FMO DATABASE

FMODB ID: R9JJ8

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	OptH
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	-1113721.698416
FMO2-HF: Nuclear repulsion	1062711.474941
FMO2-HF: Total energy	-51010.223475
FMO2-MP2: Total energy	-51155.717855

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.
-2.142	0.658	1.837	-1.781	-2.856	-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 : 0.023 / q_NPA : 0.009

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

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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	0.012	-0.012	3.861	-1.073	1.034	-0.019	-1.043	-1.045	0.003
4	A	146	GLN	0	-0.013	0.008	6.691	0.218	0.218	0.000	0.000	0.000	0.000
5	A	147	ASP	-1	-0.853	-0.930	8.931	-0.478	-0.478	0.000	0.000	0.000	0.000
6	A	148	TRP	0	-0.070	-0.030	7.692	0.033	0.033	0.000	0.000	0.000	0.000
7	A	149	ILE	0	0.013	0.007	8.071	0.059	0.059	0.000	0.000	0.000	0.000
8	A	150	ALA	0	0.012	-0.012	4.179	-0.294	-0.220	-0.001	-0.012	-0.061	0.000
9	A	151	HIS	0	-0.002	-0.003	6.007	0.326	0.326	0.000	0.000	0.000	0.000
10	A	152	GLY	0	0.012	0.009	8.244	-0.179	-0.179	0.000	0.000	0.000	0.000
11	A	153	GLU	-1	-0.953	-0.985	6.553	-0.092	-0.092	0.000	0.000	0.000	0.000
12	A	154	ASN	0	-0.083	-0.037	5.868	-0.427	-0.427	0.000	0.000	0.000	0.000
13	A	156	TYR	0	-0.013	-0.019	7.408	0.145	0.145	0.000	0.000	0.000	0.000
14	A	157	LEU	0	0.058	0.034	10.670	0.008	0.008	0.000	0.000	0.000	0.000
15	A	158	PHE	0	-0.002	0.001	13.114	0.049	0.049	0.000	0.000	0.000	0.000
16	A	159	SER	0	-0.008	-0.003	16.502	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	160	SER	0	0.026	0.001	18.997	0.025	0.025	0.000	0.000	0.000	0.000
18	A	161	GLY	0	0.010	0.006	21.076	0.024	0.024	0.000	0.000	0.000	0.000
19	A	162	SER	0	-0.004	0.009	23.608	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	163	PHE	0	0.008	-0.013	24.590	0.009	0.009	0.000	0.000	0.000	0.000
21	A	164	ASN	0	0.025	0.030	27.617	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	165	TRP	0	0.012	-0.001	24.435	-0.013	-0.013	0.000	0.000	0.000	0.000
23	A	166	GLU	-1	-0.885	-0.936	25.842	-0.165	-0.165	0.000	0.000	0.000	0.000
24	A	167	LYS	1	0.898	0.946	26.353	0.126	0.126	0.000	0.000	0.000	0.000
25	A	168	SER	0	-0.019	-0.019	22.907	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	169	GLN	0	-0.004	-0.012	21.891	-0.018	-0.018	0.000	0.000	0.000	0.000
27	A	170	GLU	-1	-0.952	-0.981	21.416	-0.269	-0.269	0.000	0.000	0.000	0.000
28	A	171	LYS	1	0.983	0.978	20.973	0.197	0.197	0.000	0.000	0.000	0.000
29	A	172	CYS	0	-0.065	-0.007	14.695	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	173	LEU	0	-0.020	0.000	17.093	-0.056	-0.056	0.000	0.000	0.000	0.000
31	A	174	SER	0	0.003	0.000	18.378	-0.030	-0.030	0.000	0.000	0.000	0.000
32	A	175	LEU	0	-0.112	-0.036	14.730	-0.020	-0.020	0.000	0.000	0.000	0.000
33	A	176	ASP	-1	-0.936	-0.959	13.174	-0.699	-0.699	0.000	0.000	0.000	0.000
34	A	177	ALA	0	-0.102	-0.048	13.257	-0.100	-0.100	0.000	0.000	0.000	0.000
35	A	178	LYS	1	0.944	0.977	14.410	0.421	0.421	0.000	0.000	0.000	0.000
36	A	179	LEU	0	0.000	0.003	16.028	-0.034	-0.034	0.000	0.000	0.000	0.000
37	A	180	LEU	0	-0.045	-0.017	15.443	0.001	0.001	0.000	0.000	0.000	0.000
38	A	181	LYS	1	0.889	0.951	16.350	0.207	0.207	0.000	0.000	0.000	0.000
