FMO DATABASE

FMODB ID: PKGJ3

Calculation Name: 2RFF-A-Xray19

Preferred Name:
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Target Type:
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Ligand Name: 1,2-ethanediol

ligand 3-letter code: EDO

PDB ID: 2RFF

Chain ID: A

ChEMBL ID:
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UniProt ID: Q97XP0

Base Structure: X-ray

Registration Date: 2018-06-04

Reference:

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water	Apo structure with with a 3 angstrom solvent shell.
Procedure	Auto-FMO protocol ver. 1.20180227

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	178
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-1104276.884633
FMO2-HF: Nuclear repulsion	1053583.904889
FMO2-HF: Total energy	-50692.979744
FMO2-MP2: Total energy	-50838.118495

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:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

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.
2.767	3.818	-0.007	-0.415	-0.629	0

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.046 / q_NPA : 0.006

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	A	2	GLY	0	0.034	0.032	3.837	1.307	2.258	-0.006	-0.407	-0.537
4	A	3	LYS	1	0.807	0.934	5.368	1.871	1.971	-0.001	-0.008	-0.092
5	A	4	GLY	0	0.049	0.021	8.290	-0.061	-0.061	0.000	0.000	0.000
6	A	5	LYS	1	0.992	0.977	10.441	0.114	0.114	0.000	0.000	0.000
7	A	6	SER	0	0.004	-0.010	12.946	0.009	0.009	0.000	0.000	0.000
8	A	7	ALA	0	0.036	0.015	12.602	0.024	0.024	0.000	0.000	0.000
9	A	8	ILE	0	0.039	0.027	10.146	0.018	0.018	0.000	0.000	0.000
10	A	9	GLU	-1	-0.918	-0.968	13.706	-0.196	-0.196	0.000	0.000	0.000
11	A	10	SER	0	-0.063	-0.041	16.977	0.034	0.034	0.000	0.000	0.000
12	A	11	GLN	0	0.041	0.024	15.287	0.057	0.057	0.000	0.000	0.000
13	A	12	ILE	0	-0.019	-0.016	15.555	0.042	0.042	0.000	0.000	0.000
14	A	13	ARG	1	0.914	0.966	18.885	0.270	0.270	0.000	0.000	0.000
15	A	14	MET	0	-0.030	-0.001	21.043	0.024	0.024	0.000	0.000	0.000
16	A	15	LEU	0	0.026	0.014	18.169	0.017	0.017	0.000	0.000	0.000
17	A	16	LYS	1	0.971	0.985	21.472	0.238	0.238	0.000	0.000	0.000
18	A	17	LEU	0	0.026	0.031	24.701	0.016	0.016	0.000	0.000	0.000
19	A	18	ALA	0	0.033	0.011	25.217	0.013	0.013	0.000	0.000	0.000
20	A	19	LYS	1	0.878	0.949	26.199	0.171	0.171	0.000	0.000	0.000
21	A	20	GLU	-1	-0.923	-0.956	27.851	-0.130	-0.130	0.000	0.000	0.000
22	A	21	ILE	0	-0.021	-0.001	29.875	0.010	0.010	0.000	0.000	0.000
23	A	22	VAL	0	-0.004	-0.014	29.018	0.009	0.009	0.000	0.000	0.000
24	A	23	GLU	-1	-0.864	-0.917	31.346	-0.126	-0.126	0.000	0.000	0.000
