FMO DATABASE

FMODB ID: LN799

Calculation Name: 5D50-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: 5D50

Chain ID: A

ChEMBL ID:
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UniProt ID: T1S9Z0

Base Structure: X-ray

Registration Date: 2023-09-22

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	171
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1532191.772115
FMO2-HF: Nuclear repulsion	1463603.577786
FMO2-HF: Total energy	-68588.194329
FMO2-MP2: Total energy	-68788.093818

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:0:ALA)

Summations of interaction energy for fragment #1(A:0: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.
-0.824	1.213	0.016	-1.101	-0.952	0.004

Interaction energy analysis for fragmet #1(A:0:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.016

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	A	2	LYS	1	0.777	0.863	3.624	0.427	2.464	0.016	-1.101	-0.952	0.004
4	A	3	SER	0	0.019	0.014	5.857	0.719	0.719	0.000	0.000	0.000	0.000
5	A	4	ILE	0	0.060	0.013	7.486	-0.061	-0.061	0.000	0.000	0.000	0.000
6	A	5	TYR	0	-0.058	-0.035	9.607	0.071	0.071	0.000	0.000	0.000	0.000
7	A	6	ASP	-1	-0.771	-0.875	5.993	-1.763	-1.763	0.000	0.000	0.000	0.000
8	A	7	ILE	0	-0.001	0.024	9.178	0.059	0.059	0.000	0.000	0.000	0.000
9	A	8	ARG	1	0.783	0.849	11.840	0.537	0.537	0.000	0.000	0.000	0.000
10	A	9	ARG	1	0.847	0.921	7.887	1.111	1.111	0.000	0.000	0.000	0.000
11	A	10	LYS	1	0.878	0.953	11.855	0.966	0.966	0.000	0.000	0.000	0.000
12	A	11	ASN	0	0.009	-0.014	13.784	0.081	0.081	0.000	0.000	0.000	0.000
13	A	12	LEU	0	-0.034	-0.021	16.797	0.066	0.066	0.000	0.000	0.000	0.000
14	A	13	ASN	0	-0.061	-0.056	15.327	0.097	0.097	0.000	0.000	0.000	0.000
15	A	14	GLU	-1	-0.810	-0.889	16.422	-0.482	-0.482	0.000	0.000	0.000	0.000
16	A	15	ILE	0	-0.019	-0.008	19.305	0.041	0.041	0.000	0.000	0.000	0.000
17	A	16	ILE	0	-0.073	-0.038	21.384	0.035	0.035	0.000	0.000	0.000	0.000
18	A	17	LEU	0	0.023	0.011	20.369	0.028	0.028	0.000	0.000	0.000	0.000
19	A	18	ARG	1	0.852	0.907	19.830	0.383	0.383	0.000	0.000	0.000	0.000
20	A	19	ASP	-1	-0.857	-0.895	25.420	-0.233	-0.233	0.000	0.000	0.000	0.000
21	A	20	PHE	0	-0.114	-0.074	25.774	0.021	0.021	0.000	0.000	0.000	0.000
22	A	21	ASP	-1	-0.881	-0.938	27.773	-0.144	-0.144	0.000	0.000	0.000	0.000
23	A	22	ASP	-1	-0.874	-0.942	21.979	-0.252	-0.252	0.000	0.000	0.000	0.000
24	A	23	THR	0	-0.075	-0.026	24.394	0.011	0.011	0.000	0.000	0.000	0.000
25	A	24	GLN	0	0.100	0.019	20.691	0.018	0.018	0.000	0.000	0.000	0.000
26	A	25	LEU	0	-0.019	-0.016	25.130	0.002	0.002	0.000	0.000	0.000	0.000
27	A	26	ARG	1	0.924	0.956	28.840	0.119	0.119	0.000	0.000	0.000	0.000
