FMO DATABASE

FMODB ID: 3G27L

Calculation Name: 2DKT-A-Other549

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2DKT

Chain ID: A

ChEMBL ID:

UniProt ID: Q9CR50

Base Structure: SolutionNMR

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1172141.793452
FMO2-HF: Nuclear repulsion	1111129.651966
FMO2-HF: Total energy	-61012.141487
FMO2-MP2: Total energy	-61174.382536

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.
13.133	14.151	-0.017	-0.441	-0.561	-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 : 0.859 / q_NPA : 0.916

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	0.031	0.028	3.832	0.078	1.096	-0.017	-0.441	-0.561	-0.001
4	A	4	GLY	0	0.039	0.027	6.748	1.415	1.415	0.000	0.000	0.000	0.000
5	A	5	SER	0	-0.006	-0.008	9.693	1.000	1.000	0.000	0.000	0.000	0.000
6	A	6	SER	0	-0.004	0.001	13.338	0.074	0.074	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.026	0.000	15.947	0.139	0.139	0.000	0.000	0.000	0.000
8	A	8	GLY	0	-0.015	0.005	19.061	0.152	0.152	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.012	0.007	22.239	0.333	0.333	0.000	0.000	0.000	0.000
10	A	10	ARG	1	0.974	0.983	24.859	11.040	11.040	0.000	0.000	0.000	0.000
11	A	11	ASN	0	-0.033	-0.017	28.473	0.147	0.147	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.010	0.003	32.052	-0.048	-0.048	0.000	0.000	0.000	0.000
13	A	13	ALA	0	0.016	0.012	35.167	0.030	0.030	0.000	0.000	0.000	0.000
14	A	14	GLN	0	0.022	0.013	38.733	-0.088	-0.088	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.070	0.023	42.380	-0.028	-0.028	0.000	0.000	0.000	0.000
16	A	16	PRO	0	0.004	0.019	43.608	0.201	0.201	0.000	0.000	0.000	0.000
17	A	17	ARG	1	0.881	0.926	43.851	6.992	6.992	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.010	0.036	48.515	0.055	0.055	0.000	0.000	0.000	0.000
19	A	19	CYS	0	-0.061	-0.002	48.318	-0.105	-0.105	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.869	-0.951	47.277	-6.707	-6.707	0.000	0.000	0.000	0.000
21	A	21	HIS	1	0.806	0.886	48.891	6.600	6.600	0.000	0.000	0.000	0.000
22	A	22	TYR	0	-0.034	-0.056	52.632	0.170	0.170	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.867	-0.927	52.768	-6.103	-6.103	0.000	0.000	0.000	0.000
24	A	24	ARG	1	0.900	0.938	52.869	5.967	5.967	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.010	-0.002	51.862	-0.142	-0.142	0.000	0.000	0.000	0.000
26	A	26	CYS	0	-0.030	-0.007	52.733	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.011	0.004	47.108	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.016	-0.010	51.854	0.126	0.126	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.842	0.918	51.040	6.085	6.085	0.000	0.000	0.000	0.000
30	A	30	ALA	0	0.041	0.005	51.652	0.120	0.120	0.000	0.000	0.000	0.000
31	A	31	PRO	0	-0.064	-0.037	53.659	-0.036	-0.036	0.000	0.000	0.000	0.000
32	A	32	CYS	0	-0.051	-0.004	54.008	0.037	0.037	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.051	-0.019	49.361	0.001	0.001	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.813	-0.891	49.808	-6.350	-6.350	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.870	0.933	43.623	7.187	7.187	0.000	0.000	0.000	0.000
36	A	36	LEU	0	0.002	-0.010	47.755	0.171	0.171	0.000	0.000	0.000	0.000
37	A	37	TYR	0	-0.014	-0.012	44.694	-0.181	-0.181	0.000	0.000	0.000	0.000
38	A	38	THR	0	-0.011	-0.027	47.607	0.128	0.128	0.000	0.000	0.000	0.000
39	A	39	CYS	0	-0.122	-0.095	49.979	0.192	0.192	0.000	0.000	0.000	0.000
40	A	40	ARG	1	1.003	0.984	51.723	5.540	5.540	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.008	-0.015	52.300	0.031	0.031	0.000	0.000	0.000	0.000
42	A	42	CYS	-1	-0.743	-0.767	47.692	-6.637	-6.637	0.000	0.000	0.000	0.000
43	A	43	HIS	0	-0.020	-0.013	47.689	-0.089	-0.089	0.000	0.000	0.000	0.000
