FMO DATABASE

FMODB ID: V53M1

Calculation Name: 3P45-B-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3P45

Chain ID: B

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	72
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-437641.342142
FMO2-HF: Nuclear repulsion	407656.409327
FMO2-HF: Total energy	-29984.932815
FMO2-MP2: Total energy	-30068.910983

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(B:198:TYR)

Summations of interaction energy for fragment #1(B:198:TYR)

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.
-12.936	-3.665	4.572	-4.4	-9.444	-0.015

Interaction energy analysis for fragmet #1(B:198:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.030

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	B	200	LEU	0	-0.016	0.000	3.532	-2.451	1.382	-0.021	-1.798	-2.014	-0.007
4	B	201	PRO	0	-0.023	-0.024	5.515	-0.056	-0.056	0.000	0.000	0.000	0.000
5	B	202	ALA	0	0.038	0.030	8.853	-0.036	-0.036	0.000	0.000	0.000	0.000
6	B	203	GLY	0	0.019	0.007	11.244	0.026	0.026	0.000	0.000	0.000	0.000
7	B	204	ALA	0	0.004	-0.012	13.849	0.024	0.024	0.000	0.000	0.000	0.000
8	B	205	ASP	-1	-0.822	-0.893	16.110	0.007	0.007	0.000	0.000	0.000	0.000
9	B	206	PHE	0	-0.005	0.022	11.148	0.006	0.006	0.000	0.000	0.000	0.000
10	B	207	LEU	0	-0.012	-0.011	10.401	0.008	0.008	0.000	0.000	0.000	0.000
11	B	208	MET	0	-0.022	0.000	6.023	0.038	0.038	0.000	0.000	0.000	0.000
12	B	209	CYS	0	-0.008	-0.016	7.764	0.122	0.122	0.000	0.000	0.000	0.000
13	B	210	TYR	0	0.063	0.026	2.695	-4.002	-0.829	2.357	-1.225	-4.306	-0.007
14	B	211	SER	0	0.038	0.017	4.571	-0.296	-0.161	-0.001	-0.013	-0.121	0.000
15	B	212	VAL	0	-0.004	0.010	2.301	-5.272	-3.142	2.237	-1.364	-3.003	-0.001
16	B	222	THR	0	0.024	0.008	16.438	-0.019	-0.019	0.000	0.000	0.000	0.000
17	B	223	VAL	0	0.021	-0.013	17.830	0.034	0.034	0.000	0.000	0.000	0.000
18	B	224	ASN	0	0.009	0.019	20.361	-0.005	-0.005	0.000	0.000	0.000	0.000
19	B	225	GLY	0	0.028	0.028	16.738	0.006	0.006	0.000	0.000	0.000	0.000
20	B	226	SER	0	0.002	-0.010	11.460	-0.024	-0.024	0.000	0.000	0.000	0.000
21	B	227	TRP	0	0.049	0.005	12.087	0.039	0.039	0.000	0.000	0.000	0.000
22	B	228	TYR	0	0.081	0.047	8.307	0.035	0.035	0.000	0.000	0.000	0.000
23	B	229	ILE	0	0.060	0.035	10.452	-0.038	-0.038	0.000	0.000	0.000	0.000
24	B	230	GLN	0	0.009	0.009	13.264	-0.068	-0.068	0.000	0.000	0.000	0.000
25	B	231	ASP	-1	-0.796	-0.901	14.699	0.308	0.308	0.000	0.000	0.000	0.000
26	B	232	LEU	0	-0.026	-0.021	11.763	-0.035	-0.035	0.000	0.000	0.000	0.000
27	B	233	CYS	0	-0.034	-0.034	15.023	-0.050	-0.050	0.000	0.000	0.000	0.000
28	B	234	GLU	-1	-0.793	-0.876	17.923	0.179	0.179	0.000	0.000	0.000	0.000
29	B	235	MET	0	-0.021	-0.020	17.934	-0.040	-0.040	0.000	0.000	0.000	0.000
30	B	236	LEU	0	0.015	0.006	16.394	-0.027	-0.027	0.000	0.000	0.000	0.000
31	B	237	GLY	0	-0.008	0.004	20.263	-0.024	-0.024	0.000	0.000	0.000	0.000
32	B	238	LYS	1	0.814	0.919	23.007	-0.199	-0.199	0.000	0.000	0.000	0.000
