FMO DATABASE

FMODB ID: XRQ18

Calculation Name: 2YH6-A-Xray42

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2YH6

Chain ID: A

ChEMBL ID:

UniProt ID: P0A903

Base Structure: X-ray

Registration Date: 2019-02-15

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	141
LigandCharge	SO4=-2
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-955702.073284
FMO2-HF: Nuclear repulsion	907859.818022
FMO2-HF: Total energy	-47842.255262
FMO2-MP2: Total energy	-47977.860769

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:77:GLY)

Summations of interaction energy for fragment #1(A:77: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.
1.264	-12.824	38.101	-12.485	-11.526	-0.043

Interaction energy analysis for fragmet #1(A:77:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.058 / q_NPA : -0.079

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	79	THR	0	0.019	0.036	3.886	-0.982	1.420	-0.011	-1.441	-0.949	-0.004
4	A	80	ALA	0	0.047	0.044	6.024	-0.329	-0.329	0.000	0.000	0.000	0.000
5	A	81	SER	0	-0.020	-0.034	7.813	0.323	0.323	0.000	0.000	0.000	0.000
6	A	82	LEU	0	0.016	0.011	11.529	-0.016	-0.016	0.000	0.000	0.000	0.000
7	A	83	LEU	0	0.010	-0.001	14.543	0.039	0.039	0.000	0.000	0.000	0.000
8	A	84	VAL	0	0.005	-0.004	18.004	0.008	0.008	0.000	0.000	0.000	0.000
9	A	85	GLU	-1	-0.921	-0.979	20.861	-0.198	-0.198	0.000	0.000	0.000	0.000
10	A	86	ASN	0	-0.015	0.000	23.559	0.026	0.026	0.000	0.000	0.000	0.000
11	A	87	GLY	0	0.086	0.028	26.594	0.001	0.001	0.000	0.000	0.000	0.000
12	A	88	ARG	1	0.841	0.915	29.855	0.122	0.122	0.000	0.000	0.000	0.000
13	A	89	GLY	0	0.056	0.033	31.667	0.003	0.003	0.000	0.000	0.000	0.000
14	A	90	ASN	0	-0.070	-0.054	27.799	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	91	THR	0	0.017	-0.004	26.703	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	92	LEU	0	0.060	0.074	20.130	0.005	0.005	0.000	0.000	0.000	0.000
17	A	93	TRP	0	0.008	-0.007	18.690	-0.013	-0.013	0.000	0.000	0.000	0.000
18	A	94	PRO	0	0.005	-0.017	23.278	-0.006	-0.006	0.000	0.000	0.000	0.000
19	A	95	GLN	0	0.005	0.005	24.075	-0.005	-0.005	0.000	0.000	0.000	0.000
20	A	96	VAL	0	0.072	0.045	18.198	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	97	VAL	0	-0.010	-0.007	20.962	-0.003	-0.003	0.000	0.000	0.000	0.000
22	A	98	SER	0	-0.012	-0.001	22.749	0.007	0.007	0.000	0.000	0.000	0.000
23	A	99	VAL	0	0.030	0.033	19.814	0.011	0.011	0.000	0.000	0.000	0.000
24	A	100	LEU	0	-0.012	-0.009	17.156	0.003	0.003	0.000	0.000	0.000	0.000
25	A	101	GLN	0	-0.050	-0.043	20.960	0.015	0.015	0.000	0.000	0.000	0.000
26	A	102	ALA	0	0.009	0.012	24.356	0.013	0.013	0.000	0.000	0.000	0.000
27	A	103	LYS	1	0.885	0.953	19.279	0.231	0.231	0.000	0.000	0.000	0.000
28	A	104	ASN	0	-0.050	-0.009	22.463	0.012	0.012	0.000	0.000	0.000	0.000
