FMO DATABASE

FMODB ID: XYNK2

Calculation Name: 1HQ1-A-Xray40

Preferred Name:

Target Type:

Ligand Name: cytidine-5'-phosphate-2',3'-cyclic phosphate

ligand 3-letter code: CCC

PDB ID: 1HQ1

Chain ID: A

ChEMBL ID:

UniProt ID: P0AGD7

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	120
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-610905.757024
FMO2-HF: Nuclear repulsion	574647.553397
FMO2-HF: Total energy	-36258.203628
FMO2-MP2: Total energy	-36357.711565

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:1:GLY)

Summations of interaction energy for fragment #1(A:1: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.
-4.525	-3.584	-0.013	-0.376	-0.552	0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.024

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

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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	3	ASP	-1	-0.774	-0.899	3.805	-2.570	-1.582	-0.011	-0.358	-0.620	0.001
4	A	4	LEU	0	0.008	-0.016	6.219	0.543	0.543	0.000	0.000	0.000	0.000
5	A	5	ASN	0	0.027	0.055	8.268	0.681	0.681	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.759	-0.860	4.872	-3.478	-3.545	-0.001	-0.017	0.086	0.000
7	A	7	PHE	0	-0.051	-0.040	8.230	0.389	0.389	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.024	-0.019	10.997	0.149	0.149	0.000	0.000	0.000	0.000
9	A	9	GLU	-1	-0.852	-0.948	11.179	-0.327	-0.327	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.048	-0.035	11.136	0.209	0.209	0.000	0.000	0.000	0.000
11	A	11	LEU	0	-0.115	-0.061	13.442	0.068	0.068	0.000	0.000	0.000	0.000
12	A	12	ARG	1	0.892	0.956	15.502	0.444	0.444	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.007	0.000	17.079	0.000	0.000	0.000	0.000	0.000	0.000
14	A	14	NME	0	0.001	0.025	15.959	0.006	0.006	0.000	0.000	0.000	0.000
15	A	20	ACE	0	0.023	0.002	27.328	0.002	0.002	0.000	0.000	0.000	0.000
16	A	21	ASP	-1	-0.923	-1.004	23.611	-0.083	-0.083	0.000	0.000	0.000	0.000
17	A	22	ASP	-1	-0.829	-0.887	25.737	-0.083	-0.083	0.000	0.000	0.000	0.000
18	A	23	LYS	1	0.803	0.910	26.629	0.067	0.067	0.000	0.000	0.000	0.000
19	A	24	VAL	0	0.009	-0.017	21.938	0.006	0.006	0.000	0.000	0.000	0.000
20	A	25	LEU	0	0.053	0.046	19.094	-0.021	-0.021	0.000	0.000	0.000	0.000
21	A	26	VAL	0	0.090	0.063	21.301	-0.025	-0.025	0.000	0.000	0.000	0.000
22	A	27	ARG	1	0.968	0.978	23.092	0.092	0.092	0.000	0.000	0.000	0.000
23	A	28	MET	0	-0.068	-0.027	17.596	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	29	GLU	-1	-0.857	-0.939	18.242	-0.276	-0.276	0.000	0.000	0.000	0.000
25	A	30	ALA	0	-0.013	0.002	19.361	-0.032	-0.032	0.000	0.000	0.000	0.000
26	A	31	ILE	0	-0.034	-0.025	18.451	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	32	ILE	0	0.024	0.000	13.966	-0.021	-0.021	0.000	0.000	0.000	0.000
28	A	33	ASN	0	0.012	0.005	17.155	-0.075	-0.075	0.000	0.000	0.000	0.000
29	A	34	SER	0	-0.002	0.008	19.476	0.011	0.011	0.000	0.000	0.000	0.000
30	A	35	MET	0	-0.102	-0.026	15.324	-0.011	-0.011	0.000	0.000	0.000	0.000
31	A	36	THR	0	-0.013	0.010	16.608	-0.014	-0.014	0.000	0.000	0.000	0.000
32	A	37	MET	0	0.089	0.016	13.408	-0.062	-0.062	0.000	0.000	0.000	0.000
33	A	38	LYS	1	0.916	0.939	12.051	0.252	0.252	0.000	0.000	0.000	0.000