25	A	24	GLU	-1	-0.831	-0.894	33.647	-0.103	-0.103	0.000	0.000	0.000
26	A	25	VAL	0	0.031	0.019	34.975	0.007	0.007	0.000	0.000	0.000
27	A	26	ALA	0	0.008	-0.007	34.553	0.006	0.006	0.000	0.000	0.000
28	A	27	SER	0	-0.035	-0.015	36.591	0.007	0.007	0.000	0.000	0.000
29	A	28	SER	0	0.012	0.021	39.353	0.008	0.008	0.000	0.000	0.000
30	A	29	PHE	0	0.001	0.015	39.504	0.005	0.005	0.000	0.000	0.000
31	A	30	PRO	0	0.013	0.026	39.963	-0.005	-0.005	0.000	0.000	0.000
32	A	31	ASN	0	0.024	-0.006	40.850	-0.003	-0.003	0.000	0.000	0.000
33	A	32	LEU	0	0.014	0.039	33.897	-0.003	-0.003	0.000	0.000	0.000
34	A	33	GLU	-1	-0.744	-0.850	35.092	-0.117	-0.117	0.000	0.000	0.000
35	A	34	GLU	-1	-0.777	-0.846	30.697	-0.160	-0.160	0.000	0.000	0.000
36	A	35	VAL	0	0.027	0.023	28.017	0.006	0.006	0.000	0.000	0.000
37	A	36	TYR	0	-0.027	-0.043	25.503	-0.009	-0.009	0.000	0.000	0.000
38	A	37	ILE	0	0.031	0.040	21.319	0.010	0.010	0.000	0.000	0.000
39	A	38	PHE	0	0.014	-0.014	22.875	-0.015	-0.015	0.000	0.000	0.000
40	A	39	GLY	0	0.058	0.044	22.175	-0.007	-0.007	0.000	0.000	0.000
41	A	40	SER	0	-0.015	-0.030	17.832	-0.038	-0.038	0.000	0.000	0.000
42	A	41	ARG	1	0.763	0.877	16.875	0.316	0.316	0.000	0.000	0.000
43	A	42	ALA	0	-0.027	0.008	17.465	-0.034	-0.034	0.000	0.000	0.000
44	A	43	ARG	1	0.818	0.887	16.695	0.325	0.325	0.000	0.000	0.000
45	A	44	GLY	0	0.025	0.021	12.847	-0.082	-0.082	0.000	0.000	0.000
46	A	45	ASP	-1	-0.833	-0.903	12.686	-0.577	-0.577	0.000	0.000	0.000
47	A	46	TYR	0	-0.016	-0.014	13.207	0.049	0.049	0.000	0.000	0.000
48	A	47	LEU	0	0.011	-0.012	14.613	-0.097	-0.097	0.000	0.000	0.000
49	A	48	ASP	-1	-0.826	-0.891	16.866	-0.294	-0.294	0.000	0.000	0.000
50	A	49	THR	0	-0.021	-0.029	18.077	0.011	0.011	0.000	0.000	0.000
51	A	50	SER	0	-0.004	0.012	19.508	0.008	0.008	0.000	0.000	0.000
52	A	51	ASP	-1	-0.710	-0.801	21.412	-0.242	-0.242	0.000	0.000	0.000
53	A	52	ILE	0	-0.028	-0.030	22.006	-0.040	-0.040	0.000	0.000	0.000
54	A	53	ASP	-1	-0.766	-0.864	23.796	-0.223	-0.223	0.000	0.000	0.000
55	A	54	ILE	0	-0.014	-0.020	25.260	-0.017	-0.017	0.000	0.000	0.000
56	A	55	LEU	0	-0.032	-0.012	27.920	0.012	0.012	0.000	0.000	0.000
57	A	56	PHE	0	0.019	-0.003	29.860	-0.004	-0.004	0.000	0.000	0.000
58	A	57	VAL	0	-0.009	-0.004	31.863	0.005	0.005	0.000	0.000	0.000
59	A	58	PHE	0	0.025	0.004	34.547	0.000	0.000	0.000	0.000	0.000
60	A	59	LYS	1	0.879	0.928	38.214	0.096	0.096	0.000	0.000	0.000
61	A	60	GLY	0	0.034	0.015	40.847	0.002	0.002	0.000	0.000	0.000
62	A	61	ILE	0	-0.005	-0.004	38.971	0.004	0.004	0.000	0.000	0.000
63	A	62	LYS	1	0.916	0.954	42.142	0.088	0.088	0.000	0.000	0.000