29	A	105	TYR	0	0.075	0.048	16.633	0.011	0.011	0.000	0.000	0.000	0.000
30	A	106	THR	0	-0.013	-0.029	20.853	0.001	0.001	0.000	0.000	0.000	0.000
31	A	107	ILE	0	-0.023	-0.007	20.065	-0.015	-0.015	0.000	0.000	0.000	0.000
32	A	108	THR	0	-0.012	-0.009	18.970	0.017	0.017	0.000	0.000	0.000	0.000
33	A	109	GLN	0	-0.026	-0.002	19.539	0.008	0.008	0.000	0.000	0.000	0.000
34	A	110	ARG	1	0.873	0.905	20.913	0.111	0.111	0.000	0.000	0.000	0.000
35	A	111	ASP	-1	-0.898	-0.931	22.641	-0.081	-0.081	0.000	0.000	0.000	0.000
36	A	112	ASP	-1	-0.762	-0.858	23.779	-0.152	-0.152	0.000	0.000	0.000	0.000
37	A	113	ALA	0	-0.046	-0.012	25.840	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	114	GLY	0	0.027	0.024	23.359	0.000	0.000	0.000	0.000	0.000	0.000
39	A	115	GLN	0	-0.049	-0.018	21.624	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	116	THR	0	0.021	0.000	17.360	-0.035	-0.035	0.000	0.000	0.000	0.000
41	A	117	LEU	0	-0.002	0.003	17.183	0.040	0.040	0.000	0.000	0.000	0.000
42	A	118	THR	0	-0.018	-0.011	15.361	-0.057	-0.057	0.000	0.000	0.000	0.000
43	A	119	THR	0	-0.012	-0.017	14.933	0.008	0.008	0.000	0.000	0.000	0.000
44	A	120	ASP	-1	-0.887	-0.963	16.454	-0.048	-0.048	0.000	0.000	0.000	0.000
45	A	121	TRP	0	-0.071	-0.038	12.247	-0.038	-0.038	0.000	0.000	0.000	0.000
46	A	122	VAL	0	-0.020	0.000	13.960	0.005	0.005	0.000	0.000	0.000	0.000
47	A	123	GLN	0	-0.019	-0.018	14.210	0.006	0.006	0.000	0.000	0.000	0.000
48	A	124	TRP	0	-0.019	-0.020	10.932	-0.048	-0.048	0.000	0.000	0.000	0.000
49	A	125	ASN	0	-0.008	0.007	15.221	0.037	0.037	0.000	0.000	0.000	0.000
50	A	126	ARG	1	0.818	0.887	13.912	0.021	0.021	0.000	0.000	0.000	0.000
51	A	127	LEU	0	-0.066	-0.023	18.936	0.012	0.012	0.000	0.000	0.000	0.000
52	A	128	ASP	-1	-0.890	-0.953	19.696	0.029	0.029	0.000	0.000	0.000	0.000
53	A	129	GLU	-1	-0.970	-0.993	19.496	0.001	0.001	0.000	0.000	0.000	0.000
54	A	130	ASP	-1	-0.935	-0.977	19.688	0.059	0.059	0.000	0.000	0.000	0.000
55	A	131	GLU	-1	-1.018	-1.010	16.156	0.066	0.066	0.000	0.000	0.000	0.000
56	A	132	GLN	0	0.015	0.023	15.155	-0.025	-0.025	0.000	0.000	0.000	0.000
57	A	133	TYR	0	-0.011	-0.035	9.826	0.027	0.027	0.000	0.000	0.000	0.000
58	A	134	ARG	1	0.814	0.902	12.607	-0.079	-0.079	0.000	0.000	0.000	0.000
59	A	135	GLY	0	0.017	0.001	10.331	0.064	0.064	0.000	0.000	0.000	0.000
60	A	136	ARG	1	0.869	0.959	10.877	0.030	0.030	0.000	0.000	0.000	0.000
61	A	137	TYR	0	0.036	-0.009	8.209	0.039	0.039	0.000	0.000	0.000	0.000
62	A	138	GLN	0	0.016	0.019	11.478	0.096	0.096	0.000	0.000	0.000	0.000
63	A	139	ILE	0	-0.029	-0.011	12.473	-0.137	-0.137	0.000	0.000	0.000	0.000
64	A	140	SER	0	-0.037	-0.040	14.867	0.085	0.085	0.000	0.000	0.000	0.000
65	A	141	VAL	0	0.028	0.011	16.466	-0.048	-0.048	0.000	0.000	0.000	0.000
66	A	142	LYS	1	0.945	0.993	16.662	0.327	0.327	0.000	0.000	0.000	0.000
