FMO DATABASE

FMODB ID: PKKR3

Calculation Name: 2V33-A-Xray42

Preferred Name:

Target Type:

Ligand Name: nitrate ion

ligand 3-letter code: NO3

PDB ID: 2V33

Chain ID: A

ChEMBL ID:

UniProt ID: P03315

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	144
LigandCharge	NO3=-1
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-672944.382582
FMO2-HF: Nuclear repulsion	634266.576759
FMO2-HF: Total energy	-38677.805824
FMO2-MP2: Total energy	-38784.93588

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:292:GLU)

Summations of interaction energy for fragment #1(A:292:GLU)

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.
-70.276	-64.244	0.965	-3.356	-3.639	0.016

Interaction energy analysis for fragmet #1(A:292:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.952 / q_NPA : -0.969

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	294	PRO	0	-0.021	-0.015	3.229	4.000	6.575	0.067	-1.404	-1.238	0.001
4	A	295	THR	0	0.003	0.009	5.039	-1.510	-1.510	0.000	0.000	0.000	0.000
5	A	296	ILE	0	-0.030	-0.011	7.005	-2.051	-2.051	0.000	0.000	0.000	0.000
6	A	297	ILE	0	0.028	0.003	10.589	-0.091	-0.091	0.000	0.000	0.000	0.000
7	A	298	ASP	-1	-0.784	-0.883	13.489	16.764	16.764	0.000	0.000	0.000	0.000
8	A	299	LEU	0	-0.007	0.014	15.402	-0.604	-0.604	0.000	0.000	0.000	0.000
9	A	300	THR	0	0.023	0.033	17.320	-0.860	-0.860	0.000	0.000	0.000	0.000
10	A	376	CYS	0	-0.067	-0.006	20.742	0.471	0.471	0.000	0.000	0.000	0.000
11	A	302	THR	0	-0.007	0.005	22.999	-0.498	-0.498	0.000	0.000	0.000	0.000
12	A	303	VAL	0	0.025	0.014	26.076	0.290	0.290	0.000	0.000	0.000	0.000
13	A	304	ALA	0	-0.042	-0.005	28.403	-0.279	-0.279	0.000	0.000	0.000	0.000
14	A	305	THR	0	0.004	-0.005	30.156	-0.299	-0.299	0.000	0.000	0.000	0.000
15	A	380	CYS	0	-0.113	-0.055	31.516	0.519	0.519	0.000	0.000	0.000	0.000
16	A	307	THR	0	0.025	0.057	33.608	-0.196	-0.196	0.000	0.000	0.000	0.000
17	A	308	HIS	0	0.012	0.002	34.842	0.338	0.338	0.000	0.000	0.000	0.000
18	A	309	SER	0	0.015	0.026	35.156	-0.241	-0.241	0.000	0.000	0.000	0.000
19	A	310	SER	0	0.007	-0.010	34.755	0.125	0.125	0.000	0.000	0.000	0.000
20	A	311	ASP	-1	-0.943	-0.945	33.220	8.570	8.570	0.000	0.000	0.000	0.000
21	A	312	PHE	0	-0.039	-0.050	27.045	0.143	0.143	0.000	0.000	0.000	0.000
22	A	313	GLY	0	0.013	0.018	30.602	0.001	0.001	0.000	0.000	0.000	0.000
23	A	314	GLY	0	0.006	0.005	29.715	-0.131	-0.131	0.000	0.000	0.000	0.000
24	A	315	VAL	0	-0.006	-0.007	26.898	0.357	0.357	0.000	0.000	0.000	0.000
25	A	316	LEU	0	-0.001	-0.007	21.767	-0.188	-0.188	0.000	0.000	0.000	0.000
26	A	317	THR	0	0.032	0.032	22.146	0.321	0.321	0.000	0.000	0.000	0.000
27	A	318	LEU	0	-0.006	0.001	17.302	-0.144	-0.144	0.000	0.000	0.000	0.000
28	A	319	THR	0	-0.039	-0.025	18.720	0.252	0.252	0.000	0.000	0.000	0.000
29	A	320	TYR	0	-0.022	-0.008	12.829	-0.024	-0.024	0.000	0.000	0.000	0.000
