FMO DATABASE

FMODB ID: 646MZ

Calculation Name: 1S3Z-A-Xray547

Preferred Name:

Target Type:

Ligand Name: coenzyme a | ribostamycin | nickel (ii) ion

Ligand 3-letter code: COA | RIO | NI

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1S3Z

Chain ID: A

ChEMBL ID:

UniProt ID: Q9R381

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	147
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1347953.275536
FMO2-HF: Nuclear repulsion	1289067.719215
FMO2-HF: Total energy	-58885.556321
FMO2-MP2: Total energy	-59055.014547

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:SER)

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

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.
-72.663	-70.454	16.191	-10.263	-8.138	-0.112

Interaction energy analysis for fragmet #1(A:-1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.783 / q_NPA : 0.868

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	1	MET	0	-0.006	0.002	3.369	-2.234	-0.597	0.023	-0.783	-0.877	-0.002
52	A	50	ALA	0	0.022	-0.001	3.520	-2.693	-2.338	0.011	-0.158	-0.209	0.001
53	A	51	ASP	-1	-0.844	-0.913	1.725	-105.778	-105.604	16.158	-9.302	-7.030	-0.111
54	A	52	GLY	0	-0.007	0.006	4.643	4.731	4.774	-0.001	-0.020	-0.022	0.000
4	A	2	ASP	-1	-0.833	-0.875	6.056	-27.222	-27.222	0.000	0.000	0.000	0.000
5	A	3	ILE	0	-0.032	-0.020	9.355	0.040	0.040	0.000	0.000	0.000	0.000
6	A	4	ARG	1	0.852	0.914	9.461	26.566	26.566	0.000	0.000	0.000	0.000
7	A	5	GLN	0	0.037	0.020	14.558	0.064	0.064	0.000	0.000	0.000	0.000
8	A	6	MET	0	-0.030	-0.009	18.220	-0.445	-0.445	0.000	0.000	0.000	0.000
9	A	7	ASN	0	0.060	0.041	18.658	0.779	0.779	0.000	0.000	0.000	0.000
10	A	8	LYS	1	0.899	0.929	20.776	10.852	10.852	0.000	0.000	0.000	0.000
11	A	9	THR	0	-0.068	-0.046	18.206	-0.220	-0.220	0.000	0.000	0.000	0.000
12	A	10	HIS	0	-0.006	-0.008	15.222	-0.525	-0.525	0.000	0.000	0.000	0.000
13	A	11	LEU	0	0.067	0.041	18.063	-0.323	-0.323	0.000	0.000	0.000	0.000
14	A	12	GLU	-1	-0.829	-0.899	19.118	-13.409	-13.409	0.000	0.000	0.000	0.000
15	A	13	HIS	0	-0.002	-0.006	13.491	-0.175	-0.175	0.000	0.000	0.000	0.000
16	A	14	TRP	0	-0.042	-0.022	16.545	-0.329	-0.329	0.000	0.000	0.000	0.000
17	A	15	ARG	1	0.885	0.921	18.753	12.717	12.717	0.000	0.000	0.000	0.000
18	A	16	GLY	0	0.005	0.008	18.298	0.361	0.361	0.000	0.000	0.000	0.000
19	A	17	LEU	0	-0.040	-0.018	13.558	-0.037	-0.037	0.000	0.000	0.000	0.000
20	A	18	ARG	1	0.782	0.866	17.906	12.336	12.336	0.000	0.000	0.000	0.000
21	A	19	LYS	1	0.821	0.891	21.357	12.227	12.227	0.000	0.000	0.000	0.000
22	A	20	GLN	0	-0.073	-0.045	16.641	-0.007	-0.007	0.000	0.000	0.000	0.000
23	A	21	LEU	0	-0.087	-0.023	20.931	0.022	0.022	0.000	0.000	0.000	0.000
24	A	22	TRP	0	0.011	0.000	22.406	0.275	0.275	0.000	0.000	0.000	0.000
25	A	23	PRO	0	0.021	0.004	24.867	0.209	0.209	0.000	0.000	0.000	0.000
26	A	24	GLY	0	-0.038	-0.017	27.100	0.238	0.238	0.000	0.000	0.000	0.000
