FMO DATABASE

FMODB ID: 3J78L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1529468.382906
FMO2-HF: Nuclear repulsion	1460880.994647
FMO2-HF: Total energy	-68587.388259
FMO2-MP2: Total energy	-68787.382356

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.
-0.372	1.546	-0.004	-1.024	-0.89	0.006

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 : 0.027 / q_NPA : 0.014

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	0.805	0.888	3.802	0.131	2.049	-0.004	-1.024	-0.890	0.006
4	A	3	SER	0	0.022	0.021	6.107	0.872	0.872	0.000	0.000	0.000	0.000
5	A	4	ILE	0	0.058	0.007	7.670	-0.061	-0.061	0.000	0.000	0.000	0.000
6	A	5	TYR	0	-0.046	-0.030	9.646	0.086	0.086	0.000	0.000	0.000	0.000
7	A	6	ASP	-1	-0.782	-0.881	6.402	-2.297	-2.297	0.000	0.000	0.000	0.000
8	A	7	ILE	0	0.038	0.036	9.305	0.113	0.113	0.000	0.000	0.000	0.000
9	A	8	ARG	1	0.799	0.870	11.853	0.673	0.673	0.000	0.000	0.000	0.000
10	A	9	ARG	1	0.888	0.943	7.890	1.326	1.326	0.000	0.000	0.000	0.000
11	A	10	LYS	1	0.878	0.956	11.264	1.020	1.020	0.000	0.000	0.000	0.000
12	A	11	ASN	0	0.003	-0.022	13.416	0.092	0.092	0.000	0.000	0.000	0.000
13	A	12	LEU	0	-0.078	-0.050	16.488	0.074	0.074	0.000	0.000	0.000	0.000
14	A	13	ASN	0	-0.079	-0.075	14.881	0.104	0.104	0.000	0.000	0.000	0.000
15	A	14	GLU	-1	-0.814	-0.879	16.305	-0.434	-0.434	0.000	0.000	0.000	0.000
16	A	15	ILE	0	-0.034	-0.010	19.158	0.045	0.045	0.000	0.000	0.000	0.000
17	A	16	ILE	0	-0.040	-0.024	21.156	0.037	0.037	0.000	0.000	0.000	0.000
18	A	17	LEU	0	0.023	0.036	20.675	0.029	0.029	0.000	0.000	0.000	0.000
19	A	18	ARG	1	0.866	0.907	19.174	0.380	0.380	0.000	0.000	0.000	0.000
20	A	19	ASP	-1	-0.872	-0.908	24.955	-0.237	-0.237	0.000	0.000	0.000	0.000
21	A	20	PHE	0	-0.134	-0.085	25.755	0.022	0.022	0.000	0.000	0.000	0.000
22	A	21	ASP	-1	-0.874	-0.931	27.222	-0.143	-0.143	0.000	0.000	0.000	0.000
23	A	22	ASP	-1	-0.927	-0.985	21.516	-0.244	-0.244	0.000	0.000	0.000	0.000
24	A	23	THR	0	-0.047	-0.007	24.145	0.013	0.013	0.000	0.000	0.000	0.000
25	A	24	GLN	0	0.081	0.007	20.903	0.010	0.010	0.000	0.000	0.000	0.000
26	A	25	LEU	0	-0.014	-0.018	24.818	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	26	ARG	1	0.952	0.975	28.503	0.122	0.122	0.000	0.000	0.000	0.000
28	A	27	PHE	0	0.024	0.019	23.844	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	28	ALA	0	-0.040	-0.027	27.033	0.000	0.000	0.000	0.000	0.000	0.000
30	A	29	GLU	-1	-0.846	-0.918	28.115	-0.113	-0.113	0.000	0.000	0.000	0.000
31	A	30	ARG	1	0.897	0.967	29.714	0.165	0.165	0.000	0.000	0.000	0.000
32	A	31	VAL	0	-0.029	-0.009	25.897	0.004	0.004	0.000	0.000	0.000	0.000
