FMO DATABASE

FMODB ID: Z98VN

Calculation Name: 1J5Y-A-Xray549

Preferred Name:

Target Type:

Ligand Name: nickel (ii) ion | potassium ion

Ligand 3-letter code: NI | K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1J5Y

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X1T8

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	172
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1658820.390829
FMO2-HF: Nuclear repulsion	1591425.691974
FMO2-HF: Total energy	-67394.698855
FMO2-MP2: Total energy	-67590.946411

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:MET)

Summations of interaction energy for fragment #1(A:3: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.
43.764	48.191	2.635	-1.928	-5.134	-0.007

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.898 / q_NPA : 0.937

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	THR	0	0.093	0.049	2.918	-1.230	1.609	0.179	-1.095	-1.922	-0.004
4	A	6	VAL	0	0.085	0.044	2.283	1.024	2.183	2.457	-0.754	-2.862	-0.003
5	A	7	ARG	1	0.924	0.970	4.024	53.932	54.361	-0.001	-0.079	-0.350	0.000
6	A	8	GLN	0	0.026	0.010	6.401	3.180	3.180	0.000	0.000	0.000	0.000
7	A	9	GLU	-1	-0.873	-0.943	5.808	-31.869	-31.869	0.000	0.000	0.000	0.000
8	A	10	ARG	1	0.834	0.901	6.276	38.220	38.220	0.000	0.000	0.000	0.000
9	A	11	LEU	0	0.002	0.001	10.111	2.514	2.514	0.000	0.000	0.000	0.000
10	A	12	LYS	1	0.891	0.922	11.247	23.321	23.321	0.000	0.000	0.000	0.000
11	A	13	SER	0	-0.046	-0.031	12.441	2.092	2.092	0.000	0.000	0.000	0.000
12	A	14	ILE	0	-0.009	-0.002	13.150	1.385	1.385	0.000	0.000	0.000	0.000
13	A	15	VAL	0	0.016	0.019	16.366	1.154	1.154	0.000	0.000	0.000	0.000
14	A	16	ARG	1	0.953	0.973	13.426	20.302	20.302	0.000	0.000	0.000	0.000
15	A	17	ILE	0	-0.042	-0.015	16.945	0.829	0.829	0.000	0.000	0.000	0.000
16	A	18	LEU	0	-0.038	-0.025	20.020	0.745	0.745	0.000	0.000	0.000	0.000
17	A	19	GLU	0	-0.048	-0.046	22.169	0.654	0.654	0.000	0.000	0.000	0.000
18	A	20	ARG	1	0.873	0.939	19.169	15.289	15.289	0.000	0.000	0.000	0.000
19	A	21	SER	0	-0.055	-0.021	25.160	0.595	0.595	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.971	0.979	26.871	9.682	9.682	0.000	0.000	0.000	0.000
21	A	23	GLU	-1	-0.944	-0.958	28.899	-9.718	-9.718	0.000	0.000	0.000	0.000
22	A	24	PRO	0	-0.041	-0.010	26.800	-0.432	-0.432	0.000	0.000	0.000	0.000
23	A	25	VAL	0	0.063	0.043	21.731	0.090	0.090	0.000	0.000	0.000	0.000
24	A	26	SER	0	0.045	0.020	23.077	-0.547	-0.547	0.000	0.000	0.000	0.000
25	A	27	GLY	0	0.016	-0.023	19.836	-0.528	-0.528	0.000	0.000	0.000	0.000
26	A	28	ALA	0	-0.040	-0.012	18.945	-0.854	-0.854	0.000	0.000	0.000	0.000
