FMO DATABASE

FMODB ID: 53V7Z

Calculation Name: 1R7L-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1R7L

Chain ID: A

ChEMBL ID:

UniProt ID: Q81EU2

Base Structure: X-ray

Registration Date: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

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	103
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-765359.959693
FMO2-HF: Nuclear repulsion	724621.776497
FMO2-HF: Total energy	-40738.183196
FMO2-MP2: Total energy	-40856.934452

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:-6:LEU)

Summations of interaction energy for fragment #1(A:-6:LEU)

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.
0.337	2.913	-0.019	-1.412	-1.145	0.007

Interaction energy analysis for fragmet #1(A:-6:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / 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	-4	PHE	0	-0.004	-0.001	3.866	-0.997	1.579	-0.019	-1.412	-1.145	0.007
4	A	-3	GLN	0	0.023	0.016	6.695	-0.119	-0.119	0.000	0.000	0.000	0.000
5	A	-2	SER	0	-0.007	-0.027	10.503	0.070	0.070	0.000	0.000	0.000	0.000
6	A	-1	ASN	0	-0.028	-0.008	12.933	0.020	0.020	0.000	0.000	0.000	0.000
7	A	0	ALA	0	0.020	0.011	16.097	0.028	0.028	0.000	0.000	0.000	0.000
8	A	1	MET	0	-0.004	0.008	11.337	-0.043	-0.043	0.000	0.000	0.000	0.000
9	A	2	LYN	0	0.074	0.050	14.911	0.071	0.071	0.000	0.000	0.000	0.000
10	A	3	PRO	0	0.052	0.021	17.214	-0.050	-0.050	0.000	0.000	0.000	0.000
11	A	4	ARG	1	0.843	0.895	13.667	0.552	0.552	0.000	0.000	0.000	0.000
12	A	5	ASP	-1	-0.806	-0.906	12.808	-0.748	-0.748	0.000	0.000	0.000	0.000
13	A	6	ILE	0	0.012	0.007	14.232	-0.055	-0.055	0.000	0.000	0.000	0.000
14	A	7	ASN	0	0.029	0.027	16.474	0.008	0.008	0.000	0.000	0.000	0.000
15	A	8	LYS	1	0.822	0.917	12.358	0.769	0.769	0.000	0.000	0.000	0.000
16	A	9	LEU	0	-0.019	0.007	10.214	-0.018	-0.018	0.000	0.000	0.000	0.000
17	A	10	ILE	0	-0.002	0.007	13.814	0.034	0.034	0.000	0.000	0.000	0.000
18	A	11	ALA	0	0.020	0.007	16.747	0.031	0.031	0.000	0.000	0.000	0.000
19	A	12	SER	0	-0.026	-0.021	12.910	0.003	0.003	0.000	0.000	0.000	0.000
20	A	13	LYS	1	0.913	0.947	9.655	0.975	0.975	0.000	0.000	0.000	0.000
21	A	14	ILE	0	-0.013	0.001	15.307	0.037	0.037	0.000	0.000	0.000	0.000
22	A	15	PHE	0	-0.012	-0.022	18.785	0.036	0.036	0.000	0.000	0.000	0.000
23	A	16	GLY	0	0.016	0.034	17.218	0.026	0.026	0.000	0.000	0.000	0.000
24	A	17	TYR	0	-0.056	-0.043	17.861	0.035	0.035	0.000	0.000	0.000	0.000
25	A	18	GLU	-1	-0.846	-0.927	14.796	-0.264	-0.264	0.000	0.000	0.000	0.000
26	A	19	ILE	0	-0.039	-0.030	12.693	0.015	0.015	0.000	0.000	0.000	0.000
27	A	20	LYS	1	0.861	0.910	12.687	0.176	0.176	0.000	0.000	0.000	0.000
28	A	21	ASP	-1	-0.809	-0.890	13.238	-0.255	-0.255	0.000	0.000	0.000	0.000
29	A	22	ASP	-1	-0.799	-0.882	13.355	-0.598	-0.598	0.000	0.000	0.000	0.000
