FMO DATABASE

FMODB ID: KV2N3

Calculation Name: 2D5K-A-Xray547

Preferred Name:

Target Type:

Ligand Name: glycerol

Ligand 3-letter code: GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2D5K

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

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	148
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1420168.362331
FMO2-HF: Nuclear repulsion	1360851.795537
FMO2-HF: Total energy	-59316.566794
FMO2-MP2: Total energy	-59489.059608

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:3:SER)

Summations of interaction energy for fragment #1(A:3:SER)

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.
-312.158	-296.812	9.958	-12.113	-13.192	-0.121

Interaction energy analysis for fragmet #1(A:3:SER)

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 : 0.899

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	5	GLN	0	0.075	0.010	3.638	-0.321	1.283	-0.004	-0.693	-0.907	-0.001
5	A	7	ASP	-1	-0.845	-0.919	2.322	-71.114	-68.441	4.211	-3.477	-3.407	-0.041
6	A	8	VAL	0	0.034	0.016	4.230	3.916	4.025	-0.001	-0.016	-0.092	0.000
114	A	116	ILE	0	-0.087	-0.054	1.995	-13.282	-11.538	2.598	-1.952	-2.391	-0.007
115	A	117	ALA	0	-0.006	-0.006	2.650	-16.153	-13.768	0.880	-1.346	-1.919	-0.020
116	A	118	GLY	0	0.131	0.080	4.984	-2.899	-2.872	-0.001	-0.004	-0.022	0.000
117	A	119	ASN	0	-0.164	-0.100	2.913	-0.464	0.922	0.271	-0.560	-1.097	0.000
118	A	120	ALA	0	-0.099	-0.056	2.240	-30.715	-25.454	1.959	-4.062	-3.158	-0.051
119	A	121	GLY	0	-0.019	0.005	3.413	6.820	6.977	0.045	-0.003	-0.199	-0.001
4	A	6	GLN	0	-0.012	-0.004	6.332	4.697	4.697	0.000	0.000	0.000	0.000
7	A	9	VAL	0	0.032	0.020	5.843	4.132	4.132	0.000	0.000	0.000	0.000
8	A	10	LYS	1	0.918	0.968	7.639	29.962	29.962	0.000	0.000	0.000	0.000
9	A	11	GLU	-1	-0.891	-0.955	6.306	-27.574	-27.574	0.000	0.000	0.000	0.000
10	A	12	LEU	0	0.009	0.007	9.149	2.342	2.342	0.000	0.000	0.000	0.000
11	A	13	ASN	0	0.019	0.000	11.515	2.914	2.914	0.000	0.000	0.000	0.000
12	A	14	GLN	0	-0.072	-0.031	12.090	1.063	1.063	0.000	0.000	0.000	0.000
13	A	15	GLN	0	0.032	0.017	12.675	2.593	2.593	0.000	0.000	0.000	0.000
14	A	16	VAL	0	0.015	0.018	15.552	1.184	1.184	0.000	0.000	0.000	0.000
15	A	17	ALA	0	0.011	0.011	17.131	1.110	1.110	0.000	0.000	0.000	0.000
16	A	18	ASN	0	-0.018	-0.023	16.063	1.264	1.264	0.000	0.000	0.000	0.000
17	A	19	TRP	0	0.006	-0.025	17.878	1.441	1.441	0.000	0.000	0.000	0.000
18	A	20	THR	0	0.010	0.001	21.440	0.878	0.878	0.000	0.000	0.000	0.000
19	A	21	VAL	0	-0.029	-0.011	22.964	0.661	0.661	0.000	0.000	0.000	0.000
20	A	22	ALA	0	-0.014	0.001	23.336	0.582	0.582	0.000	0.000	0.000	0.000
21	A	23	TYR	0	0.039	0.018	25.240	0.710	0.710	0.000	0.000	0.000	0.000
22	A	24	THR	0	0.013	0.012	27.380	0.558	0.558	0.000	0.000	0.000	0.000
23	A	25	LYS	1	0.729	0.850	25.936	11.626	11.626	0.000	0.000	0.000	0.000
24	A	26	LEU	0	0.019	0.010	26.968	0.393	0.393	0.000	0.000	0.000	0.000
