FMO DATABASE

FMODB ID: 3K57L

Calculation Name: 2F1R-B-Xray547

Preferred Name:

Target Type:

Ligand Name: praseodymium ion | chloride ion

Ligand 3-letter code: PR | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2F1R

Chain ID: B

ChEMBL ID:

UniProt ID: O28031

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1359551.423493
FMO2-HF: Nuclear repulsion	1300909.165402
FMO2-HF: Total energy	-58642.25809
FMO2-MP2: Total energy	-58815.697867

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:3:LEU)

Summations of interaction energy for fragment #1(A:3: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.
-210.773	-198.407	20.511	-14.225	-18.655	-0.143

Interaction energy analysis for fragmet #1(A:3:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.817 / q_NPA : 0.917

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	5	LEU	0	-0.009	-0.002	2.479	0.870	4.227	1.993	-1.417	-3.934	-0.010
4	A	6	SER	0	-0.012	-0.013	3.895	1.783	1.903	0.005	-0.026	-0.099	0.000
84	A	97	ASP	-1	-0.808	-0.882	4.193	-48.005	-47.552	-0.001	-0.254	-0.198	-0.001
85	A	98	LEU	0	-0.004	-0.003	1.836	-44.819	-45.416	12.342	-6.233	-5.512	-0.067
86	A	99	VAL	0	0.003	0.000	3.444	14.257	14.953	0.003	-0.245	-0.454	0.000
87	A	100	ILE	0	0.033	0.018	4.694	-1.538	-1.512	-0.001	-0.022	-0.003	0.000
97	A	110	ASP	-1	-0.756	-0.862	4.304	-26.706	-26.586	-0.001	-0.007	-0.112	0.000
117	A	130	LEU	0	-0.018	-0.002	4.699	0.713	0.796	-0.001	-0.003	-0.079	0.000
143	A	156	ILE	0	-0.007	-0.021	2.786	-2.270	-1.803	0.142	-0.095	-0.515	0.000
144	A	157	LEU	0	0.028	0.005	3.868	-5.904	-5.488	0.008	-0.114	-0.311	-0.001
146	A	159	LEU	0	-0.124	-0.058	2.320	1.639	1.780	2.332	-0.677	-1.796	0.000
147	A	160	LEU	-1	-0.928	-0.945	2.412	-111.217	-104.133	3.690	-5.132	-5.642	-0.064
5	A	7	ILE	0	0.002	0.006	7.167	0.892	0.892	0.000	0.000	0.000	0.000
6	A	8	VAL	0	-0.020	-0.019	10.254	1.222	1.222	0.000	0.000	0.000	0.000
7	A	9	GLY	0	0.082	0.033	13.483	0.185	0.185	0.000	0.000	0.000	0.000
8	A	10	THR	0	0.005	0.014	16.918	0.033	0.033	0.000	0.000	0.000	0.000
9	A	11	SER	0	0.038	-0.004	18.894	-0.311	-0.311	0.000	0.000	0.000	0.000
10	A	12	ASP	-1	-0.835	-0.910	19.435	-13.909	-13.909	0.000	0.000	0.000	0.000
11	A	13	SER	0	0.054	0.025	19.013	-0.665	-0.665	0.000	0.000	0.000	0.000
12	A	14	GLY	0	0.025	0.014	19.411	-0.225	-0.225	0.000	0.000	0.000	0.000
13	A	15	LYS	1	0.787	0.892	14.558	15.255	15.255	0.000	0.000	0.000	0.000
14	A	16	THR	0	-0.004	-0.029	14.808	-0.517	-0.517	0.000	0.000	0.000	0.000
15	A	17	THR	0	-0.040	-0.012	16.104	-0.381	-0.381	0.000	0.000	0.000	0.000
16	A	18	LEU	0	0.025	0.021	11.834	-0.045	-0.045	0.000	0.000	0.000	0.000
17	A	19	ILE	0	-0.003	-0.008	10.764	-0.679	-0.679	0.000	0.000	0.000	0.000
18	A	20	THR	0	-0.053	-0.059	12.369	-0.555	-0.555	0.000	0.000	0.000	0.000
19	A	21	ARG	1	0.889	0.942	15.138	14.390	14.390	0.000	0.000	0.000	0.000
20	A	22	MET	0	-0.006	0.005	8.853	-0.077	-0.077	0.000	0.000	0.000	0.000
