FMO DATABASE

FMODB ID: JY9V9

Calculation Name: 5U1A-B-Xray547

Preferred Name:

Target Type:

Ligand Name: glycerol | fe (iii) ion | chloride ion

Ligand 3-letter code: GOL | FE | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5U1A

Chain ID: B

ChEMBL ID:

UniProt ID: Q51006

Base Structure: X-ray

Registration Date: 2025-10-04

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	167
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1742988.546336
FMO2-HF: Nuclear repulsion	1675251.915274
FMO2-HF: Total energy	-67736.631063
FMO2-MP2: Total energy	-67934.771682

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:LEU)

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

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.
-155.064	-139.877	13.355	-10.759	-17.783	-0.099

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.864 / q_NPA : 0.945

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	LYS	1	1.003	0.982	3.349	31.165	32.983	0.028	-0.903	-0.943	0.000
5	A	6	ILE	0	0.004	0.005	2.463	1.128	2.050	1.376	-0.459	-1.840	-0.003
6	A	7	ILE	0	0.007	0.003	2.256	1.520	2.574	1.545	-0.653	-1.947	-0.004
7	A	8	LYS	1	0.912	0.964	4.351	25.908	26.031	0.000	-0.031	-0.092	0.000
9	A	10	LEU	0	0.051	0.025	2.706	1.287	1.861	0.269	-0.137	-0.706	-0.001
61	A	75	PHE	0	0.062	0.035	2.373	-4.692	-3.198	1.114	-0.843	-1.765	-0.011
62	A	76	LEU	0	-0.016	-0.007	2.917	-6.264	-5.640	0.132	-0.130	-0.626	-0.001
63	A	77	ASN	0	0.004	-0.005	5.029	-2.689	-2.668	-0.001	-0.002	-0.017	0.000
65	A	79	ASN	0	-0.122	-0.065	2.560	-8.889	-6.868	1.417	-1.126	-2.312	-0.011
66	A	80	ASN	0	-0.074	-0.035	4.382	-3.350	-3.247	-0.001	-0.024	-0.078	0.000
67	A	81	VAL	0	-0.037	-0.022	2.317	-1.890	-1.795	1.590	-0.351	-1.333	-0.002
114	A	128	ASP	-1	-0.804	-0.878	2.110	-86.945	-82.691	5.309	-5.168	-4.395	-0.056
116	A	130	ALA	0	0.006	0.017	4.173	3.058	3.143	-0.001	-0.011	-0.073	0.000
117	A	131	THR	0	0.029	-0.011	2.746	-1.280	0.706	0.579	-0.914	-1.650	-0.010
118	A	132	PHE	0	-0.027	-0.014	5.027	4.004	4.017	-0.001	-0.007	-0.006	0.000
4	A	5	ASP	-1	-0.878	-0.927	6.045	-28.313	-28.313	0.000	0.000	0.000	0.000
8	A	9	LEU	0	-0.004	-0.004	7.422	2.104	2.104	0.000	0.000	0.000	0.000
10	A	11	ASN	0	0.019	0.008	6.463	3.978	3.978	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.885	-0.935	8.508	-17.700	-17.700	0.000	0.000	0.000	0.000
12	A	13	GLN	0	-0.001	-0.010	9.811	1.377	1.377	0.000	0.000	0.000	0.000
13	A	14	VAL	0	0.006	0.009	9.072	1.345	1.345	0.000	0.000	0.000	0.000
14	A	15	ASN	0	0.022	-0.005	11.674	2.142	2.142	0.000	0.000	0.000	0.000