39	A	182	ILE	0	-0.028	-0.006	16.557	-0.008	-0.008	0.000	0.000	0.000	0.000
40	A	183	ASN	0	-0.003	-0.027	17.279	0.009	0.009	0.000	0.000	0.000	0.000
41	A	184	SER	0	-0.006	-0.004	16.689	0.026	0.026	0.000	0.000	0.000	0.000
42	A	185	THR	0	0.045	0.002	19.447	-0.013	-0.013	0.000	0.000	0.000	0.000
43	A	186	ALA	0	0.043	0.042	15.674	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	187	ASP	-1	-0.831	-0.905	14.561	-0.101	-0.101	0.000	0.000	0.000	0.000
45	A	188	LEU	0	-0.047	-0.014	16.132	-0.012	-0.012	0.000	0.000	0.000	0.000
46	A	189	ASP	-1	-0.886	-0.959	18.081	0.069	0.069	0.000	0.000	0.000	0.000
47	A	190	PHE	0	0.044	0.016	10.835	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	191	ILE	0	-0.027	-0.010	14.630	-0.011	-0.011	0.000	0.000	0.000	0.000
49	A	192	GLN	0	-0.093	-0.087	16.712	0.007	0.007	0.000	0.000	0.000	0.000
50	A	193	GLN	0	-0.009	-0.004	14.174	-0.020	-0.020	0.000	0.000	0.000	0.000
51	A	194	ALA	0	0.021	0.024	14.433	0.006	0.006	0.000	0.000	0.000	0.000
52	A	195	ILE	0	-0.034	-0.013	16.313	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	196	SER	0	-0.038	-0.008	18.713	0.008	0.008	0.000	0.000	0.000	0.000
54	A	197	TYR	0	-0.062	-0.039	21.091	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	198	SER	0	0.048	0.040	23.016	0.000	0.000	0.000	0.000	0.000	0.000
56	A	199	SER	0	-0.069	-0.041	24.822	0.000	0.000	0.000	0.000	0.000	0.000
57	A	200	PHE	0	0.028	0.021	24.614	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	201	PRO	0	-0.007	0.008	25.785	0.003	0.003	0.000	0.000	0.000	0.000
59	A	202	PHE	0	0.030	-0.005	20.845	-0.008	-0.008	0.000	0.000	0.000	0.000
60	A	203	TRP	0	-0.023	-0.028	23.117	0.005	0.005	0.000	0.000	0.000	0.000
61	A	204	MET	0	-0.025	0.005	20.712	-0.015	-0.015	0.000	0.000	0.000	0.000
62	A	205	GLY	0	0.041	0.005	20.655	0.007	0.007	0.000	0.000	0.000	0.000
63	A	206	LEU	0	-0.046	-0.017	21.955	0.006	0.006	0.000	0.000	0.000	0.000
64	A	207	SER	0	-0.001	0.001	24.887	0.007	0.007	0.000	0.000	0.000	0.000
65	A	208	ARG	1	0.894	0.947	28.319	0.069	0.069	0.000	0.000	0.000	0.000
66	A	209	ARG	1	1.001	1.000	31.622	0.079	0.079	0.000	0.000	0.000	0.000
67	A	210	ASN	0	0.028	0.016	34.619	0.003	0.003	0.000	0.000	0.000	0.000
68	A	211	PRO	0	0.011	-0.007	36.260	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	212	SER	0	-0.081	-0.028	37.859	0.003	0.003	0.000	0.000	0.000	0.000
70	A	213	TYR	0	-0.004	0.019	33.777	0.000	0.000	0.000	0.000	0.000	0.000
71	A	214	PRO	0	0.027	0.002	31.091	0.002	0.002	0.000	0.000	0.000	0.000
72	A	215	TRP	0	-0.011	-0.013	28.280	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	216	LEU	0	-0.031	-0.008	26.531	0.005	0.005	0.000	0.000	0.000	0.000
74	A	217	TRP	0	0.035	0.002	21.137	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	218	GLU	-1	-0.749	-0.885	20.161	-0.254	-0.254	0.000	0.000	0.000	0.000
76	A	219	ASP	-1	-0.890	-0.876	19.681	-0.194	-0.194	0.000	0.000	0.000	0.000
77	A	220	GLY	0	0.035	0.018	22.233	0.008	0.008	0.000	0.000	0.000	0.000
78	A	221	SER	0	-0.088	-0.097	21.754	0.013	0.013	0.000	0.000	0.000	0.000
79	A	222	PRO	0	0.007	-0.008	24.265	-0.002	-0.002	0.000	0.000	0.000	0.000
80	A	223	LEU	0	-0.023	0.000	24.307	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	224	MET	0	-0.011	-0.009	21.676	0.005	0.005	0.000	0.000	0.000	0.000
