FMO DATABASE

FMODB ID: L6ML9

Calculation Name: 2HKV-A-Xray549

Preferred Name:

Target Type:

Ligand Name: nickel (ii) ion

Ligand 3-letter code: NI

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2HKV

Chain ID: A

ChEMBL ID:

UniProt ID: B1YEV7

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	148
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1454596.903003
FMO2-HF: Nuclear repulsion	1395233.544034
FMO2-HF: Total energy	-59363.358969
FMO2-MP2: Total energy	-59538.88553

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:0:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

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.
-107.631	-106.565	-0.015	-0.483	-0.567	-0.002

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.825 / q_NPA : 0.897

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	2	THR	0	0.047	0.014	3.837	2.221	3.287	-0.015	-0.483	-0.567	-0.002
4	A	3	ASP	-1	-0.848	-0.923	7.135	-28.024	-28.024	0.000	0.000	0.000	0.000
5	A	4	TRP	0	0.026	0.005	10.053	1.013	1.013	0.000	0.000	0.000	0.000
6	A	5	GLN	0	0.036	0.021	6.702	-3.506	-3.506	0.000	0.000	0.000	0.000
7	A	6	GLN	0	0.022	0.001	7.784	2.757	2.757	0.000	0.000	0.000	0.000
8	A	7	ALA	0	-0.044	-0.021	9.233	2.199	2.199	0.000	0.000	0.000	0.000
9	A	8	LEU	0	0.017	0.006	12.603	1.662	1.662	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.851	-0.918	10.212	-27.071	-27.071	0.000	0.000	0.000	0.000
11	A	10	ARG	1	0.944	0.973	12.166	20.134	20.134	0.000	0.000	0.000	0.000
12	A	11	HIS	0	0.002	-0.005	13.964	1.514	1.514	0.000	0.000	0.000	0.000
13	A	12	VAL	0	0.038	0.038	16.165	1.419	1.419	0.000	0.000	0.000	0.000
14	A	13	GLY	0	0.058	0.043	15.805	0.825	0.825	0.000	0.000	0.000	0.000
15	A	14	VAL	0	-0.070	-0.045	16.842	0.848	0.848	0.000	0.000	0.000	0.000
16	A	15	GLY	0	0.043	0.044	19.715	0.865	0.865	0.000	0.000	0.000	0.000
17	A	16	VAL	0	0.029	0.021	18.900	0.853	0.853	0.000	0.000	0.000	0.000
18	A	17	ARG	1	0.895	0.960	16.009	18.131	18.131	0.000	0.000	0.000	0.000
19	A	18	THR	0	0.039	0.006	22.235	0.667	0.667	0.000	0.000	0.000	0.000
20	A	19	THR	0	0.006	-0.012	24.577	0.737	0.737	0.000	0.000	0.000	0.000
21	A	20	ARG	1	0.811	0.881	19.874	15.068	15.068	0.000	0.000	0.000	0.000
22	A	21	ASP	-1	-0.920	-0.960	26.038	-11.778	-11.778	0.000	0.000	0.000	0.000
23	A	22	LEU	0	-0.012	-0.012	28.413	0.427	0.427	0.000	0.000	0.000	0.000
24	A	23	ILE	0	0.005	-0.013	27.888	0.400	0.400	0.000	0.000	0.000	0.000
25	A	24	ARG	1	0.853	0.923	25.503	12.113	12.113	0.000	0.000	0.000	0.000
26	A	25	LEU	0	-0.027	-0.004	31.992	0.233	0.233	0.000	0.000	0.000	0.000
27	A	26	ILE	0	-0.063	-0.006	33.583	0.279	0.279	0.000	0.000	0.000	0.000
28	A	27	GLN	0	0.000	-0.005	36.693	-0.125	-0.125	0.000	0.000	0.000	0.000
29	A	28	PRO	0	-0.030	-0.019	40.201	-0.033	-0.033	0.000	0.000	0.000	0.000
30	A	29	GLU	-1	-0.836	-0.916	41.757	-7.270	-7.270	0.000	0.000	0.000	0.000
