FMO DATABASE

FMODB ID: 4GNRN

Calculation Name: 4ZFZ-B-Xray547

Preferred Name:

Target Type:

Ligand Name: myristic acid | 2-amino-2-hydroxymethyl-propane-1,3-diol | 1,2-ethanediol | zinc ion | chloride ion

Ligand 3-letter code: MYR | TRS | EDO | ZN | CL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4ZFZ

Chain ID: B

ChEMBL ID:

UniProt ID: Q6V7J5

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	99
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-775224.321228
FMO2-HF: Nuclear repulsion	733899.15628
FMO2-HF: Total energy	-41325.164948
FMO2-MP2: Total energy	-41445.013218

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:0:ALA)

Summations of interaction energy for fragment #1(B:0:ALA)

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.
-2.472	-0.44400000000001	0.118	-1.02	-1.126	-0.004

Interaction energy analysis for fragmet #1(B:0:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.859 / q_NPA : 0.925

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	2	GLN	0	0.042	0.011	3.204	-4.057	-2.029	0.118	-1.020	-1.126	-0.004
4	B	3	ARG	1	0.789	0.897	6.020	31.819	31.819	0.000	0.000	0.000	0.000
5	B	4	THR	0	0.051	0.028	9.493	0.260	0.260	0.000	0.000	0.000	0.000
6	B	5	PRO	0	-0.019	0.009	12.814	0.558	0.558	0.000	0.000	0.000	0.000
7	B	6	LYS	1	0.929	0.965	15.276	17.641	17.641	0.000	0.000	0.000	0.000
8	B	7	ILE	0	0.018	-0.008	18.344	-0.158	-0.158	0.000	0.000	0.000	0.000
9	B	8	GLN	0	-0.006	0.005	21.289	0.016	0.016	0.000	0.000	0.000	0.000
10	B	9	VAL	0	0.012	-0.005	24.716	-0.110	-0.110	0.000	0.000	0.000	0.000
11	B	10	TYR	0	0.033	0.014	25.938	0.047	0.047	0.000	0.000	0.000	0.000
12	B	11	SER	0	0.029	0.007	30.577	-0.126	-0.126	0.000	0.000	0.000	0.000
13	B	12	ARG	1	0.875	0.947	31.528	9.066	9.066	0.000	0.000	0.000	0.000
14	B	13	HIS	0	0.000	0.004	33.648	0.022	0.022	0.000	0.000	0.000	0.000
15	B	14	PRO	0	0.077	0.040	37.080	-0.134	-0.134	0.000	0.000	0.000	0.000
16	B	15	PRO	0	-0.006	0.013	37.465	0.100	0.100	0.000	0.000	0.000	0.000
17	B	16	GLU	-1	-0.822	-0.897	39.674	-6.722	-6.722	0.000	0.000	0.000	0.000
18	B	17	ASN	0	-0.040	-0.048	43.031	-0.191	-0.191	0.000	0.000	0.000	0.000
19	B	18	GLY	0	-0.004	-0.004	44.137	0.150	0.150	0.000	0.000	0.000	0.000
20	B	19	LYS	1	0.844	0.914	42.983	6.797	6.797	0.000	0.000	0.000	0.000
21	B	20	PRO	0	-0.016	-0.011	41.095	-0.182	-0.182	0.000	0.000	0.000	0.000
22	B	21	ASN	0	-0.001	0.002	36.701	-0.156	-0.156	0.000	0.000	0.000	0.000
23	B	22	PHE	0	0.017	-0.007	32.700	-0.046	-0.046	0.000	0.000	0.000	0.000
24	B	23	LEU	0	-0.008	0.017	30.203	-0.016	-0.016	0.000	0.000	0.000	0.000
25	B	24	ASN	0	-0.018	-0.018	27.557	-0.146	-0.146	0.000	0.000	0.000	0.000