82	A	225	PRO	0	0.043	0.018	25.334	0.002	0.002	0.000	0.000	0.000	0.000
83	A	226	HIS	0	-0.069	-0.034	26.710	0.002	0.002	0.000	0.000	0.000	0.000
84	A	227	LEU	0	-0.006	0.019	21.721	0.008	0.008	0.000	0.000	0.000	0.000
85	A	228	PHE	0	0.078	0.018	22.544	0.006	0.006	0.000	0.000	0.000	0.000
86	A	229	ARG	1	0.893	0.954	27.265	0.017	0.017	0.000	0.000	0.000	0.000
87	A	230	VAL	0	0.028	0.023	28.607	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	231	ARG	1	0.942	0.954	30.775	0.032	0.032	0.000	0.000	0.000	0.000
89	A	232	GLY	0	0.027	0.009	33.029	-0.005	-0.005	0.000	0.000	0.000	0.000
90	A	233	ALA	0	0.010	0.020	34.996	0.004	0.004	0.000	0.000	0.000	0.000
91	A	234	VAL	0	-0.029	-0.026	33.999	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	235	SER	0	0.014	0.000	36.379	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	236	GLN	0	0.025	0.023	38.827	0.002	0.002	0.000	0.000	0.000	0.000
94	A	237	THR	0	0.022	-0.003	38.930	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	238	TYR	0	0.010	0.000	36.303	0.003	0.003	0.000	0.000	0.000	0.000
96	A	239	PRO	0	-0.003	-0.011	38.141	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	240	SER	0	0.012	0.006	34.166	0.001	0.001	0.000	0.000	0.000	0.000
98	A	241	GLY	0	0.028	0.037	33.406	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	242	THR	0	-0.042	-0.032	32.569	0.004	0.004	0.000	0.000	0.000	0.000
100	A	243	CYS	0	0.065	0.046	28.012	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	244	ALA	0	0.027	0.005	26.059	0.010	0.010	0.000	0.000	0.000	0.000
102	A	245	TYR	0	-0.012	-0.002	24.772	-0.013	-0.013	0.000	0.000	0.000	0.000
103	A	246	ILE	0	-0.004	-0.002	21.352	0.014	0.014	0.000	0.000	0.000	0.000
104	A	247	GLN	0	0.011	-0.031	24.702	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	248	ARG	1	0.957	0.968	26.416	0.028	0.028	0.000	0.000	0.000	0.000
106	A	249	GLY	0	0.022	0.025	24.027	0.007	0.007	0.000	0.000	0.000	0.000
107	A	250	ALA	0	0.015	0.032	25.104	0.001	0.001	0.000	0.000	0.000	0.000
108	A	251	VAL	0	0.030	0.013	24.799	-0.007	-0.007	0.000	0.000	0.000	0.000
109	A	252	TYR	0	-0.043	-0.006	27.446	0.011	0.011	0.000	0.000	0.000	0.000
110	A	253	ALA	0	0.014	0.017	29.098	-0.009	-0.009	0.000	0.000	0.000	0.000
111	A	254	GLU	-1	-0.898	-0.958	30.576	-0.075	-0.075	0.000	0.000	0.000	0.000
112	A	255	ASN	0	0.016	-0.006	32.351	-0.012	-0.012	0.000	0.000	0.000	0.000
113	A	257	ILE	0	-0.069	-0.030	31.145	-0.008	-0.008	0.000	0.000	0.000	0.000
114	A	258	LEU	0	-0.015	-0.006	32.342	0.001	0.001	0.000	0.000	0.000	0.000
115	A	259	ALA	0	-0.005	-0.006	29.763	-0.009	-0.009	0.000	0.000	0.000	0.000
116	A	260	ALA	0	0.035	0.011	26.299	0.010	0.010	0.000	0.000	0.000	0.000
117	A	261	PHE	0	-0.017	0.007	22.169	-0.009	-0.009	0.000	0.000	0.000	0.000
118	A	262	SER	0	-0.028	-0.001	20.778	-0.002	-0.002	0.000	0.000	0.000	0.000
119	A	263	ILE	0	0.037	0.024	15.026	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	265	GLN	0	0.012	-0.012	11.552	0.035	0.035	0.000	0.000	0.000	0.000
121	A	266	LYS	1	0.968	0.994	8.704	1.242	1.242	0.000	0.000	0.000	0.000
122	A	267	LYS	1	0.929	0.965	7.652	0.440	0.440	0.000	0.000	0.000	0.000
123	A	268	ALA	0	0.011	0.011	2.072	-1.366	-0.747	1.857	-0.726	-1.750	-0.005

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