FMO DATABASE

FMODB ID: QL72Y

Calculation Name: 1IX1-A-Xray547

Preferred Name: Peptide deformylase

Target Type: SINGLE PROTEIN

Ligand Name: actinonin | (carbamoylmethyl-carboxymethyl-amino)-acetic acid | zinc ion

Ligand 3-letter code: BB2 | MHA | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1IX1

Chain ID: A

ChEMBL ID: CHEMBL1649054

UniProt ID: Q9I7A8

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	169
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1806083.014912
FMO2-HF: Nuclear repulsion	1737221.471018
FMO2-HF: Total energy	-68861.543894
FMO2-MP2: Total energy	-69061.028694

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-352.275	-359.544	37.899	-17.973	-12.658	-0.204

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.707 / q_NPA : 0.828

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	4	LEU	0	-0.006	0.000	3.670	4.641	6.079	0.010	-0.580	-0.868	0.000
29	A	30	GLN	0	0.005	0.003	3.614	5.145	5.379	0.001	-0.057	-0.178	0.000
33	A	34	ASP	-1	-0.825	-0.905	1.716	-121.510	-125.317	16.813	-7.981	-5.026	-0.089
34	A	35	MET	0	-0.081	-0.018	3.305	5.076	5.155	0.007	-0.013	-0.074	-0.001
36	A	37	GLU	-1	-0.877	-0.922	1.812	-128.757	-134.037	21.069	-9.332	-6.457	-0.114
37	A	38	THR	0	-0.020	-0.039	5.271	6.090	6.157	-0.001	-0.010	-0.055	0.000
4	A	5	ASN	0	-0.066	-0.042	5.941	4.533	4.533	0.000	0.000	0.000	0.000
5	A	6	ILE	0	0.057	0.031	9.255	0.296	0.296	0.000	0.000	0.000	0.000
6	A	7	LEU	0	-0.057	-0.016	12.349	1.721	1.721	0.000	0.000	0.000	0.000
7	A	8	GLU	-1	-0.769	-0.877	15.541	-16.288	-16.288	0.000	0.000	0.000	0.000
8	A	9	PHE	0	-0.029	-0.003	18.745	0.826	0.826	0.000	0.000	0.000	0.000
9	A	10	PRO	0	-0.105	-0.072	22.443	0.046	0.046	0.000	0.000	0.000	0.000
10	A	11	ASP	-1	-0.752	-0.862	18.695	-15.661	-15.661	0.000	0.000	0.000	0.000
11	A	12	PRO	0	0.013	-0.004	21.611	-0.100	-0.100	0.000	0.000	0.000	0.000
12	A	13	ARG	1	0.841	0.904	15.634	17.676	17.676	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.026	0.023	17.500	-0.339	-0.339	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.683	0.802	20.064	12.689	12.689	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.083	-0.040	19.507	0.796	0.796	0.000	0.000	0.000	0.000
16	A	17	ILE	0	-0.018	0.000	20.926	-0.432	-0.432	0.000	0.000	0.000	0.000
17	A	18	ALA	0	-0.021	0.005	18.285	-0.033	-0.033	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.934	0.953	19.625	14.920	14.920	0.000	0.000	0.000	0.000
19	A	20	PRO	0	0.021	-0.005	19.444	-0.853	-0.853	0.000	0.000	0.000	0.000
20	A	21	VAL	0	-0.031	-0.009	16.186	-0.319	-0.319	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.930	-0.962	19.228	-12.914	-12.914	0.000	0.000	0.000	0.000
