FMO DATABASE

FMODB ID: VQRL1

Calculation Name: 1YOZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YOZ

Chain ID: A

ChEMBL ID:

UniProt ID: O29321

Base Structure: X-ray

Registration Date: 2023-09-21

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	116
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1022525.764527
FMO2-HF: Nuclear repulsion	974303.909776
FMO2-HF: Total energy	-48221.854751
FMO2-MP2: Total energy	-48362.806733

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:9:GLY)

Summations of interaction energy for fragment #1(A:9:GLY)

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.
-4.721	1.391	4.123	-5.456	-4.78	-0.024

Interaction energy analysis for fragmet #1(A:9:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.015 / q_NPA : 0.008

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	11	MET	0	-0.037	-0.029	3.743	-1.802	1.078	-0.053	-1.493	-1.335	-0.004
4	A	12	LEU	0	-0.007	-0.002	5.229	0.144	0.144	0.000	0.000	0.000	0.000
5	A	13	TYR	0	-0.050	-0.039	6.903	-0.267	-0.267	0.000	0.000	0.000	0.000
6	A	14	ILE	0	0.032	0.034	9.732	0.057	0.057	0.000	0.000	0.000	0.000
7	A	15	ASN	0	0.019	-0.019	12.840	-0.008	-0.008	0.000	0.000	0.000	0.000
8	A	16	SER	0	0.014	-0.017	15.612	0.020	0.020	0.000	0.000	0.000	0.000
9	A	17	PHE	0	-0.009	-0.018	19.137	0.016	0.016	0.000	0.000	0.000	0.000
10	A	18	LEU	0	-0.024	-0.011	16.080	0.012	0.012	0.000	0.000	0.000	0.000
11	A	19	ASP	-1	-0.863	-0.930	17.349	-0.173	-0.173	0.000	0.000	0.000	0.000
12	A	20	ARG	1	0.773	0.864	20.206	0.105	0.105	0.000	0.000	0.000	0.000
13	A	21	MET	0	-0.027	-0.003	22.357	0.012	0.012	0.000	0.000	0.000	0.000
14	A	22	GLY	0	0.000	-0.009	22.881	0.009	0.009	0.000	0.000	0.000	0.000
15	A	23	GLU	-1	-0.794	-0.888	23.861	-0.073	-0.073	0.000	0.000	0.000	0.000
16	A	24	ILE	0	-0.038	-0.010	25.958	0.009	0.009	0.000	0.000	0.000	0.000
17	A	25	ILE	0	-0.041	-0.019	26.725	0.006	0.006	0.000	0.000	0.000	0.000
18	A	26	ARG	1	0.763	0.853	22.052	0.103	0.103	0.000	0.000	0.000	0.000
19	A	27	GLY	0	-0.019	0.003	28.620	0.006	0.006	0.000	0.000	0.000	0.000
20	A	28	GLU	-1	-0.851	-0.890	26.050	-0.072	-0.072	0.000	0.000	0.000	0.000
21	A	29	LYS	1	0.817	0.907	26.603	0.072	0.072	0.000	0.000	0.000	0.000
22	A	30	SER	0	0.024	0.017	31.114	-0.001	-0.001	0.000	0.000	0.000	0.000
23	A	31	VAL	0	0.058	0.015	32.907	-0.004	-0.004	0.000	0.000	0.000	0.000
24	A	32	GLU	-1	-0.946	-0.963	34.279	-0.047	-0.047	0.000	0.000	0.000	0.000
25	A	33	GLU	-1	-0.854	-0.940	30.360	-0.068	-0.068	0.000	0.000	0.000	0.000
26	A	34	ALA	0	-0.003	0.001	30.602	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	35	ASP	-1	-0.816	-0.902	31.531	-0.062	-0.062	0.000	0.000	0.000	0.000
28	A	36	LYS	1	0.851	0.913	31.250	0.054	0.054	0.000	0.000	0.000	0.000
29	A	37	LEU	0	0.042	0.026	25.034	-0.003	-0.003	0.000	0.000	0.000	0.000
30	A	38	LEU	0	-0.039	-0.013	28.058	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	39	ASP	-1	-0.822	-0.908	30.225	-0.071	-0.071	0.000	0.000	0.000	0.000
32	A	40	GLN	0	0.063	0.003	28.413	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	41	LYS	1	0.931	0.987	27.771	0.068	0.068	0.000	0.000	0.000	0.000
