FMO DATABASE

FMODB ID: 7ZJRK

Calculation Name: 2WCR-B-Xray549

Preferred Name:

Target Type:

Ligand Name: imidazole | nickel (ii) ion

Ligand 3-letter code: IMD | NI

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2WCR

Chain ID: B

ChEMBL ID:

UniProt ID: O25318

Base Structure: X-ray

Registration Date: 2025-10-12

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	146
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1360493.852687
FMO2-HF: Nuclear repulsion	1301528.175334
FMO2-HF: Total energy	-58965.677352
FMO2-MP2: Total energy	-59137.587467

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(B:35:SER)

Summations of interaction energy for fragment #1(B:35: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.
-87.99	-79.692	1.925	-5.286	-4.935	-0.063

Interaction energy analysis for fragmet #1(B:35:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.815 / q_NPA : 0.904

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	B	37	LEU	0	-0.017	0.002	2.772	-22.004	-18.950	0.393	-1.786	-1.660	-0.014
4	B	38	GLN	0	0.017	0.001	5.327	6.862	6.936	-0.001	-0.005	-0.068	0.000
100	B	134	ASN	0	-0.043	-0.028	2.321	-25.753	-20.649	1.534	-3.494	-3.144	-0.049
101	B	135	ASN	0	-0.029	-0.018	5.280	0.129	0.195	-0.001	-0.001	-0.063	0.000
5	B	39	ASP	-1	-0.882	-0.952	8.185	-24.726	-24.726	0.000	0.000	0.000	0.000
6	B	40	VAL	0	-0.030	-0.001	9.312	1.028	1.028	0.000	0.000	0.000	0.000
7	B	41	PRO	0	0.003	0.018	11.924	1.330	1.330	0.000	0.000	0.000	0.000
8	B	42	TYR	0	0.055	-0.005	15.496	-0.495	-0.495	0.000	0.000	0.000	0.000
9	B	43	TRP	0	-0.019	-0.003	16.996	-0.067	-0.067	0.000	0.000	0.000	0.000
10	B	44	MET	0	-0.035	-0.013	11.796	0.921	0.921	0.000	0.000	0.000	0.000
11	B	45	LEU	0	-0.033	0.009	13.744	-1.154	-1.154	0.000	0.000	0.000	0.000
12	B	46	GLN	0	0.044	0.004	14.893	0.296	0.296	0.000	0.000	0.000	0.000
13	B	47	ASN	0	-0.080	-0.036	17.156	0.188	0.188	0.000	0.000	0.000	0.000
14	B	48	ARG	1	0.912	0.944	19.884	15.122	15.122	0.000	0.000	0.000	0.000
15	B	49	SER	0	-0.026	-0.005	22.530	0.365	0.365	0.000	0.000	0.000	0.000
16	B	50	GLU	-1	-0.857	-0.938	25.108	-12.209	-12.209	0.000	0.000	0.000	0.000
17	B	51	TYR	0	-0.027	0.002	24.534	0.498	0.498	0.000	0.000	0.000	0.000
18	B	52	ILE	0	0.025	0.010	27.338	-0.214	-0.214	0.000	0.000	0.000	0.000
19	B	53	THR	0	0.033	0.014	29.269	-0.269	-0.269	0.000	0.000	0.000	0.000
20	B	54	GLN	0	-0.011	0.000	25.116	-0.510	-0.510	0.000	0.000	0.000	0.000
21	B	55	GLY	0	0.012	0.010	24.162	0.055	0.055	0.000	0.000	0.000	0.000
22	B	56	VAL	0	-0.029	-0.033	17.503	-0.142	-0.142	0.000	0.000	0.000	0.000
23	B	57	ASP	-1	-0.852	-0.923	18.649	-15.621	-15.621	0.000	0.000	0.000	0.000
24	B	58	SER	0	-0.079	-0.062	15.346	-0.121	-0.121	0.000	0.000	0.000	0.000
25	B	59	SER	0	-0.066	-0.030	16.923	1.235	1.235	0.000	0.000	0.000	0.000
26	B	60	HIS	0	0.006	0.016	13.299	-0.077	-0.077	0.000	0.000	0.000	0.000
