FMO DATABASE

FMODB ID: QYR3Y

Calculation Name: 3L0X-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3L0X

Chain ID: B

ChEMBL ID:

UniProt ID: P15873

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	91
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-554143.941021
FMO2-HF: Nuclear repulsion	519339.998424
FMO2-HF: Total energy	-34803.942597
FMO2-MP2: Total energy	-34906.283937

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(B:165:GLU)

Summations of interaction energy for fragment #1(B:165:GLU)

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.
2.096	5.685	0.212	-1.662	-2.142	0.004

Interaction energy analysis for fragmet #1(B:165:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.903 / q_NPA : -0.938

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	B	167	ILE	0	-0.001	0.015	3.629	-7.807	-5.522	-0.009	-1.254	-1.023	0.004
4	B	168	LYS	1	0.923	0.955	7.177	-27.663	-27.663	0.000	0.000	0.000	0.000
5	B	169	PHE	0	0.008	0.011	9.234	-1.753	-1.753	0.000	0.000	0.000	0.000
6	B	170	VAL	0	-0.005	-0.022	12.519	0.232	0.232	0.000	0.000	0.000	0.000
7	B	171	ALA	0	-0.030	0.003	15.207	-0.647	-0.647	0.000	0.000	0.000	0.000
8	B	172	ASP	-1	-0.892	-0.965	18.880	14.985	14.985	0.000	0.000	0.000	0.000
9	B	173	GLY	0	-0.034	-0.018	20.684	-0.340	-0.340	0.000	0.000	0.000	0.000
10	B	174	ASP	-1	-0.923	-0.961	24.378	10.533	10.533	0.000	0.000	0.000	0.000
11	B	175	ILE	0	-0.049	-0.030	26.950	-0.078	-0.078	0.000	0.000	0.000	0.000
12	B	176	GLY	0	0.012	0.006	24.775	-0.111	-0.111	0.000	0.000	0.000	0.000
13	B	177	SER	0	-0.009	0.014	19.421	0.171	0.171	0.000	0.000	0.000	0.000
14	B	178	GLY	0	-0.005	0.004	18.748	-0.226	-0.226	0.000	0.000	0.000	0.000
15	B	179	SER	0	-0.014	-0.026	12.686	0.898	0.898	0.000	0.000	0.000	0.000
16	B	180	VAL	0	-0.010	0.005	12.688	-0.026	-0.026	0.000	0.000	0.000	0.000
17	B	181	ILE	0	-0.018	-0.012	6.625	0.819	0.819	0.000	0.000	0.000	0.000
18	B	182	ILE	0	0.007	0.012	8.528	-1.346	-1.346	0.000	0.000	0.000	0.000
19	B	183	LYS	1	0.973	0.980	4.404	-45.516	-45.336	-0.001	-0.041	-0.139	0.000
20	B	184	PRO	0	0.027	0.017	3.083	-5.352	-4.893	0.024	-0.132	-0.352	0.000
21	B	185	PHE	0	-0.068	-0.035	6.290	2.629	2.629	0.000	0.000	0.000	0.000
22	B	186	VAL	0	0.006	-0.006	9.484	-1.493	-1.493	0.000	0.000	0.000	0.000
23	B	187	ASP	-1	-0.861	-0.944	12.672	17.435	17.435	0.000	0.000	0.000	0.000
24	B	188	MET	0	-0.029	-0.012	16.053	-0.351	-0.351	0.000	0.000	0.000	0.000
25	B	189	GLU	-1	-0.930	-0.959	19.507	13.718	13.718	0.000	0.000	0.000	0.000