30	A	321	LYS	1	0.942	0.981	14.159	-18.107	-18.107	0.000	0.000	0.000	0.000
31	A	322	THR	0	-0.014	-0.014	8.712	1.900	1.900	0.000	0.000	0.000	0.000
32	A	323	ASN	0	0.038	0.016	4.370	-6.230	-6.100	-0.001	-0.013	-0.116	0.000
33	A	324	LYS	1	0.854	0.928	2.635	-65.611	-63.972	0.803	-0.813	-1.628	0.009
34	A	325	ASN	0	0.012	-0.004	8.301	-0.868	-0.868	0.000	0.000	0.000	0.000
35	A	326	GLY	0	-0.007	-0.009	7.643	3.206	3.206	0.000	0.000	0.000	0.000
36	A	327	ASP	-1	-0.851	-0.906	7.881	21.701	21.701	0.000	0.000	0.000	0.000
37	A	370	CYS	0	-0.057	-0.015	7.807	4.844	4.844	0.000	0.000	0.000	0.000
38	A	329	SER	0	0.014	0.009	10.016	-0.991	-0.991	0.000	0.000	0.000	0.000
39	A	330	VAL	0	-0.044	-0.018	12.102	0.684	0.684	0.000	0.000	0.000	0.000
40	A	331	HIS	0	-0.027	-0.008	14.388	0.245	0.245	0.000	0.000	0.000	0.000
41	A	332	SER	0	0.001	-0.006	17.819	-0.092	-0.092	0.000	0.000	0.000	0.000
42	A	333	HIS	0	-0.056	-0.037	18.751	-0.469	-0.469	0.000	0.000	0.000	0.000
43	A	334	SER	0	0.002	0.007	23.323	-0.263	-0.263	0.000	0.000	0.000	0.000
44	A	335	ASN	0	-0.008	-0.009	26.688	0.042	0.042	0.000	0.000	0.000	0.000
45	A	336	VAL	0	-0.032	-0.013	29.288	-0.315	-0.315	0.000	0.000	0.000	0.000
46	A	337	ALA	0	0.020	0.020	27.165	-0.238	-0.238	0.000	0.000	0.000	0.000
47	A	338	THR	0	0.007	0.034	25.734	0.237	0.237	0.000	0.000	0.000	0.000
48	A	339	LEU	0	-0.035	-0.020	19.767	-0.201	-0.201	0.000	0.000	0.000	0.000
49	A	340	GLN	0	0.004	0.005	23.618	-0.079	-0.079	0.000	0.000	0.000	0.000
50	A	341	GLU	-1	-0.790	-0.859	18.670	13.192	13.192	0.000	0.000	0.000	0.000
51	A	342	ALA	0	0.051	0.042	16.816	0.089	0.089	0.000	0.000	0.000	0.000
52	A	343	THR	0	-0.018	-0.024	12.636	0.818	0.818	0.000	0.000	0.000	0.000
53	A	344	ALA	0	0.038	0.032	13.411	-1.031	-1.031	0.000	0.000	0.000	0.000
54	A	345	LYS	1	0.824	0.896	12.401	-18.284	-18.284	0.000	0.000	0.000	0.000
55	A	346	VAL	0	0.049	0.027	10.341	-1.122	-1.122	0.000	0.000	0.000	0.000
56	A	347	LYS	1	0.884	0.934	11.829	-18.340	-18.340	0.000	0.000	0.000	0.000
57	A	348	THR	0	0.050	0.002	11.481	-0.776	-0.776	0.000	0.000	0.000	0.000
58	A	349	ALA	0	-0.028	-0.006	13.691	-0.447	-0.447	0.000	0.000	0.000	0.000
59	A	350	GLY	0	0.025	0.027	15.539	-0.746	-0.746	0.000	0.000	0.000	0.000
60	A	351	LYS	1	0.921	0.954	16.545	-14.069	-14.069	0.000	0.000	0.000	0.000
61	A	352	VAL	0	0.000	0.028	15.230	0.526	0.526	0.000	0.000	0.000	0.000
62	A	353	THR	0	0.012	0.031	18.491	-0.543	-0.543	0.000	0.000	0.000	0.000
63	A	354	LEU	0	-0.038	-0.002	18.157	0.466	0.466	0.000	0.000	0.000	0.000
64	A	355	HIS	1	0.884	0.916	22.334	-12.207	-12.207	0.000	0.000	0.000	0.000
65	A	356	PHE	0	-0.003	0.006	24.522	0.363	0.363	0.000	0.000	0.000	0.000
66	A	357	SER	0	0.045	0.042	26.894	-0.242	-0.242	0.000	0.000	0.000	0.000
67	A	358	THR	0	-0.009	-0.023	29.578	0.161	0.161	0.000	0.000	0.000	0.000
68	A	359	ALA	0	0.060	0.035	32.149	-0.197	-0.197	0.000	0.000	0.000	0.000