28	A	27	PHE	0	0.013	0.018	24.015	0.001	0.001	0.000	0.000	0.000	0.000
29	A	28	ALA	0	-0.042	-0.029	27.117	0.005	0.005	0.000	0.000	0.000	0.000
30	A	29	GLU	-1	-0.821	-0.904	28.151	-0.104	-0.104	0.000	0.000	0.000	0.000
31	A	30	ARG	1	0.905	0.972	29.894	0.159	0.159	0.000	0.000	0.000	0.000
32	A	31	VAL	0	-0.023	-0.008	25.659	0.003	0.003	0.000	0.000	0.000	0.000
33	A	32	LYS	1	0.944	0.982	28.974	0.105	0.105	0.000	0.000	0.000	0.000
34	A	33	ARG	1	0.864	0.934	26.406	0.132	0.132	0.000	0.000	0.000	0.000
35	A	34	SER	0	0.056	0.028	27.041	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	35	GLN	0	0.118	0.046	26.129	-0.022	-0.022	0.000	0.000	0.000	0.000
37	A	36	ASN	0	0.045	0.023	24.775	-0.015	-0.015	0.000	0.000	0.000	0.000
38	A	37	LEU	0	-0.084	-0.028	21.529	0.005	0.005	0.000	0.000	0.000	0.000
39	A	38	VAL	0	0.039	0.022	21.185	-0.017	-0.017	0.000	0.000	0.000	0.000
40	A	39	ASN	0	0.035	0.019	20.457	-0.013	-0.013	0.000	0.000	0.000	0.000
41	A	40	ARG	1	0.890	0.943	18.745	0.078	0.078	0.000	0.000	0.000	0.000
42	A	41	TRP	0	-0.027	-0.023	16.700	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	42	CYS	0	-0.029	0.001	15.611	-0.051	-0.051	0.000	0.000	0.000	0.000
44	A	43	THR	0	0.019	-0.004	15.381	-0.057	-0.057	0.000	0.000	0.000	0.000
45	A	44	GLY	0	0.014	0.000	12.412	-0.025	-0.025	0.000	0.000	0.000	0.000
46	A	45	ILE	0	-0.044	-0.005	12.935	0.034	0.034	0.000	0.000	0.000	0.000
47	A	46	LYS	1	0.896	0.948	15.567	0.178	0.178	0.000	0.000	0.000	0.000
48	A	47	ASN	0	0.067	0.038	11.169	-0.115	-0.115	0.000	0.000	0.000	0.000
49	A	48	ILE	0	0.004	0.014	14.168	0.058	0.058	0.000	0.000	0.000	0.000
50	A	49	GLY	0	0.024	0.015	15.879	-0.027	-0.027	0.000	0.000	0.000	0.000
51	A	50	PRO	0	0.053	0.008	17.949	-0.011	-0.011	0.000	0.000	0.000	0.000
52	A	51	ASN	0	0.034	0.006	19.739	-0.012	-0.012	0.000	0.000	0.000	0.000
53	A	52	ALA	0	-0.017	-0.003	20.274	0.005	0.005	0.000	0.000	0.000	0.000
54	A	53	ALA	0	0.058	0.026	18.456	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	54	ARG	1	0.735	0.854	18.812	0.314	0.314	0.000	0.000	0.000	0.000
56	A	55	ILE	0	0.022	0.019	23.839	0.009	0.009	0.000	0.000	0.000	0.000
57	A	56	ILE	0	-0.031	-0.018	19.917	0.010	0.010	0.000	0.000	0.000	0.000
58	A	57	GLU	-1	-0.718	-0.848	21.417	-0.294	-0.294	0.000	0.000	0.000	0.000
59	A	58	GLU	-1	-0.847	-0.908	24.589	-0.157	-0.157	0.000	0.000	0.000	0.000
60	A	59	ALA	0	-0.037	-0.020	26.602	0.010	0.010	0.000	0.000	0.000	0.000
61	A	60	ALA	0	0.009	-0.007	24.869	0.012	0.012	0.000	0.000	0.000	0.000
62	A	61	ARG	1	0.819	0.913	26.893	0.154	0.154	0.000	0.000	0.000	0.000
63	A	62	LYS	1	0.822	0.903	23.911	0.251	0.251	0.000	0.000	0.000	0.000
64	A	63	GLU	-1	-0.821	-0.913	26.613	-0.183	-0.183	0.000	0.000	0.000	0.000
