FMO DATABASE

FMODB ID: VR4L1

Calculation Name: 2R4Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2R4Q

Chain ID: A

ChEMBL ID:

UniProt ID: P71012

Base Structure: X-ray

Registration Date: 2023-06-21

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	OptHSide
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	104
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-770888.41609
FMO2-HF: Nuclear repulsion	731323.965546
FMO2-HF: Total energy	-39564.450544
FMO2-MP2: Total energy	-39679.33687

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:170:ALA)

Summations of interaction energy for fragment #1(A:170:ALA)

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.
-2.014	2.783	1.405	-2.757	-3.445	-0.011

Interaction energy analysis for fragmet #1(A:170:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.002

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	172	ILE	0	0.032	0.018	3.774	-0.389	1.277	-0.029	-0.856	-0.780	0.003
4	A	173	LEU	0	-0.016	-0.008	6.249	0.173	0.173	0.000	0.000	0.000	0.000
5	A	174	ALA	0	0.007	0.005	9.018	-0.051	-0.051	0.000	0.000	0.000	0.000
6	A	175	VAL	0	-0.012	-0.004	12.794	0.051	0.051	0.000	0.000	0.000	0.000
7	A	176	THR	0	-0.010	-0.011	15.866	-0.017	-0.017	0.000	0.000	0.000	0.000
8	A	177	ALA	0	0.024	-0.001	19.216	0.016	0.016	0.000	0.000	0.000	0.000
9	A	178	CYS	0	-0.033	0.021	22.558	-0.009	-0.009	0.000	0.000	0.000	0.000
10	A	179	PRO	0	0.063	0.011	26.228	0.007	0.007	0.000	0.000	0.000	0.000
11	A	180	THR	0	0.037	0.026	29.539	0.004	0.004	0.000	0.000	0.000	0.000
12	A	181	GLY	0	-0.013	-0.023	26.882	0.004	0.004	0.000	0.000	0.000	0.000
13	A	182	ILE	0	0.022	-0.004	27.475	0.006	0.006	0.000	0.000	0.000	0.000
14	A	183	ALA	0	0.053	0.013	29.063	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	184	HIS	0	0.052	0.010	26.095	0.004	0.004	0.000	0.000	0.000	0.000
16	A	185	THR	0	0.006	0.002	21.750	-0.006	-0.006	0.000	0.000	0.000	0.000
17	A	186	PHE	0	0.030	0.009	21.663	0.000	0.000	0.000	0.000	0.000	0.000
18	A	187	MET	0	0.052	0.048	22.442	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	188	ALA	0	0.026	0.018	20.554	-0.008	-0.008	0.000	0.000	0.000	0.000
20	A	189	ALA	0	-0.010	-0.009	17.969	-0.010	-0.010	0.000	0.000	0.000	0.000
21	A	190	ASP	-1	-0.873	-0.933	18.129	0.026	0.026	0.000	0.000	0.000	0.000
22	A	191	ALA	0	0.035	0.032	19.868	-0.009	-0.009	0.000	0.000	0.000	0.000
23	A	192	LEU	0	-0.026	-0.023	14.946	-0.017	-0.017	0.000	0.000	0.000	0.000
24	A	193	LYS	1	0.847	0.916	15.075	-0.074	-0.074	0.000	0.000	0.000	0.000
25	A	194	GLU	-1	-0.951	-0.973	16.270	-0.036	-0.036	0.000	0.000	0.000	0.000
26	A	195	LYS	1	0.817	0.897	16.765	0.105	0.105	0.000	0.000	0.000	0.000
27	A	196	ALA	0	0.016	0.003	12.372	-0.022	-0.022	0.000	0.000	0.000	0.000
28	A	197	LYS	1	0.950	0.976	14.095	0.009	0.009	0.000	0.000	0.000	0.000