22	A	23	VAL	0	-0.010	-0.008	18.272	0.548	0.548	0.000	0.000	0.000	0.000
23	A	24	VAL	0	0.012	0.017	14.883	-0.858	-0.858	0.000	0.000	0.000	0.000
24	A	25	ASP	-1	-0.881	-0.945	14.370	-20.799	-20.799	0.000	0.000	0.000	0.000
25	A	26	ASP	-1	-0.912	-0.962	12.012	-26.800	-26.800	0.000	0.000	0.000	0.000
26	A	27	ALA	0	0.020	0.010	10.398	-2.631	-2.631	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.067	-0.038	9.820	-2.538	-2.538	0.000	0.000	0.000	0.000
28	A	29	ARG	1	0.893	0.957	10.296	19.452	19.452	0.000	0.000	0.000	0.000
30	A	31	LEU	0	-0.014	-0.009	5.311	-6.771	-6.771	0.000	0.000	0.000	0.000
31	A	32	ILE	0	0.009	-0.005	6.845	-1.448	-1.448	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.882	-0.934	5.351	-38.204	-38.204	0.000	0.000	0.000	0.000
35	A	36	PHE	0	0.025	0.011	6.892	3.892	3.892	0.000	0.000	0.000	0.000
38	A	39	MET	0	-0.051	0.003	7.256	4.833	4.833	0.000	0.000	0.000	0.000
39	A	40	TYR	0	-0.074	-0.086	8.416	2.831	2.831	0.000	0.000	0.000	0.000
40	A	41	GLU	-1	-1.027	-1.003	7.870	-27.732	-27.732	0.000	0.000	0.000	0.000
41	A	42	ALA	0	0.005	0.021	10.126	2.528	2.528	0.000	0.000	0.000	0.000
42	A	43	PRO	0	-0.040	-0.007	12.538	1.613	1.613	0.000	0.000	0.000	0.000
43	A	44	GLY	0	-0.034	-0.044	13.593	1.628	1.628	0.000	0.000	0.000	0.000
44	A	45	ILE	0	0.026	0.017	14.558	-0.723	-0.723	0.000	0.000	0.000	0.000
45	A	46	GLY	0	0.004	-0.007	15.540	0.455	0.455	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.032	-0.007	9.445	-0.848	-0.848	0.000	0.000	0.000	0.000
47	A	48	ALA	0	0.073	0.042	13.154	-0.688	-0.688	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.007	-0.001	11.919	-0.701	-0.701	0.000	0.000	0.000	0.000
49	A	50	THR	0	-0.014	-0.028	12.921	-0.794	-0.794	0.000	0.000	0.000	0.000
50	A	51	GLN	0	0.016	-0.003	13.815	-0.049	-0.049	0.000	0.000	0.000	0.000
51	A	52	VAL	0	0.027	0.031	8.781	0.067	0.067	0.000	0.000	0.000	0.000
52	A	53	ASN	0	-0.037	-0.028	10.434	0.538	0.538	0.000	0.000	0.000	0.000
53	A	54	VAL	0	0.013	0.020	9.294	0.904	0.904	0.000	0.000	0.000	0.000
54	A	55	HIS	0	0.014	0.008	12.644	0.400	0.400	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.948	0.973	13.144	23.210	23.210	0.000	0.000	0.000	0.000
56	A	57	ARG	1	0.838	0.910	16.018	13.562	13.562	0.000	0.000	0.000	0.000
57	A	58	ILE	0	0.033	0.017	11.886	0.487	0.487	0.000	0.000	0.000	0.000
58	A	59	VAL	0	0.011	0.006	14.460	-0.397	-0.397	0.000	0.000	0.000	0.000
59	A	60	VAL	0	-0.018	0.012	10.055	0.415	0.415	0.000	0.000	0.000	0.000
60	A	61	MET	0	-0.002	-0.019	13.250	1.197	1.197	0.000	0.000	0.000	0.000
61	A	62	ASP	-1	-0.737	-0.820	14.203	-20.652	-20.652	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.027	-0.017	16.124	0.173	0.173	0.000	0.000	0.000	0.000
