FMO DATABASE

FMODB ID: NLGKQ

Calculation Name: 4DGD-A-Xray547

Preferred Name:

Target Type:

Ligand Name: glycerol

Ligand 3-letter code: GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4DGD

Chain ID: A

ChEMBL ID:

UniProt ID: P62940

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	165
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1654333.844751
FMO2-HF: Nuclear repulsion	1589953.2429
FMO2-HF: Total energy	-64380.601851
FMO2-MP2: Total energy	-64563.748344

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-21.404	-19.637	7.58	-0.704	-8.644	-0.034

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.799 / q_NPA : 0.910

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	3	ASN	0	-0.004	-0.010	3.258	2.022	2.231	3.854	0.861	-4.924	-0.022
4	A	4	PRO	0	-0.008	0.016	4.190	0.815	0.698	0.036	0.212	-0.131	0.000
23	A	23	GLU	-1	-0.806	-0.897	4.752	-32.627	-32.564	-0.001	-0.002	-0.060	0.000
27	A	27	ASP	-1	-0.833	-0.914	2.479	-44.509	-43.159	3.687	-1.716	-3.321	-0.012
28	A	28	LYS	1	0.796	0.887	4.101	35.964	36.226	0.004	-0.059	-0.208	0.000
5	A	5	THR	0	0.002	-0.011	7.913	1.031	1.031	0.000	0.000	0.000	0.000
6	A	6	VAL	0	-0.002	0.001	10.807	0.754	0.754	0.000	0.000	0.000	0.000
7	A	7	PHE	0	-0.014	-0.017	14.140	-0.018	-0.018	0.000	0.000	0.000	0.000
8	A	8	PHE	0	0.009	-0.004	17.596	0.297	0.297	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.763	-0.837	20.843	-12.543	-12.543	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.017	-0.023	22.882	0.250	0.250	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.022	0.013	26.161	0.167	0.167	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.023	-0.023	29.980	-0.057	-0.057	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.867	-0.933	32.744	-7.775	-7.775	0.000	0.000	0.000	0.000
14	A	14	GLY	0	-0.014	-0.003	33.808	0.188	0.188	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.897	-0.939	33.879	-8.424	-8.424	0.000	0.000	0.000	0.000
16	A	16	PRO	0	-0.028	-0.021	30.037	-0.254	-0.254	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.040	-0.011	27.433	0.146	0.146	0.000	0.000	0.000	0.000
18	A	18	GLY	0	0.030	0.000	25.925	0.020	0.020	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.824	0.884	19.550	13.480	13.480	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.040	-0.012	17.527	0.104	0.104	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.015	0.005	14.993	-0.273	-0.273	0.000	0.000	0.000	0.000
22	A	22	PHE	0	0.016	-0.008	12.890	0.345	0.345	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.004	-0.009	8.335	1.520	1.520	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.022	-0.003	5.660	-2.385	-2.385	0.000	0.000	0.000	0.000
26	A	26	ALA	0	0.042	0.009	5.393	1.111	1.111	0.000	0.000	0.000	0.000
29	A	29	VAL	0	-0.019	0.006	7.381	2.110	2.110	0.000	0.000	0.000	0.000
30	A	30	PRO	0	0.054	0.037	7.709	0.496	0.496	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.828	0.910	9.282	15.747	15.747	0.000	0.000	0.000	0.000
32	A	32	THR	0	-0.015	-0.043	13.065	1.399	1.399	0.000	0.000	0.000	0.000
33	A	33	ALA	0	-0.007	0.001	9.421	0.718	0.718	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.793	-0.876	11.400	-19.361	-19.361	0.000	0.000	0.000	0.000
35	A	35	ASN	0	-0.019	-0.013	12.679	1.399	1.399	0.000	0.000	0.000	0.000
