FMO DATABASE

FMODB ID: K9663

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	OptAll
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	-1114228.317817
FMO2-HF: Nuclear repulsion	1063216.553177
FMO2-HF: Total energy	-51011.76464
FMO2-MP2: Total energy	-51157.006091

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.
-2.817	-0.167	0.539	-1.083	-2.106	0.001

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 : -0.011 / q_NPA : -0.037

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	0.024	0.014	3.845	-1.019	0.347	-0.013	-0.610	-0.743	0.002
4	A	146	GLN	0	-0.013	-0.019	6.676	0.410	0.410	0.000	0.000	0.000	0.000
5	A	147	ASP	-1	-0.874	-0.933	9.112	-0.027	-0.027	0.000	0.000	0.000	0.000
6	A	148	TRP	0	-0.063	-0.023	7.856	-0.012	-0.012	0.000	0.000	0.000	0.000
7	A	149	ILE	0	0.001	0.001	7.926	0.352	0.352	0.000	0.000	0.000	0.000
8	A	150	ALA	0	0.044	-0.001	5.176	-0.252	-0.190	-0.001	-0.004	-0.057	0.000
9	A	151	HIS	0	-0.035	-0.031	6.762	-0.171	-0.171	0.000	0.000	0.000	0.000
10	A	152	GLY	0	0.027	0.022	8.579	-0.199	-0.199	0.000	0.000	0.000	0.000
11	A	153	GLU	-1	-0.887	-0.941	7.040	0.162	0.162	0.000	0.000	0.000	0.000
12	A	154	ASN	0	-0.033	-0.002	6.487	-0.621	-0.621	0.000	0.000	0.000	0.000
13	A	156	TYR	0	-0.004	-0.016	7.271	-0.291	-0.291	0.000	0.000	0.000	0.000
14	A	157	LEU	0	0.029	0.028	10.915	0.100	0.100	0.000	0.000	0.000	0.000
15	A	158	PHE	0	0.003	0.002	13.365	-0.031	-0.031	0.000	0.000	0.000	0.000
16	A	159	SER	0	-0.007	-0.002	17.012	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	160	SER	0	0.012	-0.004	19.348	0.015	0.015	0.000	0.000	0.000	0.000
18	A	161	GLY	0	0.001	0.004	21.066	0.004	0.004	0.000	0.000	0.000	0.000
19	A	162	SER	0	-0.028	0.003	23.641	0.003	0.003	0.000	0.000	0.000	0.000
20	A	163	PHE	0	0.006	-0.010	23.809	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	164	ASN	0	0.050	0.045	27.715	0.002	0.002	0.000	0.000	0.000	0.000
22	A	165	TRP	0	0.019	0.012	24.551	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	166	GLU	-1	-0.868	-0.936	25.356	-0.061	-0.061	0.000	0.000	0.000	0.000
24	A	167	LYS	1	0.929	0.963	25.900	0.038	0.038	0.000	0.000	0.000	0.000
25	A	168	SER	0	-0.031	-0.032	22.491	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	169	GLN	0	0.015	-0.012	21.334	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	170	GLU	-1	-0.819	-0.876	21.226	-0.132	-0.132	0.000	0.000	0.000	0.000
28	A	171	LYS	1	0.808	0.876	20.470	0.084	0.084	0.000	0.000	0.000	0.000
29	A	172	CYS	0	-0.007	0.027	14.831	-0.023	-0.023	0.000	0.000	0.000	0.000
30	A	173	LEU	0	0.027	0.019	16.981	-0.045	-0.045	0.000	0.000	0.000	0.000
31	A	174	SER	0	-0.101	-0.065	18.488	-0.035	-0.035	0.000	0.000	0.000	0.000
32	A	175	LEU	0	-0.056	-0.017	14.744	-0.009	-0.009	0.000	0.000	0.000	0.000
33	A	176	ASP	-1	-0.853	-0.903	11.871	-0.757	-0.757	0.000	0.000	0.000	0.000
34	A	177	ALA	0	-0.031	0.000	13.087	-0.062	-0.062	0.000	0.000	0.000	0.000
35	A	178	LYS	1	0.866	0.930	14.583	0.153	0.153	0.000	0.000	0.000	0.000
36	A	179	LEU	0	0.012	-0.001	16.036	0.013	0.013	0.000	0.000	0.000	0.000
37	A	180	LEU	0	-0.037	-0.010	15.707	-0.006	-0.006	0.000	0.000	0.000	0.000
38	A	181	LYS	1	0.831	0.902	16.346	0.009	0.009	0.000	0.000	0.000	0.000
39	A	182	ILE	0	-0.007	-0.004	17.027	0.012	0.012	0.000	0.000	0.000	0.000
