FMO DATABASE

FMODB ID: 7YL4K

Calculation Name: 2CTD-A-Other547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2CTD

Chain ID: A

ChEMBL ID:

UniProt ID: Q96ME7

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	96
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-505815.74437
FMO2-HF: Nuclear repulsion	467381.97341
FMO2-HF: Total energy	-38433.77096
FMO2-MP2: Total energy	-38539.012199

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.
38.577	39.675	-0.015	-0.496	-0.587	-0.002

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 : 0.875 / q_NPA : 0.925

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	0.025	0.004	3.849	3.427	4.525	-0.015	-0.496	-0.587	-0.002
4	A	4	GLY	0	0.044	0.034	7.126	0.681	0.681	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.019	-0.014	10.914	0.840	0.840	0.000	0.000	0.000	0.000
6	A	6	SER	0	-0.018	-0.010	14.441	0.494	0.494	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.067	0.034	17.933	-0.009	-0.009	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.896	0.954	21.466	13.658	13.658	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.034	0.026	24.704	-0.041	-0.041	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.977	0.978	24.684	11.713	11.713	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.914	0.950	28.991	9.314	9.314	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.884	-0.933	30.439	-9.754	-9.754	0.000	0.000	0.000	0.000
13	A	13	PRO	0	0.002	0.011	33.080	0.033	0.033	0.000	0.000	0.000	0.000
14	A	14	PRO	0	-0.010	-0.004	33.563	-0.324	-0.324	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.012	-0.014	33.085	0.002	0.002	0.000	0.000	0.000	0.000
16	A	16	TYR	0	-0.035	-0.010	34.705	0.020	0.020	0.000	0.000	0.000	0.000
17	A	17	ALA	0	0.049	0.033	38.551	-0.047	-0.047	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.006	0.002	40.454	0.124	0.124	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.003	-0.008	43.089	0.188	0.188	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.027	-0.021	42.800	-0.042	-0.042	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.020	0.006	44.925	-0.001	-0.001	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.930	-0.965	38.247	-8.308	-8.308	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.829	-0.924	41.996	-7.700	-7.700	0.000	0.000	0.000	0.000
24	A	24	GLN	0	-0.010	-0.004	43.325	0.114	0.114	0.000	0.000	0.000	0.000
25	A	25	TRP	0	0.000	-0.025	42.444	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	26	TYR	0	0.006	0.005	38.350	-0.102	-0.102	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.020	0.007	42.653	0.016	0.016	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.902	-0.947	45.751	-6.324	-6.324	0.000	0.000	0.000	0.000
29	A	29	ILE	0	-0.090	-0.042	41.054	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	30	VAL	0	-0.054	-0.030	41.344	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	31	ASP	-1	-0.861	-0.892	43.994	-6.299	-6.299	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.827	0.898	47.586	6.311	6.311	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.029	0.027	44.533	0.040	0.040	0.000	0.000	0.000	0.000
34	A	34	SER	0	-0.169	-0.090	44.302	-0.099	-0.099	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.068	0.040	43.967	0.076	0.076	0.000	0.000	0.000	0.000
36	A	36	SER	0	0.032	0.012	46.719	-0.043	-0.043	0.000	0.000	0.000	0.000
37	A	37	CYS	0	-0.050	-0.028	47.788	-0.100	-0.100	0.000	0.000	0.000	0.000
38	A	38	PRO	0	0.033	0.008	47.771	0.137	0.137	0.000	0.000	0.000	0.000
39	A	39	THR	0	-0.006	-0.010	50.104	0.046	0.046	0.000	0.000	0.000	0.000
40	A	40	CYS	0	-0.030	-0.026	51.594	0.070	0.070	0.000	0.000	0.000	0.000
41	A	41	GLN	0	-0.032	-0.008	52.633	0.079	0.079	0.000	0.000	0.000	0.000
42	A	42	ALA	0	0.049	0.041	53.321	0.069	0.069	0.000	0.000	0.000	0.000
43	A	43	VAL	0	-0.014	-0.009	49.158	-0.017	-0.017	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.066	0.034	47.474	-0.030	-0.030	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.820	0.912	41.232	7.392	7.392	0.000	0.000	0.000	0.000
