FMO DATABASE

FMODB ID: Y9KJ2

Calculation Name: 2FZC-B-Xray547

Preferred Name:

Target Type:

Ligand Name: cytidine-5'-triphosphate | {ethane-1,2-diylbis[imino(2-oxoethane-2,1-diyl)]}bis(phosphonic acid) | zinc ion

Ligand 3-letter code: CTP | EOP | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2FZC

Chain ID: B

ChEMBL ID:

UniProt ID: P0A786

Base Structure: X-ray

Registration Date: 2025-10-04

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	152
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1364607.608507
FMO2-HF: Nuclear repulsion	1304936.563373
FMO2-HF: Total energy	-59671.045135
FMO2-MP2: Total energy	-59844.711327

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:2:THR)

Summations of interaction energy for fragment #1(A:2:THR)

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.
-49.24	-46.071	12.436	-6.07	-9.535	-0.052

Interaction energy analysis for fragmet #1(A:2:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.827 / q_NPA : 0.910

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	4	ASP	-1	-0.856	-0.928	3.631	-45.986	-43.526	0.006	-0.980	-1.485	-0.002
4	A	5	ASN	0	-0.014	-0.020	4.704	3.909	3.990	-0.001	-0.017	-0.063	0.000
8	A	9	VAL	0	0.021	0.019	1.798	-5.271	-7.709	8.669	-3.075	-3.156	-0.026
9	A	10	GLU	-1	-0.792	-0.894	3.453	-55.438	-54.408	0.017	-0.408	-0.640	-0.002
10	A	11	ALA	0	-0.022	-0.018	2.250	-14.515	-12.688	3.525	-1.960	-3.392	-0.022
11	A	12	ILE	0	-0.037	-0.016	3.115	5.621	5.105	0.111	0.567	-0.162	0.000
57	A	58	LEU	0	-0.037	-0.020	4.164	-1.927	-1.852	-0.001	-0.012	-0.062	0.000
59	A	60	LYS	1	0.807	0.905	2.877	55.558	56.208	0.110	-0.185	-0.575	0.000
5	A	6	LYS	1	0.933	0.949	8.241	24.127	24.127	0.000	0.000	0.000	0.000
6	A	7	LEU	0	0.030	0.019	8.249	2.196	2.196	0.000	0.000	0.000	0.000
7	A	8	GLN	0	-0.002	0.019	7.798	-1.705	-1.705	0.000	0.000	0.000	0.000
12	A	13	LYS	1	0.923	0.965	6.582	20.007	20.007	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.936	0.983	9.567	17.583	17.583	0.000	0.000	0.000	0.000
14	A	15	GLY	0	-0.018	0.009	11.071	0.358	0.358	0.000	0.000	0.000	0.000
15	A	16	THR	0	0.006	-0.021	10.711	-0.179	-0.179	0.000	0.000	0.000	0.000
16	A	17	VAL	0	-0.033	-0.017	5.024	-1.044	-1.044	0.000	0.000	0.000	0.000
17	A	18	ILE	0	0.022	0.022	8.269	0.318	0.318	0.000	0.000	0.000	0.000
18	A	19	ASP	-1	-0.789	-0.892	5.612	-46.531	-46.531	0.000	0.000	0.000	0.000
19	A	20	HIS	0	-0.029	-0.026	7.745	4.444	4.444	0.000	0.000	0.000	0.000
20	A	21	ILE	0	0.003	0.025	11.065	2.410	2.410	0.000	0.000	0.000	0.000
21	A	22	PRO	0	0.028	0.019	13.375	-0.849	-0.849	0.000	0.000	0.000	0.000
22	A	23	ALA	0	0.037	0.003	15.617	-0.040	-0.040	0.000	0.000	0.000	0.000
23	A	24	GLN	0	0.013	0.001	16.479	1.212	1.212	0.000	0.000	0.000	0.000
24	A	25	ILE	0	0.028	0.034	17.254	0.885	0.885	0.000	0.000	0.000	0.000
25	A	26	GLY	0	0.032	0.014	14.584	0.195	0.195	0.000	0.000	0.000	0.000
26	A	27	PHE	0	0.002	-0.012	15.424	0.208	0.208	0.000	0.000	0.000	0.000
27	A	28	LYS	1	0.872	0.937	18.124	15.139	15.139	0.000	0.000	0.000	0.000