27	A	25	HIS	0	-0.024	-0.008	28.156	0.480	0.480	0.000	0.000	0.000	0.000
28	A	26	PRO	0	0.016	-0.006	29.480	-0.222	-0.222	0.000	0.000	0.000	0.000
29	A	27	ASP	-1	-0.818	-0.892	28.145	-11.224	-11.224	0.000	0.000	0.000	0.000
30	A	28	ASP	-1	-0.876	-0.943	29.560	-9.255	-9.255	0.000	0.000	0.000	0.000
31	A	29	ALA	0	-0.009	0.004	31.258	0.028	0.028	0.000	0.000	0.000	0.000
32	A	30	HIS	0	0.008	0.005	25.363	-0.485	-0.485	0.000	0.000	0.000	0.000
33	A	31	LEU	0	-0.064	-0.027	26.874	-0.402	-0.402	0.000	0.000	0.000	0.000
34	A	32	ALA	0	0.004	0.000	28.835	-0.117	-0.117	0.000	0.000	0.000	0.000
35	A	33	ASP	-1	-0.712	-0.841	27.833	-10.582	-10.582	0.000	0.000	0.000	0.000
36	A	34	GLY	0	0.008	-0.009	25.850	-0.253	-0.253	0.000	0.000	0.000	0.000
37	A	35	GLU	-1	-0.866	-0.941	26.648	-11.124	-11.124	0.000	0.000	0.000	0.000
38	A	36	GLU	-1	-0.951	-0.958	29.195	-9.489	-9.489	0.000	0.000	0.000	0.000
39	A	37	ILE	0	-0.012	-0.021	24.470	-0.026	-0.026	0.000	0.000	0.000	0.000
40	A	38	LEU	0	-0.097	-0.040	23.117	-0.300	-0.300	0.000	0.000	0.000	0.000
41	A	39	GLN	0	-0.061	-0.029	26.714	0.188	0.188	0.000	0.000	0.000	0.000
42	A	40	ALA	0	-0.009	0.017	29.570	0.291	0.291	0.000	0.000	0.000	0.000
43	A	41	ASP	-1	-0.842	-0.901	29.157	-9.696	-9.696	0.000	0.000	0.000	0.000
44	A	42	HIS	1	0.766	0.842	30.310	9.051	9.051	0.000	0.000	0.000	0.000
45	A	43	LEU	0	0.056	0.025	27.690	-0.048	-0.048	0.000	0.000	0.000	0.000
46	A	44	ALA	0	-0.010	0.003	22.904	-0.108	-0.108	0.000	0.000	0.000	0.000
47	A	45	SER	0	0.035	-0.001	20.711	0.153	0.153	0.000	0.000	0.000	0.000
48	A	46	PHE	0	-0.046	-0.025	16.987	-0.475	-0.475	0.000	0.000	0.000	0.000
49	A	47	ILE	0	0.010	-0.006	13.102	-0.117	-0.117	0.000	0.000	0.000	0.000
50	A	48	ALA	0	0.001	-0.004	10.304	-0.782	-0.782	0.000	0.000	0.000	0.000
51	A	49	MET	0	-0.045	-0.008	8.742	0.653	0.653	0.000	0.000	0.000	0.000
55	A	53	VAL	0	-0.018	-0.004	6.675	3.660	3.660	0.000	0.000	0.000	0.000
56	A	54	ALA	0	0.047	0.011	8.296	-2.231	-2.231	0.000	0.000	0.000	0.000
57	A	55	ILE	0	-0.030	-0.025	6.414	0.739	0.739	0.000	0.000	0.000	0.000
58	A	56	GLY	0	0.003	-0.015	10.099	0.938	0.938	0.000	0.000	0.000	0.000
59	A	57	PHE	0	-0.039	-0.006	13.307	-0.833	-0.833	0.000	0.000	0.000	0.000
60	A	58	ALA	0	0.025	0.010	16.326	0.213	0.213	0.000	0.000	0.000	0.000
61	A	59	ASP	-1	-0.693	-0.811	19.588	-13.566	-13.566	0.000	0.000	0.000	0.000
62	A	60	ALA	0	-0.029	-0.025	23.081	0.032	0.032	0.000	0.000	0.000	0.000
63	A	61	SER	0	-0.024	-0.039	25.363	0.151	0.151	0.000	0.000	0.000	0.000
64	A	62	ILE	0	-0.046	-0.020	28.525	-0.143	-0.143	0.000	0.000	0.000	0.000
65	A	63	ARG	1	0.891	0.928	31.303	10.182	10.182	0.000	0.000	0.000	0.000
66	A	64	HIS	0	0.047	0.008	34.225	-0.124	-0.124	0.000	0.000	0.000	0.000
67	A	65	ASP	-1	-0.887	-0.937	37.684	-8.136	-8.136	0.000	0.000	0.000	0.000
68	A	66	TYR	0	-0.033	-0.013	38.148	-0.136	-0.136	0.000	0.000	0.000	0.000
69	A	67	VAL	0	-0.018	-0.010	33.365	-0.120	-0.120	0.000	0.000	0.000	0.000