27	A	29	GLN	0	0.076	0.037	19.729	-0.117	-0.117	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.022	-0.013	16.722	-0.688	-0.688	0.000	0.000	0.000	0.000
29	A	31	ALA	0	-0.043	-0.028	15.135	-1.261	-1.261	0.000	0.000	0.000	0.000
30	A	32	GLU	-1	-0.906	-0.946	15.417	-15.424	-15.424	0.000	0.000	0.000	0.000
31	A	33	GLU	-1	-0.859	-0.940	16.975	-16.352	-16.352	0.000	0.000	0.000	0.000
32	A	34	LEU	0	-0.073	-0.045	12.444	-0.961	-0.961	0.000	0.000	0.000	0.000
33	A	35	SER	0	-0.018	0.006	11.903	-2.137	-2.137	0.000	0.000	0.000	0.000
34	A	36	VAL	0	-0.067	-0.025	9.352	-2.572	-2.572	0.000	0.000	0.000	0.000
35	A	37	SER	0	0.056	0.018	12.044	1.883	1.883	0.000	0.000	0.000	0.000
36	A	38	ARG	1	0.958	0.959	14.075	15.540	15.540	0.000	0.000	0.000	0.000
37	A	39	GLN	0	0.038	0.015	14.774	0.960	0.960	0.000	0.000	0.000	0.000
38	A	40	VAL	0	-0.028	-0.008	9.245	-0.446	-0.446	0.000	0.000	0.000	0.000
39	A	41	ILE	0	0.042	0.026	12.069	-0.260	-0.260	0.000	0.000	0.000	0.000
40	A	42	VAL	0	-0.042	-0.010	14.521	0.741	0.741	0.000	0.000	0.000	0.000
41	A	43	GLN	0	-0.011	-0.004	10.315	-1.702	-1.702	0.000	0.000	0.000	0.000
42	A	44	ASP	-1	-0.780	-0.865	10.244	-29.784	-29.784	0.000	0.000	0.000	0.000
43	A	45	ILE	0	-0.005	-0.001	13.016	0.705	0.705	0.000	0.000	0.000	0.000
44	A	46	ALA	0	-0.017	-0.008	16.392	0.847	0.847	0.000	0.000	0.000	0.000
45	A	47	TYR	0	-0.013	0.002	11.713	0.343	0.343	0.000	0.000	0.000	0.000
46	A	48	LEU	0	0.020	0.007	14.889	0.617	0.617	0.000	0.000	0.000	0.000
47	A	49	ARG	1	0.902	0.945	16.973	14.517	14.517	0.000	0.000	0.000	0.000
48	A	50	SER	0	-0.082	-0.045	17.011	0.414	0.414	0.000	0.000	0.000	0.000
49	A	51	LEU	0	-0.052	-0.023	14.547	0.130	0.130	0.000	0.000	0.000	0.000
50	A	52	GLY	0	0.082	0.049	19.018	0.489	0.489	0.000	0.000	0.000	0.000
51	A	53	TYR	0	-0.044	-0.012	17.398	0.506	0.506	0.000	0.000	0.000	0.000
52	A	54	ASN	0	0.033	0.022	21.858	-0.097	-0.097	0.000	0.000	0.000	0.000
53	A	55	ILE	0	-0.054	-0.033	19.246	0.180	0.180	0.000	0.000	0.000	0.000
54	A	56	VAL	0	0.014	0.003	23.588	0.139	0.139	0.000	0.000	0.000	0.000
55	A	57	ALA	0	-0.022	-0.016	23.500	-0.351	-0.351	0.000	0.000	0.000	0.000
56	A	58	THR	0	-0.010	-0.018	25.285	0.585	0.585	0.000	0.000	0.000	0.000
57	A	59	PRO	0	0.017	-0.010	27.295	-0.353	-0.353	0.000	0.000	0.000	0.000
58	A	60	ARG	1	0.973	0.991	29.063	9.799	9.799	0.000	0.000	0.000	0.000
59	A	61	GLY	0	0.011	0.007	24.751	-0.213	-0.213	0.000	0.000	0.000	0.000
60	A	62	TYR	0	-0.008	0.017	19.699	0.126	0.126	0.000	0.000	0.000	0.000
61	A	63	VAL	0	0.042	0.022	23.754	0.109	0.109	0.000	0.000	0.000	0.000
62	A	64	LEU	0	-0.002	0.005	21.076	-0.309	-0.309	0.000	0.000	0.000	0.000
63	A	65	ALA	0	0.024	0.025	24.848	0.143	0.143	0.000	0.000	0.000	0.000
64	A	66	GLY	0	0.088	0.038	26.570	-0.385	-0.385	0.000	0.000	0.000	0.000