15	A	16	LYS	1	0.877	0.952	14.065	19.059	19.059	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.737	-0.830	14.002	-15.328	-15.328	0.000	0.000	0.000	0.000
17	A	18	MET	0	-0.032	-0.012	14.596	0.958	0.958	0.000	0.000	0.000	0.000
18	A	19	ASN	0	-0.032	-0.035	18.051	1.322	1.322	0.000	0.000	0.000	0.000
19	A	20	SER	0	0.017	0.008	18.873	0.763	0.763	0.000	0.000	0.000	0.000
20	A	21	SER	0	-0.038	-0.023	20.286	0.649	0.649	0.000	0.000	0.000	0.000
21	A	22	ASN	0	0.021	-0.004	22.022	0.543	0.543	0.000	0.000	0.000	0.000
22	A	23	LEU	0	-0.004	0.000	23.904	0.543	0.543	0.000	0.000	0.000	0.000
23	A	24	TYR	0	-0.031	-0.053	23.129	0.635	0.635	0.000	0.000	0.000	0.000
24	A	25	MET	0	-0.009	0.001	25.266	0.525	0.525	0.000	0.000	0.000	0.000
25	A	26	SER	0	-0.072	-0.064	28.217	0.483	0.483	0.000	0.000	0.000	0.000
26	A	27	MET	0	-0.006	-0.004	28.666	0.264	0.264	0.000	0.000	0.000	0.000
27	A	28	SER	0	-0.028	-0.021	30.467	0.358	0.358	0.000	0.000	0.000	0.000
28	A	29	SER	0	0.002	-0.007	32.229	0.353	0.353	0.000	0.000	0.000	0.000
29	A	30	TRP	0	0.012	0.007	34.113	0.157	0.157	0.000	0.000	0.000	0.000
30	A	31	CYS	0	-0.032	-0.005	34.492	0.212	0.212	0.000	0.000	0.000	0.000
31	A	32	TYR	0	-0.024	-0.013	34.114	0.309	0.309	0.000	0.000	0.000	0.000
32	A	33	THR	0	-0.125	-0.065	37.932	0.206	0.206	0.000	0.000	0.000	0.000
33	A	34	GLY	-1	-0.882	-0.917	39.123	-7.127	-7.127	0.000	0.000	0.000	0.000
34	A	48	SER	0	-0.041	-0.034	47.128	-0.048	-0.048	0.000	0.000	0.000	0.000
35	A	49	TYR	0	-0.028	-0.016	42.763	0.104	0.104	0.000	0.000	0.000	0.000
36	A	50	SER	0	0.011	0.003	41.046	-0.036	-0.036	0.000	0.000	0.000	0.000
37	A	51	LEU	0	-0.045	-0.016	38.763	0.130	0.130	0.000	0.000	0.000	0.000
38	A	52	ASP	-1	-0.780	-0.900	37.754	-7.544	-7.544	0.000	0.000	0.000	0.000
39	A	53	GLY	0	-0.023	-0.016	36.595	-0.205	-0.205	0.000	0.000	0.000	0.000
40	A	54	CYS	0	-0.045	-0.026	34.442	-0.262	-0.262	0.000	0.000	0.000	0.000
41	A	55	GLY	0	0.048	0.021	33.050	-0.287	-0.287	0.000	0.000	0.000	0.000
42	A	56	THR	0	-0.060	-0.031	32.325	-0.279	-0.279	0.000	0.000	0.000	0.000
43	A	57	PHE	0	0.021	0.006	28.399	-0.297	-0.297	0.000	0.000	0.000	0.000
44	A	58	LEU	0	-0.018	-0.006	28.640	-0.416	-0.416	0.000	0.000	0.000	0.000
45	A	59	PHE	0	-0.005	0.001	27.506	-0.405	-0.405	0.000	0.000	0.000	0.000
46	A	60	ASP	-1	-0.813	-0.914	26.645	-10.051	-10.051	0.000	0.000	0.000	0.000
47	A	61	HIS	1	0.789	0.885	22.034	11.684	11.684	0.000	0.000	0.000	0.000
48	A	62	ALA	0	0.017	-0.002	22.893	-0.557	-0.557	0.000	0.000	0.000	0.000
49	A	63	ALA	0	-0.010	0.011	22.219	-0.531	-0.531	0.000	0.000	0.000	0.000
50	A	64	GLU	-1	-0.836	-0.922	18.853	-14.472	-14.472	0.000	0.000	0.000	0.000
51	A	65	GLU	0	0.019	0.003	18.316	-0.727	-0.727	0.000	0.000	0.000	0.000