64	A	63	GLU	-1	-0.937	-0.974	43.692	-0.067	-0.067	0.000	0.000	0.000
65	A	64	MET	0	-0.047	0.005	43.714	0.003	0.003	0.000	0.000	0.000
66	A	65	ASN	0	0.063	0.034	43.813	-0.007	-0.007	0.000	0.000	0.000
67	A	66	VAL	0	0.055	-0.008	40.355	-0.002	-0.002	0.000	0.000	0.000
68	A	67	PHE	0	-0.006	0.000	41.411	-0.004	-0.004	0.000	0.000	0.000
69	A	68	ASP	-1	-0.773	-0.875	43.613	-0.074	-0.074	0.000	0.000	0.000
70	A	69	ARG	1	0.751	0.857	38.795	0.100	0.100	0.000	0.000	0.000
71	A	70	MET	0	-0.002	0.024	38.088	-0.004	-0.004	0.000	0.000	0.000
72	A	71	TYR	0	-0.035	-0.007	39.885	-0.002	-0.002	0.000	0.000	0.000
73	A	72	MET	0	-0.043	0.003	40.450	0.001	0.001	0.000	0.000	0.000
74	A	73	VAL	0	0.025	-0.005	35.709	0.000	0.000	0.000	0.000	0.000
75	A	74	SER	0	-0.035	0.000	37.629	-0.004	-0.004	0.000	0.000	0.000
76	A	75	ARG	1	0.935	0.964	38.169	0.082	0.082	0.000	0.000	0.000
77	A	76	PHE	0	-0.015	0.007	35.954	0.002	0.002	0.000	0.000	0.000
78	A	77	ILE	0	-0.011	0.011	32.453	-0.008	-0.008	0.000	0.000	0.000
79	A	78	ARG	1	0.850	0.925	32.431	0.135	0.135	0.000	0.000	0.000
80	A	79	GLY	0	-0.006	-0.005	29.901	-0.009	-0.009	0.000	0.000	0.000
81	A	80	ASN	0	-0.021	-0.009	24.647	0.016	0.016	0.000	0.000	0.000
82	A	81	VAL	0	-0.016	-0.017	26.466	-0.022	-0.022	0.000	0.000	0.000
83	A	82	ASP	-1	-0.789	-0.873	28.031	-0.144	-0.144	0.000	0.000	0.000
84	A	83	TYR	0	-0.057	-0.052	28.997	-0.009	-0.009	0.000	0.000	0.000
85	A	84	ILE	0	0.019	0.010	30.150	0.007	0.007	0.000	0.000	0.000
86	A	85	VAL	0	-0.001	0.009	32.835	-0.006	-0.006	0.000	0.000	0.000
87	A	86	LEU	0	-0.060	-0.031	32.648	0.004	0.004	0.000	0.000	0.000
88	A	87	ASP	-1	-0.676	-0.839	36.226	-0.099	-0.099	0.000	0.000	0.000
89	A	88	GLU	-1	-0.827	-0.924	36.253	-0.105	-0.105	0.000	0.000	0.000
90	A	89	GLY	0	-0.041	0.002	36.184	-0.006	-0.006	0.000	0.000	0.000
91	A	90	GLU	-1	-0.823	-0.896	36.376	-0.107	-0.107	0.000	0.000	0.000
92	A	91	LYS	1	0.863	0.918	31.533	0.143	0.143	0.000	0.000	0.000
93	A	92	ASP	-1	-0.871	-0.921	30.643	-0.164	-0.164	0.000	0.000	0.000
94	A	93	ARG	1	0.914	0.952	30.687	0.115	0.115	0.000	0.000	0.000
95	A	94	VAL	0	0.002	0.034	26.467	-0.001	-0.001	0.000	0.000	0.000
96	A	95	LYS	1	0.892	0.936	25.214	0.172	0.172	0.000	0.000	0.000
97	A	96	ASP	-1	-0.909	-0.961	20.813	-0.318	-0.318	0.000	0.000	0.000
98	A	97	LYS	1	0.856	0.913	22.351	0.210	0.210	0.000	0.000	0.000
99	A	98	VAL	0	0.007	0.018	18.895	-0.003	-0.003	0.000	0.000	0.000
100	A	99	LEU	0	-0.031	-0.007	22.144	0.020	0.020	0.000	0.000	0.000
101	A	100	PHE	0	0.021	0.015	22.935	-0.015	-0.015	0.000	0.000	0.000
102	A	101	TRP	0	0.037	0.005	25.086	0.005	0.005	0.000	0.000	0.000
