FMO DATABASE

FMODB ID: 2291R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-951410.555534
FMO2-HF: Nuclear repulsion	906219.758833
FMO2-HF: Total energy	-45190.796701
FMO2-MP2: Total energy	-45326.167342

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.
-28.055	-23.999	14.074	-8.445	-9.683	0.08

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 : -0.812 / q_NPA : -0.909

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	0.936	0.964	3.591	-33.940	-32.350	0.004	-0.634	-0.960	0.003
4	A	40	ALA	0	0.006	0.008	3.081	-5.598	-4.787	0.065	-0.260	-0.615	0.000
5	A	41	GLN	0	0.032	0.003	1.809	-41.309	-42.279	12.046	-5.556	-5.519	0.073
6	A	42	ARG	1	0.833	0.911	4.612	-35.141	-34.969	-0.001	-0.032	-0.139	0.000
7	A	43	VAL	0	0.008	-0.003	7.865	-3.602	-3.602	0.000	0.000	0.000	0.000
8	A	44	ALA	0	0.027	0.024	7.400	-3.235	-3.235	0.000	0.000	0.000	0.000
9	A	45	LEU	0	-0.005	-0.012	7.275	-3.864	-3.864	0.000	0.000	0.000	0.000
10	A	46	GLN	0	-0.023	-0.014	10.134	-1.298	-1.298	0.000	0.000	0.000	0.000
11	A	47	LEU	0	0.036	0.021	12.464	-1.821	-1.821	0.000	0.000	0.000	0.000
12	A	48	VAL	0	-0.003	0.001	11.255	-1.631	-1.631	0.000	0.000	0.000	0.000
13	A	49	ALA	0	-0.041	-0.017	14.117	-1.470	-1.470	0.000	0.000	0.000	0.000
14	A	50	ILE	0	0.068	0.038	16.118	-1.148	-1.148	0.000	0.000	0.000	0.000
15	A	51	VAL	0	0.024	0.027	17.452	-1.103	-1.103	0.000	0.000	0.000	0.000
16	A	52	LYS	1	0.933	0.965	15.886	-19.732	-19.732	0.000	0.000	0.000	0.000
17	A	53	LEU	0	-0.011	0.013	19.574	-0.858	-0.858	0.000	0.000	0.000	0.000
18	A	54	THR	0	0.023	0.003	21.893	-0.863	-0.863	0.000	0.000	0.000	0.000
19	A	55	ARG	1	0.940	0.979	19.590	-15.642	-15.642	0.000	0.000	0.000	0.000
20	A	56	THR	0	-0.066	-0.050	22.841	-0.533	-0.533	0.000	0.000	0.000	0.000
21	A	57	ALA	0	0.015	0.004	25.424	-0.513	-0.513	0.000	0.000	0.000	0.000
22	A	58	LEU	0	0.004	-0.001	27.436	-0.457	-0.457	0.000	0.000	0.000	0.000
23	A	59	LEU	0	-0.016	0.003	27.228	-0.403	-0.403	0.000	0.000	0.000	0.000
24	A	60	TYR	0	-0.030	-0.030	27.082	-0.438	-0.438	0.000	0.000	0.000	0.000
25	A	61	SER	0	-0.038	0.000	31.543	-0.385	-0.385	0.000	0.000	0.000	0.000
26	A	62	ASP	-1	-0.828	-0.916	33.490	7.978	7.978	0.000	0.000	0.000	0.000
27	A	63	PRO	0	-0.023	-0.034	37.152	0.083	0.083	0.000	0.000	0.000	0.000
28	A	64	ASP	-1	-0.949	-0.951	38.432	7.505	7.505	0.000	0.000	0.000	0.000
29	A	65	LEU	0	0.013	-0.006	37.551	0.070	0.070	0.000	0.000	0.000	0.000
30	A	66	ARG	1	0.848	0.935	33.609	-9.326	-9.326	0.000	0.000	0.000	0.000
31	A	67	ARG	1	0.938	0.951	34.660	-8.425	-8.425	0.000	0.000	0.000	0.000
32	A	68	ALA	0	0.039	0.028	36.323	0.078	0.078	0.000	0.000	0.000	0.000
33	A	69	LEU	0	0.041	0.027	30.298	0.134	0.134	0.000	0.000	0.000	0.000
34	A	70	LEU	0	-0.040	-0.024	29.974	0.276	0.276	0.000	0.000	0.000	0.000
35	A	71	GLN	0	-0.081	-0.045	32.281	-0.182	-0.182	0.000	0.000	0.000	0.000
36	A	72	ASP	-1	-0.900	-0.921	32.507	9.582	9.582	0.000	0.000	0.000	0.000