21	A	23	MET	0	-0.022	0.009	10.288	-1.295	-1.295	0.000	0.000	0.000	0.000
22	A	24	PRO	0	-0.010	-0.009	12.403	-0.915	-0.915	0.000	0.000	0.000	0.000
23	A	25	ILE	0	0.083	0.048	12.291	-0.463	-0.463	0.000	0.000	0.000	0.000
24	A	26	LEU	0	-0.015	-0.015	6.631	-0.784	-0.784	0.000	0.000	0.000	0.000
25	A	27	ARG	1	0.835	0.901	10.023	22.676	22.676	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.949	-0.970	12.542	-17.109	-17.109	0.000	0.000	0.000	0.000
27	A	29	ARG	1	0.822	0.916	10.788	21.601	21.601	0.000	0.000	0.000	0.000
28	A	30	GLY	0	0.011	0.010	12.043	-0.872	-0.872	0.000	0.000	0.000	0.000
29	A	31	LEU	0	0.010	0.028	5.869	-0.584	-0.584	0.000	0.000	0.000	0.000
30	A	32	ARG	1	0.780	0.877	8.120	31.369	31.369	0.000	0.000	0.000	0.000
31	A	33	VAL	0	0.000	-0.008	6.811	-4.578	-4.578	0.000	0.000	0.000	0.000
32	A	34	ALA	0	-0.002	0.012	7.622	4.074	4.074	0.000	0.000	0.000	0.000
33	A	35	VAL	0	-0.022	-0.020	8.903	-2.187	-2.187	0.000	0.000	0.000	0.000
34	A	36	VAL	0	0.015	0.011	10.398	2.154	2.154	0.000	0.000	0.000	0.000
35	A	37	LYS	1	0.885	0.930	12.174	16.310	16.310	0.000	0.000	0.000	0.000
36	A	38	ARG	1	0.796	0.895	14.863	15.980	15.980	0.000	0.000	0.000	0.000
37	A	39	HIS	0	-0.055	-0.030	16.937	0.000	0.000	0.000	0.000	0.000	0.000
38	A	40	ALA	-1	-0.826	-0.892	20.673	-13.072	-13.072	0.000	0.000	0.000	0.000
39	A	52	ASP	-1	-0.912	-0.945	34.020	-8.934	-8.934	0.000	0.000	0.000	0.000
40	A	53	SER	0	0.032	0.002	29.802	0.159	0.159	0.000	0.000	0.000	0.000
41	A	54	TRP	0	0.043	0.025	31.763	-0.039	-0.039	0.000	0.000	0.000	0.000
42	A	55	LYS	1	0.999	0.971	32.845	8.059	8.059	0.000	0.000	0.000	0.000
43	A	56	ILE	0	0.001	0.014	32.799	0.104	0.104	0.000	0.000	0.000	0.000
44	A	57	TYR	0	0.029	0.027	26.743	0.198	0.198	0.000	0.000	0.000	0.000
45	A	58	ASN	0	-0.068	-0.024	31.969	0.203	0.203	0.000	0.000	0.000	0.000
46	A	59	SER	0	-0.073	-0.049	34.942	0.146	0.146	0.000	0.000	0.000	0.000
47	A	60	GLY	0	0.027	0.012	34.137	0.187	0.187	0.000	0.000	0.000	0.000
48	A	61	ALA	0	-0.030	0.002	32.175	-0.226	-0.226	0.000	0.000	0.000	0.000
49	A	62	ASP	-1	-0.793	-0.889	26.456	-11.958	-11.958	0.000	0.000	0.000	0.000
50	A	63	VAL	0	-0.038	-0.028	27.066	0.240	0.240	0.000	0.000	0.000	0.000
51	A	64	VAL	0	0.006	0.008	23.927	-0.579	-0.579	0.000	0.000	0.000	0.000
52	A	65	ILE	0	-0.040	-0.018	25.410	0.581	0.581	0.000	0.000	0.000	0.000
53	A	66	ALA	0	0.025	0.007	25.192	-0.601	-0.601	0.000	0.000	0.000	0.000
54	A	67	SER	0	-0.036	-0.034	25.600	0.541	0.541	0.000	0.000	0.000	0.000
55	A	68	PRO	0	0.029	0.001	25.966	-0.399	-0.399	0.000	0.000	0.000	0.000
56	A	69	VAL	0	0.013	0.013	23.682	-0.146	-0.146	0.000	0.000	0.000	0.000
57	A	70	LYS	1	0.951	0.978	21.417	13.110	13.110	0.000	0.000	0.000	0.000
58	A	71	LEU	0	0.016	0.032	20.372	0.695	0.695	0.000	0.000	0.000	0.000
59	A	72	ALA	0	-0.019	-0.008	20.739	-0.703	-0.703	0.000	0.000	0.000	0.000
60	A	73	PHE	0	0.003	-0.012	19.650	0.525	0.525	0.000	0.000	0.000	0.000