26	B	25	CYS	0	-0.032	-0.011	23.591	-0.208	-0.208	0.000	0.000	0.000	0.000
27	B	26	TYR	0	-0.017	0.014	19.979	-0.420	-0.420	0.000	0.000	0.000	0.000
28	B	27	VAL	0	0.026	0.008	16.780	-0.141	-0.141	0.000	0.000	0.000	0.000
29	B	28	SER	0	0.036	0.005	16.334	-0.331	-0.331	0.000	0.000	0.000	0.000
30	B	29	GLY	0	0.002	-0.003	13.914	-0.015	-0.015	0.000	0.000	0.000	0.000
31	B	30	PHE	0	-0.017	0.002	11.335	-1.364	-1.364	0.000	0.000	0.000	0.000
32	B	31	HIS	0	0.015	-0.003	5.099	-3.778	-3.778	0.000	0.000	0.000	0.000
33	B	32	PRO	0	0.043	0.019	5.305	-2.024	-2.024	0.000	0.000	0.000	0.000
34	B	33	SER	0	0.028	0.003	6.939	1.421	1.421	0.000	0.000	0.000	0.000
35	B	34	ASP	-1	-0.916	-0.939	10.241	-20.872	-20.872	0.000	0.000	0.000	0.000
36	B	35	ILE	0	-0.069	-0.044	12.127	-0.756	-0.756	0.000	0.000	0.000	0.000
37	B	36	GLU	-1	-0.888	-0.914	14.877	-14.868	-14.868	0.000	0.000	0.000	0.000
38	B	37	VAL	0	-0.020	-0.036	18.359	-0.164	-0.164	0.000	0.000	0.000	0.000
39	B	38	ASP	-1	-0.817	-0.884	21.194	-11.670	-11.670	0.000	0.000	0.000	0.000
40	B	39	LEU	0	0.018	0.000	24.868	-0.085	-0.085	0.000	0.000	0.000	0.000
41	B	40	LEU	0	-0.057	-0.035	27.222	0.104	0.104	0.000	0.000	0.000	0.000
42	B	41	LYS	1	0.912	0.946	30.347	8.097	8.097	0.000	0.000	0.000	0.000
43	B	42	ASN	0	-0.011	-0.021	34.154	-0.013	-0.013	0.000	0.000	0.000	0.000
44	B	43	GLY	0	-0.007	0.008	31.639	0.065	0.065	0.000	0.000	0.000	0.000
45	B	44	GLU	-1	-0.946	-0.961	31.215	-8.709	-8.709	0.000	0.000	0.000	0.000
46	B	45	LYS	1	0.896	0.941	26.398	11.082	11.082	0.000	0.000	0.000	0.000
47	B	46	MET	0	-0.019	0.007	30.363	0.262	0.262	0.000	0.000	0.000	0.000
48	B	47	GLY	0	0.029	0.016	30.537	-0.259	-0.259	0.000	0.000	0.000	0.000
49	B	48	LYS	1	0.954	0.955	32.296	8.181	8.181	0.000	0.000	0.000	0.000
50	B	49	VAL	0	-0.008	0.030	26.262	0.046	0.046	0.000	0.000	0.000	0.000
51	B	50	GLU	-1	-0.848	-0.897	27.227	-10.027	-10.027	0.000	0.000	0.000	0.000
52	B	51	HIS	1	0.864	0.897	22.026	12.768	12.768	0.000	0.000	0.000	0.000
53	B	52	SER	0	0.000	0.015	20.887	0.193	0.193	0.000	0.000	0.000	0.000
54	B	53	ASP	-1	-0.868	-0.918	21.094	-12.803	-12.803	0.000	0.000	0.000	0.000
55	B	54	LEU	0	-0.047	-0.030	12.994	-0.230	-0.230	0.000	0.000	0.000	0.000
56	B	55	SER	0	0.028	0.018	16.767	-0.089	-0.089	0.000	0.000	0.000	0.000
57	B	56	PHE	0	-0.001	-0.010	12.883	-1.133	-1.133	0.000	0.000	0.000	0.000
58	B	57	SER	0	0.002	0.010	14.306	1.561	1.561	0.000	0.000	0.000	0.000
59	B	58	LYS	1	0.964	0.972	14.627	14.874	14.874	0.000	0.000	0.000	0.000
60	B	59	ASP	-1	-0.776	-0.862	12.375	-22.473	-22.473	0.000	0.000	0.000	0.000
61	B	60	TRP	0	-0.009	-0.005	9.365	-2.626	-2.626	0.000	0.000	0.000	0.000
62	B	61	SER	0	-0.098	-0.060	10.098	-1.060	-1.060	0.000	0.000	0.000	0.000
