FMO DATABASE

FMODB ID: YR1M2

Calculation Name: 2KDX-A-Other547

Preferred Name:

Target Type:

Ligand Name: zinc ion

Ligand 3-letter code: ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2KDX

Chain ID: A

ChEMBL ID:

UniProt ID: P0A0U4

Base Structure: SolutionNMR

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	119
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-865337.877763
FMO2-HF: Nuclear repulsion	816646.045667
FMO2-HF: Total energy	-48691.832097
FMO2-MP2: Total energy	-48826.952583

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.
-88.645	-87.618	-0.012	-0.405	-0.609	-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 : 0.854 / q_NPA : 0.913

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	MET	0	0.067	0.049	3.843	3.896	4.923	-0.012	-0.405	-0.609	-0.002
4	A	4	HIS	0	0.022	0.005	6.760	3.439	3.439	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.926	-0.971	7.684	-29.427	-29.427	0.000	0.000	0.000	0.000
6	A	6	TYR	0	0.027	0.003	9.982	1.581	1.581	0.000	0.000	0.000	0.000
7	A	7	SER	0	-0.044	0.000	11.261	2.133	2.133	0.000	0.000	0.000	0.000
8	A	8	VAL	0	0.022	-0.001	12.977	1.472	1.472	0.000	0.000	0.000	0.000
9	A	9	VAL	0	0.007	0.015	15.012	1.162	1.162	0.000	0.000	0.000	0.000
10	A	10	SER	0	0.037	0.021	15.535	0.973	0.973	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.021	-0.004	16.960	1.357	1.357	0.000	0.000	0.000	0.000
12	A	12	LEU	0	0.030	-0.001	18.914	0.933	0.933	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.010	0.009	19.018	0.868	0.868	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.063	0.028	21.054	0.710	0.710	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.035	-0.023	22.512	0.721	0.721	0.000	0.000	0.000	0.000
16	A	16	CYS	0	-0.052	0.000	24.755	0.661	0.661	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.781	-0.887	25.847	-11.139	-11.139	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.914	-0.945	26.872	-10.594	-10.594	0.000	0.000	0.000	0.000
19	A	19	HIS	0	0.014	-0.013	28.270	0.695	0.695	0.000	0.000	0.000	0.000
20	A	20	ALA	0	0.018	0.016	30.355	0.429	0.429	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.757	0.864	27.999	11.760	11.760	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.891	0.951	32.669	9.794	9.794	0.000	0.000	0.000	0.000
23	A	23	ASN	0	-0.050	-0.041	34.510	0.416	0.416	0.000	0.000	0.000	0.000
24	A	24	GLN	0	-0.082	-0.043	36.439	0.312	0.312	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.057	0.040	35.703	0.171	0.171	0.000	0.000	0.000	0.000
26	A	26	HIS	0	-0.080	-0.050	33.761	-0.164	-0.164	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.873	0.925	33.107	8.378	8.378	0.000	0.000	0.000	0.000
28	A	28	ILE	0	-0.054	-0.025	28.765	-0.161	-0.161	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.888	-0.938	32.131	-8.291	-8.291	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.829	0.894	31.000	9.593	9.593	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.008	0.014	25.384	-0.071	-0.071	0.000	0.000	0.000	0.000
32	A	32	VAL	0	0.018	0.010	28.434	-0.039	-0.039	0.000	0.000	0.000	0.000
33	A	33	VAL	0	0.004	-0.001	22.570	-0.156	-0.156	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.030	0.013	25.711	0.409	0.409	0.000	0.000	0.000	0.000
35	A	35	ILE	0	-0.004	-0.013	20.697	-0.520	-0.520	0.000	0.000	0.000	0.000
