FMO DATABASE

FMODB ID: 19G3Z

Calculation Name: 5YOL-F-Xray547

Preferred Name:

Target Type:

Ligand Name: magnesium ion

Ligand 3-letter code: MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5YOL

Chain ID: F

ChEMBL ID:

UniProt ID: V5VIC4

Base Structure: X-ray

Registration Date: 2025-10-06

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	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1253706.759285
FMO2-HF: Nuclear repulsion	1199502.832651
FMO2-HF: Total energy	-54203.926634
FMO2-MP2: Total energy	-54362.406114

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:MET)

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

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.
-121.025	-113.844	1.464	-3.184	-5.46	-0.025

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.845 / 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	ILE	0	-0.007	-0.001	3.050	-11.141	-8.867	0.145	-1.114	-1.305	-0.008
4	A	4	GLU	-1	-0.868	-0.929	3.635	-43.071	-42.061	0.013	-0.346	-0.677	-0.002
80	A	80	GLU	-1	-0.874	-0.949	2.622	-52.531	-51.668	0.414	-0.439	-0.837	-0.004
81	A	81	ASN	0	-0.066	-0.028	2.392	-1.985	0.688	0.879	-1.189	-2.363	-0.010
82	A	82	ALA	0	0.063	0.037	4.019	6.545	6.906	0.013	-0.096	-0.278	-0.001
5	A	5	ARG	1	0.845	0.890	6.460	23.206	23.206	0.000	0.000	0.000	0.000
6	A	6	THR	0	0.022	-0.001	9.720	-0.333	-0.333	0.000	0.000	0.000	0.000
7	A	7	LEU	0	-0.025	0.007	11.992	0.596	0.596	0.000	0.000	0.000	0.000
8	A	8	SER	0	0.001	0.005	15.510	-0.331	-0.331	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.026	-0.020	17.935	0.611	0.611	0.000	0.000	0.000	0.000
10	A	10	VAL	0	0.005	0.014	21.687	-0.082	-0.082	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.905	0.945	23.670	12.856	12.856	0.000	0.000	0.000	0.000
12	A	12	PRO	0	0.063	0.033	26.849	0.032	0.032	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.745	-0.867	28.486	-10.952	-10.952	0.000	0.000	0.000	0.000
14	A	14	ALA	0	-0.004	0.014	26.631	0.174	0.174	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.065	-0.026	28.129	0.014	0.014	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.048	-0.040	30.089	0.229	0.229	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.849	0.916	30.392	10.562	10.562	0.000	0.000	0.000	0.000
18	A	18	ASN	0	-0.060	-0.026	30.936	-0.017	-0.017	0.000	0.000	0.000	0.000
19	A	19	HIS	0	0.016	0.004	26.535	0.049	0.049	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.001	0.002	25.089	-0.540	-0.540	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.023	0.013	23.859	-0.577	-0.577	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.849	-0.926	23.556	-11.997	-11.997	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.007	0.000	20.579	-0.698	-0.698	0.000	0.000	0.000	0.000
24	A	24	PHE	0	-0.018	-0.017	19.499	-0.944	-0.944	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.029	0.021	18.604	-0.970	-0.970	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.769	0.867	17.829	13.727	13.727	0.000	0.000	0.000	0.000