44	A	44	ASP	-1	-0.874	-0.946	48.483	-6.340	-6.340	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.085	-0.049	45.189	-0.056	-0.056	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.112	-0.072	42.936	-0.341	-0.341	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.723	-0.826	44.618	-7.055	-7.055	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.891	-0.931	45.988	-7.040	-7.040	0.000	0.000	0.000	0.000
49	A	49	HIS	0	-0.040	-0.041	48.598	0.124	0.124	0.000	0.000	0.000	0.000
50	A	50	GLN	0	0.036	0.023	51.790	0.040	0.040	0.000	0.000	0.000	0.000
51	A	51	LEU	0	-0.012	0.000	53.279	0.049	0.049	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.930	-0.967	55.847	-5.299	-5.299	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.901	0.940	58.702	5.216	5.216	0.000	0.000	0.000	0.000
54	A	54	PHE	0	0.027	-0.001	60.308	0.015	0.015	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.964	0.980	61.169	5.259	5.259	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.013	0.029	56.772	0.031	0.031	0.000	0.000	0.000	0.000
57	A	57	LYS	1	0.933	0.959	59.904	4.986	4.986	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.843	-0.927	57.426	-5.343	-5.343	0.000	0.000	0.000	0.000
59	A	59	VAL	0	-0.055	-0.041	55.438	-0.067	-0.067	0.000	0.000	0.000	0.000
60	A	60	GLN	0	0.035	0.023	47.885	0.068	0.068	0.000	0.000	0.000	0.000
61	A	61	CYS	0	-0.064	0.006	52.515	-0.063	-0.063	0.000	0.000	0.000	0.000
62	A	62	ILE	0	-0.014	-0.011	47.942	-0.129	-0.129	0.000	0.000	0.000	0.000
63	A	63	ASN	0	-0.007	-0.032	47.966	-0.115	-0.115	0.000	0.000	0.000	0.000
64	A	64	CYS	0	0.037	0.002	49.316	-0.043	-0.043	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.951	-0.955	45.114	-7.026	-7.026	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.897	0.949	49.897	5.612	5.612	0.000	0.000	0.000	0.000
67	A	67	LEU	0	0.013	0.004	53.554	-0.020	-0.020	0.000	0.000	0.000	0.000
68	A	68	GLN	0	-0.012	-0.014	55.281	0.127	0.127	0.000	0.000	0.000	0.000
69	A	69	HIS	0	0.085	0.053	58.499	-0.077	-0.077	0.000	0.000	0.000	0.000
70	A	70	ALA	0	-0.067	-0.048	61.108	0.001	0.001	0.000	0.000	0.000	0.000
71	A	71	GLN	0	-0.020	-0.010	60.719	0.080	0.080	0.000	0.000	0.000	0.000
72	A	72	GLN	0	-0.025	-0.014	61.225	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	73	THR	0	0.002	-0.012	60.134	-0.087	-0.087	0.000	0.000	0.000	0.000
74	A	74	CYS	0	-0.048	0.009	55.559	0.023	0.023	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.888	-0.938	58.902	-5.024	-5.024	0.000	0.000	0.000	0.000
76	A	76	ASP	-1	-0.942	-0.972	55.764	-5.737	-5.737	0.000	0.000	0.000	0.000
77	A	77	CYS	0	0.015	-0.003	54.414	0.011	0.011	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.020	0.014	56.500	0.024	0.024	0.000	0.000	0.000	0.000
79	A	79	THR	0	-0.031	-0.013	53.969	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.008	0.012	57.131	0.024	0.024	0.000	0.000	0.000	0.000
81	A	81	PHE	0	-0.013	-0.027	54.804	-0.117	-0.117	0.000	0.000	0.000	0.000
82	A	82	GLY	0	0.030	0.002	57.119	-0.089	-0.089	0.000	0.000	0.000	0.000
83	A	83	GLU	-1	-0.826	-0.911	59.505	-5.163	-5.163	0.000	0.000	0.000	0.000
84	A	84	TYR	0	-0.034	-0.013	62.188	0.115	0.115	0.000	0.000	0.000	0.000
85	A	85	TYR	0	0.028	0.010	62.213	-0.114	-0.114	0.000	0.000	0.000	0.000
86	A	86	CYS	0	-0.041	0.015	63.548	0.120	0.120	0.000	0.000	0.000	0.000
87	A	87	SER	0	0.026	0.010	64.635	-0.065	-0.065	0.000	0.000	0.000	0.000
88	A	88	ILE	0	0.029	0.007	66.812	-0.038	-0.038	0.000	0.000	0.000	0.000
89	A	89	CYS	0	-0.079	-0.060	63.401	-0.022	-0.022	0.000	0.000	0.000	0.000
90	A	90	HIS	1	0.854	0.951	61.296	4.980	4.980	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.027	0.003	59.478	-0.083	-0.083	0.000	0.000	0.000	0.000
92	A	92	PHE	0	0.014	-0.008	57.807	0.087	0.087	0.000	0.000	0.000	0.000
93	A	93	ASP	-1	-0.762	-0.887	57.496	-5.638	-5.638	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.897	0.940	55.859	5.705	5.705	0.000	0.000	0.000	0.000