27	B	61	ILE	0	-0.002	-0.011	13.319	1.414	1.414	0.000	0.000	0.000	0.000
28	B	62	VAL	0	-0.036	-0.016	16.743	-0.202	-0.202	0.000	0.000	0.000	0.000
29	B	63	ASP	-1	-0.839	-0.921	19.477	-13.556	-13.556	0.000	0.000	0.000	0.000
30	B	64	GLY	0	-0.017	-0.007	21.394	0.456	0.456	0.000	0.000	0.000	0.000
31	B	65	LYS	1	0.806	0.905	21.713	13.866	13.866	0.000	0.000	0.000	0.000
32	B	66	LYS	1	0.889	0.935	22.575	11.214	11.214	0.000	0.000	0.000	0.000
33	B	67	THR	0	0.094	0.027	19.269	-0.142	-0.142	0.000	0.000	0.000	0.000
34	B	68	GLU	-1	-0.830	-0.906	21.564	-12.642	-12.642	0.000	0.000	0.000	0.000
35	B	69	GLU	-1	-0.867	-0.929	24.260	-12.199	-12.199	0.000	0.000	0.000	0.000
36	B	70	ILE	0	0.016	0.022	17.897	0.177	0.177	0.000	0.000	0.000	0.000
37	B	71	GLU	-1	-0.775	-0.886	20.039	-14.314	-14.314	0.000	0.000	0.000	0.000
38	B	72	LYS	1	0.891	0.961	21.494	11.629	11.629	0.000	0.000	0.000	0.000
39	B	73	ILE	0	-0.052	-0.014	22.216	0.386	0.386	0.000	0.000	0.000	0.000
40	B	74	ALA	0	0.057	0.035	19.374	0.214	0.214	0.000	0.000	0.000	0.000
41	B	75	THR	0	-0.006	-0.026	21.215	0.155	0.155	0.000	0.000	0.000	0.000
42	B	76	LYS	1	0.954	0.992	24.024	11.416	11.416	0.000	0.000	0.000	0.000
43	B	77	ARG	1	0.905	0.945	19.572	15.300	15.300	0.000	0.000	0.000	0.000
44	B	78	ALA	0	0.010	0.016	21.914	0.191	0.191	0.000	0.000	0.000	0.000
45	B	79	THR	0	0.011	-0.010	23.603	0.321	0.321	0.000	0.000	0.000	0.000
46	B	80	ILE	0	-0.014	-0.011	26.701	0.351	0.351	0.000	0.000	0.000	0.000
47	B	81	ARG	1	0.881	0.946	20.807	13.965	13.965	0.000	0.000	0.000	0.000
48	B	82	VAL	0	0.020	0.021	25.831	0.108	0.108	0.000	0.000	0.000	0.000
49	B	83	ALA	0	0.025	0.013	28.476	0.274	0.274	0.000	0.000	0.000	0.000
50	B	84	GLN	0	-0.009	-0.017	25.511	-0.090	-0.090	0.000	0.000	0.000	0.000
51	B	85	ASN	0	-0.030	0.003	25.343	-0.078	-0.078	0.000	0.000	0.000	0.000
52	B	86	ILE	0	0.031	0.021	28.886	0.227	0.227	0.000	0.000	0.000	0.000
53	B	87	VAL	0	0.018	0.008	31.866	0.265	0.265	0.000	0.000	0.000	0.000
54	B	88	HIS	0	0.000	-0.012	27.294	0.541	0.541	0.000	0.000	0.000	0.000
55	B	89	LYS	1	0.890	0.942	30.385	10.323	10.323	0.000	0.000	0.000	0.000
56	B	90	LEU	0	-0.014	0.003	34.259	0.308	0.308	0.000	0.000	0.000	0.000
57	B	91	LYS	1	0.857	0.945	31.514	9.945	9.945	0.000	0.000	0.000	0.000
58	B	92	GLU	-1	-0.852	-0.915	32.074	-9.585	-9.585	0.000	0.000	0.000	0.000
59	B	93	ALA	0	-0.033	-0.022	36.524	0.231	0.231	0.000	0.000	0.000	0.000
60	B	94	TYR	0	-0.047	-0.044	39.541	0.206	0.206	0.000	0.000	0.000	0.000
61	B	95	LEU	0	0.003	-0.009	36.608	0.175	0.175	0.000	0.000	0.000	0.000
62	B	96	SER	0	0.006	0.036	40.472	0.174	0.174	0.000	0.000	0.000	0.000
63	B	97	LYS	1	0.958	0.967	41.658	7.146	7.146	0.000	0.000	0.000	0.000
64	B	98	THR	0	-0.052	-0.035	43.530	0.150	0.150	0.000	0.000	0.000	0.000
65	B	99	ASN	0	0.053	0.045	43.821	0.091	0.091	0.000	0.000	0.000	0.000
66	B	100	ARG	1	0.942	0.970	45.544	6.703	6.703	0.000	0.000	0.000	0.000
67	B	101	ILE	0	0.003	0.029	43.791	0.191	0.191	0.000	0.000	0.000	0.000