33	A	32	LYS	1	0.949	0.982	29.165	0.119	0.119	0.000	0.000	0.000	0.000
34	A	33	ARG	1	0.867	0.941	26.660	0.161	0.161	0.000	0.000	0.000	0.000
35	A	34	SER	0	0.063	0.029	27.725	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	35	GLN	0	0.109	0.038	26.056	-0.021	-0.021	0.000	0.000	0.000	0.000
37	A	36	ASN	0	0.024	0.021	24.919	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	37	LEU	0	-0.063	-0.027	21.827	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	38	VAL	0	0.040	0.016	21.474	-0.024	-0.024	0.000	0.000	0.000	0.000
40	A	39	ASN	0	0.025	0.015	20.544	-0.021	-0.021	0.000	0.000	0.000	0.000
41	A	40	ARG	1	0.918	0.960	18.837	0.132	0.132	0.000	0.000	0.000	0.000
42	A	41	TRP	0	-0.034	-0.019	16.975	-0.011	-0.011	0.000	0.000	0.000	0.000
43	A	42	CYS	0	-0.018	0.005	15.616	-0.063	-0.063	0.000	0.000	0.000	0.000
44	A	43	THR	0	0.028	-0.001	15.115	-0.044	-0.044	0.000	0.000	0.000	0.000
45	A	44	GLY	0	0.026	0.011	12.554	-0.035	-0.035	0.000	0.000	0.000	0.000
46	A	45	ILE	0	-0.057	-0.009	13.366	0.004	0.004	0.000	0.000	0.000	0.000
47	A	46	LYS	1	0.892	0.946	15.837	0.249	0.249	0.000	0.000	0.000	0.000
48	A	47	ASN	0	0.055	0.031	11.734	-0.116	-0.116	0.000	0.000	0.000	0.000
49	A	48	ILE	0	-0.005	0.013	14.527	0.070	0.070	0.000	0.000	0.000	0.000
50	A	49	GLY	0	0.005	0.000	16.269	-0.030	-0.030	0.000	0.000	0.000	0.000
51	A	50	PRO	0	0.058	0.006	18.552	-0.018	-0.018	0.000	0.000	0.000	0.000
52	A	51	ASN	0	0.042	0.014	20.016	-0.004	-0.004	0.000	0.000	0.000	0.000
53	A	52	ALA	0	-0.019	0.002	20.896	0.009	0.009	0.000	0.000	0.000	0.000
54	A	53	ALA	0	0.080	0.035	18.956	0.008	0.008	0.000	0.000	0.000	0.000
55	A	54	ARG	1	0.782	0.884	19.165	0.370	0.370	0.000	0.000	0.000	0.000
56	A	55	ILE	0	0.028	0.015	24.345	0.012	0.012	0.000	0.000	0.000	0.000
57	A	56	ILE	0	-0.054	-0.022	20.478	0.014	0.014	0.000	0.000	0.000	0.000
58	A	57	GLU	-1	-0.724	-0.860	21.837	-0.333	-0.333	0.000	0.000	0.000	0.000
59	A	58	GLU	-1	-0.859	-0.927	25.020	-0.183	-0.183	0.000	0.000	0.000	0.000
60	A	59	ALA	0	-0.065	-0.040	26.987	0.011	0.011	0.000	0.000	0.000	0.000
61	A	60	ALA	0	-0.027	-0.021	24.733	0.011	0.011	0.000	0.000	0.000	0.000
62	A	61	ARG	1	0.867	0.935	26.705	0.166	0.166	0.000	0.000	0.000	0.000
63	A	62	LYS	1	0.798	0.891	23.580	0.269	0.269	0.000	0.000	0.000	0.000
64	A	63	GLU	-1	-0.829	-0.916	26.543	-0.201	-0.201	0.000	0.000	0.000	0.000
65	A	64	LYS	1	0.871	0.928	25.100	0.192	0.192	0.000	0.000	0.000	0.000
66	A	65	PHE	0	-0.057	-0.050	20.039	0.002	0.002	0.000	0.000	0.000	0.000
67	A	66	TRP	0	0.094	0.056	20.235	-0.052	-0.052	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.027	-0.001	17.672	-0.043	-0.043	0.000	0.000	0.000	0.000
