FMO DATABASE

FMODB ID: 7KR7K

Calculation Name: 6A6F-B-Xray547

Preferred Name:

Target Type:

Ligand Name: glycerol | di(hydroxyethyl)ether | nickel (ii) ion | zinc ion

Ligand 3-letter code: GOL | PEG | NI | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6A6F

Chain ID: B

ChEMBL ID:

UniProt ID: A0A1B0

Base Structure: X-ray

Registration Date: 2025-10-06

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	136
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1303997.361863
FMO2-HF: Nuclear repulsion	1247674.990462
FMO2-HF: Total energy	-56322.371401
FMO2-MP2: Total energy	-56480.580686

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:-2:GLY)

Summations of interaction energy for fragment #1(A:-2: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.
-55.379	-54.4	12.606	-6.923	-6.662	-0.094

Interaction energy analysis for fragmet #1(A:-2:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.792 / q_NPA : 0.884

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	0	HIS	0	0.088	0.043	2.055	-20.827	-18.405	7.035	-5.002	-4.455	-0.065
4	A	1	MET	0	0.030	0.008	2.734	-11.972	-13.415	5.571	-1.921	-2.207	-0.029
5	A	2	ILE	0	0.014	0.030	5.519	4.898	4.898	0.000	0.000	0.000	0.000
6	A	3	TYR	0	-0.022	-0.014	7.492	4.632	4.632	0.000	0.000	0.000	0.000
7	A	4	SER	0	0.059	0.029	9.636	-0.654	-0.654	0.000	0.000	0.000	0.000
8	A	5	GLU	-1	-0.894	-0.947	11.580	-18.320	-18.320	0.000	0.000	0.000	0.000
9	A	6	PHE	0	0.075	0.036	14.179	0.660	0.660	0.000	0.000	0.000	0.000
10	A	7	ILE	0	0.011	0.007	13.149	0.885	0.885	0.000	0.000	0.000	0.000
11	A	8	MET	0	-0.005	-0.017	11.692	0.432	0.432	0.000	0.000	0.000	0.000
12	A	9	ASP	-1	-0.867	-0.909	14.880	-16.325	-16.325	0.000	0.000	0.000	0.000
13	A	10	TYR	0	-0.040	-0.050	18.421	0.564	0.564	0.000	0.000	0.000	0.000
14	A	11	SER	0	-0.059	-0.015	16.463	0.902	0.902	0.000	0.000	0.000	0.000
15	A	12	LYS	1	0.816	0.887	16.727	18.093	18.093	0.000	0.000	0.000	0.000
16	A	13	LEU	0	-0.023	0.008	20.443	0.786	0.786	0.000	0.000	0.000	0.000
17	A	14	LYS	1	0.930	0.952	23.606	12.568	12.568	0.000	0.000	0.000	0.000
18	A	15	LYS	1	0.924	0.978	26.619	10.986	10.986	0.000	0.000	0.000	0.000
19	A	16	PHE	0	0.037	0.020	27.131	0.410	0.410	0.000	0.000	0.000	0.000
20	A	17	HIS	0	-0.010	0.008	26.732	-0.134	-0.134	0.000	0.000	0.000	0.000
21	A	18	GLY	0	0.008	0.007	28.827	0.254	0.254	0.000	0.000	0.000	0.000
22	A	19	LYS	1	0.845	0.908	32.038	9.304	9.304	0.000	0.000	0.000	0.000
23	A	20	ILE	0	-0.010	0.002	35.154	0.045	0.045	0.000	0.000	0.000	0.000
24	A	21	GLU	-1	-0.933	-0.972	38.019	-7.323	-7.323	0.000	0.000	0.000	0.000
25	A	22	ASN	0	-0.051	-0.035	41.367	0.105	0.105	0.000	0.000	0.000	0.000
26	A	23	ALA	0	-0.010	0.007	39.206	0.078	0.078	0.000	0.000	0.000	0.000
