FMO DATABASE

FMODB ID: 2MYKR

Calculation Name: 4Z2F-A-Xray547

Preferred Name:

Target Type:

Ligand Name: (4s)-2-methyl-2,4-pentanediol

Ligand 3-letter code: MPD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4Z2F

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0M3

Base Structure: X-ray

Registration Date: 2025-10-05

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	142
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1387562.131821
FMO2-HF: Nuclear repulsion	1330778.042119
FMO2-HF: Total energy	-56784.089702
FMO2-MP2: Total energy	-56950.261332

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:MET)

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

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.
-32.537	-25.101	2.281	-3.63	-6.086	-0.034

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

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 : 0.905

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	TYR	0	0.003	0.012	2.711	-9.033	-5.632	0.519	-1.666	-2.253	-0.016
47	A	46	GLY	0	-0.050	-0.038	3.151	-23.330	-22.114	0.024	-0.814	-0.426	-0.007
48	A	47	SER	0	0.013	0.011	4.390	10.332	10.544	-0.001	-0.026	-0.184	0.000
73	A	72	TYR	0	-0.009	-0.020	4.799	2.576	2.679	-0.001	-0.003	-0.099	0.000
133	A	132	ASN	0	-0.044	-0.049	2.751	2.593	5.045	1.741	-1.113	-3.081	-0.011
134	A	133	ASP	-1	-0.831	-0.900	4.610	-27.071	-27.019	-0.001	-0.008	-0.043	0.000
4	A	3	LYS	1	0.846	0.927	5.519	28.797	28.797	0.000	0.000	0.000	0.000
5	A	4	ILE	0	-0.005	0.003	8.588	0.206	0.206	0.000	0.000	0.000	0.000
6	A	5	THR	0	-0.008	0.004	11.829	0.686	0.686	0.000	0.000	0.000	0.000
7	A	6	VAL	0	-0.013	-0.007	14.098	0.540	0.540	0.000	0.000	0.000	0.000
8	A	7	ARG	1	0.902	0.950	17.705	14.814	14.814	0.000	0.000	0.000	0.000
9	A	8	VAL	0	0.002	-0.010	20.702	-0.081	-0.081	0.000	0.000	0.000	0.000
10	A	9	TYR	0	-0.015	-0.004	22.306	0.173	0.173	0.000	0.000	0.000	0.000
11	A	10	GLN	0	0.034	0.012	26.852	0.201	0.201	0.000	0.000	0.000	0.000
12	A	11	THR	0	-0.073	-0.061	30.077	0.184	0.184	0.000	0.000	0.000	0.000
13	A	12	ASN	0	-0.045	-0.024	32.698	0.407	0.407	0.000	0.000	0.000	0.000
14	A	13	PRO	0	0.001	-0.009	35.909	-0.107	-0.107	0.000	0.000	0.000	0.000
15	A	14	ASP	-1	-0.843	-0.880	38.265	-8.089	-8.089	0.000	0.000	0.000	0.000
16	A	15	ALA	0	-0.010	-0.019	36.081	0.083	0.083	0.000	0.000	0.000	0.000
17	A	16	PHE	0	0.009	0.014	31.852	-0.147	-0.147	0.000	0.000	0.000	0.000
18	A	17	PHE	0	-0.005	-0.017	30.402	-0.039	-0.039	0.000	0.000	0.000	0.000
19	A	18	HIS	0	-0.021	-0.008	29.430	-0.174	-0.174	0.000	0.000	0.000	0.000
20	A	19	PRO	0	-0.022	-0.009	25.161	0.023	0.023	0.000	0.000	0.000	0.000
21	A	20	VAL	0	0.010	0.002	27.130	0.089	0.089	0.000	0.000	0.000	0.000
22	A	21	GLU	-1	-0.753	-0.862	24.764	-12.275	-12.275	0.000	0.000	0.000	0.000
