FMO DATABASE

FMODB ID: 3Z9QL

Calculation Name: 3COQ-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: 3COQ

Chain ID: A

ChEMBL ID:

UniProt ID: P04386

Base Structure: X-ray

Registration Date: 2025-10-04

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	89
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-507525.636951
FMO2-HF: Nuclear repulsion	469627.66565
FMO2-HF: Total energy	-37897.971302
FMO2-MP2: Total energy	-38003.369001

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:8:GLU)

Summations of interaction energy for fragment #1(A:8: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.
-40.744	-35.967	7.038	-5.401	-6.415	0.022

Interaction energy analysis for fragmet #1(A:8:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / q_NPA : -0.030

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	10	ALA	0	0.028	0.018	3.113	-10.948	-8.659	0.043	-1.270	-1.063	-0.005
16	A	23	LYS	1	0.836	0.897	1.950	-35.041	-32.600	6.996	-4.129	-5.307	0.027
17	A	24	GLU	-1	-0.755	-0.823	4.981	-7.360	-7.313	-0.001	-0.002	-0.045	0.000
4	A	11	CYS	0	0.004	-0.002	5.734	0.747	0.747	0.000	0.000	0.000	0.000
5	A	12	ASP	-1	-0.760	-0.860	8.670	-0.526	-0.526	0.000	0.000	0.000	0.000
6	A	13	ILE	0	0.042	0.019	11.956	0.638	0.638	0.000	0.000	0.000	0.000
7	A	14	CYS	0	-0.039	-0.020	9.482	0.136	0.136	0.000	0.000	0.000	0.000
8	A	15	ARG	1	0.889	0.939	7.364	-0.156	-0.156	0.000	0.000	0.000	0.000
9	A	16	LEU	0	0.026	0.005	11.497	0.478	0.478	0.000	0.000	0.000	0.000
10	A	17	LYS	1	0.907	0.958	14.702	-0.055	-0.055	0.000	0.000	0.000	0.000
11	A	18	LYS	1	0.973	0.999	12.199	-2.585	-2.585	0.000	0.000	0.000	0.000
12	A	19	LEU	0	0.006	0.015	12.497	0.150	0.150	0.000	0.000	0.000	0.000
13	A	20	LYS	1	0.987	0.989	8.469	-0.987	-0.987	0.000	0.000	0.000	0.000
14	A	21	CYS	0	-0.068	-0.017	6.250	-1.751	-1.751	0.000	0.000	0.000	0.000
15	A	22	SER	0	-0.020	-0.036	7.144	0.489	0.489	0.000	0.000	0.000	0.000
18	A	25	LYS	1	0.939	0.975	6.360	10.452	10.452	0.000	0.000	0.000	0.000
19	A	26	PRO	0	0.069	0.038	9.819	0.237	0.237	0.000	0.000	0.000	0.000
20	A	27	LYS	1	0.931	0.938	11.653	1.725	1.725	0.000	0.000	0.000	0.000
21	A	28	CYS	0	-0.029	-0.013	8.576	0.284	0.284	0.000	0.000	0.000	0.000
22	A	29	ALA	0	0.083	0.019	11.028	0.697	0.697	0.000	0.000	0.000	0.000
23	A	30	LYS	1	0.930	0.973	12.847	0.499	0.499	0.000	0.000	0.000	0.000
24	A	31	CYS	0	0.009	0.012	12.937	0.225	0.225	0.000	0.000	0.000	0.000
25	A	32	LEU	0	0.018	0.022	14.730	0.073	0.073	0.000	0.000	0.000	0.000
26	A	33	LYS	1	0.988	0.982	16.445	0.934	0.934	0.000	0.000	0.000	0.000
27	A	34	ASN	0	-0.075	-0.036	18.191	0.094	0.094	0.000	0.000	0.000	0.000
28	A	35	ASN	0	0.017	0.006	19.460	-0.065	-0.065	0.000	0.000	0.000	0.000
29	A	36	TRP	0	0.039	0.017	16.376	0.112	0.112	0.000	0.000	0.000	0.000
30	A	37	GLU	-1	-0.807	-0.898	17.130	-1.441	-1.441	0.000	0.000	0.000	0.000
31	A	38	CYS	0	-0.124	-0.047	11.506	-0.257	-0.257	0.000	0.000	0.000	0.000
32	A	39	ARG	1	0.956	0.980	12.493	1.134	1.134	0.000	0.000	0.000	0.000
33	A	40	TYR	0	-0.025	-0.033	5.402	-0.686	-0.686	0.000	0.000	0.000	0.000
34	A	41	SER	0	-0.030	-0.040	9.544	-0.292	-0.292	0.000	0.000	0.000	0.000
35	A	42	PRO	0	-0.004	-0.002	10.468	-0.233	-0.233	0.000	0.000	0.000	0.000
36	A	43	LYS	1	0.946	0.961	6.175	3.586	3.586	0.000	0.000	0.000	0.000
37	A	44	THR	0	0.035	0.020	10.261	-0.052	-0.052	0.000	0.000	0.000	0.000
38	A	45	LYS	1	0.956	0.973	13.329	0.470	0.470	0.000	0.000	0.000	0.000
39	A	46	ARG	1	0.982	1.000	13.938	-2.034	-2.034	0.000	0.000	0.000	0.000
40	A	47	SER	0	0.056	0.039	17.588	-0.095	-0.095	0.000	0.000	0.000	0.000
41	A	48	PRO	0	-0.003	-0.002	18.891	0.181	0.181	0.000	0.000	0.000	0.000