28	A	29	LEU	0	0.025	0.012	15.526	0.500	0.500	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.019	-0.018	14.868	0.303	0.303	0.000	0.000	0.000	0.000
30	A	31	SER	0	-0.010	-0.005	18.488	0.609	0.609	0.000	0.000	0.000	0.000
31	A	32	LEU	0	-0.032	-0.010	22.240	0.396	0.396	0.000	0.000	0.000	0.000
32	A	33	PHE	0	-0.038	-0.031	20.048	0.410	0.410	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.949	0.990	21.502	11.290	11.290	0.000	0.000	0.000	0.000
34	A	35	LEU	0	-0.013	0.002	15.735	-0.188	-0.188	0.000	0.000	0.000	0.000
35	A	36	THR	0	-0.006	-0.022	17.081	-0.652	-0.652	0.000	0.000	0.000	0.000
36	A	37	GLU	-1	-0.954	-0.962	19.046	-11.584	-11.584	0.000	0.000	0.000	0.000
37	A	38	THR	0	-0.050	-0.036	18.236	0.048	0.048	0.000	0.000	0.000	0.000
38	A	39	ASP	-1	-0.882	-0.931	19.679	-13.019	-13.019	0.000	0.000	0.000	0.000
39	A	40	GLN	0	-0.002	0.008	15.399	-1.013	-1.013	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.871	0.940	8.791	25.245	25.245	0.000	0.000	0.000	0.000
41	A	42	ILE	0	0.053	0.024	11.820	-1.301	-1.301	0.000	0.000	0.000	0.000
42	A	43	THR	0	-0.094	-0.060	7.435	-0.743	-0.743	0.000	0.000	0.000	0.000
43	A	44	ILE	0	0.012	0.008	9.409	-1.038	-1.038	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.021	0.020	9.354	-0.308	-0.308	0.000	0.000	0.000	0.000
45	A	46	LEU	0	-0.022	-0.023	10.249	0.372	0.372	0.000	0.000	0.000	0.000
46	A	47	ASN	0	-0.056	-0.042	13.198	0.840	0.840	0.000	0.000	0.000	0.000
47	A	48	LEU	0	0.010	0.035	7.281	0.542	0.542	0.000	0.000	0.000	0.000
48	A	49	PRO	0	0.010	0.002	10.096	1.283	1.283	0.000	0.000	0.000	0.000
49	A	50	SER	0	-0.034	-0.015	9.663	-3.326	-3.326	0.000	0.000	0.000	0.000
50	A	51	GLY	0	0.023	0.024	10.269	-1.162	-1.162	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.834	-0.920	8.468	-32.092	-32.092	0.000	0.000	0.000	0.000
52	A	53	MET	0	-0.028	-0.011	12.841	1.290	1.290	0.000	0.000	0.000	0.000
53	A	54	GLY	0	0.027	0.003	14.137	1.260	1.260	0.000	0.000	0.000	0.000
54	A	55	ARG	1	0.913	0.952	13.849	15.944	15.944	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.780	0.885	6.090	40.926	40.926	0.000	0.000	0.000	0.000
56	A	57	ASP	-1	-0.789	-0.890	11.688	-20.190	-20.190	0.000	0.000	0.000	0.000
58	A	59	ILE	0	0.008	0.001	8.902	0.965	0.965	0.000	0.000	0.000	0.000
60	A	61	ILE	0	0.046	0.021	8.727	1.446	1.446	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.770	-0.872	9.766	-24.873	-24.873	0.000	0.000	0.000	0.000
62	A	63	ASN	0	-0.076	-0.066	11.620	0.989	0.989	0.000	0.000	0.000	0.000
63	A	64	THR	0	0.018	0.013	13.744	1.524	1.524	0.000	0.000	0.000	0.000
64	A	65	PHE	0	-0.037	-0.015	13.051	-1.192	-1.192	0.000	0.000	0.000	0.000
65	A	66	LEU	0	0.003	0.022	15.575	0.778	0.778	0.000	0.000	0.000	0.000
66	A	67	SER	0	0.022	0.000	17.722	-0.321	-0.321	0.000	0.000	0.000	0.000
67	A	68	GLU	-1	-0.839	-0.938	20.255	-13.908	-13.908	0.000	0.000	0.000	0.000
68	A	69	ASP	-1	-0.816	-0.903	21.703	-11.872	-11.872	0.000	0.000	0.000	0.000
69	A	70	GLN	0	-0.040	-0.020	20.250	-0.066	-0.066	0.000	0.000	0.000	0.000
70	A	71	VAL	0	-0.025	-0.012	16.785	-0.553	-0.553	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.753	-0.864	19.116	-13.934	-13.934	0.000	0.000	0.000	0.000