61	A	74	ILE	0	-0.010	0.000	21.608	-0.479	-0.479	0.000	0.000	0.000	0.000
62	A	75	ARG	1	0.825	0.894	20.566	14.904	14.904	0.000	0.000	0.000	0.000
63	A	76	ARG	1	0.842	0.905	24.375	10.398	10.398	0.000	0.000	0.000	0.000
64	A	77	VAL	0	-0.037	-0.008	20.766	-0.441	-0.441	0.000	0.000	0.000	0.000
65	A	78	SER	0	-0.002	-0.023	24.042	0.292	0.292	0.000	0.000	0.000	0.000
66	A	79	GLU	-1	-0.906	-0.954	23.592	-11.890	-11.890	0.000	0.000	0.000	0.000
67	A	80	GLU	-1	-0.865	-0.910	21.726	-12.952	-12.952	0.000	0.000	0.000	0.000
68	A	81	GLU	-1	-0.798	-0.896	19.698	-14.741	-14.741	0.000	0.000	0.000	0.000
69	A	82	GLY	0	-0.009	-0.006	18.687	-0.941	-0.941	0.000	0.000	0.000	0.000
70	A	83	ASN	0	-0.110	-0.073	18.025	-0.698	-0.698	0.000	0.000	0.000	0.000
71	A	84	ASP	-1	-0.830	-0.899	14.737	-20.600	-20.600	0.000	0.000	0.000	0.000
72	A	85	LEU	0	-0.017	-0.026	8.747	-0.328	-0.328	0.000	0.000	0.000	0.000
73	A	86	ASP	-1	-0.803	-0.861	9.523	-30.614	-30.614	0.000	0.000	0.000	0.000
74	A	87	TRP	0	0.016	0.010	11.592	-0.660	-0.660	0.000	0.000	0.000	0.000
75	A	88	ILE	0	-0.044	-0.033	12.445	0.036	0.036	0.000	0.000	0.000	0.000
76	A	89	TYR	0	-0.034	-0.011	4.841	-0.200	-0.200	0.000	0.000	0.000	0.000
77	A	90	GLU	-1	-0.857	-0.949	9.612	-29.939	-29.939	0.000	0.000	0.000	0.000
78	A	91	ARG	1	0.828	0.925	11.385	18.449	18.449	0.000	0.000	0.000	0.000
79	A	92	TYR	0	-0.058	-0.035	12.810	1.931	1.931	0.000	0.000	0.000	0.000
80	A	93	LEU	0	-0.024	-0.013	8.518	0.560	0.560	0.000	0.000	0.000	0.000
81	A	94	SER	0	0.038	0.030	7.647	-4.150	-4.150	0.000	0.000	0.000	0.000
82	A	95	ASP	-1	-0.843	-0.899	7.949	-28.018	-28.018	0.000	0.000	0.000	0.000
83	A	96	TYR	0	-0.078	-0.040	6.453	2.983	2.983	0.000	0.000	0.000	0.000
88	A	101	THR	0	0.016	0.011	6.842	1.756	1.756	0.000	0.000	0.000	0.000
89	A	102	GLU	-1	-0.803	-0.874	9.400	-17.149	-17.149	0.000	0.000	0.000	0.000
90	A	103	GLY	0	-0.020	-0.019	12.579	1.116	1.116	0.000	0.000	0.000	0.000
91	A	104	PHE	0	0.046	0.001	11.623	-1.252	-1.252	0.000	0.000	0.000	0.000
92	A	105	SER	0	0.011	0.000	12.622	-0.840	-0.840	0.000	0.000	0.000	0.000
93	A	106	LYS	1	0.967	0.979	13.348	14.527	14.527	0.000	0.000	0.000	0.000
94	A	107	ALA	0	0.029	0.027	11.434	0.579	0.579	0.000	0.000	0.000	0.000
95	A	108	GLY	0	-0.001	0.010	11.254	-1.076	-1.076	0.000	0.000	0.000	0.000
96	A	109	LYS	1	0.826	0.892	6.323	29.748	29.748	0.000	0.000	0.000	0.000
98	A	111	ARG	1	0.749	0.853	6.095	19.455	19.455	0.000	0.000	0.000	0.000
99	A	112	ILE	0	0.009	0.022	6.484	0.985	0.985	0.000	0.000	0.000	0.000
100	A	113	VAL	0	-0.020	-0.010	9.357	0.245	0.245	0.000	0.000	0.000	0.000
101	A	114	VAL	0	0.006	0.002	13.112	0.366	0.366	0.000	0.000	0.000	0.000
102	A	115	VAL	0	-0.022	-0.010	15.464	0.399	0.399	0.000	0.000	0.000	0.000
103	A	116	LYS	1	0.843	0.923	19.100	11.883	11.883	0.000	0.000	0.000	0.000
104	A	117	LYS	1	0.886	0.931	22.682	10.455	10.455	0.000	0.000	0.000	0.000