52	A	66	TYR	0	-0.021	-0.010	17.072	-0.949	-0.949	0.000	0.000	0.000	0.000
53	A	67	GLU	-1	-0.811	-0.886	16.623	-14.767	-14.767	0.000	0.000	0.000	0.000
54	A	68	HIS	1	0.764	0.874	14.329	13.968	13.968	0.000	0.000	0.000	0.000
55	A	69	ALA	0	0.005	-0.002	12.596	-1.462	-1.462	0.000	0.000	0.000	0.000
56	A	70	LYS	1	0.798	0.876	11.919	12.864	12.864	0.000	0.000	0.000	0.000
57	A	71	LYS	1	0.892	0.968	10.917	17.455	17.455	0.000	0.000	0.000	0.000
58	A	72	LEU	0	-0.019	-0.006	7.908	-2.245	-2.245	0.000	0.000	0.000	0.000
59	A	73	ILE	0	-0.006	-0.007	7.056	-2.715	-2.715	0.000	0.000	0.000	0.000
60	A	74	VAL	0	-0.030	-0.001	8.499	-1.295	-1.295	0.000	0.000	0.000	0.000
64	A	78	GLU	-1	-0.941	-0.969	7.397	-24.929	-24.929	0.000	0.000	0.000	0.000
68	A	82	PRO	0	-0.036	-0.024	5.469	2.979	2.979	0.000	0.000	0.000	0.000
69	A	83	VAL	0	0.032	0.024	8.092	-1.158	-1.158	0.000	0.000	0.000	0.000
70	A	84	GLN	0	-0.064	-0.032	9.490	2.651	2.651	0.000	0.000	0.000	0.000
71	A	85	LEU	0	0.018	0.011	11.781	-0.163	-0.163	0.000	0.000	0.000	0.000
72	A	86	THR	0	-0.042	-0.036	14.288	0.117	0.117	0.000	0.000	0.000	0.000
73	A	87	SER	0	-0.025	-0.014	16.958	0.380	0.380	0.000	0.000	0.000	0.000
74	A	88	ILE	0	-0.025	-0.005	17.148	-0.501	-0.501	0.000	0.000	0.000	0.000
75	A	89	SER	0	-0.027	-0.019	20.959	0.502	0.502	0.000	0.000	0.000	0.000
76	A	90	ALA	0	-0.004	-0.001	23.947	0.011	0.011	0.000	0.000	0.000	0.000
77	A	91	PRO	0	-0.016	0.010	26.428	-0.114	-0.114	0.000	0.000	0.000	0.000
78	A	92	GLU	-1	-0.836	-0.909	27.589	-8.620	-8.620	0.000	0.000	0.000	0.000
79	A	93	HIS	0	-0.035	0.000	30.587	0.166	0.166	0.000	0.000	0.000	0.000
80	A	94	LYS	1	0.904	0.954	33.592	7.904	7.904	0.000	0.000	0.000	0.000
81	A	95	PHE	0	0.013	-0.012	30.786	-0.213	-0.213	0.000	0.000	0.000	0.000
82	A	96	GLU	-1	-0.894	-0.935	36.658	-7.524	-7.524	0.000	0.000	0.000	0.000
83	A	97	GLY	0	0.031	0.012	38.599	0.231	0.231	0.000	0.000	0.000	0.000
84	A	98	LEU	0	0.007	0.003	36.697	-0.190	-0.190	0.000	0.000	0.000	0.000
85	A	99	THR	0	0.033	0.012	36.759	-0.178	-0.178	0.000	0.000	0.000	0.000
86	A	100	GLN	0	0.041	0.010	35.911	-0.265	-0.265	0.000	0.000	0.000	0.000
87	A	101	ILE	0	-0.063	-0.010	32.409	-0.278	-0.278	0.000	0.000	0.000	0.000
88	A	102	PHE	0	0.034	-0.002	31.248	-0.332	-0.332	0.000	0.000	0.000	0.000
89	A	103	GLN	0	-0.044	-0.018	31.477	-0.259	-0.259	0.000	0.000	0.000	0.000
90	A	104	LYS	1	0.961	0.975	29.962	8.654	8.654	0.000	0.000	0.000	0.000
91	A	105	ALA	0	0.000	0.007	27.519	-0.371	-0.371	0.000	0.000	0.000	0.000
92	A	106	TYR	0	0.014	0.006	26.598	-0.321	-0.321	0.000	0.000	0.000	0.000
93	A	107	GLU	-1	-0.924	-0.963	26.648	-10.019	-10.019	0.000	0.000	0.000	0.000
