FMO DATABASE

FMODB ID: Z643N

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

Total energy (hartree)

FMO2-HF: Electronic energy	-395656.606179
FMO2-HF: Nuclear repulsion	367306.757263
FMO2-HF: Total energy	-28349.848916
FMO2-MP2: Total energy	-28428.782248

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.
-5.855	-1.642	5.807	-3.913	-6.106	-0.018

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 : 0.010 / q_NPA : 0.015

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	-0.029	-0.025	3.900	-1.477	0.753	-0.016	-1.401	-0.813	0.005
4	F	205	ASP	-1	-0.835	-0.896	6.486	-0.906	-0.906	0.000	0.000	0.000	0.000
5	F	206	PHE	0	-0.025	0.009	2.657	-1.727	-0.540	3.834	-1.601	-3.420	-0.017
6	F	207	LEU	0	0.004	-0.015	4.688	0.061	0.092	-0.001	-0.009	-0.021	0.000
7	F	208	MET	0	-0.008	0.016	4.471	-0.051	0.245	0.016	-0.058	-0.253	0.000
8	F	209	CYS	0	-0.019	-0.018	7.344	-0.217	-0.217	0.000	0.000	0.000	0.000
9	F	210	TYR	0	0.032	0.005	6.834	0.011	0.011	0.000	0.000	0.000	0.000
10	F	211	SER	0	0.029	-0.004	12.722	-0.066	-0.066	0.000	0.000	0.000	0.000
11	F	212	VAL	0	0.001	0.016	15.730	-0.045	-0.045	0.000	0.000	0.000	0.000
12	F	223	VAL	0	0.010	-0.012	30.126	0.004	0.004	0.000	0.000	0.000	0.000
13	F	224	ASN	0	-0.037	-0.017	29.798	0.001	0.001	0.000	0.000	0.000	0.000
14	F	225	GLY	0	0.086	0.057	26.109	-0.003	-0.003	0.000	0.000	0.000	0.000
15	F	226	SER	0	-0.026	-0.018	20.677	-0.004	-0.004	0.000	0.000	0.000	0.000
16	F	227	TRP	0	0.076	0.015	23.877	-0.006	-0.006	0.000	0.000	0.000	0.000
17	F	228	TYR	0	0.039	0.029	15.024	0.001	0.001	0.000	0.000	0.000	0.000
18	F	229	ILE	0	0.054	0.024	17.471	-0.004	-0.004	0.000	0.000	0.000	0.000
19	F	230	GLN	0	0.024	0.011	20.857	-0.018	-0.018	0.000	0.000	0.000	0.000
20	F	231	ASP	-1	-0.803	-0.906	22.874	0.159	0.159	0.000	0.000	0.000	0.000
21	F	232	LEU	0	-0.009	-0.006	16.492	-0.016	-0.016	0.000	0.000	0.000	0.000
22	F	233	CYS	0	-0.023	-0.022	20.563	-0.022	-0.022	0.000	0.000	0.000	0.000
23	F	234	GLU	-1	-0.901	-0.946	22.713	0.087	0.087	0.000	0.000	0.000	0.000
24	F	235	MET	0	-0.049	-0.039	21.927	-0.019	-0.019	0.000	0.000	0.000	0.000
25	F	236	LEU	0	0.010	-0.002	18.143	-0.017	-0.017	0.000	0.000	0.000	0.000
26	F	237	GLY	0	-0.006	0.002	22.296	-0.016	-0.016	0.000	0.000	0.000	0.000
27	F	238	LYS	1	0.822	0.932	25.809	-0.090	-0.090	0.000	0.000	0.000	0.000
28	F	239	TYR	0	0.025	-0.015	23.990	-0.005	-0.005	0.000	0.000	0.000	0.000
29	F	240	GLY	0	0.037	0.018	21.404	-0.007	-0.007	0.000	0.000	0.000	0.000
30	F	241	SER	0	-0.034	-0.008	21.747	-0.009	-0.009	0.000	0.000	0.000	0.000
31	F	242	SER	0	-0.028	-0.024	24.090	-0.010	-0.010	0.000	0.000	0.000	0.000
32	F	243	LEU	0	0.006	0.001	22.046	-0.010	-0.010	0.000	0.000	0.000	0.000