69	A	68	ASP	-1	-0.775	-0.853	16.091	-0.558	-0.558	0.000	0.000	0.000	0.000
70	A	69	VAL	0	0.004	0.025	15.477	-0.077	-0.077	0.000	0.000	0.000	0.000
71	A	70	ASP	-1	-0.824	-0.908	11.569	-1.222	-1.222	0.000	0.000	0.000	0.000
72	A	71	HIS	0	-0.004	-0.021	14.766	0.069	0.069	0.000	0.000	0.000	0.000
73	A	72	GLU	-1	-0.840	-0.908	11.210	-1.029	-1.029	0.000	0.000	0.000	0.000
74	A	73	LEU	0	-0.025	-0.017	14.987	0.041	0.041	0.000	0.000	0.000	0.000
75	A	74	ASP	-1	-0.949	-0.959	17.921	-0.276	-0.276	0.000	0.000	0.000	0.000
76	A	75	ALA	0	-0.035	-0.007	19.721	-0.010	-0.010	0.000	0.000	0.000	0.000
77	A	76	VAL	0	-0.017	-0.007	20.998	0.002	0.002	0.000	0.000	0.000	0.000
78	A	90	TRP	0	0.007	-0.001	30.456	-0.005	-0.005	0.000	0.000	0.000	0.000
79	A	91	THR	0	-0.063	-0.045	33.540	0.003	0.003	0.000	0.000	0.000	0.000
80	A	92	VAL	0	0.063	0.035	32.473	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	93	GLU	-1	-0.823	-0.885	34.009	-0.015	-0.015	0.000	0.000	0.000	0.000
82	A	94	LYS	1	0.928	0.937	36.319	0.032	0.032	0.000	0.000	0.000	0.000
83	A	95	GLN	0	0.028	0.019	27.210	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	96	ALA	0	0.035	0.031	31.885	0.003	0.003	0.000	0.000	0.000	0.000
85	A	97	ALA	0	0.009	-0.003	33.726	0.005	0.005	0.000	0.000	0.000	0.000
86	A	98	ALA	0	0.008	0.000	31.677	0.001	0.001	0.000	0.000	0.000	0.000
87	A	99	THR	0	0.007	0.001	28.296	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	100	LEU	0	0.033	0.019	30.371	0.003	0.003	0.000	0.000	0.000	0.000
89	A	101	ASN	0	-0.052	-0.008	33.229	0.005	0.005	0.000	0.000	0.000	0.000
90	A	102	ALA	0	-0.069	-0.045	28.600	0.000	0.000	0.000	0.000	0.000	0.000
91	A	103	TRP	0	-0.008	-0.007	26.309	0.004	0.004	0.000	0.000	0.000	0.000
92	A	104	MET	0	-0.031	0.003	30.687	0.007	0.007	0.000	0.000	0.000	0.000
93	A	105	ARG	1	0.902	0.943	28.191	0.042	0.042	0.000	0.000	0.000	0.000
94	A	106	LYS	1	0.918	0.985	28.976	-0.036	-0.036	0.000	0.000	0.000	0.000
95	A	120	ALA	0	0.027	-0.004	39.356	0.000	0.000	0.000	0.000	0.000	0.000
96	A	121	GLY	0	-0.006	-0.014	39.983	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	122	ILE	0	-0.047	0.007	40.611	0.000	0.000	0.000	0.000	0.000	0.000
98	A	123	GLY	0	0.053	-0.016	39.264	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	124	PRO	0	-0.010	-0.012	38.946	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	125	ALA	0	0.055	0.032	39.985	0.001	0.001	0.000	0.000	0.000	0.000
101	A	126	THR	0	-0.034	-0.030	41.636	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	127	VAL	0	0.016	0.029	40.779	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	128	ASN	0	0.033	0.022	43.546	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	129	ARG	1	0.895	0.956	42.764	-0.010	-0.010	0.000	0.000	0.000	0.000
