FMO DATABASE

FMODB ID: 941J2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-410947.034099
FMO2-HF: Nuclear repulsion	382023.256889
FMO2-HF: Total energy	-28923.77721
FMO2-MP2: Total energy	-29004.489794

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.
-7.358	-2.123	4.364	-3.148	-6.451	-0.017

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 : -0.027 / q_NPA : -0.057

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	0.050	0.037	3.843	-2.177	0.568	-0.024	-1.267	-1.455	-0.005
4	J	204	ALA	0	-0.021	-0.022	6.664	0.113	0.113	0.000	0.000	0.000	0.000
5	J	205	ASP	-1	-0.814	-0.898	9.043	-0.152	-0.152	0.000	0.000	0.000	0.000
6	J	206	PHE	0	-0.026	0.005	4.624	0.265	0.354	-0.001	-0.009	-0.079	0.000
7	J	207	LEU	0	-0.003	-0.003	6.321	-0.212	-0.212	0.000	0.000	0.000	0.000
8	J	208	MET	0	-0.024	-0.006	2.213	-1.171	-0.335	1.519	-0.977	-1.378	-0.003
9	J	209	CYS	0	-0.015	-0.006	5.566	-0.460	-0.460	0.000	0.000	0.000	0.000
10	J	210	TYR	0	0.047	0.015	2.981	-1.196	-0.086	0.176	-0.410	-0.875	-0.004
11	J	211	SER	0	0.037	0.008	9.224	-0.122	-0.122	0.000	0.000	0.000	0.000
12	J	212	VAL	0	-0.025	-0.003	11.070	-0.069	-0.069	0.000	0.000	0.000	0.000
13	J	222	THR	0	0.000	-0.011	25.319	-0.007	-0.007	0.000	0.000	0.000	0.000
14	J	223	VAL	0	0.045	0.005	26.685	0.013	0.013	0.000	0.000	0.000	0.000
15	J	224	ASN	0	0.015	0.023	28.231	0.009	0.009	0.000	0.000	0.000	0.000
16	J	225	GLY	0	0.033	0.031	24.341	0.003	0.003	0.000	0.000	0.000	0.000
17	J	226	SER	0	-0.002	-0.006	18.998	-0.014	-0.014	0.000	0.000	0.000	0.000
18	J	227	TRP	0	0.046	0.008	20.509	0.003	0.003	0.000	0.000	0.000	0.000
19	J	228	TYR	0	0.093	0.047	12.768	0.014	0.014	0.000	0.000	0.000	0.000
20	J	229	ILE	0	0.059	0.027	16.299	-0.003	-0.003	0.000	0.000	0.000	0.000
21	J	230	GLN	0	0.001	0.007	19.283	-0.023	-0.023	0.000	0.000	0.000	0.000
22	J	231	ASP	-1	-0.756	-0.875	20.364	0.138	0.138	0.000	0.000	0.000	0.000
23	J	232	LEU	0	-0.022	-0.012	15.252	-0.015	-0.015	0.000	0.000	0.000	0.000
24	J	233	CYS	0	-0.022	-0.032	19.097	-0.010	-0.010	0.000	0.000	0.000	0.000
25	J	234	GLU	-1	-0.839	-0.903	21.746	0.091	0.091	0.000	0.000	0.000	0.000
26	J	235	MET	0	-0.042	-0.016	20.331	-0.024	-0.024	0.000	0.000	0.000	0.000
27	J	236	LEU	0	0.002	-0.005	17.801	-0.012	-0.012	0.000	0.000	0.000	0.000
28	J	237	GLY	0	0.000	0.013	21.693	-0.012	-0.012	0.000	0.000	0.000	0.000
29	J	238	LYS	1	0.834	0.917	25.463	-0.098	-0.098	0.000	0.000	0.000	0.000
30	J	239	TYR	0	0.008	-0.020	22.739	-0.009	-0.009	0.000	0.000	0.000	0.000
31	J	240	GLY	0	0.039	0.023	21.253	-0.006	-0.006	0.000	0.000	0.000	0.000
32	J	241	SER	0	-0.058	-0.021	21.775	-0.002	-0.002	0.000	0.000	0.000	0.000
33	J	242	SER	0	-0.010	-0.012	23.975	-0.011	-0.011	0.000	0.000	0.000	0.000
