FMO DATABASE

FMODB ID: Q13LY

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	OptAll
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	-600386.957941
FMO2-HF: Nuclear repulsion	563757.774675
FMO2-HF: Total energy	-36629.183266
FMO2-MP2: Total energy	-36733.803825

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.
-30.212	-25.1	16.671	-8.144	-13.637	-0.009

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 : -0.015 / q_NPA : 0.001

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	-0.013	0.006	3.238	-1.779	0.862	0.081	-1.231	-1.491	-0.001
4	B	4	LEU	0	-0.005	0.000	4.726	0.936	1.065	-0.001	-0.017	-0.110	0.000
5	B	5	GLU	-1	-0.783	-0.865	7.793	-1.035	-1.035	0.000	0.000	0.000	0.000
6	B	6	SER	0	0.005	-0.011	11.009	0.032	0.032	0.000	0.000	0.000	0.000
7	B	7	GLU	-1	-0.826	-0.905	12.545	-0.455	-0.455	0.000	0.000	0.000	0.000
8	B	8	GLN	0	0.039	0.012	10.867	-0.169	-0.169	0.000	0.000	0.000	0.000
9	B	9	PHE	0	-0.013	-0.008	6.729	0.086	0.086	0.000	0.000	0.000	0.000
10	B	10	LEU	0	0.009	0.003	10.001	0.246	0.246	0.000	0.000	0.000	0.000
11	B	11	THR	0	0.006	0.009	13.425	0.150	0.150	0.000	0.000	0.000	0.000
12	B	12	GLU	-1	-0.796	-0.877	9.439	-0.831	-0.831	0.000	0.000	0.000	0.000
13	B	13	LEU	0	-0.018	-0.010	10.109	0.208	0.208	0.000	0.000	0.000	0.000
14	B	14	THR	0	-0.013	-0.015	11.325	0.165	0.165	0.000	0.000	0.000	0.000
15	B	15	ARG	1	0.818	0.866	12.140	0.759	0.759	0.000	0.000	0.000	0.000
16	B	16	LEU	0	-0.066	-0.029	7.617	0.079	0.079	0.000	0.000	0.000	0.000
17	B	17	PHE	0	0.048	0.002	12.357	0.112	0.112	0.000	0.000	0.000	0.000
18	B	18	GLN	0	-0.036	-0.019	15.301	-0.013	-0.013	0.000	0.000	0.000	0.000
19	B	19	LYS	1	0.921	0.964	13.142	0.177	0.177	0.000	0.000	0.000	0.000
20	B	20	CYS	0	-0.076	-0.024	14.080	0.079	0.079	0.000	0.000	0.000	0.000
21	B	21	ARG	1	0.831	0.893	17.000	-0.176	-0.176	0.000	0.000	0.000	0.000
22	B	22	THR	0	0.011	0.006	20.446	-0.003	-0.003	0.000	0.000	0.000	0.000
23	B	23	SER	0	0.014	0.004	20.377	0.025	0.025	0.000	0.000	0.000	0.000
24	B	24	GLY	0	0.012	0.005	16.446	-0.009	-0.009	0.000	0.000	0.000	0.000
25	B	25	SER	0	0.001	0.003	14.653	-0.081	-0.081	0.000	0.000	0.000	0.000
26	B	26	VAL	0	0.009	0.004	12.005	0.181	0.181	0.000	0.000	0.000	0.000
27	B	27	TYR	0	-0.003	0.011	9.903	-0.002	-0.002	0.000	0.000	0.000	0.000
28	B	28	ILE	0	0.000	-0.010	9.513	0.248	0.248	0.000	0.000	0.000	0.000
29	B	29	THR	0	-0.056	-0.025	7.526	0.041	0.041	0.000	0.000	0.000	0.000
30	B	30	LEU	0	0.042	0.017	8.953	0.236	0.236	0.000	0.000	0.000	0.000
31	B	31	LYS	1	0.940	0.976	9.059	-1.537	-1.537	0.000	0.000	0.000	0.000
32	B	32	LYS	1	0.921	0.961	10.492	-0.301	-0.301	0.000	0.000	0.000	0.000
33	B	33	TYR	0	-0.061	-0.043	7.451	0.130	0.130	0.000	0.000	0.000	0.000
34	B	34	ASP	-1	-0.765	-0.872	10.668	0.107	0.107	0.000	0.000	0.000	0.000
35	B	35	GLY	0	0.001	0.003	10.293	-0.049	-0.049	0.000	0.000	0.000	0.000
36	B	36	ARG	1	0.816	0.898	10.037	-0.426	-0.426	0.000	0.000	0.000	0.000
37	B	37	THR	0	-0.006	-0.005	8.546	-0.177	-0.177	0.000	0.000	0.000	0.000
38	B	38	LYS	1	0.887	0.947	10.111	0.552	0.552	0.000	0.000	0.000	0.000
39	B	39	PRO	0	0.006	-0.006	11.711	0.124	0.124	0.000	0.000	0.000	0.000
40	B	40	ILE	0	0.008	0.012	13.113	-0.070	-0.070	0.000	0.000	0.000	0.000
41	B	41	PRO	0	0.041	0.029	15.906	0.054	0.054	0.000	0.000	0.000	0.000
42	B	42	LYS	1	0.937	0.967	18.539	-0.193	-0.193	0.000	0.000	0.000	0.000
43	B	50	GLU	-1	-0.784	-0.898	13.307	-0.569	-0.569	0.000	0.000	0.000	0.000
44	B	51	PRO	0	-0.047	-0.013	15.128	-0.039	-0.039	0.000	0.000	0.000	0.000
