FMO DATABASE

FMODB ID: 9RG82

Calculation Name: 1PSR-A-Xray547

Preferred Name:

Target Type:

Ligand Name: holmium atom

Ligand 3-letter code: HO

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1PSR

Chain ID: A

ChEMBL ID:

UniProt ID: P31151

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	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-727197.760507
FMO2-HF: Nuclear repulsion	686475.282747
FMO2-HF: Total energy	-40722.47776
FMO2-MP2: Total energy	-40838.003779

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.
-2.55	-0.955	-0.017	-0.673	-0.904	-0.002

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 : 0.842 / q_NPA : 0.909

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	THR	0	0.041	-0.017	3.840	5.136	6.656	-0.016	-0.668	-0.836	-0.002
7	A	7	ARG	1	0.868	0.936	4.465	41.317	41.392	-0.001	-0.005	-0.068	0.000
4	A	4	GLN	0	0.011	-0.009	6.477	-0.270	-0.270	0.000	0.000	0.000	0.000
5	A	5	ALA	0	0.040	0.041	9.420	1.330	1.330	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.757	-0.854	6.511	-45.809	-45.809	0.000	0.000	0.000	0.000
8	A	8	SER	0	-0.010	-0.014	8.939	2.363	2.363	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.001	0.002	12.117	1.413	1.413	0.000	0.000	0.000	0.000
10	A	10	ILE	0	0.002	-0.008	7.649	0.739	0.739	0.000	0.000	0.000	0.000
11	A	11	GLY	0	0.018	0.012	11.680	1.284	1.284	0.000	0.000	0.000	0.000
12	A	12	MET	0	-0.005	-0.003	13.735	1.657	1.657	0.000	0.000	0.000	0.000
13	A	13	ILE	0	-0.017	-0.003	14.567	1.050	1.050	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.943	-0.969	14.566	-17.335	-17.335	0.000	0.000	0.000	0.000
15	A	15	MET	0	-0.035	-0.015	16.524	1.115	1.115	0.000	0.000	0.000	0.000
16	A	16	PHE	0	-0.028	-0.017	19.218	0.876	0.876	0.000	0.000	0.000	0.000
17	A	17	HIS	0	0.017	0.010	19.180	0.607	0.607	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.918	0.979	20.329	14.549	14.549	0.000	0.000	0.000	0.000
19	A	19	TYR	0	-0.072	-0.069	22.055	0.360	0.360	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.031	-0.014	24.004	0.568	0.568	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.812	0.896	26.315	9.602	9.602	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.957	0.957	27.381	9.672	9.672	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.837	-0.912	28.636	-10.336	-10.336	0.000	0.000	0.000	0.000
24	A	24	ASP	-1	-0.896	-0.949	23.109	-13.857	-13.857	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.852	0.915	25.920	10.090	10.090	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.011	0.016	24.437	0.185	0.185	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.769	-0.853	28.670	-9.351	-9.351	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.899	0.931	31.710	8.119	8.119	0.000	0.000	0.000	0.000
29	A	29	PRO	0	-0.015	-0.023	33.332	-0.117	-0.117	0.000	0.000	0.000	0.000
30	A	30	SER	0	0.005	0.002	28.830	-0.136	-0.136	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.041	0.024	27.838	-0.365	-0.365	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.024	-0.022	29.437	-0.181	-0.181	0.000	0.000	0.000	0.000
33	A	33	THR	0	-0.065	-0.042	28.841	0.127	0.127	0.000	0.000	0.000	0.000
34	A	34	MET	0	0.026	0.041	24.160	-0.289	-0.289	0.000	0.000	0.000	0.000
35	A	35	MET	0	0.012	0.004	26.054	-0.451	-0.451	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.896	0.948	28.281	9.385	9.385	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.865	-0.898	25.089	-11.906	-11.906	0.000	0.000	0.000	0.000
38	A	38	ASN	0	-0.075	-0.059	21.829	-0.811	-0.811	0.000	0.000	0.000	0.000
39	A	39	PHE	0	0.012	0.004	22.351	-0.329	-0.329	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.047	0.035	26.066	0.448	0.448	0.000	0.000	0.000	0.000
41	A	41	ASN	0	-0.009	-0.027	25.890	0.683	0.683	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.013	0.006	28.010	0.245	0.245	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.017	0.002	29.863	0.351	0.351	0.000	0.000	0.000	0.000
44	A	44	SER	0	0.036	0.025	32.400	0.400	0.400	0.000	0.000	0.000	0.000
45	A	45	ALA	0	-0.018	-0.010	32.414	0.308	0.308	0.000	0.000	0.000	0.000
