FMO DATABASE

FMODB ID: QLL9Y

Calculation Name: 2UZH-A-Xray547

Preferred Name:

Target Type:

Ligand Name: cytidine-5'-diphosphate | 3-methylbut-3-enyl trihydrogen diphosphate | acetate ion | di(hydroxyethyl)ether

Ligand 3-letter code: CDP | IPE | ACT | PEG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2UZH

Chain ID: A

ChEMBL ID:

UniProt ID: A0R559

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	155
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1275865.256624
FMO2-HF: Nuclear repulsion	1220305.764389
FMO2-HF: Total energy	-55559.492235
FMO2-MP2: Total energy	-55720.482766

3D Structure Molmil

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:3:LEU)

Summations of interaction energy for fragment #1(A:3:LEU)

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.
-119.692	-117.48	0.157	-1.19	-1.18	-0.006

Interaction energy analysis for fragmet #1(A:3:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.822 / q_NPA : 0.901

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

Sort

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	5	ARG	1	0.889	0.946	3.084	28.316	30.528	0.157	-1.190	-1.180	-0.006
4	A	6	VAL	0	-0.005	-0.001	5.961	2.611	2.611	0.000	0.000	0.000	0.000
5	A	7	GLY	0	0.026	0.020	8.582	-0.128	-0.128	0.000	0.000	0.000	0.000
6	A	8	LEU	0	-0.058	-0.040	12.198	0.429	0.429	0.000	0.000	0.000	0.000
7	A	9	GLY	0	0.038	0.035	15.588	0.066	0.066	0.000	0.000	0.000	0.000
8	A	10	THR	0	-0.062	-0.050	19.222	0.090	0.090	0.000	0.000	0.000	0.000
9	A	11	ASP	-1	-0.764	-0.884	22.681	-11.104	-11.104	0.000	0.000	0.000	0.000
10	A	12	VAL	0	-0.028	-0.038	26.187	0.126	0.126	0.000	0.000	0.000	0.000
11	A	13	HIS	0	-0.060	-0.016	29.818	0.136	0.136	0.000	0.000	0.000	0.000
12	A	14	PRO	0	0.051	0.021	33.111	0.046	0.046	0.000	0.000	0.000	0.000
13	A	15	ILE	0	-0.049	-0.014	36.470	-0.120	-0.120	0.000	0.000	0.000	0.000
14	A	16	GLU	-1	-0.937	-0.967	38.781	-7.344	-7.344	0.000	0.000	0.000	0.000
15	A	17	ALA	0	-0.008	-0.014	41.890	-0.048	-0.048	0.000	0.000	0.000	0.000
16	A	18	GLY	0	-0.001	0.000	44.518	0.104	0.104	0.000	0.000	0.000	0.000
17	A	19	ARG	1	0.822	0.918	37.006	8.348	8.348	0.000	0.000	0.000	0.000
18	A	20	PRO	0	0.002	-0.014	40.207	-0.099	-0.099	0.000	0.000	0.000	0.000
19	A	21	CYS	0	-0.033	-0.008	36.327	-0.312	-0.312	0.000	0.000	0.000	0.000
20	A	22	ARG	1	0.806	0.892	33.836	8.435	8.435	0.000	0.000	0.000	0.000
21	A	23	LEU	0	0.003	-0.011	29.631	-0.153	-0.153	0.000	0.000	0.000	0.000