27	A	27	PHE	0	0.045	0.011	14.699	-1.192	-1.192	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.912	-0.956	13.858	-18.355	-18.355	0.000	0.000	0.000	0.000
29	A	29	LYS	1	0.893	0.950	14.939	16.096	16.096	0.000	0.000	0.000	0.000
30	A	30	ALA	0	-0.026	-0.004	11.766	-0.259	-0.259	0.000	0.000	0.000	0.000
31	A	31	GLY	0	-0.011	-0.001	10.484	-2.831	-2.831	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.059	-0.023	8.839	-1.910	-1.910	0.000	0.000	0.000	0.000
33	A	33	LYS	1	0.887	0.944	8.373	35.045	35.045	0.000	0.000	0.000	0.000
34	A	34	ILE	0	0.055	0.030	13.776	-0.503	-0.503	0.000	0.000	0.000	0.000
35	A	35	VAL	0	-0.015	0.002	14.917	0.501	0.501	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.036	0.021	17.635	0.833	0.833	0.000	0.000	0.000	0.000
37	A	37	THR	0	-0.029	-0.032	19.960	-0.276	-0.276	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.809	0.893	22.719	12.986	12.986	0.000	0.000	0.000	0.000
39	A	39	MET	0	0.006	0.017	25.920	-0.033	-0.033	0.000	0.000	0.000	0.000
40	A	40	LYS	1	0.925	0.954	27.028	10.919	10.919	0.000	0.000	0.000	0.000
41	A	41	HIS	0	-0.001	0.014	29.994	-0.162	-0.162	0.000	0.000	0.000	0.000
42	A	42	LEU	0	-0.051	-0.009	26.826	0.034	0.034	0.000	0.000	0.000	0.000
43	A	43	SER	0	-0.001	-0.035	31.334	0.318	0.318	0.000	0.000	0.000	0.000
44	A	44	GLN	0	0.006	-0.023	32.346	-0.130	-0.130	0.000	0.000	0.000	0.000
45	A	45	ALA	0	0.013	0.006	32.534	-0.180	-0.180	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.819	-0.876	28.996	-9.935	-9.935	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.034	0.020	27.795	-0.460	-0.460	0.000	0.000	0.000	0.000
48	A	48	GLU	-1	-0.888	-0.943	27.912	-8.990	-8.990	0.000	0.000	0.000	0.000
49	A	49	GLY	0	-0.010	-0.004	27.860	-0.035	-0.035	0.000	0.000	0.000	0.000
50	A	50	PHE	0	-0.032	-0.003	19.838	-0.285	-0.285	0.000	0.000	0.000	0.000
51	A	51	TYR	0	0.008	-0.009	22.814	-0.392	-0.392	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.027	0.020	25.322	0.226	0.226	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.919	-0.960	20.561	-13.196	-13.196	0.000	0.000	0.000	0.000
54	A	54	HIS	0	-0.006	-0.019	22.113	0.526	0.526	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.883	0.944	27.169	9.349	9.349	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.939	-0.962	30.254	-8.970	-8.970	0.000	0.000	0.000	0.000
57	A	57	ARG	1	0.866	0.946	25.197	10.917	10.917	0.000	0.000	0.000	0.000
58	A	58	GLY	0	0.017	0.000	31.282	0.049	0.049	0.000	0.000	0.000	0.000
59	A	59	PHE	0	0.022	0.008	26.573	0.139	0.139	0.000	0.000	0.000	0.000
60	A	60	PHE	0	-0.005	0.008	28.685	-0.062	-0.062	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.028	0.012	31.462	-0.056	-0.056	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.852	-0.927	33.707	-8.562	-8.562	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.053	-0.015	26.243	-0.134	-0.134	0.000	0.000	0.000	0.000
