FMO DATABASE

FMODB ID: 9GYQ2

Calculation Name: 4UYK-B-Xray323

Preferred Name:

Target Type:

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

ligand 3-letter code: CCC

PDB ID: 4UYK

Chain ID: B

ChEMBL ID:

UniProt ID: P49458

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	93
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-602790.143127
FMO2-HF: Nuclear repulsion	565971.836729
FMO2-HF: Total energy	-36818.306397
FMO2-MP2: Total energy	-36923.581683

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(B:1:MET )

Summations of interaction energy for fragment #1(B:1:MET )

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.
-24.62	-14.605	6.746	-5.311	-11.451	-0.02

Interaction energy analysis for fragmet #1(B:1:MET )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.017

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	B	3	LEU	0	-0.028	-0.004	3.163	-1.502	1.203	0.142	-1.222	-1.625	-0.002
4	B	4	LEU	0	-0.016	-0.011	4.464	0.876	1.029	0.000	-0.022	-0.130	0.000
5	B	5	GLU	-1	-0.846	-0.922	7.579	-1.122	-1.122	0.000	0.000	0.000	0.000
6	B	6	SER	0	-0.016	-0.029	10.945	0.084	0.084	0.000	0.000	0.000	0.000
7	B	7	GLU	-1	-0.891	-0.942	12.374	-0.493	-0.493	0.000	0.000	0.000	0.000
8	B	8	GLN	0	0.082	0.046	10.612	-0.093	-0.093	0.000	0.000	0.000	0.000
9	B	9	PHE	0	0.031	0.020	7.078	0.116	0.116	0.000	0.000	0.000	0.000
10	B	10	LEU	0	0.020	0.007	9.838	0.274	0.274	0.000	0.000	0.000	0.000
11	B	11	THR	0	-0.002	-0.018	13.225	0.133	0.133	0.000	0.000	0.000	0.000
12	B	12	GLU	-1	-0.961	-0.999	8.937	-0.714	-0.714	0.000	0.000	0.000	0.000
13	B	13	LEU	0	-0.073	-0.033	10.336	0.223	0.223	0.000	0.000	0.000	0.000
14	B	14	THR	0	0.003	-0.002	11.202	0.137	0.137	0.000	0.000	0.000	0.000
15	B	15	ARG	1	0.938	0.963	12.370	0.570	0.570	0.000	0.000	0.000	0.000
16	B	16	LEU	0	-0.037	-0.008	7.692	0.074	0.074	0.000	0.000	0.000	0.000
17	B	17	PHE	0	0.049	0.007	12.266	0.069	0.069	0.000	0.000	0.000	0.000
18	B	18	GLN	0	-0.016	-0.005	15.328	-0.022	-0.022	0.000	0.000	0.000	0.000
19	B	19	LYS	1	0.894	0.948	13.981	-0.027	-0.027	0.000	0.000	0.000	0.000
20	B	20	CYS	0	-0.093	-0.017	14.047	0.086	0.086	0.000	0.000	0.000	0.000
21	B	21	ARG	1	0.936	0.974	16.954	-0.225	-0.225	0.000	0.000	0.000	0.000
22	B	22	THR	0	0.009	0.004	20.457	0.003	0.003	0.000	0.000	0.000	0.000
23	B	23	SER	0	-0.010	-0.008	20.480	0.025	0.025	0.000	0.000	0.000	0.000
24	B	24	GLY	0	0.040	0.025	16.632	0.008	0.008	0.000	0.000	0.000	0.000
