FMO DATABASE

FMODB ID: 6697Z

Calculation Name: 3V3K-B-Xray372

Preferred Name: Caspase-9

Target Type: SINGLE PROTEIN

Ligand Name:
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ligand 3-letter code:
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PDB ID: 3V3K

Chain ID: B

ChEMBL ID: CHEMBL2273

UniProt ID: P55211

Base Structure: X-ray

Registration Date: 2023-06-20

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	165
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1650698.175357
FMO2-HF: Nuclear repulsion	1582895.628985
FMO2-HF: Total energy	-67802.546372
FMO2-MP2: Total energy	-67994.689824

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:25:THR)

Summations of interaction energy for fragment #1(B:25:THR)

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.
-3.776	0.504	0.52	-1.77	-3.03	-0.007

Interaction energy analysis for fragmet #1(B:25:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / 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].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	B	27	GLU	-1	-0.829	-0.871	2.543	-4.208	-1.886	0.246	-0.942	-1.625	-0.001
4	B	28	SER	0	-0.029	-0.053	3.120	0.333	0.815	0.009	-0.114	-0.377	0.000
5	B	29	VAL	0	-0.059	-0.034	2.945	-2.893	-1.892	0.265	-0.625	-0.642	-0.006
6	B	30	SER	0	0.031	0.014	5.190	0.254	0.319	-0.001	-0.002	-0.062	0.000
7	B	31	GLU	-1	-0.921	-0.958	7.148	0.206	0.206	0.000	0.000	0.000	0.000
8	B	32	LEU	0	-0.027	-0.012	8.341	-0.138	-0.138	0.000	0.000	0.000	0.000
9	B	33	ASN	0	-0.023	-0.021	7.152	0.142	0.142	0.000	0.000	0.000	0.000
10	B	34	HIS	0	0.047	0.006	11.101	0.025	0.025	0.000	0.000	0.000	0.000
11	B	35	ASN	0	-0.068	-0.037	10.085	0.126	0.126	0.000	0.000	0.000	0.000
12	B	36	HIS	0	-0.029	-0.020	8.247	0.130	0.130	0.000	0.000	0.000	0.000
13	B	37	PHE	0	0.005	0.022	13.726	0.022	0.022	0.000	0.000	0.000	0.000
14	B	38	LEU	0	-0.008	0.009	17.349	-0.021	-0.021	0.000	0.000	0.000	0.000
15	B	39	SER	0	0.022	0.011	20.284	0.014	0.014	0.000	0.000	0.000	0.000
16	B	40	PRO	0	0.035	-0.011	21.728	0.007	0.007	0.000	0.000	0.000	0.000
17	B	41	GLU	-1	-0.933	-0.955	24.943	-0.169	-0.169	0.000	0.000	0.000	0.000
18	B	42	LEU	0	-0.010	-0.005	20.651	0.008	0.008	0.000	0.000	0.000	0.000
19	B	43	GLN	0	-0.052	-0.041	24.714	-0.005	-0.005	0.000	0.000	0.000	0.000
20	B	44	ASP	-1	-0.926	-0.960	26.080	-0.105	-0.105	0.000	0.000	0.000	0.000
21	B	45	LYS	1	0.854	0.911	27.255	0.160	0.160	0.000	0.000	0.000	0.000
22	B	46	LEU	0	-0.039	-0.012	24.816	0.007	0.007	0.000	0.000	0.000	0.000
23	B	47	ASP	-1	-0.834	-0.928	28.277	-0.112	-0.112	0.000	0.000	0.000	0.000