29	A	198	GLU	-1	-0.900	-0.932	15.775	-0.118	-0.118	0.000	0.000	0.000	0.000
30	A	199	LEU	0	-0.033	-0.019	14.235	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	200	GLY	0	-0.029	0.011	13.596	-0.036	-0.036	0.000	0.000	0.000	0.000
32	A	201	VAL	0	-0.051	-0.029	9.099	-0.103	-0.103	0.000	0.000	0.000	0.000
33	A	202	GLU	-1	-0.911	-0.958	6.092	0.605	0.605	0.000	0.000	0.000	0.000
34	A	203	ILE	0	-0.036	-0.026	8.177	-0.155	-0.155	0.000	0.000	0.000	0.000
35	A	204	LYS	1	0.768	0.886	9.017	-0.405	-0.405	0.000	0.000	0.000	0.000
36	A	205	VAL	0	0.002	-0.007	10.537	-0.040	-0.040	0.000	0.000	0.000	0.000
37	A	206	GLU	-1	-0.774	-0.823	13.673	0.197	0.197	0.000	0.000	0.000	0.000
38	A	207	THR	0	-0.017	-0.008	15.507	-0.031	-0.031	0.000	0.000	0.000	0.000
39	A	208	ASN	0	-0.045	-0.048	18.833	0.006	0.006	0.000	0.000	0.000	0.000
40	A	209	GLY	0	0.037	0.004	21.870	-0.012	-0.012	0.000	0.000	0.000	0.000
41	A	210	SER	0	-0.033	-0.004	25.139	0.006	0.006	0.000	0.000	0.000	0.000
42	A	211	SER	0	0.017	0.009	26.778	0.000	0.000	0.000	0.000	0.000	0.000
43	A	212	GLY	0	0.003	0.004	25.299	0.006	0.006	0.000	0.000	0.000	0.000
44	A	213	ILE	0	-0.044	-0.023	18.937	-0.003	-0.003	0.000	0.000	0.000	0.000
45	A	214	LYS	1	0.905	0.956	19.714	-0.107	-0.107	0.000	0.000	0.000	0.000
46	A	215	HIS	0	0.052	0.018	14.732	0.017	0.017	0.000	0.000	0.000	0.000
47	A	216	LYS	1	0.958	0.982	14.497	-0.174	-0.174	0.000	0.000	0.000	0.000
48	A	217	LEU	0	0.009	0.011	10.149	0.066	0.066	0.000	0.000	0.000	0.000
49	A	218	THR	0	-0.014	-0.024	9.865	-0.026	-0.026	0.000	0.000	0.000	0.000
50	A	219	ALA	0	0.025	0.001	10.188	0.024	0.024	0.000	0.000	0.000	0.000
51	A	220	GLN	0	0.031	0.012	6.676	-0.250	-0.250	0.000	0.000	0.000	0.000
52	A	221	GLU	-1	-0.731	-0.836	5.660	1.013	1.013	0.000	0.000	0.000	0.000
53	A	222	ILE	0	-0.022	-0.021	5.624	-0.096	-0.096	0.000	0.000	0.000	0.000
54	A	223	GLU	-1	-0.937	-0.962	7.629	0.124	0.124	0.000	0.000	0.000	0.000
55	A	224	ASP	-1	-0.859	-0.924	2.478	0.839	1.371	0.505	-0.485	-0.553	-0.004
56	A	225	ALA	0	-0.091	-0.029	2.948	-2.106	-0.118	0.472	-1.172	-1.288	-0.011
57	A	226	PRO	0	0.020	0.019	2.449	-0.622	-0.040	0.458	-0.241	-0.799	0.001
58	A	227	ALA	0	0.015	0.008	5.005	0.054	0.083	-0.001	-0.003	-0.025	0.000
59	A	228	ILE	0	-0.028	-0.007	7.821	-0.021	-0.021	0.000	0.000	0.000	0.000
60	A	229	ILE	0	0.004	0.005	10.507	0.001	0.001	0.000	0.000	0.000	0.000
61	A	230	VAL	0	-0.010	-0.008	13.448	0.031	0.031	0.000	0.000	0.000	0.000
62	A	231	ALA	0	0.011	0.010	16.619	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	232	ALA	0	-0.036	-0.034	19.366	0.013	0.013	0.000	0.000	0.000	0.000
64	A	233	ASP	-1	-0.835	-0.912	22.300	-0.010	-0.010	0.000	0.000	0.000	0.000
65	A	234	LYS	1	0.841	0.927	24.656	-0.048	-0.048	0.000	0.000	0.000	0.000
66	A	235	GLN	0	0.007	0.007	24.217	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	236	VAL	0	-0.014	-0.004	18.270	0.006	0.006	0.000	0.000	0.000	0.000