94	A	108	HIS	0	-0.081	-0.045	21.126	-0.195	-0.195	0.000	0.000	0.000	0.000
95	A	109	GLU	-1	-0.760	-0.860	22.254	-13.211	-13.211	0.000	0.000	0.000	0.000
96	A	110	GLN	0	0.003	0.020	21.643	-0.478	-0.478	0.000	0.000	0.000	0.000
97	A	111	HIS	1	0.840	0.902	21.270	11.674	11.674	0.000	0.000	0.000	0.000
98	A	112	ILE	0	0.005	0.028	16.732	-0.912	-0.912	0.000	0.000	0.000	0.000
99	A	113	SER	0	0.032	-0.017	17.097	-1.264	-1.264	0.000	0.000	0.000	0.000
100	A	114	GLU	-1	-0.934	-0.944	17.309	-14.180	-14.180	0.000	0.000	0.000	0.000
101	A	115	SER	0	-0.101	-0.060	15.060	-1.033	-1.033	0.000	0.000	0.000	0.000
102	A	116	ILE	0	0.034	0.015	12.280	-1.642	-1.642	0.000	0.000	0.000	0.000
103	A	117	ASN	0	0.032	0.006	12.345	-2.070	-2.070	0.000	0.000	0.000	0.000
104	A	118	ASN	0	0.007	0.013	12.736	-0.256	-0.256	0.000	0.000	0.000	0.000
105	A	119	ILE	0	-0.015	-0.004	7.304	-1.668	-1.668	0.000	0.000	0.000	0.000
106	A	120	VAL	0	0.014	0.010	8.883	-2.726	-2.726	0.000	0.000	0.000	0.000
107	A	121	ASP	-1	-0.788	-0.885	10.802	-20.127	-20.127	0.000	0.000	0.000	0.000
108	A	122	HIS	0	-0.013	-0.021	8.833	-0.443	-0.443	0.000	0.000	0.000	0.000
109	A	123	ALA	0	-0.026	0.013	6.926	-2.301	-2.301	0.000	0.000	0.000	0.000
110	A	124	ILE	0	-0.020	-0.001	8.051	-0.658	-0.658	0.000	0.000	0.000	0.000
111	A	125	LYS	1	0.786	0.880	11.214	19.088	19.088	0.000	0.000	0.000	0.000
112	A	126	SER	0	-0.088	-0.077	6.576	-1.136	-1.136	0.000	0.000	0.000	0.000
113	A	127	LYS	1	0.926	0.971	7.509	22.248	22.248	0.000	0.000	0.000	0.000
115	A	129	HIS	0	0.017	-0.024	5.532	1.581	1.581	0.000	0.000	0.000	0.000
119	A	133	ASN	0	-0.042	-0.015	8.457	2.292	2.292	0.000	0.000	0.000	0.000
120	A	134	PHE	0	0.024	0.015	6.334	1.995	1.995	0.000	0.000	0.000	0.000
121	A	135	LEU	0	-0.005	-0.010	7.347	1.824	1.824	0.000	0.000	0.000	0.000
122	A	136	GLN	0	-0.054	-0.022	10.210	2.916	2.916	0.000	0.000	0.000	0.000
123	A	137	TRP	0	0.010	-0.005	12.842	0.355	0.355	0.000	0.000	0.000	0.000
124	A	138	TYR	0	-0.028	-0.057	10.800	0.139	0.139	0.000	0.000	0.000	0.000
125	A	139	VAL	0	0.013	-0.005	13.616	0.730	0.730	0.000	0.000	0.000	0.000
126	A	140	SER	0	-0.016	-0.003	15.995	0.949	0.949	0.000	0.000	0.000	0.000
127	A	141	GLU	-1	-0.856	-0.926	17.223	-13.441	-13.441	0.000	0.000	0.000	0.000
128	A	142	GLN	0	-0.003	-0.005	17.250	0.244	0.244	0.000	0.000	0.000	0.000
129	A	143	HIS	0	-0.001	0.002	19.208	0.362	0.362	0.000	0.000	0.000	0.000
130	A	144	GLU	-1	-0.956	-0.981	21.861	-11.411	-11.411	0.000	0.000	0.000	0.000
131	A	145	GLU	-1	-0.797	-0.856	20.003	-13.168	-13.168	0.000	0.000	0.000	0.000
132	A	146	GLU	-1	-0.841	-0.908	23.153	-11.677	-11.677	0.000	0.000	0.000	0.000
