FMO DATABASE

FMODB ID: 3M9JL

Calculation Name: 1TWF-I-Xray547

Preferred Name:

Target Type:

Ligand Name: uridine 5'-triphosphate | manganese (ii) ion | zinc ion

Ligand 3-letter code: UTP | MN | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1TWF

Chain ID: I

ChEMBL ID:

UniProt ID: P20434

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	122
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-909794.867595
FMO2-HF: Nuclear repulsion	857438.973037
FMO2-HF: Total energy	-52355.894558
FMO2-MP2: Total energy	-52500.607319

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:1:MET)

Summations of interaction energy for fragment #1(A: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.
35.982	40.481	2.378	-2.083	-4.794	-0.006

Interaction energy analysis for fragmet #1(A:1:MET)

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 : 0.898

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	A	3	THR	0	0.000	0.012	3.795	1.435	3.305	-0.022	-0.757	-1.092	-0.002
42	A	42	LEU	0	-0.051	-0.012	3.518	-1.176	-0.770	0.011	-0.104	-0.313	0.000
45	A	45	ARG	1	0.832	0.895	2.312	55.668	56.911	2.376	-0.853	-2.766	-0.002
46	A	46	HIS	0	0.027	0.019	4.763	-4.485	-4.430	-0.001	-0.004	-0.050	0.000
47	A	47	GLU	-1	-0.837	-0.911	3.562	-52.196	-51.359	0.015	-0.360	-0.491	-0.002
118	A	118	ARG	1	0.871	0.943	4.734	31.021	31.109	-0.001	-0.005	-0.082	0.000
4	A	4	PHE	0	0.018	0.021	5.936	3.901	3.901	0.000	0.000	0.000	0.000
5	A	5	ARG	1	0.860	0.897	9.158	21.820	21.820	0.000	0.000	0.000	0.000
6	A	6	PHE	0	0.024	0.007	12.163	-0.099	-0.099	0.000	0.000	0.000	0.000
7	A	7	CYS	0	-0.070	0.000	15.802	0.653	0.653	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.885	0.916	19.359	13.045	13.045	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.788	-0.885	21.239	-12.309	-12.309	0.000	0.000	0.000	0.000
10	A	10	CYS	0	-0.015	-0.030	22.858	0.186	0.186	0.000	0.000	0.000	0.000
11	A	11	ASN	0	0.000	0.010	18.220	-0.419	-0.419	0.000	0.000	0.000	0.000
12	A	12	ASN	0	0.030	0.011	18.628	-0.890	-0.890	0.000	0.000	0.000	0.000
13	A	13	MET	0	-0.027	-0.014	11.626	-0.139	-0.139	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.028	0.001	14.744	1.182	1.182	0.000	0.000	0.000	0.000
15	A	15	TYR	0	-0.035	-0.033	13.984	-1.808	-1.808	0.000	0.000	0.000	0.000
16	A	16	PRO	0	-0.015	0.009	13.193	0.835	0.835	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.782	0.866	15.431	15.941	15.941	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.864	-0.943	18.462	-14.950	-14.950	0.000	0.000	0.000	0.000
19	A	19	ASP	-1	-0.799	-0.882	20.561	-12.460	-12.460	0.000	0.000	0.000	0.000
20	A	20	LYS	1	0.922	0.943	23.084	12.510	12.510	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.942	-0.939	25.416	-10.239	-10.239	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.072	-0.061	24.385	0.333	0.333	0.000	0.000	0.000	0.000
23	A	23	ASN	0	-0.067	-0.015	22.417	-0.589	-0.589	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.901	0.952	18.946	13.743	13.743	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.040	-0.014	12.581	0.085	0.085	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.004	0.005	17.007	-0.057	-0.057	0.000	0.000	0.000	0.000
27	A	27	PHE	0	0.006	-0.019	11.026	-1.493	-1.493	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.779	-0.869	16.838	-13.842	-13.842	0.000	0.000	0.000	0.000
