FMO DATABASE

FMODB ID: 17R6Z

Calculation Name: 4JQZ-B-Xray372

Preferred Name: Caspase-3

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4JQZ

Chain ID: B

ChEMBL ID: CHEMBL2334

UniProt ID: P42574

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	188
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-2259575.260052
FMO2-HF: Nuclear repulsion	2181516.644887
FMO2-HF: Total energy	-78058.615165
FMO2-MP2: Total energy	-78281.866953

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:33:ALA)

Summations of interaction energy for fragment #1(B:33: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.
0.825	3.498	0.057	-0.964	-1.767	0

Interaction energy analysis for fragmet #1(B:33:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : -0.003

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

Sort

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].
3	B	35	ASN	0	-0.020	-0.013	3.059	0.776	3.130	0.057	-0.905	-1.507
4	B	36	SER	0	0.030	0.025	4.068	-0.283	0.036	0.000	-0.059	-0.260
5	B	37	TYR	0	-0.028	-0.058	5.462	-0.111	-0.111	0.000	0.000	0.000
6	B	38	LYS	1	0.842	0.907	7.015	0.392	0.392	0.000	0.000	0.000
7	B	39	MET	0	-0.034	-0.025	7.948	0.191	0.191	0.000	0.000	0.000
8	B	40	ASP	-1	-0.829	-0.891	8.024	-0.639	-0.639	0.000	0.000	0.000
9	B	41	TYR	0	-0.075	-0.030	10.730	0.029	0.029	0.000	0.000	0.000
10	B	42	PRO	0	-0.050	-0.031	13.700	0.013	0.013	0.000	0.000	0.000
11	B	43	GLU	-1	-0.851	-0.921	17.078	-0.131	-0.131	0.000	0.000	0.000
12	B	44	MET	0	0.027	0.033	13.651	-0.039	-0.039	0.000	0.000	0.000
13	B	45	GLY	0	0.049	0.013	16.823	-0.011	-0.011	0.000	0.000	0.000
14	B	46	LEU	0	-0.025	0.002	19.557	0.008	0.008	0.000	0.000	0.000
15	B	47	CYS	0	-0.029	-0.006	22.272	-0.002	-0.002	0.000	0.000	0.000
16	B	48	ILE	0	0.008	0.006	24.365	0.006	0.006	0.000	0.000	0.000
17	B	49	ILE	0	0.013	0.010	27.485	0.002	0.002	0.000	0.000	0.000
18	B	50	ILE	0	-0.008	-0.005	29.743	0.002	0.002	0.000	0.000	0.000
19	B	51	ASN	0	-0.019	0.023	32.839	0.003	0.003	0.000	0.000	0.000
20	B	52	ASN	0	0.017	0.020	35.574	-0.001	-0.001	0.000	0.000	0.000
21	B	53	LYS	1	0.875	0.922	38.469	0.031	0.031	0.000	0.000	0.000
22	B	54	ASN	0	-0.008	0.008	40.787	0.003	0.003	0.000	0.000	0.000
23	B	67	THR	0	0.037	-0.027	35.932	0.001	0.001	0.000	0.000	0.000
24	B	68	ASP	-1	-0.813	-0.893	35.426	-0.037	-0.037	0.000	0.000	0.000
25	B	69	VAL	0	0.015	0.004	35.641	-0.003	-0.003	0.000	0.000	0.000
26	B	70	ASP	-1	-0.784	-0.880	32.171	-0.041	-0.041	0.000	0.000	0.000
27	B	71	ALA	0	-0.008	-0.010	31.248	-0.005	-0.005	0.000	0.000	0.000
28	B	72	ALA	0	-0.011	-0.009	31.288	-0.005	-0.005	0.000	0.000	0.000
29	B	73	ASN	0	0.065	0.034	29.669	-0.008	-0.008	0.000	0.000	0.000