36	A	36	PHE	0	0.066	0.020	14.164	0.668	0.668	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.781	0.848	11.073	20.426	20.426	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.002	0.001	14.331	0.725	0.725	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.056	-0.020	17.184	0.957	0.957	0.000	0.000	0.000	0.000
40	A	40	SER	0	-0.003	-0.018	16.513	0.795	0.795	0.000	0.000	0.000	0.000
41	A	41	THR	0	-0.022	-0.027	16.711	0.537	0.537	0.000	0.000	0.000	0.000
42	A	42	GLY	0	-0.005	0.015	19.471	0.585	0.585	0.000	0.000	0.000	0.000
43	A	43	GLU	-1	-0.780	-0.847	17.183	-16.465	-16.465	0.000	0.000	0.000	0.000
44	A	44	LYS	1	0.835	0.910	17.019	15.900	15.900	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.001	0.010	22.923	0.437	0.437	0.000	0.000	0.000	0.000
46	A	46	PHE	0	-0.050	-0.033	23.293	0.485	0.485	0.000	0.000	0.000	0.000
47	A	47	GLY	0	0.033	0.001	22.745	-0.573	-0.573	0.000	0.000	0.000	0.000
48	A	48	TYR	0	-0.059	-0.042	18.264	0.464	0.464	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.907	0.965	23.565	11.475	11.475	0.000	0.000	0.000	0.000
50	A	50	GLY	0	-0.003	0.005	25.719	0.267	0.267	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.093	-0.045	25.367	0.262	0.262	0.000	0.000	0.000	0.000
52	A	52	CYS	0	-0.047	-0.034	27.918	0.086	0.086	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.056	0.005	21.829	-0.306	-0.306	0.000	0.000	0.000	0.000
54	A	54	HIS	0	-0.023	-0.012	27.161	0.308	0.308	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.862	0.931	27.652	10.043	10.043	0.000	0.000	0.000	0.000
56	A	56	ILE	0	0.044	0.030	27.328	-0.363	-0.363	0.000	0.000	0.000	0.000
57	A	57	ILE	0	-0.047	-0.017	28.219	0.381	0.381	0.000	0.000	0.000	0.000
58	A	58	PRO	0	-0.008	-0.014	28.378	-0.243	-0.243	0.000	0.000	0.000	0.000
59	A	59	GLY	0	-0.013	0.001	28.147	0.240	0.240	0.000	0.000	0.000	0.000
60	A	60	PHE	0	-0.053	-0.025	24.807	-0.065	-0.065	0.000	0.000	0.000	0.000
61	A	61	MET	0	-0.021	0.003	23.132	-0.552	-0.552	0.000	0.000	0.000	0.000
62	A	62	CYS	0	0.005	0.015	23.196	0.595	0.595	0.000	0.000	0.000	0.000
63	A	63	GLN	0	0.046	0.013	22.978	-0.356	-0.356	0.000	0.000	0.000	0.000
64	A	64	GLY	0	0.003	-0.001	23.900	0.432	0.432	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.032	0.027	23.525	-0.275	-0.275	0.000	0.000	0.000	0.000
66	A	66	ASN	0	-0.058	-0.016	24.483	-0.227	-0.227	0.000	0.000	0.000	0.000
67	A	67	PHE	0	0.093	0.024	23.969	0.019	0.019	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.017	-0.011	29.360	0.078	0.078	0.000	0.000	0.000	0.000
69	A	69	HIS	0	-0.032	-0.020	29.753	-0.159	-0.159	0.000	0.000	0.000	0.000
70	A	70	CYS	0	-0.006	-0.015	31.898	0.159	0.159	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.012	0.011	32.497	0.461	0.461	0.000	0.000	0.000	0.000
72	A	72	GLY	0	-0.006	0.000	34.076	0.094	0.094	0.000	0.000	0.000	0.000
73	A	73	THR	0	0.012	-0.005	33.018	-0.191	-0.191	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.003	0.008	30.454	-0.125	-0.125	0.000	0.000	0.000	0.000
75	A	75	GLY	0	0.051	0.040	26.920	-0.309	-0.309	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.837	0.934	25.662	10.961	10.961	0.000	0.000	0.000	0.000
77	A	77	SER	0	0.006	-0.003	20.698	-0.422	-0.422	0.000	0.000	0.000	0.000
78	A	78	ILE	0	0.005	-0.007	16.537	0.515	0.515	0.000	0.000	0.000	0.000
