FMO DATABASE

FMODB ID: VVZJ1

Calculation Name: 1F9Z-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: 1F9Z

Chain ID: A

ChEMBL ID:

UniProt ID: P0AC81

Base Structure: X-ray

Registration Date: 2025-09-02

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	128
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1045352.204378
FMO2-HF: Nuclear repulsion	995280.423308
FMO2-HF: Total energy	-50071.78107
FMO2-MP2: Total energy	-50217.46313

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.
-144.293	-142.358	-0.019	-0.957	-0.96	-0.003

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 : 0.832 / q_NPA : 0.901

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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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	LEU	0	0.045	0.034	3.873	-0.451	1.484	-0.019	-0.957	-0.960	-0.003
4	A	4	LEU	0	-0.011	-0.003	6.137	0.114	0.114	0.000	0.000	0.000	0.000
5	A	5	HIS	0	-0.003	-0.013	8.760	0.282	0.282	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.018	0.001	11.530	-0.767	-0.767	0.000	0.000	0.000	0.000
7	A	7	MET	0	-0.056	-0.013	14.268	0.907	0.907	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.002	0.016	17.044	0.190	0.190	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.909	0.957	20.663	13.284	13.284	0.000	0.000	0.000	0.000
10	A	10	VAL	0	0.033	0.034	23.879	0.197	0.197	0.000	0.000	0.000	0.000
11	A	11	GLY	0	-0.028	-0.019	26.854	0.048	0.048	0.000	0.000	0.000	0.000
12	A	12	ASP	-1	-0.867	-0.949	29.970	-9.133	-9.133	0.000	0.000	0.000	0.000
13	A	13	LEU	0	0.020	0.017	24.913	-0.204	-0.204	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.024	-0.003	28.266	-0.417	-0.417	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.914	0.947	30.697	9.511	9.511	0.000	0.000	0.000	0.000
16	A	16	SER	0	0.000	-0.012	26.188	-0.099	-0.099	0.000	0.000	0.000	0.000
17	A	17	ILE	0	0.010	0.003	25.693	-0.307	-0.307	0.000	0.000	0.000	0.000
18	A	18	ASP	-1	-0.845	-0.887	27.430	-9.885	-9.885	0.000	0.000	0.000	0.000
19	A	19	PHE	0	0.036	0.017	26.844	0.028	0.028	0.000	0.000	0.000	0.000
20	A	20	TYR	0	0.015	-0.044	22.713	-0.223	-0.223	0.000	0.000	0.000	0.000
21	A	21	THR	0	-0.075	-0.057	25.238	-0.105	-0.105	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.804	0.884	27.175	10.029	10.029	0.000	0.000	0.000	0.000
23	A	23	VAL	0	-0.046	-0.008	30.012	0.267	0.267	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.008	0.002	24.737	0.037	0.037	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.028	0.037	25.809	-0.427	-0.427	0.000	0.000	0.000	0.000
26	A	26	MET	0	-0.072	-0.008	20.688	-0.449	-0.449	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.788	0.886	19.585	15.990	15.990	0.000	0.000	0.000	0.000
28	A	28	LEU	0	0.005	-0.006	22.178	-0.464	-0.464	0.000	0.000	0.000	0.000
29	A	29	LEU	0	-0.072	-0.024	17.107	0.121	0.121	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.773	0.847	15.246	17.877	17.877	0.000	0.000	0.000	0.000
31	A	31	THR	0	0.031	0.005	21.883	-0.342	-0.342	0.000	0.000	0.000	0.000
32	A	32	SER	0	-0.032	-0.010	22.706	-0.186	-0.186	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.832	-0.877	24.854	-10.917	-10.917	0.000	0.000	0.000	0.000
34	A	34	ASN	0	-0.011	-0.002	24.083	0.237	0.237	0.000	0.000	0.000	0.000
35	A	35	PRO	0	0.016	-0.018	27.258	0.193	0.193	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.953	-0.940	28.544	-10.293	-10.293	0.000	0.000	0.000	0.000
37	A	37	TYR	0	-0.100	-0.083	26.409	0.175	0.175	0.000	0.000	0.000	0.000