30	B	74	LEU	0	0.028	0.030	26.513	-0.007	-0.007	0.000	0.000	0.000
31	B	75	ARG	1	0.861	0.918	26.353	0.059	0.059	0.000	0.000	0.000
32	B	76	GLU	-1	-0.952	-0.986	26.771	-0.078	-0.078	0.000	0.000	0.000
33	B	77	THR	0	-0.021	-0.035	22.939	-0.006	-0.006	0.000	0.000	0.000
34	B	78	PHE	0	0.028	-0.010	20.223	-0.010	-0.010	0.000	0.000	0.000
35	B	79	ARG	1	0.924	0.965	22.128	0.076	0.076	0.000	0.000	0.000
36	B	80	ASN	0	0.006	0.015	22.622	-0.006	-0.006	0.000	0.000	0.000
37	B	81	LEU	0	-0.057	-0.006	17.324	-0.012	-0.012	0.000	0.000	0.000
38	B	82	LYS	1	0.933	0.962	14.889	0.230	0.230	0.000	0.000	0.000
39	B	83	TYR	0	-0.007	-0.007	16.607	-0.012	-0.012	0.000	0.000	0.000
40	B	84	GLU	-1	-0.861	-0.915	21.280	-0.094	-0.094	0.000	0.000	0.000
41	B	85	VAL	0	-0.049	-0.029	24.351	0.005	0.005	0.000	0.000	0.000
42	B	86	ARG	1	0.737	0.857	26.732	0.086	0.086	0.000	0.000	0.000
43	B	87	ASN	0	0.033	0.027	29.820	-0.002	-0.002	0.000	0.000	0.000
44	B	88	LYS	1	0.926	0.962	32.343	0.055	0.055	0.000	0.000	0.000
45	B	89	ASN	0	-0.006	-0.016	34.868	0.000	0.000	0.000	0.000	0.000
46	B	90	ASP	-1	-0.834	-0.922	38.055	-0.027	-0.027	0.000	0.000	0.000
47	B	91	LEU	0	-0.014	0.010	35.278	0.000	0.000	0.000	0.000	0.000
48	B	92	THR	0	0.058	0.029	39.383	0.001	0.001	0.000	0.000	0.000
49	B	93	ARG	1	0.924	0.957	38.954	0.012	0.012	0.000	0.000	0.000
50	B	94	GLU	-1	-0.843	-0.929	38.694	-0.019	-0.019	0.000	0.000	0.000
51	B	95	GLU	-1	-0.818	-0.913	38.868	-0.030	-0.030	0.000	0.000	0.000
52	B	96	ILE	0	-0.043	-0.011	33.694	-0.003	-0.003	0.000	0.000	0.000
53	B	97	VAL	0	-0.059	-0.040	33.971	-0.003	-0.003	0.000	0.000	0.000
54	B	98	GLU	-1	-0.979	-0.989	34.444	-0.034	-0.034	0.000	0.000	0.000
55	B	99	LEU	0	0.049	0.033	31.453	-0.003	-0.003	0.000	0.000	0.000
56	B	100	MET	0	-0.041	-0.033	27.488	-0.005	-0.005	0.000	0.000	0.000
57	B	101	ARG	1	0.947	0.983	29.588	0.027	0.027	0.000	0.000	0.000
58	B	102	ASP	-1	-0.853	-0.891	31.125	-0.044	-0.044	0.000	0.000	0.000
59	B	103	VAL	0	0.000	-0.004	25.930	-0.004	-0.004	0.000	0.000	0.000
60	B	104	SER	0	-0.126	-0.076	26.305	-0.006	-0.006	0.000	0.000	0.000
61	B	105	LYS	1	0.920	0.950	26.914	0.038	0.038	0.000	0.000	0.000
62	B	106	GLU	-1	-0.812	-0.881	26.382	-0.082	-0.082	0.000	0.000	0.000
63	B	107	ASP	-1	-0.824	-0.863	23.758	-0.109	-0.109	0.000	0.000	0.000
64	B	108	HIS	0	-0.038	-0.045	20.239	-0.016	-0.016	0.000	0.000	0.000
65	B	109	SER	0	-0.046	-0.084	19.044	-0.022	-0.022	0.000	0.000	0.000
66	B	110	LYS	1	0.920	0.960	17.866	0.130	0.130	0.000	0.000	0.000
67	B	111	ARG	1	0.861	0.943	17.537	0.101	0.101	0.000	0.000	0.000
68	B	112	SER	0	0.030	0.001	12.856	-0.018	-0.018	0.000	0.000	0.000
69	B	113	SER	0	-0.030	-0.013	14.367	-0.005	-0.005	0.000	0.000	0.000