25	A	27	HIS	1	0.846	0.927	30.704	9.828	9.828	0.000	0.000	0.000	0.000
26	A	28	ASN	0	-0.034	-0.014	32.933	0.377	0.377	0.000	0.000	0.000	0.000
27	A	29	PHE	0	0.049	-0.007	30.550	0.306	0.306	0.000	0.000	0.000	0.000
28	A	30	HIS	0	-0.034	-0.020	34.670	0.282	0.282	0.000	0.000	0.000	0.000
29	A	31	TRP	0	-0.015	0.002	35.971	0.199	0.199	0.000	0.000	0.000	0.000
30	A	32	TYR	0	-0.054	-0.033	37.520	0.275	0.275	0.000	0.000	0.000	0.000
31	A	33	VAL	0	0.039	0.045	37.686	0.194	0.194	0.000	0.000	0.000	0.000
32	A	34	LYS	1	0.828	0.897	39.577	7.434	7.434	0.000	0.000	0.000	0.000
33	A	35	GLY	0	0.054	0.031	42.246	-0.107	-0.107	0.000	0.000	0.000	0.000
34	A	36	PRO	0	0.006	-0.006	44.843	-0.015	-0.015	0.000	0.000	0.000	0.000
35	A	37	ASN	0	0.037	0.005	40.428	0.146	0.146	0.000	0.000	0.000	0.000
36	A	38	PHE	0	-0.016	0.004	40.892	-0.161	-0.161	0.000	0.000	0.000	0.000
37	A	39	PHE	0	0.023	-0.006	40.811	-0.147	-0.147	0.000	0.000	0.000	0.000
38	A	40	SER	0	-0.003	0.009	38.946	-0.076	-0.076	0.000	0.000	0.000	0.000
39	A	41	LEU	0	-0.013	-0.006	35.260	-0.208	-0.208	0.000	0.000	0.000	0.000
40	A	42	HIS	0	-0.075	-0.029	35.967	-0.157	-0.157	0.000	0.000	0.000	0.000
41	A	43	VAL	0	0.053	0.024	36.617	-0.163	-0.163	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.847	0.921	31.562	8.993	8.993	0.000	0.000	0.000	0.000
43	A	45	PHE	0	0.028	-0.021	31.750	-0.312	-0.312	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.854	-0.917	31.591	-8.600	-8.600	0.000	0.000	0.000	0.000
45	A	47	GLU	-1	-0.900	-0.942	31.533	-9.265	-9.265	0.000	0.000	0.000	0.000
46	A	48	LEU	0	-0.010	-0.006	26.904	-0.336	-0.336	0.000	0.000	0.000	0.000
47	A	49	TYR	0	0.001	0.002	27.124	-0.407	-0.407	0.000	0.000	0.000	0.000
48	A	50	ASN	0	-0.004	-0.007	28.123	-0.263	-0.263	0.000	0.000	0.000	0.000
49	A	51	GLU	-1	-0.750	-0.800	24.194	-12.226	-12.226	0.000	0.000	0.000	0.000
50	A	52	ALA	0	-0.008	-0.002	23.574	-0.434	-0.434	0.000	0.000	0.000	0.000
51	A	53	SER	0	-0.010	-0.016	23.299	-0.321	-0.321	0.000	0.000	0.000	0.000
52	A	54	GLN	0	-0.033	-0.009	24.156	0.003	0.003	0.000	0.000	0.000	0.000
53	A	55	TYR	0	0.010	-0.019	19.356	-0.470	-0.470	0.000	0.000	0.000	0.000
54	A	56	VAL	0	-0.049	-0.025	19.084	-0.757	-0.757	0.000	0.000	0.000	0.000
55	A	57	ASP	-1	-0.920	-0.953	19.926	-13.097	-13.097	0.000	0.000	0.000	0.000
56	A	58	GLU	-1	-0.893	-0.951	17.813	-16.199	-16.199	0.000	0.000	0.000	0.000
57	A	59	LEU	0	0.009	-0.011	14.169	-0.980	-0.980	0.000	0.000	0.000	0.000
58	A	60	ALA	0	-0.013	-0.002	15.447	-1.044	-1.044	0.000	0.000	0.000	0.000
59	A	61	GLU	-1	-0.914	-0.970	17.483	-13.791	-13.791	0.000	0.000	0.000	0.000
60	A	62	ARG	1	0.829	0.892	11.064	23.114	23.114	0.000	0.000	0.000	0.000
61	A	63	ILE	0	-0.040	-0.020	12.430	-1.277	-1.277	0.000	0.000	0.000	0.000
62	A	64	LEU	0	-0.012	0.001	14.072	-0.398	-0.398	0.000	0.000	0.000	0.000
63	A	65	ALA	0	-0.068	-0.028	16.086	0.061	0.061	0.000	0.000	0.000	0.000
64	A	66	VAL	0	-0.078	-0.031	10.556	-0.496	-0.496	0.000	0.000	0.000	0.000