24	B	48	VAL	0	0.012	0.027	31.300	0.009	0.009	0.000	0.000	0.000	0.000
25	B	49	MET	0	-0.011	0.002	29.453	0.004	0.004	0.000	0.000	0.000	0.000
26	B	50	VAL	0	0.018	0.014	29.995	0.006	0.006	0.000	0.000	0.000	0.000
27	B	51	SER	0	-0.054	-0.036	32.902	0.008	0.008	0.000	0.000	0.000	0.000
28	B	52	ILE	0	-0.008	-0.010	36.064	0.006	0.006	0.000	0.000	0.000	0.000
29	B	53	TYR	0	-0.062	-0.099	34.519	0.004	0.004	0.000	0.000	0.000	0.000
30	B	54	SER	0	-0.021	-0.010	36.552	0.005	0.005	0.000	0.000	0.000	0.000
31	B	55	CYS	0	-0.048	-0.021	38.246	0.006	0.006	0.000	0.000	0.000	0.000
32	B	56	ALA	0	-0.043	-0.002	40.076	0.004	0.004	0.000	0.000	0.000	0.000
33	B	57	ARG	1	0.842	0.911	41.926	0.056	0.056	0.000	0.000	0.000	0.000
34	B	58	ASN	0	-0.032	-0.024	43.683	0.000	0.000	0.000	0.000	0.000	0.000
35	B	59	ASN	0	0.032	-0.010	40.966	0.000	0.000	0.000	0.000	0.000	0.000
36	B	60	ASN	0	-0.024	-0.018	41.746	-0.002	-0.002	0.000	0.000	0.000	0.000
37	B	61	GLU	-1	-0.802	-0.886	42.546	-0.060	-0.060	0.000	0.000	0.000	0.000
38	B	62	LEU	0	0.034	0.029	37.032	-0.003	-0.003	0.000	0.000	0.000	0.000
39	B	63	GLU	-1	-0.877	-0.931	37.392	-0.084	-0.084	0.000	0.000	0.000	0.000
40	B	64	GLU	-1	-0.931	-0.958	37.865	-0.081	-0.081	0.000	0.000	0.000	0.000
41	B	65	ILE	0	0.022	0.006	33.100	-0.006	-0.006	0.000	0.000	0.000	0.000
42	B	66	PHE	0	-0.024	-0.024	32.930	-0.009	-0.009	0.000	0.000	0.000	0.000
43	B	67	GLN	0	-0.004	0.001	32.824	-0.009	-0.009	0.000	0.000	0.000	0.000
44	B	68	GLU	-1	-0.802	-0.869	30.826	-0.138	-0.138	0.000	0.000	0.000	0.000
45	B	69	LEU	0	0.042	0.016	26.858	-0.011	-0.011	0.000	0.000	0.000	0.000
46	B	70	SER	0	-0.033	-0.019	27.688	-0.012	-0.012	0.000	0.000	0.000	0.000
47	B	71	ALA	0	0.013	0.029	28.734	-0.005	-0.005	0.000	0.000	0.000	0.000
48	B	72	PHE	0	-0.024	-0.013	21.954	-0.006	-0.006	0.000	0.000	0.000	0.000
49	B	73	VAL	0	0.002	-0.014	23.621	-0.020	-0.020	0.000	0.000	0.000	0.000
50	B	74	SER	0	-0.054	-0.044	23.335	-0.015	-0.015	0.000	0.000	0.000	0.000
51	B	75	GLY	0	0.051	0.033	24.151	-0.003	-0.003	0.000	0.000	0.000	0.000
52	B	76	LEU	0	-0.033	-0.015	18.026	-0.019	-0.019	0.000	0.000	0.000	0.000
53	B	77	MET	0	-0.010	-0.021	19.026	-0.029	-0.029	0.000	0.000	0.000	0.000
54	B	78	ASP	-1	-0.875	-0.931	19.610	-0.203	-0.203	0.000	0.000	0.000	0.000
55	B	79	LYS	1	0.808	0.914	16.693	0.382	0.382	0.000	0.000	0.000	0.000
56	B	80	ARG	1	0.813	0.905	13.668	0.375	0.375	0.000	0.000	0.000	0.000
57	B	81	ASN	0	-0.027	-0.019	15.005	-0.022	-0.022	0.000	0.000	0.000	0.000
58	B	82	SER	0	-0.043	-0.018	17.385	0.012	0.012	0.000	0.000	0.000	0.000
59	B	83	VAL	0	-0.011	0.001	11.528	0.011	0.011	0.000	0.000	0.000	0.000