72	A	73	GLN	0	-0.053	-0.039	22.232	0.415	0.415	0.000	0.000	0.000	0.000
73	A	74	LEU	0	-0.009	-0.002	15.955	-0.032	-0.032	0.000	0.000	0.000	0.000
74	A	75	ALA	0	-0.017	-0.007	20.052	-0.201	-0.201	0.000	0.000	0.000	0.000
75	A	76	LEU	0	-0.023	-0.017	21.891	0.145	0.145	0.000	0.000	0.000	0.000
76	A	77	TYR	0	-0.017	0.000	20.283	0.164	0.164	0.000	0.000	0.000	0.000
77	A	78	ALA	0	-0.006	-0.018	16.045	-0.417	-0.417	0.000	0.000	0.000	0.000
78	A	79	PRO	0	0.010	0.013	17.461	-0.786	-0.786	0.000	0.000	0.000	0.000
79	A	80	GLN	0	-0.021	-0.017	16.377	-0.134	-0.134	0.000	0.000	0.000	0.000
80	A	81	ALA	0	0.009	0.022	13.280	-1.057	-1.057	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.029	-0.036	9.933	1.705	1.705	0.000	0.000	0.000	0.000
82	A	83	VAL	0	-0.004	0.002	10.435	-2.475	-2.475	0.000	0.000	0.000	0.000
83	A	84	ASN	0	-0.025	-0.009	8.420	0.629	0.629	0.000	0.000	0.000	0.000
84	A	85	ARG	1	0.906	0.946	10.361	17.334	17.334	0.000	0.000	0.000	0.000
85	A	86	ILE	0	-0.017	-0.014	6.215	-1.010	-1.010	0.000	0.000	0.000	0.000
86	A	87	ASP	-1	-0.867	-0.966	9.700	-17.260	-17.260	0.000	0.000	0.000	0.000
87	A	88	ASN	0	-0.029	-0.004	11.348	-0.318	-0.318	0.000	0.000	0.000	0.000
88	A	89	TYR	0	-0.021	-0.027	6.620	0.880	0.880	0.000	0.000	0.000	0.000
89	A	90	GLU	-1	-0.857	-0.898	6.724	-36.180	-36.180	0.000	0.000	0.000	0.000
90	A	91	VAL	0	-0.081	-0.064	6.508	1.094	1.094	0.000	0.000	0.000	0.000
91	A	92	VAL	0	0.003	0.014	9.281	1.426	1.426	0.000	0.000	0.000	0.000
92	A	93	GLY	0	0.002	0.001	12.316	1.746	1.746	0.000	0.000	0.000	0.000
93	A	94	LYS	1	0.880	0.935	8.080	30.207	30.207	0.000	0.000	0.000	0.000
94	A	95	SER	0	-0.013	-0.004	12.962	1.808	1.808	0.000	0.000	0.000	0.000
95	A	96	ARG	1	0.914	0.943	14.475	15.923	15.923	0.000	0.000	0.000	0.000
96	A	97	PRO	0	-0.044	0.010	16.284	0.801	0.801	0.000	0.000	0.000	0.000
97	A	98	SER	0	-0.087	-0.049	19.507	0.326	0.326	0.000	0.000	0.000	0.000
98	A	99	LEU	0	-0.016	-0.032	23.236	0.030	0.030	0.000	0.000	0.000	0.000
99	A	100	PRO	0	0.041	0.046	25.136	0.261	0.261	0.000	0.000	0.000	0.000
100	A	101	GLU	-1	-0.898	-0.962	27.682	-9.220	-9.220	0.000	0.000	0.000	0.000
101	A	102	ARG	1	0.836	0.882	30.142	9.807	9.807	0.000	0.000	0.000	0.000
102	A	103	ILE	0	0.002	0.021	26.292	-0.440	-0.440	0.000	0.000	0.000	0.000
103	A	104	ASP	-1	-0.735	-0.842	28.949	-9.061	-9.061	0.000	0.000	0.000	0.000
104	A	105	ASN	0	-0.047	-0.021	28.691	-0.178	-0.178	0.000	0.000	0.000	0.000
105	A	106	VAL	0	-0.011	-0.001	25.126	0.143	0.143	0.000	0.000	0.000	0.000
106	A	107	LEU	0	-0.017	0.013	28.280	-0.091	-0.091	0.000	0.000	0.000	0.000
107	A	108	VAL	0	0.098	0.063	30.923	0.254	0.254	0.000	0.000	0.000	0.000
108	A	109	CYS	0	-0.076	-0.049	34.271	0.027	0.027	0.000	0.000	0.000	0.000
109	A	110	PRO	0	0.061	0.018	36.417	0.154	0.154	0.000	0.000	0.000	0.000
110	A	111	ASN	0	-0.027	-0.021	38.912	0.268	0.268	0.000	0.000	0.000	0.000
111	A	112	SER	0	0.056	0.024	42.198	-0.041	-0.041	0.000	0.000	0.000	0.000
112	A	113	ASN	0	-0.002	0.002	43.565	0.040	0.040	0.000	0.000	0.000	0.000