70	A	68	ASN	0	-0.028	-0.044	35.828	-0.032	-0.032	0.000	0.000	0.000	0.000
71	A	69	GLY	0	0.009	0.009	35.586	-0.281	-0.281	0.000	0.000	0.000	0.000
72	A	70	CYS	0	-0.085	-0.022	34.386	-0.309	-0.309	0.000	0.000	0.000	0.000
73	A	71	ASP	-1	-0.897	-0.949	36.780	-7.883	-7.883	0.000	0.000	0.000	0.000
74	A	72	SER	0	-0.215	-0.143	36.353	0.215	0.215	0.000	0.000	0.000	0.000
75	A	73	SER	0	0.016	0.011	37.067	-0.127	-0.127	0.000	0.000	0.000	0.000
76	A	74	PRO	0	-0.054	-0.038	34.084	0.169	0.169	0.000	0.000	0.000	0.000
77	A	75	VAL	0	0.024	0.000	31.535	-0.120	-0.120	0.000	0.000	0.000	0.000
78	A	76	VAL	0	-0.052	-0.019	26.349	-0.075	-0.075	0.000	0.000	0.000	0.000
79	A	77	PHE	0	0.020	0.004	28.730	-0.062	-0.062	0.000	0.000	0.000	0.000
80	A	78	LEU	0	-0.039	-0.025	21.536	-0.489	-0.489	0.000	0.000	0.000	0.000
81	A	79	GLU	-1	-0.726	-0.807	25.651	-10.343	-10.343	0.000	0.000	0.000	0.000
82	A	80	GLY	0	0.022	0.009	24.016	0.231	0.231	0.000	0.000	0.000	0.000
83	A	81	ILE	0	-0.058	-0.024	17.574	-0.683	-0.683	0.000	0.000	0.000	0.000
84	A	82	PHE	0	0.031	0.015	16.123	0.252	0.252	0.000	0.000	0.000	0.000
85	A	83	VAL	0	-0.016	-0.011	12.091	-1.106	-1.106	0.000	0.000	0.000	0.000
86	A	84	LEU	0	0.069	0.051	11.114	1.234	1.234	0.000	0.000	0.000	0.000
87	A	85	PRO	0	0.020	-0.006	13.185	-1.202	-1.202	0.000	0.000	0.000	0.000
88	A	86	SER	0	0.009	0.004	11.024	0.319	0.319	0.000	0.000	0.000	0.000
89	A	87	PHE	0	0.002	-0.009	5.644	-2.486	-2.486	0.000	0.000	0.000	0.000
90	A	88	ARG	1	0.882	0.945	10.390	16.883	16.883	0.000	0.000	0.000	0.000
91	A	89	GLN	0	-0.021	-0.024	12.174	-0.443	-0.443	0.000	0.000	0.000	0.000
92	A	90	ARG	1	0.943	0.988	4.882	38.716	38.716	0.000	0.000	0.000	0.000
93	A	91	GLY	0	0.029	0.018	8.825	-2.461	-2.461	0.000	0.000	0.000	0.000
94	A	92	VAL	0	0.021	0.005	8.855	1.177	1.177	0.000	0.000	0.000	0.000
95	A	93	ALA	0	0.046	0.014	11.218	0.783	0.783	0.000	0.000	0.000	0.000
96	A	94	LYS	1	0.990	1.010	14.040	18.833	18.833	0.000	0.000	0.000	0.000
97	A	95	GLN	0	-0.011	-0.015	10.076	-0.435	-0.435	0.000	0.000	0.000	0.000
98	A	96	LEU	0	-0.016	0.000	14.116	0.545	0.545	0.000	0.000	0.000	0.000
99	A	97	ILE	0	0.071	0.038	16.224	0.725	0.725	0.000	0.000	0.000	0.000
100	A	98	ALA	0	0.015	0.008	16.946	0.713	0.713	0.000	0.000	0.000	0.000
101	A	99	ALA	0	-0.081	-0.034	16.836	0.238	0.238	0.000	0.000	0.000	0.000
102	A	100	VAL	0	0.048	0.027	18.936	0.675	0.675	0.000	0.000	0.000	0.000
103	A	101	GLN	0	0.082	0.030	22.028	0.193	0.193	0.000	0.000	0.000	0.000
104	A	102	ARG	1	0.873	0.962	16.544	17.903	17.903	0.000	0.000	0.000	0.000
105	A	103	TRP	0	-0.020	-0.002	22.772	0.420	0.420	0.000	0.000	0.000	0.000
106	A	104	GLY	0	0.075	0.023	24.389	0.493	0.493	0.000	0.000	0.000	0.000
107	A	105	THR	0	-0.031	-0.026	26.409	0.501	0.501	0.000	0.000	0.000	0.000
108	A	106	ASN	0	-0.059	-0.040	25.158	0.424	0.424	0.000	0.000	0.000	0.000
109	A	107	LYS	1	0.885	0.956	27.902	11.036	11.036	0.000	0.000	0.000	0.000