36	A	36	GLY	0	0.019	0.028	23.839	0.484	0.484	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.774	-0.871	23.856	-10.678	-10.678	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.799	0.873	24.339	11.102	11.102	0.000	0.000	0.000	0.000
39	A	39	SER	0	0.010	0.008	19.771	-0.474	-0.474	0.000	0.000	0.000	0.000
40	A	40	ALA	0	-0.073	-0.031	18.881	-0.763	-0.763	0.000	0.000	0.000	0.000
41	A	41	MET	0	0.000	0.008	16.373	-0.958	-0.958	0.000	0.000	0.000	0.000
42	A	42	ASP	-1	-0.894	-0.943	17.649	-14.661	-14.661	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.923	0.950	18.951	11.074	11.074	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.015	0.000	21.224	0.025	0.025	0.000	0.000	0.000	0.000
45	A	45	LEU	0	0.037	0.016	13.328	0.053	0.053	0.000	0.000	0.000	0.000
46	A	46	PHE	0	0.019	0.001	16.947	-0.464	-0.464	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.040	0.015	18.114	-0.193	-0.193	0.000	0.000	0.000	0.000
48	A	48	SER	0	0.000	0.010	18.372	0.019	0.019	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.021	0.016	14.877	-0.151	-0.151	0.000	0.000	0.000	0.000
50	A	50	PHE	0	-0.006	-0.023	16.754	-0.196	-0.196	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.878	-0.966	19.444	-12.353	-12.353	0.000	0.000	0.000	0.000
52	A	52	THR	0	-0.077	-0.039	16.746	0.215	0.215	0.000	0.000	0.000	0.000
53	A	53	PHE	0	-0.015	-0.018	13.200	-0.360	-0.360	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.862	0.933	18.906	13.075	13.075	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.972	-1.007	22.335	-12.440	-12.440	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.993	-0.974	18.783	-16.608	-16.608	0.000	0.000	0.000	0.000
57	A	57	SER	0	-0.014	-0.018	22.530	0.252	0.252	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.025	-0.017	25.895	0.132	0.132	0.000	0.000	0.000	0.000
59	A	59	VAL	0	0.042	0.020	28.816	0.103	0.103	0.000	0.000	0.000	0.000
60	A	60	CYS	0	-0.041	-0.009	25.088	0.233	0.233	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.920	0.972	26.736	11.092	11.092	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.920	-0.940	28.526	-9.205	-9.205	0.000	0.000	0.000	0.000
63	A	63	ALA	0	0.005	-0.006	27.988	0.025	0.025	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.003	0.001	28.262	-0.025	-0.025	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.009	0.004	22.344	0.116	0.116	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.868	-0.917	26.668	-9.995	-9.995	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.010	-0.012	23.726	-0.274	-0.274	0.000	0.000	0.000	0.000
68	A	68	VAL	0	0.020	0.008	26.952	0.225	0.225	0.000	0.000	0.000	0.000
69	A	69	ASP	-1	-0.974	-0.981	27.327	-11.359	-11.359	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.799	-0.882	27.277	-9.899	-9.899	0.000	0.000	0.000	0.000
71	A	71	LYS	1	0.858	0.914	28.443	9.352	9.352	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.000	-0.012	27.888	-0.316	-0.316	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.922	-0.969	30.072	-8.574	-8.574	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.035	-0.021	30.097	-0.410	-0.410	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.851	-0.924	31.760	-9.405	-9.405	0.000	0.000	0.000	0.000
76	A	76	CYS	0	-0.047	-0.024	32.946	-0.057	-0.057	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.926	0.969	29.087	10.355	10.355	0.000	0.000	0.000	0.000
