FMO DATABASE

FMODB ID: ZYQZN

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	OptH
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	-597911.37729
FMO2-HF: Nuclear repulsion	561283.235117
FMO2-HF: Total energy	-36628.142173
FMO2-MP2: Total energy	-36732.759908

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.
-24.644	-14.621	6.34	-5.175	-11.189	-0.019

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 : -0.031 / 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	-0.031	-0.006	3.170	-1.463	1.276	0.134	-1.234	-1.639	-0.002
4	B	4	LEU	0	-0.014	-0.009	4.476	0.772	0.930	-0.001	-0.023	-0.134	0.000
5	B	5	GLU	-1	-0.848	-0.923	7.593	-1.139	-1.139	0.000	0.000	0.000	0.000
6	B	6	SER	0	-0.016	-0.029	10.964	0.074	0.074	0.000	0.000	0.000	0.000
7	B	7	GLU	-1	-0.893	-0.943	12.395	-0.495	-0.495	0.000	0.000	0.000	0.000
8	B	8	GLN	0	0.084	0.046	10.623	-0.091	-0.091	0.000	0.000	0.000	0.000
9	B	9	PHE	0	0.030	0.020	7.098	0.118	0.118	0.000	0.000	0.000	0.000
10	B	10	LEU	0	0.020	0.006	9.853	0.262	0.262	0.000	0.000	0.000	0.000
11	B	11	THR	0	-0.001	-0.017	13.241	0.133	0.133	0.000	0.000	0.000	0.000
12	B	12	GLU	-1	-0.962	-0.998	8.981	-0.720	-0.720	0.000	0.000	0.000	0.000
13	B	13	LEU	0	-0.066	-0.029	10.386	0.212	0.212	0.000	0.000	0.000	0.000
14	B	14	THR	0	-0.004	-0.006	11.252	0.136	0.136	0.000	0.000	0.000	0.000
15	B	15	ARG	1	0.939	0.964	12.409	0.559	0.559	0.000	0.000	0.000	0.000
16	B	16	LEU	0	-0.040	-0.009	7.729	0.069	0.069	0.000	0.000	0.000	0.000
17	B	17	PHE	0	0.051	0.007	12.301	0.068	0.068	0.000	0.000	0.000	0.000
18	B	18	GLN	0	-0.016	-0.006	15.366	-0.020	-0.020	0.000	0.000	0.000	0.000
19	B	19	LYS	1	0.894	0.948	14.005	-0.022	-0.022	0.000	0.000	0.000	0.000
20	B	20	CYS	0	-0.095	-0.017	14.072	0.082	0.082	0.000	0.000	0.000	0.000
21	B	21	ARG	1	0.937	0.974	16.978	-0.222	-0.222	0.000	0.000	0.000	0.000
22	B	22	THR	0	0.010	0.004	20.484	0.003	0.003	0.000	0.000	0.000	0.000
23	B	23	SER	0	-0.009	-0.008	20.498	0.023	0.023	0.000	0.000	0.000	0.000
24	B	24	GLY	0	0.037	0.024	16.646	0.005	0.005	0.000	0.000	0.000	0.000
25	B	25	SER	0	-0.008	0.001	15.204	-0.061	-0.061	0.000	0.000	0.000	0.000
26	B	26	VAL	0	0.033	0.008	11.668	0.139	0.139	0.000	0.000	0.000	0.000
27	B	27	TYR	0	-0.024	0.000	9.939	-0.036	-0.036	0.000	0.000	0.000	0.000
28	B	28	ILE	0	0.008	-0.010	9.456	0.317	0.317	0.000	0.000	0.000	0.000
29	B	29	THR	0	-0.072	-0.030	7.459	-0.072	-0.072	0.000	0.000	0.000	0.000
30	B	30	LEU	0	0.047	0.015	8.334	0.131	0.131	0.000	0.000	0.000	0.000
31	B	31	LYS	1	0.953	0.982	8.124	-1.147	-1.147	0.000	0.000	0.000	0.000
32	B	32	LYS	1	0.969	0.997	10.246	-0.116	-0.116	0.000	0.000	0.000	0.000
33	B	33	TYR	0	-0.078	-0.062	8.139	0.036	0.036	0.000	0.000	0.000	0.000
34	B	34	ASP	-1	-0.789	-0.890	10.956	-0.067	-0.067	0.000	0.000	0.000	0.000
35	B	35	GLY	0	0.007	0.003	11.007	-0.019	-0.019	0.000	0.000	0.000	0.000
36	B	36	ARG	1	0.874	0.939	10.369	-0.246	-0.246	0.000	0.000	0.000	0.000
37	B	37	THR	0	0.037	0.027	9.313	-0.146	-0.146	0.000	0.000	0.000	0.000
38	B	38	LYS	1	0.956	0.981	10.466	0.571	0.571	0.000	0.000	0.000	0.000
39	B	39	PRO	0	0.007	-0.004	12.310	0.078	0.078	0.000	0.000	0.000	0.000
40	B	40	ILE	0	0.019	0.011	13.799	-0.056	-0.056	0.000	0.000	0.000	0.000
41	B	41	PRO	0	0.022	0.018	16.898	0.056	0.056	0.000	0.000	0.000	0.000
42	B	42	LYS	1	0.970	0.993	19.502	-0.159	-0.159	0.000	0.000	0.000	0.000
43	B	50	GLU	-1	-0.951	-0.993	15.078	-0.437	-0.437	0.000	0.000	0.000	0.000
44	B	51	PRO	0	-0.048	-0.005	16.450	-0.040	-0.040	0.000	0.000	0.000	0.000
