FMO DATABASE

FMODB ID: 8GYRY

Calculation Name: 1X3C-A-Other547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1X3C

Chain ID: A

ChEMBL ID:

UniProt ID: O60281

Base Structure: SolutionNMR

Registration Date: 2025-10-03

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	73
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-323795.726047
FMO2-HF: Nuclear repulsion	295641.11211
FMO2-HF: Total energy	-28154.613936
FMO2-MP2: Total energy	-28236.360363

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:GLY)

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

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.
21.424	22.466	-0.014	-0.45	-0.579	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.872 / q_NPA : 0.922

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	SER	0	0.011	0.011	3.848	3.113	4.155	-0.014	-0.450	-0.579	-0.001
4	A	4	GLY	0	0.059	0.028	6.999	0.574	0.574	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.028	-0.004	10.821	0.841	0.841	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.014	0.002	14.215	0.267	0.267	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.059	0.029	17.954	0.134	0.134	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.951	0.975	21.310	11.984	11.984	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.960	0.973	25.007	10.321	10.321	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.963	0.991	28.569	9.818	9.818	0.000	0.000	0.000	0.000
11	A	11	PRO	0	0.038	0.018	31.747	-0.022	-0.022	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.032	0.009	35.066	-0.024	-0.024	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.022	-0.011	38.027	0.093	0.093	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.035	-0.027	41.198	0.048	0.048	0.000	0.000	0.000	0.000
15	A	15	SER	0	0.028	0.024	43.749	0.048	0.048	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.031	-0.009	47.276	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.868	-0.942	50.593	-6.327	-6.327	0.000	0.000	0.000	0.000
18	A	18	PHE	0	-0.063	-0.018	53.216	0.112	0.112	0.000	0.000	0.000	0.000
19	A	19	PRO	0	0.043	0.031	56.452	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.012	-0.036	59.532	0.038	0.038	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.940	0.976	59.137	5.228	5.228	0.000	0.000	0.000	0.000
22	A	22	TYR	0	0.006	0.004	60.078	-0.030	-0.030	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.009	-0.005	63.250	0.007	0.007	0.000	0.000	0.000	0.000
24	A	24	PRO	0	-0.028	-0.006	65.589	0.024	0.024	0.000	0.000	0.000	0.000
25	A	25	TYR	0	0.065	0.030	69.335	0.040	0.040	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.868	0.926	66.529	4.704	4.704	0.000	0.000	0.000	0.000
27	A	27	PRO	0	0.039	0.030	66.928	0.069	0.069	0.000	0.000	0.000	0.000
28	A	28	TYR	0	0.024	0.019	63.965	0.038	0.038	0.000	0.000	0.000	0.000
29	A	29	ARG	1	0.943	0.951	68.967	4.298	4.298	0.000	0.000	0.000	0.000
30	A	30	CYS	0	-0.061	0.009	72.029	0.014	0.014	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.052	0.022	73.258	0.046	0.046	0.000	0.000	0.000	0.000
32	A	32	HIS	0	-0.012	-0.014	74.087	0.083	0.083	0.000	0.000	0.000	0.000
33	A	33	GLN	0	0.012	-0.005	77.778	0.006	0.006	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.015	0.016	80.624	0.036	0.036	0.000	0.000	0.000	0.000
35	A	35	CYS	0	-0.026	-0.004	74.272	-0.033	-0.033	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.005	0.002	76.138	-0.031	-0.031	0.000	0.000	0.000	0.000
37	A	37	ALA	0	0.004	0.011	71.106	-0.043	-0.043	0.000	0.000	0.000	0.000
38	A	38	ALA	0	0.033	0.007	70.032	0.026	0.026	0.000	0.000	0.000	0.000
39	A	39	PHE	0	-0.017	-0.001	64.472	-0.035	-0.035	0.000	0.000	0.000	0.000
40	A	40	THR	0	0.007	-0.013	62.640	0.035	0.035	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.011	0.017	57.722	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	42	GLN	0	0.087	0.037	60.963	-0.036	-0.036	0.000	0.000	0.000	0.000
43	A	43	GLN	0	0.086	0.033	57.095	0.090	0.090	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.013	-0.030	59.505	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.007	0.007	62.070	0.061	0.061	0.000	0.000	0.000	0.000
46	A	46	ILE	0	0.032	0.018	60.987	0.087	0.087	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.036	0.015	59.859	0.066	0.066	0.000	0.000	0.000	0.000
48	A	48	HIS	0	0.008	-0.005	63.848	0.105	0.105	0.000	0.000	0.000	0.000
49	A	49	TYR	0	0.033	0.014	67.166	0.072	0.072	0.000	0.000	0.000	0.000
50	A	50	GLN	0	-0.006	-0.008	63.348	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	51	ALA	0	-0.051	-0.019	65.930	0.012	0.012	0.000	0.000	0.000	0.000
52	A	52	VAL	0	-0.062	-0.035	67.868	0.051	0.051	0.000	0.000	0.000	0.000
53	A	53	HIS	0	-0.003	-0.028	71.519	0.008	0.008	0.000	0.000	0.000	0.000
54	A	54	LYS	1	0.845	0.952	69.037	4.638	4.638	0.000	0.000	0.000	0.000
55	A	55	SER	0	0.003	0.003	70.161	0.027	0.027	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.831	-0.910	65.629	-5.018	-5.018	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.039	-0.026	66.268	0.071	0.071	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.014	0.001	69.403	-0.007	-0.007	0.000	0.000	0.000	0.000
59	A	59	ALA	0	0.022	0.012	70.547	-0.056	-0.056	0.000	0.000	0.000	0.000
60	A	60	PHE	0	-0.043	-0.036	71.229	0.075	0.075	0.000	0.000	0.000	0.000
61	A	61	SER	0	-0.019	-0.007	68.669	-0.013	-0.013	0.000	0.000	0.000	0.000
62	A	62	ALA	0	0.023	0.011	69.209	0.028	0.028	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.952	-0.974	64.691	-4.890	-4.890	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.036	-0.016	65.716	0.013	0.013	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.964	-0.979	58.733	-5.537	-5.537	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.928	-0.935	62.010	-4.820	-4.820	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.977	-0.983	63.858	-4.979	-4.979	0.000	0.000	0.000	0.000
68	A	68	SER	0	-0.076	-0.080	65.732	0.051	0.051	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.029	0.027	68.304	0.080	0.080	0.000	0.000	0.000	0.000
70	A	70	PRO	0	-0.065	-0.032	70.101	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	71	SER	0	0.012	-0.003	69.413	-0.053	-0.053	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.075	-0.038	70.231	0.078	0.078	0.000	0.000	0.000	0.000
73	A	73	GLY	-1	-0.930	-0.952	72.055	-4.251	-4.251	0.000	0.000	0.000	0.000

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