FMO DATABASE

FMODB ID: LVZ49

Calculation Name: 1VCD-A-Xray547

Preferred Name:

Target Type:

Ligand Name: glycerol

Ligand 3-letter code: GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1VCD

Chain ID: A

ChEMBL ID:

UniProt ID: Q75UV1

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	126
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1099411.519535
FMO2-HF: Nuclear repulsion	1049977.442968
FMO2-HF: Total energy	-49434.076567
FMO2-MP2: Total energy	-49579.035542

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.
-130.997	-127.379	16.219	-5.264	-14.572	-0.063

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 : 0.770 / q_NPA : 0.900

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	LEU	0	0.051	0.018	2.234	-1.145	0.883	4.616	-1.602	-5.041	-0.016
4	A	4	GLY	0	0.020	0.009	3.020	2.867	2.068	0.051	0.999	-0.251	-0.001
65	A	65	ARG	1	0.816	0.879	4.277	36.302	36.560	-0.001	-0.019	-0.238	0.000
72	A	72	VAL	0	-0.025	-0.010	3.430	-2.802	-2.546	0.013	-0.062	-0.206	0.000
73	A	73	GLU	-1	-0.942	-0.969	2.454	-58.138	-56.994	1.872	-1.145	-1.872	-0.005
74	A	74	ARG	1	0.807	0.886	2.530	21.373	24.815	2.199	-2.710	-2.931	-0.030
75	A	75	GLU	-1	-0.783	-0.873	2.158	-33.953	-36.631	7.449	-1.162	-3.609	-0.008
76	A	76	VAL	0	-0.020	-0.001	3.417	-1.016	-1.049	0.020	0.437	-0.424	-0.003
5	A	5	ALA	0	0.006	0.029	6.099	-0.120	-0.120	0.000	0.000	0.000	0.000
6	A	6	GLY	0	0.025	-0.001	9.266	0.147	0.147	0.000	0.000	0.000	0.000
7	A	7	GLY	0	0.041	0.006	11.976	0.290	0.290	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.035	-0.014	15.641	0.356	0.356	0.000	0.000	0.000	0.000
9	A	9	VAL	0	-0.014	-0.008	18.032	0.391	0.391	0.000	0.000	0.000	0.000
10	A	10	PHE	0	0.019	0.004	20.992	0.208	0.208	0.000	0.000	0.000	0.000
11	A	11	ASN	0	0.014	-0.001	24.520	0.110	0.110	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.040	-0.039	27.921	0.018	0.018	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.829	0.920	31.225	8.954	8.954	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.813	0.910	27.691	9.888	9.888	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.866	-0.909	28.406	-9.181	-9.181	0.000	0.000	0.000	0.000
16	A	16	VAL	0	-0.015	-0.017	21.965	-0.192	-0.192	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.021	-0.008	21.135	0.257	0.257	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.044	-0.019	21.227	-0.577	-0.577	0.000	0.000	0.000	0.000
19	A	19	LEU	0	0.044	0.014	18.730	0.516	0.516	0.000	0.000	0.000	0.000
20	A	20	ARG	1	0.869	0.950	21.773	10.944	10.944	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.719	-0.866	19.055	-14.536	-14.536	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.967	0.980	20.105	14.396	14.396	0.000	0.000	0.000	0.000
23	A	23	MET	0	-0.116	-0.054	20.464	0.299	0.299	0.000	0.000	0.000	0.000
24	A	24	GLY	0	-0.026	-0.004	23.073	0.478	0.478	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.034	-0.019	19.685	0.460	0.460	0.000	0.000	0.000	0.000
26	A	26	TRP	0	0.027	0.007	21.659	-0.114	-0.114	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.003	-0.005	16.817	-0.371	-0.371	0.000	0.000	0.000	0.000
28	A	28	PHE	0	0.039	0.020	15.641	0.772	0.772	0.000	0.000	0.000	0.000
29	A	29	PRO	0	0.010	0.015	15.729	-0.789	-0.789	0.000	0.000	0.000	0.000
30	A	30	LYS	1	0.930	0.945	10.084	20.554	20.554	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.065	0.051	11.015	0.389	0.389	0.000	0.000	0.000	0.000