65	A	67	GLY	0	-0.027	-0.017	27.627	0.163	0.163	0.000	0.000	0.000	0.000
66	A	68	LYS	1	0.849	0.919	26.914	10.579	10.579	0.000	0.000	0.000	0.000
67	A	69	SER	0	0.018	0.004	27.980	0.052	0.052	0.000	0.000	0.000	0.000
68	A	70	GLY	0	-0.004	0.007	23.988	-0.031	-0.031	0.000	0.000	0.000	0.000
69	A	71	VAL	0	-0.026	-0.021	21.291	-0.326	-0.326	0.000	0.000	0.000	0.000
70	A	72	SER	0	-0.009	-0.030	24.608	0.459	0.459	0.000	0.000	0.000	0.000
71	A	73	ARG	1	0.965	0.968	24.013	11.941	11.941	0.000	0.000	0.000	0.000
72	A	74	LEU	0	0.033	0.029	29.003	0.240	0.240	0.000	0.000	0.000	0.000
73	A	75	VAL	0	-0.051	-0.032	30.078	-0.311	-0.311	0.000	0.000	0.000	0.000
74	A	76	ALA	0	0.038	0.028	32.695	0.271	0.271	0.000	0.000	0.000	0.000
75	A	77	VAL	0	-0.010	-0.013	35.152	-0.200	-0.200	0.000	0.000	0.000	0.000
76	A	78	LYS	1	0.963	0.984	37.581	7.352	7.352	0.000	0.000	0.000	0.000
77	A	79	HIS	1	0.769	0.872	39.498	7.700	7.700	0.000	0.000	0.000	0.000
78	A	80	ALA	0	0.074	0.049	42.944	0.039	0.039	0.000	0.000	0.000	0.000
79	A	81	PRO	0	0.018	0.006	44.894	-0.177	-0.177	0.000	0.000	0.000	0.000
80	A	82	GLU	-1	-0.851	-0.932	45.873	-6.508	-6.508	0.000	0.000	0.000	0.000
81	A	83	GLU	-1	-0.934	-0.968	41.850	-7.282	-7.282	0.000	0.000	0.000	0.000
82	A	84	ILE	0	-0.028	-0.011	41.167	-0.262	-0.262	0.000	0.000	0.000	0.000
83	A	85	LYS	1	0.964	0.985	40.470	6.835	6.835	0.000	0.000	0.000	0.000
84	A	86	GLU	-1	-0.828	-0.901	38.002	-8.256	-8.256	0.000	0.000	0.000	0.000
85	A	87	GLU	-1	-0.785	-0.877	36.286	-8.554	-8.554	0.000	0.000	0.000	0.000
86	A	88	LEU	0	0.013	-0.010	35.525	-0.324	-0.324	0.000	0.000	0.000	0.000
87	A	89	LEU	0	-0.005	-0.008	35.376	-0.244	-0.244	0.000	0.000	0.000	0.000
88	A	90	CYS	0	-0.046	0.003	32.387	-0.360	-0.360	0.000	0.000	0.000	0.000
89	A	91	VAL	0	0.049	0.028	30.467	-0.414	-0.414	0.000	0.000	0.000	0.000
90	A	92	VAL	0	-0.030	-0.002	30.238	-0.364	-0.364	0.000	0.000	0.000	0.000
91	A	93	ARG	1	0.785	0.861	31.042	8.236	8.236	0.000	0.000	0.000	0.000
92	A	94	ASN	0	-0.036	-0.020	27.059	-0.550	-0.550	0.000	0.000	0.000	0.000
93	A	95	GLY	0	0.009	0.007	26.138	-0.591	-0.591	0.000	0.000	0.000	0.000
94	A	96	GLY	0	0.008	-0.006	27.319	-0.307	-0.307	0.000	0.000	0.000	0.000
95	A	97	ARG	1	0.813	0.901	28.834	9.852	9.852	0.000	0.000	0.000	0.000
96	A	98	ILE	0	-0.015	0.003	31.925	-0.247	-0.247	0.000	0.000	0.000	0.000
97	A	99	VAL	0	0.032	0.021	33.598	0.206	0.206	0.000	0.000	0.000	0.000
98	A	100	ASP	-1	-0.763	-0.857	36.221	-8.407	-8.407	0.000	0.000	0.000	0.000
99	A	101	VAL	0	0.015	0.025	38.138	-0.173	-0.173	0.000	0.000	0.000	0.000
100	A	102	ILE	0	0.018	0.015	38.620	0.123	0.123	0.000	0.000	0.000	0.000
101	A	103	VAL	0	-0.001	-0.004	41.624	-0.114	-0.114	0.000	0.000	0.000	0.000