29	A	29	CYS	0	-0.057	-0.015	18.545	-0.904	-0.904	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.929	0.971	18.518	16.697	16.697	0.000	0.000	0.000	0.000
31	A	31	THR	0	-0.005	-0.001	22.579	0.134	0.134	0.000	0.000	0.000	0.000
32	A	32	CYS	0	0.018	0.015	24.579	0.309	0.309	0.000	0.000	0.000	0.000
33	A	33	SER	0	0.039	0.005	25.049	-0.236	-0.236	0.000	0.000	0.000	0.000
34	A	34	TYR	0	-0.038	-0.046	18.921	0.473	0.473	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.004	-0.014	20.835	-0.480	-0.480	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.779	-0.829	15.516	-19.074	-19.074	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.890	-0.957	17.120	-16.067	-16.067	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.040	-0.018	12.676	-0.920	-0.920	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.015	0.011	11.640	0.571	0.571	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.030	-0.024	7.264	-0.215	-0.215	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.067	0.030	10.255	-0.243	-0.243	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.040	0.013	7.136	-3.887	-3.887	0.000	0.000	0.000	0.000
44	A	44	TYR	0	0.001	-0.006	6.479	-1.365	-1.365	0.000	0.000	0.000	0.000
48	A	48	LEU	0	0.031	0.018	7.555	1.947	1.947	0.000	0.000	0.000	0.000
49	A	49	ILE	0	0.014	0.011	10.321	1.495	1.495	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.035	-0.011	7.239	-1.259	-1.259	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.009	-0.011	7.900	0.907	0.907	0.000	0.000	0.000	0.000
52	A	52	ILE	0	0.040	0.032	5.638	1.457	1.457	0.000	0.000	0.000	0.000
53	A	53	GLY	0	0.026	0.007	8.454	0.684	0.684	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.873	-0.900	11.799	-18.386	-18.386	0.000	0.000	0.000	0.000
55	A	55	THR	0	0.019	-0.017	12.674	1.799	1.799	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.029	-0.010	14.113	0.357	0.357	0.000	0.000	0.000	0.000
57	A	57	GLY	0	0.049	0.016	15.293	0.845	0.845	0.000	0.000	0.000	0.000
58	A	58	VAL	0	-0.025	0.001	16.754	0.858	0.858	0.000	0.000	0.000	0.000
59	A	59	VAL	0	0.003	0.003	17.847	-0.613	-0.613	0.000	0.000	0.000	0.000
60	A	60	GLN	0	-0.009	-0.007	20.606	0.115	0.115	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.852	-0.923	23.362	-10.681	-10.681	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.029	0.001	21.203	0.307	0.307	0.000	0.000	0.000	0.000
63	A	63	GLY	0	0.015	-0.009	24.655	0.204	0.204	0.000	0.000	0.000	0.000
64	A	64	SER	0	-0.090	-0.062	27.702	0.434	0.434	0.000	0.000	0.000	0.000
65	A	65	ASP	-1	-0.802	-0.875	27.069	-10.661	-10.661	0.000	0.000	0.000	0.000
66	A	66	PRO	0	-0.045	-0.027	29.223	0.064	0.064	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.100	-0.074	29.071	0.163	0.163	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.015	0.005	24.672	-0.102	-0.102	0.000	0.000	0.000	0.000
69	A	69	PRO	0	-0.012	0.010	27.472	0.350	0.350	0.000	0.000	0.000	0.000
70	A	70	ARG	1	0.956	0.965	28.487	9.351	9.351	0.000	0.000	0.000	0.000
71	A	71	SER	0	-0.059	-0.030	28.703	0.087	0.087	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.856	-0.918	30.182	-9.084	-9.084	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.960	0.974	25.216	10.934	10.934	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.801	-0.861	28.776	-9.328	-9.328	0.000	0.000	0.000	0.000
75	A	75	CYS	0	-0.059	-0.016	24.200	-0.342	-0.342	0.000	0.000	0.000	0.000