103	A	102	LYS	1	0.821	0.885	28.455	0.137	0.137	0.000	0.000	0.000
104	A	103	ARG	1	0.848	0.963	31.299	0.108	0.108	0.000	0.000	0.000
105	A	104	GLH	0	-0.058	-0.074	34.377	0.006	0.006	0.000	0.000	0.000
106	A	105	LYS	1	0.897	0.949	27.244	0.178	0.178	0.000	0.000	0.000
107	A	106	GLY	0	0.042	0.052	29.820	-0.001	-0.001	0.000	0.000	0.000
108	A	107	PHE	0	0.003	-0.019	25.947	-0.004	-0.004	0.000	0.000	0.000
109	A	108	VAL	0	-0.027	-0.005	22.102	0.006	0.006	0.000	0.000	0.000
110	A	109	LEU	0	-0.044	-0.040	18.354	-0.016	-0.016	0.000	0.000	0.000
111	A	110	LEU	-1	-0.934	-0.932	20.623	-0.196	-0.196	0.000	0.000	0.000
112	A	111	EDO	0	-0.050	-0.052	38.746	0.002	0.002	0.000	0.000	0.000
113	A	112	EDO	0	-0.038	-0.035	34.257	0.005	0.005	0.000	0.000	0.000
114	A	113	HOH	0	-0.012	-0.020	21.901	-0.009	-0.009	0.000	0.000	0.000
115	A	114	HOH	0	0.007	0.004	46.520	-0.001	-0.001	0.000	0.000	0.000
116	A	115	HOH	0	-0.036	-0.027	40.498	0.000	0.000	0.000	0.000	0.000
117	A	116	HOH	0	0.002	0.008	22.430	-0.011	-0.011	0.000	0.000	0.000
118	A	117	HOH	0	0.027	0.018	35.846	-0.002	-0.002	0.000	0.000	0.000
119	A	118	HOH	0	-0.011	-0.014	48.058	-0.001	-0.001	0.000	0.000	0.000
120	A	119	HOH	0	-0.002	-0.008	37.415	0.003	0.003	0.000	0.000	0.000
121	A	120	HOH	0	-0.062	-0.049	24.081	-0.008	-0.008	0.000	0.000	0.000
122	A	121	HOH	0	-0.009	-0.009	36.464	0.000	0.000	0.000	0.000	0.000
123	A	122	HOH	0	-0.032	-0.026	23.721	0.008	0.008	0.000	0.000	0.000
124	A	123	HOH	0	-0.001	-0.012	42.403	-0.001	-0.001	0.000	0.000	0.000
125	A	124	HOH	0	0.037	0.029	44.437	-0.001	-0.001	0.000	0.000	0.000
126	A	125	HOH	0	-0.022	-0.019	21.135	0.005	0.005	0.000	0.000	0.000
127	A	126	HOH	0	-0.013	-0.013	44.445	0.000	0.000	0.000	0.000	0.000
128	A	127	HOH	0	-0.018	-0.010	25.634	0.001	0.001	0.000	0.000	0.000
129	A	128	HOH	0	0.001	-0.003	38.198	0.001	0.001	0.000	0.000	0.000
130	A	130	HOH	0	-0.061	-0.079	26.439	0.000	0.000	0.000	0.000	0.000
131	A	132	HOH	0	0.029	0.031	34.756	0.000	0.000	0.000	0.000	0.000
132	A	133	HOH	0	-0.005	-0.005	29.704	-0.004	-0.004	0.000	0.000	0.000
133	A	134	HOH	0	-0.017	-0.018	42.889	-0.001	-0.001	0.000	0.000	0.000
134	A	136	HOH	0	0.006	-0.001	33.262	-0.004	-0.004	0.000	0.000	0.000
135	A	137	HOH	0	0.025	0.020	27.308	-0.001	-0.001	0.000	0.000	0.000
136	A	138	HOH	0	0.013	0.003	39.605	0.001	0.001	0.000	0.000	0.000
137	A	139	HOH	0	-0.016	0.003	21.846	-0.015	-0.015	0.000	0.000	0.000
138	A	140	HOH	0	-0.008	-0.002	38.467	0.002	0.002	0.000	0.000	0.000
139	A	141	HOH	0	0.007	0.007	25.618	0.005	0.005	0.000	0.000	0.000
140	A	142	HOH	0	-0.035	-0.034	23.243	0.004	0.004	0.000	0.000	0.000