23	A	22	LYS	1	0.897	0.959	20.307	14.775	14.775	0.000	0.000	0.000	0.000
24	A	23	THR	0	-0.009	0.010	19.893	-0.145	-0.145	0.000	0.000	0.000	0.000
25	A	24	VAL	0	0.004	-0.006	13.327	-0.425	-0.425	0.000	0.000	0.000	0.000
26	A	25	TRP	0	0.010	0.015	14.098	1.317	1.317	0.000	0.000	0.000	0.000
27	A	26	LYS	1	0.959	0.969	13.439	14.987	14.987	0.000	0.000	0.000	0.000
28	A	27	TYR	0	0.001	0.015	11.521	-0.324	-0.324	0.000	0.000	0.000	0.000
29	A	28	ALA	0	0.027	0.006	6.445	-0.451	-0.451	0.000	0.000	0.000	0.000
30	A	29	ASN	0	-0.028	-0.020	7.020	-1.723	-1.723	0.000	0.000	0.000	0.000
31	A	30	GLY	0	0.031	0.039	9.206	1.362	1.362	0.000	0.000	0.000	0.000
32	A	31	GLY	0	0.012	-0.021	9.441	-3.832	-3.832	0.000	0.000	0.000	0.000
33	A	32	THR	0	-0.062	-0.020	11.464	2.381	2.381	0.000	0.000	0.000	0.000
34	A	33	TRP	0	0.037	0.017	14.171	-1.050	-1.050	0.000	0.000	0.000	0.000
35	A	34	SER	0	0.001	0.002	15.920	1.547	1.547	0.000	0.000	0.000	0.000
36	A	35	ILE	0	0.009	-0.005	17.554	0.089	0.089	0.000	0.000	0.000	0.000
37	A	36	THR	0	-0.052	-0.025	16.668	-0.535	-0.535	0.000	0.000	0.000	0.000
38	A	37	ASP	-1	-0.883	-0.931	18.934	-13.941	-13.941	0.000	0.000	0.000	0.000
39	A	38	ASP	-1	-0.917	-0.953	21.697	-11.683	-11.683	0.000	0.000	0.000	0.000
40	A	39	GLN	0	-0.038	-0.005	17.648	-0.102	-0.102	0.000	0.000	0.000	0.000
41	A	40	HIS	0	0.013	-0.001	18.690	-0.639	-0.639	0.000	0.000	0.000	0.000
42	A	41	VAL	0	-0.006	-0.012	12.796	-0.681	-0.681	0.000	0.000	0.000	0.000
43	A	42	LEU	0	0.003	0.023	12.154	-0.176	-0.176	0.000	0.000	0.000	0.000
44	A	43	THR	0	-0.013	-0.016	8.415	-1.824	-1.824	0.000	0.000	0.000	0.000
45	A	44	MET	0	0.001	0.004	8.387	2.481	2.481	0.000	0.000	0.000	0.000
46	A	45	GLY	0	0.041	0.022	5.441	-5.313	-5.313	0.000	0.000	0.000	0.000
49	A	48	GLY	0	-0.030	-0.015	6.587	-0.618	-0.618	0.000	0.000	0.000	0.000
50	A	49	THR	0	-0.036	-0.012	9.211	3.107	3.107	0.000	0.000	0.000	0.000
51	A	50	SER	0	0.038	0.025	11.453	-0.791	-0.791	0.000	0.000	0.000	0.000
52	A	51	GLY	0	0.006	-0.006	13.887	-0.048	-0.048	0.000	0.000	0.000	0.000
53	A	52	THR	0	-0.026	-0.015	16.485	0.051	0.051	0.000	0.000	0.000	0.000
54	A	53	LEU	0	-0.028	0.000	19.913	0.159	0.159	0.000	0.000	0.000	0.000
55	A	54	ARG	1	0.882	0.918	22.427	11.290	11.290	0.000	0.000	0.000	0.000
56	A	55	PHE	0	-0.007	-0.008	23.544	-0.044	-0.044	0.000	0.000	0.000	0.000
57	A	56	HIS	0	0.018	-0.004	28.486	-0.075	-0.075	0.000	0.000	0.000	0.000
58	A	57	ALA	0	0.031	0.026	32.274	-0.078	-0.078	0.000	0.000	0.000	0.000
59	A	58	ASP	-1	-0.868	-0.939	35.250	-8.213	-8.213	0.000	0.000	0.000	0.000
60	A	59	ASN	0	-0.065	-0.037	38.359	0.036	0.036	0.000	0.000	0.000	0.000
61	A	60	GLY	0	-0.006	-0.004	38.735	0.144	0.144	0.000	0.000	0.000	0.000
62	A	61	GLU	-1	-0.771	-0.825	35.162	-8.811	-8.811	0.000	0.000	0.000	0.000
63	A	62	SER	0	-0.008	-0.006	31.958	-0.227	-0.227	0.000	0.000	0.000	0.000