67	A	143	PRO	0	0.026	0.014	20.489	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	144	GLN	0	-0.015	-0.009	18.956	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	145	GLY	0	0.035	0.034	21.918	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	146	TYR	0	-0.096	-0.037	24.779	0.006	0.006	0.000	0.000	0.000	0.000
71	A	147	GLN	0	0.077	0.038	22.488	0.013	0.013	0.000	0.000	0.000	0.000
72	A	148	GLN	0	-0.004	0.023	21.603	0.010	0.010	0.000	0.000	0.000	0.000
73	A	149	ALA	0	0.022	0.018	16.199	-0.016	-0.016	0.000	0.000	0.000	0.000
74	A	150	VAL	0	0.032	0.017	14.532	0.034	0.034	0.000	0.000	0.000	0.000
75	A	151	THR	0	-0.041	-0.015	10.960	-0.032	-0.032	0.000	0.000	0.000	0.000
76	A	152	VAL	0	0.001	0.005	8.967	0.146	0.146	0.000	0.000	0.000	0.000
77	A	153	LYS	1	0.919	0.963	8.063	0.012	0.012	0.000	0.000	0.000	0.000
78	A	154	LEU	0	0.010	0.008	4.181	0.247	0.348	-0.001	-0.019	-0.080	0.000
79	A	155	LEU	0	-0.080	-0.033	6.958	0.154	0.154	0.000	0.000	0.000	0.000
80	A	156	ASN	0	-0.024	-0.021	9.409	0.126	0.126	0.000	0.000	0.000	0.000
81	A	157	LEU	0	0.013	0.010	6.027	-0.160	-0.160	0.000	0.000	0.000	0.000
82	A	158	GLU	-1	-0.881	-0.936	9.340	0.258	0.258	0.000	0.000	0.000	0.000
83	A	159	GLN	0	0.025	0.008	12.391	-0.080	-0.080	0.000	0.000	0.000	0.000
84	A	160	ALA	0	0.086	0.048	13.905	0.023	0.023	0.000	0.000	0.000	0.000
85	A	161	GLY	0	-0.050	-0.022	16.509	0.006	0.006	0.000	0.000	0.000	0.000
86	A	162	LYS	1	0.904	0.961	14.998	-0.266	-0.266	0.000	0.000	0.000	0.000
87	A	163	PRO	0	-0.005	-0.002	12.675	0.016	0.016	0.000	0.000	0.000	0.000
88	A	164	VAL	0	-0.016	0.001	8.811	0.045	0.045	0.000	0.000	0.000	0.000
89	A	165	ALA	0	0.002	-0.026	7.018	-0.038	-0.038	0.000	0.000	0.000	0.000
90	A	166	ASP	-1	-0.804	-0.865	6.617	1.563	1.563	0.000	0.000	0.000	0.000
91	A	167	ALA	0	0.024	-0.003	2.811	-0.497	0.441	0.236	-0.523	-0.651	0.004
92	A	168	ALA	0	0.014	0.007	2.176	-6.694	-5.984	2.854	-1.566	-1.997	-0.028
93	A	169	SER	0	0.084	0.007	4.852	-0.325	-0.307	-0.001	-0.005	-0.012	0.000
94	A	170	MET	0	-0.044	0.015	1.986	-0.914	-4.165	12.441	-6.252	-2.938	0.006
95	A	171	GLN	0	-0.046	-0.011	1.973	-0.108	-5.450	21.439	-11.436	-4.661	-0.009
96	A	172	ARG	1	0.771	0.871	2.402	8.780	-0.954	1.143	8.813	-0.223	-0.012
97	A	173	TYR	0	0.081	0.012	5.686	-0.128	-0.128	0.000	0.000	0.000	0.000
98	A	174	SER	0	-0.050	-0.014	3.657	-0.155	-0.085	0.001	-0.056	-0.015	0.000
99	A	175	THR	0	-0.019	-0.015	5.902	0.337	0.337	0.000	0.000	0.000	0.000
100	A	176	GLU	-1	-0.797	-0.868	7.897	-0.257	-0.257	0.000	0.000	0.000	0.000
101	A	177	MET	0	0.004	0.011	9.780	0.138	0.138	0.000	0.000	0.000	0.000
102	A	178	MET	0	-0.074	-0.042	10.194	0.144	0.144	0.000	0.000	0.000	0.000
103	A	179	ASN	0	-0.021	-0.017	11.845	0.106	0.106	0.000	0.000	0.000	0.000
104	A	180	VAL	0	0.025	0.038	13.910	0.072	0.072	0.000	0.000	0.000	0.000