40	A	183	ASN	0	0.004	0.003	17.318	-0.040	-0.040	0.000	0.000	0.000	0.000
41	A	184	SER	0	-0.016	-0.035	16.784	0.003	0.003	0.000	0.000	0.000	0.000
42	A	185	THR	0	0.019	-0.011	19.425	0.000	0.000	0.000	0.000	0.000	0.000
43	A	186	ALA	0	0.075	0.049	15.994	0.002	0.002	0.000	0.000	0.000	0.000
44	A	187	ASP	-1	-0.802	-0.873	14.402	0.264	0.264	0.000	0.000	0.000	0.000
45	A	188	LEU	0	-0.040	-0.011	16.455	0.002	0.002	0.000	0.000	0.000	0.000
46	A	189	ASP	-1	-0.879	-0.949	18.410	0.312	0.312	0.000	0.000	0.000	0.000
47	A	190	PHE	0	0.029	0.017	11.383	0.012	0.012	0.000	0.000	0.000	0.000
48	A	191	ILE	0	0.001	0.000	14.876	0.006	0.006	0.000	0.000	0.000	0.000
49	A	192	GLN	0	-0.090	-0.065	17.540	-0.009	-0.009	0.000	0.000	0.000	0.000
50	A	193	GLN	0	-0.020	-0.003	14.829	-0.013	-0.013	0.000	0.000	0.000	0.000
51	A	194	ALA	0	0.039	0.027	15.412	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	195	ILE	0	-0.041	-0.018	17.384	-0.028	-0.028	0.000	0.000	0.000	0.000
53	A	196	SER	0	-0.040	-0.017	19.700	-0.020	-0.020	0.000	0.000	0.000	0.000
54	A	197	TYR	0	-0.049	-0.033	22.130	-0.023	-0.023	0.000	0.000	0.000	0.000
55	A	198	SER	0	0.020	0.027	24.194	-0.023	-0.023	0.000	0.000	0.000	0.000
56	A	199	SER	0	-0.034	-0.030	25.896	0.000	0.000	0.000	0.000	0.000	0.000
57	A	200	PHE	0	-0.013	-0.003	24.756	-0.011	-0.011	0.000	0.000	0.000	0.000
58	A	201	PRO	0	0.010	0.019	26.421	0.010	0.010	0.000	0.000	0.000	0.000
59	A	202	PHE	0	0.026	-0.005	21.488	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	203	TRP	0	-0.048	-0.042	23.168	0.007	0.007	0.000	0.000	0.000	0.000
61	A	204	MET	0	-0.010	-0.001	20.719	0.007	0.007	0.000	0.000	0.000	0.000
62	A	205	GLY	0	0.055	0.038	20.526	-0.010	-0.010	0.000	0.000	0.000	0.000
63	A	206	LEU	0	-0.071	-0.037	21.816	-0.007	-0.007	0.000	0.000	0.000	0.000
64	A	207	SER	0	-0.010	-0.009	24.959	0.003	0.003	0.000	0.000	0.000	0.000
65	A	208	ARG	1	0.848	0.913	28.473	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	209	ARG	1	0.972	0.988	31.968	0.025	0.025	0.000	0.000	0.000	0.000
67	A	210	ASN	0	0.029	0.026	34.745	0.002	0.002	0.000	0.000	0.000	0.000
68	A	211	PRO	0	0.030	0.007	36.603	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	212	SER	0	-0.048	-0.029	38.237	0.001	0.001	0.000	0.000	0.000	0.000
70	A	213	TYR	0	0.019	0.026	34.191	-0.002	-0.002	0.000	0.000	0.000	0.000
71	A	214	PRO	0	0.023	0.010	31.659	0.005	0.005	0.000	0.000	0.000	0.000
72	A	215	TRP	0	0.003	-0.009	28.718	-0.003	-0.003	0.000	0.000	0.000	0.000
73	A	216	LEU	0	-0.026	-0.004	27.120	0.004	0.004	0.000	0.000	0.000	0.000
74	A	217	TRP	0	0.006	-0.008	21.346	0.005	0.005	0.000	0.000	0.000	0.000
75	A	218	GLU	-1	-0.778	-0.886	19.948	-0.090	-0.090	0.000	0.000	0.000	0.000
76	A	219	ASP	-1	-0.816	-0.880	19.922	-0.078	-0.078	0.000	0.000	0.000	0.000
77	A	220	GLY	0	0.013	0.011	22.677	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	221	SER	0	-0.042	-0.035	22.364	0.014	0.014	0.000	0.000	0.000	0.000
79	A	222	PRO	0	0.027	0.000	24.992	0.002	0.002	0.000	0.000	0.000	0.000
80	A	223	LEU	0	0.000	0.008	24.992	0.003	0.003	0.000	0.000	0.000	0.000
81	A	224	MET	0	0.003	0.005	22.065	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	225	PRO	0	0.028	0.010	25.995	0.007	0.007	0.000	0.000	0.000	0.000