30	A	23	ASN	0	-0.089	-0.033	15.388	0.063	0.063	0.000	0.000	0.000	0.000
31	A	24	ILE	0	0.013	0.006	16.683	-0.044	-0.044	0.000	0.000	0.000	0.000
32	A	25	ILE	0	-0.061	-0.031	16.680	0.031	0.031	0.000	0.000	0.000	0.000
33	A	26	LYS	1	0.945	0.982	19.631	0.173	0.173	0.000	0.000	0.000	0.000
34	A	27	ASP	-1	-0.836	-0.928	22.064	-0.103	-0.103	0.000	0.000	0.000	0.000
35	A	28	GLY	0	0.037	0.036	19.733	0.016	0.016	0.000	0.000	0.000	0.000
36	A	29	ARG	1	0.847	0.911	20.793	0.070	0.070	0.000	0.000	0.000	0.000
37	A	30	TYR	0	-0.005	0.000	23.202	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	31	ARG	1	0.960	0.982	20.625	0.164	0.164	0.000	0.000	0.000	0.000
39	A	32	LEU	0	0.000	0.001	21.851	0.017	0.017	0.000	0.000	0.000	0.000
40	A	33	GLY	0	0.033	0.022	21.492	-0.025	-0.025	0.000	0.000	0.000	0.000
41	A	34	ILE	0	-0.013	-0.012	17.022	0.001	0.001	0.000	0.000	0.000	0.000
42	A	35	PRO	0	0.031	0.020	21.266	0.006	0.006	0.000	0.000	0.000	0.000
43	A	36	LEU	0	0.016	0.011	22.149	-0.030	-0.030	0.000	0.000	0.000	0.000
44	A	37	TYR	0	0.026	-0.006	20.380	0.007	0.007	0.000	0.000	0.000	0.000
45	A	38	SER	0	0.002	-0.035	21.062	0.017	0.017	0.000	0.000	0.000	0.000
46	A	39	GLN	0	-0.054	-0.043	23.115	-0.009	-0.009	0.000	0.000	0.000	0.000
47	A	40	ASN	0	0.049	0.025	26.235	0.014	0.014	0.000	0.000	0.000	0.000
48	A	41	ILE	0	0.024	0.000	28.173	-0.009	-0.009	0.000	0.000	0.000	0.000
49	A	42	GLU	-1	-0.891	-0.936	30.353	-0.132	-0.132	0.000	0.000	0.000	0.000
50	A	43	SER	0	-0.010	-0.007	25.548	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	44	ALA	0	0.000	-0.010	25.618	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	45	TRP	0	-0.024	-0.007	26.690	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	46	GLN	0	0.031	0.014	26.335	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	47	VAL	0	-0.037	-0.021	22.182	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	48	VAL	0	-0.055	-0.032	24.913	0.000	0.000	0.000	0.000	0.000	0.000
56	A	49	GLU	-1	-0.881	-0.949	27.761	-0.118	-0.118	0.000	0.000	0.000	0.000
57	A	50	LYS	1	0.780	0.900	22.887	0.182	0.182	0.000	0.000	0.000	0.000
58	A	51	LEU	0	-0.071	-0.030	22.378	-0.008	-0.008	0.000	0.000	0.000	0.000
59	A	52	GLU	-1	-0.798	-0.891	24.915	-0.143	-0.143	0.000	0.000	0.000	0.000
60	A	53	TYR	0	-0.068	-0.033	21.600	0.019	0.019	0.000	0.000	0.000	0.000
61	A	54	ASP	-1	-0.799	-0.896	27.876	-0.102	-0.102	0.000	0.000	0.000	0.000
62	A	55	VAL	0	-0.012	-0.016	27.480	-0.010	-0.010	0.000	0.000	0.000	0.000
63	A	56	LYS	1	0.854	0.939	30.053	0.107	0.107	0.000	0.000	0.000	0.000
64	A	57	VAL	0	0.026	-0.002	29.815	-0.012	-0.012	0.000	0.000	0.000	0.000
65	A	58	THR	0	0.013	0.016	32.022	0.011	0.011	0.000	0.000	0.000	0.000
66	A	59	LYS	1	0.812	0.901	33.430	0.085	0.085	0.000	0.000	0.000	0.000
