FMO DATABASE

FMODB ID: LNZ39

Calculation Name: 3CU5-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3CU5

Chain ID: A

ChEMBL ID:
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UniProt ID: A9KIW7

Base Structure: X-ray

Registration Date: 2023-09-21

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	130
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1174305.211837
FMO2-HF: Nuclear repulsion	1122335.814078
FMO2-HF: Total energy	-51969.39776
FMO2-MP2: Total energy	-52120.945039

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(A:2:SER)

Summations of interaction energy for fragment #1(A:2:SER)

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.
-9.549	-4.456	1.762	-2.68	-4.176	-0.009

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.034

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	A	4	ARG	1	0.849	0.934	2.625	0.220	2.057	0.616	-0.745	-1.709	-0.001
4	A	5	ILE	0	-0.003	0.012	4.357	0.202	0.255	0.000	-0.018	-0.036	0.000
5	A	6	LEU	0	-0.016	-0.015	8.058	0.180	0.180	0.000	0.000	0.000	0.000
6	A	7	ILE	0	-0.023	-0.015	10.264	0.034	0.034	0.000	0.000	0.000	0.000
7	A	8	VAL	0	-0.025	-0.037	13.628	0.053	0.053	0.000	0.000	0.000	0.000
8	A	9	ASP	-1	-0.885	-0.964	16.554	-0.207	-0.207	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.880	-0.939	19.910	-0.113	-0.113	0.000	0.000	0.000	0.000
10	A	11	GLU	-1	-0.942	-0.948	22.896	-0.092	-0.092	0.000	0.000	0.000	0.000
11	A	12	LYS	1	0.879	0.925	21.154	0.049	0.049	0.000	0.000	0.000	0.000
12	A	13	LEU	0	0.019	-0.009	21.416	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	14	THR	0	0.054	0.030	20.778	0.000	0.000	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.896	0.966	16.786	0.138	0.138	0.000	0.000	0.000	0.000
15	A	16	ASP	-1	-0.874	-0.919	18.147	-0.120	-0.120	0.000	0.000	0.000	0.000
16	A	17	GLY	0	0.005	0.009	19.515	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	18	LEU	0	0.027	0.024	16.039	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	19	ILE	0	0.010	-0.014	13.790	-0.022	-0.022	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.063	-0.024	16.454	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	21	ASN	0	-0.094	-0.069	19.487	0.015	0.015	0.000	0.000	0.000	0.000
21	A	22	ILE	0	0.001	0.029	14.309	-0.012	-0.012	0.000	0.000	0.000	0.000
22	A	23	ASN	0	0.025	0.012	16.250	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	24	TRP	0	0.006	-0.061	10.923	-0.045	-0.045	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.932	0.980	12.575	0.128	0.128	0.000	0.000	0.000	0.000
25	A	26	ALA	0	-0.080	-0.037	13.997	-0.028	-0.028	0.000	0.000	0.000	0.000
26	A	27	LEU	0	-0.023	-0.019	11.832	0.001	0.001	0.000	0.000	0.000	0.000
27	A	28	SER	0	0.020	-0.006	7.903	0.122	0.122	0.000	0.000	0.000	0.000
28	A	29	PHE	0	-0.035	0.000	6.310	-0.270	-0.270	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.877	-0.933	2.331	-7.907	-5.248	1.125	-1.748	-2.036	-0.009
30	A	31	GLN	0	-0.056	-0.046	3.340	1.329	1.934	0.023	-0.159	-0.468	0.001
31	A	32	ILE	0	0.011	0.003	5.284	-0.604	-0.605	-0.001	0.000	0.002	0.000
32	A	33	ASP	-1	-0.843	-0.882	6.784	-0.056	-0.056	0.000	0.000	0.000	0.000
33	A	34	GLN	0	0.020	-0.020	9.594	-0.129	-0.129	0.000	0.000	0.000	0.000
34	A	35	ALA	0	-0.025	-0.010	13.257	0.062	0.062	0.000	0.000	0.000	0.000
35	A	36	ASH	0	-0.115	-0.102	15.797	-0.015	-0.015	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.701	-0.774	19.221	-0.131	-0.131	0.000	0.000	0.000	0.000
37	A	38	GLY	0	0.095	0.018	18.861	-0.017	-0.017	0.000	0.000	0.000	0.000