46	A	46	CYS	0	-0.085	-0.009	32.429	0.479	0.479	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.853	-0.930	36.153	-8.291	-8.291	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.886	0.947	37.134	8.384	8.384	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.804	0.902	37.485	8.470	8.470	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.013	0.007	40.812	0.113	0.113	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.065	-0.030	38.194	0.100	0.100	0.000	0.000	0.000	0.000
52	A	52	ASN	0	0.081	0.027	38.275	-0.409	-0.409	0.000	0.000	0.000	0.000
53	A	53	TYR	0	0.051	0.003	30.892	0.097	0.097	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.034	-0.024	32.301	-0.154	-0.154	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.056	-0.012	35.853	0.057	0.057	0.000	0.000	0.000	0.000
56	A	56	ASP	-1	-0.800	-0.911	37.772	-8.320	-8.320	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.002	0.008	31.559	-0.092	-0.092	0.000	0.000	0.000	0.000
58	A	58	PHE	0	-0.016	-0.005	32.642	-0.233	-0.233	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.781	-0.885	34.664	-8.451	-8.451	0.000	0.000	0.000	0.000
60	A	60	LYS	1	0.817	0.920	35.839	8.694	8.694	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.744	0.851	29.985	10.292	10.292	0.000	0.000	0.000	0.000
62	A	62	ASP	-1	-0.786	-0.893	32.398	-9.123	-9.123	0.000	0.000	0.000	0.000
63	A	63	LYS	1	0.915	0.958	32.457	10.004	10.004	0.000	0.000	0.000	0.000
64	A	64	ASN	0	-0.085	-0.061	34.235	0.230	0.230	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.929	-0.945	36.709	-7.453	-7.453	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.819	-0.892	34.157	-9.265	-9.265	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.838	0.915	36.881	8.052	8.052	0.000	0.000	0.000	0.000
68	A	68	LYS	1	0.758	0.862	31.554	9.553	9.553	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.024	0.032	27.481	0.030	0.030	0.000	0.000	0.000	0.000
70	A	70	ASP	-1	-0.793	-0.895	27.228	-11.535	-11.535	0.000	0.000	0.000	0.000
71	A	71	PHE	0	0.047	0.005	18.313	-0.197	-0.197	0.000	0.000	0.000	0.000
72	A	72	SER	0	-0.070	-0.051	23.920	-0.219	-0.219	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.776	-0.882	25.899	-10.257	-10.257	0.000	0.000	0.000	0.000
74	A	74	PHE	0	-0.002	-0.003	20.137	0.149	0.149	0.000	0.000	0.000	0.000
75	A	75	LEU	0	-0.012	-0.006	19.835	-0.167	-0.167	0.000	0.000	0.000	0.000
76	A	76	SER	0	-0.012	0.001	23.778	0.178	0.178	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.002	0.006	26.935	0.245	0.245	0.000	0.000	0.000	0.000
78	A	78	LEU	0	-0.008	-0.018	20.371	0.030	0.030	0.000	0.000	0.000	0.000
79	A	79	GLY	0	0.018	0.014	24.357	-0.120	-0.120	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.818	-0.878	25.997	-10.324	-10.324	0.000	0.000	0.000	0.000
81	A	81	ILE	0	-0.023	-0.008	25.299	0.162	0.162	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.003	-0.001	23.225	0.048	0.048	0.000	0.000	0.000	0.000
83	A	83	THR	0	-0.021	-0.022	24.989	0.108	0.108	0.000	0.000	0.000	0.000
84	A	84	ASP	-1	-0.784	-0.861	28.245	-9.681	-9.681	0.000	0.000	0.000	0.000
85	A	85	TYR	0	0.037	0.005	24.972	0.149	0.149	0.000	0.000	0.000	0.000
86	A	86	HIS	0	0.017	0.026	25.930	-0.021	-0.021	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.908	0.971	27.252	9.608	9.608	0.000	0.000	0.000	0.000
88	A	88	GLN	0	-0.024	-0.014	28.775	0.127	0.127	0.000	0.000	0.000	0.000
89	A	89	SER	0	-0.103	-0.059	26.368	0.081	0.081	0.000	0.000	0.000	0.000
90	A	90	HIS	1	0.806	0.879	28.297	10.792	10.792	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.041	0.030	31.717	0.302	0.302	0.000	0.000	0.000	0.000
92	A	92	ALA	0	-0.024	0.005	33.465	0.299	0.299	0.000	0.000	0.000	0.000
93	A	93	ALA	0	0.005	-0.008	33.731	-0.193	-0.193	0.000	0.000	0.000	0.000
94	A	94	PRO	0	0.011	-0.014	31.791	-0.056	-0.056	0.000	0.000	0.000	0.000
95	A	96	SER	0	-0.054	-0.033	33.681	0.358	0.358	0.000	0.000	0.000	0.000
96	A	97	GLY	0	0.031	0.009	34.574	0.274	0.274	0.000	0.000	0.000	0.000
97	A	98	GLY	0	-0.042	-0.023	35.365	-0.195	-0.195	0.000	0.000	0.000	0.000
98	A	99	SER	0	-0.049	-0.044	37.001	-0.181	-0.181	0.000	0.000	0.000	0.000
99	A	100	GLN	-1	-0.914	-0.929	38.921	-7.514	-7.514	0.000	0.000	0.000	0.000

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