79	A	79	TYR	0	-0.081	-0.056	15.065	0.061	0.061	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.037	0.032	21.712	0.404	0.404	0.000	0.000	0.000	0.000
81	A	81	GLU	-1	-0.840	-0.925	24.738	-10.101	-10.101	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.851	0.914	24.375	10.465	10.465	0.000	0.000	0.000	0.000
83	A	83	PHE	0	-0.011	0.001	16.842	0.028	0.028	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.749	-0.861	18.461	-14.172	-14.172	0.000	0.000	0.000	0.000
85	A	85	ASP	-1	-0.818	-0.904	18.994	-13.294	-13.294	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.788	-0.855	12.292	-20.337	-20.337	0.000	0.000	0.000	0.000
87	A	87	ASN	0	-0.005	-0.027	11.421	-0.157	-0.157	0.000	0.000	0.000	0.000
88	A	88	PHE	0	0.007	-0.001	15.432	0.040	0.040	0.000	0.000	0.000	0.000
89	A	89	ILE	0	-0.015	0.000	10.428	0.446	0.446	0.000	0.000	0.000	0.000
90	A	90	LEU	0	-0.056	-0.012	8.388	-0.148	-0.148	0.000	0.000	0.000	0.000
91	A	91	LYS	1	0.974	0.987	12.785	14.853	14.853	0.000	0.000	0.000	0.000
92	A	92	HIS	0	0.009	-0.005	15.290	-0.596	-0.596	0.000	0.000	0.000	0.000
93	A	93	THR	0	-0.034	-0.033	15.130	0.747	0.747	0.000	0.000	0.000	0.000
94	A	94	GLY	0	0.005	-0.007	17.741	0.551	0.551	0.000	0.000	0.000	0.000
95	A	95	PRO	0	0.007	0.011	18.261	-0.285	-0.285	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.046	0.024	16.539	-0.571	-0.571	0.000	0.000	0.000	0.000
97	A	97	ILE	0	-0.046	-0.006	13.228	-0.820	-0.820	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.012	0.009	13.520	0.973	0.973	0.000	0.000	0.000	0.000
99	A	99	SER	0	0.009	-0.022	14.369	-0.975	-0.975	0.000	0.000	0.000	0.000
100	A	100	MET	0	0.014	0.026	16.952	0.329	0.329	0.000	0.000	0.000	0.000
101	A	101	ALA	0	-0.037	-0.019	19.198	0.430	0.430	0.000	0.000	0.000	0.000
102	A	102	ASN	0	-0.046	-0.029	22.306	0.241	0.241	0.000	0.000	0.000	0.000
103	A	103	ALA	0	-0.018	-0.016	25.118	0.244	0.244	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.015	0.018	27.052	0.347	0.347	0.000	0.000	0.000	0.000
105	A	105	PRO	0	0.006	-0.009	24.573	-0.248	-0.248	0.000	0.000	0.000	0.000
106	A	106	ASN	0	-0.032	-0.015	22.930	-0.128	-0.128	0.000	0.000	0.000	0.000
107	A	107	THR	0	0.001	0.002	24.268	0.232	0.232	0.000	0.000	0.000	0.000
108	A	108	ASN	0	-0.025	-0.023	20.040	0.371	0.371	0.000	0.000	0.000	0.000
109	A	109	GLY	0	0.035	0.005	22.485	0.124	0.124	0.000	0.000	0.000	0.000
110	A	110	SER	0	0.032	0.007	21.315	-0.467	-0.467	0.000	0.000	0.000	0.000
111	A	111	GLN	0	-0.057	-0.020	21.410	-0.329	-0.329	0.000	0.000	0.000	0.000
112	A	112	PHE	0	0.019	0.030	18.772	-0.335	-0.335	0.000	0.000	0.000	0.000
113	A	113	PHE	0	-0.036	-0.039	19.845	0.670	0.670	0.000	0.000	0.000	0.000
114	A	114	ILE	0	0.047	0.034	17.948	-0.666	-0.666	0.000	0.000	0.000	0.000
115	A	115	CYS	0	-0.054	-0.019	18.885	0.612	0.612	0.000	0.000	0.000	0.000
116	A	116	THR	0	-0.005	-0.043	20.226	-0.462	-0.462	0.000	0.000	0.000	0.000
117	A	117	ALA	0	0.006	0.010	22.857	0.174	0.174	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.871	0.927	21.014	10.884	10.884	0.000	0.000	0.000	0.000
119	A	119	THR	0	-0.014	-0.025	21.269	0.380	0.380	0.000	0.000	0.000	0.000
120	A	120	GLU	-1	-0.776	-0.874	21.620	-11.039	-11.039	0.000	0.000	0.000	0.000
121	A	121	TRP	0	-0.030	0.000	22.656	-0.119	-0.119	0.000	0.000	0.000	0.000
122	A	122	LEU	0	-0.060	-0.035	21.909	0.311	0.311	0.000	0.000	0.000	0.000