27	A	24	HIS	0	0.020	0.013	41.207	0.018	0.018	0.000	0.000	0.000	0.000
28	A	25	LYS	1	0.855	0.941	37.467	8.588	8.588	0.000	0.000	0.000	0.000
29	A	26	VAL	0	0.006	0.002	35.722	-0.147	-0.147	0.000	0.000	0.000	0.000
30	A	27	GLU	-1	-0.872	-0.939	33.338	-8.800	-8.800	0.000	0.000	0.000	0.000
31	A	28	GLU	-1	-0.847	-0.917	30.813	-10.419	-10.419	0.000	0.000	0.000	0.000
32	A	29	GLY	0	0.032	0.035	28.651	0.129	0.129	0.000	0.000	0.000	0.000
33	A	30	LYS	1	0.831	0.900	26.126	10.284	10.284	0.000	0.000	0.000	0.000
34	A	31	ASN	0	-0.059	-0.047	19.528	0.521	0.521	0.000	0.000	0.000	0.000
35	A	32	LEU	0	0.047	0.008	22.066	-0.705	-0.705	0.000	0.000	0.000	0.000
36	A	33	SER	0	-0.039	-0.011	20.259	0.026	0.026	0.000	0.000	0.000	0.000
37	A	34	CYS	0	-0.083	-0.050	16.641	-1.296	-1.296	0.000	0.000	0.000	0.000
38	A	35	GLY	0	-0.007	0.009	18.504	-0.430	-0.430	0.000	0.000	0.000	0.000
39	A	36	ASP	-1	-0.715	-0.819	18.712	-17.078	-17.078	0.000	0.000	0.000	0.000
40	A	37	GLU	-1	-0.947	-0.978	21.694	-11.158	-11.158	0.000	0.000	0.000	0.000
41	A	38	VAL	0	-0.002	-0.009	25.012	-0.240	-0.240	0.000	0.000	0.000	0.000
42	A	39	THR	0	0.006	0.010	27.094	0.397	0.397	0.000	0.000	0.000	0.000
43	A	40	LEU	0	-0.009	-0.006	28.379	-0.125	-0.125	0.000	0.000	0.000	0.000
44	A	41	TYR	0	0.035	-0.003	31.932	0.442	0.442	0.000	0.000	0.000	0.000
45	A	42	PHE	0	0.028	0.003	33.117	-0.210	-0.210	0.000	0.000	0.000	0.000
46	A	43	LEU	0	-0.007	0.005	37.284	0.236	0.236	0.000	0.000	0.000	0.000
47	A	44	PHE	0	-0.013	-0.022	38.294	-0.183	-0.183	0.000	0.000	0.000	0.000
48	A	45	ASP	-1	-0.861	-0.922	42.333	-6.793	-6.793	0.000	0.000	0.000	0.000
49	A	46	GLY	0	0.028	0.016	45.249	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	47	ASP	-1	-0.842	-0.924	43.127	-7.359	-7.359	0.000	0.000	0.000	0.000
51	A	48	LYS	1	0.841	0.924	41.003	7.169	7.169	0.000	0.000	0.000	0.000
52	A	49	ILE	0	0.011	0.001	35.603	0.099	0.099	0.000	0.000	0.000	0.000
53	A	50	VAL	0	-0.060	-0.033	38.804	-0.031	-0.031	0.000	0.000	0.000	0.000
54	A	51	ASP	-1	-0.807	-0.911	35.473	-9.044	-9.044	0.000	0.000	0.000	0.000
55	A	52	VAL	0	-0.009	-0.009	31.962	0.087	0.087	0.000	0.000	0.000	0.000
56	A	53	LYS	1	0.818	0.921	31.254	9.042	9.042	0.000	0.000	0.000	0.000
57	A	54	PHE	0	-0.002	-0.007	24.318	0.031	0.031	0.000	0.000	0.000	0.000
58	A	55	GLU	-1	-0.828	-0.904	29.078	-10.355	-10.355	0.000	0.000	0.000	0.000
59	A	56	GLY	0	0.042	0.035	27.045	-0.070	-0.070	0.000	0.000	0.000	0.000
60	A	57	HIS	0	-0.042	-0.025	22.327	-0.579	-0.579	0.000	0.000	0.000	0.000
61	A	58	GLY	0	0.085	0.037	20.002	0.241	0.241	0.000	0.000	0.000	0.000
62	A	59	CYS	0	-0.105	-0.034	14.432	-0.987	-0.987	0.000	0.000	0.000	0.000
63	A	60	ALA	0	0.027	-0.003	13.449	0.676	0.676	0.000	0.000	0.000	0.000