105	A	118	PRO	0	0.047	0.009	21.302	-0.425	-0.425	0.000	0.000	0.000	0.000
106	A	119	GLU	-1	-0.830	-0.904	21.617	-10.393	-10.393	0.000	0.000	0.000	0.000
107	A	120	GLU	-1	-0.822	-0.908	21.270	-11.964	-11.964	0.000	0.000	0.000	0.000
108	A	121	VAL	0	0.031	0.011	16.478	-0.462	-0.462	0.000	0.000	0.000	0.000
109	A	122	GLU	-1	-0.819	-0.891	18.188	-13.367	-13.367	0.000	0.000	0.000	0.000
110	A	123	HIS	0	-0.015	0.004	20.213	0.225	0.225	0.000	0.000	0.000	0.000
111	A	124	PHE	0	-0.007	0.005	14.996	-0.211	-0.211	0.000	0.000	0.000	0.000
112	A	125	ARG	1	0.842	0.910	14.522	11.437	11.437	0.000	0.000	0.000	0.000
113	A	126	GLN	0	-0.025	-0.015	14.440	-0.439	-0.439	0.000	0.000	0.000	0.000
114	A	127	GLY	0	0.081	0.041	10.917	-0.382	-0.382	0.000	0.000	0.000	0.000
115	A	128	ARG	1	0.846	0.919	7.309	25.204	25.204	0.000	0.000	0.000	0.000
116	A	129	ILE	0	-0.002	0.004	8.773	-1.683	-1.683	0.000	0.000	0.000	0.000
118	A	131	ALA	0	-0.026	-0.025	8.968	0.488	0.488	0.000	0.000	0.000	0.000
119	A	132	VAL	0	-0.011	0.004	11.039	-0.237	-0.237	0.000	0.000	0.000	0.000
120	A	133	VAL	0	-0.006	0.007	12.446	0.304	0.304	0.000	0.000	0.000	0.000
121	A	134	CYS	0	-0.053	-0.026	15.221	0.492	0.492	0.000	0.000	0.000	0.000
122	A	135	ASP	-1	-0.758	-0.870	19.049	-12.533	-12.533	0.000	0.000	0.000	0.000
123	A	136	GLU	-1	-0.921	-0.972	22.097	-10.044	-10.044	0.000	0.000	0.000	0.000
124	A	137	ARG	1	0.882	0.917	21.836	10.163	10.163	0.000	0.000	0.000	0.000
125	A	138	VAL	0	-0.017	-0.004	18.034	0.244	0.244	0.000	0.000	0.000	0.000
126	A	139	ASP	-1	-0.803	-0.885	20.300	-11.083	-11.083	0.000	0.000	0.000	0.000
127	A	140	GLY	0	-0.024	-0.025	19.867	-0.255	-0.255	0.000	0.000	0.000	0.000
128	A	141	HIS	0	0.020	0.016	14.865	-1.103	-1.103	0.000	0.000	0.000	0.000
129	A	142	LYS	1	0.912	0.968	10.510	19.842	19.842	0.000	0.000	0.000	0.000
130	A	143	TRP	0	-0.060	-0.029	13.762	-0.321	-0.321	0.000	0.000	0.000	0.000
131	A	144	PHE	0	0.026	0.012	10.517	-0.297	-0.297	0.000	0.000	0.000	0.000
132	A	145	ARG	1	0.907	0.956	15.908	12.120	12.120	0.000	0.000	0.000	0.000
133	A	146	ARG	1	0.805	0.872	17.026	11.830	11.830	0.000	0.000	0.000	0.000
134	A	147	ASP	-1	-0.834	-0.910	17.257	-13.614	-13.614	0.000	0.000	0.000	0.000
135	A	148	GLU	-1	-0.953	-0.964	16.237	-14.463	-14.463	0.000	0.000	0.000	0.000
136	A	149	VAL	0	-0.008	-0.023	13.820	-0.939	-0.939	0.000	0.000	0.000	0.000
137	A	150	GLU	-1	-0.883	-0.934	12.515	-17.774	-17.774	0.000	0.000	0.000	0.000
138	A	151	ARG	1	0.957	0.979	12.367	14.025	14.025	0.000	0.000	0.000	0.000
139	A	152	ILE	0	-0.026	-0.004	9.333	-1.146	-1.146	0.000	0.000	0.000	0.000
140	A	153	ALA	0	0.046	0.010	8.263	-2.215	-2.215	0.000	0.000	0.000	0.000
141	A	154	GLU	-1	-0.876	-0.942	7.746	-21.923	-21.923	0.000	0.000	0.000	0.000
142	A	155	PHE	0	-0.029	-0.018	7.587	-1.085	-1.085	0.000	0.000	0.000	0.000
145	A	158	SER	0	-0.070	-0.033	6.360	0.228	0.228	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LEU)