65	A	64	LYS	1	0.841	0.904	24.814	0.165	0.165	0.000	0.000	0.000	0.000
66	A	65	PHE	0	-0.037	-0.049	20.097	0.002	0.002	0.000	0.000	0.000	0.000
67	A	66	TRP	0	0.085	0.050	20.043	-0.048	-0.048	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.022	-0.004	17.444	-0.039	-0.039	0.000	0.000	0.000	0.000
69	A	68	ASP	-1	-0.757	-0.830	15.498	-0.473	-0.473	0.000	0.000	0.000	0.000
70	A	69	VAL	0	-0.002	0.014	15.330	-0.055	-0.055	0.000	0.000	0.000	0.000
71	A	70	ASP	-1	-0.795	-0.896	11.862	-1.263	-1.263	0.000	0.000	0.000	0.000
72	A	71	HIS	0	-0.014	-0.008	14.902	0.018	0.018	0.000	0.000	0.000	0.000
73	A	72	GLU	-1	-0.847	-0.913	12.003	-1.056	-1.056	0.000	0.000	0.000	0.000
74	A	73	LEU	0	-0.029	-0.018	15.359	0.017	0.017	0.000	0.000	0.000	0.000
75	A	74	ASP	-1	-0.913	-0.940	18.535	-0.297	-0.297	0.000	0.000	0.000	0.000
76	A	75	ALA	0	-0.048	-0.017	20.581	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	76	VAL	0	-0.032	-0.015	21.297	0.010	0.010	0.000	0.000	0.000	0.000
78	A	90	TRP	0	0.026	0.014	30.396	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	91	THR	0	-0.077	-0.062	33.604	0.005	0.005	0.000	0.000	0.000	0.000
80	A	92	VAL	0	0.049	0.040	32.479	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	93	GLU	-1	-0.809	-0.881	33.876	-0.035	-0.035	0.000	0.000	0.000	0.000
82	A	94	LYS	1	0.894	0.920	36.051	0.043	0.043	0.000	0.000	0.000	0.000
83	A	95	GLN	0	0.046	0.022	27.144	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	96	ALA	0	0.030	0.026	31.536	0.002	0.002	0.000	0.000	0.000	0.000
85	A	97	ALA	0	-0.010	-0.013	33.276	0.005	0.005	0.000	0.000	0.000	0.000
86	A	98	ALA	0	-0.017	-0.006	31.635	0.002	0.002	0.000	0.000	0.000	0.000
87	A	99	THR	0	-0.021	-0.015	28.329	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	100	LEU	0	0.020	0.008	30.441	0.004	0.004	0.000	0.000	0.000	0.000
89	A	101	ASN	0	-0.024	-0.015	33.400	0.007	0.007	0.000	0.000	0.000	0.000
90	A	102	ALA	0	-0.038	-0.027	28.372	0.002	0.002	0.000	0.000	0.000	0.000
91	A	103	TRP	0	-0.009	-0.008	26.229	0.006	0.006	0.000	0.000	0.000	0.000
92	A	104	MET	0	0.039	0.041	30.626	0.008	0.008	0.000	0.000	0.000	0.000
93	A	105	ARG	1	0.884	0.957	27.944	0.040	0.040	0.000	0.000	0.000	0.000
94	A	106	LYS	1	0.824	0.918	28.493	-0.032	-0.032	0.000	0.000	0.000	0.000
95	A	120	ALA	0	0.034	-0.001	39.377	0.000	0.000	0.000	0.000	0.000	0.000
96	A	121	GLY	0	-0.020	-0.018	39.990	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	122	ILE	0	-0.043	0.002	40.673	0.000	0.000	0.000	0.000	0.000	0.000
98	A	123	GLY	0	0.050	0.008	38.732	0.000	0.000	0.000	0.000	0.000	0.000
99	A	124	PRO	0	-0.007	-0.015	38.575	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	125	ALA	0	0.061	0.032	40.250	0.002	0.002	0.000	0.000	0.000	0.000