60	B	84	PHE	0	-0.029	-0.022	8.517	-0.035	-0.035	0.000	0.000	0.000	0.000
61	B	85	GLU	-1	-0.856	-0.916	11.065	-0.055	-0.055	0.000	0.000	0.000	0.000
62	B	86	VAL	0	0.006	0.000	11.041	-0.045	-0.045	0.000	0.000	0.000	0.000
63	B	87	ARG	1	0.844	0.918	10.729	0.039	0.039	0.000	0.000	0.000	0.000
64	B	88	ASN	0	-0.034	-0.019	13.824	-0.008	-0.008	0.000	0.000	0.000	0.000
65	B	89	GLU	-1	-0.796	-0.899	16.288	-0.169	-0.169	0.000	0.000	0.000	0.000
66	B	90	ASN	0	-0.055	-0.042	17.903	0.013	0.013	0.000	0.000	0.000	0.000
67	B	91	THR	0	-0.053	-0.018	17.705	0.017	0.017	0.000	0.000	0.000	0.000
68	B	92	ASP	-1	-0.771	-0.866	17.546	-0.027	-0.027	0.000	0.000	0.000	0.000
69	B	93	GLU	-1	-0.992	-0.985	14.574	0.025	0.025	0.000	0.000	0.000	0.000
70	B	94	VAL	0	-0.034	-0.001	12.561	0.004	0.004	0.000	0.000	0.000	0.000
71	B	95	VAL	0	-0.031	-0.020	7.472	0.007	0.007	0.000	0.000	0.000	0.000
72	B	96	GLY	0	0.030	0.020	7.864	0.026	0.026	0.000	0.000	0.000	0.000
73	B	97	ALA	0	-0.051	-0.040	6.916	0.138	0.138	0.000	0.000	0.000	0.000
74	B	98	LEU	0	-0.005	0.001	7.123	-0.110	-0.110	0.000	0.000	0.000	0.000
75	B	99	ARG	1	0.847	0.930	9.531	0.383	0.383	0.000	0.000	0.000	0.000
76	B	100	ALA	0	-0.042	-0.033	13.081	-0.008	-0.008	0.000	0.000	0.000	0.000
77	B	101	GLY	0	-0.048	-0.019	14.890	-0.004	-0.004	0.000	0.000	0.000	0.000
78	B	102	MET	0	0.010	0.010	12.419	0.013	0.013	0.000	0.000	0.000	0.000
79	B	103	THR	0	-0.038	-0.027	11.220	-0.055	-0.055	0.000	0.000	0.000	0.000
80	B	104	ILE	0	0.024	-0.016	5.013	-0.092	-0.092	0.000	0.000	0.000	0.000
81	B	105	GLU	-1	-0.936	-0.965	8.745	-0.492	-0.492	0.000	0.000	0.000	0.000
82	B	106	ASP	-1	-0.822	-0.902	11.961	-0.437	-0.437	0.000	0.000	0.000	0.000
83	B	107	ARG	1	0.830	0.921	3.906	3.305	3.467	-0.001	-0.043	-0.119	0.000
84	B	108	ASP	-1	-0.775	-0.887	8.758	-1.245	-1.245	0.000	0.000	0.000	0.000
85	B	109	SER	0	-0.035	-0.016	11.513	0.130	0.130	0.000	0.000	0.000	0.000
86	B	110	TYR	0	-0.028	-0.030	12.836	0.080	0.080	0.000	0.000	0.000	0.000
87	B	111	ILE	0	0.025	0.011	8.946	0.048	0.048	0.000	0.000	0.000	0.000
88	B	112	ARG	1	0.941	0.989	13.585	0.461	0.461	0.000	0.000	0.000	0.000
89	B	113	ASP	-1	-0.830	-0.910	16.606	-0.289	-0.289	0.000	0.000	0.000	0.000
90	B	114	LEU	0	-0.040	-0.019	13.931	0.041	0.041	0.000	0.000	0.000	0.000
91	B	115	PHE	0	0.045	0.003	16.139	0.045	0.045	0.000	0.000	0.000	0.000
92	B	116	PHE	0	-0.027	0.001	18.094	0.040	0.040	0.000	0.000	0.000	0.000
93	B	117	LEU	0	0.013	0.003	20.338	0.027	0.027	0.000	0.000	0.000	0.000
94	B	118	HIS	0	0.002	0.016	19.420	0.010	0.010	0.000	0.000	0.000	0.000
95	B	119	SER	0	-0.010	-0.036	21.455	0.026	0.026	0.000	0.000	0.000	0.000
