FMO DATABASE

FMODB ID: GRK91

Calculation Name: 9ANT-A-Xray547

Preferred Name:

Target Type:

Ligand Name: nickel (ii) ion

Ligand 3-letter code: NI

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 9ANT

Chain ID: A

ChEMBL ID:

UniProt ID: P02833

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	56
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-371253.53381
FMO2-HF: Nuclear repulsion	346102.819097
FMO2-HF: Total energy	-25150.714713
FMO2-MP2: Total energy	-25225.647843

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:5:ARG)

Summations of interaction energy for fragment #1(A:5:ARG)

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.
243.629	248.021	1.175	-2.133	-3.434	-0.019

Interaction energy analysis for fragmet #1(A:5:ARG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.840 / q_NPA : 1.910

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

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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	7	THR	0	-0.007	-0.016	2.828	-24.992	-20.791	1.174	-2.098	-3.277	-0.019
4	A	8	TYR	0	-0.008	0.005	4.152	6.204	6.395	0.001	-0.035	-0.157	0.000
5	A	9	THR	0	0.063	0.015	7.087	1.195	1.195	0.000	0.000	0.000	0.000
6	A	10	ARG	1	1.003	0.993	10.088	36.289	36.289	0.000	0.000	0.000	0.000
7	A	11	TYR	0	0.066	0.040	12.152	0.985	0.985	0.000	0.000	0.000	0.000
8	A	12	GLN	0	0.066	0.025	10.600	-2.205	-2.205	0.000	0.000	0.000	0.000
9	A	13	THR	0	-0.032	-0.027	9.141	-0.828	-0.828	0.000	0.000	0.000	0.000
10	A	14	LEU	0	0.007	0.005	11.285	1.525	1.525	0.000	0.000	0.000	0.000
11	A	15	GLU	-1	-0.834	-0.899	14.886	-28.212	-28.212	0.000	0.000	0.000	0.000
12	A	16	LEU	0	-0.041	-0.018	11.229	1.026	1.026	0.000	0.000	0.000	0.000
13	A	17	GLU	-1	-0.844	-0.910	13.083	-36.185	-36.185	0.000	0.000	0.000	0.000
14	A	18	LYS	1	0.875	0.921	15.321	30.045	30.045	0.000	0.000	0.000	0.000
15	A	19	GLU	-1	-0.773	-0.856	17.793	-25.823	-25.823	0.000	0.000	0.000	0.000
16	A	20	PHE	0	-0.068	-0.048	16.183	0.926	0.926	0.000	0.000	0.000	0.000
17	A	21	HIS	0	-0.031	-0.002	18.314	0.871	0.871	0.000	0.000	0.000	0.000
18	A	22	PHE	0	-0.022	0.010	21.042	1.151	1.151	0.000	0.000	0.000	0.000
19	A	23	ASN	0	-0.032	-0.022	21.629	1.307	1.307	0.000	0.000	0.000	0.000
20	A	24	ARG	1	0.990	0.993	19.130	24.257	24.257	0.000	0.000	0.000	0.000
21	A	25	TYR	0	-0.030	-0.027	18.951	-2.093	-2.093	0.000	0.000	0.000	0.000
22	A	26	LEU	0	0.023	0.030	17.999	0.718	0.718	0.000	0.000	0.000	0.000
23	A	27	THR	0	0.058	0.025	21.589	-0.112	-0.112	0.000	0.000	0.000	0.000
24	A	28	ARG	1	0.896	0.934	21.326	25.735	25.735	0.000	0.000	0.000	0.000
25	A	29	ARG	1	0.990	0.996	22.504	19.964	19.964	0.000	0.000	0.000	0.000
26	A	30	ARG	1	0.920	0.935	21.734	25.949	25.949	0.000	0.000	0.000	0.000
27	A	31	ARG	1	0.823	0.890	17.028	29.829	29.829	0.000	0.000	0.000	0.000
28	A	32	ILE	0	-0.028	-0.013	18.584	-1.617	-1.617	0.000	0.000	0.000	0.000
29	A	33	GLU	-1	-0.841	-0.909	20.213	-24.925	-24.925	0.000	0.000	0.000	0.000
30	A	34	ILE	0	0.003	-0.001	16.444	-0.687	-0.687	0.000	0.000	0.000	0.000
31	A	35	ALA	0	-0.059	-0.029	15.629	-1.584	-1.584	0.000	0.000	0.000	0.000
32	A	36	HIS	0	0.047	0.016	16.249	-2.354	-2.354	0.000	0.000	0.000	0.000
33	A	37	ALA	0	0.008	0.015	18.719	-0.460	-0.460	0.000	0.000	0.000	0.000
34	A	38	LEU	0	-0.034	-0.014	13.785	-0.604	-0.604	0.000	0.000	0.000	0.000
35	A	39	SER	0	-0.006	0.016	14.069	-2.491	-2.491	0.000	0.000	0.000	0.000
36	A	40	LEU	0	-0.070	-0.026	9.479	-4.440	-4.440	0.000	0.000	0.000	0.000
37	A	41	THR	0	0.054	0.003	10.406	3.395	3.395	0.000	0.000	0.000	0.000
38	A	42	GLU	-1	-0.701	-0.856	12.963	-31.111	-31.111	0.000	0.000	0.000	0.000
39	A	43	ARG	1	0.953	0.977	9.044	49.794	49.794	0.000	0.000	0.000	0.000
40	A	44	GLN	0	0.038	0.030	6.699	4.020	4.020	0.000	0.000	0.000	0.000
41	A	45	ILE	0	0.054	0.046	10.307	-1.465	-1.465	0.000	0.000	0.000	0.000
42	A	46	LYS	1	0.933	0.964	13.649	36.298	36.298	0.000	0.000	0.000	0.000
43	A	47	ILE	0	-0.028	-0.022	8.982	1.020	1.020	0.000	0.000	0.000	0.000
44	A	48	TRP	0	0.020	0.025	8.268	-0.787	-0.787	0.000	0.000	0.000	0.000
45	A	49	PHE	0	0.076	0.025	10.692	0.634	0.634	0.000	0.000	0.000	0.000
46	A	50	GLN	0	-0.080	-0.037	12.935	3.570	3.570	0.000	0.000	0.000	0.000
47	A	51	ASN	0	0.005	-0.012	7.607	4.236	4.236	0.000	0.000	0.000	0.000
48	A	52	ARG	1	0.772	0.887	10.897	37.118	37.118	0.000	0.000	0.000	0.000
49	A	53	ARG	1	0.939	0.961	12.647	34.300	34.300	0.000	0.000	0.000	0.000
50	A	54	MET	0	-0.030	0.008	12.399	2.097	2.097	0.000	0.000	0.000	0.000
51	A	55	LYS	1	0.806	0.885	10.187	41.515	41.515	0.000	0.000	0.000	0.000
52	A	56	TRP	0	0.080	0.026	13.057	1.072	1.072	0.000	0.000	0.000	0.000
53	A	57	LYS	1	0.921	0.937	16.488	31.966	31.966	0.000	0.000	0.000	0.000
54	A	58	LYS	1	0.859	0.931	12.042	38.221	38.221	0.000	0.000	0.000	0.000
55	A	59	GLU	-1	-0.815	-0.887	14.412	-36.498	-36.498	0.000	0.000	0.000	0.000
56	A	60	ASN	-1	-0.925	-0.931	17.465	-24.130	-24.130	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:5:ARG)