FMO DATABASE

FMODB ID: MVQGZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-412921.083614
FMO2-HF: Nuclear repulsion	383997.035266
FMO2-HF: Total energy	-28924.048348
FMO2-MP2: Total energy	-29004.779676

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.
-8.088	-2.875	6.592	-3.925	-7.878	-0.013

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 : -0.028 / q_NPA : -0.056

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	0.046	0.027	3.841	-2.460	0.390	-0.029	-1.362	-1.458	-0.004
4	J	204	ALA	0	0.012	-0.010	6.001	0.251	0.251	0.000	0.000	0.000	0.000
5	J	205	ASP	-1	-0.782	-0.871	8.732	0.026	0.026	0.000	0.000	0.000	0.000
6	J	206	PHE	0	0.008	0.020	4.728	0.220	0.298	-0.001	-0.006	-0.071	0.000
7	J	207	LEU	0	-0.010	-0.017	6.130	-0.203	-0.203	0.000	0.000	0.000	0.000
8	J	208	MET	0	0.000	0.026	2.338	-2.360	-0.923	2.430	-1.461	-2.405	0.000
9	J	209	CYS	0	-0.023	-0.017	5.362	-0.772	-0.727	-0.001	-0.001	-0.042	0.000
10	J	210	TYR	0	0.030	0.006	2.858	-1.116	-0.106	0.349	-0.401	-0.958	-0.004
11	J	211	SER	0	0.045	0.014	9.134	-0.117	-0.117	0.000	0.000	0.000	0.000
12	J	212	VAL	0	-0.037	-0.006	10.619	-0.044	-0.044	0.000	0.000	0.000	0.000
13	J	222	THR	0	-0.007	-0.014	25.179	-0.007	-0.007	0.000	0.000	0.000	0.000
14	J	223	VAL	0	0.040	0.006	26.568	0.013	0.013	0.000	0.000	0.000	0.000
15	J	224	ASN	0	0.034	0.033	27.917	0.008	0.008	0.000	0.000	0.000	0.000
16	J	225	GLY	0	0.029	0.032	23.935	0.006	0.006	0.000	0.000	0.000	0.000
17	J	226	SER	0	0.010	-0.004	18.690	-0.015	-0.015	0.000	0.000	0.000	0.000
18	J	227	TRP	0	0.006	-0.010	20.274	0.009	0.009	0.000	0.000	0.000	0.000
19	J	228	TYR	0	0.093	0.042	11.943	0.014	0.014	0.000	0.000	0.000	0.000
20	J	229	ILE	0	0.037	0.025	15.992	0.009	0.009	0.000	0.000	0.000	0.000
21	J	230	GLN	0	0.031	0.012	18.848	-0.017	-0.017	0.000	0.000	0.000	0.000
22	J	231	ASP	-1	-0.755	-0.866	19.848	0.164	0.164	0.000	0.000	0.000	0.000
23	J	232	LEU	0	0.002	0.003	14.985	-0.014	-0.014	0.000	0.000	0.000	0.000
24	J	233	CYS	0	-0.024	-0.018	18.719	-0.008	-0.008	0.000	0.000	0.000	0.000
25	J	234	GLU	-1	-0.820	-0.896	21.771	0.116	0.116	0.000	0.000	0.000	0.000
26	J	235	MET	0	-0.035	-0.023	20.120	-0.024	-0.024	0.000	0.000	0.000	0.000
27	J	236	LEU	0	0.001	-0.009	17.836	-0.014	-0.014	0.000	0.000	0.000	0.000
28	J	237	GLY	0	-0.002	0.002	21.709	-0.012	-0.012	0.000	0.000	0.000	0.000
29	J	238	LYS	1	0.823	0.911	25.211	-0.132	-0.132	0.000	0.000	0.000	0.000
30	J	239	TYR	0	0.021	-0.002	22.841	-0.011	-0.011	0.000	0.000	0.000	0.000
31	J	240	GLY	0	0.024	0.011	20.911	-0.004	-0.004	0.000	0.000	0.000	0.000
32	J	241	SER	0	-0.040	-0.007	21.617	0.002	0.002	0.000	0.000	0.000	0.000
33	J	242	SER	0	-0.010	-0.020	23.464	-0.016	-0.016	0.000	0.000	0.000	0.000