31	A	30	ASP	-1	-0.766	-0.857	40.596	-7.500	-7.500	0.000	0.000	0.000	0.000
32	A	31	TRP	0	0.022	0.019	33.867	-0.117	-0.117	0.000	0.000	0.000	0.000
33	A	32	ASP	-1	-0.864	-0.939	39.878	-7.759	-7.759	0.000	0.000	0.000	0.000
34	A	33	LYS	1	0.768	0.868	42.567	7.350	7.350	0.000	0.000	0.000	0.000
35	A	34	ARG	1	0.869	0.923	41.604	7.413	7.413	0.000	0.000	0.000	0.000
36	A	35	PRO	0	-0.017	0.003	40.519	0.177	0.177	0.000	0.000	0.000	0.000
37	A	36	ILE	0	0.023	0.027	39.842	0.106	0.106	0.000	0.000	0.000	0.000
38	A	37	SER	0	0.019	0.005	43.500	-0.019	-0.019	0.000	0.000	0.000	0.000
39	A	38	GLY	0	-0.003	-0.010	45.252	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	39	LYS	1	0.877	0.942	39.754	7.726	7.726	0.000	0.000	0.000	0.000
41	A	40	ARG	1	0.971	0.992	33.470	9.609	9.609	0.000	0.000	0.000	0.000
42	A	41	SER	0	0.047	0.031	39.147	-0.016	-0.016	0.000	0.000	0.000	0.000
43	A	42	VAL	0	0.045	0.015	36.387	-0.272	-0.272	0.000	0.000	0.000	0.000
44	A	43	TYR	0	-0.022	-0.023	34.989	-0.243	-0.243	0.000	0.000	0.000	0.000
45	A	44	GLU	-1	-0.809	-0.898	34.609	-8.392	-8.392	0.000	0.000	0.000	0.000
46	A	45	VAL	0	-0.082	-0.041	32.374	-0.243	-0.243	0.000	0.000	0.000	0.000
47	A	46	ALA	0	0.036	0.019	30.993	-0.398	-0.398	0.000	0.000	0.000	0.000
48	A	47	VAL	0	0.049	0.019	29.851	-0.451	-0.451	0.000	0.000	0.000	0.000
49	A	48	HIS	0	-0.076	-0.035	29.384	-0.440	-0.440	0.000	0.000	0.000	0.000
50	A	49	LEU	0	-0.007	-0.019	26.803	-0.433	-0.433	0.000	0.000	0.000	0.000
51	A	50	ALA	0	-0.003	0.012	25.351	-0.580	-0.580	0.000	0.000	0.000	0.000
52	A	51	VAL	0	0.037	0.037	24.885	-0.493	-0.493	0.000	0.000	0.000	0.000
53	A	52	LEU	0	-0.020	-0.003	23.303	-0.470	-0.470	0.000	0.000	0.000	0.000
54	A	53	LEU	0	-0.018	-0.004	18.733	-0.244	-0.244	0.000	0.000	0.000	0.000
55	A	54	GLU	-1	-0.751	-0.846	19.796	-14.821	-14.821	0.000	0.000	0.000	0.000
56	A	55	ALA	0	-0.008	-0.010	21.477	0.009	0.009	0.000	0.000	0.000	0.000
57	A	56	ASP	-1	-0.756	-0.833	22.568	-12.790	-12.790	0.000	0.000	0.000	0.000
58	A	57	LEU	0	0.002	-0.001	16.899	-0.114	-0.114	0.000	0.000	0.000	0.000
59	A	58	ARG	1	0.846	0.933	20.934	13.380	13.380	0.000	0.000	0.000	0.000
60	A	59	ILE	0	-0.010	-0.010	23.477	0.315	0.315	0.000	0.000	0.000	0.000
61	A	60	ALA	0	-0.018	-0.009	21.207	0.230	0.230	0.000	0.000	0.000	0.000
62	A	61	THR	0	-0.060	-0.047	19.727	-0.149	-0.149	0.000	0.000	0.000	0.000
63	A	62	GLY	0	0.035	0.033	22.715	0.163	0.163	0.000	0.000	0.000	0.000
64	A	63	ALA	0	-0.032	0.000	26.064	0.452	0.452	0.000	0.000	0.000	0.000
65	A	64	THR	0	-0.034	-0.059	27.735	0.393	0.393	0.000	0.000	0.000	0.000
66	A	65	ALA	0	-0.014	-0.019	31.569	-0.078	-0.078	0.000	0.000	0.000	0.000
67	A	66	ASP	-1	-0.924	-0.956	34.087	-8.852	-8.852	0.000	0.000	0.000	0.000
68	A	67	GLU	-1	-0.805	-0.875	29.605	-10.961	-10.961	0.000	0.000	0.000	0.000
69	A	68	MET	0	-0.028	-0.009	27.160	-0.356	-0.356	0.000	0.000	0.000	0.000
70	A	69	ALA	0	-0.031	-0.011	30.902	0.003	0.003	0.000	0.000	0.000	0.000