63	A	64	SER	0	-0.028	-0.015	17.438	0.686	0.686	0.000	0.000	0.000	0.000
64	A	65	GLU	-1	-0.953	-0.988	18.479	-13.773	-13.773	0.000	0.000	0.000	0.000
65	A	66	ASP	-1	-0.919	-0.942	17.990	-16.371	-16.371	0.000	0.000	0.000	0.000
66	A	67	LYS	1	0.861	0.943	10.829	24.882	24.882	0.000	0.000	0.000	0.000
67	A	68	SER	0	-0.032	-0.035	14.698	-0.785	-0.785	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.912	-0.943	17.047	-14.015	-14.015	0.000	0.000	0.000	0.000
69	A	70	PRO	0	0.000	0.015	12.807	-0.032	-0.032	0.000	0.000	0.000	0.000
70	A	71	ARG	1	0.805	0.892	14.767	15.922	15.922	0.000	0.000	0.000	0.000
71	A	72	VAL	0	0.019	-0.002	13.003	-1.431	-1.431	0.000	0.000	0.000	0.000
72	A	73	PHE	0	-0.018	-0.005	15.603	1.224	1.224	0.000	0.000	0.000	0.000
73	A	74	ILE	0	0.020	0.006	14.984	-0.847	-0.847	0.000	0.000	0.000	0.000
74	A	75	ASN	0	-0.033	-0.031	17.948	0.657	0.657	0.000	0.000	0.000	0.000
75	A	76	PRO	0	-0.007	0.007	19.182	0.641	0.641	0.000	0.000	0.000	0.000
76	A	77	GLU	-1	-0.891	-0.943	22.092	-11.041	-11.041	0.000	0.000	0.000	0.000
77	A	78	PHE	0	-0.010	-0.029	25.593	-0.187	-0.187	0.000	0.000	0.000	0.000
78	A	79	GLU	-1	-0.891	-0.930	27.805	-9.630	-9.630	0.000	0.000	0.000	0.000
79	A	80	PRO	0	-0.025	-0.026	31.620	-0.063	-0.063	0.000	0.000	0.000	0.000
80	A	81	LEU	0	-0.072	-0.032	33.256	0.247	0.247	0.000	0.000	0.000	0.000
81	A	82	THR	0	-0.063	-0.027	35.237	0.338	0.338	0.000	0.000	0.000	0.000
82	A	83	GLU	-1	-0.954	-0.973	37.202	-7.671	-7.671	0.000	0.000	0.000	0.000
83	A	84	ASP	-1	-0.928	-0.958	38.502	-8.166	-8.166	0.000	0.000	0.000	0.000
84	A	85	MET	0	-0.060	-0.033	34.671	-0.356	-0.356	0.000	0.000	0.000	0.000
85	A	86	ASP	-1	-0.853	-0.926	32.579	-9.490	-9.490	0.000	0.000	0.000	0.000
86	A	87	GLN	0	-0.050	-0.018	32.907	-0.126	-0.126	0.000	0.000	0.000	0.000
87	A	88	TYR	0	-0.001	-0.013	25.786	0.079	0.079	0.000	0.000	0.000	0.000
88	A	89	GLN	0	-0.023	-0.024	28.871	0.201	0.201	0.000	0.000	0.000	0.000
89	A	90	GLU	-1	-0.731	-0.824	25.182	-13.040	-13.040	0.000	0.000	0.000	0.000
90	A	91	GLY	0	0.037	0.008	23.685	0.456	0.456	0.000	0.000	0.000	0.000
91	A	92	CYS	0	-0.121	-0.049	19.679	-0.561	-0.561	0.000	0.000	0.000	0.000
92	A	93	LEU	0	0.105	0.054	13.489	0.580	0.580	0.000	0.000	0.000	0.000
93	A	94	SER	0	0.024	0.004	16.671	-0.254	-0.254	0.000	0.000	0.000	0.000
94	A	95	VAL	0	-0.101	-0.066	18.443	0.964	0.964	0.000	0.000	0.000	0.000
95	A	96	PRO	0	0.074	0.059	18.804	0.670	0.670	0.000	0.000	0.000	0.000
96	A	97	GLY	0	-0.010	-0.015	20.858	0.577	0.577	0.000	0.000	0.000	0.000
97	A	98	PHE	0	-0.091	-0.051	23.826	0.931	0.931	0.000	0.000	0.000	0.000
98	A	99	TYR	0	0.053	0.017	22.605	-0.540	-0.540	0.000	0.000	0.000	0.000