22	A	24	LEU	0	-0.045	-0.027	26.016	0.060	0.060	0.000	0.000	0.000	0.000
23	A	25	CYS	0	-0.064	-0.041	28.335	-0.215	-0.215	0.000	0.000	0.000	0.000
24	A	26	LEU	0	-0.040	0.004	30.242	0.156	0.156	0.000	0.000	0.000	0.000
25	A	27	GLU	-1	-0.811	-0.880	33.302	-8.341	-8.341	0.000	0.000	0.000	0.000
26	A	28	PHE	0	-0.009	-0.018	32.868	0.039	0.039	0.000	0.000	0.000	0.000
27	A	29	ASP	-1	-0.893	-0.946	38.227	-7.749	-7.749	0.000	0.000	0.000	0.000
28	A	30	ASP	-1	-1.015	-0.999	40.186	-7.619	-7.619	0.000	0.000	0.000	0.000
29	A	31	ALA	0	-0.046	-0.036	38.991	0.125	0.125	0.000	0.000	0.000	0.000
30	A	32	ASP	-1	-0.759	-0.848	40.518	-7.375	-7.375	0.000	0.000	0.000	0.000
31	A	33	GLY	0	0.050	-0.002	37.393	-0.171	-0.171	0.000	0.000	0.000	0.000
32	A	34	CYS	0	-0.099	-0.027	33.285	0.136	0.136	0.000	0.000	0.000	0.000
33	A	35	ALA	0	0.080	0.032	36.216	-0.049	-0.049	0.000	0.000	0.000	0.000
34	A	36	GLY	0	-0.047	-0.016	33.861	0.064	0.064	0.000	0.000	0.000	0.000
35	A	37	HIS	0	0.002	-0.004	30.145	-0.243	-0.243	0.000	0.000	0.000	0.000
36	A	38	SER	0	0.018	0.013	33.279	0.350	0.350	0.000	0.000	0.000	0.000
37	A	39	ASP	-1	-0.785	-0.900	31.528	-9.921	-9.921	0.000	0.000	0.000	0.000
38	A	40	GLY	0	0.047	0.028	33.437	0.206	0.206	0.000	0.000	0.000	0.000
39	A	41	ASP	-1	-0.738	-0.870	28.782	-11.098	-11.098	0.000	0.000	0.000	0.000
40	A	42	VAL	0	0.015	0.000	27.610	-0.453	-0.453	0.000	0.000	0.000	0.000
41	A	43	ALA	0	-0.005	-0.004	25.357	-0.490	-0.490	0.000	0.000	0.000	0.000
42	A	44	ALA	0	0.008	0.006	23.984	-0.650	-0.650	0.000	0.000	0.000	0.000
43	A	45	HIS	1	0.818	0.928	23.855	10.584	10.584	0.000	0.000	0.000	0.000
44	A	46	ALA	0	0.041	0.024	21.986	-0.510	-0.510	0.000	0.000	0.000	0.000
45	A	47	LEU	0	0.015	-0.013	19.207	-0.863	-0.863	0.000	0.000	0.000	0.000
46	A	48	CYS	0	-0.060	-0.009	18.954	-0.786	-0.786	0.000	0.000	0.000	0.000
47	A	49	ASP	-1	-0.745	-0.885	18.929	-15.043	-15.043	0.000	0.000	0.000	0.000
48	A	50	ALA	0	-0.045	0.004	15.909	-1.028	-1.028	0.000	0.000	0.000	0.000
49	A	51	LEU	0	0.023	0.001	14.426	-1.727	-1.727	0.000	0.000	0.000	0.000
50	A	52	LEU	0	-0.033	-0.001	14.604	-1.387	-1.387	0.000	0.000	0.000	0.000
51	A	53	SER	0	-0.001	-0.019	14.372	-1.354	-1.354	0.000	0.000	0.000	0.000
52	A	54	ALA	0	-0.014	0.007	10.488	-1.467	-1.467	0.000	0.000	0.000	0.000
53	A	55	ALA	0	0.012	0.004	9.964	-3.326	-3.326	0.000	0.000	0.000	0.000
54	A	56	GLY	0	-0.063	-0.026	12.152	-0.636	-0.636	0.000	0.000	0.000	0.000
55	A	57	LEU	0	-0.058	-0.026	13.331	0.960	0.960	0.000	0.000	0.000	0.000