70	B	114	PHE	0	-0.006	-0.008	16.486	0.014	0.014	0.000	0.000	0.000
71	B	115	VAL	0	0.010	0.021	19.514	0.004	0.004	0.000	0.000	0.000
72	B	116	CYS	0	-0.056	-0.024	21.861	0.006	0.006	0.000	0.000	0.000
73	B	117	VAL	0	-0.004	-0.009	25.462	0.003	0.003	0.000	0.000	0.000
74	B	118	LEU	0	-0.004	-0.001	27.718	0.002	0.002	0.000	0.000	0.000
75	B	119	LEU	0	-0.011	-0.002	30.801	0.002	0.002	0.000	0.000	0.000
76	B	120	SER	0	0.013	-0.006	33.846	0.000	0.000	0.000	0.000	0.000
77	B	121	HIS	0	0.060	0.054	37.078	-0.001	-0.001	0.000	0.000	0.000
78	B	122	GLY	0	0.006	-0.063	36.022	-0.002	-0.002	0.000	0.000	0.000
79	B	123	GLU	-1	-0.904	-0.950	36.821	-0.001	-0.001	0.000	0.000	0.000
80	B	124	GLU	-1	-0.935	-0.968	35.180	0.007	0.007	0.000	0.000	0.000
81	B	125	GLY	0	-0.025	-0.001	31.938	0.000	0.000	0.000	0.000	0.000
82	B	126	ILE	0	-0.084	-0.032	31.787	-0.004	-0.004	0.000	0.000	0.000
83	B	127	ILE	0	0.013	0.000	32.743	-0.001	-0.001	0.000	0.000	0.000
84	B	128	PHE	0	-0.047	-0.006	35.497	0.001	0.001	0.000	0.000	0.000
85	B	129	GLY	0	0.012	-0.011	38.589	-0.002	-0.002	0.000	0.000	0.000
86	B	130	THR	0	-0.016	-0.013	39.729	0.002	0.002	0.000	0.000	0.000
87	B	131	ASN	0	-0.064	-0.031	42.739	0.002	0.002	0.000	0.000	0.000
88	B	132	GLY	0	0.020	0.004	42.694	0.002	0.002	0.000	0.000	0.000
89	B	133	PRO	0	0.000	0.011	40.088	-0.002	-0.002	0.000	0.000	0.000
90	B	134	VAL	0	-0.036	-0.024	35.674	0.001	0.001	0.000	0.000	0.000
91	B	135	ASP	-1	-0.846	-0.933	35.232	-0.006	-0.006	0.000	0.000	0.000
92	B	136	LEU	0	0.050	0.021	28.245	-0.002	-0.002	0.000	0.000	0.000
93	B	137	LYS	1	1.010	0.998	30.161	-0.006	-0.006	0.000	0.000	0.000
94	B	138	LYS	1	0.894	0.947	31.344	0.015	0.015	0.000	0.000	0.000
95	B	139	ILE	0	0.007	0.011	28.922	-0.002	-0.002	0.000	0.000	0.000
96	B	140	THR	0	0.076	0.027	26.501	-0.003	-0.003	0.000	0.000	0.000
97	B	141	ASN	0	-0.059	-0.036	26.925	-0.001	-0.001	0.000	0.000	0.000
98	B	142	PHE	0	-0.040	-0.022	28.574	0.002	0.002	0.000	0.000	0.000
99	B	143	PHE	0	0.050	0.014	23.327	-0.003	-0.003	0.000	0.000	0.000
100	B	144	ARG	1	0.861	0.928	23.131	-0.007	-0.007	0.000	0.000	0.000
101	B	145	GLY	0	0.009	0.000	21.496	-0.005	-0.005	0.000	0.000	0.000
102	B	146	ASP	-1	-0.806	-0.873	22.272	-0.018	-0.018	0.000	0.000	0.000
103	B	147	ARG	1	0.885	0.970	25.012	0.019	0.019	0.000	0.000	0.000
104	B	148	CYS	0	-0.018	0.010	23.444	-0.007	-0.007	0.000	0.000	0.000
105	B	149	ARG	1	0.989	0.991	18.733	0.073	0.073	0.000	0.000	0.000
106	B	150	SER	0	0.018	0.010	20.676	-0.014	-0.014	0.000	0.000	0.000
107	B	151	LEU	0	0.034	-0.004	18.511	-0.019	-0.019	0.000	0.000	0.000
108	B	152	THR	0	-0.075	-0.060	18.012	-0.003	-0.003	0.000	0.000	0.000
109	B	153	GLY	0	-0.013	0.006	14.709	-0.014	-0.014	0.000	0.000	0.000