25	B	25	SER	0	-0.010	0.000	15.183	-0.059	-0.059	0.000	0.000	0.000	0.000
26	B	26	VAL	0	0.030	0.007	11.633	0.145	0.145	0.000	0.000	0.000	0.000
27	B	27	TYR	0	-0.021	0.001	9.912	-0.031	-0.031	0.000	0.000	0.000	0.000
28	B	28	ILE	0	0.011	-0.009	9.415	0.322	0.322	0.000	0.000	0.000	0.000
29	B	29	THR	0	-0.075	-0.030	7.419	-0.079	-0.079	0.000	0.000	0.000	0.000
30	B	30	LEU	0	0.049	0.016	8.285	0.122	0.122	0.000	0.000	0.000	0.000
31	B	31	LYS	1	0.950	0.981	8.105	-1.133	-1.133	0.000	0.000	0.000	0.000
32	B	32	LYS	1	0.967	0.996	10.213	-0.117	-0.117	0.000	0.000	0.000	0.000
33	B	33	TYR	0	-0.078	-0.062	8.149	0.034	0.034	0.000	0.000	0.000	0.000
34	B	34	ASP	-1	-0.788	-0.889	10.939	-0.080	-0.080	0.000	0.000	0.000	0.000
35	B	35	GLY	0	0.008	0.003	11.009	-0.024	-0.024	0.000	0.000	0.000	0.000
36	B	36	ARG	1	0.875	0.937	10.386	-0.234	-0.234	0.000	0.000	0.000	0.000
37	B	37	THR	0	0.041	0.029	9.327	-0.157	-0.157	0.000	0.000	0.000	0.000
38	B	38	LYS	1	0.953	0.979	10.494	0.585	0.585	0.000	0.000	0.000	0.000
39	B	39	PRO	0	0.012	-0.001	12.323	0.082	0.082	0.000	0.000	0.000	0.000
40	B	40	ILE	0	0.026	0.015	13.812	-0.055	-0.055	0.000	0.000	0.000	0.000
41	B	41	PRO	0	0.032	0.021	16.903	0.057	0.057	0.000	0.000	0.000	0.000
42	B	42	LYS	1	0.887	0.932	20.010	-0.107	-0.107	0.000	0.000	0.000	0.000
43	B	43	NME	0	0.060	0.049	23.762	-0.021	-0.021	0.000	0.000	0.000	0.000
44	B	49	ACE	0	0.004	-0.011	22.695	0.009	0.009	0.000	0.000	0.000	0.000
45	B	50	GLU	-1	-0.969	-0.998	15.381	-0.453	-0.453	0.000	0.000	0.000	0.000
46	B	51	PRO	0	-0.034	0.014	16.455	-0.039	-0.039	0.000	0.000	0.000	0.000
47	B	52	ALA	0	0.017	0.008	15.616	0.016	0.016	0.000	0.000	0.000	0.000
48	B	53	ASP	-1	-0.879	-0.940	15.836	-0.128	-0.128	0.000	0.000	0.000	0.000
49	B	54	ASN	0	-0.027	-0.018	17.236	0.034	0.034	0.000	0.000	0.000	0.000
50	B	55	LYS	1	0.933	0.960	11.946	0.625	0.625	0.000	0.000	0.000	0.000
51	B	56	CYS	0	0.000	-0.001	11.438	0.117	0.117	0.000	0.000	0.000	0.000
52	B	57	LEU	0	-0.048	-0.009	3.789	-0.299	-0.108	0.003	-0.038	-0.157	0.000
53	B	58	LEU	0	0.026	0.011	7.262	0.343	0.343	0.000	0.000	0.000	0.000
54	B	59	ARG	1	0.932	0.965	2.611	-5.849	-4.315	0.844	-0.490	-1.887	0.005
55	B	60	ALA	0	0.034	0.010	5.058	-1.121	-1.053	0.000	-0.021	-0.047	0.000
56	B	61	THR	0	-0.062	-0.058	5.576	0.706	0.706	0.000	0.000	0.000	0.000
57	B	62	ASP	-1	-0.729	-0.858	7.507	0.995	0.995	0.000	0.000	0.000	0.000
58	B	63	GLY	0	-0.040	-0.010	9.109	-0.241	-0.241	0.000	0.000	0.000	0.000
59	B	64	LYS	1	0.889	0.944	9.602	-0.803	-0.803	0.000	0.000	0.000	0.000