99	A	100	GLU	-1	-0.894	-0.925	27.483	-9.626	-9.626	0.000	0.000	0.000	0.000
100	A	101	ASN	0	0.007	0.009	29.566	-0.423	-0.423	0.000	0.000	0.000	0.000
101	A	102	VAL	0	-0.056	-0.028	28.677	0.155	0.155	0.000	0.000	0.000	0.000
102	A	103	ASP	-1	-0.882	-0.935	31.408	-9.254	-9.254	0.000	0.000	0.000	0.000
103	A	104	ARG	1	0.732	0.818	25.722	11.978	11.978	0.000	0.000	0.000	0.000
104	A	105	PRO	0	0.022	0.007	31.787	0.130	0.130	0.000	0.000	0.000	0.000
105	A	106	GLN	0	0.019	0.020	31.740	-0.245	-0.245	0.000	0.000	0.000	0.000
106	A	107	LYS	1	0.840	0.923	32.103	9.002	9.002	0.000	0.000	0.000	0.000
107	A	108	VAL	0	-0.003	-0.003	27.774	0.206	0.206	0.000	0.000	0.000	0.000
108	A	109	ARG	1	0.832	0.894	29.934	9.760	9.760	0.000	0.000	0.000	0.000
109	A	110	ILE	0	0.012	0.009	23.253	0.033	0.033	0.000	0.000	0.000	0.000
110	A	111	LYS	1	0.882	0.937	26.130	10.766	10.766	0.000	0.000	0.000	0.000
111	A	112	ALA	0	-0.013	-0.003	20.832	-0.377	-0.377	0.000	0.000	0.000	0.000
112	A	113	LEU	0	-0.022	-0.002	20.079	0.586	0.586	0.000	0.000	0.000	0.000
113	A	114	ASP	-1	-0.738	-0.877	19.322	-15.998	-15.998	0.000	0.000	0.000	0.000
114	A	115	ARG	1	0.879	0.921	14.843	18.822	18.822	0.000	0.000	0.000	0.000
115	A	116	ASP	-1	-0.953	-0.983	15.764	-18.540	-18.540	0.000	0.000	0.000	0.000
116	A	117	GLY	0	-0.024	-0.020	18.537	0.156	0.156	0.000	0.000	0.000	0.000
117	A	118	ASN	0	-0.074	-0.029	20.358	0.993	0.993	0.000	0.000	0.000	0.000
118	A	119	PRO	0	-0.014	-0.009	23.028	-0.388	-0.388	0.000	0.000	0.000	0.000
119	A	120	PHE	0	-0.041	-0.018	20.817	0.433	0.433	0.000	0.000	0.000	0.000
120	A	121	GLU	-1	-0.817	-0.909	25.999	-10.282	-10.282	0.000	0.000	0.000	0.000
121	A	122	GLU	-1	-0.873	-0.946	23.439	-13.608	-13.608	0.000	0.000	0.000	0.000
122	A	123	VAL	0	-0.065	-0.028	27.297	0.147	0.147	0.000	0.000	0.000	0.000
123	A	124	ALA	0	0.019	0.015	26.415	-0.151	-0.151	0.000	0.000	0.000	0.000
124	A	125	GLU	-1	-0.817	-0.922	28.389	-9.143	-9.143	0.000	0.000	0.000	0.000
125	A	126	GLY	0	0.055	0.031	28.418	-0.380	-0.380	0.000	0.000	0.000	0.000
126	A	127	LEU	0	0.011	-0.001	22.836	-0.112	-0.112	0.000	0.000	0.000	0.000
127	A	128	LEU	0	0.024	0.019	22.221	-0.454	-0.454	0.000	0.000	0.000	0.000
128	A	129	ALA	0	0.003	0.012	24.447	-0.324	-0.324	0.000	0.000	0.000	0.000
129	A	130	VAL	0	0.014	0.015	25.330	-0.048	-0.048	0.000	0.000	0.000	0.000
130	A	131	CYS	0	-0.011	0.003	19.672	-0.398	-0.398	0.000	0.000	0.000	0.000
131	A	132	ILE	0	0.038	0.003	20.925	-0.473	-0.473	0.000	0.000	0.000	0.000
132	A	133	GLN	0	-0.005	-0.014	22.580	0.117	0.117	0.000	0.000	0.000	0.000
133	A	134	HIS	0	0.015	0.009	19.692	-0.617	-0.617	0.000	0.000	0.000	0.000