42	A	49	LEU	0	0.028	0.015	17.435	-0.070	-0.070	0.000	0.000	0.000	0.000
43	A	50	THR	0	0.007	-0.001	19.864	0.048	0.048	0.000	0.000	0.000	0.000
44	A	51	ARG	1	1.037	1.014	22.448	-0.954	-0.954	0.000	0.000	0.000	0.000
45	A	52	ALA	0	0.034	0.034	25.904	-0.045	-0.045	0.000	0.000	0.000	0.000
46	A	53	HIS	0	-0.002	-0.011	23.266	-0.115	-0.115	0.000	0.000	0.000	0.000
47	A	54	LEU	0	-0.005	-0.003	25.281	-0.020	-0.020	0.000	0.000	0.000	0.000
48	A	55	THR	0	0.065	0.021	26.971	-0.037	-0.037	0.000	0.000	0.000	0.000
49	A	56	GLU	-1	-0.853	-0.894	29.520	0.327	0.327	0.000	0.000	0.000	0.000
50	A	57	VAL	0	-0.040	-0.026	27.154	-0.040	-0.040	0.000	0.000	0.000	0.000
51	A	58	GLU	-1	-0.897	-0.957	30.245	0.705	0.705	0.000	0.000	0.000	0.000
52	A	59	SER	0	-0.021	-0.025	32.447	-0.041	-0.041	0.000	0.000	0.000	0.000
53	A	60	ARG	1	0.741	0.847	31.925	-0.371	-0.371	0.000	0.000	0.000	0.000
54	A	61	LEU	0	0.033	0.027	32.818	-0.022	-0.022	0.000	0.000	0.000	0.000
55	A	62	GLU	-1	-0.827	-0.907	35.310	0.380	0.380	0.000	0.000	0.000	0.000
56	A	63	ARG	1	0.878	0.946	35.824	-0.358	-0.358	0.000	0.000	0.000	0.000
57	A	64	LEU	0	-0.008	-0.004	36.417	-0.024	-0.024	0.000	0.000	0.000	0.000
58	A	65	GLU	-1	-0.886	-0.941	38.040	0.392	0.392	0.000	0.000	0.000	0.000
59	A	66	GLN	0	-0.065	-0.046	40.684	-0.034	-0.034	0.000	0.000	0.000	0.000
60	A	67	LEU	0	-0.058	-0.018	43.098	-0.018	-0.018	0.000	0.000	0.000	0.000
61	A	68	PHE	0	0.021	-0.019	40.316	-0.017	-0.017	0.000	0.000	0.000	0.000
62	A	69	LEU	0	-0.002	0.017	44.455	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	70	LEU	0	-0.047	-0.032	46.503	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	71	ILE	0	-0.062	-0.013	46.529	-0.013	-0.013	0.000	0.000	0.000	0.000
65	A	72	PHE	0	0.015	-0.002	44.102	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	73	PRO	0	0.004	0.007	47.912	0.013	0.013	0.000	0.000	0.000	0.000
67	A	74	ARG	1	0.827	0.899	50.313	-0.217	-0.217	0.000	0.000	0.000	0.000
68	A	75	GLU	-1	-0.901	-0.954	47.221	0.282	0.282	0.000	0.000	0.000	0.000
69	A	76	ASP	-1	-0.874	-0.938	43.040	0.352	0.352	0.000	0.000	0.000	0.000
70	A	77	LEU	0	0.063	0.037	40.585	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	78	ASP	-1	-0.917	-0.965	37.976	0.444	0.444	0.000	0.000	0.000	0.000
72	A	79	MET	0	-0.030	-0.009	39.678	0.001	0.001	0.000	0.000	0.000	0.000
73	A	80	ILE	0	-0.022	-0.021	41.571	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	81	LEU	0	-0.043	-0.021	36.696	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	82	LYS	1	0.888	0.953	35.799	-0.403	-0.403	0.000	0.000	0.000	0.000
76	A	83	MET	0	-0.059	-0.004	37.630	-0.011	-0.011	0.000	0.000	0.000	0.000
77	A	84	ASP	-1	-0.937	-0.963	35.764	0.226	0.226	0.000	0.000	0.000	0.000
78	A	85	SER	0	-0.020	-0.017	38.282	-0.026	-0.026	0.000	0.000	0.000	0.000
79	A	86	LEU	0	0.041	0.000	39.228	0.000	0.000	0.000	0.000	0.000	0.000
80	A	87	GLN	0	-0.069	-0.028	42.653	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	88	ASP	-1	-0.836	-0.913	44.522	0.158	0.158	0.000	0.000	0.000	0.000
82	A	89	ILE	0	0.020	0.010	40.315	0.000	0.000	0.000	0.000	0.000	0.000
83	A	90	LYS	1	0.926	0.964	44.921	-0.093	-0.093	0.000	0.000	0.000	0.000
84	A	91	ALA	0	0.003	0.002	47.497	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	92	LEU	0	-0.018	0.000	47.063	-0.002	-0.002	0.000	0.000	0.000	0.000
86	A	93	LEU	0	0.009	-0.005	45.033	0.001	0.001	0.000	0.000	0.000	0.000
87	A	94	THR	0	-0.110	-0.060	49.478	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	95	GLY	0	-0.051	-0.017	52.374	-0.008	-0.008	0.000	0.000	0.000	0.000
89	A	96	LEU	-1	-0.975	-0.971	50.377	0.156	0.156	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:8:GLU)