96	B	120	LEU	0	-0.009	-0.005	23.369	0.019	0.019	0.000	0.000	0.000	0.000
97	B	121	LYS	1	0.847	0.909	24.415	0.161	0.161	0.000	0.000	0.000	0.000
98	B	122	VAL	0	0.006	0.010	23.901	0.012	0.012	0.000	0.000	0.000	0.000
99	B	123	LYS	1	0.962	0.997	26.755	0.131	0.131	0.000	0.000	0.000	0.000
100	B	124	ILE	0	-0.041	-0.013	29.402	0.010	0.010	0.000	0.000	0.000	0.000
101	B	125	GLU	-1	-0.857	-0.925	27.855	-0.108	-0.108	0.000	0.000	0.000	0.000
102	B	126	GLU	-1	-0.925	-0.954	29.670	-0.088	-0.088	0.000	0.000	0.000	0.000
103	B	127	SER	0	-0.074	-0.048	33.016	0.007	0.007	0.000	0.000	0.000	0.000
104	B	128	ARG	1	0.791	0.917	33.860	0.085	0.085	0.000	0.000	0.000	0.000
105	B	129	GLN	0	0.063	0.036	35.142	-0.002	-0.002	0.000	0.000	0.000	0.000
106	B	130	GLY	0	-0.038	-0.010	37.368	0.003	0.003	0.000	0.000	0.000	0.000
107	B	131	LYS	1	0.933	0.958	40.917	0.054	0.054	0.000	0.000	0.000	0.000
108	B	132	GLU	-1	-0.894	-0.938	36.429	-0.060	-0.060	0.000	0.000	0.000	0.000
109	B	133	ASP	-1	-0.928	-0.968	37.270	-0.055	-0.055	0.000	0.000	0.000	0.000
110	B	134	SER	0	-0.053	-0.045	38.701	0.002	0.002	0.000	0.000	0.000	0.000
111	B	135	LYS	1	0.898	0.960	35.611	0.075	0.075	0.000	0.000	0.000	0.000
112	B	136	CYM	-1	-0.833	-0.789	35.439	-0.089	-0.089	0.000	0.000	0.000	0.000
113	B	137	LYS	1	0.870	0.902	34.959	0.072	0.072	0.000	0.000	0.000	0.000
114	B	138	VAL	0	0.065	0.004	31.548	-0.005	-0.005	0.000	0.000	0.000	0.000
115	B	139	TYR	0	-0.003	-0.064	29.217	-0.006	-0.006	0.000	0.000	0.000	0.000
116	B	140	ASN	0	-0.058	-0.041	29.724	-0.005	-0.005	0.000	0.000	0.000	0.000
117	B	141	LEU	0	-0.039	0.003	28.193	-0.003	-0.003	0.000	0.000	0.000	0.000
118	B	142	LEU	0	0.025	0.023	25.118	-0.012	-0.012	0.000	0.000	0.000	0.000
119	B	143	CYS	0	-0.088	-0.014	25.286	-0.007	-0.007	0.000	0.000	0.000	0.000
120	B	144	PRO	0	0.038	0.032	22.732	0.012	0.012	0.000	0.000	0.000	0.000
121	B	145	HIS	0	0.053	0.035	25.531	-0.004	-0.004	0.000	0.000	0.000	0.000
122	B	146	HIS	0	0.057	0.020	23.342	-0.009	-0.009	0.000	0.000	0.000	0.000
123	B	147	SER	0	-0.036	-0.018	22.334	-0.007	-0.007	0.000	0.000	0.000	0.000
124	B	148	SER	0	-0.056	-0.041	21.313	-0.014	-0.014	0.000	0.000	0.000	0.000
125	B	149	GLU	-1	-0.773	-0.905	16.525	-0.304	-0.304	0.000	0.000	0.000	0.000
126	B	150	LEU	0	0.028	0.013	17.167	-0.025	-0.025	0.000	0.000	0.000	0.000
127	B	151	TYR	0	0.004	0.008	18.937	-0.008	-0.008	0.000	0.000	0.000	0.000
128	B	152	GLY	0	0.046	0.019	16.389	0.007	0.007	0.000	0.000	0.000	0.000
129	B	153	ASP	-1	-0.791	-0.874	13.560	-0.545	-0.545	0.000	0.000	0.000	0.000
130	B	154	LEU	0	-0.003	-0.008	15.351	-0.009	-0.009	0.000	0.000	0.000	0.000