65	A	67	GLY	0	-0.054	-0.023	12.926	-1.008	-1.008	0.000	0.000	0.000	0.000
66	A	68	GLY	0	-0.011	0.001	13.284	0.005	0.005	0.000	0.000	0.000	0.000
67	A	69	ASN	0	-0.011	-0.024	14.166	1.229	1.229	0.000	0.000	0.000	0.000
68	A	70	PRO	0	0.010	0.010	15.543	-0.858	-0.858	0.000	0.000	0.000	0.000
69	A	71	VAL	0	-0.032	-0.010	16.621	0.668	0.668	0.000	0.000	0.000	0.000
70	A	72	GLY	0	0.025	0.025	18.952	0.298	0.298	0.000	0.000	0.000	0.000
71	A	73	THR	0	-0.100	-0.080	22.574	0.813	0.813	0.000	0.000	0.000	0.000
72	A	74	LEU	0	0.056	0.009	23.434	-0.341	-0.341	0.000	0.000	0.000	0.000
73	A	75	THR	0	-0.036	-0.012	24.951	0.013	0.013	0.000	0.000	0.000	0.000
74	A	76	GLU	-1	-0.763	-0.857	19.823	-14.195	-14.195	0.000	0.000	0.000	0.000
75	A	77	CYS	0	-0.048	-0.018	20.071	-0.683	-0.683	0.000	0.000	0.000	0.000
76	A	78	LEU	0	-0.032	-0.031	21.247	-0.272	-0.272	0.000	0.000	0.000	0.000
77	A	79	GLU	-1	-0.992	-0.992	20.805	-13.096	-13.096	0.000	0.000	0.000	0.000
78	A	80	GLN	0	-0.027	-0.015	15.489	-1.207	-1.207	0.000	0.000	0.000	0.000
79	A	81	SER	0	-0.014	0.004	17.452	-0.878	-0.878	0.000	0.000	0.000	0.000
80	A	82	ILE	0	-0.048	-0.025	16.261	0.442	0.442	0.000	0.000	0.000	0.000
81	A	83	VAL	0	-0.057	-0.003	19.528	0.565	0.565	0.000	0.000	0.000	0.000
82	A	84	LYS	1	0.940	0.975	22.349	11.114	11.114	0.000	0.000	0.000	0.000
83	A	85	GLU	-1	-0.826	-0.926	25.693	-10.291	-10.291	0.000	0.000	0.000	0.000
84	A	86	ALA	0	-0.031	-0.006	28.639	0.060	0.060	0.000	0.000	0.000	0.000
85	A	87	ALA	0	-0.004	-0.001	31.663	0.189	0.189	0.000	0.000	0.000	0.000
86	A	88	LYS	1	0.888	0.926	33.991	8.458	8.458	0.000	0.000	0.000	0.000
87	A	89	GLY	0	0.003	0.005	37.641	0.200	0.200	0.000	0.000	0.000	0.000
88	A	90	TYR	0	-0.035	-0.035	31.265	-0.054	-0.054	0.000	0.000	0.000	0.000
89	A	91	SER	0	-0.044	-0.034	37.823	0.111	0.111	0.000	0.000	0.000	0.000
90	A	92	ALA	0	0.035	0.002	37.230	-0.211	-0.211	0.000	0.000	0.000	0.000
91	A	93	GLU	-1	-0.789	-0.869	35.981	-7.950	-7.950	0.000	0.000	0.000	0.000
92	A	94	GLN	0	0.084	0.042	34.442	-0.218	-0.218	0.000	0.000	0.000	0.000
93	A	95	MET	0	-0.063	-0.003	32.760	-0.250	-0.250	0.000	0.000	0.000	0.000
94	A	96	VAL	0	-0.003	0.010	31.183	-0.363	-0.363	0.000	0.000	0.000	0.000
95	A	97	GLU	-1	-0.936	-0.974	30.075	-9.137	-9.137	0.000	0.000	0.000	0.000
96	A	98	GLU	-1	-0.829	-0.888	27.616	-10.619	-10.619	0.000	0.000	0.000	0.000
97	A	99	LEU	0	0.024	0.019	26.587	-0.454	-0.454	0.000	0.000	0.000	0.000
98	A	100	SER	0	-0.016	-0.007	25.420	-0.432	-0.432	0.000	0.000	0.000	0.000
99	A	101	GLN	0	-0.037	-0.005	24.559	-0.777	-0.777	0.000	0.000	0.000	0.000
100	A	102	ASP	-1	-0.785	-0.887	22.256	-12.612	-12.612	0.000	0.000	0.000	0.000
101	A	103	PHE	0	-0.010	-0.015	20.719	-0.686	-0.686	0.000	0.000	0.000	0.000
102	A	104	THR	0	-0.035	-0.027	20.197	-0.487	-0.487	0.000	0.000	0.000	0.000
103	A	105	ASN	0	-0.052	-0.027	18.472	-0.800	-0.800	0.000	0.000	0.000	0.000
