FMO DATABASE

FMODB ID: QY33Y

Calculation Name: 3VLG-A-Xray372

Preferred Name: Oxidized low-density lipoprotein receptor 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3VLG

Chain ID: A

ChEMBL ID: CHEMBL3421522

UniProt ID: P78380

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	123
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1114393.673587
FMO2-HF: Nuclear repulsion	1063382.318845
FMO2-HF: Total energy	-51011.354741
FMO2-MP2: Total energy	-51156.741658

3D Structure

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:143:PRO)

Summations of interaction energy for fragment #1(A:143:PRO)

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.
-2.567	0.833	0.143	-1.414	-2.13	-0.002

Interaction energy analysis for fragmet #1(A:143:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : -0.013

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	145	PRO	0	0.025	0.005	3.842	-0.604	1.212	-0.016	-0.870	-0.930	0.001
4	A	146	GLN	0	-0.012	0.000	6.691	0.322	0.322	0.000	0.000	0.000	0.000
5	A	147	ASP	-1	-0.878	-0.944	8.912	-0.366	-0.366	0.000	0.000	0.000	0.000
6	A	148	TRP	0	-0.057	-0.022	7.627	-0.007	-0.007	0.000	0.000	0.000	0.000
7	A	149	ILE	0	0.005	0.003	8.282	0.185	0.185	0.000	0.000	0.000	0.000
8	A	150	ALA	0	0.016	-0.010	4.585	-0.353	-0.290	-0.001	-0.006	-0.056	0.000
9	A	151	HIS	0	-0.019	-0.024	6.285	0.251	0.251	0.000	0.000	0.000	0.000
10	A	152	GLY	0	0.018	0.014	8.265	-0.264	-0.264	0.000	0.000	0.000	0.000
11	A	153	GLU	-1	-0.872	-0.931	6.778	-0.148	-0.148	0.000	0.000	0.000	0.000
12	A	154	ASN	0	-0.047	-0.014	6.539	-0.633	-0.633	0.000	0.000	0.000	0.000
13	A	156	TYR	0	-0.001	-0.011	7.252	0.056	0.056	0.000	0.000	0.000	0.000
14	A	157	LEU	0	0.067	0.043	10.632	0.052	0.052	0.000	0.000	0.000	0.000
15	A	158	PHE	0	-0.004	-0.003	13.084	0.032	0.032	0.000	0.000	0.000	0.000
16	A	159	SER	0	0.006	0.009	16.544	-0.010	-0.010	0.000	0.000	0.000	0.000
17	A	160	SER	0	0.021	0.001	18.950	0.026	0.026	0.000	0.000	0.000	0.000
18	A	161	GLY	0	0.003	0.002	21.074	0.023	0.023	0.000	0.000	0.000	0.000
19	A	162	SER	0	-0.016	-0.001	23.553	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	163	PHE	0	-0.005	-0.017	24.113	0.006	0.006	0.000	0.000	0.000	0.000
21	A	164	ASN	0	0.035	0.030	27.496	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	165	TRP	0	0.009	0.003	24.575	-0.015	-0.015	0.000	0.000	0.000	0.000
23	A	166	GLU	-1	-0.888	-0.937	25.687	-0.160	-0.160	0.000	0.000	0.000	0.000
24	A	167	LYS	1	0.928	0.955	26.289	0.116	0.116	0.000	0.000	0.000	0.000
25	A	168	SER	0	-0.010	-0.016	22.732	-0.017	-0.017	0.000	0.000	0.000	0.000
26	A	169	GLN	0	-0.008	-0.017	21.664	-0.021	-0.021	0.000	0.000	0.000	0.000
27	A	170	GLU	-1	-0.788	-0.885	21.442	-0.267	-0.267	0.000	0.000	0.000	0.000
28	A	171	LYS	1	0.814	0.878	20.719	0.207	0.207	0.000	0.000	0.000	0.000
29	A	172	CYS	0	-0.039	0.007	14.559	-0.012	-0.012	0.000	0.000	0.000	0.000
30	A	173	LEU	0	-0.006	0.007	17.121	-0.063	-0.063	0.000	0.000	0.000	0.000
31	A	174	SER	0	-0.057	-0.032	18.413	-0.034	-0.034	0.000	0.000	0.000	0.000
32	A	175	LEU	0	-0.077	-0.017	14.661	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	176	ASP	-1	-0.867	-0.915	12.475	-1.032	-1.032	0.000	0.000	0.000	0.000
34	A	177	ALA	0	-0.064	-0.026	13.301	-0.110	-0.110	0.000	0.000	0.000	0.000
35	A	178	LYS	1	0.879	0.942	14.752	0.391	0.391	0.000	0.000	0.000	0.000
36	A	179	LEU	0	-0.004	0.003	16.047	-0.023	-0.023	0.000	0.000	0.000	0.000