34	A	39	GLU	-1	-0.771	-0.853	11.876	-0.405	-0.405	0.000	0.000	0.000	0.000
35	A	40	ARG	1	0.931	0.960	11.268	0.568	0.568	0.000	0.000	0.000	0.000
36	A	41	ALA	0	0.031	0.035	7.783	-0.195	-0.195	0.000	0.000	0.000	0.000
37	A	42	LYS	1	0.898	0.977	7.034	0.032	0.032	0.000	0.000	0.000	0.000
38	A	43	PRO	0	0.126	0.059	8.621	0.223	0.223	0.000	0.000	0.000	0.000
39	A	44	GLU	-1	-0.787	-0.887	9.761	-0.333	-0.333	0.000	0.000	0.000	0.000
40	A	45	ILE	0	-0.123	-0.073	13.086	0.091	0.091	0.000	0.000	0.000	0.000
41	A	46	ILE	0	-0.021	-0.014	14.471	0.045	0.045	0.000	0.000	0.000	0.000
42	A	47	LYS	1	0.946	0.986	16.951	0.187	0.187	0.000	0.000	0.000	0.000
43	A	48	GLY	0	0.045	0.015	20.394	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	49	SER	0	-0.034	-0.029	23.911	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	50	ARG	1	0.821	0.875	18.099	0.297	0.297	0.000	0.000	0.000	0.000
46	A	51	LYS	1	0.889	0.950	19.743	0.127	0.127	0.000	0.000	0.000	0.000
47	A	52	ARG	1	0.988	1.002	22.133	0.120	0.120	0.000	0.000	0.000	0.000
48	A	53	ARG	1	0.815	0.903	19.390	0.286	0.286	0.000	0.000	0.000	0.000
49	A	54	ILE	0	0.020	0.008	18.469	0.003	0.003	0.000	0.000	0.000	0.000
50	A	55	ALA	0	-0.003	0.007	22.563	0.001	0.001	0.000	0.000	0.000	0.000
51	A	56	ALA	0	0.025	0.024	25.051	0.005	0.005	0.000	0.000	0.000	0.000
52	A	57	GLY	0	-0.017	-0.002	25.510	0.007	0.007	0.000	0.000	0.000	0.000
53	A	58	SER	0	-0.047	-0.024	23.331	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	59	GLY	0	0.028	0.034	25.501	0.006	0.006	0.000	0.000	0.000	0.000
55	A	60	MET	0	-0.057	-0.021	24.384	0.015	0.015	0.000	0.000	0.000	0.000
56	A	61	GLN	0	0.080	0.050	27.396	0.004	0.004	0.000	0.000	0.000	0.000
57	A	62	VAL	0	0.053	0.001	24.081	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	63	GLN	0	-0.035	-0.005	23.907	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	64	ASP	-1	-0.759	-0.884	23.903	-0.101	-0.101	0.000	0.000	0.000	0.000
60	A	65	VAL	0	-0.007	0.001	19.625	-0.013	-0.013	0.000	0.000	0.000	0.000
61	A	66	ASN	0	0.018	0.006	19.340	-0.029	-0.029	0.000	0.000	0.000	0.000
62	A	67	ARG	1	0.941	0.973	19.319	0.083	0.083	0.000	0.000	0.000	0.000
63	A	68	LEU	0	0.025	0.022	15.571	0.013	0.013	0.000	0.000	0.000	0.000
64	A	69	LEU	0	-0.005	-0.010	14.505	-0.021	-0.021	0.000	0.000	0.000	0.000
65	A	70	LYS	1	0.851	0.931	14.513	-0.040	-0.040	0.000	0.000	0.000	0.000
66	A	71	GLN	0	0.092	0.040	15.517	0.007	0.007	0.000	0.000	0.000	0.000
67	A	72	PHE	0	0.019	0.011	7.375	0.090	0.090	0.000	0.000	0.000	0.000
68	A	73	ASP	-1	-0.735	-0.788	11.015	0.100	0.100	0.000	0.000	0.000	0.000
69	A	74	ASP	-1	-0.834	-0.906	11.610	0.176	0.176	0.000	0.000	0.000	0.000
70	A	75	MET	0	0.033	0.021	10.483	0.092	0.092	0.000	0.000	0.000	0.000
71	A	76	GLN	0	0.028	0.038	5.268	0.545	0.545	0.000	0.000	0.000	0.000
72	A	77	ARG	1	0.816	0.885	7.803	0.194	0.194	0.000	0.000	0.000	0.000
73	A	78	MET	0	0.023	0.015	10.342	0.174	0.174	0.000	0.000	0.000	0.000
74	A	79	MET	0	0.004	0.028	7.263	0.232	0.232	0.000	0.000	0.000	0.000
75	A	80	LYS	1	0.921	0.949	5.859	-1.510	-1.510	0.000	0.000	0.000	0.000
76	A	81	LYS	1	0.923	0.963	7.899	-0.600	-0.600	0.000	0.000	0.000	0.000
77	A	82	MET	0	-0.046	0.003	11.325	-0.052	-0.052	0.000	0.000	0.000	0.000
78	A	83	LYS	1	0.912	0.973	7.866	-1.354	-1.354	0.000	0.000	0.000	0.000