101	A	126	THR	0	-0.035	-0.020	41.707	-0.003	-0.003	0.000	0.000	0.000	0.000
102	A	127	VAL	0	0.016	0.014	40.707	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	128	ASN	0	0.017	0.011	43.424	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	129	ARG	1	0.907	0.941	43.038	0.001	0.001	0.000	0.000	0.000	0.000
105	A	130	ILE	0	0.023	0.027	42.005	0.000	0.000	0.000	0.000	0.000	0.000
106	A	131	MET	0	0.001	0.014	36.810	0.002	0.002	0.000	0.000	0.000	0.000
107	A	132	LYS	1	0.945	0.954	40.109	0.020	0.020	0.000	0.000	0.000	0.000
108	A	133	ALA	0	0.012	0.007	38.485	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	134	GLU	-1	-0.819	-0.893	39.811	-0.035	-0.035	0.000	0.000	0.000	0.000
110	A	135	VAL	0	-0.037	-0.034	41.675	0.001	0.001	0.000	0.000	0.000	0.000
111	A	136	SER	0	0.009	-0.019	40.714	0.001	0.001	0.000	0.000	0.000	0.000
112	A	137	THR	0	-0.053	-0.011	38.506	0.002	0.002	0.000	0.000	0.000	0.000
113	A	138	THR	0	0.030	0.008	39.507	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	139	ILE	0	0.106	0.031	36.121	0.001	0.001	0.000	0.000	0.000	0.000
115	A	140	GLY	0	0.020	0.026	37.039	0.003	0.003	0.000	0.000	0.000	0.000
116	A	141	VAL	0	-0.022	-0.020	39.047	0.003	0.003	0.000	0.000	0.000	0.000
117	A	142	LEU	0	0.016	0.011	34.614	0.002	0.002	0.000	0.000	0.000	0.000
118	A	143	SER	0	0.043	0.015	34.137	0.002	0.002	0.000	0.000	0.000	0.000
119	A	144	SER	0	-0.092	-0.037	35.027	0.006	0.006	0.000	0.000	0.000	0.000
120	A	145	LEU	0	0.004	-0.011	35.688	0.003	0.003	0.000	0.000	0.000	0.000
121	A	146	ALA	0	-0.002	0.006	30.810	0.002	0.002	0.000	0.000	0.000	0.000
122	A	147	ARG	1	0.990	1.002	30.220	-0.058	-0.058	0.000	0.000	0.000	0.000
123	A	148	ALA	0	-0.051	-0.021	33.113	0.005	0.005	0.000	0.000	0.000	0.000
124	A	149	PHE	0	-0.040	-0.019	30.903	0.001	0.001	0.000	0.000	0.000	0.000
125	A	150	GLY	0	-0.019	-0.005	29.928	0.003	0.003	0.000	0.000	0.000	0.000
126	A	151	HIS	0	0.005	0.009	26.333	0.013	0.013	0.000	0.000	0.000	0.000
127	A	152	GLU	-1	-0.849	-0.938	26.678	0.058	0.058	0.000	0.000	0.000	0.000
128	A	153	ALA	0	-0.024	-0.029	28.594	-0.008	-0.008	0.000	0.000	0.000	0.000
129	A	154	TYR	0	-0.055	-0.037	22.981	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	155	GLU	-1	-0.866	-0.902	22.903	0.010	0.010	0.000	0.000	0.000	0.000
131	A	156	MET	0	-0.020	-0.013	22.029	0.000	0.000	0.000	0.000	0.000	0.000
132	A	157	ILE	0	0.002	0.002	26.422	-0.011	-0.011	0.000	0.000	0.000	0.000
133	A	158	ILE	0	0.018	0.002	24.767	-0.004	-0.004	0.000	0.000	0.000	0.000
134	A	159	PRO	0	-0.083	-0.008	24.465	-0.006	-0.006	0.000	0.000	0.000	0.000
135	A	160	VAL	0	0.073	0.012	22.143	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	161	GLY	0	0.011	0.024	20.000	-0.026	-0.026	0.000	0.000	0.000	0.000