64	A	61	ILE	0	0.005	0.000	12.143	0.568	0.568	0.000	0.000	0.000	0.000
65	A	62	SER	0	0.032	0.017	16.080	1.125	1.125	0.000	0.000	0.000	0.000
66	A	63	GLN	0	0.010	0.015	18.801	1.288	1.288	0.000	0.000	0.000	0.000
67	A	64	ALA	0	0.005	0.007	17.740	0.686	0.686	0.000	0.000	0.000	0.000
68	A	65	SER	0	-0.045	-0.034	19.670	0.759	0.759	0.000	0.000	0.000	0.000
69	A	66	THR	0	0.018	-0.010	21.410	0.788	0.788	0.000	0.000	0.000	0.000
70	A	67	ASN	0	-0.033	-0.033	22.359	1.130	1.130	0.000	0.000	0.000	0.000
71	A	68	VAL	0	-0.002	0.000	21.529	0.460	0.460	0.000	0.000	0.000	0.000
72	A	69	MET	0	-0.025	0.006	24.580	0.459	0.459	0.000	0.000	0.000	0.000
73	A	70	ILE	0	-0.014	-0.012	26.885	0.452	0.452	0.000	0.000	0.000	0.000
74	A	71	GLU	-1	-0.912	-0.941	26.740	-11.460	-11.460	0.000	0.000	0.000	0.000
75	A	72	GLN	0	-0.006	0.004	27.495	0.515	0.515	0.000	0.000	0.000	0.000
76	A	73	ILE	0	0.006	0.000	30.218	0.346	0.346	0.000	0.000	0.000	0.000
77	A	74	ILE	0	-0.001	0.008	32.708	0.360	0.360	0.000	0.000	0.000	0.000
78	A	75	GLY	0	-0.042	-0.016	34.894	-0.034	-0.034	0.000	0.000	0.000	0.000
79	A	76	LYS	1	0.850	0.943	33.106	9.773	9.773	0.000	0.000	0.000	0.000
80	A	77	THR	0	-0.007	-0.043	37.660	0.120	0.120	0.000	0.000	0.000	0.000
81	A	78	LYS	1	0.887	0.925	37.607	7.328	7.328	0.000	0.000	0.000	0.000
82	A	79	GLN	0	-0.013	0.004	37.458	-0.205	-0.205	0.000	0.000	0.000	0.000
83	A	80	GLU	-1	-0.765	-0.861	36.158	-8.504	-8.504	0.000	0.000	0.000	0.000
84	A	81	ALA	0	0.001	0.007	33.339	-0.341	-0.341	0.000	0.000	0.000	0.000
85	A	82	LEU	0	-0.014	-0.004	32.554	-0.395	-0.395	0.000	0.000	0.000	0.000
86	A	83	GLU	-1	-0.961	-0.978	33.472	-9.159	-9.159	0.000	0.000	0.000	0.000
87	A	84	MET	0	-0.025	-0.006	28.944	-0.382	-0.382	0.000	0.000	0.000	0.000
88	A	85	MET	0	-0.015	0.005	28.788	-0.401	-0.401	0.000	0.000	0.000	0.000
89	A	86	LYS	1	0.960	0.981	28.673	8.945	8.945	0.000	0.000	0.000	0.000
90	A	87	ASN	0	-0.012	-0.013	28.947	-0.235	-0.235	0.000	0.000	0.000	0.000
91	A	88	ALA	0	0.036	0.028	24.772	-0.429	-0.429	0.000	0.000	0.000	0.000
92	A	89	GLU	-1	-0.882	-0.955	24.295	-12.126	-12.126	0.000	0.000	0.000	0.000
93	A	90	ASN	0	-0.042	-0.033	25.585	-0.311	-0.311	0.000	0.000	0.000	0.000
94	A	91	MET	0	0.005	0.035	21.068	-0.297	-0.297	0.000	0.000	0.000	0.000
95	A	92	MET	0	-0.094	-0.034	18.429	-0.906	-0.906	0.000	0.000	0.000	0.000
96	A	93	LEU	0	-0.056	-0.038	21.824	-0.420	-0.420	0.000	0.000	0.000	0.000
97	A	94	GLY	0	-0.056	-0.021	23.786	0.185	0.185	0.000	0.000	0.000	0.000
98	A	95	LYS	1	0.864	0.947	24.494	11.074	11.074	0.000	0.000	0.000	0.000
99	A	96	GLU	-1	-0.866	-0.934	27.255	-11.301	-11.301	0.000	0.000	0.000	0.000
100	A	97	PHE	0	-0.031	-0.034	24.202	0.087	0.087	0.000	0.000	0.000	0.000