45	B	52	ALA	0	0.021	0.003	15.000	0.006	0.006	0.000	0.000	0.000	0.000
46	B	53	ASP	-1	-0.866	-0.938	15.096	-0.034	-0.034	0.000	0.000	0.000	0.000
47	B	54	ASN	0	0.016	0.000	16.640	0.032	0.032	0.000	0.000	0.000	0.000
48	B	55	LYS	1	0.915	0.961	11.711	0.482	0.482	0.000	0.000	0.000	0.000
49	B	56	CYS	0	-0.059	-0.028	11.294	0.144	0.144	0.000	0.000	0.000	0.000
50	B	57	LEU	0	-0.002	0.000	3.805	-0.371	-0.182	0.002	-0.031	-0.159	0.000
51	B	58	LEU	0	0.013	0.012	7.502	0.400	0.400	0.000	0.000	0.000	0.000
52	B	59	ARG	1	0.918	0.940	2.432	-12.692	-15.730	10.499	-2.595	-4.866	0.023
53	B	60	ALA	0	0.031	0.019	5.146	-0.902	-0.902	0.000	0.000	0.000	0.000
54	B	61	THR	0	-0.063	-0.060	5.210	0.154	0.154	0.000	0.000	0.000	0.000
55	B	62	ASP	-1	-0.689	-0.821	7.371	0.848	0.848	0.000	0.000	0.000	0.000
56	B	63	GLY	0	-0.019	-0.004	9.204	-0.159	-0.159	0.000	0.000	0.000	0.000
57	B	64	LYS	1	0.826	0.905	9.456	-0.626	-0.626	0.000	0.000	0.000	0.000
58	B	65	LYS	1	0.925	0.960	5.987	-0.011	-0.011	0.000	0.000	0.000	0.000
59	B	66	LYS	1	0.971	0.997	2.329	-6.774	-5.679	1.730	-0.850	-1.975	0.000
60	B	67	ILE	0	0.024	0.034	2.854	-5.535	-3.471	0.672	-1.364	-1.372	-0.014
61	B	68	SER	0	-0.011	-0.034	2.564	-1.416	0.528	3.686	-2.008	-3.622	-0.017
62	B	69	THR	0	-0.001	-0.014	4.391	-1.591	-1.503	0.002	-0.048	-0.042	0.000
63	B	70	VAL	0	0.006	-0.003	6.433	0.700	0.700	0.000	0.000	0.000	0.000
64	B	71	VAL	0	-0.008	0.009	8.873	-0.100	-0.100	0.000	0.000	0.000	0.000
65	B	72	SER	0	-0.031	-0.043	12.604	0.121	0.121	0.000	0.000	0.000	0.000
66	B	73	SER	0	0.034	0.011	15.668	-0.004	-0.004	0.000	0.000	0.000	0.000
67	B	74	LYS	1	0.945	0.992	17.896	0.444	0.444	0.000	0.000	0.000	0.000
68	B	75	GLU	-1	-0.772	-0.868	15.157	-0.489	-0.489	0.000	0.000	0.000	0.000
69	B	76	VAL	0	-0.004	-0.009	16.256	0.022	0.022	0.000	0.000	0.000	0.000
70	B	77	ASN	0	0.034	0.013	18.015	0.041	0.041	0.000	0.000	0.000	0.000
71	B	78	LYS	1	0.897	0.955	19.400	0.430	0.430	0.000	0.000	0.000	0.000
72	B	79	PHE	0	-0.009	-0.010	12.754	0.007	0.007	0.000	0.000	0.000	0.000
73	B	80	GLN	0	0.026	0.005	17.780	0.016	0.016	0.000	0.000	0.000	0.000
74	B	81	MET	0	0.036	0.033	19.730	0.043	0.043	0.000	0.000	0.000	0.000
75	B	82	ALA	0	0.024	0.016	18.600	0.019	0.019	0.000	0.000	0.000	0.000
76	B	83	TYR	0	0.025	0.003	12.981	0.052	0.052	0.000	0.000	0.000	0.000
77	B	84	SER	0	0.014	-0.009	17.542	0.068	0.068	0.000	0.000	0.000	0.000
78	B	85	ASN	0	0.002	0.011	20.558	0.043	0.043	0.000	0.000	0.000	0.000
79	B	86	LEU	0	-0.005	0.009	14.540	0.013	0.013	0.000	0.000	0.000	0.000
80	B	87	LEU	0	0.030	0.005	15.396	0.027	0.027	0.000	0.000	0.000	0.000
81	B	88	ARG	1	0.896	0.932	18.816	-0.070	-0.070	0.000	0.000	0.000	0.000
82	B	89	ALA	0	-0.065	-0.028	21.228	-0.005	-0.005	0.000	0.000	0.000	0.000
83	B	90	ASN	0	-0.034	-0.020	18.188	-0.038	-0.038	0.000	0.000	0.000	0.000
84	B	91	MET	0	-0.052	-0.002	18.430	0.077	0.077	0.000	0.000	0.000	0.000
85	B	92	ASP	-1	-0.814	-0.869	21.086	0.190	0.190	0.000	0.000	0.000	0.000
86	B	93	GLY	0	0.022	0.012	23.990	0.029	0.029	0.000	0.000	0.000	0.000
87	B	94	LEU	0	-0.003	0.006	23.864	0.015	0.015	0.000	0.000	0.000	0.000
88	B	95	LYS	1	0.978	0.977	27.804	-0.275	-0.275	0.000	0.000	0.000	0.000
89	B	96	LYS	1	1.011	0.999	30.743	-0.139	-0.139	0.000	0.000	0.000	0.000
90	B	97	ARG	1	0.938	0.987	30.393	-0.217	-0.217	0.000	0.000	0.000	0.000

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Highlights

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Support

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