56	A	58	GLY	0	-0.013	-0.001	16.803	1.108	1.108	0.000	0.000	0.000	0.000
57	A	59	ASP	-1	-0.823	-0.899	18.397	-14.069	-14.069	0.000	0.000	0.000	0.000
58	A	60	LEU	0	0.003	-0.022	21.193	0.409	0.409	0.000	0.000	0.000	0.000
59	A	61	GLY	0	0.004	0.009	24.391	0.451	0.451	0.000	0.000	0.000	0.000
60	A	62	THR	0	-0.063	-0.051	21.937	0.324	0.324	0.000	0.000	0.000	0.000
61	A	63	ILE	0	-0.006	0.002	20.633	0.451	0.451	0.000	0.000	0.000	0.000
62	A	64	PHE	0	-0.027	0.001	24.381	0.410	0.410	0.000	0.000	0.000	0.000
63	A	65	GLY	0	-0.019	-0.002	28.032	0.478	0.478	0.000	0.000	0.000	0.000
64	A	66	THR	0	-0.025	-0.027	29.969	0.005	0.005	0.000	0.000	0.000	0.000
65	A	67	ASP	-1	-0.824	-0.904	33.080	-8.204	-8.204	0.000	0.000	0.000	0.000
66	A	68	ARG	1	0.886	0.961	27.910	11.150	11.150	0.000	0.000	0.000	0.000
67	A	69	PRO	0	-0.007	-0.021	34.709	-0.041	-0.041	0.000	0.000	0.000	0.000
68	A	70	GLN	0	0.005	-0.001	32.057	0.355	0.355	0.000	0.000	0.000	0.000
69	A	71	TRP	0	-0.006	-0.004	28.402	-0.132	-0.132	0.000	0.000	0.000	0.000
70	A	72	ARG	1	0.837	0.914	33.460	8.119	8.119	0.000	0.000	0.000	0.000
71	A	73	GLY	0	-0.014	-0.011	36.299	0.100	0.100	0.000	0.000	0.000	0.000
72	A	74	ALA	0	-0.027	0.003	31.687	0.036	0.036	0.000	0.000	0.000	0.000
73	A	75	SER	0	-0.025	-0.032	32.201	-0.078	-0.078	0.000	0.000	0.000	0.000
74	A	76	GLY	0	0.065	0.010	28.251	-0.311	-0.311	0.000	0.000	0.000	0.000
75	A	77	ALA	0	0.046	0.017	27.139	-0.480	-0.480	0.000	0.000	0.000	0.000
76	A	78	ASP	-1	-0.859	-0.891	27.827	-10.409	-10.409	0.000	0.000	0.000	0.000
77	A	79	MET	0	-0.056	-0.017	26.012	-0.277	-0.277	0.000	0.000	0.000	0.000
78	A	80	ILE	0	0.047	0.008	22.154	-0.494	-0.494	0.000	0.000	0.000	0.000
79	A	81	ARG	1	0.902	0.944	22.747	10.335	10.335	0.000	0.000	0.000	0.000
80	A	82	HIS	0	-0.015	0.000	23.751	-0.454	-0.454	0.000	0.000	0.000	0.000
81	A	83	VAL	0	-0.003	-0.008	19.295	-0.454	-0.454	0.000	0.000	0.000	0.000
82	A	84	ARG	1	0.812	0.901	18.937	14.565	14.565	0.000	0.000	0.000	0.000
83	A	85	GLY	0	0.035	0.024	18.854	-0.777	-0.777	0.000	0.000	0.000	0.000
84	A	86	LEU	0	-0.069	-0.042	19.442	-0.280	-0.280	0.000	0.000	0.000	0.000
85	A	87	VAL	0	-0.004	-0.008	13.734	-0.867	-0.867	0.000	0.000	0.000	0.000
86	A	88	GLU	-1	-0.806	-0.891	14.704	-17.930	-17.930	0.000	0.000	0.000	0.000
87	A	89	ASN	0	-0.049	-0.032	16.091	-0.481	-0.481	0.000	0.000	0.000	0.000
88	A	90	ALA	0	-0.078	-0.028	14.121	0.178	0.178	0.000	0.000	0.000	0.000
89	A	91	GLY	0	-0.012	0.010	12.863	-1.266	-1.266	0.000	0.000	0.000	0.000