33	F	244	GLU	-1	-0.764	-0.830	16.298	-0.059	-0.059	0.000	0.000	0.000	0.000
34	F	245	PHE	0	0.036	-0.002	12.759	0.027	0.027	0.000	0.000	0.000	0.000
35	F	246	THR	0	-0.016	-0.035	13.092	0.048	0.048	0.000	0.000	0.000	0.000
36	F	247	GLU	-1	-0.904	-0.952	15.711	0.034	0.034	0.000	0.000	0.000	0.000
37	F	248	LEU	0	0.003	0.003	18.218	0.023	0.023	0.000	0.000	0.000	0.000
38	F	249	LEU	0	-0.003	-0.019	13.143	0.025	0.025	0.000	0.000	0.000	0.000
39	F	250	THR	0	-0.028	-0.004	17.264	0.037	0.037	0.000	0.000	0.000	0.000
40	F	251	LEU	0	-0.052	-0.035	18.947	0.003	0.003	0.000	0.000	0.000	0.000
41	F	252	VAL	0	-0.004	0.018	18.917	-0.001	-0.001	0.000	0.000	0.000	0.000
42	F	253	ASN	0	0.014	0.016	16.255	0.021	0.021	0.000	0.000	0.000	0.000
43	F	254	ARG	1	0.953	0.974	20.198	-0.107	-0.107	0.000	0.000	0.000	0.000
44	F	255	LYS	1	0.919	0.956	23.757	-0.125	-0.125	0.000	0.000	0.000	0.000
45	F	256	VAL	0	0.032	0.004	21.334	-0.005	-0.005	0.000	0.000	0.000	0.000
46	F	257	SER	0	-0.034	0.011	23.575	-0.004	-0.004	0.000	0.000	0.000	0.000
47	F	258	GLN	0	-0.043	-0.026	24.960	-0.010	-0.010	0.000	0.000	0.000	0.000
48	F	259	ARG	1	0.874	0.960	26.502	-0.174	-0.174	0.000	0.000	0.000	0.000
49	F	260	ARG	1	0.893	0.959	28.506	-0.136	-0.136	0.000	0.000	0.000	0.000
50	F	274	GLN	0	-0.026	-0.031	19.787	-0.028	-0.028	0.000	0.000	0.000	0.000
51	F	275	VAL	0	-0.024	-0.019	18.844	-0.028	-0.028	0.000	0.000	0.000	0.000
52	F	276	PRO	0	-0.008	0.026	16.966	0.034	0.034	0.000	0.000	0.000	0.000
53	F	277	CYS	0	-0.016	-0.016	12.664	0.003	0.003	0.000	0.000	0.000	0.000
54	F	278	PHE	0	-0.016	-0.017	10.874	0.038	0.038	0.000	0.000	0.000	0.000
55	F	279	ALA	0	0.048	0.036	6.663	-0.074	-0.074	0.000	0.000	0.000	0.000
56	F	280	SER	0	-0.010	-0.011	6.688	0.041	0.041	0.000	0.000	0.000	0.000
57	F	281	MET	0	0.006	0.008	2.400	-1.557	-1.088	1.974	-0.844	-1.599	-0.006
58	F	282	LEU	0	-0.026	-0.002	6.338	-0.184	-0.184	0.000	0.000	0.000	0.000
59	F	283	THR	0	-0.010	-0.031	9.526	0.097	0.097	0.000	0.000	0.000	0.000
60	F	284	LYS	1	0.927	0.955	12.062	0.441	0.441	0.000	0.000	0.000	0.000
61	F	285	LYS	1	0.931	0.973	14.137	0.105	0.105	0.000	0.000	0.000	0.000
62	F	286	LEU	0	-0.002	0.003	12.659	-0.019	-0.019	0.000	0.000	0.000	0.000
63	F	287	HIS	0	-0.023	-0.015	16.358	0.025	0.025	0.000	0.000	0.000	0.000
64	F	288	PHE	0	-0.024	-0.010	14.874	-0.018	-0.018	0.000	0.000	0.000	0.000
65	F	289	PHE	0	0.009	0.012	20.529	0.011	0.011	0.000	0.000	0.000	0.000
66	F	290	PRO	0	-0.007	-0.003	23.828	-0.005	-0.005	0.000	0.000	0.000	0.000
67	F	291	LYS	1	0.945	0.974	21.698	0.080	0.080	0.000	0.000	0.000	0.000
68	F	292	SER	0	0.031	0.023	26.211	0.007	0.007	0.000	0.000	0.000	0.000

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