64	A	64	VAL	0	-0.007	-0.009	30.215	-0.204	-0.204	0.000	0.000	0.000	0.000
65	A	65	ALA	0	0.017	0.023	31.630	0.021	0.021	0.000	0.000	0.000	0.000
66	A	66	PHE	0	0.024	0.011	28.489	0.005	0.005	0.000	0.000	0.000	0.000
67	A	67	MET	0	-0.026	-0.006	25.505	-0.110	-0.110	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.053	-0.040	30.060	-0.049	-0.049	0.000	0.000	0.000	0.000
69	A	69	SER	0	-0.058	-0.029	33.020	0.258	0.258	0.000	0.000	0.000	0.000
70	A	70	GLY	0	-0.012	-0.020	33.474	0.282	0.282	0.000	0.000	0.000	0.000
71	A	71	PRO	0	-0.040	-0.026	31.867	-0.230	-0.230	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.050	0.028	26.308	-0.117	-0.117	0.000	0.000	0.000	0.000
73	A	73	VAL	0	-0.026	-0.022	24.036	0.211	0.211	0.000	0.000	0.000	0.000
74	A	74	VAL	0	0.008	0.024	21.403	-0.564	-0.564	0.000	0.000	0.000	0.000
75	A	75	SER	0	0.027	0.002	19.406	0.435	0.435	0.000	0.000	0.000	0.000
76	A	76	VAL	0	0.000	0.009	14.562	-0.422	-0.422	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.012	0.005	12.899	0.301	0.301	0.000	0.000	0.000	0.000
78	A	78	GLU	-1	-0.798	-0.899	10.674	-24.898	-24.898	0.000	0.000	0.000	0.000
79	A	79	GLY	0	0.010	-0.006	7.853	1.786	1.786	0.000	0.000	0.000	0.000
83	A	83	VAL	0	0.011	0.008	7.124	4.065	4.065	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.020	-0.012	5.535	3.170	3.170	0.000	0.000	0.000	0.000
85	A	85	ALA	0	0.053	0.031	7.317	2.846	2.846	0.000	0.000	0.000	0.000
86	A	86	HIS	0	-0.013	-0.010	9.108	3.644	3.644	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.885	0.945	11.436	22.514	22.514	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.966	-0.973	10.080	-26.889	-26.889	0.000	0.000	0.000	0.000
89	A	89	ILE	0	-0.040	-0.021	12.785	1.749	1.749	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.009	0.002	15.325	1.522	1.522	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.035	0.029	16.441	1.176	1.176	0.000	0.000	0.000	0.000
92	A	92	ALA	0	-0.003	-0.003	18.173	-0.085	-0.085	0.000	0.000	0.000	0.000
93	A	93	THR	0	0.009	-0.011	19.960	0.108	0.108	0.000	0.000	0.000	0.000
94	A	94	ASN	0	-0.014	-0.006	21.881	0.802	0.802	0.000	0.000	0.000	0.000
95	A	95	PRO	0	0.101	0.049	24.290	-0.319	-0.319	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.896	0.953	25.863	9.837	9.837	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.943	-0.966	22.711	-12.486	-12.486	0.000	0.000	0.000	0.000
98	A	98	ALA	0	-0.043	-0.002	21.397	-0.603	-0.603	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.027	0.018	19.368	0.441	0.441	0.000	0.000	0.000	0.000
100	A	100	PRO	0	0.025	0.011	21.460	-0.110	-0.110	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.002	0.008	21.564	-0.531	-0.531	0.000	0.000	0.000	0.000
102	A	102	THR	0	-0.065	-0.043	17.785	-0.601	-0.601	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.007	-0.012	18.165	0.784	0.784	0.000	0.000	0.000	0.000
104	A	104	ARG	1	0.832	0.904	19.135	15.707	15.707	0.000	0.000	0.000	0.000
105	A	105	ALA	0	-0.025	-0.005	22.826	0.582	0.582	0.000	0.000	0.000	0.000