64	A	63	PHE	0	-0.022	-0.011	25.927	0.097	0.097	0.000	0.000	0.000	0.000
65	A	64	THR	0	0.009	0.002	24.408	-0.071	-0.071	0.000	0.000	0.000	0.000
66	A	65	ALA	0	0.012	0.011	22.194	0.205	0.205	0.000	0.000	0.000	0.000
67	A	66	THR	0	-0.011	-0.001	18.060	-0.404	-0.404	0.000	0.000	0.000	0.000
68	A	67	PHE	0	0.037	0.014	15.276	0.271	0.271	0.000	0.000	0.000	0.000
69	A	68	GLY	0	0.079	0.017	12.744	-0.433	-0.433	0.000	0.000	0.000	0.000
70	A	69	VAL	0	-0.027	0.004	7.698	0.267	0.267	0.000	0.000	0.000	0.000
71	A	70	HIS	0	0.062	0.037	10.460	-1.638	-1.638	0.000	0.000	0.000	0.000
72	A	71	ASN	0	0.015	0.005	10.126	-0.336	-0.336	0.000	0.000	0.000	0.000
74	A	73	LYS	1	0.812	0.914	8.533	21.027	21.027	0.000	0.000	0.000	0.000
75	A	74	ARG	1	0.807	0.889	11.513	18.972	18.972	0.000	0.000	0.000	0.000
76	A	75	TRP	0	-0.010	0.006	12.844	1.728	1.728	0.000	0.000	0.000	0.000
77	A	76	CYS	0	-0.059	-0.019	16.138	-0.383	-0.383	0.000	0.000	0.000	0.000
78	A	77	ASP	-1	-0.787	-0.873	18.968	-12.984	-12.984	0.000	0.000	0.000	0.000
79	A	78	ILE	0	-0.053	-0.018	22.245	-0.262	-0.262	0.000	0.000	0.000	0.000
80	A	79	VAL	0	0.003	0.014	25.408	0.353	0.353	0.000	0.000	0.000	0.000
81	A	80	THR	0	0.009	-0.015	27.934	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	81	ASN	0	-0.013	-0.020	31.436	0.101	0.101	0.000	0.000	0.000	0.000
83	A	82	LEU	0	0.003	0.022	28.868	0.078	0.078	0.000	0.000	0.000	0.000
84	A	83	ALA	0	0.029	0.021	32.943	0.318	0.318	0.000	0.000	0.000	0.000
85	A	84	ALA	0	-0.025	-0.024	33.667	-0.237	-0.237	0.000	0.000	0.000	0.000
86	A	85	ASP	-1	-0.921	-0.958	33.337	-9.465	-9.465	0.000	0.000	0.000	0.000
87	A	86	GLU	-1	-0.894	-0.946	29.897	-10.809	-10.809	0.000	0.000	0.000	0.000
88	A	87	THR	0	-0.001	-0.010	27.964	-0.225	-0.225	0.000	0.000	0.000	0.000
89	A	88	GLY	0	0.003	-0.018	24.736	-0.217	-0.217	0.000	0.000	0.000	0.000
90	A	89	MET	0	-0.040	-0.026	22.446	-0.501	-0.501	0.000	0.000	0.000	0.000
91	A	90	VAL	0	-0.023	0.007	23.176	-0.442	-0.442	0.000	0.000	0.000	0.000
92	A	91	ILE	0	0.010	0.004	23.538	-0.296	-0.296	0.000	0.000	0.000	0.000
93	A	92	ASN	0	-0.004	-0.020	17.522	-0.971	-0.971	0.000	0.000	0.000	0.000
94	A	93	GLN	0	0.024	0.002	19.700	-1.011	-1.011	0.000	0.000	0.000	0.000
95	A	94	GLN	0	0.075	0.070	21.403	-0.174	-0.174	0.000	0.000	0.000	0.000
96	A	95	TYR	0	-0.040	-0.050	18.750	0.087	0.087	0.000	0.000	0.000	0.000
97	A	96	TYR	0	-0.048	-0.047	14.364	-1.456	-1.456	0.000	0.000	0.000	0.000
98	A	97	SER	0	0.007	-0.003	19.640	0.336	0.336	0.000	0.000	0.000	0.000
99	A	98	GLN	0	-0.031	-0.004	23.378	0.637	0.637	0.000	0.000	0.000	0.000
100	A	99	LYS	1	0.903	0.945	24.654	10.991	10.991	0.000	0.000	0.000	0.000
101	A	100	ASN	0	0.023	0.007	24.904	-0.412	-0.412	0.000	0.000	0.000	0.000
102	A	101	ARG	1	0.871	0.937	22.903	11.979	11.979	0.000	0.000	0.000	0.000
103	A	102	GLU	-1	-0.931	-0.960	20.351	-14.939	-14.939	0.000	0.000	0.000	0.000