69	A	360	SER	0	-0.026	0.000	33.978	-0.342	-0.342	0.000	0.000	0.000	0.000
70	A	361	ALA	0	0.081	0.033	35.547	0.108	0.108	0.000	0.000	0.000	0.000
71	A	362	SER	0	-0.023	-0.002	35.602	-0.020	-0.020	0.000	0.000	0.000	0.000
72	A	363	PRO	0	-0.023	0.021	30.442	0.135	0.135	0.000	0.000	0.000	0.000
73	A	364	SER	0	0.023	-0.009	28.880	0.198	0.198	0.000	0.000	0.000	0.000
74	A	365	PHE	0	0.012	0.020	24.098	-0.097	-0.097	0.000	0.000	0.000	0.000
75	A	366	VAL	0	-0.020	0.000	20.245	0.255	0.255	0.000	0.000	0.000	0.000
76	A	367	VAL	0	0.036	0.021	18.364	-0.050	-0.050	0.000	0.000	0.000	0.000
77	A	368	SER	0	-0.021	-0.019	14.619	0.530	0.530	0.000	0.000	0.000	0.000
78	A	369	LEU	0	0.031	0.012	12.469	-0.370	-0.370	0.000	0.000	0.000	0.000
79	A	371	SER	0	0.004	0.005	9.147	-1.754	-1.754	0.000	0.000	0.000	0.000
80	A	372	ALA	0	-0.009	0.023	10.869	-1.181	-1.181	0.000	0.000	0.000	0.000
81	A	373	ARG	1	0.960	0.950	13.634	-16.947	-16.947	0.000	0.000	0.000	0.000
82	A	374	ALA	0	0.029	0.027	17.233	-0.147	-0.147	0.000	0.000	0.000	0.000
83	A	375	THR	0	-0.009	0.015	20.384	-0.197	-0.197	0.000	0.000	0.000	0.000
84	A	377	SER	0	0.055	0.007	25.661	-0.105	-0.105	0.000	0.000	0.000	0.000
85	A	378	ALA	0	0.013	0.018	29.429	0.085	0.085	0.000	0.000	0.000	0.000
86	A	379	SER	0	0.003	0.008	32.420	-0.188	-0.188	0.000	0.000	0.000	0.000
87	A	381	GLU	-1	-0.841	-0.915	36.621	8.048	8.048	0.000	0.000	0.000	0.000
88	A	382	PRO	-1	-0.907	-0.951	38.833	7.672	7.672	0.000	0.000	0.000	0.000
89	A	1383	NO3	-1	-0.833	-0.902	17.325	15.358	15.358	0.000	0.000	0.000	0.000
90	A	1384	NO3	-1	-0.962	-0.989	22.885	12.280	12.280	0.000	0.000	0.000	0.000
91	A	2001	HOH	0	-0.013	-0.008	9.901	1.268	1.268	0.000	0.000	0.000	0.000
92	A	2002	HOH	0	-0.020	-0.010	19.139	-0.231	-0.231	0.000	0.000	0.000	0.000
93	A	2003	HOH	0	-0.049	-0.042	18.595	-0.065	-0.065	0.000	0.000	0.000	0.000
94	A	2004	HOH	0	-0.035	-0.029	19.518	-0.085	-0.085	0.000	0.000	0.000	0.000
95	A	2005	HOH	0	-0.062	-0.048	18.884	0.098	0.098	0.000	0.000	0.000	0.000
96	A	2007	HOH	0	-0.052	-0.040	21.317	-0.226	-0.226	0.000	0.000	0.000	0.000
97	A	2008	HOH	0	-0.019	-0.022	26.772	-0.165	-0.165	0.000	0.000	0.000	0.000
98	A	2009	HOH	0	-0.024	-0.019	31.005	0.061	0.061	0.000	0.000	0.000	0.000
99	A	2010	HOH	0	-0.073	-0.066	32.088	-0.023	-0.023	0.000	0.000	0.000	0.000
100	A	2012	HOH	0	0.004	-0.008	33.039	0.125	0.125	0.000	0.000	0.000	0.000
101	A	2015	HOH	0	-0.007	-0.029	35.453	0.053	0.053	0.000	0.000	0.000	0.000
102	A	2018	HOH	0	-0.067	-0.085	24.142	-0.152	-0.152	0.000	0.000	0.000	0.000
103	A	2019	HOH	0	-0.001	0.000	22.808	-0.117	-0.117	0.000	0.000	0.000	0.000
104	A	2020	HOH	0	-0.028	-0.015	17.642	-0.169	-0.169	0.000	0.000	0.000	0.000
105	A	2021	HOH	0	0.024	0.011	18.776	0.196	0.196	0.000	0.000	0.000	0.000
106	A	2022	HOH	0	-0.020	-0.013	9.113	0.363	0.363	0.000	0.000	0.000	0.000
107	A	2023	HOH	0	0.037	0.040	3.042	-7.586	-5.898	0.096	-1.126	-0.657	0.006