90	A	92	PHE	0	-0.052	-0.041	7.838	-3.663	-3.663	0.000	0.000	0.000	0.000
91	A	93	VAL	0	0.073	0.054	10.534	2.749	2.749	0.000	0.000	0.000	0.000
92	A	94	ILE	0	-0.020	-0.025	10.986	-2.669	-2.669	0.000	0.000	0.000	0.000
93	A	95	GLY	0	-0.005	0.001	11.202	0.519	0.519	0.000	0.000	0.000	0.000
94	A	96	ASN	0	-0.049	-0.044	12.141	0.383	0.383	0.000	0.000	0.000	0.000
95	A	97	ALA	0	0.021	0.017	13.943	-1.051	-1.051	0.000	0.000	0.000	0.000
96	A	98	THR	0	-0.071	-0.033	16.106	0.959	0.959	0.000	0.000	0.000	0.000
97	A	99	VAL	0	0.048	0.017	18.530	-0.146	-0.146	0.000	0.000	0.000	0.000
98	A	100	GLN	0	-0.031	-0.002	21.621	0.604	0.604	0.000	0.000	0.000	0.000
99	A	101	VAL	0	0.030	0.010	24.340	-0.031	-0.031	0.000	0.000	0.000	0.000
100	A	102	ILE	0	-0.009	-0.012	25.487	0.082	0.082	0.000	0.000	0.000	0.000
101	A	103	GLY	0	0.042	0.008	29.563	0.150	0.150	0.000	0.000	0.000	0.000
102	A	104	ASN	0	-0.047	-0.029	33.410	-0.164	-0.164	0.000	0.000	0.000	0.000
103	A	105	ARG	1	0.814	0.903	36.396	7.756	7.756	0.000	0.000	0.000	0.000
104	A	106	PRO	0	0.126	0.072	34.573	-0.072	-0.072	0.000	0.000	0.000	0.000
105	A	107	LYS	1	0.870	0.923	35.126	8.247	8.247	0.000	0.000	0.000	0.000
106	A	108	VAL	0	0.067	0.031	29.447	0.066	0.066	0.000	0.000	0.000	0.000
107	A	109	GLY	0	-0.015	-0.007	32.303	-0.085	-0.085	0.000	0.000	0.000	0.000
108	A	110	PRO	0	-0.013	-0.024	33.275	-0.166	-0.166	0.000	0.000	0.000	0.000
109	A	111	ARG	1	0.837	0.885	33.852	8.874	8.874	0.000	0.000	0.000	0.000
110	A	112	ARG	1	0.876	0.947	25.917	11.042	11.042	0.000	0.000	0.000	0.000
111	A	113	GLU	-1	-0.952	-0.986	28.485	-10.566	-10.566	0.000	0.000	0.000	0.000
112	A	114	GLU	-1	-0.757	-0.841	29.092	-9.366	-9.366	0.000	0.000	0.000	0.000
113	A	115	ALA	0	0.046	0.021	27.922	-0.213	-0.213	0.000	0.000	0.000	0.000
114	A	116	GLN	0	0.020	0.009	24.540	-0.580	-0.580	0.000	0.000	0.000	0.000
115	A	117	GLN	0	-0.014	0.016	25.043	-0.316	-0.316	0.000	0.000	0.000	0.000
116	A	118	VAL	0	0.038	0.022	26.753	-0.293	-0.293	0.000	0.000	0.000	0.000
117	A	119	LEU	0	-0.008	-0.012	23.533	-0.251	-0.251	0.000	0.000	0.000	0.000
118	A	120	SER	0	-0.009	-0.026	22.015	-0.787	-0.787	0.000	0.000	0.000	0.000
119	A	121	GLU	-1	-0.959	-0.965	22.596	-12.443	-12.443	0.000	0.000	0.000	0.000
120	A	122	LEU	0	-0.082	-0.033	24.470	-0.202	-0.202	0.000	0.000	0.000	0.000
121	A	123	VAL	0	-0.011	-0.026	18.397	-0.267	-0.267	0.000	0.000	0.000	0.000
122	A	124	GLY	0	-0.008	0.004	19.567	-0.656	-0.656	0.000	0.000	0.000	0.000