26	B	190	HIS	0	-0.005	-0.011	20.411	-0.263	-0.263	0.000	0.000	0.000	0.000
27	B	191	PRO	0	0.061	0.034	17.468	0.751	0.751	0.000	0.000	0.000	0.000
28	B	192	GLU	-1	-0.899	-0.952	16.751	15.333	15.333	0.000	0.000	0.000	0.000
29	B	193	THR	0	-0.021	-0.003	16.623	-0.145	-0.145	0.000	0.000	0.000	0.000
30	B	194	SER	0	-0.055	-0.023	12.568	1.181	1.181	0.000	0.000	0.000	0.000
31	B	195	ILE	0	-0.034	0.005	8.022	-0.610	-0.610	0.000	0.000	0.000	0.000
32	B	196	LYS	1	0.832	0.892	8.484	-19.415	-19.415	0.000	0.000	0.000	0.000
33	B	197	LEU	0	0.013	-0.010	2.653	-0.374	0.065	0.192	-0.183	-0.447	0.000
34	B	198	GLU	-1	-0.831	-0.887	5.735	23.246	23.246	0.000	0.000	0.000	0.000
35	B	199	MET	0	-0.032	-0.016	4.529	1.436	1.662	0.006	-0.052	-0.181	0.000
36	B	200	ASP	-1	-0.886	-0.924	6.512	21.389	21.389	0.000	0.000	0.000	0.000
37	B	201	GLN	0	-0.065	-0.057	9.294	-1.295	-1.295	0.000	0.000	0.000	0.000
38	B	202	PRO	0	-0.006	0.008	6.968	1.543	1.543	0.000	0.000	0.000	0.000
39	B	203	VAL	0	-0.025	-0.015	8.107	-2.720	-2.720	0.000	0.000	0.000	0.000
40	B	204	ASP	-1	-0.919	-0.962	9.827	22.789	22.789	0.000	0.000	0.000	0.000
41	B	205	LEU	0	-0.012	-0.003	12.558	-1.650	-1.650	0.000	0.000	0.000	0.000
42	B	206	THR	0	0.031	0.026	15.592	0.209	0.209	0.000	0.000	0.000	0.000
43	B	207	PHE	0	0.039	0.009	15.927	-0.851	-0.851	0.000	0.000	0.000	0.000
44	B	208	GLY	0	-0.038	-0.020	20.794	-0.075	-0.075	0.000	0.000	0.000	0.000
45	B	209	ALA	0	0.076	0.026	23.234	0.006	0.006	0.000	0.000	0.000	0.000
46	B	210	LYS	1	0.931	0.958	24.161	-9.919	-9.919	0.000	0.000	0.000	0.000
47	B	211	TYR	0	0.064	0.022	24.742	-0.371	-0.371	0.000	0.000	0.000	0.000
48	B	212	LEU	0	0.057	0.040	19.317	-0.104	-0.104	0.000	0.000	0.000	0.000
49	B	213	LEU	0	-0.007	-0.006	22.754	0.086	0.086	0.000	0.000	0.000	0.000
50	B	214	ASP	-1	-0.898	-0.945	25.463	10.021	10.021	0.000	0.000	0.000	0.000
51	B	215	ILE	0	-0.039	-0.006	20.965	-0.147	-0.147	0.000	0.000	0.000	0.000
52	B	216	ILE	0	0.018	0.011	20.762	-0.062	-0.062	0.000	0.000	0.000	0.000
53	B	217	LYS	1	0.889	0.950	23.265	-10.428	-10.428	0.000	0.000	0.000	0.000
54	B	218	GLY	0	-0.010	0.002	24.894	-0.313	-0.313	0.000	0.000	0.000	0.000
55	B	219	SER	0	0.009	-0.023	22.677	0.294	0.294	0.000	0.000	0.000	0.000
56	B	220	SER	0	-0.105	-0.037	23.926	-0.098	-0.098	0.000	0.000	0.000	0.000
57	B	221	LEU	0	-0.058	-0.033	25.899	-0.404	-0.404	0.000	0.000	0.000	0.000
58	B	222	SER	0	-0.067	-0.032	21.200	-0.254	-0.254	0.000	0.000	0.000	0.000
