FMO DATABASE

FMODB ID: R5JL8

Calculation Name: 4UYK-B-Xray372

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: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-598664.282156
FMO2-HF: Nuclear repulsion	562035.556088
FMO2-HF: Total energy	-36628.726069
FMO2-MP2: Total energy	-36733.328703

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.
-22.405	-14.619	9.342	-5.442	-11.688	-0.005

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 : -0.012 / q_NPA : -0.008

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	0.002	3.270	-1.195	1.390	0.092	-1.122	-1.555	0.000
4	B	4	LEU	0	0.003	0.001	4.463	0.812	0.972	-0.001	-0.025	-0.135	0.000
5	B	5	GLU	-1	-0.855	-0.904	7.625	-1.046	-1.046	0.000	0.000	0.000	0.000
6	B	6	SER	0	-0.002	-0.025	10.967	0.089	0.089	0.000	0.000	0.000	0.000
7	B	7	GLU	-1	-0.841	-0.909	12.408	-0.409	-0.409	0.000	0.000	0.000	0.000
8	B	8	GLN	0	0.116	0.046	10.625	-0.107	-0.107	0.000	0.000	0.000	0.000
9	B	9	PHE	0	0.032	0.022	7.043	0.101	0.101	0.000	0.000	0.000	0.000
10	B	10	LEU	0	0.030	0.017	9.935	0.247	0.247	0.000	0.000	0.000	0.000
11	B	11	THR	0	0.001	0.004	13.324	0.130	0.130	0.000	0.000	0.000	0.000
12	B	12	GLU	-1	-0.831	-0.899	9.144	-0.681	-0.681	0.000	0.000	0.000	0.000
13	B	13	LEU	0	-0.059	-0.032	10.073	0.198	0.198	0.000	0.000	0.000	0.000
14	B	14	THR	0	-0.020	-0.024	11.264	0.129	0.129	0.000	0.000	0.000	0.000
15	B	15	ARG	1	0.802	0.864	11.826	0.619	0.619	0.000	0.000	0.000	0.000
16	B	16	LEU	0	-0.039	-0.010	7.723	0.072	0.072	0.000	0.000	0.000	0.000
17	B	17	PHE	0	0.059	0.014	12.383	0.068	0.068	0.000	0.000	0.000	0.000
18	B	18	GLN	0	-0.023	-0.005	15.395	-0.023	-0.023	0.000	0.000	0.000	0.000
19	B	19	LYS	1	0.903	0.954	13.863	-0.011	-0.011	0.000	0.000	0.000	0.000
20	B	20	CYS	0	-0.117	-0.034	14.189	0.078	0.078	0.000	0.000	0.000	0.000
21	B	21	ARG	1	0.877	0.916	17.048	-0.221	-0.221	0.000	0.000	0.000	0.000
22	B	22	THR	0	0.017	0.006	20.547	0.005	0.005	0.000	0.000	0.000	0.000
23	B	23	SER	0	0.005	-0.001	20.579	0.023	0.023	0.000	0.000	0.000	0.000
24	B	24	GLY	0	0.023	0.018	16.702	0.002	0.002	0.000	0.000	0.000	0.000
25	B	25	SER	0	0.004	0.006	15.070	-0.082	-0.082	0.000	0.000	0.000	0.000
26	B	26	VAL	0	0.019	0.002	11.625	0.128	0.128	0.000	0.000	0.000	0.000
27	B	27	TYR	0	-0.028	-0.002	10.135	-0.056	-0.056	0.000	0.000	0.000	0.000
28	B	28	ILE	0	0.012	-0.011	9.578	0.329	0.329	0.000	0.000	0.000	0.000
29	B	29	THR	0	-0.056	-0.021	7.421	-0.097	-0.097	0.000	0.000	0.000	0.000
30	B	30	LEU	0	0.039	0.015	8.613	0.206	0.206	0.000	0.000	0.000	0.000
31	B	31	LYS	1	0.955	0.981	8.601	-1.149	-1.149	0.000	0.000	0.000	0.000
32	B	32	LYS	1	0.924	0.966	10.170	-0.139	-0.139	0.000	0.000	0.000	0.000
33	B	33	TYR	0	-0.063	-0.058	7.834	0.055	0.055	0.000	0.000	0.000	0.000
34	B	34	ASP	-1	-0.780	-0.864	10.679	-0.018	-0.018	0.000	0.000	0.000	0.000
35	B	35	GLY	0	0.020	0.009	10.575	-0.019	-0.019	0.000	0.000	0.000	0.000
36	B	36	ARG	1	0.839	0.901	10.221	-0.262	-0.262	0.000	0.000	0.000	0.000
37	B	37	THR	0	0.042	0.031	8.827	-0.161	-0.161	0.000	0.000	0.000	0.000
38	B	38	LYS	1	0.957	0.985	10.129	0.593	0.593	0.000	0.000	0.000	0.000
39	B	39	PRO	0	0.010	-0.005	11.994	0.087	0.087	0.000	0.000	0.000	0.000
40	B	40	ILE	0	0.013	0.009	13.513	-0.054	-0.054	0.000	0.000	0.000	0.000
41	B	41	PRO	0	0.016	0.015	16.629	0.055	0.055	0.000	0.000	0.000	0.000
42	B	42	LYS	1	0.978	0.995	19.180	-0.150	-0.150	0.000	0.000	0.000	0.000
43	B	50	GLU	-1	-0.952	-0.993	14.577	-0.475	-0.475	0.000	0.000	0.000	0.000