46	A	46	LYS	1	1.031	1.010	40.563	7.743	7.743	0.000	0.000	0.000	0.000
47	A	47	THR	0	0.078	0.041	37.107	0.019	0.019	0.000	0.000	0.000	0.000
48	A	48	ILE	0	0.084	0.036	38.636	0.059	0.059	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.962	-0.975	32.761	-9.614	-9.614	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.002	-0.008	37.114	-0.014	-0.014	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.021	0.018	39.201	0.120	0.120	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.953	0.978	35.164	9.034	9.034	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.893	0.934	36.255	8.776	8.776	0.000	0.000	0.000	0.000
54	A	54	HIS	0	0.005	-0.003	39.914	0.018	0.018	0.000	0.000	0.000	0.000
55	A	55	MET	0	0.058	0.019	43.240	0.116	0.116	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.908	-0.923	38.252	-8.363	-8.363	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.049	-0.009	43.030	0.190	0.190	0.000	0.000	0.000	0.000
58	A	58	CYS	0	-0.015	-0.010	45.701	0.186	0.186	0.000	0.000	0.000	0.000
59	A	59	LYS	1	0.860	0.923	44.172	7.368	7.368	0.000	0.000	0.000	0.000
60	A	60	GLN	0	-0.024	-0.012	49.245	0.043	0.043	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.899	-0.944	52.503	-5.707	-5.707	0.000	0.000	0.000	0.000
62	A	62	MET	0	-0.041	-0.017	55.687	0.051	0.051	0.000	0.000	0.000	0.000
63	A	63	PHE	0	0.054	0.024	57.954	0.061	0.061	0.000	0.000	0.000	0.000
64	A	64	THR	0	-0.020	-0.031	62.364	0.016	0.016	0.000	0.000	0.000	0.000
65	A	65	CYS	0	-0.071	0.006	65.895	0.038	0.038	0.000	0.000	0.000	0.000
66	A	66	HIS	0	0.061	0.018	67.742	0.058	0.058	0.000	0.000	0.000	0.000
67	A	67	HIS	0	0.038	0.017	71.804	0.059	0.059	0.000	0.000	0.000	0.000
68	A	68	CYS	0	-0.050	-0.015	73.317	0.023	0.023	0.000	0.000	0.000	0.000
69	A	69	GLY	0	0.093	0.058	70.351	0.012	0.012	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.905	0.954	68.382	4.570	4.570	0.000	0.000	0.000	0.000
71	A	71	GLN	0	0.028	0.003	63.612	-0.039	-0.039	0.000	0.000	0.000	0.000
72	A	72	LEU	0	-0.011	-0.019	63.385	0.029	0.029	0.000	0.000	0.000	0.000
73	A	73	ARG	1	1.006	1.004	54.842	5.755	5.755	0.000	0.000	0.000	0.000
74	A	74	SER	0	-0.006	-0.002	59.301	-0.067	-0.067	0.000	0.000	0.000	0.000
75	A	75	LEU	0	0.041	0.027	60.522	0.113	0.113	0.000	0.000	0.000	0.000
76	A	76	ALA	0	0.023	0.007	62.101	0.089	0.089	0.000	0.000	0.000	0.000
77	A	77	GLY	0	0.039	0.019	64.023	0.083	0.083	0.000	0.000	0.000	0.000
78	A	78	MET	0	-0.040	0.000	64.639	0.080	0.080	0.000	0.000	0.000	0.000
79	A	79	LYS	1	0.946	0.957	64.698	5.021	5.021	0.000	0.000	0.000	0.000
80	A	80	TYR	0	0.039	0.027	68.133	0.070	0.070	0.000	0.000	0.000	0.000
81	A	81	HIS	0	0.020	-0.011	69.420	0.028	0.028	0.000	0.000	0.000	0.000
82	A	82	VAL	0	-0.001	0.005	70.737	0.069	0.069	0.000	0.000	0.000	0.000
83	A	83	MET	0	-0.010	-0.011	70.314	0.061	0.061	0.000	0.000	0.000	0.000
84	A	84	ALA	0	-0.020	0.008	74.187	0.059	0.059	0.000	0.000	0.000	0.000
85	A	85	ASN	0	-0.090	-0.062	74.412	0.082	0.082	0.000	0.000	0.000	0.000
86	A	86	HIS	0	0.006	-0.010	74.484	0.009	0.009	0.000	0.000	0.000	0.000
87	A	87	ASN	0	-0.023	0.006	77.897	0.012	0.012	0.000	0.000	0.000	0.000
88	A	88	SER	0	0.001	-0.002	79.537	0.073	0.073	0.000	0.000	0.000	0.000
89	A	89	LEU	0	0.011	0.008	80.892	-0.043	-0.043	0.000	0.000	0.000	0.000
90	A	90	PRO	0	-0.011	-0.003	80.952	0.040	0.040	0.000	0.000	0.000	0.000
91	A	91	SER	0	-0.021	-0.031	83.781	0.019	0.019	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.028	0.017	87.569	0.038	0.038	0.000	0.000	0.000	0.000
93	A	93	PRO	0	-0.025	-0.011	88.595	-0.036	-0.036	0.000	0.000	0.000	0.000
94	A	94	SER	0	-0.030	-0.016	90.350	0.020	0.020	0.000	0.000	0.000	0.000
95	A	95	SER	0	-0.025	-0.022	90.355	-0.034	-0.034	0.000	0.000	0.000	0.000
96	A	96	GLY	-1	-0.931	-0.936	91.851	-3.404	-3.404	0.000	0.000	0.000	0.000

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