38	A	38	LYS	1	0.914	0.974	28.628	8.791	8.791	0.000	0.000	0.000	0.000
39	A	39	TYR	0	0.048	0.032	22.684	-0.092	-0.092	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.033	-0.044	26.359	0.156	0.156	0.000	0.000	0.000	0.000
41	A	41	LEU	0	-0.051	-0.009	19.766	-0.043	-0.043	0.000	0.000	0.000	0.000
42	A	42	ALA	0	0.024	0.005	22.378	0.348	0.348	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.018	0.016	14.938	-0.351	-0.351	0.000	0.000	0.000	0.000
44	A	44	VAL	0	0.020	-0.002	19.259	0.607	0.607	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.082	0.029	17.922	-0.900	-0.900	0.000	0.000	0.000	0.000
46	A	46	TYR	0	0.063	0.026	18.541	0.533	0.533	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.021	0.018	17.196	0.911	0.911	0.000	0.000	0.000	0.000
48	A	48	PRO	0	-0.015	-0.014	15.009	0.360	0.360	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.723	-0.824	12.737	-20.760	-20.760	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.048	-0.022	10.791	-2.355	-2.355	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.979	-0.983	9.974	-23.424	-23.424	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.850	-0.929	10.200	-22.359	-22.359	0.000	0.000	0.000	0.000
53	A	53	ALA	0	-0.059	-0.024	10.375	-0.646	-0.646	0.000	0.000	0.000	0.000
54	A	54	VAL	0	-0.011	0.000	11.876	1.707	1.707	0.000	0.000	0.000	0.000
55	A	55	ILE	0	0.034	0.007	14.593	-0.612	-0.612	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.866	-0.930	16.492	-16.876	-16.876	0.000	0.000	0.000	0.000
57	A	57	LEU	0	-0.006	-0.007	18.132	0.313	0.313	0.000	0.000	0.000	0.000
58	A	58	THR	0	0.030	-0.003	20.633	0.111	0.111	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.028	0.026	23.124	0.316	0.316	0.000	0.000	0.000	0.000
60	A	60	ASN	0	-0.005	-0.024	25.471	-0.151	-0.151	0.000	0.000	0.000	0.000
61	A	61	TRP	0	-0.018	-0.026	28.675	0.466	0.466	0.000	0.000	0.000	0.000
62	A	62	GLY	0	-0.027	-0.014	32.114	0.146	0.146	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.071	-0.025	30.441	0.208	0.208	0.000	0.000	0.000	0.000
64	A	64	ASP	-1	-0.895	-0.945	31.283	-8.886	-8.886	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.934	0.968	31.922	9.199	9.199	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.044	0.016	27.546	-0.216	-0.216	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.970	-0.984	29.280	-9.253	-9.253	0.000	0.000	0.000	0.000
68	A	68	LEU	0	-0.002	0.005	24.961	-0.295	-0.295	0.000	0.000	0.000	0.000
69	A	69	GLY	0	-0.011	0.000	25.830	-0.379	-0.379	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.025	-0.035	27.262	0.036	0.036	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.019	-0.004	22.338	-0.041	-0.041	0.000	0.000	0.000	0.000
72	A	72	TYR	0	0.006	0.006	18.511	-0.346	-0.346	0.000	0.000	0.000	0.000
73	A	73	GLY	0	0.007	0.010	21.070	0.540	0.540	0.000	0.000	0.000	0.000
74	A	74	HIS	0	-0.059	-0.052	20.906	0.721	0.721	0.000	0.000	0.000	0.000
75	A	75	ILE	0	-0.004	0.010	17.195	-0.836	-0.836	0.000	0.000	0.000	0.000
76	A	76	ALA	0	0.004	0.001	18.460	0.792	0.792	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.035	-0.015	18.580	-0.934	-0.934	0.000	0.000	0.000	0.000
78	A	78	SER	0	0.031	0.036	20.687	0.543	0.543	0.000	0.000	0.000	0.000
79	A	79	VAL	0	-0.057	-0.037	22.476	0.126	0.126	0.000	0.000	0.000	0.000
80	A	80	ASP	-1	-0.881	-0.938	25.934	-11.915	-11.915	0.000	0.000	0.000	0.000
81	A	81	ASN	0	-0.022	-0.020	28.361	0.457	0.457	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.047	0.021	29.741	0.031	0.031	0.000	0.000	0.000	0.000