79	A	0	NME	0	-0.038	-0.005	6.714	-0.006	-0.006	0.000	0.000	0.000	0.000
80	B	9007	HOH	0	0.069	0.049	17.438	-0.014	-0.014	0.000	0.000	0.000	0.000
81	B	9019	HOH	0	0.010	0.004	17.212	0.018	0.018	0.000	0.000	0.000	0.000
82	B	9056	HOH	0	-0.026	-0.016	22.709	0.001	0.001	0.000	0.000	0.000	0.000
83	B	9065	HOH	0	-0.030	-0.014	31.284	0.003	0.003	0.000	0.000	0.000	0.000
84	A	9001	HOH	0	-0.026	-0.021	26.528	0.002	0.002	0.000	0.000	0.000	0.000
85	A	9004	HOH	0	-0.028	-0.017	25.813	0.003	0.003	0.000	0.000	0.000	0.000
86	A	9005	HOH	0	0.042	0.017	17.203	0.008	0.008	0.000	0.000	0.000	0.000
87	A	9010	HOH	0	0.043	0.030	19.859	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	9012	HOH	0	0.031	0.011	20.987	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	9013	HOH	0	-0.004	-0.006	16.512	-0.008	-0.008	0.000	0.000	0.000	0.000
90	A	9032	HOH	0	-0.013	-0.003	20.231	-0.018	-0.018	0.000	0.000	0.000	0.000
91	A	9051	HOH	0	-0.043	-0.028	15.107	0.018	0.018	0.000	0.000	0.000	0.000
92	A	9059	HOH	0	-0.019	-0.018	10.794	0.057	0.057	0.000	0.000	0.000	0.000
93	A	9069	HOH	0	-0.040	-0.028	27.941	0.003	0.003	0.000	0.000	0.000	0.000
94	A	9071	HOH	0	0.034	0.030	20.081	-0.010	-0.010	0.000	0.000	0.000	0.000
95	A	9080	HOH	0	0.032	0.025	13.171	0.021	0.021	0.000	0.000	0.000	0.000
96	A	9088	HOH	0	-0.030	-0.018	24.133	0.001	0.001	0.000	0.000	0.000	0.000
97	A	9089	HOH	0	-0.008	-0.009	24.515	0.005	0.005	0.000	0.000	0.000	0.000
98	A	9096	HOH	0	0.046	0.028	28.286	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	9105	HOH	0	-0.075	-0.056	4.938	-0.055	-0.035	-0.001	-0.001	-0.018	0.000
100	A	9117	HOH	0	-0.025	-0.015	15.196	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	9122	HOH	0	-0.020	-0.018	11.593	0.010	0.010	0.000	0.000	0.000	0.000
102	A	9125	HOH	0	0.021	0.009	20.440	-0.008	-0.008	0.000	0.000	0.000	0.000
103	A	9141	HOH	0	-0.053	-0.057	10.258	0.048	0.048	0.000	0.000	0.000	0.000
104	A	9142	HOH	0	-0.042	-0.031	13.873	0.020	0.020	0.000	0.000	0.000	0.000
105	A	9143	HOH	0	0.012	0.009	29.451	-0.003	-0.003	0.000	0.000	0.000	0.000
106	A	9151	HOH	0	-0.027	-0.019	29.675	0.004	0.004	0.000	0.000	0.000	0.000
107	A	9154	HOH	0	-0.035	-0.020	18.090	0.004	0.004	0.000	0.000	0.000	0.000
108	A	9157	HOH	0	-0.033	-0.023	4.847	0.343	0.343	0.000	0.000	0.000	0.000
109	A	9159	HOH	0	-0.029	-0.032	29.219	0.004	0.004	0.000	0.000	0.000	0.000
110	A	9177	HOH	0	0.010	0.008	20.741	0.010	0.010	0.000	0.000	0.000	0.000
111	A	9214	HOH	0	0.044	0.034	16.672	-0.008	-0.008	0.000	0.000	0.000	0.000
112	A	9217	HOH	0	0.011	-0.012	11.898	0.050	0.050	0.000	0.000	0.000	0.000
113	A	9220	HOH	0	-0.015	-0.014	28.746	0.000	0.000	0.000	0.000	0.000	0.000
114	A	9241	HOH	0	0.020	0.026	10.734	-0.015	-0.015	0.000	0.000	0.000	0.000
115	A	9242	HOH	0	-0.005	-0.012	30.132	0.002	0.002	0.000	0.000	0.000	0.000
116	A	9250	HOH	0	0.032	0.019	16.681	0.025	0.025	0.000	0.000	0.000	0.000
117	A	9258	HOH	0	-0.054	-0.064	12.588	0.044	0.044	0.000	0.000	0.000	0.000
118	A	9259	HOH	0	-0.089	-0.092	9.367	0.055	0.055	0.000	0.000	0.000	0.000
119	A	9271	HOH	0	-0.098	-0.096	14.741	0.004	0.004	0.000	0.000	0.000	0.000
120	A	9278	HOH	0	0.003	0.003	13.426	0.010	0.010	0.000	0.000	0.000	0.000

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