133	A	147	VAL	0	-0.004	-0.012	24.885	0.548	0.548	0.000	0.000	0.000	0.000
134	A	148	LEU	0	-0.034	-0.004	26.856	0.478	0.478	0.000	0.000	0.000	0.000
135	A	149	PHE	0	-0.002	-0.022	25.642	0.434	0.434	0.000	0.000	0.000	0.000
136	A	150	LYS	1	0.813	0.903	29.124	9.205	9.205	0.000	0.000	0.000	0.000
137	A	151	ASP	-1	-0.793	-0.865	31.091	-8.183	-8.183	0.000	0.000	0.000	0.000
138	A	152	ILE	0	-0.007	-0.004	30.834	0.339	0.339	0.000	0.000	0.000	0.000
139	A	153	LEU	0	-0.023	0.001	32.861	0.252	0.252	0.000	0.000	0.000	0.000
140	A	154	ASP	-1	-0.770	-0.868	34.787	-8.305	-8.305	0.000	0.000	0.000	0.000
141	A	155	LYS	1	0.808	0.893	36.785	8.318	8.318	0.000	0.000	0.000	0.000
142	A	156	ILE	0	-0.043	-0.016	35.755	0.249	0.249	0.000	0.000	0.000	0.000
143	A	157	GLU	-1	-0.906	-0.960	38.102	-7.797	-7.797	0.000	0.000	0.000	0.000
144	A	158	LEU	0	-0.080	-0.026	40.822	0.189	0.189	0.000	0.000	0.000	0.000
145	A	159	ILE	0	-0.090	-0.033	41.401	0.198	0.198	0.000	0.000	0.000	0.000
146	A	160	GLY	0	0.030	0.027	43.514	0.186	0.186	0.000	0.000	0.000	0.000
147	A	161	ASN	0	-0.037	-0.045	44.597	-0.055	-0.055	0.000	0.000	0.000	0.000
148	A	162	GLU	-1	-0.900	-0.940	46.293	-5.818	-5.818	0.000	0.000	0.000	0.000
149	A	163	ASN	0	-0.037	-0.020	49.672	-0.084	-0.084	0.000	0.000	0.000	0.000
150	A	164	HIS	0	0.030	0.010	49.103	-0.004	-0.004	0.000	0.000	0.000	0.000
151	A	165	GLY	0	0.018	0.014	46.570	-0.097	-0.097	0.000	0.000	0.000	0.000
152	A	166	LEU	0	0.071	0.018	42.288	-0.145	-0.145	0.000	0.000	0.000	0.000
153	A	167	TYR	0	0.001	0.006	42.696	-0.128	-0.128	0.000	0.000	0.000	0.000
154	A	168	LEU	0	-0.041	-0.022	43.610	-0.089	-0.089	0.000	0.000	0.000	0.000
155	A	169	ALA	0	0.048	0.028	39.868	-0.120	-0.120	0.000	0.000	0.000	0.000
156	A	170	ASP	-1	-0.742	-0.871	38.845	-7.802	-7.802	0.000	0.000	0.000	0.000
157	A	171	GLN	0	0.002	-0.008	38.941	-0.230	-0.230	0.000	0.000	0.000	0.000
158	A	172	TYR	0	-0.070	-0.053	35.734	0.033	0.033	0.000	0.000	0.000	0.000
159	A	173	VAL	0	0.047	0.019	33.568	-0.158	-0.158	0.000	0.000	0.000	0.000
160	A	174	LYS	1	0.799	0.909	34.780	7.071	7.071	0.000	0.000	0.000	0.000
161	A	175	GLY	0	-0.061	-0.018	36.409	-0.062	-0.062	0.000	0.000	0.000	0.000
162	A	176	ILE	0	0.011	0.006	31.446	-0.134	-0.134	0.000	0.000	0.000	0.000
163	A	177	ALA	0	0.007	0.006	31.376	-0.230	-0.230	0.000	0.000	0.000	0.000
164	A	178	LYS	1	0.900	0.940	31.848	7.468	7.468	0.000	0.000	0.000	0.000
165	A	179	SER	0	-0.100	-0.047	32.942	-0.027	-0.027	0.000	0.000	0.000	0.000
166	A	180	ARG	1	0.943	0.966	24.483	10.787	10.787	0.000	0.000	0.000	0.000
167	A	181	LYS	0	-0.083	-0.012	27.951	-0.454	-0.454	0.000	0.000	0.000	0.000

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