FMO DATABASE

FMODB ID: VR821

Calculation Name: 3LR3-A-Xray317

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	116
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-954171.273806
FMO2-HF: Nuclear repulsion	908810.330549
FMO2-HF: Total energy	-45360.943256
FMO2-MP2: Total energy	-45496.883602

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:36:ACE )

Summations of interaction energy for fragment #1(A:36:ACE )

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.
0.256	2.025	0.42	-0.999	-1.191	-0.003

Interaction energy analysis for fragmet #1(A:36:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.023

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	38	PRO	0	0.049	0.035	3.556	0.660	1.847	0.005	-0.595	-0.597	-0.001
4	A	39	ARG	1	0.916	0.954	4.931	-0.372	-0.372	0.000	0.000	0.000	0.000
5	A	40	ALA	0	-0.001	0.002	4.123	0.097	0.164	0.000	-0.020	-0.048	0.000
6	A	41	GLN	0	0.054	0.027	5.811	0.453	0.453	0.000	0.000	0.000	0.000
7	A	42	ARG	1	0.836	0.924	8.425	0.037	0.037	0.000	0.000	0.000	0.000
8	A	43	VAL	0	-0.002	-0.007	9.149	0.052	0.052	0.000	0.000	0.000	0.000
9	A	44	ALA	0	0.044	0.034	10.071	0.033	0.033	0.000	0.000	0.000	0.000
10	A	45	LEU	0	-0.002	-0.007	11.915	0.049	0.049	0.000	0.000	0.000	0.000
11	A	46	GLN	0	-0.037	-0.020	13.675	0.043	0.043	0.000	0.000	0.000	0.000
12	A	47	LEU	0	0.036	0.017	13.336	0.015	0.015	0.000	0.000	0.000	0.000
13	A	48	VAL	0	0.012	0.005	15.804	0.009	0.009	0.000	0.000	0.000	0.000
14	A	49	ALA	0	-0.049	-0.017	17.929	0.013	0.013	0.000	0.000	0.000	0.000
15	A	50	ILE	0	0.062	0.030	19.348	0.008	0.008	0.000	0.000	0.000	0.000
16	A	51	VAL	0	0.029	0.036	20.152	0.007	0.007	0.000	0.000	0.000	0.000
17	A	52	LYS	1	0.921	0.949	21.287	0.133	0.133	0.000	0.000	0.000	0.000
18	A	53	LEU	0	0.000	0.018	23.559	0.005	0.005	0.000	0.000	0.000	0.000
19	A	54	THR	0	0.046	0.019	24.774	0.007	0.007	0.000	0.000	0.000	0.000
20	A	55	ARG	1	0.931	0.973	24.687	0.091	0.091	0.000	0.000	0.000	0.000
21	A	56	THR	0	-0.071	-0.053	27.586	0.001	0.001	0.000	0.000	0.000	0.000
22	A	57	ALA	0	0.038	0.019	29.730	0.003	0.003	0.000	0.000	0.000	0.000
23	A	58	LEU	0	0.009	-0.003	31.134	0.003	0.003	0.000	0.000	0.000	0.000
24	A	59	LEU	0	-0.033	-0.001	31.503	0.002	0.002	0.000	0.000	0.000	0.000
25	A	60	TYR	0	-0.046	-0.030	32.438	0.001	0.001	0.000	0.000	0.000	0.000
26	A	61	SER	0	-0.044	0.001	35.919	0.003	0.003	0.000	0.000	0.000	0.000
27	A	62	ASP	-1	-0.819	-0.924	37.491	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	63	PRO	0	-0.034	-0.033	40.786	0.001	0.001	0.000	0.000	0.000	0.000
29	A	64	ASP	-1	-0.940	-0.959	42.006	-0.012	-0.012	0.000	0.000	0.000	0.000
30	A	65	LEU	0	-0.009	-0.001	40.661	0.002	0.002	0.000	0.000	0.000	0.000
31	A	66	ARG	1	0.880	0.948	36.735	0.028	0.028	0.000	0.000	0.000	0.000
32	A	67	ARG	1	0.944	0.948	36.871	0.012	0.012	0.000	0.000	0.000	0.000
33	A	68	ALA	0	0.032	0.019	37.814	0.002	0.002	0.000	0.000	0.000	0.000
34	A	69	LEU	0	0.030	0.014	32.864	0.001	0.001	0.000	0.000	0.000	0.000
35	A	70	LEU	0	-0.045	-0.028	32.260	0.001	0.001	0.000	0.000	0.000	0.000
