FMO DATABASE

FMODB ID: M347Z

Calculation Name: 3LR3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LR3

Chain ID: A

ChEMBL ID:

UniProt ID: Q63T74

Base Structure: X-ray

Registration Date: 2023-06-19

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	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	114
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-948036.683858
FMO2-HF: Nuclear repulsion	902846.669405
FMO2-HF: Total energy	-45190.014453
FMO2-MP2: Total energy	-45325.412315

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:37:GLU)

Summations of interaction energy for fragment #1(A:37: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.
-25.277	-20.449	10.013	-6.637	-8.205	0.06

Interaction energy analysis for fragmet #1(A:37:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.859 / q_NPA : -0.926

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	39	ARG	1	0.934	0.961	3.564	-35.573	-33.861	0.007	-0.696	-1.024	0.004
4	A	40	ALA	0	0.004	0.003	2.928	-6.883	-6.040	0.127	-0.294	-0.676	0.001
5	A	41	GLN	0	0.049	0.021	1.874	-38.434	-37.900	8.289	-4.321	-4.502	0.057
6	A	42	ARG	1	0.855	0.935	4.896	-35.214	-35.086	-0.001	-0.012	-0.115	0.000
7	A	43	VAL	0	0.005	-0.005	8.104	-3.737	-3.737	0.000	0.000	0.000	0.000
8	A	44	ALA	0	0.036	0.032	7.774	-3.199	-3.199	0.000	0.000	0.000	0.000
9	A	45	LEU	0	-0.001	-0.007	7.457	-3.720	-3.720	0.000	0.000	0.000	0.000
10	A	46	GLN	0	-0.034	-0.020	10.456	-1.196	-1.196	0.000	0.000	0.000	0.000
11	A	47	LEU	0	0.031	0.017	12.485	-1.779	-1.779	0.000	0.000	0.000	0.000
12	A	48	VAL	0	0.018	0.007	11.788	-1.590	-1.590	0.000	0.000	0.000	0.000
13	A	49	ALA	0	-0.053	-0.019	14.516	-1.565	-1.565	0.000	0.000	0.000	0.000
14	A	50	ILE	0	0.065	0.031	16.460	-1.141	-1.141	0.000	0.000	0.000	0.000
15	A	51	VAL	0	0.026	0.035	17.833	-1.085	-1.085	0.000	0.000	0.000	0.000
16	A	52	LYS	1	0.925	0.950	16.298	-19.340	-19.340	0.000	0.000	0.000	0.000
17	A	53	LEU	0	-0.001	0.017	19.997	-0.845	-0.845	0.000	0.000	0.000	0.000
18	A	54	THR	0	0.042	0.019	22.246	-0.849	-0.849	0.000	0.000	0.000	0.000
19	A	55	ARG	1	0.934	0.975	20.082	-15.352	-15.352	0.000	0.000	0.000	0.000
20	A	56	THR	0	-0.072	-0.054	23.241	-0.549	-0.549	0.000	0.000	0.000	0.000
21	A	57	ALA	0	0.038	0.019	25.800	-0.483	-0.483	0.000	0.000	0.000	0.000
22	A	58	LEU	0	0.006	-0.003	27.909	-0.478	-0.478	0.000	0.000	0.000	0.000
23	A	59	LEU	0	-0.030	-0.001	26.899	-0.369	-0.369	0.000	0.000	0.000	0.000
24	A	60	TYR	0	-0.045	-0.029	27.514	-0.378	-0.378	0.000	0.000	0.000	0.000
25	A	61	SER	0	-0.048	0.000	31.900	-0.388	-0.388	0.000	0.000	0.000	0.000
26	A	62	ASP	-1	-0.814	-0.922	33.951	7.922	7.922	0.000	0.000	0.000	0.000
27	A	63	PRO	0	-0.035	-0.034	37.675	0.084	0.084	0.000	0.000	0.000	0.000
28	A	64	ASP	-1	-0.941	-0.959	38.795	7.439	7.439	0.000	0.000	0.000	0.000
29	A	65	LEU	0	-0.009	0.000	37.807	-0.017	-0.017	0.000	0.000	0.000	0.000
30	A	66	ARG	1	0.884	0.948	33.993	-9.030	-9.030	0.000	0.000	0.000	0.000
31	A	67	ARG	1	0.939	0.947	34.902	-8.496	-8.496	0.000	0.000	0.000	0.000
32	A	68	ALA	0	0.033	0.019	36.432	0.092	0.092	0.000	0.000	0.000	0.000