63	B	62	PHE	0	0.035	0.004	8.071	1.472	1.472	0.000	0.000	0.000	0.000
64	B	63	TYR	0	-0.044	-0.030	12.869	0.443	0.443	0.000	0.000	0.000	0.000
65	B	64	LEU	0	-0.017	0.003	16.456	0.018	0.018	0.000	0.000	0.000	0.000
66	B	65	LEU	0	-0.018	0.008	19.111	0.059	0.059	0.000	0.000	0.000	0.000
67	B	66	TYR	0	0.040	0.008	18.978	0.237	0.237	0.000	0.000	0.000	0.000
68	B	67	TYR	0	-0.072	-0.055	24.327	0.058	0.058	0.000	0.000	0.000	0.000
69	B	68	THR	0	0.001	-0.024	28.167	0.048	0.048	0.000	0.000	0.000	0.000
70	B	69	GLU	-1	-0.939	-0.953	31.506	-8.112	-8.112	0.000	0.000	0.000	0.000
71	B	70	PHE	0	-0.053	-0.038	35.010	-0.053	-0.053	0.000	0.000	0.000	0.000
72	B	71	THR	0	-0.011	-0.007	36.982	0.211	0.211	0.000	0.000	0.000	0.000
73	B	72	PRO	0	-0.026	0.016	38.432	-0.014	-0.014	0.000	0.000	0.000	0.000
74	B	73	ASN	0	0.020	-0.019	40.022	0.366	0.366	0.000	0.000	0.000	0.000
75	B	74	GLU	-1	-0.807	-0.892	41.508	-7.404	-7.404	0.000	0.000	0.000	0.000
76	B	75	LYS	1	0.835	0.915	42.526	7.237	7.237	0.000	0.000	0.000	0.000
77	B	76	ASP	-1	-0.845	-0.891	38.781	-7.725	-7.725	0.000	0.000	0.000	0.000
78	B	77	GLU	-1	-0.838	-0.905	35.202	-8.785	-8.785	0.000	0.000	0.000	0.000
79	B	78	TYR	0	0.021	0.000	32.680	0.004	0.004	0.000	0.000	0.000	0.000
80	B	79	ALA	0	-0.004	0.004	28.757	-0.052	-0.052	0.000	0.000	0.000	0.000
81	B	81	ARG	1	0.859	0.928	22.466	11.943	11.943	0.000	0.000	0.000	0.000
82	B	82	VAL	0	0.030	0.013	17.224	-0.078	-0.078	0.000	0.000	0.000	0.000
83	B	83	ASN	0	-0.050	-0.039	17.174	-0.309	-0.309	0.000	0.000	0.000	0.000
84	B	84	HIS	0	0.053	0.024	8.980	0.201	0.201	0.000	0.000	0.000	0.000
85	B	85	VAL	0	0.042	0.032	7.657	0.504	0.504	0.000	0.000	0.000	0.000
86	B	86	THR	0	-0.070	-0.055	8.770	-0.230	-0.230	0.000	0.000	0.000	0.000
87	B	87	LEU	0	-0.058	-0.029	11.049	1.123	1.123	0.000	0.000	0.000	0.000
88	B	88	SER	0	-0.007	-0.010	14.812	-0.447	-0.447	0.000	0.000	0.000	0.000
89	B	89	GLY	0	0.031	0.020	17.063	0.672	0.672	0.000	0.000	0.000	0.000
90	B	90	PRO	0	-0.019	-0.009	18.739	-0.286	-0.286	0.000	0.000	0.000	0.000
91	B	91	ARG	1	0.958	0.997	17.775	16.842	16.842	0.000	0.000	0.000	0.000
92	B	92	THR	0	-0.005	-0.016	21.237	0.054	0.054	0.000	0.000	0.000	0.000
93	B	93	VAL	0	-0.031	-0.012	23.548	0.045	0.045	0.000	0.000	0.000	0.000
94	B	94	LYS	1	0.982	0.978	26.334	9.441	9.441	0.000	0.000	0.000	0.000
95	B	95	TRP	0	-0.008	-0.017	29.759	-0.110	-0.110	0.000	0.000	0.000	0.000
96	B	96	ASP	-1	-0.864	-0.936	31.558	-8.732	-8.732	0.000	0.000	0.000	0.000
97	B	97	ARG	1	0.773	0.861	33.797	8.030	8.030	0.000	0.000	0.000	0.000
98	B	98	ASP	-1	-0.957	-0.974	36.775	-7.457	-7.457	0.000	0.000	0.000	0.000
99	B	99	MET	-1	-0.988	-0.968	31.708	-8.654	-8.654	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:0:ALA)