37	A	180	LEU	0	-0.043	-0.015	15.336	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	181	LYS	1	0.827	0.907	16.431	0.176	0.176	0.000	0.000	0.000	0.000
39	A	182	ILE	0	-0.024	-0.008	16.736	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	183	ASN	0	0.013	-0.003	17.517	-0.019	-0.019	0.000	0.000	0.000	0.000
41	A	184	SER	0	-0.026	-0.033	16.962	0.027	0.027	0.000	0.000	0.000	0.000
42	A	185	THR	0	0.041	-0.004	19.570	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	186	ALA	0	0.060	0.050	15.943	0.000	0.000	0.000	0.000	0.000	0.000
44	A	187	ASP	-1	-0.805	-0.871	14.429	0.033	0.033	0.000	0.000	0.000	0.000
45	A	188	LEU	0	-0.024	-0.006	16.221	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	189	ASP	-1	-0.908	-0.965	18.092	0.209	0.209	0.000	0.000	0.000	0.000
47	A	190	PHE	0	0.060	0.025	11.048	0.011	0.011	0.000	0.000	0.000	0.000
48	A	191	ILE	0	-0.033	-0.021	14.521	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	192	GLN	0	-0.097	-0.072	16.903	0.005	0.005	0.000	0.000	0.000	0.000
50	A	193	GLN	0	-0.024	-0.008	14.221	-0.014	-0.014	0.000	0.000	0.000	0.000
51	A	194	ALA	0	0.046	0.033	14.733	0.000	0.000	0.000	0.000	0.000	0.000
52	A	195	ILE	0	-0.040	-0.012	16.635	-0.020	-0.020	0.000	0.000	0.000	0.000
53	A	196	SER	0	-0.041	-0.013	18.929	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	197	TYR	0	-0.057	-0.037	21.459	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	198	SER	0	0.045	0.040	23.356	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	199	SER	0	-0.045	-0.035	25.093	0.002	0.002	0.000	0.000	0.000	0.000
57	A	200	PHE	0	-0.007	-0.002	24.473	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	201	PRO	0	-0.001	0.012	25.923	0.007	0.007	0.000	0.000	0.000	0.000
59	A	202	PHE	0	0.021	-0.008	20.921	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	203	TRP	0	-0.026	-0.026	23.108	0.009	0.009	0.000	0.000	0.000	0.000
61	A	204	MET	0	-0.019	0.000	20.581	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	205	GLY	0	0.040	0.007	20.638	0.002	0.002	0.000	0.000	0.000	0.000
63	A	206	LEU	0	-0.053	-0.021	22.025	0.002	0.002	0.000	0.000	0.000	0.000
64	A	207	SER	0	0.003	0.000	25.003	0.008	0.008	0.000	0.000	0.000	0.000
65	A	208	ARG	1	0.868	0.942	28.463	0.053	0.053	0.000	0.000	0.000	0.000
66	A	209	ARG	1	0.978	0.986	31.866	0.073	0.073	0.000	0.000	0.000	0.000
67	A	210	ASN	0	0.028	0.029	34.856	0.004	0.004	0.000	0.000	0.000	0.000
68	A	211	PRO	0	0.010	-0.002	36.496	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	212	SER	0	-0.070	-0.044	38.037	0.003	0.003	0.000	0.000	0.000	0.000
70	A	213	TYR	0	0.016	0.027	34.275	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	214	PRO	0	0.032	0.009	31.630	0.004	0.004	0.000	0.000	0.000	0.000
72	A	215	TRP	0	0.004	-0.011	28.516	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	216	LEU	0	-0.039	-0.009	27.017	0.006	0.006	0.000	0.000	0.000	0.000
74	A	217	TRP	0	0.013	-0.007	21.494	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	218	GLU	-1	-0.740	-0.866	20.181	-0.253	-0.253	0.000	0.000	0.000	0.000
76	A	219	ASP	-1	-0.836	-0.889	19.982	-0.211	-0.211	0.000	0.000	0.000	0.000
77	A	220	GLY	0	0.034	0.021	22.970	0.005	0.005	0.000	0.000	0.000	0.000
78	A	221	SER	0	-0.069	-0.051	22.405	0.019	0.019	0.000	0.000	0.000	0.000
79	A	222	PRO	0	0.027	0.006	24.991	0.000	0.000	0.000	0.000	0.000	0.000
80	A	223	LEU	0	-0.013	0.002	24.747	-0.006	-0.006	0.000	0.000	0.000	0.000