78	A	78	ASP	-1	-0.913	-0.953	34.084	-8.368	-8.368	0.000	0.000	0.000	0.000
79	A	79	CYS	0	-0.051	-0.017	37.234	0.355	0.355	0.000	0.000	0.000	0.000
80	A	80	SER	0	-0.024	-0.038	39.458	0.028	0.028	0.000	0.000	0.000	0.000
81	A	81	HIS	0	-0.028	-0.022	38.653	0.242	0.242	0.000	0.000	0.000	0.000
82	A	82	VAL	0	0.044	0.027	34.744	-0.223	-0.223	0.000	0.000	0.000	0.000
83	A	83	PHE	0	-0.046	-0.014	35.933	0.266	0.266	0.000	0.000	0.000	0.000
84	A	84	LYS	1	1.063	1.044	34.887	8.202	8.202	0.000	0.000	0.000	0.000
85	A	85	PRO	0	-0.021	0.000	31.440	0.195	0.195	0.000	0.000	0.000	0.000
86	A	86	ASN	0	-0.043	-0.036	34.418	0.055	0.055	0.000	0.000	0.000	0.000
87	A	87	ALA	0	0.013	0.023	37.307	0.077	0.077	0.000	0.000	0.000	0.000
88	A	88	LEU	0	0.037	0.009	35.731	-0.209	-0.209	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.905	-0.952	37.117	-7.555	-7.555	0.000	0.000	0.000	0.000
90	A	90	TYR	0	0.055	0.027	39.944	-0.087	-0.087	0.000	0.000	0.000	0.000
91	A	91	GLY	0	-0.031	-0.002	37.620	0.064	0.064	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.073	-0.039	37.134	-0.237	-0.237	0.000	0.000	0.000	0.000
93	A	93	CYS	0	-0.041	-0.018	38.060	0.049	0.049	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.908	-0.952	39.696	-7.071	-7.071	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.910	0.949	42.552	7.319	7.319	0.000	0.000	0.000	0.000
96	A	96	CYS	0	0.013	0.004	40.233	0.097	0.097	0.000	0.000	0.000	0.000
97	A	97	HIS	0	0.039	0.035	41.095	-0.201	-0.201	0.000	0.000	0.000	0.000
98	A	98	SER	0	-0.004	-0.013	37.777	-0.076	-0.076	0.000	0.000	0.000	0.000
99	A	99	LYS	1	0.879	0.916	34.672	8.347	8.347	0.000	0.000	0.000	0.000
100	A	100	ASN	0	0.007	0.013	33.122	-0.371	-0.371	0.000	0.000	0.000	0.000
101	A	101	VAL	0	0.007	0.011	32.147	-0.171	-0.171	0.000	0.000	0.000	0.000
102	A	102	ILE	0	0.001	-0.008	27.333	-0.292	-0.292	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.026	-0.018	25.620	0.313	0.313	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.031	-0.005	26.682	-0.432	-0.432	0.000	0.000	0.000	0.000
105	A	105	GLN	0	0.007	0.002	27.189	-0.373	-0.373	0.000	0.000	0.000	0.000
106	A	106	GLY	0	0.026	0.005	26.237	0.289	0.289	0.000	0.000	0.000	0.000
107	A	107	ASN	0	-0.015	-0.016	21.346	0.261	0.261	0.000	0.000	0.000	0.000
108	A	108	GLU	-1	-0.893	-0.942	19.168	-16.343	-16.343	0.000	0.000	0.000	0.000
109	A	109	MET	0	-0.074	-0.021	18.760	0.614	0.614	0.000	0.000	0.000	0.000
110	A	110	ARG	1	0.846	0.906	21.779	10.729	10.729	0.000	0.000	0.000	0.000
111	A	111	LEU	0	0.029	0.013	24.032	0.146	0.146	0.000	0.000	0.000	0.000
112	A	112	LEU	0	-0.072	-0.042	25.912	0.228	0.228	0.000	0.000	0.000	0.000
113	A	113	SER	0	0.010	0.002	29.653	0.299	0.299	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.057	-0.032	27.148	-0.489	-0.489	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.883	-0.930	31.109	-8.615	-8.615	0.000	0.000	0.000	0.000
116	A	116	MET	0	-0.054	-0.037	32.316	-0.210	-0.210	0.000	0.000	0.000	0.000
117	A	117	LEU	0	0.012	0.039	35.407	0.240	0.240	0.000	0.000	0.000	0.000
118	A	118	ALA	0	-0.048	-0.035	37.913	-0.097	-0.097	0.000	0.000	0.000	0.000
119	A	119	GLU	-2	-1.817	-1.875	40.382	-15.055	-15.055	0.000	0.000	0.000	0.000

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