108	A	2024	HOH	0	0.020	0.009	8.119	0.393	0.393	0.000	0.000	0.000	0.000
109	A	2025	HOH	0	-0.025	-0.026	15.199	-0.061	-0.061	0.000	0.000	0.000	0.000
110	A	2027	HOH	0	0.035	0.018	20.266	0.006	0.006	0.000	0.000	0.000	0.000
111	A	2030	HOH	0	-0.002	-0.013	24.323	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	2031	HOH	0	-0.017	-0.018	26.985	-0.028	-0.028	0.000	0.000	0.000	0.000
113	A	2032	HOH	0	-0.021	-0.022	22.324	-0.083	-0.083	0.000	0.000	0.000	0.000
114	A	2033	HOH	0	-0.050	-0.033	22.589	0.117	0.117	0.000	0.000	0.000	0.000
115	A	2034	HOH	0	-0.010	-0.010	18.346	-0.190	-0.190	0.000	0.000	0.000	0.000
116	A	2035	HOH	0	0.009	0.005	17.900	0.239	0.239	0.000	0.000	0.000	0.000
117	A	2036	HOH	0	-0.006	-0.002	17.360	0.419	0.419	0.000	0.000	0.000	0.000
118	A	2037	HOH	0	0.014	0.009	11.811	-0.613	-0.613	0.000	0.000	0.000	0.000
119	A	2038	HOH	0	0.026	0.021	13.353	0.079	0.079	0.000	0.000	0.000	0.000
120	A	2039	HOH	0	-0.005	-0.009	13.845	0.090	0.090	0.000	0.000	0.000	0.000
121	A	2041	HOH	0	0.042	0.015	23.706	0.068	0.068	0.000	0.000	0.000	0.000
122	A	2042	HOH	0	-0.015	-0.028	16.130	0.303	0.303	0.000	0.000	0.000	0.000
123	A	2043	HOH	0	-0.033	-0.039	20.936	0.177	0.177	0.000	0.000	0.000	0.000
124	A	2044	HOH	0	0.027	0.014	19.645	-0.056	-0.056	0.000	0.000	0.000	0.000
125	A	2045	HOH	0	0.026	0.016	27.896	0.097	0.097	0.000	0.000	0.000	0.000
126	A	2046	HOH	0	-0.018	-0.011	31.002	0.010	0.010	0.000	0.000	0.000	0.000
127	A	2047	HOH	0	-0.037	-0.026	36.836	0.031	0.031	0.000	0.000	0.000	0.000
128	A	2048	HOH	0	0.035	0.020	39.519	0.088	0.088	0.000	0.000	0.000	0.000
129	A	2049	HOH	0	-0.006	-0.020	38.357	-0.055	-0.055	0.000	0.000	0.000	0.000
130	A	2050	HOH	0	-0.010	-0.015	33.281	0.058	0.058	0.000	0.000	0.000	0.000
131	A	2051	HOH	0	-0.047	-0.036	37.727	0.024	0.024	0.000	0.000	0.000	0.000
132	A	2052	HOH	0	0.024	0.020	40.030	0.051	0.051	0.000	0.000	0.000	0.000
133	A	2053	HOH	0	-0.007	-0.019	28.115	0.013	0.013	0.000	0.000	0.000	0.000
134	A	2054	HOH	0	-0.036	-0.032	27.254	0.000	0.000	0.000	0.000	0.000	0.000
135	A	2056	HOH	0	-0.024	-0.035	12.583	0.080	0.080	0.000	0.000	0.000	0.000
136	A	2058	HOH	0	-0.009	-0.003	13.892	-0.537	-0.537	0.000	0.000	0.000	0.000
137	A	2059	HOH	0	0.034	0.033	20.918	0.319	0.319	0.000	0.000	0.000	0.000
138	A	2060	HOH	0	0.001	-0.009	15.623	-0.015	-0.015	0.000	0.000	0.000	0.000
139	A	2061	HOH	0	-0.001	-0.007	25.755	-0.107	-0.107	0.000	0.000	0.000	0.000
140	A	2062	HOH	0	0.014	-0.002	23.828	0.247	0.247	0.000	0.000	0.000	0.000
141	A	2063	HOH	0	-0.020	0.005	34.276	0.141	0.141	0.000	0.000	0.000	0.000
142	A	2065	HOH	0	-0.001	-0.003	35.834	0.133	0.133	0.000	0.000	0.000	0.000
143	A	2066	HOH	0	0.009	0.004	21.247	-0.266	-0.266	0.000	0.000	0.000	0.000
144	B	2045	HOH	0	0.031	0.019	25.951	-0.103	-0.103	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:292:GLU)