37	A	73	LEU	0	0.021	0.006	26.561	0.189	0.189	0.000	0.000	0.000	0.000
38	A	74	GLU	-1	-0.852	-0.893	28.327	10.441	10.441	0.000	0.000	0.000	0.000
39	A	75	SER	0	-0.065	-0.051	29.814	0.036	0.036	0.000	0.000	0.000	0.000
40	A	76	ASN	0	-0.086	-0.042	30.626	-0.159	-0.159	0.000	0.000	0.000	0.000
41	A	77	GLU	-1	-0.905	-0.966	25.110	11.530	11.530	0.000	0.000	0.000	0.000
42	A	78	GLY	0	-0.025	0.007	25.066	0.541	0.541	0.000	0.000	0.000	0.000
43	A	79	VAL	0	-0.087	-0.051	23.076	0.506	0.506	0.000	0.000	0.000	0.000
44	A	80	ARG	1	0.863	0.919	25.583	-10.549	-10.549	0.000	0.000	0.000	0.000
45	A	81	VAL	0	-0.011	-0.017	26.066	0.541	0.541	0.000	0.000	0.000	0.000
46	A	82	TYR	0	-0.027	-0.006	27.720	-0.694	-0.694	0.000	0.000	0.000	0.000
47	A	83	PRO	0	0.041	0.021	28.604	0.385	0.385	0.000	0.000	0.000	0.000
48	A	84	ARG	1	0.920	0.955	23.777	-12.842	-12.842	0.000	0.000	0.000	0.000
49	A	85	GLU	-1	-0.873	-0.935	29.275	9.322	9.322	0.000	0.000	0.000	0.000
50	A	86	LYS	1	0.846	0.900	30.478	-10.145	-10.145	0.000	0.000	0.000	0.000
51	A	87	THR	0	-0.020	-0.012	31.216	0.037	0.037	0.000	0.000	0.000	0.000
52	A	88	ASP	-1	-0.811	-0.875	28.446	10.596	10.596	0.000	0.000	0.000	0.000
53	A	89	LYS	1	0.919	0.958	28.343	-9.449	-9.449	0.000	0.000	0.000	0.000
54	A	90	PHE	0	0.027	0.012	21.809	0.153	0.153	0.000	0.000	0.000	0.000
55	A	91	LYS	1	0.914	0.970	21.883	-12.824	-12.824	0.000	0.000	0.000	0.000
56	A	92	LEU	0	0.054	0.029	17.694	0.309	0.309	0.000	0.000	0.000	0.000
57	A	93	GLN	0	0.009	0.000	12.819	-1.056	-1.056	0.000	0.000	0.000	0.000
58	A	94	PRO	0	0.020	0.017	15.107	0.037	0.037	0.000	0.000	0.000	0.000
59	A	95	ASP	-1	-0.809	-0.904	12.959	21.841	21.841	0.000	0.000	0.000	0.000
60	A	96	GLU	-1	-0.917	-0.962	12.006	16.898	16.898	0.000	0.000	0.000	0.000
61	A	97	SER	0	-0.027	-0.019	8.564	2.046	2.046	0.000	0.000	0.000	0.000
62	A	98	VAL	0	0.020	0.004	3.612	1.209	1.371	0.002	-0.032	-0.131	0.000
63	A	99	ASN	0	-0.040	-0.012	6.564	3.471	3.471	0.000	0.000	0.000	0.000
64	A	100	ARG	1	0.787	0.863	9.723	-19.898	-19.898	0.000	0.000	0.000	0.000
65	A	101	LEU	0	-0.032	0.006	2.196	-5.364	-3.240	1.959	-1.926	-2.158	0.004
66	A	102	ILE	0	0.032	0.016	6.611	1.664	1.664	0.000	0.000	0.000	0.000
67	A	103	GLU	-1	-0.805	-0.901	8.063	20.410	20.410	0.000	0.000	0.000	0.000
68	A	104	HIS	0	-0.051	-0.027	5.993	-5.840	-5.840	0.000	0.000	0.000	0.000
69	A	105	ASP	-1	-0.788	-0.897	5.010	61.624	61.791	-0.001	-0.005	-0.161	0.000
70	A	106	ILE	0	0.003	-0.005	7.672	-2.675	-2.675	0.000	0.000	0.000	0.000
71	A	107	ARG	1	0.878	0.951	11.170	-22.604	-22.604	0.000	0.000	0.000	0.000
72	A	108	SER	0	-0.007	-0.003	8.917	-1.551	-1.551	0.000	0.000	0.000	0.000
73	A	109	ARG	1	0.787	0.878	9.417	-28.674	-28.674	0.000	0.000	0.000	0.000
74	A	110	LEU	0	-0.073	-0.031	12.676	-1.633	-1.633	0.000	0.000	0.000	0.000
75	A	111	GLY	0	0.037	0.033	15.271	-1.432	-1.432	0.000	0.000	0.000	0.000
76	A	112	ASP	-1	-0.886	-0.950	14.438	22.167	22.167	0.000	0.000	0.000	0.000