110	B	154	LYS	1	0.795	0.915	13.301	0.161	0.161	0.000	0.000	0.000
111	B	155	PRO	0	-0.005	0.009	12.917	0.040	0.040	0.000	0.000	0.000
112	B	156	LYS	1	0.872	0.938	15.773	0.075	0.075	0.000	0.000	0.000
113	B	157	LEU	0	-0.030	-0.021	16.607	0.015	0.015	0.000	0.000	0.000
114	B	158	PHE	0	0.020	0.005	20.603	0.000	0.000	0.000	0.000	0.000
115	B	159	ILE	0	-0.028	-0.011	21.974	0.006	0.006	0.000	0.000	0.000
116	B	160	ILE	0	0.030	0.012	25.673	-0.001	-0.001	0.000	0.000	0.000
117	B	161	GLN	0	0.036	0.003	29.153	0.001	0.001	0.000	0.000	0.000
118	B	162	ALA	0	0.021	0.037	32.004	0.000	0.000	0.000	0.000	0.000
119	B	185	HIS	0	-0.003	-0.012	35.887	0.002	0.002	0.000	0.000	0.000
120	B	186	LYS	1	0.966	0.986	32.194	-0.021	-0.021	0.000	0.000	0.000
121	B	187	ILE	0	0.070	0.039	26.904	-0.003	-0.003	0.000	0.000	0.000
122	B	188	PRO	0	-0.079	-0.042	26.928	0.006	0.006	0.000	0.000	0.000
123	B	189	VAL	0	0.026	0.016	23.769	-0.003	-0.003	0.000	0.000	0.000
124	B	190	GLU	-1	-0.923	-0.961	23.053	0.012	0.012	0.000	0.000	0.000
125	B	191	ALA	0	0.050	0.011	17.907	-0.002	-0.002	0.000	0.000	0.000
126	B	192	ASP	-1	-0.857	-0.896	14.698	-0.079	-0.079	0.000	0.000	0.000
127	B	193	PHE	0	-0.014	-0.005	16.988	-0.027	-0.027	0.000	0.000	0.000
128	B	194	LEU	0	0.013	0.001	17.195	0.009	0.009	0.000	0.000	0.000
129	B	195	TYR	0	0.017	0.004	20.407	-0.011	-0.011	0.000	0.000	0.000
130	B	196	ALA	0	0.008	0.018	22.435	0.007	0.007	0.000	0.000	0.000
131	B	197	TYR	0	0.034	0.015	24.382	-0.005	-0.005	0.000	0.000	0.000
132	B	198	SER	0	0.012	0.017	28.181	0.006	0.006	0.000	0.000	0.000
133	B	199	THR	0	0.006	0.007	30.934	0.000	0.000	0.000	0.000	0.000
134	B	212	GLY	0	0.013	0.007	35.804	0.000	0.000	0.000	0.000	0.000
135	B	213	SER	0	-0.072	-0.055	33.365	0.002	0.002	0.000	0.000	0.000
136	B	214	TRP	0	0.082	0.019	33.195	-0.003	-0.003	0.000	0.000	0.000
137	B	215	PHE	0	0.003	0.012	25.732	-0.002	-0.002	0.000	0.000	0.000
138	B	216	ILE	0	0.021	0.015	28.247	-0.005	-0.005	0.000	0.000	0.000
139	B	217	GLN	0	0.017	0.015	28.545	-0.007	-0.007	0.000	0.000	0.000
140	B	218	SER	0	-0.053	-0.041	27.949	-0.004	-0.004	0.000	0.000	0.000
141	B	219	LEU	0	0.038	0.023	22.216	-0.004	-0.004	0.000	0.000	0.000
142	B	220	CYS	0	-0.024	-0.010	23.915	-0.010	-0.010	0.000	0.000	0.000
143	B	221	ALA	0	-0.032	-0.011	24.936	-0.006	-0.006	0.000	0.000	0.000
144	B	222	MET	0	-0.066	-0.025	21.835	-0.004	-0.004	0.000	0.000	0.000
145	B	223	LEU	0	0.005	0.003	18.986	-0.010	-0.010	0.000	0.000	0.000
146	B	224	LYS	1	0.952	0.989	20.428	0.060	0.060	0.000	0.000	0.000
147	B	225	GLN	0	-0.040	-0.013	22.045	-0.001	-0.001	0.000	0.000	0.000
148	B	226	TYR	0	-0.010	-0.049	18.047	0.002	0.002	0.000	0.000	0.000
149	B	227	ALA	0	0.055	0.040	16.344	-0.008	-0.008	0.000	0.000	0.000