102	A	104	GLU	-1	-0.879	-0.932	44.371	-7.023	-7.023	0.000	0.000	0.000	0.000
103	A	105	HIS	0	0.023	-0.004	46.893	0.088	0.088	0.000	0.000	0.000	0.000
104	A	106	PRO	0	-0.016	-0.007	50.519	0.007	0.007	0.000	0.000	0.000	0.000
105	A	107	VAL	0	-0.053	-0.023	53.863	0.111	0.111	0.000	0.000	0.000	0.000
106	A	108	TYR	0	-0.015	-0.028	51.142	0.053	0.053	0.000	0.000	0.000	0.000
107	A	109	GLY	0	0.027	0.042	49.408	-0.101	-0.101	0.000	0.000	0.000	0.000
108	A	110	GLU	-1	-0.956	-0.982	42.958	-7.706	-7.706	0.000	0.000	0.000	0.000
109	A	111	ILE	0	-0.036	-0.014	46.382	0.125	0.125	0.000	0.000	0.000	0.000
110	A	112	ARG	1	0.861	0.913	38.433	8.082	8.082	0.000	0.000	0.000	0.000
111	A	113	GLY	0	0.005	0.009	43.405	0.171	0.171	0.000	0.000	0.000	0.000
112	A	114	ILE	0	-0.031	-0.027	40.624	-0.203	-0.203	0.000	0.000	0.000	0.000
113	A	115	ILE	0	-0.069	-0.038	39.187	0.157	0.157	0.000	0.000	0.000	0.000
114	A	116	ASP	-1	-0.922	-0.969	37.175	-8.479	-8.479	0.000	0.000	0.000	0.000
115	A	117	VAL	0	-0.010	0.021	36.881	0.103	0.103	0.000	0.000	0.000	0.000
116	A	118	SER	0	-0.047	-0.059	32.725	-0.351	-0.351	0.000	0.000	0.000	0.000
117	A	119	SER	0	-0.016	-0.017	32.988	-0.232	-0.232	0.000	0.000	0.000	0.000
118	A	120	GLU	-1	-0.759	-0.856	35.413	-8.093	-8.093	0.000	0.000	0.000	0.000
119	A	121	GLU	-1	-0.873	-0.935	37.641	-7.322	-7.322	0.000	0.000	0.000	0.000
120	A	122	GLU	-1	-0.789	-0.874	36.919	-8.411	-8.411	0.000	0.000	0.000	0.000
121	A	123	VAL	0	0.008	0.009	37.153	0.164	0.164	0.000	0.000	0.000	0.000
122	A	124	LEU	0	-0.009	-0.013	40.212	0.192	0.192	0.000	0.000	0.000	0.000
123	A	125	LYS	1	0.861	0.934	42.927	7.478	7.478	0.000	0.000	0.000	0.000
124	A	126	PHE	0	0.037	0.018	42.443	0.156	0.156	0.000	0.000	0.000	0.000
125	A	127	VAL	0	-0.006	-0.006	43.008	0.103	0.103	0.000	0.000	0.000	0.000
126	A	128	ASN	0	0.037	0.018	45.642	0.211	0.211	0.000	0.000	0.000	0.000
127	A	129	LEU	0	-0.036	-0.028	47.081	0.151	0.151	0.000	0.000	0.000	0.000
128	A	130	MET	0	-0.040	-0.010	46.288	0.080	0.080	0.000	0.000	0.000	0.000
129	A	131	GLU	-1	-0.953	-0.985	48.547	-6.404	-6.404	0.000	0.000	0.000	0.000
130	A	132	MET	0	-0.066	-0.028	51.496	0.181	0.181	0.000	0.000	0.000	0.000
131	A	133	ALA	0	-0.040	0.003	52.546	0.124	0.124	0.000	0.000	0.000	0.000
132	A	134	LYS	1	0.929	0.944	54.345	5.356	5.356	0.000	0.000	0.000	0.000
133	A	135	THR	0	-0.021	-0.001	53.067	0.088	0.088	0.000	0.000	0.000	0.000
134	A	136	GLU	-1	-0.917	-0.954	53.714	-5.875	-5.875	0.000	0.000	0.000	0.000
135	A	137	PRO	0	0.007	-0.002	50.452	-0.106	-0.106	0.000	0.000	0.000	0.000
136	A	138	LEU	0	0.073	0.030	47.616	0.000	0.000	0.000	0.000	0.000	0.000
137	A	139	LEU	0	-0.034	-0.010	43.207	-0.029	-0.029	0.000	0.000	0.000	0.000