71	A	70	GLN	0	-0.016	-0.015	32.652	-0.056	-0.056	0.000	0.000	0.000	0.000
72	A	71	PHE	0	-0.033	-0.022	25.077	-0.070	-0.070	0.000	0.000	0.000	0.000
73	A	72	TYR	0	-0.043	-0.040	28.954	-0.229	-0.229	0.000	0.000	0.000	0.000
74	A	73	ALA	0	-0.022	0.008	32.236	0.191	0.191	0.000	0.000	0.000	0.000
75	A	74	VAL	0	-0.031	-0.004	30.451	0.237	0.237	0.000	0.000	0.000	0.000
76	A	75	PRO	0	-0.040	-0.009	32.637	-0.126	-0.126	0.000	0.000	0.000	0.000
77	A	76	VAL	0	0.017	0.006	29.638	-0.248	-0.248	0.000	0.000	0.000	0.000
78	A	77	LEU	0	0.008	0.020	32.534	0.196	0.196	0.000	0.000	0.000	0.000
79	A	78	PRO	0	0.027	-0.004	33.211	-0.328	-0.328	0.000	0.000	0.000	0.000
80	A	79	GLU	-1	-0.878	-0.952	33.107	-9.140	-9.140	0.000	0.000	0.000	0.000
81	A	80	GLN	0	0.006	0.008	30.366	-0.315	-0.315	0.000	0.000	0.000	0.000
82	A	81	LEU	0	-0.039	-0.005	28.688	-0.462	-0.462	0.000	0.000	0.000	0.000
83	A	82	VAL	0	-0.004	-0.005	25.354	-0.428	-0.428	0.000	0.000	0.000	0.000
84	A	83	ASP	-1	-0.851	-0.923	24.685	-12.302	-12.302	0.000	0.000	0.000	0.000
85	A	84	ARG	1	0.821	0.907	23.181	12.400	12.400	0.000	0.000	0.000	0.000
86	A	85	LEU	0	0.024	0.016	22.649	-0.472	-0.472	0.000	0.000	0.000	0.000
87	A	86	ASP	-1	-0.830	-0.893	20.309	-15.318	-15.318	0.000	0.000	0.000	0.000
88	A	87	GLN	0	-0.037	-0.013	19.137	-0.828	-0.828	0.000	0.000	0.000	0.000
89	A	88	SER	0	-0.024	-0.050	19.280	-0.759	-0.759	0.000	0.000	0.000	0.000
90	A	89	TRP	0	-0.030	-0.011	13.882	-0.455	-0.455	0.000	0.000	0.000	0.000
91	A	90	GLN	0	-0.022	-0.016	12.192	-0.604	-0.604	0.000	0.000	0.000	0.000
92	A	91	TYR	0	0.003	0.002	14.303	-1.375	-1.375	0.000	0.000	0.000	0.000
93	A	92	TYR	0	0.021	-0.027	14.653	-1.334	-1.334	0.000	0.000	0.000	0.000
94	A	93	GLN	0	-0.039	-0.032	10.900	-0.213	-0.213	0.000	0.000	0.000	0.000
95	A	94	ASP	-1	-0.875	-0.933	10.271	-26.438	-26.438	0.000	0.000	0.000	0.000
96	A	95	ARG	1	0.818	0.914	10.705	18.065	18.065	0.000	0.000	0.000	0.000
97	A	96	LEU	0	-0.014	0.016	9.938	-0.038	-0.038	0.000	0.000	0.000	0.000
98	A	97	MET	0	-0.042	-0.023	5.892	-5.457	-5.457	0.000	0.000	0.000	0.000
99	A	98	ALA	0	-0.048	-0.016	7.097	-4.287	-4.287	0.000	0.000	0.000	0.000
100	A	99	ASP	-1	-0.893	-0.956	9.460	-20.813	-20.813	0.000	0.000	0.000	0.000
101	A	100	PHE	0	-0.063	-0.036	11.868	0.826	0.826	0.000	0.000	0.000	0.000
102	A	101	SER	0	0.016	0.012	15.471	0.137	0.137	0.000	0.000	0.000	0.000
103	A	102	THR	0	-0.076	-0.046	18.915	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	103	GLU	-1	-0.955	-0.976	21.106	-12.320	-12.320	0.000	0.000	0.000	0.000
105	A	104	THR	0	-0.087	-0.046	24.872	-0.043	-0.043	0.000	0.000	0.000	0.000
106	A	105	THR	0	0.020	0.014	27.272	0.222	0.222	0.000	0.000	0.000	0.000
107	A	106	TYR	0	0.025	0.002	29.306	0.303	0.303	0.000	0.000	0.000	0.000
108	A	107	TRP	0	-0.060	-0.035	29.461	0.289	0.289	0.000	0.000	0.000	0.000
109	A	108	GLY	0	0.021	0.006	32.556	0.209	0.209	0.000	0.000	0.000	0.000