36	A	71	GLN	0	-0.018	-0.005	33.078	0.003	0.003	0.000	0.000	0.000	0.000
37	A	72	ASP	-1	-0.897	-0.922	33.989	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	73	LEU	0	0.030	0.004	28.674	0.001	0.001	0.000	0.000	0.000	0.000
39	A	74	GLU	-1	-0.913	-0.951	29.287	0.008	0.008	0.000	0.000	0.000	0.000
40	A	75	SER	0	-0.064	-0.038	30.011	0.005	0.005	0.000	0.000	0.000	0.000
41	A	76	ASN	0	-0.096	-0.055	31.575	0.007	0.007	0.000	0.000	0.000	0.000
42	A	77	GLU	-1	-0.939	-0.968	27.074	-0.004	-0.004	0.000	0.000	0.000	0.000
43	A	78	GLY	0	-0.018	0.013	25.871	0.002	0.002	0.000	0.000	0.000	0.000
44	A	79	VAL	0	-0.089	-0.055	24.093	-0.001	-0.001	0.000	0.000	0.000	0.000
45	A	80	ARG	1	0.906	0.968	26.204	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	81	VAL	0	-0.002	-0.006	27.004	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	82	TYR	0	-0.034	-0.022	28.216	0.005	0.005	0.000	0.000	0.000	0.000
48	A	83	PRO	0	0.020	0.018	30.209	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	84	ARG	1	0.944	0.975	26.309	0.056	0.056	0.000	0.000	0.000	0.000
50	A	85	GLU	-1	-0.891	-0.952	30.776	-0.026	-0.026	0.000	0.000	0.000	0.000
51	A	86	LYS	1	0.842	0.900	31.456	0.043	0.043	0.000	0.000	0.000	0.000
52	A	87	THR	0	-0.021	-0.020	31.930	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	88	ASP	-1	-0.802	-0.865	29.338	-0.018	-0.018	0.000	0.000	0.000	0.000
54	A	89	LYS	1	0.918	0.955	28.722	0.009	0.009	0.000	0.000	0.000	0.000
55	A	90	PHE	0	0.059	0.022	21.984	0.000	0.000	0.000	0.000	0.000	0.000
56	A	91	LYS	1	0.937	0.987	21.450	-0.038	-0.038	0.000	0.000	0.000	0.000
57	A	92	LEU	0	0.022	0.009	17.452	0.001	0.001	0.000	0.000	0.000	0.000
58	A	93	GLN	0	0.023	0.022	13.372	0.043	0.043	0.000	0.000	0.000	0.000
59	A	94	PRO	0	0.030	0.020	14.510	-0.030	-0.030	0.000	0.000	0.000	0.000
60	A	95	ASP	-1	-0.959	-0.975	10.911	0.020	0.020	0.000	0.000	0.000	0.000
61	A	96	GLU	-1	-0.871	-0.944	11.036	0.266	0.266	0.000	0.000	0.000	0.000
62	A	97	SER	0	-0.047	-0.020	7.441	-0.003	-0.003	0.000	0.000	0.000	0.000
63	A	98	VAL	0	0.022	-0.006	2.651	-0.205	0.132	0.397	-0.300	-0.434	-0.002
64	A	99	ASN	0	-0.017	-0.009	5.728	-0.313	-0.313	0.000	0.000	0.000	0.000
65	A	100	ARG	1	0.883	0.927	9.270	-0.023	-0.023	0.000	0.000	0.000	0.000
66	A	101	LEU	0	-0.006	0.007	3.591	-0.334	-0.156	0.018	-0.084	-0.112	0.000
67	A	102	ILE	0	0.005	0.003	7.081	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	103	GLU	-1	-0.798	-0.906	9.047	-0.081	-0.081	0.000	0.000	0.000	0.000
69	A	104	HIS	0	-0.021	0.003	10.419	0.082	0.082	0.000	0.000	0.000	0.000
70	A	105	ASP	-1	-0.823	-0.930	8.473	-0.971	-0.971	0.000	0.000	0.000	0.000
71	A	106	ILE	0	-0.033	-0.022	11.773	0.071	0.071	0.000	0.000	0.000	0.000
72	A	107	ARG	1	0.884	0.934	14.479	0.203	0.203	0.000	0.000	0.000	0.000
73	A	108	SER	0	-0.031	0.003	14.338	0.023	0.023	0.000	0.000	0.000	0.000
74	A	109	ARG	1	0.861	0.929	15.735	0.297	0.297	0.000	0.000	0.000	0.000
75	A	110	LEU	0	-0.063	-0.047	18.170	0.027	0.027	0.000	0.000	0.000	0.000
76	A	111	GLY	0	0.012	0.020	19.633	0.021	0.021	0.000	0.000	0.000	0.000