106	A	106	ASP	-1	-0.823	-0.889	23.743	-12.758	-12.758	0.000	0.000	0.000	0.000
107	A	107	PHE	0	-0.043	-0.029	23.027	0.245	0.245	0.000	0.000	0.000	0.000
108	A	108	ALA	0	-0.056	-0.003	25.668	0.264	0.264	0.000	0.000	0.000	0.000
109	A	109	VAL	0	0.002	0.004	27.641	0.211	0.211	0.000	0.000	0.000	0.000
110	A	110	SER	0	-0.028	-0.018	29.767	0.149	0.149	0.000	0.000	0.000	0.000
111	A	111	ILE	0	-0.013	-0.023	26.792	-0.398	-0.398	0.000	0.000	0.000	0.000
112	A	112	ASP	-1	-0.904	-0.938	27.096	-10.275	-10.275	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-0.950	-0.974	28.405	-9.762	-9.762	0.000	0.000	0.000	0.000
114	A	114	ASN	0	0.002	-0.008	23.597	-0.117	-0.117	0.000	0.000	0.000	0.000
115	A	115	ALA	0	0.064	0.032	23.960	-0.720	-0.720	0.000	0.000	0.000	0.000
116	A	116	ALA	0	-0.036	-0.041	20.728	-0.042	-0.042	0.000	0.000	0.000	0.000
117	A	117	HIS	0	-0.076	-0.042	18.061	0.668	0.668	0.000	0.000	0.000	0.000
118	A	118	GLY	0	0.059	0.013	16.224	-0.264	-0.264	0.000	0.000	0.000	0.000
119	A	119	SER	0	-0.064	-0.037	12.966	0.201	0.201	0.000	0.000	0.000	0.000
120	A	120	ASP	-1	-0.839	-0.928	12.891	-18.871	-18.871	0.000	0.000	0.000	0.000
121	A	121	SER	0	-0.049	-0.027	10.075	-1.106	-1.106	0.000	0.000	0.000	0.000
122	A	122	VAL	0	0.062	0.033	5.543	0.834	0.834	0.000	0.000	0.000	0.000
123	A	123	ALA	0	0.036	0.020	8.948	1.027	1.027	0.000	0.000	0.000	0.000
124	A	124	SER	0	-0.014	-0.011	12.124	1.012	1.012	0.000	0.000	0.000	0.000
125	A	125	ALA	0	0.024	0.006	10.826	0.841	0.841	0.000	0.000	0.000	0.000
126	A	126	GLU	-1	-0.938	-0.969	10.490	-20.452	-20.452	0.000	0.000	0.000	0.000
127	A	127	ARG	1	0.846	0.926	13.849	15.031	15.031	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.807	-0.886	16.288	-15.338	-15.338	0.000	0.000	0.000	0.000
129	A	129	ILE	0	-0.028	-0.024	13.151	0.548	0.548	0.000	0.000	0.000	0.000
130	A	130	ALA	0	0.013	0.006	17.227	0.683	0.683	0.000	0.000	0.000	0.000
131	A	131	TYR	0	-0.075	-0.024	19.293	0.769	0.769	0.000	0.000	0.000	0.000
132	A	132	PHE	0	0.005	-0.005	21.016	0.659	0.659	0.000	0.000	0.000	0.000
133	A	133	PHE	0	-0.071	-0.042	19.796	0.412	0.412	0.000	0.000	0.000	0.000
134	A	134	ALA	0	0.041	0.038	20.978	-0.186	-0.186	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.879	-0.956	17.586	-15.817	-15.817	0.000	0.000	0.000	0.000
136	A	136	ASN	0	-0.071	-0.042	20.056	-0.305	-0.305	0.000	0.000	0.000	0.000
137	A	137	GLU	-1	-0.829	-0.905	22.477	-12.063	-12.063	0.000	0.000	0.000	0.000
138	A	138	ILE	0	-0.061	-0.020	16.340	-0.240	-0.240	0.000	0.000	0.000	0.000
139	A	139	CYS	0	-0.033	-0.010	19.776	0.344	0.344	0.000	0.000	0.000	0.000
140	A	140	PRO	0	0.013	0.006	16.662	-0.776	-0.776	0.000	0.000	0.000	0.000
141	A	141	ARG	1	0.851	0.904	15.855	19.159	19.159	0.000	0.000	0.000	0.000
142	A	142	THR	0	-0.020	-0.014	17.536	-0.533	-0.533	0.000	0.000	0.000	0.000
143	A	143	ARG	0	0.028	0.035	19.990	-1.549	-1.549	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:1:MET)