81	A	224	MET	0	-0.001	-0.005	21.956	0.002	0.002	0.000	0.000	0.000	0.000
82	A	225	PRO	0	0.055	0.029	25.761	0.004	0.004	0.000	0.000	0.000	0.000
83	A	226	HIS	0	-0.060	-0.040	26.889	0.001	0.001	0.000	0.000	0.000	0.000
84	A	227	LEU	0	-0.002	0.027	21.796	0.010	0.010	0.000	0.000	0.000	0.000
85	A	228	PHE	0	0.083	0.020	22.694	0.008	0.008	0.000	0.000	0.000	0.000
86	A	229	ARG	1	0.848	0.930	27.310	-0.017	-0.017	0.000	0.000	0.000	0.000
87	A	230	VAL	0	0.031	0.024	28.488	0.001	0.001	0.000	0.000	0.000	0.000
88	A	231	ARG	1	0.953	0.962	30.758	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	232	GLY	0	0.027	0.013	33.015	-0.006	-0.006	0.000	0.000	0.000	0.000
90	A	233	ALA	0	-0.010	0.004	34.988	0.002	0.002	0.000	0.000	0.000	0.000
91	A	234	VAL	0	-0.016	-0.019	33.914	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	235	SER	0	0.014	-0.001	36.290	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	236	GLN	0	0.042	0.028	38.805	0.000	0.000	0.000	0.000	0.000	0.000
94	A	237	THR	0	0.022	-0.005	38.905	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	238	TYR	0	0.000	0.002	36.105	0.004	0.004	0.000	0.000	0.000	0.000
96	A	239	PRO	0	0.000	-0.010	38.176	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	240	SER	0	0.027	0.018	34.056	-0.002	-0.002	0.000	0.000	0.000	0.000
98	A	241	GLY	0	0.002	0.021	33.442	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	242	THR	0	-0.037	-0.033	32.720	0.002	0.002	0.000	0.000	0.000	0.000
100	A	243	CYS	0	0.040	0.038	27.860	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	244	ALA	0	0.024	0.002	25.956	0.011	0.011	0.000	0.000	0.000	0.000
102	A	245	TYR	0	-0.063	-0.040	24.735	-0.010	-0.010	0.000	0.000	0.000	0.000
103	A	246	ILE	0	-0.004	-0.003	21.297	0.013	0.013	0.000	0.000	0.000	0.000
104	A	247	GLN	0	0.017	-0.021	24.763	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	248	ARG	1	0.951	0.965	26.618	-0.020	-0.020	0.000	0.000	0.000	0.000
106	A	249	GLY	0	0.037	0.031	24.227	0.006	0.006	0.000	0.000	0.000	0.000
107	A	250	ALA	0	0.002	0.018	25.310	0.001	0.001	0.000	0.000	0.000	0.000
108	A	251	VAL	0	0.020	0.011	24.797	-0.007	-0.007	0.000	0.000	0.000	0.000
109	A	252	TYR	0	-0.028	-0.001	27.493	0.006	0.006	0.000	0.000	0.000	0.000
110	A	253	ALA	0	0.005	0.016	29.063	-0.009	-0.009	0.000	0.000	0.000	0.000
111	A	254	GLU	-1	-0.854	-0.923	30.794	-0.044	-0.044	0.000	0.000	0.000	0.000
112	A	255	ASN	0	0.013	-0.010	32.222	-0.012	-0.012	0.000	0.000	0.000	0.000
113	A	257	ILE	0	-0.046	-0.023	30.961	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	258	LEU	0	-0.008	0.003	32.274	0.000	0.000	0.000	0.000	0.000	0.000
115	A	259	ALA	0	-0.001	-0.008	29.658	-0.009	-0.009	0.000	0.000	0.000	0.000
116	A	260	ALA	0	0.023	0.006	26.333	0.012	0.012	0.000	0.000	0.000	0.000
117	A	261	PHE	0	-0.001	0.016	22.177	-0.011	-0.011	0.000	0.000	0.000	0.000
118	A	262	SER	0	-0.040	-0.008	20.690	-0.006	-0.006	0.000	0.000	0.000	0.000
119	A	263	ILE	0	0.037	0.023	14.994	0.004	0.004	0.000	0.000	0.000	0.000
120	A	265	GLN	0	0.029	0.003	11.539	0.069	0.069	0.000	0.000	0.000	0.000
121	A	266	LYS	1	0.857	0.918	8.958	1.216	1.216	0.000	0.000	0.000	0.000
122	A	267	LYS	1	0.791	0.879	8.437	0.527	0.527	0.000	0.000	0.000	0.000
123	A	268	ALA	0	0.007	0.008	2.879	-1.816	-0.295	0.160	-0.538	-1.144	-0.003

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Interactive mode: IFIE and PIEDA for fragment #1(A:143:PRO)