76	A	76	PRO	0	-0.002	-0.022	21.495	0.211	0.211	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.904	0.971	18.288	14.290	14.290	0.000	0.000	0.000	0.000
78	A	78	CYS	0	0.011	0.009	24.376	0.361	0.361	0.000	0.000	0.000	0.000
79	A	79	HIS	1	0.842	0.909	27.393	10.397	10.397	0.000	0.000	0.000	0.000
80	A	80	SER	0	0.033	0.021	28.481	0.220	0.220	0.000	0.000	0.000	0.000
81	A	81	ARG	1	0.926	0.940	29.128	8.472	8.472	0.000	0.000	0.000	0.000
82	A	82	GLU	-1	-0.868	-0.912	30.480	-9.165	-9.165	0.000	0.000	0.000	0.000
83	A	83	ASN	0	-0.107	-0.071	26.093	-0.706	-0.706	0.000	0.000	0.000	0.000
84	A	84	VAL	0	0.042	0.032	24.417	0.359	0.359	0.000	0.000	0.000	0.000
85	A	85	PHE	0	-0.038	-0.030	23.875	-0.432	-0.432	0.000	0.000	0.000	0.000
86	A	86	PHE	0	0.048	0.025	18.043	0.227	0.227	0.000	0.000	0.000	0.000
87	A	87	GLN	0	0.017	0.009	21.789	0.092	0.092	0.000	0.000	0.000	0.000
88	A	88	SER	0	-0.018	-0.039	16.145	-0.369	-0.369	0.000	0.000	0.000	0.000
89	A	89	GLN	0	-0.014	-0.004	16.391	0.985	0.985	0.000	0.000	0.000	0.000
90	A	90	GLN	0	-0.031	-0.009	12.245	-1.372	-1.372	0.000	0.000	0.000	0.000
91	A	91	ARG	1	0.871	0.921	16.395	15.951	15.951	0.000	0.000	0.000	0.000
92	A	92	ARG	1	0.916	0.968	10.813	24.136	24.136	0.000	0.000	0.000	0.000
93	A	93	LYS	1	0.963	0.980	18.829	13.266	13.266	0.000	0.000	0.000	0.000
94	A	94	ASP	-1	-0.885	-0.941	16.919	-16.768	-16.768	0.000	0.000	0.000	0.000
95	A	95	THR	0	-0.040	-0.024	17.515	-0.889	-0.889	0.000	0.000	0.000	0.000
96	A	96	SER	0	-0.007	-0.002	18.316	0.769	0.769	0.000	0.000	0.000	0.000
97	A	97	MET	0	0.000	-0.010	20.195	-0.085	-0.085	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.026	-0.002	17.300	0.457	0.457	0.000	0.000	0.000	0.000
99	A	99	LEU	0	0.015	0.005	20.703	-0.290	-0.290	0.000	0.000	0.000	0.000
100	A	100	PHE	0	0.022	0.005	14.878	-0.230	-0.230	0.000	0.000	0.000	0.000
101	A	101	PHE	0	-0.005	-0.011	20.301	0.540	0.540	0.000	0.000	0.000	0.000
102	A	102	VAL	0	0.013	0.000	19.907	-0.627	-0.627	0.000	0.000	0.000	0.000
103	A	103	CYS	0	-0.015	0.017	22.391	0.575	0.575	0.000	0.000	0.000	0.000
104	A	104	LEU	0	0.032	-0.002	24.573	-0.311	-0.311	0.000	0.000	0.000	0.000
105	A	105	SER	0	0.021	-0.010	26.892	0.137	0.137	0.000	0.000	0.000	0.000
106	A	106	CYS	0	-0.066	-0.034	24.254	-0.058	-0.058	0.000	0.000	0.000	0.000
107	A	107	SER	0	-0.010	0.006	20.759	-0.631	-0.631	0.000	0.000	0.000	0.000
108	A	108	HIS	0	0.020	0.000	17.611	-0.673	-0.673	0.000	0.000	0.000	0.000
109	A	109	ILE	0	0.058	0.033	15.263	0.498	0.498	0.000	0.000	0.000	0.000
110	A	110	PHE	0	-0.070	-0.041	17.817	-0.282	-0.282	0.000	0.000	0.000	0.000
111	A	111	THR	0	0.024	0.018	16.124	0.302	0.302	0.000	0.000	0.000	0.000
112	A	112	SER	0	-0.051	-0.035	19.363	0.412	0.412	0.000	0.000	0.000	0.000
113	A	113	ASP	-1	-0.834	-0.917	16.770	-14.684	-14.684	0.000	0.000	0.000	0.000
114	A	114	GLN	0	-0.017	-0.014	19.280	-0.127	-0.127	0.000	0.000	0.000	0.000
115	A	115	LYS	1	0.879	0.943	17.914	13.138	13.138	0.000	0.000	0.000	0.000
116	A	116	ASN	0	0.054	0.021	14.416	-1.585	-1.585	0.000	0.000	0.000	0.000
117	A	117	LYS	1	0.927	0.967	11.175	17.198	17.198	0.000	0.000	0.000	0.000
119	A	119	THR	0	0.025	0.004	9.365	0.858	0.858	0.000	0.000	0.000	0.000
120	A	120	GLN	0	-0.008	-0.014	8.179	0.475	0.475	0.000	0.000	0.000	0.000
121	A	121	PHE	0	-0.041	-0.011	10.707	0.425	0.425	0.000	0.000	0.000	0.000
122	A	122	SER	-1	-0.856	-0.894	6.621	-31.387	-31.387	0.000	0.000	0.000	0.000

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