101	A	98	ASP	-1	-0.804	-0.898	29.508	-9.780	-9.780	0.000	0.000	0.000	0.000
102	A	99	GLU	-1	-0.915	-0.964	26.354	-12.266	-12.266	0.000	0.000	0.000	0.000
103	A	100	ASN	0	-0.075	-0.053	28.855	-0.132	-0.132	0.000	0.000	0.000	0.000
104	A	101	VAL	0	-0.036	-0.005	31.076	0.067	0.067	0.000	0.000	0.000	0.000
105	A	102	LEU	0	-0.030	-0.014	25.037	-0.111	-0.111	0.000	0.000	0.000	0.000
106	A	103	GLY	0	0.077	0.042	26.871	-0.212	-0.212	0.000	0.000	0.000	0.000
107	A	104	PRO	0	-0.014	-0.007	24.005	-0.559	-0.559	0.000	0.000	0.000	0.000
108	A	105	ILE	0	0.004	-0.004	22.318	-0.884	-0.884	0.000	0.000	0.000	0.000
109	A	106	ILE	0	0.054	0.023	21.614	-0.778	-0.778	0.000	0.000	0.000	0.000
110	A	107	ASN	0	-0.054	-0.030	18.086	-1.086	-1.086	0.000	0.000	0.000	0.000
111	A	108	PHE	0	-0.027	-0.019	16.810	-1.438	-1.438	0.000	0.000	0.000	0.000
112	A	109	TYR	0	0.051	0.024	17.445	-0.187	-0.187	0.000	0.000	0.000	0.000
113	A	110	ASP	-1	-0.871	-0.951	12.881	-21.876	-21.876	0.000	0.000	0.000	0.000
114	A	111	VAL	0	-0.058	-0.044	13.704	-1.788	-1.788	0.000	0.000	0.000	0.000
115	A	112	LYS	1	0.923	0.965	14.916	14.964	14.964	0.000	0.000	0.000	0.000
116	A	113	ASN	0	-0.048	-0.002	12.556	1.437	1.437	0.000	0.000	0.000	0.000
117	A	114	TYR	0	-0.034	-0.017	7.704	-3.508	-3.508	0.000	0.000	0.000	0.000
118	A	115	PRO	0	0.075	0.030	13.170	0.732	0.732	0.000	0.000	0.000	0.000
119	A	116	MET	0	0.001	-0.004	15.174	1.146	1.146	0.000	0.000	0.000	0.000
120	A	117	ARG	1	0.814	0.858	10.968	25.425	25.425	0.000	0.000	0.000	0.000
121	A	118	VAL	0	0.089	0.051	15.777	0.514	0.514	0.000	0.000	0.000	0.000
122	A	119	LYS	1	0.902	0.959	18.833	14.628	14.628	0.000	0.000	0.000	0.000
123	A	120	CYS	0	-0.041	-0.010	16.939	0.122	0.122	0.000	0.000	0.000	0.000
124	A	121	PHE	0	0.027	0.013	18.219	0.323	0.323	0.000	0.000	0.000	0.000
125	A	122	LEU	0	0.012	0.006	19.849	0.653	0.653	0.000	0.000	0.000	0.000
126	A	123	LEU	0	-0.027	0.018	22.600	0.565	0.565	0.000	0.000	0.000	0.000
127	A	124	PRO	0	0.017	0.024	23.036	0.642	0.642	0.000	0.000	0.000	0.000
128	A	125	TRP	0	0.078	0.026	23.589	0.798	0.798	0.000	0.000	0.000	0.000
129	A	126	LYS	1	0.899	0.940	25.850	12.359	12.359	0.000	0.000	0.000	0.000
130	A	127	THR	0	-0.024	-0.019	27.945	0.393	0.393	0.000	0.000	0.000	0.000
131	A	128	LEU	0	0.002	-0.015	29.963	0.392	0.392	0.000	0.000	0.000	0.000
132	A	129	GLU	-1	-0.891	-0.953	31.422	-9.430	-9.430	0.000	0.000	0.000	0.000
133	A	130	ILE	0	-0.023	-0.011	32.241	0.274	0.274	0.000	0.000	0.000	0.000
134	A	131	ALA	0	-0.027	-0.006	34.404	0.279	0.279	0.000	0.000	0.000	0.000
135	A	132	LEU	0	-0.069	-0.040	35.428	0.282	0.282	0.000	0.000	0.000	0.000
136	A	133	LYS	0	-0.080	-0.025	35.846	1.104	1.104	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-2:GLY)