105	A	130	ILE	0	0.006	0.015	42.182	0.001	0.001	0.000	0.000	0.000	0.000
106	A	131	MET	0	0.026	0.020	37.111	0.002	0.002	0.000	0.000	0.000	0.000
107	A	132	LYS	1	0.947	0.950	40.389	0.011	0.011	0.000	0.000	0.000	0.000
108	A	133	ALA	0	0.010	0.008	37.897	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	134	GLU	-1	-0.842	-0.911	39.345	-0.025	-0.025	0.000	0.000	0.000	0.000
110	A	135	VAL	0	-0.039	-0.029	41.873	0.000	0.000	0.000	0.000	0.000	0.000
111	A	136	SER	0	0.003	-0.028	40.518	0.001	0.001	0.000	0.000	0.000	0.000
112	A	137	THR	0	-0.025	-0.001	38.606	0.001	0.001	0.000	0.000	0.000	0.000
113	A	138	THR	0	0.012	-0.003	39.949	0.001	0.001	0.000	0.000	0.000	0.000
114	A	139	ILE	0	0.107	0.034	36.184	0.000	0.000	0.000	0.000	0.000	0.000
115	A	140	GLY	0	0.038	0.030	37.040	0.004	0.004	0.000	0.000	0.000	0.000
116	A	141	VAL	0	-0.024	-0.017	39.212	0.002	0.002	0.000	0.000	0.000	0.000
117	A	142	LEU	0	0.030	0.015	34.539	0.001	0.001	0.000	0.000	0.000	0.000
118	A	143	SER	0	0.036	0.019	34.473	0.004	0.004	0.000	0.000	0.000	0.000
119	A	144	SER	0	-0.110	-0.051	35.474	0.005	0.005	0.000	0.000	0.000	0.000
120	A	145	LEU	0	-0.010	-0.017	35.925	0.001	0.001	0.000	0.000	0.000	0.000
121	A	146	ALA	0	-0.028	-0.004	31.231	0.000	0.000	0.000	0.000	0.000	0.000
122	A	147	ARG	1	1.016	1.003	31.314	-0.078	-0.078	0.000	0.000	0.000	0.000
123	A	148	ALA	0	-0.051	-0.017	33.382	0.004	0.004	0.000	0.000	0.000	0.000
124	A	149	PHE	0	-0.061	-0.033	30.628	0.000	0.000	0.000	0.000	0.000	0.000
125	A	150	GLY	0	-0.014	-0.003	29.885	0.004	0.004	0.000	0.000	0.000	0.000
126	A	151	HIS	0	-0.032	-0.009	26.636	0.012	0.012	0.000	0.000	0.000	0.000
127	A	152	GLU	-1	-0.867	-0.936	26.396	0.093	0.093	0.000	0.000	0.000	0.000
128	A	153	ALA	0	-0.021	-0.032	28.728	-0.008	-0.008	0.000	0.000	0.000	0.000
129	A	154	TYR	0	-0.072	-0.057	23.214	-0.008	-0.008	0.000	0.000	0.000	0.000
130	A	155	GLU	-1	-0.854	-0.887	23.294	0.061	0.061	0.000	0.000	0.000	0.000
131	A	156	MET	0	-0.002	-0.005	22.227	-0.002	-0.002	0.000	0.000	0.000	0.000
132	A	157	ILE	0	-0.010	-0.006	26.567	-0.010	-0.010	0.000	0.000	0.000	0.000
133	A	158	ILE	0	-0.006	-0.009	24.618	-0.006	-0.006	0.000	0.000	0.000	0.000
134	A	159	PRO	0	-0.046	-0.008	24.762	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	160	VAL	0	0.017	0.005	21.549	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	161	GLY	0	0.018	0.007	20.303	-0.017	-0.017	0.000	0.000	0.000	0.000
137	A	162	ALA	0	0.033	0.006	18.427	0.008	0.008	0.000	0.000	0.000	0.000