68	B	102	LYS	1	0.877	0.920	47.800	6.148	6.148	0.000	0.000	0.000	0.000
69	B	103	GLN	0	0.028	0.036	47.101	-0.006	-0.006	0.000	0.000	0.000	0.000
70	B	104	LYS	0	0.008	0.018	43.719	-0.161	-0.161	0.000	0.000	0.000	0.000
71	B	105	ILE	0	0.006	-0.007	40.710	0.025	0.025	0.000	0.000	0.000	0.000
72	B	106	THR	0	0.030	-0.012	39.592	-0.060	-0.060	0.000	0.000	0.000	0.000
73	B	107	ASN	0	0.034	0.006	32.729	-0.211	-0.211	0.000	0.000	0.000	0.000
74	B	108	GLU	-1	-0.831	-0.911	35.504	-8.643	-8.643	0.000	0.000	0.000	0.000
75	B	109	MET	0	0.026	0.043	36.833	-0.062	-0.062	0.000	0.000	0.000	0.000
76	B	110	PHE	0	0.038	-0.010	35.553	-0.075	-0.075	0.000	0.000	0.000	0.000
77	B	111	ILE	0	-0.036	-0.009	31.746	-0.210	-0.210	0.000	0.000	0.000	0.000
78	B	112	GLN	0	0.003	0.007	34.206	-0.106	-0.106	0.000	0.000	0.000	0.000
79	B	113	MET	0	0.004	0.010	36.629	-0.011	-0.011	0.000	0.000	0.000	0.000
80	B	114	THR	0	-0.043	-0.039	30.448	-0.102	-0.102	0.000	0.000	0.000	0.000
81	B	115	GLN	0	-0.090	-0.040	33.463	-0.366	-0.366	0.000	0.000	0.000	0.000
82	B	116	PRO	0	0.021	0.011	35.370	-0.007	-0.007	0.000	0.000	0.000	0.000
83	B	117	ILE	0	0.004	0.016	34.039	0.056	0.056	0.000	0.000	0.000	0.000
84	B	118	TYR	0	-0.018	-0.013	29.456	-0.235	-0.235	0.000	0.000	0.000	0.000
85	B	119	ASP	-1	-0.872	-0.936	33.817	-8.710	-8.710	0.000	0.000	0.000	0.000
86	B	120	SER	0	-0.064	-0.017	36.939	0.176	0.176	0.000	0.000	0.000	0.000
87	B	121	LEU	0	-0.008	-0.005	31.561	0.049	0.049	0.000	0.000	0.000	0.000
88	B	122	MET	0	-0.013	-0.009	35.398	0.066	0.066	0.000	0.000	0.000	0.000
89	B	123	ASN	0	-0.060	-0.037	35.044	-0.143	-0.143	0.000	0.000	0.000	0.000
90	B	124	VAL	0	0.034	0.017	28.915	-0.126	-0.126	0.000	0.000	0.000	0.000
91	B	125	ASP	-1	-0.779	-0.832	29.248	-10.060	-10.060	0.000	0.000	0.000	0.000
92	B	126	ARG	1	0.812	0.873	22.667	13.029	13.029	0.000	0.000	0.000	0.000
93	B	127	LEU	0	-0.013	-0.005	24.316	0.021	0.021	0.000	0.000	0.000	0.000
94	B	128	GLY	0	-0.003	0.001	20.560	-0.246	-0.246	0.000	0.000	0.000	0.000
95	B	129	ILE	0	-0.024	-0.011	16.981	0.293	0.293	0.000	0.000	0.000	0.000
96	B	130	TYR	0	0.023	0.005	8.708	-0.523	-0.523	0.000	0.000	0.000	0.000
97	B	131	ILE	0	0.011	0.007	11.032	0.778	0.778	0.000	0.000	0.000	0.000
98	B	132	ASN	0	0.026	0.015	6.826	-6.003	-6.003	0.000	0.000	0.000	0.000
99	B	133	PRO	0	0.023	-0.004	5.152	0.761	0.761	0.000	0.000	0.000	0.000
102	B	136	GLU	-1	-0.887	-0.931	8.955	-22.743	-22.743	0.000	0.000	0.000	0.000
103	B	137	GLU	-1	-0.823	-0.874	10.866	-17.925	-17.925	0.000	0.000	0.000	0.000
104	B	138	VAL	0	-0.004	-0.012	12.360	-1.224	-1.224	0.000	0.000	0.000	0.000
105	B	139	PHE	0	0.015	-0.013	11.563	0.873	0.873	0.000	0.000	0.000	0.000
106	B	140	ALA	0	-0.010	-0.009	16.044	0.219	0.219	0.000	0.000	0.000	0.000
107	B	141	LEU	0	-0.024	-0.008	19.532	-0.083	-0.083	0.000	0.000	0.000	0.000
108	B	142	VAL	0	-0.034	-0.029	21.453	0.372	0.372	0.000	0.000	0.000	0.000