33	A	69	LEU	0	0.030	0.014	30.386	0.097	0.097	0.000	0.000	0.000	0.000
34	A	70	LEU	0	-0.043	-0.028	30.729	0.220	0.220	0.000	0.000	0.000	0.000
35	A	71	GLN	0	-0.017	-0.005	32.140	0.116	0.116	0.000	0.000	0.000	0.000
36	A	72	ASP	-1	-0.898	-0.923	32.601	9.809	9.809	0.000	0.000	0.000	0.000
37	A	73	LEU	0	0.031	0.004	26.848	0.239	0.239	0.000	0.000	0.000	0.000
38	A	74	GLU	-1	-0.914	-0.953	28.619	10.398	10.398	0.000	0.000	0.000	0.000
39	A	75	SER	0	-0.063	-0.038	29.820	0.078	0.078	0.000	0.000	0.000	0.000
40	A	76	ASN	0	-0.096	-0.055	31.159	-0.125	-0.125	0.000	0.000	0.000	0.000
41	A	77	GLU	-1	-0.941	-0.968	25.974	11.259	11.259	0.000	0.000	0.000	0.000
42	A	78	GLY	0	-0.015	0.014	25.394	0.596	0.596	0.000	0.000	0.000	0.000
43	A	79	VAL	0	-0.088	-0.054	23.329	0.604	0.604	0.000	0.000	0.000	0.000
44	A	80	ARG	1	0.906	0.969	25.656	-10.626	-10.626	0.000	0.000	0.000	0.000
45	A	81	VAL	0	-0.003	-0.006	26.258	0.502	0.502	0.000	0.000	0.000	0.000
46	A	82	TYR	0	-0.033	-0.022	27.774	-0.682	-0.682	0.000	0.000	0.000	0.000
47	A	83	PRO	0	0.019	0.018	29.004	0.408	0.408	0.000	0.000	0.000	0.000
48	A	84	ARG	1	0.945	0.974	24.619	-12.596	-12.596	0.000	0.000	0.000	0.000
49	A	85	GLU	-1	-0.892	-0.951	29.579	9.301	9.301	0.000	0.000	0.000	0.000
50	A	86	LYS	1	0.840	0.898	30.479	-10.199	-10.199	0.000	0.000	0.000	0.000
51	A	87	THR	0	-0.020	-0.020	31.018	0.078	0.078	0.000	0.000	0.000	0.000
52	A	88	ASP	-1	-0.802	-0.865	28.881	10.464	10.464	0.000	0.000	0.000	0.000
53	A	89	LYS	1	0.918	0.955	28.579	-9.555	-9.555	0.000	0.000	0.000	0.000
54	A	90	PHE	0	0.059	0.021	21.652	0.156	0.156	0.000	0.000	0.000	0.000
55	A	91	LYS	1	0.936	0.988	22.414	-12.451	-12.451	0.000	0.000	0.000	0.000
56	A	92	LEU	0	0.020	0.008	17.892	0.333	0.333	0.000	0.000	0.000	0.000
57	A	93	GLN	0	0.025	0.023	13.824	-1.619	-1.619	0.000	0.000	0.000	0.000
58	A	94	PRO	0	0.029	0.019	15.830	0.112	0.112	0.000	0.000	0.000	0.000
59	A	95	ASP	-1	-0.958	-0.976	11.936	23.007	23.007	0.000	0.000	0.000	0.000
60	A	96	GLU	-1	-0.875	-0.945	12.356	16.283	16.283	0.000	0.000	0.000	0.000
61	A	97	SER	0	-0.047	-0.020	9.469	2.146	2.146	0.000	0.000	0.000	0.000
62	A	98	VAL	0	0.025	-0.003	4.320	1.238	1.354	-0.001	-0.019	-0.096	0.000
63	A	99	ASN	0	-0.017	-0.010	7.029	3.236	3.236	0.000	0.000	0.000	0.000
64	A	100	ARG	1	0.881	0.927	9.798	-19.933	-19.933	0.000	0.000	0.000	0.000
65	A	101	LEU	0	-0.002	0.006	2.197	-3.076	-1.760	1.593	-1.291	-1.618	-0.002
66	A	102	ILE	0	0.007	0.004	6.557	2.294	2.294	0.000	0.000	0.000	0.000
67	A	103	GLU	-1	-0.795	-0.905	7.880	21.409	21.409	0.000	0.000	0.000	0.000
68	A	104	HIS	0	-0.028	0.000	6.643	-4.921	-4.921	0.000	0.000	0.000	0.000
69	A	105	ASP	-1	-0.821	-0.930	4.864	61.339	61.518	-0.001	-0.004	-0.174	0.000
70	A	106	ILE	0	-0.028	-0.019	7.913	-2.751	-2.751	0.000	0.000	0.000	0.000
71	A	107	ARG	1	0.882	0.933	11.351	-22.458	-22.458	0.000	0.000	0.000	0.000
72	A	108	SER	0	-0.033	0.001	9.204	-1.193	-1.193	0.000	0.000	0.000	0.000
73	A	109	ARG	1	0.861	0.930	10.015	-28.472	-28.472	0.000	0.000	0.000	0.000