113	A	114	CYS	0	-0.068	-0.020	40.740	0.110	0.110	0.000	0.000	0.000	0.000
114	A	115	ILE	0	0.067	0.024	43.321	-0.072	-0.072	0.000	0.000	0.000	0.000
115	A	116	SER	0	0.001	-0.016	38.824	0.004	0.004	0.000	0.000	0.000	0.000
116	A	117	HIS	0	-0.073	-0.018	38.390	-0.265	-0.265	0.000	0.000	0.000	0.000
117	A	118	ALA	0	-0.004	0.002	40.726	-0.063	-0.063	0.000	0.000	0.000	0.000
118	A	119	GLU	-1	-0.903	-0.943	42.108	-6.903	-6.903	0.000	0.000	0.000	0.000
119	A	120	PRO	0	-0.020	0.005	39.438	-0.238	-0.238	0.000	0.000	0.000	0.000
120	A	121	VAL	0	-0.067	-0.043	38.380	-0.017	-0.017	0.000	0.000	0.000	0.000
121	A	122	SER	0	0.001	-0.003	32.691	-0.045	-0.045	0.000	0.000	0.000	0.000
122	A	123	SER	0	-0.038	-0.028	32.791	0.160	0.160	0.000	0.000	0.000	0.000
123	A	124	SER	0	-0.070	-0.070	33.504	-0.131	-0.131	0.000	0.000	0.000	0.000
124	A	125	PHE	0	-0.003	-0.003	32.930	0.374	0.374	0.000	0.000	0.000	0.000
125	A	126	ALA	0	0.032	0.024	33.175	-0.282	-0.282	0.000	0.000	0.000	0.000
126	A	127	VAL	0	-0.035	-0.007	29.601	0.132	0.132	0.000	0.000	0.000	0.000
127	A	128	ARG	1	0.820	0.862	32.919	8.207	8.207	0.000	0.000	0.000	0.000
128	A	129	LYS	1	0.974	0.987	28.149	10.980	10.980	0.000	0.000	0.000	0.000
129	A	130	ARG	1	0.860	0.931	32.926	8.690	8.690	0.000	0.000	0.000	0.000
130	A	131	ALA	0	-0.024	-0.012	33.486	0.139	0.139	0.000	0.000	0.000	0.000
131	A	132	ASN	0	-0.020	-0.021	33.471	0.138	0.138	0.000	0.000	0.000	0.000
132	A	133	ASP	-1	-0.794	-0.845	31.461	-9.349	-9.349	0.000	0.000	0.000	0.000
133	A	134	ILE	0	0.000	-0.009	28.015	-0.021	-0.021	0.000	0.000	0.000	0.000
134	A	135	ALA	0	-0.026	0.005	31.964	0.088	0.088	0.000	0.000	0.000	0.000
135	A	136	LEU	0	0.033	0.013	30.838	-0.208	-0.208	0.000	0.000	0.000	0.000
136	A	137	LYS	1	0.855	0.921	35.015	7.672	7.672	0.000	0.000	0.000	0.000
137	A	138	CYS	0	-0.010	0.025	37.560	-0.055	-0.055	0.000	0.000	0.000	0.000
138	A	139	LYS	1	0.904	0.947	37.312	8.496	8.496	0.000	0.000	0.000	0.000
139	A	140	TYR	0	0.050	0.013	38.278	0.076	0.076	0.000	0.000	0.000	0.000
140	A	141	CYS	0	-0.007	-0.007	41.607	0.152	0.152	0.000	0.000	0.000	0.000
141	A	142	GLU	-1	-0.877	-0.923	42.521	-6.889	-6.889	0.000	0.000	0.000	0.000
142	A	143	LYS	1	0.948	0.971	41.996	6.814	6.814	0.000	0.000	0.000	0.000
143	A	144	GLU	-1	-0.786	-0.856	38.878	-8.303	-8.303	0.000	0.000	0.000	0.000
144	A	145	PHE	0	0.014	0.004	36.758	0.187	0.187	0.000	0.000	0.000	0.000
145	A	146	SER	0	-0.018	-0.033	34.709	-0.208	-0.208	0.000	0.000	0.000	0.000
146	A	147	HIS	0	0.105	0.033	28.086	0.334	0.334	0.000	0.000	0.000	0.000
147	A	148	ASN	0	-0.035	-0.026	30.957	-0.418	-0.418	0.000	0.000	0.000	0.000
148	A	149	VAL	0	-0.010	-0.003	32.159	0.051	0.051	0.000	0.000	0.000	0.000
149	A	150	VAL	0	-0.023	-0.021	31.994	0.044	0.044	0.000	0.000	0.000	0.000
150	A	151	LEU	0	-0.038	-0.020	26.680	-0.126	-0.126	0.000	0.000	0.000	0.000
151	A	152	ALA	0	-0.057	-0.018	29.550	-0.272	-0.272	0.000	0.000	0.000	0.000
152	A	153	ASN	-1	-0.945	-0.958	31.899	-9.219	-9.219	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:THR)