110	A	108	GLY	0	-0.021	0.004	30.568	0.346	0.346	0.000	0.000	0.000	0.000
111	A	109	CYS	0	-0.073	-0.016	30.266	0.297	0.297	0.000	0.000	0.000	0.000
112	A	110	ARG	1	0.931	0.958	31.238	8.463	8.463	0.000	0.000	0.000	0.000
113	A	111	GLU	-1	-0.730	-0.814	31.304	-9.136	-9.136	0.000	0.000	0.000	0.000
114	A	112	MET	0	-0.052	-0.028	23.196	-0.357	-0.357	0.000	0.000	0.000	0.000
115	A	113	ALA	0	0.005	0.012	28.627	0.097	0.097	0.000	0.000	0.000	0.000
116	A	114	SER	0	-0.023	-0.047	25.556	-0.372	-0.372	0.000	0.000	0.000	0.000
117	A	115	ASP	-1	-0.882	-0.927	28.307	-9.925	-9.925	0.000	0.000	0.000	0.000
118	A	116	THR	0	-0.017	-0.031	26.660	-0.374	-0.374	0.000	0.000	0.000	0.000
119	A	117	SER	0	0.013	0.023	29.469	0.388	0.388	0.000	0.000	0.000	0.000
120	A	118	PRO	0	0.053	0.009	30.603	-0.306	-0.306	0.000	0.000	0.000	0.000
121	A	119	GLU	-1	-0.872	-0.924	31.949	-9.306	-9.306	0.000	0.000	0.000	0.000
122	A	120	ASN	0	-0.008	0.005	24.903	-0.581	-0.581	0.000	0.000	0.000	0.000
123	A	121	THR	0	0.031	-0.011	27.317	-0.433	-0.433	0.000	0.000	0.000	0.000
124	A	122	ILE	0	-0.046	-0.023	20.836	-0.239	-0.239	0.000	0.000	0.000	0.000
125	A	123	SER	0	0.021	0.020	22.988	-0.248	-0.248	0.000	0.000	0.000	0.000
126	A	124	GLN	0	0.032	0.007	24.148	0.054	0.054	0.000	0.000	0.000	0.000
127	A	125	LYS	1	0.911	0.977	23.219	12.126	12.126	0.000	0.000	0.000	0.000
128	A	126	VAL	0	-0.031	-0.022	19.083	-0.299	-0.299	0.000	0.000	0.000	0.000
129	A	127	HIS	0	0.036	0.028	21.430	-0.498	-0.498	0.000	0.000	0.000	0.000
130	A	128	GLN	0	0.017	0.015	23.880	0.173	0.173	0.000	0.000	0.000	0.000
131	A	129	ALA	0	-0.044	-0.018	20.607	-0.031	-0.031	0.000	0.000	0.000	0.000
132	A	130	LEU	0	-0.136	-0.079	17.310	-0.835	-0.835	0.000	0.000	0.000	0.000
133	A	131	GLY	0	-0.001	0.008	21.313	-0.107	-0.107	0.000	0.000	0.000	0.000
134	A	132	PHE	0	-0.010	-0.003	22.934	0.169	0.169	0.000	0.000	0.000	0.000
135	A	133	GLU	-1	-0.918	-0.962	27.047	-9.942	-9.942	0.000	0.000	0.000	0.000
136	A	134	GLU	-1	-0.845	-0.892	30.460	-9.391	-9.391	0.000	0.000	0.000	0.000
137	A	135	THR	0	0.001	0.017	32.598	0.187	0.187	0.000	0.000	0.000	0.000
138	A	136	GLU	-1	-0.829	-0.919	35.502	-7.865	-7.865	0.000	0.000	0.000	0.000
139	A	137	ARG	1	0.738	0.834	33.001	8.984	8.984	0.000	0.000	0.000	0.000
140	A	138	VAL	0	0.005	0.011	37.751	0.248	0.248	0.000	0.000	0.000	0.000
141	A	139	ILE	0	-0.036	-0.014	38.995	-0.152	-0.152	0.000	0.000	0.000	0.000
142	A	140	PHE	0	0.026	0.018	36.519	0.192	0.192	0.000	0.000	0.000	0.000
143	A	141	TYR	0	0.004	-0.006	41.293	0.088	0.088	0.000	0.000	0.000	0.000
144	A	142	ARG	0	0.079	0.063	42.255	0.134	0.134	0.000	0.000	0.000	0.000
145	A	143	LYS	1	0.908	0.951	44.993	6.219	6.219	0.000	0.000	0.000	0.000
146	A	144	ARG	1	0.857	0.911	45.808	6.703	6.703	0.000	0.000	0.000	0.000
147	A	145	CYS	-1	-0.871	-0.932	48.926	-6.060	-6.060	0.000	0.000	0.000	0.000

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