131	B	155	ARG	1	0.907	0.959	16.745	0.188	0.188	0.000	0.000	0.000	0.000
132	B	156	ALA	0	0.020	0.023	12.663	0.027	0.027	0.000	0.000	0.000	0.000
133	B	157	MET	0	-0.023	-0.029	14.153	-0.009	-0.009	0.000	0.000	0.000	0.000
134	B	158	LYS	1	0.829	0.905	15.354	0.154	0.154	0.000	0.000	0.000	0.000
135	B	159	CYS	0	-0.041	-0.007	15.177	0.028	0.028	0.000	0.000	0.000	0.000
136	B	160	LEU	0	-0.041	-0.021	10.343	0.023	0.023	0.000	0.000	0.000	0.000
137	B	161	VAL	0	-0.057	-0.023	14.756	0.022	0.022	0.000	0.000	0.000	0.000
138	B	162	GLU	-1	-0.847	-0.925	17.651	-0.110	-0.110	0.000	0.000	0.000	0.000
139	B	163	GLY	0	-0.005	0.020	18.138	0.018	0.018	0.000	0.000	0.000	0.000
140	B	164	CYS	0	-0.060	-0.015	17.312	0.013	0.013	0.000	0.000	0.000	0.000
141	B	165	SER	0	-0.037	-0.054	18.309	-0.019	-0.019	0.000	0.000	0.000	0.000
142	B	166	ASP	-1	-0.884	-0.939	20.555	-0.010	-0.010	0.000	0.000	0.000	0.000
143	B	167	ASP	-1	-0.867	-0.907	21.022	-0.105	-0.105	0.000	0.000	0.000	0.000
144	B	168	PHE	0	-0.066	-0.061	17.422	0.004	0.004	0.000	0.000	0.000	0.000
145	B	169	ASN	0	-0.065	-0.025	19.063	0.020	0.020	0.000	0.000	0.000	0.000
146	B	170	PRO	0	0.001	0.024	16.271	0.011	0.011	0.000	0.000	0.000	0.000
147	B	171	PHE	0	-0.008	-0.023	14.356	0.002	0.002	0.000	0.000	0.000	0.000
148	B	172	ASP	-1	-0.935	-0.958	12.623	0.118	0.118	0.000	0.000	0.000	0.000
149	B	173	ILE	0	-0.016	-0.015	7.861	0.006	0.006	0.000	0.000	0.000	0.000
150	B	174	ILE	0	0.038	0.020	10.491	-0.085	-0.085	0.000	0.000	0.000	0.000
151	B	175	ARG	1	0.867	0.934	3.453	0.794	1.042	0.002	-0.044	-0.205	0.000
152	B	176	VAL	0	0.049	0.008	7.894	0.062	0.062	0.000	0.000	0.000	0.000
153	B	177	PRO	0	-0.064	-0.009	7.949	0.063	0.063	0.000	0.000	0.000	0.000
154	B	178	ASP	-1	-0.826	-0.932	9.301	-0.537	-0.537	0.000	0.000	0.000	0.000
155	B	179	LEU	0	-0.035	-0.030	7.873	0.121	0.121	0.000	0.000	0.000	0.000
156	B	180	THR	0	-0.011	-0.003	9.879	0.059	0.059	0.000	0.000	0.000	0.000
157	B	181	TYR	0	-0.069	-0.023	12.404	0.070	0.070	0.000	0.000	0.000	0.000
158	B	182	ASN	0	-0.014	-0.017	15.236	0.023	0.023	0.000	0.000	0.000	0.000
159	B	183	LYS	1	0.866	0.936	15.475	0.244	0.244	0.000	0.000	0.000	0.000
160	B	184	GLY	0	0.050	0.019	16.633	-0.002	-0.002	0.000	0.000	0.000	0.000
161	B	185	SER	0	-0.051	-0.035	18.547	0.000	0.000	0.000	0.000	0.000	0.000
162	B	186	LEU	0	-0.048	-0.023	21.109	0.006	0.006	0.000	0.000	0.000	0.000
163	B	187	GLN	0	-0.010	0.000	21.010	-0.012	-0.012	0.000	0.000	0.000	0.000
164	B	188	CYS	0	-0.062	-0.019	22.856	0.011	0.011	0.000	0.000	0.000	0.000
165	B	189	GLY	0	-0.016	-0.006	25.454	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:25:THR)