150	B	228	ASP	-1	-0.891	-0.945	14.114	-0.193	-0.193	0.000	0.000	0.000
151	B	229	LYS	1	0.838	0.930	14.284	0.106	0.106	0.000	0.000	0.000
152	B	230	LEU	0	-0.058	-0.031	12.884	-0.004	-0.004	0.000	0.000	0.000
153	B	231	GLU	-1	-0.706	-0.843	9.970	-0.114	-0.114	0.000	0.000	0.000
154	B	232	PHE	0	0.034	-0.006	12.417	0.040	0.040	0.000	0.000	0.000
155	B	233	MET	0	0.031	0.027	14.283	0.025	0.025	0.000	0.000	0.000
156	B	234	HIS	0	-0.002	0.023	13.500	-0.007	-0.007	0.000	0.000	0.000
157	B	235	ILE	0	-0.057	-0.029	15.948	0.010	0.010	0.000	0.000	0.000
158	B	236	LEU	0	0.030	0.002	18.617	0.009	0.009	0.000	0.000	0.000
159	B	237	THR	0	-0.023	-0.029	19.185	0.012	0.012	0.000	0.000	0.000
160	B	238	ARG	1	0.882	0.937	19.100	0.043	0.043	0.000	0.000	0.000
161	B	239	VAL	0	0.002	0.014	22.989	0.002	0.002	0.000	0.000	0.000
162	B	240	ASN	0	0.043	0.022	24.426	-0.003	-0.003	0.000	0.000	0.000
163	B	241	ARG	1	0.972	0.991	23.159	0.011	0.011	0.000	0.000	0.000
164	B	242	LYS	1	0.922	0.973	27.064	0.040	0.040	0.000	0.000	0.000
165	B	243	VAL	0	0.024	0.012	28.817	0.001	0.001	0.000	0.000	0.000
166	B	244	ALA	0	0.012	0.004	30.241	0.001	0.001	0.000	0.000	0.000
167	B	245	THR	0	-0.005	-0.015	30.884	0.002	0.002	0.000	0.000	0.000
168	B	246	GLU	-1	-0.911	-0.971	32.962	-0.025	-0.025	0.000	0.000	0.000
169	B	247	PHE	0	-0.069	-0.048	34.410	0.000	0.000	0.000	0.000	0.000
170	B	248	GLU	-1	-1.002	-0.973	34.550	0.003	0.003	0.000	0.000	0.000
171	B	249	SER	0	-0.061	-0.018	38.006	0.000	0.000	0.000	0.000	0.000
172	B	261	GLN	0	-0.001	-0.023	34.950	0.001	0.001	0.000	0.000	0.000
173	B	262	ILE	0	-0.023	-0.003	28.157	-0.001	-0.001	0.000	0.000	0.000
174	B	263	PRO	0	-0.037	-0.008	26.983	0.001	0.001	0.000	0.000	0.000
175	B	264	CYS	0	-0.008	0.010	26.823	0.006	0.006	0.000	0.000	0.000
176	B	265	ILE	0	-0.013	-0.012	20.077	-0.007	-0.007	0.000	0.000	0.000
177	B	266	VAL	0	-0.009	-0.008	23.031	0.010	0.010	0.000	0.000	0.000
178	B	267	SER	0	0.005	-0.019	16.543	-0.015	-0.015	0.000	0.000	0.000
179	B	268	MET	0	-0.011	-0.001	18.666	0.018	0.018	0.000	0.000	0.000
180	B	269	LEU	0	-0.051	-0.014	13.417	-0.003	-0.003	0.000	0.000	0.000
181	B	270	THR	0	-0.037	-0.018	12.875	0.030	0.030	0.000	0.000	0.000
182	B	271	LYS	1	0.896	0.960	7.747	0.388	0.388	0.000	0.000	0.000
183	B	272	GLU	-1	-0.857	-0.886	6.932	0.069	0.069	0.000	0.000	0.000
184	B	273	LEU	0	-0.036	-0.036	8.499	-0.193	-0.193	0.000	0.000	0.000
185	B	274	TYR	0	-0.013	-0.047	6.530	0.073	0.073	0.000	0.000	0.000
186	B	275	PHE	0	-0.031	-0.019	10.438	-0.040	-0.040	0.000	0.000	0.000
187	B	276	TYR	0	-0.031	-0.019	9.593	0.024	0.024	0.000	0.000	0.000
188	B	277	HIS	0	0.014	0.022	8.368	-0.019	-0.019	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:33:ALA)