34	J	243	LEU	0	0.015	0.012	20.871	-0.010	-0.010	0.000	0.000	0.000	0.000
35	J	244	GLU	-1	-0.783	-0.850	15.105	0.121	0.121	0.000	0.000	0.000	0.000
36	J	245	PHE	0	0.040	0.004	12.149	0.007	0.007	0.000	0.000	0.000	0.000
37	J	246	THR	0	-0.006	-0.035	11.313	0.021	0.021	0.000	0.000	0.000	0.000
38	J	247	GLU	-1	-0.802	-0.876	14.014	0.048	0.048	0.000	0.000	0.000	0.000
39	J	248	LEU	0	-0.018	-0.002	17.595	0.001	0.001	0.000	0.000	0.000	0.000
40	J	249	LEU	0	0.007	-0.006	11.445	0.004	0.004	0.000	0.000	0.000	0.000
41	J	250	THR	0	-0.024	-0.020	15.279	-0.008	-0.008	0.000	0.000	0.000	0.000
42	J	251	LEU	0	-0.058	-0.029	16.618	-0.016	-0.016	0.000	0.000	0.000	0.000
43	J	252	VAL	0	-0.018	0.001	16.126	-0.008	-0.008	0.000	0.000	0.000	0.000
44	J	253	ASN	0	0.021	-0.001	12.577	0.033	0.033	0.000	0.000	0.000	0.000
45	J	254	ARG	1	0.942	0.987	16.484	-0.091	-0.091	0.000	0.000	0.000	0.000
46	J	255	LYS	1	0.822	0.913	20.092	-0.148	-0.148	0.000	0.000	0.000	0.000
47	J	256	VAL	0	0.006	-0.006	17.609	-0.005	-0.005	0.000	0.000	0.000	0.000
48	J	257	SER	0	-0.088	-0.045	19.113	-0.016	-0.016	0.000	0.000	0.000	0.000
49	J	258	GLN	0	-0.053	-0.028	20.729	-0.011	-0.011	0.000	0.000	0.000	0.000
50	J	259	ARG	1	0.791	0.903	22.409	-0.168	-0.168	0.000	0.000	0.000	0.000
51	J	273	LYS	1	1.020	1.016	20.616	-0.062	-0.062	0.000	0.000	0.000	0.000
52	J	274	GLN	0	-0.034	-0.034	17.291	0.020	0.020	0.000	0.000	0.000	0.000
53	J	275	VAL	0	0.010	-0.012	14.558	-0.017	-0.017	0.000	0.000	0.000	0.000
54	J	276	PRO	0	-0.035	0.019	12.683	0.007	0.007	0.000	0.000	0.000	0.000
55	J	277	CYS	0	-0.021	-0.017	8.260	-0.086	-0.086	0.000	0.000	0.000	0.000
56	J	278	PHE	0	0.021	-0.003	7.250	0.150	0.150	0.000	0.000	0.000	0.000
57	J	279	ALA	0	0.025	0.014	3.271	-0.785	-0.276	0.058	-0.128	-0.440	0.000
58	J	280	SER	0	0.008	-0.004	4.672	0.353	0.468	-0.001	-0.009	-0.105	0.000
59	J	281	MET	0	-0.048	0.001	2.288	-0.800	-1.631	3.787	-0.557	-2.399	-0.005
60	J	282	LEU	0	-0.034	0.000	6.357	-0.021	-0.021	0.000	0.000	0.000	0.000
61	J	283	THR	0	-0.046	-0.053	10.010	-0.044	-0.044	0.000	0.000	0.000	0.000
62	J	284	LYS	1	0.834	0.915	12.865	0.071	0.071	0.000	0.000	0.000	0.000
63	J	285	LYS	1	0.838	0.924	14.398	-0.017	-0.017	0.000	0.000	0.000	0.000
64	J	286	LEU	0	-0.009	-0.007	13.231	0.000	0.000	0.000	0.000	0.000	0.000
65	J	287	HIS	0	0.016	-0.004	16.554	0.002	0.002	0.000	0.000	0.000	0.000
66	J	288	PHE	0	-0.031	-0.015	15.053	-0.002	-0.002	0.000	0.000	0.000	0.000
67	J	289	PHE	0	0.005	0.009	21.060	0.001	0.001	0.000	0.000	0.000	0.000
68	J	290	PRO	0	-0.005	-0.008	24.742	0.006	0.006	0.000	0.000	0.000	0.000
69	J	291	LYS	1	0.923	0.972	23.860	-0.112	-0.112	0.000	0.000	0.000	0.000
70	J	292	SER	0	0.038	0.029	27.795	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)