105	A	181	ILE	0	-0.002	-0.012	14.209	0.057	0.057	0.000	0.000	0.000	0.000
106	A	182	SER	0	-0.016	-0.013	15.846	0.061	0.061	0.000	0.000	0.000	0.000
107	A	183	ALA	0	0.052	0.026	17.530	0.038	0.038	0.000	0.000	0.000	0.000
108	A	184	GLY	0	-0.063	-0.042	19.636	0.034	0.034	0.000	0.000	0.000	0.000
109	A	185	LEU	0	-0.079	-0.055	18.990	0.023	0.023	0.000	0.000	0.000	0.000
110	A	186	ASP	-1	-0.895	-0.910	22.115	-0.200	-0.200	0.000	0.000	0.000	0.000
111	A	187	LYS	1	0.882	0.950	23.712	0.188	0.188	0.000	0.000	0.000	0.000
112	A	0	NME	0	-0.010	-0.006	25.235	0.011	0.011	0.000	0.000	0.000	0.000
113	A	1188	SO4	-2	-1.720	-1.822	17.775	-0.148	-0.148	0.000	0.000	0.000	0.000
114	A	1189	SO4	-2	-1.832	-1.885	14.318	-0.550	-0.550	0.000	0.000	0.000	0.000
115	A	1190	SO4	-2	-1.946	-1.977	19.234	-0.350	-0.350	0.000	0.000	0.000	0.000
116	A	2002	HOH	0	-0.062	-0.042	8.041	-0.009	-0.009	0.000	0.000	0.000	0.000
117	A	2004	HOH	0	-0.013	-0.024	9.937	0.069	0.069	0.000	0.000	0.000	0.000
118	A	2008	HOH	0	0.006	0.003	24.894	-0.005	-0.005	0.000	0.000	0.000	0.000
119	A	2009	HOH	0	-0.041	-0.029	26.495	0.005	0.005	0.000	0.000	0.000	0.000
120	A	2013	HOH	0	0.024	0.018	23.985	0.000	0.000	0.000	0.000	0.000	0.000
121	A	2014	HOH	0	0.015	0.007	17.384	0.013	0.013	0.000	0.000	0.000	0.000
122	A	2018	HOH	0	0.027	-0.001	23.406	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	2020	HOH	0	-0.053	-0.031	26.044	0.003	0.003	0.000	0.000	0.000	0.000
124	A	2021	HOH	0	-0.049	-0.037	20.110	0.009	0.009	0.000	0.000	0.000	0.000
125	A	2022	HOH	0	-0.047	-0.035	19.721	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	2023	HOH	0	0.033	0.003	23.714	-0.004	-0.004	0.000	0.000	0.000	0.000
127	A	2026	HOH	0	-0.004	-0.007	19.041	0.004	0.004	0.000	0.000	0.000	0.000
128	A	2027	HOH	0	-0.017	-0.014	18.024	0.007	0.007	0.000	0.000	0.000	0.000
129	A	2028	HOH	0	0.019	0.005	13.876	0.017	0.017	0.000	0.000	0.000	0.000
130	A	2030	HOH	0	0.010	0.004	10.917	-0.005	-0.005	0.000	0.000	0.000	0.000
131	A	2031	HOH	0	-0.001	0.006	23.739	-0.004	-0.004	0.000	0.000	0.000	0.000
132	A	2033	HOH	0	0.006	0.014	9.601	-0.051	-0.051	0.000	0.000	0.000	0.000
133	A	2035	HOH	0	0.001	-0.003	8.901	-0.054	-0.054	0.000	0.000	0.000	0.000
134	A	2036	HOH	0	0.011	0.010	12.909	0.032	0.032	0.000	0.000	0.000	0.000
135	A	2039	HOH	0	-0.039	-0.034	15.433	0.024	0.024	0.000	0.000	0.000	0.000
136	A	2040	HOH	0	-0.045	-0.035	25.046	0.004	0.004	0.000	0.000	0.000	0.000
137	A	2041	HOH	0	-0.005	0.000	8.258	-0.126	-0.126	0.000	0.000	0.000	0.000
138	A	2042	HOH	0	0.039	0.029	10.639	0.044	0.044	0.000	0.000	0.000	0.000
139	A	2045	HOH	0	-0.022	-0.010	13.548	0.014	0.014	0.000	0.000	0.000	0.000
140	A	2046	HOH	0	-0.029	-0.026	19.563	0.007	0.007	0.000	0.000	0.000	0.000
141	A	2047	HOH	0	-0.061	-0.032	25.129	0.004	0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:77:GLY)