141	A	143	HOH	0	-0.003	0.014	41.165	0.000	0.000	0.000	0.000	0.000
142	A	145	HOH	0	-0.039	-0.035	36.064	0.000	0.000	0.000	0.000	0.000
143	A	147	HOH	0	0.002	-0.004	28.295	0.002	0.002	0.000	0.000	0.000
144	A	148	HOH	0	-0.027	-0.028	40.069	0.002	0.002	0.000	0.000	0.000
145	A	150	HOH	0	-0.038	-0.023	48.019	0.000	0.000	0.000	0.000	0.000
146	A	151	HOH	0	-0.026	-0.023	13.344	-0.051	-0.051	0.000	0.000	0.000
147	A	152	HOH	0	-0.043	-0.028	18.736	0.011	0.011	0.000	0.000	0.000
148	A	153	HOH	0	-0.021	-0.017	21.845	0.008	0.008	0.000	0.000	0.000
149	A	155	HOH	0	-0.003	-0.011	18.410	0.008	0.008	0.000	0.000	0.000
150	A	156	HOH	0	0.002	-0.008	12.795	0.012	0.012	0.000	0.000	0.000
151	A	157	HOH	0	0.056	0.032	15.637	-0.034	-0.034	0.000	0.000	0.000
152	A	159	HOH	0	-0.049	-0.043	23.299	-0.003	-0.003	0.000	0.000	0.000
153	A	160	HOH	0	-0.040	-0.022	49.320	0.001	0.001	0.000	0.000	0.000
154	A	162	HOH	0	0.011	0.024	20.812	-0.002	-0.002	0.000	0.000	0.000
155	A	163	HOH	0	-0.033	-0.026	44.331	0.000	0.000	0.000	0.000	0.000
156	A	164	HOH	0	-0.031	-0.023	27.594	-0.004	-0.004	0.000	0.000	0.000
157	A	165	HOH	0	-0.040	-0.026	29.894	0.001	0.001	0.000	0.000	0.000
158	A	167	HOH	0	0.022	0.024	37.959	0.002	0.002	0.000	0.000	0.000
159	A	169	HOH	0	-0.009	0.008	38.422	0.002	0.002	0.000	0.000	0.000
160	A	173	HOH	0	-0.027	-0.027	19.223	0.002	0.002	0.000	0.000	0.000
161	A	174	HOH	0	0.048	0.036	11.118	-0.004	-0.004	0.000	0.000	0.000
162	A	176	HOH	0	0.010	0.002	42.253	0.001	0.001	0.000	0.000	0.000
163	A	177	HOH	0	0.028	0.017	44.318	-0.001	-0.001	0.000	0.000	0.000
164	A	178	HOH	0	0.020	0.015	24.870	0.005	0.005	0.000	0.000	0.000
165	A	179	HOH	0	-0.030	-0.028	35.716	-0.001	-0.001	0.000	0.000	0.000
166	A	182	HOH	0	-0.042	-0.029	40.826	0.000	0.000	0.000	0.000	0.000
167	A	183	HOH	0	-0.097	-0.080	41.711	0.001	0.001	0.000	0.000	0.000
168	A	184	HOH	0	0.029	0.030	12.027	0.018	0.018	0.000	0.000	0.000
169	A	186	HOH	0	-0.032	-0.022	43.684	-0.001	-0.001	0.000	0.000	0.000
170	A	187	HOH	0	-0.034	-0.028	8.185	0.140	0.140	0.000	0.000	0.000
171	A	188	HOH	0	-0.020	-0.025	30.190	-0.005	-0.005	0.000	0.000	0.000
172	A	194	HOH	0	-0.038	-0.025	40.207	0.002	0.002	0.000	0.000	0.000
173	A	195	HOH	0	-0.040	-0.041	41.002	0.000	0.000	0.000	0.000	0.000
174	A	204	HOH	0	0.014	0.010	40.324	0.001	0.001	0.000	0.000	0.000
175	A	205	HOH	0	-0.033	-0.016	38.555	0.002	0.002	0.000	0.000	0.000
176	A	207	HOH	0	-0.044	-0.031	36.524	0.000	0.000	0.000	0.000	0.000
177	A	208	HOH	0	0.051	0.054	22.377	-0.005	-0.005	0.000	0.000	0.000
178	A	218	HOH	0	0.034	0.025	32.310	0.000	0.000	0.000	0.000	0.000

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