68	A	237	GLU	-1	-0.872	-0.943	19.814	0.064	0.064	0.000	0.000	0.000	0.000
69	A	238	MET	0	0.036	0.023	17.680	0.013	0.013	0.000	0.000	0.000	0.000
70	A	239	GLU	-1	-0.800	-0.869	17.866	0.034	0.034	0.000	0.000	0.000	0.000
71	A	240	ARG	1	0.763	0.849	14.720	-0.149	-0.149	0.000	0.000	0.000	0.000
72	A	241	PHE	0	-0.006	-0.017	12.269	0.020	0.020	0.000	0.000	0.000	0.000
73	A	242	LYS	1	0.901	0.950	14.541	-0.048	-0.048	0.000	0.000	0.000	0.000
74	A	243	GLY	0	0.015	0.006	14.902	0.014	0.014	0.000	0.000	0.000	0.000
75	A	244	LYS	1	0.812	0.908	6.636	-0.048	-0.048	0.000	0.000	0.000	0.000
76	A	245	ARG	1	0.911	0.964	10.307	0.188	0.188	0.000	0.000	0.000	0.000
77	A	246	VAL	0	0.010	-0.001	11.162	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	247	LEU	0	0.012	0.016	13.686	0.000	0.000	0.000	0.000	0.000	0.000
79	A	248	GLN	0	-0.020	-0.009	15.394	0.007	0.007	0.000	0.000	0.000	0.000
80	A	249	VAL	0	-0.022	-0.014	18.324	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	250	PRO	0	0.054	0.020	20.843	0.007	0.007	0.000	0.000	0.000	0.000
82	A	251	VAL	0	0.004	0.001	22.067	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	252	THR	0	-0.008	-0.023	22.830	-0.006	-0.006	0.000	0.000	0.000	0.000
84	A	253	ALA	0	-0.032	-0.007	21.171	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	254	GLY	0	0.047	0.016	19.304	-0.009	-0.009	0.000	0.000	0.000	0.000
86	A	255	ILE	0	-0.016	-0.009	20.253	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	256	ARG	1	0.904	0.947	23.302	0.028	0.028	0.000	0.000	0.000	0.000
88	A	257	ARG	1	0.870	0.931	20.939	0.080	0.080	0.000	0.000	0.000	0.000
89	A	258	PRO	0	0.043	0.032	17.918	-0.013	-0.013	0.000	0.000	0.000	0.000
90	A	259	GLN	0	0.015	-0.001	16.454	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	260	GLU	-1	-0.786	-0.890	16.197	-0.127	-0.127	0.000	0.000	0.000	0.000
92	A	261	LEU	0	-0.038	-0.023	15.486	-0.013	-0.013	0.000	0.000	0.000	0.000
93	A	262	ILE	0	0.011	0.006	11.350	-0.022	-0.022	0.000	0.000	0.000	0.000
94	A	263	GLU	-1	-0.829	-0.913	11.362	-0.272	-0.272	0.000	0.000	0.000	0.000
95	A	264	LYS	1	0.821	0.912	12.812	0.121	0.121	0.000	0.000	0.000	0.000
96	A	265	ALA	0	-0.027	-0.012	9.412	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	266	MET	0	-0.016	-0.014	6.855	-0.107	-0.107	0.000	0.000	0.000	0.000
98	A	267	ASN	0	-0.045	-0.021	8.613	-0.047	-0.047	0.000	0.000	0.000	0.000
99	A	268	GLN	0	-0.087	-0.050	7.494	0.028	0.028	0.000	0.000	0.000	0.000
100	A	269	ASP	-1	-0.848	-0.895	10.673	-0.121	-0.121	0.000	0.000	0.000	0.000
101	A	270	ALA	0	-0.009	-0.029	12.737	0.017	0.017	0.000	0.000	0.000	0.000
102	A	271	PRO	0	-0.013	0.008	14.267	-0.012	-0.012	0.000	0.000	0.000	0.000
103	A	272	ILE	0	0.004	0.001	13.702	0.001	0.001	0.000	0.000	0.000	0.000
104	A	273	TYR	0	-0.041	-0.040	15.324	0.009	0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:170:ALA)