137	A	162	ALA	0	0.009	-0.020	18.462	0.012	0.012	0.000	0.000	0.000	0.000
138	A	163	PRO	0	-0.054	-0.030	19.153	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	164	GLY	0	0.020	0.021	19.549	0.020	0.020	0.000	0.000	0.000	0.000
140	A	165	ILE	0	-0.004	0.005	13.078	-0.020	-0.020	0.000	0.000	0.000	0.000
141	A	166	ILE	0	-0.007	-0.018	15.997	0.043	0.043	0.000	0.000	0.000	0.000
142	A	167	ASP	-1	-0.968	-0.975	10.006	-0.043	-0.043	0.000	0.000	0.000	0.000
143	A	168	TYR	0	-0.021	0.004	12.209	0.094	0.094	0.000	0.000	0.000	0.000
144	A	169	ASP	-1	-0.760	-0.886	13.061	0.327	0.327	0.000	0.000	0.000	0.000
145	A	170	HIS	0	0.016	-0.002	15.125	0.010	0.010	0.000	0.000	0.000	0.000
146	A	171	ARG	1	0.891	0.949	18.327	-0.233	-0.233	0.000	0.000	0.000	0.000
147	A	172	MET	0	0.017	0.000	11.636	0.029	0.029	0.000	0.000	0.000	0.000
148	A	173	TYR	0	0.042	0.024	15.909	-0.008	-0.008	0.000	0.000	0.000	0.000
149	A	174	ALA	0	-0.020	-0.005	17.457	-0.027	-0.027	0.000	0.000	0.000	0.000
150	A	175	ALA	0	-0.020	-0.015	19.250	-0.017	-0.017	0.000	0.000	0.000	0.000
151	A	176	LEU	0	-0.008	0.019	14.936	0.003	0.003	0.000	0.000	0.000	0.000
152	A	177	PRO	0	0.062	0.030	19.238	-0.045	-0.045	0.000	0.000	0.000	0.000
153	A	178	GLN	0	0.030	0.003	21.133	0.014	0.014	0.000	0.000	0.000	0.000
154	A	179	GLU	-1	-0.863	-0.925	22.604	0.190	0.190	0.000	0.000	0.000	0.000
155	A	180	GLU	-1	-0.823	-0.899	17.202	0.323	0.323	0.000	0.000	0.000	0.000
156	A	181	LYS	1	0.786	0.891	18.168	-0.242	-0.242	0.000	0.000	0.000	0.000
157	A	182	ASN	0	0.019	0.024	19.846	-0.026	-0.026	0.000	0.000	0.000	0.000
158	A	183	LYS	1	0.783	0.872	17.945	-0.275	-0.275	0.000	0.000	0.000	0.000
159	A	184	ILE	0	0.004	0.002	14.237	-0.025	-0.025	0.000	0.000	0.000	0.000
160	A	185	THR	0	-0.020	-0.034	16.678	-0.044	-0.044	0.000	0.000	0.000	0.000
161	A	186	SER	0	0.000	0.000	19.569	-0.028	-0.028	0.000	0.000	0.000	0.000
162	A	187	PHE	0	-0.022	-0.003	13.145	-0.017	-0.017	0.000	0.000	0.000	0.000
163	A	188	ILE	0	0.011	0.003	15.230	-0.033	-0.033	0.000	0.000	0.000	0.000
164	A	189	ASN	0	0.001	-0.007	17.845	-0.034	-0.034	0.000	0.000	0.000	0.000
165	A	190	PHE	0	0.011	0.013	19.360	-0.014	-0.014	0.000	0.000	0.000	0.000
166	A	191	VAL	0	0.012	0.002	15.691	-0.019	-0.019	0.000	0.000	0.000	0.000
167	A	192	PHE	0	-0.025	-0.011	18.914	-0.022	-0.022	0.000	0.000	0.000	0.000
168	A	193	GLU	-1	-0.940	-0.965	21.611	-0.056	-0.056	0.000	0.000	0.000	0.000
169	A	194	GLN	0	-0.072	-0.031	21.139	-0.009	-0.009	0.000	0.000	0.000	0.000
170	A	195	ASN	0	-0.071	-0.027	18.790	-0.037	-0.037	0.000	0.000	0.000	0.000
171	A	196	LYS	1	0.920	0.964	22.879	0.132	0.132	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:ALA)