123	A	123	ASP	-1	-0.756	-0.879	19.156	-14.021	-14.021	0.000	0.000	0.000	0.000
124	A	124	GLY	0	-0.046	-0.025	19.510	0.486	0.486	0.000	0.000	0.000	0.000
125	A	125	LYS	1	0.896	0.959	21.158	10.562	10.562	0.000	0.000	0.000	0.000
126	A	126	HIS	1	0.844	0.928	20.027	12.265	12.265	0.000	0.000	0.000	0.000
127	A	127	VAL	0	0.027	0.033	14.270	-0.193	-0.193	0.000	0.000	0.000	0.000
128	A	128	VAL	0	0.015	0.016	12.156	0.012	0.012	0.000	0.000	0.000	0.000
129	A	129	PHE	0	-0.006	-0.025	11.093	-0.825	-0.825	0.000	0.000	0.000	0.000
130	A	130	GLY	0	0.055	0.020	9.708	-1.617	-1.617	0.000	0.000	0.000	0.000
131	A	131	LYS	1	0.838	0.942	7.535	25.711	25.711	0.000	0.000	0.000	0.000
132	A	132	VAL	0	-0.002	-0.002	12.002	-0.702	-0.702	0.000	0.000	0.000	0.000
133	A	133	LYS	1	0.819	0.927	9.982	23.213	23.213	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.888	-0.950	13.323	-15.557	-15.557	0.000	0.000	0.000	0.000
135	A	135	GLY	0	0.088	0.035	16.988	0.046	0.046	0.000	0.000	0.000	0.000
136	A	136	MET	0	-0.009	0.008	18.812	0.128	0.128	0.000	0.000	0.000	0.000
137	A	137	ASN	0	0.048	0.019	20.490	-0.024	-0.024	0.000	0.000	0.000	0.000
138	A	138	ILE	0	-0.047	-0.011	22.925	0.517	0.517	0.000	0.000	0.000	0.000
139	A	139	VAL	0	0.041	0.006	20.022	0.372	0.372	0.000	0.000	0.000	0.000
140	A	140	GLU	-1	-0.876	-0.955	23.425	-10.801	-10.801	0.000	0.000	0.000	0.000
141	A	141	ALA	0	-0.084	-0.042	25.932	0.468	0.468	0.000	0.000	0.000	0.000
142	A	142	MET	0	-0.020	-0.002	23.675	0.235	0.235	0.000	0.000	0.000	0.000
143	A	143	GLU	-1	-0.782	-0.868	26.696	-9.934	-9.934	0.000	0.000	0.000	0.000
144	A	144	ARG	1	0.888	0.953	28.563	9.687	9.687	0.000	0.000	0.000	0.000
145	A	145	PHE	0	-0.006	0.005	31.002	0.356	0.356	0.000	0.000	0.000	0.000
146	A	146	GLY	0	0.044	0.023	31.418	0.083	0.083	0.000	0.000	0.000	0.000
147	A	147	SER	0	-0.062	-0.058	32.280	0.306	0.306	0.000	0.000	0.000	0.000
148	A	148	ARG	1	0.996	0.976	33.370	7.538	7.538	0.000	0.000	0.000	0.000
149	A	149	ASN	0	-0.025	-0.008	34.501	-0.141	-0.141	0.000	0.000	0.000	0.000
150	A	150	GLY	0	0.012	0.010	31.799	-0.088	-0.088	0.000	0.000	0.000	0.000
151	A	151	LYS	1	0.954	0.989	32.397	7.187	7.187	0.000	0.000	0.000	0.000
152	A	152	THR	0	0.008	0.009	31.316	0.120	0.120	0.000	0.000	0.000	0.000
153	A	153	SER	0	-0.052	-0.028	34.366	0.165	0.165	0.000	0.000	0.000	0.000
154	A	154	LYS	1	0.908	0.957	35.056	7.958	7.958	0.000	0.000	0.000	0.000
155	A	155	LYS	1	0.927	0.961	33.920	7.892	7.892	0.000	0.000	0.000	0.000
156	A	156	ILE	0	0.052	0.042	27.739	-0.041	-0.041	0.000	0.000	0.000	0.000
157	A	157	THR	0	-0.024	-0.026	28.519	-0.086	-0.086	0.000	0.000	0.000	0.000
158	A	158	ILE	0	0.027	0.027	22.499	-0.108	-0.108	0.000	0.000	0.000	0.000
159	A	159	ALA	0	-0.014	0.000	26.088	0.173	0.173	0.000	0.000	0.000	0.000
160	A	160	ASP	-1	-0.820	-0.917	25.004	-11.769	-11.769	0.000	0.000	0.000	0.000
161	A	161	CYS	0	-0.090	-0.036	20.266	0.009	0.009	0.000	0.000	0.000	0.000
162	A	162	GLY	0	0.053	0.039	18.747	0.328	0.328	0.000	0.000	0.000	0.000
163	A	163	GLN	0	-0.055	-0.045	11.136	0.896	0.896	0.000	0.000	0.000	0.000
164	A	164	LEU	0	-0.078	-0.036	14.050	0.959	0.959	0.000	0.000	0.000	0.000
165	A	165	GLU	-2	-1.720	-1.842	10.366	-51.418	-51.418	0.000	0.000	0.000	0.000

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