95	A	95	ASP	-1	-0.839	-0.920	59.227	-5.028	-5.028	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.892	0.963	56.096	5.633	5.633	0.000	0.000	0.000	0.000
97	A	97	ARG	1	0.896	0.962	61.263	4.937	4.937	0.000	0.000	0.000	0.000
98	A	98	GLN	0	-0.002	-0.001	61.348	-0.006	-0.006	0.000	0.000	0.000	0.000
99	A	99	TYR	0	0.017	-0.009	65.321	0.059	0.059	0.000	0.000	0.000	0.000
100	A	100	HIS	0	0.015	-0.002	67.474	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	101	CYS	0	-0.082	-0.031	69.254	0.099	0.099	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.847	-0.936	71.791	-4.291	-4.291	0.000	0.000	0.000	0.000
103	A	103	SER	0	-0.013	-0.013	74.095	-0.007	-0.007	0.000	0.000	0.000	0.000
104	A	104	CYS	0	-0.065	-0.025	70.509	0.011	0.011	0.000	0.000	0.000	0.000
105	A	105	GLY	0	0.071	0.059	70.253	-0.055	-0.055	0.000	0.000	0.000	0.000
106	A	106	ILE	0	-0.052	-0.048	65.869	-0.106	-0.106	0.000	0.000	0.000	0.000
107	A	107	CYS	0	-0.005	-0.003	63.711	0.061	0.061	0.000	0.000	0.000	0.000
108	A	108	ARG	1	0.909	0.953	64.965	4.835	4.835	0.000	0.000	0.000	0.000
109	A	109	ILE	0	0.051	0.025	60.966	0.013	0.013	0.000	0.000	0.000	0.000
110	A	110	GLY	0	-0.014	0.013	64.853	0.067	0.067	0.000	0.000	0.000	0.000
111	A	111	PRO	0	0.077	0.017	66.596	-0.066	-0.066	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.847	0.913	69.258	4.403	4.403	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.941	-0.966	72.084	-4.383	-4.383	0.000	0.000	0.000	0.000
114	A	114	ASP	-1	-0.834	-0.891	71.106	-4.457	-4.457	0.000	0.000	0.000	0.000
115	A	115	PHE	0	0.015	0.000	67.375	-0.033	-0.033	0.000	0.000	0.000	0.000
116	A	116	PHE	0	-0.080	-0.024	73.013	0.075	0.075	0.000	0.000	0.000	0.000
117	A	117	HIS	0	0.042	0.007	74.074	-0.019	-0.019	0.000	0.000	0.000	0.000
118	A	118	CYS	0	-0.057	-0.022	76.031	0.086	0.086	0.000	0.000	0.000	0.000
119	A	119	LEU	0	0.101	0.035	77.972	-0.028	-0.028	0.000	0.000	0.000	0.000
120	A	120	LYS	1	0.945	0.959	80.066	3.832	3.832	0.000	0.000	0.000	0.000
121	A	121	CYS	0	-0.007	0.027	76.239	0.008	0.008	0.000	0.000	0.000	0.000
122	A	122	ASN	0	0.043	0.033	75.951	-0.044	-0.044	0.000	0.000	0.000	0.000
123	A	123	LEU	0	0.028	0.018	71.741	-0.068	-0.068	0.000	0.000	0.000	0.000
124	A	124	CYS	0	-0.051	-0.024	70.235	0.062	0.062	0.000	0.000	0.000	0.000
125	A	125	LEU	0	-0.015	-0.008	71.146	-0.051	-0.051	0.000	0.000	0.000	0.000
126	A	126	THR	0	0.068	0.047	70.184	0.036	0.036	0.000	0.000	0.000	0.000
127	A	127	THR	0	-0.032	-0.055	72.201	0.047	0.047	0.000	0.000	0.000	0.000
128	A	128	ASN	0	0.008	0.013	72.699	0.076	0.076	0.000	0.000	0.000	0.000
129	A	129	LEU	0	0.025	0.008	71.626	0.037	0.037	0.000	0.000	0.000	0.000
130	A	130	ARG	1	0.929	0.971	75.815	4.053	4.053	0.000	0.000	0.000	0.000
131	A	131	GLY	0	0.011	-0.002	79.012	0.056	0.056	0.000	0.000	0.000	0.000
132	A	132	LYS	1	0.973	1.000	74.709	4.361	4.361	0.000	0.000	0.000	0.000
133	A	133	HIS	1	0.780	0.883	76.037	4.198	4.198	0.000	0.000	0.000	0.000
134	A	134	LYS	1	1.015	1.011	77.847	4.144	4.144	0.000	0.000	0.000	0.000
135	A	135	CYS	0	-0.009	-0.042	78.655	-0.058	-0.058	0.000	0.000	0.000	0.000
136	A	136	ILE	0	0.011	0.017	80.733	-0.015	-0.015	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.951	-0.984	80.576	-4.079	-4.079	0.000	0.000	0.000	0.000
138	A	138	SER	0	-0.004	-0.007	83.217	0.053	0.053	0.000	0.000	0.000	0.000
139	A	139	GLY	0	0.033	0.022	85.261	-0.030	-0.030	0.000	0.000	0.000	0.000
140	A	140	PRO	0	-0.012	-0.001	86.030	-0.031	-0.031	0.000	0.000	0.000	0.000
141	A	141	SER	0	-0.024	-0.012	86.452	-0.022	-0.022	0.000	0.000	0.000	0.000
142	A	142	SER	0	-0.030	-0.028	80.650	-0.031	-0.031	0.000	0.000	0.000	0.000
143	A	143	GLY	-1	-0.920	-0.938	77.827	-4.169	-4.169	0.000	0.000	0.000	0.000

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