FMO DATABASE

FMODB ID: 8Q59Y

Calculation Name: 1TWF-J-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: J

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	65
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-381090.996471
FMO2-HF: Nuclear repulsion	353375.296224
FMO2-HF: Total energy	-27715.700247
FMO2-MP2: Total energy	-27792.838319

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.
-40.748	-30.419	8.325	-7.258	-11.397	-0.074

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 : 0.782 / q_NPA : 0.895

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	3	VAL	0	0.043	0.023	3.060	-11.482	-8.675	0.029	-1.608	-1.229	-0.012
4	A	4	PRO	0	-0.020	0.000	4.728	3.451	3.545	-0.001	-0.005	-0.088	0.000
53	A	53	HIS	0	-0.109	-0.044	2.654	-6.759	-5.842	0.165	-0.325	-0.758	-0.002
54	A	54	VAL	0	0.018	0.010	3.898	5.061	5.381	-0.001	-0.087	-0.232	0.000
55	A	55	ASP	-1	-0.776	-0.889	2.161	-91.038	-87.444	1.779	-2.949	-2.424	-0.046
56	A	56	LEU	0	-0.076	-0.044	2.373	8.308	9.671	2.383	-1.035	-2.711	-0.006
57	A	57	ILE	0	0.025	0.023	3.662	6.061	6.706	0.004	-0.161	-0.488	0.000
58	A	58	GLU	-1	-0.834	-0.914	4.852	-25.930	-25.770	-0.001	-0.010	-0.149	0.000
60	A	60	PHE	0	-0.020	-0.028	2.304	-1.245	-0.816	3.968	-1.078	-3.318	-0.008
5	A	5	VAL	0	0.077	0.034	6.829	3.737	3.737	0.000	0.000	0.000	0.000
6	A	6	ARG	1	0.899	0.939	10.247	21.834	21.834	0.000	0.000	0.000	0.000
7	A	7	CYS	0	-0.006	0.018	10.807	-1.714	-1.714	0.000	0.000	0.000	0.000
8	A	8	PHE	0	0.069	0.008	6.756	2.651	2.651	0.000	0.000	0.000	0.000
9	A	9	SER	0	0.017	0.012	12.844	0.674	0.674	0.000	0.000	0.000	0.000
10	A	10	CYS	0	-0.067	-0.035	16.169	1.115	1.115	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.079	0.051	15.785	0.744	0.744	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.863	0.923	16.607	17.223	17.223	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.001	-0.006	14.652	-1.232	-1.232	0.000	0.000	0.000	0.000
14	A	14	VAL	0	-0.005	-0.006	10.487	1.600	1.600	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.034	0.018	9.913	-0.783	-0.783	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.876	-0.938	10.706	-20.442	-20.442	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.860	0.931	12.745	19.313	19.313	0.000	0.000	0.000	0.000
18	A	18	TRP	0	0.010	-0.004	8.110	0.542	0.542	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.859	-0.927	11.765	-21.644	-21.644	0.000	0.000	0.000	0.000
20	A	20	SER	0	0.019	0.002	14.344	0.930	0.930	0.000	0.000	0.000	0.000
21	A	21	TYR	0	-0.039	-0.022	12.030	1.487	1.487	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.031	0.006	11.155	0.540	0.540	0.000	0.000	0.000	0.000
23	A	23	ASN	0	0.044	0.030	15.081	0.265	0.265	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.048	-0.028	18.469	0.815	0.815	0.000	0.000	0.000	0.000
25	A	25	LEU	0	-0.036	-0.014	14.835	0.391	0.391	0.000	0.000	0.000	0.000
26	A	26	GLN	0	-0.059	-0.027	18.579	0.877	0.877	0.000	0.000	0.000	0.000
27	A	27	GLU	-1	-0.951	-0.977	20.304	-13.827	-13.827	0.000	0.000	0.000	0.000
28	A	28	ASP	-1	-0.944	-0.980	22.505	-12.774	-12.774	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.980	-0.978	22.945	-11.664	-11.664	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.070	-0.031	21.429	0.392	0.392	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.751	-0.837	21.015	-14.302	-14.302	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.840	-0.944	15.847	-17.388	-17.388	0.000	0.000	0.000	0.000
33	A	33	GLY	0	-0.063	-0.033	18.275	-0.397	-0.397	0.000	0.000	0.000	0.000
34	A	34	THR	0	-0.028	-0.053	20.796	0.118	0.118	0.000	0.000	0.000	0.000
35	A	35	ALA	0	0.042	0.033	18.320	0.120	0.120	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.022	-0.020	14.261	-0.276	-0.276	0.000	0.000	0.000	0.000
37	A	37	SER	0	-0.050	-0.031	18.228	-0.080	-0.080	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.909	0.986	21.732	13.121	13.121	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.065	0.051	15.681	0.028	0.028	0.000	0.000	0.000	0.000
40	A	40	GLY	0	-0.026	-0.019	19.101	-0.366	-0.366	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.076	-0.028	14.751	0.156	0.156	0.000	0.000	0.000	0.000
42	A	42	LYS	1	1.009	0.998	18.833	12.257	12.257	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.932	0.954	19.236	15.267	15.267	0.000	0.000	0.000	0.000
44	A	44	TYR	0	0.131	0.046	18.459	-1.123	-1.123	0.000	0.000	0.000	0.000
45	A	45	CYS	0	-0.024	-0.010	16.147	-0.929	-0.929	0.000	0.000	0.000	0.000
46	A	46	CYS	0	-0.034	-0.020	14.432	-1.088	-1.088	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.868	0.925	13.680	14.264	14.264	0.000	0.000	0.000	0.000
48	A	48	ARG	1	0.978	0.993	11.688	22.039	22.039	0.000	0.000	0.000	0.000
49	A	49	MET	0	-0.067	-0.015	8.905	-2.031	-2.031	0.000	0.000	0.000	0.000
50	A	50	ILE	0	0.016	0.014	8.463	-3.808	-3.808	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.003	0.004	9.944	-1.477	-1.477	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.031	-0.026	9.246	1.571	1.571	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.891	0.938	7.159	38.392	38.392	0.000	0.000	0.000	0.000
61	A	61	LEU	0	0.025	0.012	7.372	2.531	2.531	0.000	0.000	0.000	0.000
62	A	62	ARG	1	0.895	0.956	9.810	22.051	22.051	0.000	0.000	0.000	0.000
63	A	63	TYR	0	-0.056	-0.018	8.523	1.837	1.837	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.027	-0.021	12.775	0.109	0.109	0.000	0.000	0.000	0.000
65	A	65	PRO	-1	-0.934	-0.946	13.191	-18.821	-18.821	0.000	0.000	0.000	0.000

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