138	A	140	THR	0	-0.013	-0.019	47.106	0.001	0.001	0.000	0.000	0.000	0.000
139	A	141	LEU	0	-0.008	0.006	48.836	0.061	0.061	0.000	0.000	0.000	0.000
140	A	142	SER	0	0.040	0.011	46.390	-0.053	-0.053	0.000	0.000	0.000	0.000
141	A	143	GLY	0	-0.002	0.007	46.628	-0.123	-0.123	0.000	0.000	0.000	0.000
142	A	144	GLY	0	0.046	0.019	45.532	-0.075	-0.075	0.000	0.000	0.000	0.000
143	A	145	VAL	0	-0.056	-0.016	41.334	-0.204	-0.204	0.000	0.000	0.000	0.000
144	A	146	HIS	0	-0.052	-0.043	40.298	0.029	0.029	0.000	0.000	0.000	0.000
145	A	147	LEU	0	0.039	0.020	35.993	-0.252	-0.252	0.000	0.000	0.000	0.000
146	A	148	HIS	1	0.799	0.863	35.119	8.619	8.619	0.000	0.000	0.000	0.000
147	A	149	THR	0	0.015	0.010	32.838	-0.351	-0.351	0.000	0.000	0.000	0.000
148	A	150	ILE	0	-0.030	-0.019	29.069	0.181	0.181	0.000	0.000	0.000	0.000
149	A	151	GLU	-1	-0.835	-0.893	28.244	-10.754	-10.754	0.000	0.000	0.000	0.000
150	A	152	ALA	0	0.023	0.014	24.340	0.195	0.195	0.000	0.000	0.000	0.000
151	A	153	PRO	0	0.009	0.010	22.335	-0.120	-0.120	0.000	0.000	0.000	0.000
152	A	154	ASP	-1	-0.797	-0.880	18.471	-15.788	-15.788	0.000	0.000	0.000	0.000
153	A	155	GLU	-1	-0.817	-0.926	18.053	-14.180	-14.180	0.000	0.000	0.000	0.000
154	A	156	GLU	-1	-0.882	-0.912	15.218	-18.563	-18.563	0.000	0.000	0.000	0.000
155	A	157	THR	0	-0.085	-0.064	18.784	0.730	0.730	0.000	0.000	0.000	0.000
156	A	158	MET	0	0.010	0.022	22.318	0.722	0.722	0.000	0.000	0.000	0.000
157	A	159	GLU	-1	-0.953	-0.985	18.727	-15.615	-15.615	0.000	0.000	0.000	0.000
158	A	160	ARG	1	0.770	0.887	21.162	13.385	13.385	0.000	0.000	0.000	0.000
159	A	161	ILE	0	0.017	0.011	24.068	0.472	0.472	0.000	0.000	0.000	0.000
160	A	162	MET	0	0.001	0.003	25.841	0.455	0.455	0.000	0.000	0.000	0.000
161	A	163	ARG	1	0.947	0.981	20.588	13.683	13.683	0.000	0.000	0.000	0.000
162	A	164	GLU	-1	-0.845	-0.912	27.061	-10.112	-10.112	0.000	0.000	0.000	0.000
163	A	165	LEU	0	0.014	-0.005	29.801	0.355	0.355	0.000	0.000	0.000	0.000
164	A	166	LYS	1	0.812	0.896	29.011	10.494	10.494	0.000	0.000	0.000	0.000
165	A	167	LYS	1	0.783	0.867	28.833	10.429	10.429	0.000	0.000	0.000	0.000
166	A	168	LYS	1	0.819	0.899	32.615	8.898	8.898	0.000	0.000	0.000	0.000
167	A	169	GLY	0	0.006	0.018	35.001	0.229	0.229	0.000	0.000	0.000	0.000
168	A	170	PHE	0	0.000	-0.008	35.440	0.116	0.116	0.000	0.000	0.000	0.000
169	A	171	LEU	0	-0.051	-0.025	30.173	0.056	0.056	0.000	0.000	0.000	0.000
170	A	172	ILE	0	-0.003	0.007	34.810	0.186	0.186	0.000	0.000	0.000	0.000
171	A	173	GLU	-1	-0.894	-0.935	31.477	-10.194	-10.194	0.000	0.000	0.000	0.000
172	A	174	GLU	-2	-1.899	-1.932	33.949	-17.231	-17.231	0.000	0.000	0.000	0.000

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