138	A	163	PRO	0	-0.056	-0.035	18.916	0.004	0.004	0.000	0.000	0.000	0.000
139	A	164	GLY	0	0.007	0.021	19.076	0.018	0.018	0.000	0.000	0.000	0.000
140	A	165	ILE	0	0.003	0.013	13.012	-0.024	-0.024	0.000	0.000	0.000	0.000
141	A	166	ILE	0	0.007	-0.013	15.778	0.033	0.033	0.000	0.000	0.000	0.000
142	A	167	ASP	-1	-0.961	-0.973	9.645	0.261	0.261	0.000	0.000	0.000	0.000
143	A	168	TYR	0	-0.039	-0.008	12.216	0.097	0.097	0.000	0.000	0.000	0.000
144	A	169	ASP	-1	-0.765	-0.901	13.143	0.335	0.335	0.000	0.000	0.000	0.000
145	A	170	HIS	0	0.024	0.004	15.469	0.006	0.006	0.000	0.000	0.000	0.000
146	A	171	ARG	1	0.922	0.962	18.726	-0.255	-0.255	0.000	0.000	0.000	0.000
147	A	172	MET	0	0.014	0.012	11.609	0.025	0.025	0.000	0.000	0.000	0.000
148	A	173	TYR	0	0.047	0.026	16.511	0.000	0.000	0.000	0.000	0.000	0.000
149	A	174	ALA	0	-0.044	-0.030	17.770	-0.025	-0.025	0.000	0.000	0.000	0.000
150	A	175	ALA	0	-0.018	-0.014	19.339	-0.022	-0.022	0.000	0.000	0.000	0.000
151	A	176	LEU	0	-0.022	0.017	15.545	-0.006	-0.006	0.000	0.000	0.000	0.000
152	A	177	PRO	0	0.076	0.036	19.875	-0.047	-0.047	0.000	0.000	0.000	0.000
153	A	178	GLN	0	0.032	-0.002	21.798	0.020	0.020	0.000	0.000	0.000	0.000
154	A	179	GLU	-1	-0.892	-0.940	23.319	0.256	0.256	0.000	0.000	0.000	0.000
155	A	180	GLU	-1	-0.857	-0.951	17.995	0.424	0.424	0.000	0.000	0.000	0.000
156	A	181	LYS	1	0.777	0.896	18.490	-0.281	-0.281	0.000	0.000	0.000	0.000
157	A	182	ASN	0	0.016	0.013	19.923	-0.012	-0.012	0.000	0.000	0.000	0.000
158	A	183	LYS	1	0.855	0.940	18.164	-0.342	-0.342	0.000	0.000	0.000	0.000
159	A	184	ILE	0	0.012	0.012	14.646	-0.014	-0.014	0.000	0.000	0.000	0.000
160	A	185	THR	0	-0.021	-0.026	17.019	-0.037	-0.037	0.000	0.000	0.000	0.000
161	A	186	SER	0	0.003	-0.005	19.898	-0.033	-0.033	0.000	0.000	0.000	0.000
162	A	187	PHE	0	-0.019	-0.007	13.331	-0.021	-0.021	0.000	0.000	0.000	0.000
163	A	188	ILE	0	0.010	0.007	15.736	-0.032	-0.032	0.000	0.000	0.000	0.000
164	A	189	ASN	0	0.003	-0.008	18.132	-0.037	-0.037	0.000	0.000	0.000	0.000
165	A	190	PHE	0	-0.009	0.006	19.246	-0.019	-0.019	0.000	0.000	0.000	0.000
166	A	191	VAL	0	0.022	0.004	15.738	-0.024	-0.024	0.000	0.000	0.000	0.000
167	A	192	PHE	0	-0.036	-0.019	19.079	-0.025	-0.025	0.000	0.000	0.000	0.000
168	A	193	GLU	-1	-0.957	-0.976	21.756	0.007	0.007	0.000	0.000	0.000	0.000
169	A	194	GLN	0	-0.052	-0.014	21.139	-0.014	-0.014	0.000	0.000	0.000	0.000
170	A	195	ASN	0	-0.089	-0.030	18.890	-0.037	-0.037	0.000	0.000	0.000	0.000
171	A	196	LYS	1	0.951	0.978	23.002	0.071	0.071	0.000	0.000	0.000	0.000

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