32	A	32	HIS	0	-0.111	-0.067	7.141	-5.228	-5.228	0.000	0.000	0.000	0.000
33	A	33	PRO	0	0.002	0.023	7.232	1.465	1.465	0.000	0.000	0.000	0.000
34	A	34	GLU	-1	-0.907	-0.960	10.085	-18.731	-18.731	0.000	0.000	0.000	0.000
35	A	35	PRO	0	-0.069	-0.061	12.307	-0.563	-0.563	0.000	0.000	0.000	0.000
36	A	36	GLY	0	-0.038	-0.016	12.599	1.342	1.342	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.776	-0.836	12.639	-17.922	-17.922	0.000	0.000	0.000	0.000
38	A	38	SER	0	-0.049	-0.052	11.820	-1.397	-1.397	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.005	-0.023	6.967	-0.488	-0.488	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.859	-0.942	10.872	-17.840	-17.840	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.863	-0.900	14.466	-15.035	-15.035	0.000	0.000	0.000	0.000
42	A	42	ALA	0	0.024	0.027	11.299	0.355	0.355	0.000	0.000	0.000	0.000
43	A	43	ALA	0	-0.007	-0.010	13.126	0.254	0.254	0.000	0.000	0.000	0.000
44	A	44	VAL	0	-0.052	-0.031	14.177	0.668	0.668	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.714	0.819	12.918	19.114	19.114	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.772	-0.896	12.245	-19.363	-19.363	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.019	-0.008	15.707	0.491	0.491	0.000	0.000	0.000	0.000
48	A	48	TRP	0	0.000	0.019	18.213	1.022	1.022	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.893	-0.948	17.932	-15.430	-15.430	0.000	0.000	0.000	0.000
50	A	50	GLU	-1	-0.925	-0.952	16.013	-16.083	-16.083	0.000	0.000	0.000	0.000
51	A	51	THR	0	-0.049	-0.060	19.413	0.628	0.628	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.018	0.018	22.372	0.606	0.606	0.000	0.000	0.000	0.000
53	A	53	VAL	0	-0.042	-0.017	23.145	0.475	0.475	0.000	0.000	0.000	0.000
54	A	54	ARG	1	0.823	0.918	23.031	10.796	10.796	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.007	-0.012	20.938	0.324	0.324	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.938	-0.958	21.210	-10.991	-10.991	0.000	0.000	0.000	0.000
57	A	57	VAL	0	-0.005	-0.009	16.271	-0.033	-0.033	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.051	-0.009	19.386	0.459	0.459	0.000	0.000	0.000	0.000
59	A	59	LEU	0	0.005	-0.010	19.075	0.168	0.168	0.000	0.000	0.000	0.000
60	A	60	PRO	0	0.027	0.026	14.346	-0.371	-0.371	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.022	-0.009	14.186	0.784	0.784	0.000	0.000	0.000	0.000
62	A	62	TYR	0	-0.024	-0.028	11.819	0.277	0.277	0.000	0.000	0.000	0.000
63	A	63	PRO	0	0.022	0.016	6.753	-0.063	-0.063	0.000	0.000	0.000	0.000
64	A	64	THR	0	0.030	0.030	8.241	1.322	1.322	0.000	0.000	0.000	0.000
66	A	66	TYR	0	0.029	0.016	6.231	2.877	2.877	0.000	0.000	0.000	0.000
67	A	67	VAL	0	0.011	0.012	6.127	-5.272	-5.272	0.000	0.000	0.000	0.000
68	A	68	ASN	0	0.041	0.026	7.323	4.382	4.382	0.000	0.000	0.000	0.000
69	A	69	PRO	0	0.042	-0.003	9.256	-0.144	-0.144	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.891	0.953	9.742	24.389	24.389	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.013	0.011	8.944	-0.312	-0.312	0.000	0.000	0.000	0.000
77	A	77	HIS	0	-0.019	-0.023	5.177	3.743	3.743	0.000	0.000	0.000	0.000
78	A	78	TRP	0	0.021	0.010	8.143	0.997	0.997	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.004	-0.003	10.765	0.526	0.526	0.000	0.000	0.000	0.000
80	A	80	LEU	0	0.003	0.025	14.858	0.227	0.227	0.000	0.000	0.000	0.000
81	A	81	MET	0	-0.007	0.002	17.330	-0.202	-0.202	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.896	0.958	20.330	10.348	10.348	0.000	0.000	0.000	0.000