34	J	243	LEU	0	-0.005	-0.004	20.900	-0.010	-0.010	0.000	0.000	0.000	0.000
35	J	244	GLU	-1	-0.785	-0.856	15.561	0.007	0.007	0.000	0.000	0.000	0.000
36	J	245	PHE	0	0.033	0.009	12.344	0.011	0.011	0.000	0.000	0.000	0.000
37	J	246	THR	0	-0.008	-0.042	11.503	0.018	0.018	0.000	0.000	0.000	0.000
38	J	247	GLU	-1	-0.851	-0.933	13.918	-0.004	-0.004	0.000	0.000	0.000	0.000
39	J	248	LEU	0	-0.026	0.000	17.338	0.007	0.007	0.000	0.000	0.000	0.000
40	J	249	LEU	0	0.001	-0.007	11.030	0.016	0.016	0.000	0.000	0.000	0.000
41	J	250	THR	0	-0.004	0.002	14.836	0.002	0.002	0.000	0.000	0.000	0.000
42	J	251	LEU	0	-0.036	-0.023	16.181	-0.005	-0.005	0.000	0.000	0.000	0.000
43	J	252	VAL	0	-0.019	0.005	16.248	-0.002	-0.002	0.000	0.000	0.000	0.000
44	J	253	ASN	0	0.022	-0.001	12.583	0.038	0.038	0.000	0.000	0.000	0.000
45	J	254	ARG	1	0.939	0.986	16.728	-0.055	-0.055	0.000	0.000	0.000	0.000
46	J	255	LYS	1	0.829	0.917	20.341	-0.122	-0.122	0.000	0.000	0.000	0.000
47	J	256	VAL	0	0.008	-0.008	17.953	-0.001	-0.001	0.000	0.000	0.000	0.000
48	J	257	SER	0	-0.094	-0.047	19.766	-0.009	-0.009	0.000	0.000	0.000	0.000
49	J	258	GLN	0	-0.064	-0.034	21.256	-0.008	-0.008	0.000	0.000	0.000	0.000
50	J	259	ARG	1	0.815	0.925	22.831	-0.153	-0.153	0.000	0.000	0.000	0.000
51	J	273	LYS	1	1.023	1.015	20.461	-0.054	-0.054	0.000	0.000	0.000	0.000
52	J	274	GLN	0	-0.032	-0.042	17.418	0.026	0.026	0.000	0.000	0.000	0.000
53	J	275	VAL	0	-0.037	-0.025	14.966	-0.014	-0.014	0.000	0.000	0.000	0.000
54	J	276	PRO	0	-0.015	0.026	12.826	0.010	0.010	0.000	0.000	0.000	0.000
55	J	277	CYS	0	-0.008	-0.013	7.998	-0.084	-0.084	0.000	0.000	0.000	0.000
56	J	278	PHE	0	0.015	0.001	7.655	0.137	0.137	0.000	0.000	0.000	0.000
57	J	279	ALA	0	0.019	0.017	3.040	-0.620	-0.244	0.094	-0.113	-0.357	0.000
58	J	280	SER	0	-0.004	-0.014	4.860	0.224	0.305	-0.001	-0.004	-0.076	0.000
59	J	281	MET	0	-0.031	0.002	2.405	-1.724	-1.726	2.601	-0.368	-2.231	-0.005
60	J	282	LEU	0	-0.012	0.011	6.597	0.036	0.036	0.000	0.000	0.000	0.000
61	J	283	THR	0	-0.054	-0.042	10.222	-0.032	-0.032	0.000	0.000	0.000	0.000
62	J	284	LYS	1	0.920	0.957	13.007	0.164	0.164	0.000	0.000	0.000	0.000
63	J	285	LYS	1	0.887	0.956	14.737	0.052	0.052	0.000	0.000	0.000	0.000
64	J	286	LEU	0	-0.011	0.000	13.758	0.003	0.003	0.000	0.000	0.000	0.000
65	J	287	HIS	0	0.005	-0.006	17.132	-0.004	-0.004	0.000	0.000	0.000	0.000
66	J	288	PHE	0	-0.011	-0.012	15.531	0.000	0.000	0.000	0.000	0.000	0.000
67	J	289	PHE	0	0.002	0.008	21.544	0.006	0.006	0.000	0.000	0.000	0.000
68	J	290	PRO	0	0.018	0.004	25.241	0.005	0.005	0.000	0.000	0.000	0.000
69	J	291	LYS	1	0.914	0.968	24.152	-0.066	-0.066	0.000	0.000	0.000	0.000
70	J	292	SER	0	0.052	0.035	28.023	0.003	0.003	0.000	0.000	0.000	0.000

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