123	A	125	ALA	0	-0.001	0.007	16.060	-0.604	-0.604	0.000	0.000	0.000	0.000
124	A	126	PRO	0	-0.034	-0.021	16.598	0.717	0.717	0.000	0.000	0.000	0.000
125	A	127	VAL	0	0.036	0.022	18.028	-0.921	-0.921	0.000	0.000	0.000	0.000
126	A	128	SER	0	-0.052	-0.022	19.471	0.740	0.740	0.000	0.000	0.000	0.000
127	A	129	VAL	0	0.008	-0.002	21.334	-0.132	-0.132	0.000	0.000	0.000	0.000
128	A	130	SER	0	-0.039	-0.022	23.682	0.328	0.328	0.000	0.000	0.000	0.000
129	A	131	ALA	0	0.001	-0.016	26.009	0.008	0.008	0.000	0.000	0.000	0.000
130	A	132	THR	0	-0.003	0.008	27.997	0.121	0.121	0.000	0.000	0.000	0.000
131	A	133	THR	0	-0.010	0.001	30.219	0.028	0.028	0.000	0.000	0.000	0.000
132	A	134	THR	0	0.006	-0.014	31.138	-0.292	-0.292	0.000	0.000	0.000	0.000
133	A	135	ASP	-1	-0.927	-0.963	33.517	-8.011	-8.011	0.000	0.000	0.000	0.000
134	A	136	GLY	0	0.030	0.026	36.783	0.152	0.152	0.000	0.000	0.000	0.000
135	A	137	LEU	0	-0.025	-0.007	35.264	0.112	0.112	0.000	0.000	0.000	0.000
136	A	138	GLY	0	0.016	0.009	34.918	-0.231	-0.231	0.000	0.000	0.000	0.000
137	A	139	LEU	0	0.029	0.019	32.625	0.137	0.137	0.000	0.000	0.000	0.000
138	A	140	THR	0	0.020	-0.003	31.461	0.103	0.103	0.000	0.000	0.000	0.000
139	A	141	GLY	0	-0.029	0.001	34.879	0.068	0.068	0.000	0.000	0.000	0.000
140	A	142	ARG	1	0.856	0.912	37.151	8.068	8.068	0.000	0.000	0.000	0.000
141	A	143	GLY	0	-0.025	-0.001	38.304	0.181	0.181	0.000	0.000	0.000	0.000
142	A	144	GLU	-1	-0.834	-0.910	38.444	-7.740	-7.740	0.000	0.000	0.000	0.000
143	A	145	GLY	0	0.008	-0.013	35.443	0.009	0.009	0.000	0.000	0.000	0.000
144	A	146	LEU	0	-0.026	-0.006	31.501	0.036	0.036	0.000	0.000	0.000	0.000
145	A	147	ALA	0	0.001	0.000	28.130	-0.065	-0.065	0.000	0.000	0.000	0.000
146	A	148	ALA	0	-0.017	-0.001	25.022	0.106	0.106	0.000	0.000	0.000	0.000
147	A	149	ILE	0	-0.012	-0.004	19.745	-0.078	-0.078	0.000	0.000	0.000	0.000
148	A	150	ALA	0	0.017	0.012	19.288	0.250	0.250	0.000	0.000	0.000	0.000
149	A	151	THR	0	-0.020	-0.010	13.830	-0.288	-0.288	0.000	0.000	0.000	0.000
150	A	152	ALA	0	0.028	0.016	13.414	0.872	0.872	0.000	0.000	0.000	0.000
151	A	153	LEU	0	-0.032	-0.007	6.973	-1.873	-1.873	0.000	0.000	0.000	0.000
152	A	154	VAL	0	0.040	0.020	8.649	2.051	2.051	0.000	0.000	0.000	0.000
153	A	155	ALA	0	-0.026	-0.023	6.110	-7.349	-7.349	0.000	0.000	0.000	0.000
154	A	156	ALA	0	-0.040	-0.024	5.843	4.008	4.008	0.000	0.000	0.000	0.000
155	A	157	GLU	-2	-1.877	-1.918	7.351	-58.695	-58.695	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:3:LEU)