104	A	103	GLU	-1	-0.758	-0.891	20.356	-12.188	-12.188	0.000	0.000	0.000	0.000
105	A	104	ALA	0	-0.075	-0.035	22.027	0.053	0.053	0.000	0.000	0.000	0.000
106	A	105	ARG	1	0.778	0.878	14.780	17.669	17.669	0.000	0.000	0.000	0.000
107	A	106	GLU	-1	-0.893	-0.954	17.056	-16.961	-16.961	0.000	0.000	0.000	0.000
108	A	107	ARG	1	0.936	0.979	18.610	13.044	13.044	0.000	0.000	0.000	0.000
109	A	108	GLN	0	-0.088	-0.041	13.603	0.971	0.971	0.000	0.000	0.000	0.000
110	A	109	LEU	0	0.029	0.028	17.149	-0.157	-0.157	0.000	0.000	0.000	0.000
111	A	110	SER	0	0.036	0.017	17.116	-0.526	-0.526	0.000	0.000	0.000	0.000
112	A	111	ASN	0	-0.025	-0.025	18.082	0.577	0.577	0.000	0.000	0.000	0.000
113	A	112	TYR	0	0.039	0.022	21.346	0.112	0.112	0.000	0.000	0.000	0.000
114	A	113	GLN	0	0.040	0.030	24.121	0.125	0.125	0.000	0.000	0.000	0.000
115	A	114	VAL	0	-0.020	0.009	27.536	0.180	0.180	0.000	0.000	0.000	0.000
116	A	115	LYS	1	0.927	0.949	30.358	9.214	9.214	0.000	0.000	0.000	0.000
117	A	116	ASN	0	0.013	0.009	33.572	0.022	0.022	0.000	0.000	0.000	0.000
118	A	117	ALA	0	-0.004	-0.015	35.358	0.166	0.166	0.000	0.000	0.000	0.000
119	A	118	LYS	1	0.825	0.911	38.499	8.282	8.282	0.000	0.000	0.000	0.000
120	A	119	GLY	0	0.005	0.012	38.468	0.137	0.137	0.000	0.000	0.000	0.000
121	A	120	ARG	1	0.693	0.805	33.691	8.694	8.694	0.000	0.000	0.000	0.000
122	A	121	ASN	0	-0.022	-0.025	30.353	-0.019	-0.019	0.000	0.000	0.000	0.000
123	A	122	PHE	0	0.045	0.023	28.110	-0.007	-0.007	0.000	0.000	0.000	0.000
124	A	123	GLN	0	-0.009	-0.013	24.992	-0.061	-0.061	0.000	0.000	0.000	0.000
125	A	124	ILE	0	-0.001	0.011	19.390	-0.102	-0.102	0.000	0.000	0.000	0.000
126	A	125	VAL	0	0.019	-0.001	20.266	0.132	0.132	0.000	0.000	0.000	0.000
127	A	126	TYR	0	-0.028	-0.045	13.348	-0.533	-0.533	0.000	0.000	0.000	0.000
128	A	127	THR	0	-0.027	-0.013	16.199	0.496	0.496	0.000	0.000	0.000	0.000
129	A	128	GLU	-1	-0.915	-0.935	11.609	-17.610	-17.610	0.000	0.000	0.000	0.000
130	A	129	ALA	0	-0.002	-0.014	12.595	-1.116	-1.116	0.000	0.000	0.000	0.000
131	A	130	GLU	-1	-0.783	-0.882	10.902	-21.381	-21.381	0.000	0.000	0.000	0.000
132	A	131	GLY	0	0.030	0.024	6.856	-0.024	-0.024	0.000	0.000	0.000	0.000
135	A	134	LEU	0	-0.004	0.017	7.050	2.318	2.318	0.000	0.000	0.000	0.000
136	A	135	HIS	0	-0.007	-0.016	10.236	1.236	1.236	0.000	0.000	0.000	0.000
137	A	136	ALA	0	-0.003	-0.009	13.702	0.374	0.374	0.000	0.000	0.000	0.000
138	A	137	ASN	0	0.014	0.011	16.984	-0.072	-0.072	0.000	0.000	0.000	0.000
139	A	138	LEU	0	0.002	0.001	20.708	-0.028	-0.028	0.000	0.000	0.000	0.000
140	A	139	ILE	0	-0.036	-0.023	22.928	0.286	0.286	0.000	0.000	0.000	0.000
141	A	140	ILE	0	-0.024	-0.007	26.450	-0.067	-0.067	0.000	0.000	0.000	0.000
142	A	141	GLY	-1	-0.738	-0.841	29.782	-8.886	-8.886	0.000	0.000	0.000	0.000

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