44	B	51	PRO	0	-0.047	-0.014	16.026	-0.038	-0.038	0.000	0.000	0.000	0.000
45	B	52	ALA	0	0.017	0.014	15.149	0.017	0.017	0.000	0.000	0.000	0.000
46	B	53	ASP	-1	-0.874	-0.940	15.469	-0.095	-0.095	0.000	0.000	0.000	0.000
47	B	54	ASN	0	0.019	0.005	16.831	0.020	0.020	0.000	0.000	0.000	0.000
48	B	55	LYS	1	0.924	0.969	11.695	0.552	0.552	0.000	0.000	0.000	0.000
49	B	56	CYS	0	-0.057	-0.020	11.293	0.124	0.124	0.000	0.000	0.000	0.000
50	B	57	LEU	0	-0.012	-0.008	3.790	-0.312	-0.110	0.003	-0.038	-0.167	0.000
51	B	58	LEU	0	0.030	0.018	7.303	0.333	0.333	0.000	0.000	0.000	0.000
52	B	59	ARG	1	0.927	0.955	2.389	-7.491	-7.418	4.553	-1.242	-3.384	0.013
53	B	60	ALA	0	0.032	0.017	5.289	-1.155	-1.103	-0.001	-0.020	-0.031	0.000
54	B	61	THR	0	-0.062	-0.056	5.541	0.442	0.442	0.000	0.000	0.000	0.000
55	B	62	ASP	-1	-0.677	-0.828	7.499	0.923	0.923	0.000	0.000	0.000	0.000
56	B	63	GLY	0	-0.039	-0.006	9.150	-0.218	-0.218	0.000	0.000	0.000	0.000
57	B	64	LYS	1	0.832	0.914	9.563	-0.724	-0.724	0.000	0.000	0.000	0.000
58	B	65	LYS	1	0.940	0.970	6.196	0.203	0.203	0.000	0.000	0.000	0.000
59	B	66	LYS	1	0.965	0.990	2.508	-7.662	-6.185	1.163	-0.637	-2.002	0.000
60	B	67	ILE	0	0.007	0.022	3.060	-4.259	-2.845	0.326	-0.714	-1.026	-0.007
61	B	68	SER	0	-0.019	-0.033	2.533	0.049	1.818	3.205	-1.617	-3.358	-0.011
62	B	69	THR	0	-0.011	-0.024	4.634	-1.681	-1.627	0.002	-0.027	-0.030	0.000
63	B	70	VAL	0	0.011	-0.001	6.744	0.533	0.533	0.000	0.000	0.000	0.000
64	B	71	VAL	0	0.005	0.015	9.062	-0.045	-0.045	0.000	0.000	0.000	0.000
65	B	72	SER	0	-0.053	-0.062	12.705	0.116	0.116	0.000	0.000	0.000	0.000
66	B	73	SER	0	0.073	0.017	15.695	0.011	0.011	0.000	0.000	0.000	0.000
67	B	74	LYS	1	0.936	0.972	18.269	0.444	0.444	0.000	0.000	0.000	0.000
68	B	75	GLU	-1	-0.803	-0.866	15.113	-0.562	-0.562	0.000	0.000	0.000	0.000
69	B	76	VAL	0	-0.004	0.001	16.452	0.018	0.018	0.000	0.000	0.000	0.000
70	B	77	ASN	0	0.028	0.015	18.276	0.036	0.036	0.000	0.000	0.000	0.000
71	B	78	LYS	1	0.936	0.979	19.088	0.398	0.398	0.000	0.000	0.000	0.000
72	B	79	PHE	0	0.010	-0.001	12.693	0.015	0.015	0.000	0.000	0.000	0.000
73	B	80	GLN	0	0.018	-0.014	17.856	0.029	0.029	0.000	0.000	0.000	0.000
74	B	81	MET	0	0.013	0.029	19.434	0.050	0.050	0.000	0.000	0.000	0.000
75	B	82	ALA	0	0.013	0.004	18.443	0.021	0.021	0.000	0.000	0.000	0.000
76	B	83	TYR	0	0.025	0.010	13.167	0.059	0.059	0.000	0.000	0.000	0.000
77	B	84	SER	0	0.017	-0.012	17.521	0.062	0.062	0.000	0.000	0.000	0.000
78	B	85	ASN	0	-0.001	0.009	20.358	0.046	0.046	0.000	0.000	0.000	0.000
79	B	86	LEU	0	0.000	0.016	14.613	0.013	0.013	0.000	0.000	0.000	0.000
80	B	87	LEU	0	0.013	-0.001	15.505	0.037	0.037	0.000	0.000	0.000	0.000
81	B	88	ARG	1	0.902	0.944	19.115	-0.079	-0.079	0.000	0.000	0.000	0.000
82	B	89	ALA	0	-0.070	-0.042	21.221	0.002	0.002	0.000	0.000	0.000	0.000
83	B	90	ASN	0	-0.031	-0.016	18.280	-0.022	-0.022	0.000	0.000	0.000	0.000
84	B	91	MET	0	-0.056	-0.004	18.715	0.066	0.066	0.000	0.000	0.000	0.000
85	B	92	ASP	-1	-0.848	-0.893	21.284	0.204	0.204	0.000	0.000	0.000	0.000
86	B	93	GLY	0	0.016	0.011	23.884	0.026	0.026	0.000	0.000	0.000	0.000
87	B	94	LEU	0	0.035	0.016	24.069	0.021	0.021	0.000	0.000	0.000	0.000
88	B	95	LYS	1	0.946	0.963	27.908	-0.258	-0.258	0.000	0.000	0.000	0.000
89	B	96	LYS	1	0.967	0.965	30.890	-0.148	-0.148	0.000	0.000	0.000	0.000
90	B	97	ARG	1	1.007	1.032	30.622	-0.197	-0.197	0.000	0.000	0.000	0.000

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Highlights

Manual

Support

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