67	A	60	THR	0	-0.001	-0.007	34.708	0.009	0.009	0.000	0.000	0.000	0.000
68	A	61	ASP	-1	-0.820	-0.917	36.876	-0.093	-0.093	0.000	0.000	0.000	0.000
69	A	62	LEU	0	0.049	0.043	35.455	0.003	0.003	0.000	0.000	0.000	0.000
70	A	63	LYS	1	0.835	0.906	32.203	0.117	0.117	0.000	0.000	0.000	0.000
71	A	64	PRO	0	-0.008	-0.008	27.737	0.002	0.002	0.000	0.000	0.000	0.000
72	A	65	LYS	1	0.881	0.929	30.611	0.110	0.110	0.000	0.000	0.000	0.000
73	A	66	TYR	0	-0.005	-0.002	29.794	0.009	0.009	0.000	0.000	0.000	0.000
74	A	67	GLN	0	0.013	0.004	29.088	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	68	VAL	0	-0.023	-0.014	26.217	0.005	0.005	0.000	0.000	0.000	0.000
76	A	69	HIS	0	-0.017	-0.008	27.538	-0.006	-0.006	0.000	0.000	0.000	0.000
77	A	70	VAL	0	0.028	0.016	24.434	0.001	0.001	0.000	0.000	0.000	0.000
78	A	71	PHE	0	-0.012	-0.015	26.403	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	72	VAL	0	0.022	0.020	22.829	0.001	0.001	0.000	0.000	0.000	0.000
80	A	73	PRO	0	0.020	0.010	25.126	0.010	0.010	0.000	0.000	0.000	0.000
81	A	74	GLY	0	0.007	0.003	26.544	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	75	GLY	0	-0.018	-0.012	27.114	0.003	0.003	0.000	0.000	0.000	0.000
83	A	76	VAL	0	-0.040	-0.010	27.369	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	77	LYS	1	0.865	0.943	19.640	0.199	0.199	0.000	0.000	0.000	0.000
85	A	78	MET	0	0.006	0.016	24.481	0.002	0.002	0.000	0.000	0.000	0.000
86	A	79	VAL	0	-0.041	-0.011	21.676	-0.012	-0.012	0.000	0.000	0.000	0.000
87	A	80	PHE	0	0.107	0.035	24.769	0.014	0.014	0.000	0.000	0.000	0.000
88	A	81	ALA	0	-0.058	-0.032	24.792	-0.025	-0.025	0.000	0.000	0.000	0.000
89	A	82	GLU	-1	-0.711	-0.843	26.583	-0.125	-0.125	0.000	0.000	0.000	0.000
90	A	83	THR	0	-0.020	-0.008	27.366	0.006	0.006	0.000	0.000	0.000	0.000
91	A	84	ALA	0	0.073	0.038	27.865	-0.010	-0.010	0.000	0.000	0.000	0.000
92	A	85	PRO	0	0.034	0.018	26.568	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	86	MET	0	0.010	0.020	21.418	-0.029	-0.029	0.000	0.000	0.000	0.000
94	A	87	ALA	0	-0.032	-0.019	23.113	-0.021	-0.021	0.000	0.000	0.000	0.000
95	A	88	ILE	0	0.044	0.016	24.366	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	89	CYS	0	-0.033	0.013	20.216	-0.011	-0.011	0.000	0.000	0.000	0.000
97	A	90	LYS	1	0.909	0.939	19.116	0.247	0.247	0.000	0.000	0.000	0.000
98	A	91	GLY	0	0.031	0.023	20.139	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	92	ALA	0	0.051	0.026	20.880	0.005	0.005	0.000	0.000	0.000	0.000
100	A	93	LEU	0	-0.004	0.005	14.869	-0.011	-0.011	0.000	0.000	0.000	0.000
101	A	94	ALA	0	-0.014	0.010	17.106	-0.009	-0.009	0.000	0.000	0.000	0.000
102	A	95	SER	0	-0.080	-0.047	19.065	0.028	0.028	0.000	0.000	0.000	0.000
103	A	96	VAL	0	-0.045	-0.024	15.722	0.009	0.009	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:-6:LEU)