0.032	6.720	-0.071	-0.071	0.000	0.000	0.000	0.000
56	F	280	SER	0	-0.006	-0.017	6.724	0.095	0.095	0.000	0.000	0.000	0.000
57	F	281	MET	0	-0.014	0.004	2.420	-2.118	-2.711	4.295	-1.556	-2.146	-0.008
58	F	282	LEU	0	-0.015	0.013	6.330	-0.208	-0.208	0.000	0.000	0.000	0.000
59	F	283	THR	0	-0.044	-0.059	9.521	0.066	0.066	0.000	0.000	0.000	0.000
60	F	284	LYS	1	0.860	0.926	12.042	0.593	0.593	0.000	0.000	0.000	0.000
61	F	285	LYS	1	0.892	0.961	14.135	0.056	0.056	0.000	0.000	0.000	0.000
62	F	286	LEU	0	-0.031	-0.017	12.535	-0.017	-0.017	0.000	0.000	0.000	0.000
63	F	287	HIS	0	-0.015	-0.014	16.332	0.025	0.025	0.000	0.000	0.000	0.000
64	F	288	PHE	0	-0.021	-0.012	14.590	-0.017	-0.017	0.000	0.000	0.000	0.000
65	F	289	PHE	0	0.023	0.019	20.498	0.011	0.011	0.000	0.000	0.000	0.000
66	F	290	PRO	0	-0.014	-0.010	23.800	-0.005	-0.005	0.000	0.000	0.000	0.000
67	F	291	LYS	1	0.943	0.977	21.405	0.068	0.068	0.000	0.000	0.000	0.000
68	F	292	SER	0	0.037	0.026	26.187	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:202:ALA)