83	A	83	ALA	0	0.008	0.000	31.014	0.143	0.143	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.895	-0.954	33.705	-9.289	-9.289	0.000	0.000	0.000	0.000
85	A	85	ALA	0	0.051	0.036	29.951	0.111	0.111	0.000	0.000	0.000	0.000
86	A	86	CYS	0	-0.038	-0.019	31.992	0.057	0.057	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.796	-0.879	33.951	-8.045	-8.045	0.000	0.000	0.000	0.000
88	A	88	LYS	1	0.839	0.945	32.296	9.990	9.990	0.000	0.000	0.000	0.000
89	A	89	ILE	0	0.027	0.003	29.637	0.085	0.085	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.736	0.814	33.753	8.448	8.448	0.000	0.000	0.000	0.000
91	A	91	GLN	0	-0.107	-0.057	37.141	0.242	0.242	0.000	0.000	0.000	0.000
92	A	92	ASN	0	-0.123	-0.070	34.975	0.200	0.200	0.000	0.000	0.000	0.000
93	A	93	GLY	0	-0.021	-0.007	36.138	-0.109	-0.109	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.016	0.020	33.529	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	95	ASN	0	-0.061	-0.042	33.378	0.418	0.418	0.000	0.000	0.000	0.000
96	A	96	VAL	0	0.017	0.010	32.455	-0.370	-0.370	0.000	0.000	0.000	0.000
97	A	97	THR	0	-0.058	-0.040	30.650	0.189	0.189	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.740	0.866	31.041	10.053	10.053	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.741	-0.847	32.461	-8.806	-8.806	0.000	0.000	0.000	0.000
100	A	100	ALA	0	0.014	0.011	32.761	-0.196	-0.196	0.000	0.000	0.000	0.000
101	A	101	GLY	0	0.012	0.002	32.844	0.374	0.374	0.000	0.000	0.000	0.000
102	A	102	PRO	0	0.008	0.024	32.341	-0.314	-0.314	0.000	0.000	0.000	0.000
103	A	103	VAL	0	0.042	0.037	27.990	0.251	0.251	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.940	0.956	31.074	9.107	9.107	0.000	0.000	0.000	0.000
105	A	105	GLY	0	-0.025	-0.016	31.792	-0.179	-0.179	0.000	0.000	0.000	0.000
106	A	106	GLY	0	-0.014	-0.001	30.545	-0.108	-0.108	0.000	0.000	0.000	0.000
107	A	107	THR	0	-0.029	-0.026	30.862	0.180	0.180	0.000	0.000	0.000	0.000
108	A	108	THR	0	0.056	0.038	25.780	0.276	0.276	0.000	0.000	0.000	0.000
109	A	109	VAL	0	-0.006	0.010	29.188	0.197	0.197	0.000	0.000	0.000	0.000
110	A	110	ILE	0	0.021	0.010	26.584	-0.368	-0.368	0.000	0.000	0.000	0.000
111	A	111	ALA	0	0.020	-0.002	28.281	0.543	0.543	0.000	0.000	0.000	0.000
112	A	112	PHE	0	-0.046	-0.015	25.043	-0.424	-0.424	0.000	0.000	0.000	0.000
113	A	113	VAL	0	0.025	0.019	27.598	0.497	0.497	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.902	-0.952	28.135	-9.960	-9.960	0.000	0.000	0.000	0.000
115	A	115	ASP	-1	-0.750	-0.852	25.650	-11.483	-11.483	0.000	0.000	0.000	0.000
116	A	116	PRO	0	-0.019	-0.030	28.532	0.267	0.267	0.000	0.000	0.000	0.000
117	A	117	ASP	-1	-0.837	-0.901	27.706	-10.126	-10.126	0.000	0.000	0.000	0.000
118	A	118	GLY	0	-0.039	-0.008	29.446	0.173	0.173	0.000	0.000	0.000	0.000
119	A	119	TYR	0	-0.088	-0.064	23.214	-0.259	-0.259	0.000	0.000	0.000	0.000
120	A	120	LYS	1	0.894	0.955	24.936	10.688	10.688	0.000	0.000	0.000	0.000
121	A	121	ILE	0	-0.001	-0.005	22.727	-0.599	-0.599	0.000	0.000	0.000	0.000
122	A	122	GLU	-1	-0.886	-0.933	22.467	-12.984	-12.984	0.000	0.000	0.000	0.000
123	A	123	LEU	0	-0.019	-0.017	23.309	-0.469	-0.469	0.000	0.000	0.000	0.000
124	A	124	ILE	0	0.010	-0.010	21.338	0.616	0.616	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.862	-0.936	25.015	-10.567	-10.567	0.000	0.000	0.000	0.000
126	A	126	GLU	-2	-1.914	-1.955	20.957	-28.101	-28.101	0.000	0.000	0.000	0.000
127	A	134	GLY	0	-0.044	-0.044	17.448	-0.316	-0.316	0.000	0.000	0.000	0.000
128	A	135	ASN	-1	-0.956	-0.956	18.434	-14.884	-14.884	0.000	0.000	0.000	0.000

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