104	A	106	ILE	0	0.016	0.008	16.417	-0.907	-0.907	0.000	0.000	0.000	0.000
105	A	107	SER	0	-0.001	-0.013	15.321	-1.428	-1.428	0.000	0.000	0.000	0.000
106	A	108	LYS	1	0.932	0.962	14.620	15.557	15.557	0.000	0.000	0.000	0.000
107	A	109	GLN	0	0.014	0.003	11.941	-0.393	-0.393	0.000	0.000	0.000	0.000
108	A	110	LEU	0	0.007	0.001	10.673	-1.926	-1.926	0.000	0.000	0.000	0.000
109	A	111	GLU	-1	-0.878	-0.920	10.445	-21.738	-21.738	0.000	0.000	0.000	0.000
110	A	112	ASN	0	-0.086	-0.043	6.805	-2.478	-2.478	0.000	0.000	0.000	0.000
111	A	113	ALA	0	0.014	0.006	6.095	-4.753	-4.753	0.000	0.000	0.000	0.000
112	A	114	ILE	0	-0.001	0.000	6.653	-3.812	-3.812	0.000	0.000	0.000	0.000
113	A	115	GLU	-1	-0.850	-0.902	5.352	-38.126	-38.126	0.000	0.000	0.000	0.000
120	A	122	ASP	-1	-0.781	-0.839	6.169	-25.120	-25.120	0.000	0.000	0.000	0.000
121	A	123	ASP	-1	-0.833	-0.937	7.908	-27.533	-27.533	0.000	0.000	0.000	0.000
122	A	124	VAL	0	-0.062	-0.026	10.449	1.894	1.894	0.000	0.000	0.000	0.000
123	A	125	SER	0	-0.007	-0.045	9.061	2.393	2.393	0.000	0.000	0.000	0.000
124	A	126	GLU	-1	-0.947	-0.964	8.959	-27.932	-27.932	0.000	0.000	0.000	0.000
125	A	127	ASP	-1	-0.931	-0.963	10.522	-16.158	-16.158	0.000	0.000	0.000	0.000
126	A	128	MET	0	0.007	0.011	13.957	0.762	0.762	0.000	0.000	0.000	0.000
127	A	129	PHE	0	-0.015	-0.012	8.445	1.233	1.233	0.000	0.000	0.000	0.000
128	A	130	ILE	0	0.049	0.032	13.013	1.231	1.231	0.000	0.000	0.000	0.000
129	A	131	GLY	0	0.004	0.015	15.322	1.233	1.233	0.000	0.000	0.000	0.000
130	A	132	MET	0	0.009	0.025	16.281	0.629	0.629	0.000	0.000	0.000	0.000
131	A	133	GLN	0	-0.040	-0.028	14.729	0.466	0.466	0.000	0.000	0.000	0.000
132	A	134	THR	0	-0.041	-0.030	17.558	1.034	1.034	0.000	0.000	0.000	0.000
133	A	135	SER	0	-0.086	-0.067	20.527	0.973	0.973	0.000	0.000	0.000	0.000
134	A	136	VAL	0	-0.018	-0.009	19.067	0.770	0.770	0.000	0.000	0.000	0.000
135	A	137	ASP	-1	-0.795	-0.890	19.464	-14.021	-14.021	0.000	0.000	0.000	0.000
136	A	138	LYS	1	0.923	0.966	22.454	11.420	11.420	0.000	0.000	0.000	0.000
137	A	139	HIS	1	0.817	0.868	24.534	11.919	11.919	0.000	0.000	0.000	0.000
138	A	140	ASN	0	0.047	0.019	22.714	0.883	0.883	0.000	0.000	0.000	0.000
139	A	141	TRP	0	-0.023	-0.002	25.943	0.314	0.314	0.000	0.000	0.000	0.000
140	A	142	MET	0	-0.037	-0.010	28.285	0.380	0.380	0.000	0.000	0.000	0.000
141	A	143	PHE	0	0.004	-0.002	26.112	0.394	0.394	0.000	0.000	0.000	0.000
142	A	144	LYS	1	0.946	0.969	24.928	11.702	11.702	0.000	0.000	0.000	0.000
143	A	145	SER	0	-0.054	-0.025	31.120	0.289	0.289	0.000	0.000	0.000	0.000
144	A	146	TYR	0	-0.054	-0.043	33.756	0.291	0.291	0.000	0.000	0.000	0.000
145	A	147	LEU	0	-0.043	-0.025	31.533	0.181	0.181	0.000	0.000	0.000	0.000
146	A	148	SER	0	-0.093	-0.037	34.867	0.016	0.016	0.000	0.000	0.000	0.000
147	A	149	LEU	0	-0.049	-0.017	36.978	0.104	0.104	0.000	0.000	0.000	0.000
148	A	150	GLU	-2	-1.906	-1.943	40.412	-14.016	-14.016	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)