45	B	52	ALA	0	0.017	0.006	15.625	0.015	0.015	0.000	0.000	0.000	0.000
46	B	53	ASP	-1	-0.879	-0.940	15.846	-0.123	-0.123	0.000	0.000	0.000	0.000
47	B	54	ASN	0	-0.028	-0.018	17.256	0.034	0.034	0.000	0.000	0.000	0.000
48	B	55	LYS	1	0.932	0.960	11.969	0.616	0.616	0.000	0.000	0.000	0.000
49	B	56	CYS	0	-0.001	-0.002	11.471	0.114	0.114	0.000	0.000	0.000	0.000
50	B	57	LEU	0	-0.048	-0.009	3.813	-0.286	-0.104	0.002	-0.034	-0.150	0.000
51	B	58	LEU	0	0.030	0.013	7.311	0.326	0.326	0.000	0.000	0.000	0.000
52	B	59	ARG	1	0.929	0.964	2.627	-5.896	-4.368	0.768	-0.477	-1.819	0.005
53	B	60	ALA	0	0.034	0.010	5.103	-1.087	-1.023	-0.001	-0.018	-0.045	0.000
54	B	61	THR	0	-0.062	-0.058	5.613	0.706	0.706	0.000	0.000	0.000	0.000
55	B	62	ASP	-1	-0.730	-0.858	7.530	1.008	1.008	0.000	0.000	0.000	0.000
56	B	63	GLY	0	-0.040	-0.009	9.112	-0.244	-0.244	0.000	0.000	0.000	0.000
57	B	64	LYS	1	0.890	0.944	9.621	-0.795	-0.795	0.000	0.000	0.000	0.000
58	B	65	LYS	1	0.953	0.979	6.249	0.239	0.239	0.000	0.000	0.000	0.000
59	B	66	LYS	1	0.965	0.995	2.381	-10.009	-8.504	2.243	-0.936	-2.812	0.002
60	B	67	ILE	0	0.022	0.030	2.835	-4.848	-3.242	0.637	-0.927	-1.317	-0.011
61	B	68	SER	0	-0.027	-0.037	2.541	-0.580	1.610	2.555	-1.504	-3.241	-0.013
62	B	69	THR	0	0.059	0.029	4.543	-1.634	-1.583	0.003	-0.022	-0.032	0.000
63	B	70	VAL	0	-0.008	-0.008	6.873	0.507	0.507	0.000	0.000	0.000	0.000
64	B	71	VAL	0	0.027	0.030	9.079	-0.027	-0.027	0.000	0.000	0.000	0.000
65	B	72	SER	0	-0.037	-0.021	12.681	0.103	0.103	0.000	0.000	0.000	0.000
66	B	73	SER	0	0.087	0.014	15.758	0.009	0.009	0.000	0.000	0.000	0.000
67	B	74	LYS	1	0.929	0.970	18.558	0.461	0.461	0.000	0.000	0.000	0.000
68	B	75	GLU	-1	-0.860	-0.929	14.153	-0.668	-0.668	0.000	0.000	0.000	0.000
69	B	76	VAL	0	-0.006	0.005	16.668	0.013	0.013	0.000	0.000	0.000	0.000
70	B	77	ASN	0	0.026	0.008	18.217	0.038	0.038	0.000	0.000	0.000	0.000
71	B	78	LYS	1	1.005	1.015	19.235	0.352	0.352	0.000	0.000	0.000	0.000
72	B	79	PHE	0	0.009	0.000	12.346	0.015	0.015	0.000	0.000	0.000	0.000
73	B	80	GLN	0	0.022	-0.013	17.712	0.027	0.027	0.000	0.000	0.000	0.000
74	B	81	MET	0	0.002	0.013	19.349	0.048	0.048	0.000	0.000	0.000	0.000
75	B	82	ALA	0	0.010	0.005	18.370	0.021	0.021	0.000	0.000	0.000	0.000
76	B	83	TYR	0	0.021	0.008	13.168	0.010	0.010	0.000	0.000	0.000	0.000
77	B	84	SER	0	0.017	0.001	17.488	0.063	0.063	0.000	0.000	0.000	0.000
78	B	85	ASN	0	-0.011	-0.006	20.298	0.050	0.050	0.000	0.000	0.000	0.000
79	B	86	LEU	0	-0.009	0.016	14.590	0.013	0.013	0.000	0.000	0.000	0.000
80	B	87	LEU	0	0.012	-0.009	15.510	0.041	0.041	0.000	0.000	0.000	0.000
81	B	88	ARG	1	0.909	0.962	18.998	-0.064	-0.064	0.000	0.000	0.000	0.000
82	B	89	ALA	0	-0.063	-0.042	21.271	0.005	0.005	0.000	0.000	0.000	0.000
83	B	90	ASN	0	-0.006	0.004	18.286	-0.007	-0.007	0.000	0.000	0.000	0.000
84	B	91	MET	0	-0.070	-0.012	18.494	0.069	0.069	0.000	0.000	0.000	0.000
85	B	92	ASP	-1	-0.911	-0.942	21.333	0.195	0.195	0.000	0.000	0.000	0.000
86	B	93	GLY	0	0.021	0.005	23.929	0.027	0.027	0.000	0.000	0.000	0.000
87	B	94	LEU	0	0.027	0.010	23.809	0.022	0.022	0.000	0.000	0.000	0.000
88	B	95	LYS	1	0.943	0.964	27.828	-0.254	-0.254	0.000	0.000	0.000	0.000
89	B	96	LYS	1	0.960	0.960	30.744	-0.145	-0.145	0.000	0.000	0.000	0.000
90	B	97	ARG	1	1.014	1.038	30.319	-0.194	-0.194	0.000	0.000	0.000	0.000

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Graph

Overview

Highlights

Manual

Support

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