77	A	112	ASP	-1	-0.907	-0.962	19.268	-0.227	-0.227	0.000	0.000	0.000	0.000
78	A	113	ASP	-1	-0.915	-0.937	20.663	-0.108	-0.108	0.000	0.000	0.000	0.000
79	A	114	THR	0	-0.125	-0.063	19.213	0.018	0.018	0.000	0.000	0.000	0.000
80	A	115	VAL	0	-0.020	-0.003	19.893	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	116	ILE	0	0.006	-0.003	15.072	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	117	ALA	0	-0.072	-0.033	18.321	0.001	0.001	0.000	0.000	0.000	0.000
83	A	118	GLN	0	-0.028	-0.036	18.204	0.010	0.010	0.000	0.000	0.000	0.000
84	A	119	SER	0	-0.038	-0.016	19.748	0.008	0.008	0.000	0.000	0.000	0.000
85	A	120	VAL	0	0.061	0.023	23.520	-0.008	-0.008	0.000	0.000	0.000	0.000
86	A	121	ASN	0	-0.054	-0.030	26.308	0.003	0.003	0.000	0.000	0.000	0.000
87	A	122	ASP	-1	-0.939	-0.965	27.594	0.015	0.015	0.000	0.000	0.000	0.000
88	A	123	ILE	0	-0.028	-0.006	27.183	0.006	0.006	0.000	0.000	0.000	0.000
89	A	124	PRO	0	0.003	-0.014	23.812	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	125	GLY	0	0.008	0.008	22.007	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	126	VAL	0	-0.028	-0.005	16.734	0.003	0.003	0.000	0.000	0.000	0.000
92	A	127	TRP	0	-0.014	0.001	19.322	-0.011	-0.011	0.000	0.000	0.000	0.000
93	A	128	ILE	0	0.000	-0.014	17.144	-0.012	-0.012	0.000	0.000	0.000	0.000
94	A	129	SER	0	-0.007	0.021	20.769	0.005	0.005	0.000	0.000	0.000	0.000
95	A	130	PHE	0	-0.049	-0.041	22.763	-0.014	-0.014	0.000	0.000	0.000	0.000
96	A	131	LYS	1	0.927	0.972	25.350	0.072	0.072	0.000	0.000	0.000	0.000
97	A	132	ILE	0	-0.039	-0.030	28.684	-0.005	-0.005	0.000	0.000	0.000	0.000
98	A	133	ASP	-1	-0.884	-0.927	31.664	-0.048	-0.048	0.000	0.000	0.000	0.000
99	A	134	ASP	-1	-0.956	-0.990	32.626	-0.057	-0.057	0.000	0.000	0.000	0.000
100	A	135	ASP	-1	-0.944	-0.950	33.794	-0.036	-0.036	0.000	0.000	0.000	0.000
101	A	136	ASP	-1	-0.898	-0.951	29.537	-0.062	-0.062	0.000	0.000	0.000	0.000
102	A	137	TYR	0	0.002	-0.008	28.482	0.008	0.008	0.000	0.000	0.000	0.000
103	A	138	TRP	0	-0.055	-0.055	23.318	-0.009	-0.009	0.000	0.000	0.000	0.000
104	A	139	VAL	0	0.011	0.008	22.447	0.003	0.003	0.000	0.000	0.000	0.000
105	A	140	ALA	0	-0.031	-0.021	23.152	-0.002	-0.002	0.000	0.000	0.000	0.000
106	A	141	LEU	0	0.000	-0.004	19.088	0.000	0.000	0.000	0.000	0.000	0.000
107	A	142	ASP	-1	-0.776	-0.882	21.856	0.062	0.062	0.000	0.000	0.000	0.000
108	A	143	ARG	1	0.904	0.947	12.534	-0.158	-0.158	0.000	0.000	0.000	0.000
109	A	144	ASP	-1	-0.853	-0.921	18.537	0.114	0.114	0.000	0.000	0.000	0.000
110	A	145	GLN	0	-0.008	-0.021	20.293	0.006	0.006	0.000	0.000	0.000	0.000
111	A	146	LEU	0	-0.019	-0.010	15.498	-0.004	-0.004	0.000	0.000	0.000	0.000
112	A	147	ASP	-1	-0.908	-0.961	15.666	0.164	0.164	0.000	0.000	0.000	0.000
113	A	148	THR	0	-0.100	-0.047	16.485	0.016	0.016	0.000	0.000	0.000	0.000
114	A	149	VAL	0	-0.012	0.005	18.174	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	150	THR	0	-0.049	-0.026	12.680	-0.009	-0.009	0.000	0.000	0.000	0.000
116	A	151	NME	0	0.003	0.003	12.479	0.052	0.052	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:36:ACE )