38	A	39	ILE	0	-0.022	-0.009	18.605	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	40	ASN	0	0.003	-0.010	16.407	-0.035	-0.035	0.000	0.000	0.000	0.000
40	A	41	ALA	0	0.054	0.029	14.685	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	42	ILE	0	-0.004	0.011	13.944	-0.043	-0.043	0.000	0.000	0.000	0.000
42	A	43	GLN	0	-0.045	-0.032	14.307	-0.028	-0.028	0.000	0.000	0.000	0.000
43	A	44	ILE	0	0.004	0.006	10.063	0.045	0.045	0.000	0.000	0.000	0.000
44	A	45	ALA	0	0.028	0.025	10.014	-0.043	-0.043	0.000	0.000	0.000	0.000
45	A	46	LEU	0	0.001	0.045	10.502	-0.096	-0.096	0.000	0.000	0.000	0.000
46	A	47	LYS	1	0.865	0.932	10.095	-0.051	-0.051	0.000	0.000	0.000	0.000
47	A	48	HIS	0	-0.041	-0.035	5.679	0.284	0.284	0.000	0.000	0.000	0.000
48	A	49	PRO	0	0.028	0.018	5.345	-0.128	-0.128	0.000	0.000	0.000	0.000
49	A	50	PRO	0	-0.019	0.015	5.653	-0.931	-0.931	0.000	0.000	0.000	0.000
50	A	51	ASN	0	0.023	-0.011	5.080	-1.385	-1.445	-0.001	-0.010	0.071	0.000
51	A	52	VAL	0	0.032	0.009	8.045	0.358	0.358	0.000	0.000	0.000	0.000
52	A	53	LEU	0	0.002	0.002	10.225	-0.023	-0.023	0.000	0.000	0.000	0.000
53	A	54	LEU	0	-0.025	0.004	13.011	0.049	0.049	0.000	0.000	0.000	0.000
54	A	55	THR	0	0.036	0.000	15.233	0.024	0.024	0.000	0.000	0.000	0.000
55	A	56	ASP	-1	-0.759	-0.846	18.191	-0.209	-0.209	0.000	0.000	0.000	0.000
56	A	57	VAL	0	0.000	-0.013	21.939	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.944	0.979	24.218	0.156	0.156	0.000	0.000	0.000	0.000
58	A	59	MET	0	-0.004	0.007	20.266	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	60	PRO	0	0.046	0.009	25.861	0.004	0.004	0.000	0.000	0.000	0.000
60	A	61	ARG	1	0.854	0.926	23.145	0.111	0.111	0.000	0.000	0.000	0.000
61	A	62	MET	0	0.036	0.032	20.563	-0.003	-0.003	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.914	-0.945	23.299	-0.188	-0.188	0.000	0.000	0.000	0.000
63	A	64	GLY	0	0.033	0.010	21.065	-0.015	-0.015	0.000	0.000	0.000	0.000
64	A	65	ILE	0	-0.062	-0.043	21.198	-0.028	-0.028	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.888	-0.930	23.039	-0.179	-0.179	0.000	0.000	0.000	0.000
66	A	67	LEU	0	0.022	-0.004	16.605	-0.014	-0.014	0.000	0.000	0.000	0.000
67	A	68	VAL	0	-0.065	-0.041	17.920	-0.041	-0.041	0.000	0.000	0.000	0.000
68	A	69	ASP	-1	-0.894	-0.940	18.750	-0.292	-0.292	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.046	-0.034	19.099	0.012	0.012	0.000	0.000	0.000	0.000
70	A	71	ILE	0	0.025	0.001	13.636	-0.017	-0.017	0.000	0.000	0.000	0.000
71	A	72	LEU	0	-0.002	0.003	15.144	-0.037	-0.037	0.000	0.000	0.000	0.000
72	A	73	LYS	1	0.891	0.948	16.867	0.239	0.239	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.088	-0.039	14.093	0.034	0.034	0.000	0.000	0.000	0.000
74	A	75	TYR	0	-0.051	-0.082	9.744	-0.063	-0.063	0.000	0.000	0.000	0.000
75	A	76	PRO	0	-0.008	0.011	12.629	-0.058	-0.058	0.000	0.000	0.000	0.000
76	A	77	ASP	-1	-0.883	-0.944	11.035	-0.501	-0.501	0.000	0.000	0.000	0.000
77	A	78	CYS	0	-0.116	-0.028	11.157	-0.142	-0.142	0.000	0.000	0.000	0.000
78	A	79	SER	0	0.002	0.011	12.045	0.135	0.135	0.000	0.000	0.000	0.000
79	A	80	VAL	0	0.047	0.008	13.233	-0.087	-0.087	0.000	0.000	0.000	0.000
80	A	81	ILE	0	-0.046	-0.029	15.246	0.070	0.070	0.000	0.000	0.000	0.000
81	A	82	PHE	0	0.027	0.007	17.640	0.004	0.004	0.000	0.000	0.000	0.000
82	A	83	MET	0	-0.001	-0.005	19.126	0.011	0.011	0.000	0.000	0.000	0.000
83	A	84	SER	0	-0.042	-0.043	22.620	0.010	0.010	0.000	0.000	0.000	0.000
84	A	85	GLY	0	-0.056	0.006	26.246	0.009	0.009	0.000	0.000	0.000	0.000