83	A	83	GLY	0	0.056	0.015	23.694	-0.265	-0.265	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.837	-0.910	25.322	-9.032	-9.032	0.000	0.000	0.000	0.000
85	A	85	GLY	0	0.005	0.004	28.225	-0.127	-0.127	0.000	0.000	0.000	0.000
86	A	86	ALA	0	-0.021	-0.011	29.545	-0.083	-0.083	0.000	0.000	0.000	0.000
87	A	87	PRO	0	0.036	0.029	25.526	-0.056	-0.056	0.000	0.000	0.000	0.000
88	A	88	ARG	1	0.766	0.866	26.116	11.320	11.320	0.000	0.000	0.000	0.000
89	A	89	LEU	0	-0.042	-0.015	25.461	-0.323	-0.323	0.000	0.000	0.000	0.000
90	A	90	GLU	-1	-0.761	-0.860	22.121	-11.542	-11.542	0.000	0.000	0.000	0.000
91	A	91	GLU	-1	-0.954	-0.984	22.930	-12.758	-12.758	0.000	0.000	0.000	0.000
92	A	92	GLY	0	-0.051	-0.024	22.546	-0.538	-0.538	0.000	0.000	0.000	0.000
93	A	93	MET	0	-0.017	0.002	19.602	-0.205	-0.205	0.000	0.000	0.000	0.000
94	A	94	THR	0	-0.093	-0.070	24.085	0.680	0.680	0.000	0.000	0.000	0.000
95	A	95	GLY	0	0.002	-0.017	25.848	0.455	0.455	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.009	0.011	24.874	-0.537	-0.537	0.000	0.000	0.000	0.000
97	A	97	GLY	0	-0.028	-0.013	25.522	0.478	0.478	0.000	0.000	0.000	0.000
98	A	98	TRP	0	-0.029	-0.016	24.850	-0.476	-0.476	0.000	0.000	0.000	0.000
99	A	99	PHE	0	0.013	0.011	25.984	0.283	0.283	0.000	0.000	0.000	0.000
100	A	100	SER	0	0.008	-0.028	27.793	-0.179	-0.179	0.000	0.000	0.000	0.000
101	A	101	PRO	0	0.027	-0.013	26.877	-0.208	-0.208	0.000	0.000	0.000	0.000
102	A	102	GLU	-1	-0.986	-0.982	27.573	-8.830	-8.830	0.000	0.000	0.000	0.000
103	A	103	GLU	-1	-0.811	-0.876	29.344	-9.297	-9.297	0.000	0.000	0.000	0.000
104	A	104	ALA	0	0.011	0.001	23.980	-0.235	-0.235	0.000	0.000	0.000	0.000
105	A	105	ARG	1	0.843	0.891	24.664	9.903	9.903	0.000	0.000	0.000	0.000
106	A	106	ALA	0	-0.050	-0.007	26.175	-0.073	-0.073	0.000	0.000	0.000	0.000
107	A	107	LEU	0	-0.056	-0.018	25.841	0.078	0.078	0.000	0.000	0.000	0.000
108	A	108	LEU	0	-0.051	-0.016	19.448	-0.294	-0.294	0.000	0.000	0.000	0.000
109	A	109	ALA	0	-0.018	-0.007	20.288	0.129	0.129	0.000	0.000	0.000	0.000
110	A	110	PHE	0	-0.038	-0.004	15.540	-0.231	-0.231	0.000	0.000	0.000	0.000
111	A	111	PRO	0	0.002	-0.011	17.867	0.248	0.248	0.000	0.000	0.000	0.000
112	A	112	GLU	-1	-0.894	-0.957	12.944	-18.432	-18.432	0.000	0.000	0.000	0.000
113	A	113	ASP	-1	-0.858	-0.938	15.154	-17.017	-17.017	0.000	0.000	0.000	0.000
114	A	114	LEU	0	-0.002	-0.002	17.268	0.579	0.579	0.000	0.000	0.000	0.000
115	A	115	GLY	0	0.012	0.007	18.116	0.478	0.478	0.000	0.000	0.000	0.000
116	A	116	LEU	0	-0.040	-0.019	12.986	0.230	0.230	0.000	0.000	0.000	0.000
117	A	117	LEU	0	-0.001	0.006	17.327	0.339	0.339	0.000	0.000	0.000	0.000
118	A	118	GLU	-1	-0.813	-0.894	20.789	-10.668	-10.668	0.000	0.000	0.000	0.000
119	A	119	VAL	0	0.011	0.006	18.377	0.227	0.227	0.000	0.000	0.000	0.000
120	A	120	ALA	0	-0.006	-0.006	19.104	0.099	0.099	0.000	0.000	0.000	0.000
121	A	121	LEU	0	-0.030	-0.022	20.811	0.473	0.473	0.000	0.000	0.000	0.000
122	A	122	GLU	-1	-0.979	-0.983	23.448	-11.097	-11.097	0.000	0.000	0.000	0.000
123	A	123	ARG	1	0.839	0.920	16.862	14.219	14.219	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.012	0.013	23.515	0.114	0.114	0.000	0.000	0.000	0.000
125	A	125	PRO	0	-0.024	-0.010	25.054	0.352	0.352	0.000	0.000	0.000	0.000
126	A	126	LEU	-1	-0.923	-0.951	28.273	-8.784	-8.784	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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