83	A	226	HIS	0	0.001	-0.005	26.904	0.001	0.001	0.000	0.000	0.000	0.000
84	A	227	LEU	0	-0.007	0.030	21.559	0.009	0.009	0.000	0.000	0.000	0.000
85	A	228	PHE	0	0.068	0.020	22.742	0.008	0.008	0.000	0.000	0.000	0.000
86	A	229	ARG	1	0.803	0.884	27.282	-0.070	-0.070	0.000	0.000	0.000	0.000
87	A	230	VAL	0	0.033	0.033	28.332	0.004	0.004	0.000	0.000	0.000	0.000
88	A	231	ARG	1	0.946	0.974	30.650	-0.057	-0.057	0.000	0.000	0.000	0.000
89	A	232	GLY	0	0.056	0.022	33.066	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	233	ALA	0	-0.006	0.010	35.331	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	234	VAL	0	-0.002	-0.016	33.606	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	235	SER	0	-0.013	-0.005	36.051	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	236	GLN	0	0.027	0.022	38.922	0.000	0.000	0.000	0.000	0.000	0.000
94	A	237	THR	0	0.024	-0.008	38.492	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	238	TYR	0	0.001	0.003	36.305	0.002	0.002	0.000	0.000	0.000	0.000
96	A	239	PRO	0	-0.005	-0.010	38.371	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	240	SER	0	0.022	0.021	34.028	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	241	GLY	0	-0.001	0.008	33.560	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	242	THR	0	-0.031	-0.029	32.932	0.001	0.001	0.000	0.000	0.000	0.000
100	A	243	CYS	0	0.019	0.025	27.892	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	244	ALA	0	0.032	0.005	26.343	0.005	0.005	0.000	0.000	0.000	0.000
102	A	245	TYR	0	-0.068	-0.048	24.787	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	246	ILE	0	-0.006	0.003	21.581	0.003	0.003	0.000	0.000	0.000	0.000
104	A	247	GLN	0	0.024	-0.016	25.054	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	248	ARG	1	0.934	0.959	27.167	-0.091	-0.091	0.000	0.000	0.000	0.000
106	A	249	GLY	0	0.051	0.040	24.431	0.003	0.003	0.000	0.000	0.000	0.000
107	A	250	ALA	0	0.004	0.017	25.482	0.001	0.001	0.000	0.000	0.000	0.000
108	A	251	VAL	0	0.022	0.006	24.989	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	252	TYR	0	-0.042	-0.019	27.673	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	253	ALA	0	0.034	0.015	29.009	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	254	GLU	-1	-0.882	-0.924	31.244	0.025	0.025	0.000	0.000	0.000	0.000
112	A	255	ASN	0	0.035	0.013	32.574	-0.006	-0.006	0.000	0.000	0.000	0.000
113	A	257	ILE	0	-0.034	-0.022	30.784	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	258	LEU	0	-0.011	0.003	32.671	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	259	ALA	0	-0.005	-0.014	30.013	-0.005	-0.005	0.000	0.000	0.000	0.000
116	A	260	ALA	0	0.020	0.014	26.818	0.007	0.007	0.000	0.000	0.000	0.000
117	A	261	PHE	0	0.001	0.009	22.602	-0.009	-0.009	0.000	0.000	0.000	0.000
118	A	262	SER	0	-0.042	-0.022	20.893	-0.009	-0.009	0.000	0.000	0.000	0.000
119	A	263	ILE	0	0.018	0.016	15.486	0.013	0.013	0.000	0.000	0.000	0.000
120	A	265	GLN	0	0.026	0.005	11.398	0.088	0.088	0.000	0.000	0.000	0.000
121	A	266	LYS	1	0.814	0.892	8.781	0.706	0.706	0.000	0.000	0.000	0.000
122	A	267	LYS	1	0.812	0.891	7.824	0.421	0.421	0.000	0.000	0.000	0.000
123	A	268	ALA	0	-0.002	0.003	2.280	-1.691	-0.469	0.553	-0.469	-1.306	-0.001

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