59	B	223	ASP	-1	-0.888	-0.931	21.354	12.418	12.418	0.000	0.000	0.000	0.000
60	B	224	ARG	1	0.807	0.910	13.178	-16.950	-16.950	0.000	0.000	0.000	0.000
61	B	225	VAL	0	-0.006	-0.001	15.683	-0.629	-0.629	0.000	0.000	0.000	0.000
62	B	226	GLY	0	-0.004	0.000	14.779	1.071	1.071	0.000	0.000	0.000	0.000
63	B	227	ILE	0	-0.034	-0.031	12.805	-0.762	-0.762	0.000	0.000	0.000	0.000
64	B	228	ARG	1	0.943	0.981	12.687	-14.401	-14.401	0.000	0.000	0.000	0.000
65	B	229	LEU	0	0.004	-0.006	10.785	-0.916	-0.916	0.000	0.000	0.000	0.000
66	B	230	SER	0	0.029	0.000	13.551	0.539	0.539	0.000	0.000	0.000	0.000
67	B	231	SER	0	0.005	-0.021	15.667	0.060	0.060	0.000	0.000	0.000	0.000
68	B	232	GLU	-1	-0.899	-0.915	17.234	13.639	13.639	0.000	0.000	0.000	0.000
69	B	233	ALA	0	-0.058	-0.027	19.532	-0.822	-0.822	0.000	0.000	0.000	0.000
70	B	234	PRO	0	-0.037	-0.030	20.014	0.459	0.459	0.000	0.000	0.000	0.000
71	B	235	ALA	0	0.011	0.033	17.083	0.172	0.172	0.000	0.000	0.000	0.000
72	B	236	LEU	0	-0.048	-0.018	17.363	-0.760	-0.760	0.000	0.000	0.000	0.000
73	B	237	PHE	0	0.006	-0.003	16.703	0.967	0.967	0.000	0.000	0.000	0.000
74	B	238	GLN	0	-0.029	-0.028	18.487	-0.720	-0.720	0.000	0.000	0.000	0.000
75	B	239	PHE	0	0.073	0.042	19.451	0.601	0.601	0.000	0.000	0.000	0.000
76	B	240	ASP	-1	-0.847	-0.914	20.418	12.508	12.508	0.000	0.000	0.000	0.000
77	B	241	LEU	0	0.021	0.008	23.501	-0.150	-0.150	0.000	0.000	0.000	0.000
78	B	242	LYS	1	0.964	0.969	26.679	-8.968	-8.968	0.000	0.000	0.000	0.000
79	B	243	SER	0	-0.069	-0.045	28.207	-0.326	-0.326	0.000	0.000	0.000	0.000
80	B	244	GLY	0	0.037	0.018	27.726	-0.374	-0.374	0.000	0.000	0.000	0.000
81	B	245	PHE	0	-0.011	0.009	24.236	0.342	0.342	0.000	0.000	0.000	0.000
82	B	246	LEU	0	0.004	0.017	24.988	-0.431	-0.431	0.000	0.000	0.000	0.000
83	B	247	GLN	0	-0.049	-0.034	22.163	0.142	0.142	0.000	0.000	0.000	0.000
84	B	248	PHE	0	0.021	0.001	22.419	-0.464	-0.464	0.000	0.000	0.000	0.000
85	B	249	PHE	0	0.022	0.012	21.680	0.604	0.604	0.000	0.000	0.000	0.000
86	B	250	LEU	0	-0.041	-0.020	21.253	-0.543	-0.543	0.000	0.000	0.000	0.000
87	B	251	ALA	0	0.000	-0.008	21.367	0.541	0.541	0.000	0.000	0.000	0.000
88	B	252	PRO	0	0.031	0.024	19.156	-0.205	-0.205	0.000	0.000	0.000	0.000
89	B	253	LYS	1	0.906	0.940	21.295	-12.808	-12.808	0.000	0.000	0.000	0.000
90	B	254	PHE	0	0.015	0.005	21.733	0.343	0.343	0.000	0.000	0.000	0.000
91	B	255	ASN	0	0.005	0.017	22.886	0.422	0.422	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:165:GLU)