34	A	42	ASN	0	-0.050	-0.039	27.930	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	43	ILE	0	-0.004	0.008	23.619	-0.006	-0.006	0.000	0.000	0.000	0.000
36	A	44	PHE	0	0.023	-0.004	23.283	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	45	GLU	-1	-0.845	-0.924	23.115	-0.098	-0.098	0.000	0.000	0.000	0.000
38	A	46	MET	0	-0.027	-0.008	21.487	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	47	PHE	0	0.063	0.026	17.490	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	48	ARG	1	0.793	0.912	18.319	0.093	0.093	0.000	0.000	0.000	0.000
41	A	49	SER	0	0.062	0.029	19.324	0.002	0.002	0.000	0.000	0.000	0.000
42	A	50	ASP	-1	-0.777	-0.848	15.364	-0.194	-0.194	0.000	0.000	0.000	0.000
43	A	51	CYS	0	-0.096	-0.059	14.851	-0.018	-0.018	0.000	0.000	0.000	0.000
44	A	52	GLU	-1	-0.930	-0.967	15.252	-0.085	-0.085	0.000	0.000	0.000	0.000
45	A	53	GLU	-1	-0.922	-0.965	14.979	-0.101	-0.101	0.000	0.000	0.000	0.000
46	A	54	ILE	0	-0.018	-0.017	9.786	0.017	0.017	0.000	0.000	0.000	0.000
47	A	55	LEU	0	-0.040	-0.023	11.815	0.024	0.024	0.000	0.000	0.000	0.000
48	A	56	ASN	0	-0.016	-0.008	13.869	0.028	0.028	0.000	0.000	0.000	0.000
49	A	57	LEU	0	-0.017	0.012	11.140	0.030	0.030	0.000	0.000	0.000	0.000
50	A	58	TYR	0	0.038	0.021	10.365	0.032	0.032	0.000	0.000	0.000	0.000
51	A	59	LYS	1	0.807	0.898	11.774	0.109	0.109	0.000	0.000	0.000	0.000
52	A	60	SER	0	-0.094	-0.070	15.341	0.017	0.017	0.000	0.000	0.000	0.000
53	A	61	GLY	0	0.002	-0.003	12.908	0.010	0.010	0.000	0.000	0.000	0.000
54	A	62	LYS	1	0.891	0.961	12.597	0.032	0.032	0.000	0.000	0.000	0.000
55	A	63	ALA	0	-0.002	0.008	7.734	0.022	0.022	0.000	0.000	0.000	0.000
56	A	64	GLU	-1	-0.893	-0.947	5.810	0.768	0.768	0.000	0.000	0.000	0.000
57	A	65	LYS	1	0.892	0.934	6.156	0.160	0.160	0.000	0.000	0.000	0.000
58	A	66	GLU	-1	-0.884	-0.947	2.005	-1.463	-0.616	1.612	-1.227	-1.233	0.004
59	A	67	GLU	-1	-0.709	-0.832	2.530	-3.755	-1.475	2.475	-2.832	-1.923	-0.024
60	A	68	VAL	0	-0.014	-0.010	3.330	-0.375	-0.704	0.021	0.260	0.048	0.000
61	A	69	GLN	0	-0.005	-0.002	5.542	-0.162	-0.162	0.000	0.000	0.000	0.000
62	A	70	ARG	1	0.881	0.961	3.148	1.479	1.895	0.069	-0.162	-0.322	0.000
63	A	71	ASN	0	0.011	0.007	5.083	0.238	0.256	-0.001	-0.002	-0.015	0.000
64	A	72	PHE	0	0.032	0.019	7.708	0.116	0.116	0.000	0.000	0.000	0.000
65	A	73	TYR	0	0.023	0.027	8.088	0.096	0.096	0.000	0.000	0.000	0.000
66	A	74	LEU	0	-0.025	-0.014	8.019	0.125	0.125	0.000	0.000	0.000	0.000
67	A	75	LEU	0	-0.003	0.010	10.709	0.103	0.103	0.000	0.000	0.000	0.000
68	A	76	LYS	1	0.864	0.918	13.068	0.344	0.344	0.000	0.000	0.000	0.000
69	A	77	THR	0	0.001	-0.010	12.607	0.068	0.068	0.000	0.000	0.000	0.000
70	A	78	TYR	0	-0.016	-0.025	14.695	0.052	0.052	0.000	0.000	0.000	0.000
71	A	79	VAL	0	-0.008	-0.006	16.583	0.040	0.040	0.000	0.000	0.000	0.000
72	A	80	VAL	0	-0.021	-0.010	18.505	0.026	0.026	0.000	0.000	0.000	0.000
73	A	81	SER	0	-0.029	-0.018	17.759	0.025	0.025	0.000	0.000	0.000	0.000
74	A	82	GLN	0	-0.082	-0.052	19.413	0.029	0.029	0.000	0.000	0.000	0.000
75	A	83	LEU	0	0.033	0.049	20.948	0.018	0.018	0.000	0.000	0.000	0.000