134	A	135	GLU	-1	-0.853	-0.954	16.733	-18.911	-18.911	0.000	0.000	0.000	0.000
135	A	136	CYS	0	-0.022	-0.017	19.561	-0.366	-0.366	0.000	0.000	0.000	0.000
136	A	137	ASP	-1	-0.810	-0.878	22.020	-11.990	-11.990	0.000	0.000	0.000	0.000
137	A	138	HIS	0	0.001	0.000	18.253	0.137	0.137	0.000	0.000	0.000	0.000
138	A	139	LEU	0	-0.032	0.010	16.643	-0.046	-0.046	0.000	0.000	0.000	0.000
139	A	140	ASN	0	0.001	0.008	20.247	0.208	0.208	0.000	0.000	0.000	0.000
140	A	141	GLY	0	0.000	0.025	22.271	0.615	0.615	0.000	0.000	0.000	0.000
141	A	142	LYS	1	0.867	0.937	23.441	11.730	11.730	0.000	0.000	0.000	0.000
142	A	143	LEU	0	0.051	0.015	21.293	-0.543	-0.543	0.000	0.000	0.000	0.000
143	A	144	PHE	0	0.115	0.052	23.597	0.541	0.541	0.000	0.000	0.000	0.000
144	A	145	VAL	0	0.013	-0.001	25.976	0.601	0.601	0.000	0.000	0.000	0.000
145	A	146	ASP	-1	-0.824	-0.885	27.460	-11.320	-11.320	0.000	0.000	0.000	0.000
146	A	147	TYR	0	-0.039	-0.023	27.527	0.579	0.579	0.000	0.000	0.000	0.000
147	A	148	LEU	0	0.010	0.036	29.807	0.387	0.387	0.000	0.000	0.000	0.000
148	A	149	SER	0	0.024	0.010	33.409	0.046	0.046	0.000	0.000	0.000	0.000
149	A	150	THR	0	0.040	0.005	35.060	-0.270	-0.270	0.000	0.000	0.000	0.000
150	A	151	LEU	0	0.028	0.008	35.034	-0.213	-0.213	0.000	0.000	0.000	0.000
151	A	152	LYS	1	0.798	0.896	32.482	9.617	9.617	0.000	0.000	0.000	0.000
152	A	153	ARG	1	0.954	0.963	29.500	9.874	9.874	0.000	0.000	0.000	0.000
153	A	154	ASP	-1	-0.810	-0.902	30.384	-9.888	-9.888	0.000	0.000	0.000	0.000
154	A	155	ARG	1	0.888	0.948	31.987	8.919	8.919	0.000	0.000	0.000	0.000
155	A	156	ILE	0	0.027	0.019	26.838	-0.018	-0.018	0.000	0.000	0.000	0.000
156	A	157	ARG	1	0.908	0.963	27.380	10.334	10.334	0.000	0.000	0.000	0.000
157	A	158	LYS	1	0.838	0.912	27.892	9.380	9.380	0.000	0.000	0.000	0.000
158	A	159	LYS	1	0.900	0.967	27.931	9.886	9.886	0.000	0.000	0.000	0.000
159	A	160	LEU	0	0.084	0.056	22.256	0.009	0.009	0.000	0.000	0.000	0.000
160	A	161	GLU	-1	-0.899	-0.966	24.299	-10.994	-10.994	0.000	0.000	0.000	0.000
161	A	162	LYS	1	0.855	0.934	26.292	9.947	9.947	0.000	0.000	0.000	0.000
162	A	163	GLN	0	0.037	0.007	23.127	0.422	0.422	0.000	0.000	0.000	0.000
163	A	164	HIS	1	0.861	0.909	20.353	14.505	14.505	0.000	0.000	0.000	0.000
164	A	165	ARG	1	0.914	0.962	22.678	10.496	10.496	0.000	0.000	0.000	0.000
165	A	166	GLN	0	-0.028	-0.026	25.581	0.178	0.178	0.000	0.000	0.000	0.000
166	A	167	GLN	0	0.059	0.019	19.312	0.277	0.277	0.000	0.000	0.000	0.000
167	A	168	ALA	0	-0.025	-0.002	21.134	-0.323	-0.323	0.000	0.000	0.000	0.000
168	A	169	HIS	0	-0.126	-0.061	22.503	0.618	0.618	0.000	0.000	0.000	0.000
169	A	170	HIS	-1	-0.926	-0.941	21.074	-13.167	-13.167	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)