FMO DATABASE

FMODB ID: 34N3L

Calculation Name: 2NZC-A-Xray549

Preferred Name:

Target Type:

Ligand Name: phosphate ion | glycerol | acetic acid

Ligand 3-letter code: PO4 | GOL | ACY

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2NZC

Chain ID: A

ChEMBL ID:

UniProt ID: Q9X0Z3

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	80
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-527482.683489
FMO2-HF: Nuclear repulsion	495965.617707
FMO2-HF: Total energy	-31517.065782
FMO2-MP2: Total energy	-31610.902113

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:GLU)

Summations of interaction energy for fragment #1(A:2:GLU)

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.
25.545	27.695	0.682	-1.113	-1.72	-0.001

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.080 / q_NPA : -0.049

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	4	ARG	1	0.917	0.960	3.845	6.585	7.932	-0.008	-0.620	-0.719	0.000
55	A	56	ASP	-1	-0.821	-0.884	2.405	3.786	4.393	0.689	-0.440	-0.856	-0.001
56	A	57	ASN	0	0.009	-0.017	4.124	-0.464	-0.268	0.001	-0.053	-0.145	0.000
4	A	5	PHE	0	0.052	0.017	6.493	2.418	2.418	0.000	0.000	0.000	0.000
5	A	6	TYR	0	-0.026	-0.009	7.336	-1.222	-1.222	0.000	0.000	0.000	0.000
6	A	7	ILE	0	0.023	0.021	12.470	0.513	0.513	0.000	0.000	0.000	0.000
7	A	8	LEU	0	0.007	0.003	14.620	-0.064	-0.064	0.000	0.000	0.000	0.000
8	A	9	THR	0	-0.034	-0.017	17.791	0.045	0.045	0.000	0.000	0.000	0.000
9	A	10	ILE	0	-0.008	-0.004	19.746	-0.013	-0.013	0.000	0.000	0.000	0.000
10	A	11	VAL	0	-0.024	-0.018	23.248	-0.025	-0.025	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.019	-0.012	26.054	0.026	0.026	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.782	-0.886	28.714	0.077	0.077	0.000	0.000	0.000	0.000
13	A	14	ASP	-1	-0.946	-0.978	31.916	0.290	0.290	0.000	0.000	0.000	0.000
14	A	15	ARG	1	0.845	0.904	32.376	-0.195	-0.195	0.000	0.000	0.000	0.000
15	A	16	GLU	-1	-0.878	-0.933	32.066	0.434	0.434	0.000	0.000	0.000	0.000
16	A	17	LYS	1	0.910	0.949	30.503	-0.496	-0.496	0.000	0.000	0.000	0.000
17	A	18	ALA	0	0.021	0.018	28.435	0.067	0.067	0.000	0.000	0.000	0.000
18	A	19	TYR	0	0.023	0.005	27.172	0.060	0.060	0.000	0.000	0.000	0.000
19	A	20	ARG	1	0.856	0.922	27.038	-0.756	-0.756	0.000	0.000	0.000	0.000
20	A	21	GLN	0	0.024	0.002	25.304	0.051	0.051	0.000	0.000	0.000	0.000
21	A	22	VAL	0	0.010	0.004	22.389	0.110	0.110	0.000	0.000	0.000	0.000
22	A	23	ASN	0	0.003	0.004	21.939	0.081	0.081	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.842	-0.911	22.047	1.131	1.131	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.003	0.003	17.806	0.186	0.186	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.030	-0.036	17.371	0.210	0.210	0.000	0.000	0.000	0.000
26	A	27	HIS	0	-0.016	0.004	17.567	0.009	0.009	0.000	0.000	0.000	0.000
27	A	28	ASN	0	-0.076	-0.042	15.776	0.019	0.019	0.000	0.000	0.000	0.000
28	A	29	PHE	0	0.019	0.015	11.297	0.353	0.353	0.000	0.000	0.000	0.000
29	A	30	SER	0	-0.044	-0.032	13.637	-0.340	-0.340	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.859	-0.920	10.846	3.675	3.675	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.849	-0.919	8.357	6.869	6.869	0.000	0.000	0.000	0.000
32	A	33	ILE	0	-0.076	-0.041	10.972	-1.097	-1.097	0.000	0.000	0.000	0.000
33	A	34	LEU	0	-0.027	-0.015	12.322	-0.080	-0.080	0.000	0.000	0.000	0.000