85	A	86	TYR	0	0.055	0.006	29.355	0.011	0.011	0.000	0.000	0.000	0.000
86	A	87	SER	0	-0.046	-0.022	31.676	0.006	0.006	0.000	0.000	0.000	0.000
87	A	88	ASP	-1	-0.883	-0.950	28.754	-0.165	-0.165	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.933	0.963	29.392	0.144	0.144	0.000	0.000	0.000	0.000
89	A	90	GLU	-1	-0.940	-0.981	30.465	-0.125	-0.125	0.000	0.000	0.000	0.000
90	A	91	TYR	0	-0.040	-0.006	27.145	0.010	0.010	0.000	0.000	0.000	0.000
91	A	92	LEU	0	0.008	-0.013	29.188	-0.017	-0.017	0.000	0.000	0.000	0.000
92	A	93	LYS	1	0.864	0.972	24.050	0.243	0.243	0.000	0.000	0.000	0.000
93	A	94	ALA	0	-0.049	-0.025	25.660	-0.017	-0.017	0.000	0.000	0.000	0.000
94	A	95	ALA	0	0.060	0.039	25.010	-0.014	-0.014	0.000	0.000	0.000	0.000
95	A	96	ILE	0	-0.036	-0.025	25.930	0.015	0.015	0.000	0.000	0.000	0.000
96	A	97	LYS	1	0.951	0.965	24.610	0.145	0.145	0.000	0.000	0.000	0.000
97	A	98	PHE	0	0.023	-0.030	23.176	0.024	0.024	0.000	0.000	0.000	0.000
98	A	99	ARG	1	0.983	1.003	22.478	0.193	0.193	0.000	0.000	0.000	0.000
99	A	100	ALA	0	-0.012	0.015	22.838	0.009	0.009	0.000	0.000	0.000	0.000
100	A	101	ILE	0	0.019	0.032	19.559	-0.023	-0.023	0.000	0.000	0.000	0.000
101	A	102	ARG	1	0.820	0.956	19.336	0.375	0.375	0.000	0.000	0.000	0.000
102	A	103	TYR	0	0.042	-0.038	21.170	-0.007	-0.007	0.000	0.000	0.000	0.000
103	A	104	VAL	0	0.025	0.019	21.232	0.006	0.006	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.871	-0.919	24.000	-0.167	-0.167	0.000	0.000	0.000	0.000
105	A	106	LYS	1	0.871	0.923	24.707	0.201	0.201	0.000	0.000	0.000	0.000
106	A	107	PRO	0	-0.011	-0.027	28.082	0.007	0.007	0.000	0.000	0.000	0.000
107	A	108	ILE	0	0.018	-0.006	22.618	-0.011	-0.011	0.000	0.000	0.000	0.000
108	A	109	ASP	-1	-0.792	-0.884	25.606	-0.185	-0.185	0.000	0.000	0.000	0.000
109	A	110	PRO	0	0.022	0.005	21.999	-0.022	-0.022	0.000	0.000	0.000	0.000
110	A	111	SER	0	-0.023	-0.005	21.477	-0.026	-0.026	0.000	0.000	0.000	0.000
111	A	112	GLU	-1	-0.900	-0.952	22.529	-0.230	-0.230	0.000	0.000	0.000	0.000
112	A	113	ILE	0	-0.036	-0.022	17.667	-0.019	-0.019	0.000	0.000	0.000	0.000
113	A	114	MET	0	-0.049	-0.008	17.544	-0.067	-0.067	0.000	0.000	0.000	0.000
114	A	115	ASP	-1	-0.898	-0.944	17.894	-0.325	-0.325	0.000	0.000	0.000	0.000
115	A	116	ALA	0	-0.031	-0.013	18.530	-0.032	-0.032	0.000	0.000	0.000	0.000
116	A	117	LEU	0	0.009	0.001	12.514	-0.064	-0.064	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.973	0.989	14.018	0.243	0.243	0.000	0.000	0.000	0.000
118	A	119	GLN	0	0.002	-0.005	15.722	-0.032	-0.032	0.000	0.000	0.000	0.000
119	A	120	SER	0	-0.006	-0.005	13.426	0.014	0.014	0.000	0.000	0.000	0.000
120	A	121	ILE	0	-0.003	0.006	9.418	-0.070	-0.070	0.000	0.000	0.000	0.000
121	A	122	GLN	0	-0.039	-0.016	12.051	0.000	0.000	0.000	0.000	0.000	0.000
122	A	123	THR	0	-0.010	-0.013	13.996	0.071	0.071	0.000	0.000	0.000	0.000
123	A	124	VAL	0	0.044	0.025	8.087	0.025	0.025	0.000	0.000	0.000	0.000
124	A	125	LEU	0	-0.012	0.003	8.490	0.112	0.112	0.000	0.000	0.000	0.000
125	A	126	GLN	0	-0.018	-0.020	11.381	0.100	0.100	0.000	0.000	0.000	0.000
126	A	127	HIS	0	-0.004	-0.001	11.383	0.119	0.119	0.000	0.000	0.000	0.000
127	A	128	GLN	0	-0.002	-0.003	6.476	0.119	0.119	0.000	0.000	0.000	0.000
128	A	129	ALA	0	-0.096	-0.023	10.906	0.170	0.170	0.000	0.000	0.000	0.000
129	A	130	GLN	0	-0.040	-0.012	12.947	0.014	0.014	0.000	0.000	0.000	0.000
130	A	131	GLN	0	-0.052	-0.025	12.047	0.085	0.085	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)