33	B	239	TYR	0	0.020	-0.024	21.999	-0.012	-0.012	0.000	0.000	0.000	0.000
34	B	240	GLY	0	0.027	0.017	21.619	-0.003	-0.003	0.000	0.000	0.000	0.000
35	B	241	SER	0	-0.044	-0.010	22.441	-0.005	-0.005	0.000	0.000	0.000	0.000
36	B	242	SER	0	-0.034	-0.030	25.261	-0.012	-0.012	0.000	0.000	0.000	0.000
37	B	243	LEU	0	0.005	0.005	22.564	-0.007	-0.007	0.000	0.000	0.000	0.000
38	B	244	GLU	-1	-0.757	-0.840	19.397	0.169	0.169	0.000	0.000	0.000	0.000
39	B	245	PHE	0	0.042	0.000	14.031	0.023	0.023	0.000	0.000	0.000	0.000
40	B	246	THR	0	-0.032	-0.041	14.867	0.044	0.044	0.000	0.000	0.000	0.000
41	B	247	GLU	-1	-0.854	-0.922	16.589	0.186	0.186	0.000	0.000	0.000	0.000
42	B	248	LEU	0	-0.016	0.005	17.061	0.018	0.018	0.000	0.000	0.000	0.000
43	B	249	LEU	0	0.012	-0.012	11.948	0.031	0.031	0.000	0.000	0.000	0.000
44	B	250	THR	0	-0.063	-0.035	14.381	0.055	0.055	0.000	0.000	0.000	0.000
45	B	251	LEU	0	-0.061	-0.042	16.305	-0.008	-0.008	0.000	0.000	0.000	0.000
46	B	252	VAL	0	-0.017	0.003	12.762	-0.005	-0.005	0.000	0.000	0.000	0.000
47	B	253	ASN	0	0.021	-0.002	11.921	0.097	0.097	0.000	0.000	0.000	0.000
48	B	254	ARG	1	0.925	0.970	13.607	-0.228	-0.228	0.000	0.000	0.000	0.000
49	B	255	LYS	1	0.832	0.924	16.567	-0.259	-0.259	0.000	0.000	0.000	0.000
50	B	256	VAL	0	0.029	0.003	10.741	-0.016	-0.016	0.000	0.000	0.000	0.000
51	B	257	SER	0	-0.077	-0.018	13.290	-0.051	-0.051	0.000	0.000	0.000	0.000
52	B	258	GLN	0	-0.023	-0.012	14.141	-0.035	-0.035	0.000	0.000	0.000	0.000
53	B	259	ARG	1	0.784	0.900	14.829	-0.332	-0.332	0.000	0.000	0.000	0.000
54	B	260	ARG	1	0.982	1.002	15.718	-0.095	-0.095	0.000	0.000	0.000	0.000
55	B	274	GLN	0	0.008	-0.004	7.334	-0.175	-0.175	0.000	0.000	0.000	0.000
56	B	275	VAL	0	-0.053	-0.051	7.592	0.027	0.027	0.000	0.000	0.000	0.000
57	B	276	PRO	0	-0.047	0.018	6.844	0.060	0.060	0.000	0.000	0.000	0.000
58	B	277	CYS	0	0.001	-0.013	6.191	-0.338	-0.338	0.000	0.000	0.000	0.000
59	B	278	PHE	0	-0.012	-0.012	7.841	0.158	0.158	0.000	0.000	0.000	0.000
60	B	279	ALA	0	0.039	0.029	6.180	-0.084	-0.084	0.000	0.000	0.000	0.000
61	B	280	SER	0	-0.002	-0.012	8.103	-0.098	-0.098	0.000	0.000	0.000	0.000
62	B	281	MET	0	0.022	0.021	10.682	-0.021	-0.021	0.000	0.000	0.000	0.000
63	B	282	LEU	0	-0.049	-0.011	13.194	-0.015	-0.015	0.000	0.000	0.000	0.000
64	B	283	THR	0	-0.024	-0.034	16.008	0.001	0.001	0.000	0.000	0.000	0.000
65	B	284	LYS	1	0.865	0.926	19.412	-0.019	-0.019	0.000	0.000	0.000	0.000
66	B	285	LYS	1	0.935	0.983	19.982	-0.093	-0.093	0.000	0.000	0.000	0.000
67	B	286	LEU	0	-0.019	-0.004	17.509	-0.011	-0.011	0.000	0.000	0.000	0.000
68	B	287	HIS	0	0.015	0.002	21.257	0.013	0.013	0.000	0.000	0.000	0.000
69	B	288	PHE	0	-0.028	-0.015	18.904	-0.009	-0.009	0.000	0.000	0.000	0.000
70	B	289	PHE	0	0.009	0.019	24.340	0.002	0.002	0.000	0.000	0.000	0.000
71	B	290	PRO	0	0.002	0.002	28.060	-0.001	-0.001	0.000	0.000	0.000	0.000
72	B	291	LYS	1	0.983	0.996	27.311	-0.078	-0.078	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:198:TYR)