76	A	84	SER	0	0.028	0.006	22.403	0.017	0.017	0.000	0.000	0.000	0.000
77	A	85	ILE	0	-0.008	-0.007	23.968	0.011	0.011	0.000	0.000	0.000	0.000
78	A	86	HIS	0	-0.006	0.007	20.433	0.006	0.006	0.000	0.000	0.000	0.000
79	A	87	PHE	0	0.065	0.038	25.130	0.008	0.008	0.000	0.000	0.000	0.000
80	A	88	GLU	-1	-0.765	-0.867	27.472	-0.074	-0.074	0.000	0.000	0.000	0.000
81	A	89	ARG	1	0.947	0.982	23.878	0.135	0.135	0.000	0.000	0.000	0.000
82	A	90	LEU	0	0.009	0.007	27.173	0.006	0.006	0.000	0.000	0.000	0.000
83	A	91	LYS	1	0.802	0.893	29.698	0.074	0.074	0.000	0.000	0.000	0.000
84	A	92	GLU	-1	-0.913	-0.960	32.602	-0.068	-0.068	0.000	0.000	0.000	0.000
85	A	93	PHE	0	-0.035	-0.009	31.563	0.005	0.005	0.000	0.000	0.000	0.000
86	A	94	ALA	0	0.007	-0.003	33.463	0.005	0.005	0.000	0.000	0.000	0.000
87	A	95	GLU	-1	-0.748	-0.857	35.083	-0.058	-0.058	0.000	0.000	0.000	0.000
88	A	96	SER	0	-0.095	-0.055	36.444	0.004	0.004	0.000	0.000	0.000	0.000
89	A	97	LYS	1	0.775	0.859	35.609	0.057	0.057	0.000	0.000	0.000	0.000
90	A	98	GLY	0	0.013	0.029	39.830	0.002	0.002	0.000	0.000	0.000	0.000
91	A	99	PHE	0	0.014	-0.025	38.072	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	100	LYS	1	0.741	0.876	34.390	0.065	0.065	0.000	0.000	0.000	0.000
93	A	101	ILE	0	-0.002	-0.024	39.455	0.001	0.001	0.000	0.000	0.000	0.000
94	A	102	GLU	-1	-0.797	-0.886	36.849	-0.061	-0.061	0.000	0.000	0.000	0.000
95	A	103	LYS	1	0.819	0.954	33.667	0.066	0.066	0.000	0.000	0.000	0.000
96	A	104	LYS	1	0.819	0.888	29.997	0.093	0.093	0.000	0.000	0.000	0.000
97	A	105	LEU	0	-0.028	-0.005	25.715	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	106	ASP	-1	-0.819	-0.903	30.426	-0.079	-0.079	0.000	0.000	0.000	0.000
99	A	107	PRO	0	0.003	-0.023	28.376	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	108	GLU	-1	-0.921	-0.966	27.633	-0.090	-0.090	0.000	0.000	0.000	0.000
101	A	109	VAL	0	0.020	0.012	26.671	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	110	ILE	0	-0.005	-0.004	23.045	-0.008	-0.008	0.000	0.000	0.000	0.000
103	A	111	ASN	0	-0.030	-0.007	23.007	-0.022	-0.022	0.000	0.000	0.000	0.000
104	A	112	GLU	-1	-0.869	-0.939	23.470	-0.120	-0.120	0.000	0.000	0.000	0.000
105	A	113	ILE	0	-0.067	-0.021	19.789	-0.006	-0.006	0.000	0.000	0.000	0.000
106	A	114	ALA	0	0.026	0.006	18.963	-0.016	-0.016	0.000	0.000	0.000	0.000
107	A	115	LEU	0	-0.007	-0.004	19.022	-0.017	-0.017	0.000	0.000	0.000	0.000
108	A	116	TYR	0	-0.017	-0.015	19.383	0.005	0.005	0.000	0.000	0.000	0.000
109	A	117	ILE	0	0.050	0.013	14.432	0.003	0.003	0.000	0.000	0.000	0.000
110	A	118	ASP	-1	-0.808	-0.895	15.716	-0.266	-0.266	0.000	0.000	0.000	0.000
111	A	119	ARG	1	0.791	0.909	17.073	0.126	0.126	0.000	0.000	0.000	0.000
112	A	120	VAL	0	0.004	-0.002	15.312	0.003	0.003	0.000	0.000	0.000	0.000
113	A	121	GLU	-1	-0.852	-0.926	10.238	-0.507	-0.507	0.000	0.000	0.000	0.000
114	A	122	LYS	1	0.849	0.931	13.885	0.200	0.200	0.000	0.000	0.000	0.000
115	A	123	GLU	-1	-0.832	-0.900	15.948	-0.098	-0.098	0.000	0.000	0.000	0.000
116	A	124	VAL	0	-0.054	-0.014	9.444	0.047	0.047	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:9:GLY)