74	A	110	LEU	0	-0.063	-0.046	12.810	-1.722	-1.722	0.000	0.000	0.000	0.000
75	A	111	GLY	0	0.014	0.021	15.208	-1.472	-1.472	0.000	0.000	0.000	0.000
76	A	112	ASP	-1	-0.908	-0.963	14.918	21.688	21.688	0.000	0.000	0.000	0.000
77	A	113	ASP	-1	-0.915	-0.937	16.973	14.788	14.788	0.000	0.000	0.000	0.000
78	A	114	THR	0	-0.124	-0.063	16.768	-0.816	-0.816	0.000	0.000	0.000	0.000
79	A	115	VAL	0	-0.014	0.000	18.114	0.774	0.774	0.000	0.000	0.000	0.000
80	A	116	ILE	0	-0.004	-0.007	13.682	0.201	0.201	0.000	0.000	0.000	0.000
81	A	117	ALA	0	-0.069	-0.032	17.570	-0.027	-0.027	0.000	0.000	0.000	0.000
82	A	118	GLN	0	-0.025	-0.035	19.231	-0.125	-0.125	0.000	0.000	0.000	0.000
83	A	119	SER	0	-0.037	-0.016	20.572	-0.672	-0.672	0.000	0.000	0.000	0.000
84	A	120	VAL	0	0.060	0.024	24.119	0.311	0.311	0.000	0.000	0.000	0.000
85	A	121	ASN	0	-0.053	-0.030	26.482	-0.282	-0.282	0.000	0.000	0.000	0.000
86	A	122	ASP	-1	-0.939	-0.966	28.553	10.022	10.022	0.000	0.000	0.000	0.000
87	A	123	ILE	0	-0.029	-0.005	27.792	-0.140	-0.140	0.000	0.000	0.000	0.000
88	A	124	PRO	0	0.004	-0.013	24.913	0.459	0.459	0.000	0.000	0.000	0.000
89	A	125	GLY	0	0.006	0.008	22.860	-0.335	-0.335	0.000	0.000	0.000	0.000
90	A	126	VAL	0	-0.026	-0.004	16.689	0.548	0.548	0.000	0.000	0.000	0.000
91	A	127	TRP	0	-0.014	0.001	19.578	-0.382	-0.382	0.000	0.000	0.000	0.000
92	A	128	ILE	0	-0.002	-0.014	16.094	0.987	0.987	0.000	0.000	0.000	0.000
93	A	129	SER	0	-0.001	0.023	19.643	-0.635	-0.635	0.000	0.000	0.000	0.000
94	A	130	PHE	0	-0.052	-0.042	20.505	0.922	0.922	0.000	0.000	0.000	0.000
95	A	131	LYS	1	0.927	0.972	22.641	-12.523	-12.523	0.000	0.000	0.000	0.000
96	A	132	ILE	0	-0.037	-0.029	25.099	0.480	0.480	0.000	0.000	0.000	0.000
97	A	133	ASP	-1	-0.886	-0.928	27.890	10.145	10.145	0.000	0.000	0.000	0.000
98	A	134	ASP	-1	-0.956	-0.991	28.741	10.664	10.664	0.000	0.000	0.000	0.000
99	A	135	ASP	-1	-0.943	-0.949	30.687	9.696	9.696	0.000	0.000	0.000	0.000
100	A	136	ASP	-1	-0.899	-0.951	27.083	12.299	12.299	0.000	0.000	0.000	0.000
101	A	137	TYR	0	0.001	-0.008	26.213	-0.530	-0.530	0.000	0.000	0.000	0.000
102	A	138	TRP	0	-0.054	-0.054	22.454	0.960	0.960	0.000	0.000	0.000	0.000
103	A	139	VAL	0	0.007	0.007	21.571	-0.459	-0.459	0.000	0.000	0.000	0.000
104	A	140	ALA	0	-0.032	-0.022	22.416	0.498	0.498	0.000	0.000	0.000	0.000
105	A	141	LEU	0	0.002	-0.003	18.578	-0.216	-0.216	0.000	0.000	0.000	0.000
106	A	142	ASP	-1	-0.777	-0.882	22.243	12.725	12.725	0.000	0.000	0.000	0.000
107	A	143	ARG	1	0.904	0.946	13.909	-17.821	-17.821	0.000	0.000	0.000	0.000
108	A	144	ASP	-1	-0.854	-0.922	19.647	13.602	13.602	0.000	0.000	0.000	0.000
109	A	145	GLN	0	-0.008	-0.020	21.330	0.202	0.202	0.000	0.000	0.000	0.000
110	A	146	LEU	0	-0.019	-0.011	15.656	0.489	0.489	0.000	0.000	0.000	0.000
111	A	147	ASP	-1	-0.920	-0.966	16.612	18.390	18.390	0.000	0.000	0.000	0.000
112	A	148	THR	0	-0.111	-0.052	17.309	0.273	0.273	0.000	0.000	0.000	0.000
113	A	149	VAL	0	-0.008	0.010	17.855	0.137	0.137	0.000	0.000	0.000	0.000
114	A	150	THR	0	-0.055	-0.030	12.939	2.708	2.708	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:37:GLU)