109	B	143	ARG	1	0.860	0.915	25.257	9.807	9.807	0.000	0.000	0.000	0.000
110	B	144	ALA	0	-0.001	0.016	28.281	0.181	0.181	0.000	0.000	0.000	0.000
111	B	145	ARG	1	0.800	0.838	31.646	9.352	9.352	0.000	0.000	0.000	0.000
112	B	146	GLY	0	0.012	0.007	34.550	0.232	0.232	0.000	0.000	0.000	0.000
113	B	147	PHE	0	-0.031	-0.016	36.009	-0.249	-0.249	0.000	0.000	0.000	0.000
114	B	148	ASP	-1	-0.798	-0.895	38.434	-7.157	-7.157	0.000	0.000	0.000	0.000
115	B	149	LYS	1	0.905	0.922	41.734	6.664	6.664	0.000	0.000	0.000	0.000
116	B	150	ASP	-1	-0.858	-0.887	43.864	-6.621	-6.621	0.000	0.000	0.000	0.000
117	B	151	ALA	0	0.036	0.012	42.235	0.044	0.044	0.000	0.000	0.000	0.000
118	B	152	LEU	0	-0.020	-0.004	39.137	-0.043	-0.043	0.000	0.000	0.000	0.000
119	B	153	SER	0	-0.035	-0.045	42.210	0.041	0.041	0.000	0.000	0.000	0.000
120	B	154	GLU	-1	-0.917	-0.956	45.713	-6.579	-6.579	0.000	0.000	0.000	0.000
121	B	155	GLY	0	-0.039	-0.025	42.296	0.029	0.029	0.000	0.000	0.000	0.000
122	B	156	LEU	0	-0.006	-0.018	39.945	-0.066	-0.066	0.000	0.000	0.000	0.000
123	B	157	HIS	0	0.011	-0.016	43.543	-0.012	-0.012	0.000	0.000	0.000	0.000
124	B	158	LYS	1	0.910	0.957	44.313	7.269	7.269	0.000	0.000	0.000	0.000
125	B	159	MET	0	-0.098	-0.018	40.584	-0.082	-0.082	0.000	0.000	0.000	0.000
126	B	160	SER	0	-0.023	-0.012	44.278	0.033	0.033	0.000	0.000	0.000	0.000
127	B	161	LEU	0	-0.022	0.007	42.084	0.042	0.042	0.000	0.000	0.000	0.000
128	B	162	ASP	-1	-0.791	-0.905	46.760	-6.284	-6.284	0.000	0.000	0.000	0.000
129	B	163	ASN	0	0.050	0.010	49.033	-0.172	-0.172	0.000	0.000	0.000	0.000
130	B	164	GLN	0	-0.049	-0.017	50.450	-0.061	-0.061	0.000	0.000	0.000	0.000
131	B	165	ALA	0	0.030	0.004	45.710	-0.087	-0.087	0.000	0.000	0.000	0.000
132	B	166	VAL	0	0.002	0.011	45.255	-0.156	-0.156	0.000	0.000	0.000	0.000
133	B	167	SER	0	-0.004	-0.018	45.463	-0.114	-0.114	0.000	0.000	0.000	0.000
134	B	168	ILE	0	-0.059	-0.028	44.527	-0.065	-0.065	0.000	0.000	0.000	0.000
135	B	169	LEU	0	-0.004	-0.013	40.393	-0.150	-0.150	0.000	0.000	0.000	0.000
136	B	170	VAL	0	0.044	0.020	41.323	-0.211	-0.211	0.000	0.000	0.000	0.000
137	B	171	ALA	0	0.027	0.014	42.405	-0.119	-0.119	0.000	0.000	0.000	0.000
138	B	172	LYS	1	0.812	0.902	39.770	7.551	7.551	0.000	0.000	0.000	0.000
139	B	173	VAL	0	-0.015	0.001	36.907	-0.236	-0.236	0.000	0.000	0.000	0.000
140	B	174	GLU	-1	-0.924	-0.975	38.725	-7.289	-7.289	0.000	0.000	0.000	0.000
141	B	175	GLU	-1	-0.926	-0.958	39.846	-7.710	-7.710	0.000	0.000	0.000	0.000
142	B	176	ILE	0	-0.013	-0.017	34.174	-0.144	-0.144	0.000	0.000	0.000	0.000
143	B	177	PHE	0	-0.015	-0.019	34.096	-0.261	-0.261	0.000	0.000	0.000	0.000
144	B	178	LYS	1	0.789	0.900	37.281	7.804	7.804	0.000	0.000	0.000	0.000
145	B	179	ASP	-1	-0.881	-0.924	36.732	-8.138	-8.138	0.000	0.000	0.000	0.000
146	B	180	SER	-1	-0.905	-0.924	32.690	-9.830	-9.830	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:35:SER)