34	A	35	LEU	0	-0.005	-0.002	15.663	-0.097	-0.097	0.000	0.000	0.000	0.000
35	A	36	ARG	1	0.917	0.953	18.401	-0.670	-0.670	0.000	0.000	0.000	0.000
36	A	37	VAL	0	-0.004	0.004	20.959	0.006	0.006	0.000	0.000	0.000	0.000
37	A	38	GLY	0	0.007	0.003	24.420	0.006	0.006	0.000	0.000	0.000	0.000
38	A	39	TYR	0	-0.002	-0.006	27.025	-0.012	-0.012	0.000	0.000	0.000	0.000
39	A	40	PRO	0	-0.013	-0.017	30.217	-0.009	-0.009	0.000	0.000	0.000	0.000
40	A	41	VAL	0	0.016	0.010	32.439	-0.025	-0.025	0.000	0.000	0.000	0.000
41	A	42	ARG	1	0.982	0.965	35.048	-0.136	-0.136	0.000	0.000	0.000	0.000
42	A	43	GLU	-1	-0.951	-0.955	38.003	-0.085	-0.085	0.000	0.000	0.000	0.000
43	A	44	GLU	-1	-0.899	-0.952	36.339	-0.099	-0.099	0.000	0.000	0.000	0.000
44	A	45	ASN	0	-0.071	-0.021	37.174	0.029	0.029	0.000	0.000	0.000	0.000
45	A	46	MET	0	-0.007	-0.001	31.466	0.000	0.000	0.000	0.000	0.000	0.000
46	A	47	ALA	0	-0.016	0.004	29.519	0.004	0.004	0.000	0.000	0.000	0.000
47	A	48	ILE	0	-0.012	0.006	26.195	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	49	ILE	0	-0.023	-0.022	22.072	0.072	0.072	0.000	0.000	0.000	0.000
49	A	50	PHE	0	-0.002	0.007	21.796	-0.062	-0.062	0.000	0.000	0.000	0.000
50	A	51	LEU	0	0.028	-0.001	16.847	0.161	0.161	0.000	0.000	0.000	0.000
51	A	52	VAL	0	-0.009	-0.002	14.670	-0.315	-0.315	0.000	0.000	0.000	0.000
52	A	53	LEU	0	0.041	0.023	11.176	0.362	0.362	0.000	0.000	0.000	0.000
53	A	54	LYS	1	0.885	0.947	6.812	3.323	3.323	0.000	0.000	0.000	0.000
54	A	55	THR	0	0.044	0.017	5.821	2.648	2.648	0.000	0.000	0.000	0.000
57	A	58	ASP	-1	-0.926	-0.944	6.512	2.357	2.357	0.000	0.000	0.000	0.000
58	A	59	THR	0	-0.010	-0.028	6.324	-0.948	-0.948	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.004	-0.002	8.330	-0.545	-0.545	0.000	0.000	0.000	0.000
60	A	61	GLY	0	0.017	0.030	10.363	-0.312	-0.312	0.000	0.000	0.000	0.000
61	A	62	ALA	0	-0.004	-0.008	11.707	-0.108	-0.108	0.000	0.000	0.000	0.000
62	A	63	LEU	0	-0.002	0.006	12.769	-0.173	-0.173	0.000	0.000	0.000	0.000
63	A	64	SER	0	-0.026	-0.034	14.015	-0.311	-0.311	0.000	0.000	0.000	0.000
64	A	65	GLY	0	-0.001	0.000	16.130	-0.095	-0.095	0.000	0.000	0.000	0.000
65	A	66	LYS	1	0.939	0.971	16.149	-1.814	-1.814	0.000	0.000	0.000	0.000
66	A	67	LEU	0	0.009	-0.001	17.865	-0.056	-0.056	0.000	0.000	0.000	0.000
67	A	68	GLY	0	-0.002	0.002	20.558	-0.063	-0.063	0.000	0.000	0.000	0.000
68	A	69	GLN	0	-0.040	-0.016	21.138	0.043	0.043	0.000	0.000	0.000	0.000
69	A	70	ILE	0	-0.055	-0.006	22.934	0.023	0.023	0.000	0.000	0.000	0.000
70	A	71	SER	0	0.011	-0.005	26.079	-0.087	-0.087	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.041	0.016	29.630	0.039	0.039	0.000	0.000	0.000	0.000
72	A	73	VAL	0	-0.034	0.000	23.482	-0.023	-0.023	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.935	0.977	25.655	0.186	0.186	0.000	0.000	0.000	0.000
74	A	75	VAL	0	0.034	0.011	19.269	0.011	0.011	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.901	0.953	20.723	0.656	0.656	0.000	0.000	0.000	0.000
76	A	77	THR	0	0.048	0.008	14.040	0.113	0.113	0.000	0.000	0.000	0.000
77	A	78	VAL	0	-0.014	-0.004	16.447	-0.114	-0.114	0.000	0.000	0.000	0.000
78	A	79	PRO	0	-0.019	-0.004	11.486	-0.036	-0.036	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.023	-0.023	12.045	0.208	0.208	0.000	0.000	0.000	0.000
80	A	81	LYS	0	0.025	0.024	10.966	-0.742	-0.742	0.000	0.000	0.000	0.000

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