77	A	113	ASP	-1	-0.950	-0.965	16.662	15.117	15.117	0.000	0.000	0.000	0.000
78	A	114	THR	0	-0.095	-0.051	16.383	-0.782	-0.782	0.000	0.000	0.000	0.000
79	A	115	VAL	0	0.003	0.007	17.612	0.925	0.925	0.000	0.000	0.000	0.000
80	A	116	ILE	0	-0.008	-0.008	13.881	0.105	0.105	0.000	0.000	0.000	0.000
81	A	117	ALA	0	-0.055	-0.025	17.722	-0.022	-0.022	0.000	0.000	0.000	0.000
82	A	118	GLN	0	0.000	-0.011	18.638	-0.385	-0.385	0.000	0.000	0.000	0.000
83	A	119	SER	0	-0.015	-0.008	20.038	-0.333	-0.333	0.000	0.000	0.000	0.000
84	A	120	VAL	0	0.038	0.013	23.761	0.321	0.321	0.000	0.000	0.000	0.000
85	A	121	ASN	0	-0.061	-0.054	26.241	-0.318	-0.318	0.000	0.000	0.000	0.000
86	A	122	ASP	-1	-0.948	-0.972	27.660	10.383	10.383	0.000	0.000	0.000	0.000
87	A	123	ILE	0	-0.012	0.014	27.660	-0.082	-0.082	0.000	0.000	0.000	0.000
88	A	124	PRO	0	-0.001	-0.019	24.402	0.458	0.458	0.000	0.000	0.000	0.000
89	A	125	GLY	0	0.008	0.015	22.308	-0.308	-0.308	0.000	0.000	0.000	0.000
90	A	126	VAL	0	-0.033	-0.013	16.117	0.549	0.549	0.000	0.000	0.000	0.000
91	A	127	TRP	0	-0.011	-0.004	19.227	-0.337	-0.337	0.000	0.000	0.000	0.000
92	A	128	ILE	0	0.003	-0.012	15.748	0.982	0.982	0.000	0.000	0.000	0.000
93	A	129	SER	0	-0.032	0.004	19.665	-0.738	-0.738	0.000	0.000	0.000	0.000
94	A	130	PHE	0	-0.051	-0.039	20.399	0.889	0.889	0.000	0.000	0.000	0.000
95	A	131	LYS	1	0.828	0.911	22.442	-12.264	-12.264	0.000	0.000	0.000	0.000
96	A	132	ILE	0	-0.018	-0.024	24.925	0.447	0.447	0.000	0.000	0.000	0.000
97	A	133	ASP	-1	-0.884	-0.930	27.713	10.304	10.304	0.000	0.000	0.000	0.000
98	A	134	ASP	-1	-0.873	-0.943	28.369	10.582	10.582	0.000	0.000	0.000	0.000
99	A	135	ASP	-1	-0.883	-0.896	30.356	9.891	9.891	0.000	0.000	0.000	0.000
100	A	136	ASP	-1	-0.884	-0.939	27.078	12.222	12.222	0.000	0.000	0.000	0.000
101	A	137	TYR	0	-0.067	-0.062	26.088	-0.468	-0.468	0.000	0.000	0.000	0.000
102	A	138	TRP	0	-0.060	-0.051	22.149	0.919	0.919	0.000	0.000	0.000	0.000
103	A	139	VAL	0	0.005	0.004	21.079	-0.456	-0.456	0.000	0.000	0.000	0.000
104	A	140	ALA	0	-0.030	-0.018	22.446	0.444	0.444	0.000	0.000	0.000	0.000
105	A	141	LEU	0	0.015	0.010	18.584	-0.218	-0.218	0.000	0.000	0.000	0.000
106	A	142	ASP	-1	-0.747	-0.884	21.878	12.890	12.890	0.000	0.000	0.000	0.000
107	A	143	ARG	1	0.818	0.900	13.277	-17.572	-17.572	0.000	0.000	0.000	0.000
108	A	144	ASP	-1	-0.872	-0.934	18.619	13.707	13.707	0.000	0.000	0.000	0.000
109	A	145	GLN	0	0.012	-0.006	20.173	0.269	0.269	0.000	0.000	0.000	0.000
110	A	146	LEU	0	0.015	0.018	15.204	0.509	0.509	0.000	0.000	0.000	0.000
111	A	147	ASP	-1	-0.824	-0.887	15.186	19.117	19.117	0.000	0.000	0.000	0.000
112	A	148	THR	0	-0.112	-0.046	16.156	0.523	0.523	0.000	0.000	0.000	0.000
113	A	149	VAL	0	0.005	0.019	17.296	0.043	0.043	0.000	0.000	0.000	0.000
114	A	150	THR	0	-0.115	-0.079	12.023	3.279	3.279	0.000	0.000	0.000	0.000

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