60	B	65	LYS	1	0.952	0.979	6.228	0.227	0.227	0.000	0.000	0.000	0.000
61	B	66	LYS	1	0.967	0.997	2.401	-10.055	-8.520	2.244	-0.950	-2.830	0.002
62	B	67	ILE	0	0.022	0.030	2.810	-5.056	-3.395	0.708	-0.985	-1.384	-0.012
63	B	68	SER	0	-0.030	-0.038	2.535	-0.445	1.672	2.801	-1.563	-3.355	-0.013
64	B	69	THR	0	0.058	0.029	4.534	-1.697	-1.646	0.004	-0.020	-0.036	0.000
65	B	70	VAL	0	-0.008	-0.009	6.868	0.518	0.518	0.000	0.000	0.000	0.000
66	B	71	VAL	0	0.023	0.029	9.077	-0.018	-0.018	0.000	0.000	0.000	0.000
67	B	72	SER	0	-0.030	-0.020	12.678	0.106	0.106	0.000	0.000	0.000	0.000
68	B	73	SER	0	0.084	0.013	15.756	0.011	0.011	0.000	0.000	0.000	0.000
69	B	74	LYS	1	0.930	0.972	18.558	0.464	0.464	0.000	0.000	0.000	0.000
70	B	75	GLU	-1	-0.859	-0.929	14.152	-0.674	-0.674	0.000	0.000	0.000	0.000
71	B	76	VAL	0	-0.009	0.003	16.625	0.015	0.015	0.000	0.000	0.000	0.000
72	B	77	ASN	0	0.028	0.010	18.212	0.039	0.039	0.000	0.000	0.000	0.000
73	B	78	LYS	1	1.005	1.016	19.230	0.354	0.354	0.000	0.000	0.000	0.000
74	B	79	PHE	0	0.009	-0.001	12.337	0.016	0.016	0.000	0.000	0.000	0.000
75	B	80	GLN	0	0.022	-0.013	17.706	0.030	0.030	0.000	0.000	0.000	0.000
76	B	81	MET	0	0.004	0.014	19.308	0.048	0.048	0.000	0.000	0.000	0.000
77	B	82	ALA	0	0.009	0.004	18.347	0.021	0.021	0.000	0.000	0.000	0.000
78	B	83	TYR	0	0.021	0.008	13.122	0.011	0.011	0.000	0.000	0.000	0.000
79	B	84	SER	0	0.016	0.001	17.470	0.065	0.065	0.000	0.000	0.000	0.000
80	B	85	ASN	0	-0.009	-0.006	20.253	0.050	0.050	0.000	0.000	0.000	0.000
81	B	86	LEU	0	-0.014	0.015	14.536	0.014	0.014	0.000	0.000	0.000	0.000
82	B	87	LEU	0	0.010	-0.010	15.465	0.043	0.043	0.000	0.000	0.000	0.000
83	B	88	ARG	1	0.914	0.964	18.953	-0.064	-0.064	0.000	0.000	0.000	0.000
84	B	89	ALA	0	-0.063	-0.042	21.220	0.005	0.005	0.000	0.000	0.000	0.000
85	B	90	ASN	0	-0.007	0.003	18.241	-0.005	-0.005	0.000	0.000	0.000	0.000
86	B	91	MET	0	-0.071	-0.013	18.447	0.071	0.071	0.000	0.000	0.000	0.000
87	B	92	ASP	-1	-0.909	-0.940	21.290	0.194	0.194	0.000	0.000	0.000	0.000
88	B	93	GLY	0	0.020	0.005	23.890	0.028	0.028	0.000	0.000	0.000	0.000
89	B	94	LEU	0	0.029	0.010	23.768	0.022	0.022	0.000	0.000	0.000	0.000
90	B	95	LYS	1	0.948	0.966	27.789	-0.255	-0.255	0.000	0.000	0.000	0.000
91	B	96	LYS	1	0.958	0.955	30.701	-0.144	-0.144	0.000	0.000	0.000	0.000
92	B	97	ARG	1	0.930	0.981	30.491	-0.196	-0.196	0.000	0.000	0.000	0.000
93	B	98	NME	0	0.076	0.055	36.583	-0.005	-0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:1:MET )