110	A	109	VAL	0	-0.044	-0.012	27.751	-0.043	-0.043	0.000	0.000	0.000	0.000
111	A	110	THR	0	0.046	0.019	26.416	-0.181	-0.181	0.000	0.000	0.000	0.000
112	A	111	ASP	-1	-0.810	-0.889	22.835	-14.244	-14.244	0.000	0.000	0.000	0.000
113	A	112	SER	0	-0.016	-0.005	19.233	-0.459	-0.459	0.000	0.000	0.000	0.000
114	A	113	THR	0	0.049	0.023	14.461	0.690	0.690	0.000	0.000	0.000	0.000
115	A	114	THR	0	-0.021	-0.017	14.337	-0.107	-0.107	0.000	0.000	0.000	0.000
116	A	115	GLY	0	0.002	0.019	16.496	0.042	0.042	0.000	0.000	0.000	0.000
117	A	116	TRP	0	0.058	0.011	19.868	0.448	0.448	0.000	0.000	0.000	0.000
118	A	117	LEU	0	-0.018	0.004	13.491	0.211	0.211	0.000	0.000	0.000	0.000
119	A	118	LEU	0	0.002	0.015	17.540	-0.056	-0.056	0.000	0.000	0.000	0.000
120	A	119	GLU	0	-0.057	-0.061	19.324	0.860	0.860	0.000	0.000	0.000	0.000
121	A	120	ALA	0	0.038	0.016	19.708	0.510	0.510	0.000	0.000	0.000	0.000
122	A	121	ALA	0	-0.013	0.003	18.640	0.329	0.329	0.000	0.000	0.000	0.000
123	A	122	VAL	0	-0.003	-0.016	20.690	0.589	0.589	0.000	0.000	0.000	0.000
124	A	123	HIS	1	0.793	0.895	24.053	12.746	12.746	0.000	0.000	0.000	0.000
125	A	124	LEU	0	0.025	0.007	21.116	0.543	0.543	0.000	0.000	0.000	0.000
126	A	125	TYR	0	-0.058	-0.056	20.417	0.751	0.751	0.000	0.000	0.000	0.000
127	A	126	HIS	0	-0.036	-0.009	25.715	0.711	0.711	0.000	0.000	0.000	0.000
128	A	127	HIS	0	-0.011	-0.028	28.553	0.309	0.309	0.000	0.000	0.000	0.000
129	A	128	ARG	1	0.871	0.930	24.576	12.823	12.823	0.000	0.000	0.000	0.000
130	A	129	SER	0	0.000	0.012	28.807	0.222	0.222	0.000	0.000	0.000	0.000
131	A	130	GLN	0	0.003	0.016	31.469	0.052	0.052	0.000	0.000	0.000	0.000
132	A	131	LEU	0	0.004	-0.002	30.538	0.309	0.309	0.000	0.000	0.000	0.000
133	A	132	LEU	0	0.011	0.009	31.655	0.232	0.232	0.000	0.000	0.000	0.000
134	A	133	ASP	-1	-0.877	-0.947	33.751	-8.763	-8.763	0.000	0.000	0.000	0.000
135	A	134	TYR	0	-0.116	-0.089	36.562	0.294	0.294	0.000	0.000	0.000	0.000
136	A	135	LEU	0	0.028	0.016	34.433	0.252	0.252	0.000	0.000	0.000	0.000
137	A	136	ASN	0	0.010	0.003	36.041	0.272	0.272	0.000	0.000	0.000	0.000
138	A	137	LEU	0	-0.055	-0.025	39.411	0.242	0.242	0.000	0.000	0.000	0.000
139	A	138	LEU	0	-0.080	-0.029	40.497	0.232	0.232	0.000	0.000	0.000	0.000
140	A	139	GLY	0	0.002	0.005	42.589	0.085	0.085	0.000	0.000	0.000	0.000
141	A	140	TYR	0	-0.065	-0.074	37.174	-0.067	-0.067	0.000	0.000	0.000	0.000
142	A	141	ASP	-1	-0.891	-0.921	39.345	-7.951	-7.951	0.000	0.000	0.000	0.000
143	A	142	ILE	0	0.037	0.016	33.134	-0.094	-0.094	0.000	0.000	0.000	0.000
144	A	143	LYS	1	0.765	0.874	34.361	8.065	8.065	0.000	0.000	0.000	0.000
145	A	144	LEU	0	0.013	0.011	27.820	-0.150	-0.150	0.000	0.000	0.000	0.000
146	A	145	ASP	0	-0.077	-0.068	26.181	0.149	0.149	0.000	0.000	0.000	0.000
147	A	146	LEU	0	0.013	0.001	26.293	-0.381	-0.381	0.000	0.000	0.000	0.000
148	A	147	PHE	-1	-0.858	-0.885	22.987	-13.404	-13.404	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)