FMO DATABASE

FMODB ID: VQGR1

Calculation Name: 1Y6X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y6X

Chain ID: A

ChEMBL ID:

UniProt ID: P9WMM9

Base Structure: X-ray

Registration Date: 2023-09-23

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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-545482.699028
FMO2-HF: Nuclear repulsion	512154.809196
FMO2-HF: Total energy	-33327.889832
FMO2-MP2: Total energy	-33426.704595

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:7:VAL)

Summations of interaction energy for fragment #1(A:7:VAL)

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.
-8.144	-0.671	3.674	-3.855	-7.293	-0.012

Interaction energy analysis for fragmet #1(A:7:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.023 / q_NPA : -0.018

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

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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	9	THR	0	0.009	0.001	3.255	-2.858	0.035	0.072	-1.365	-1.600	0.002
4	A	10	PHE	0	0.071	0.028	2.676	-0.992	-0.067	1.028	-0.602	-1.352	-0.008
5	A	11	GLU	-1	-0.915	-0.974	4.762	-0.026	0.081	-0.001	-0.007	-0.099	0.000
6	A	12	ASP	-1	-0.794	-0.861	2.211	0.799	2.069	1.470	-1.125	-1.615	-0.003
7	A	13	LEU	0	0.040	0.024	2.612	-1.909	0.008	1.089	-0.719	-2.287	-0.003
8	A	14	PHE	0	0.026	0.016	3.886	0.015	0.169	0.017	-0.024	-0.147	0.000
9	A	15	ALA	0	-0.021	-0.018	6.799	0.046	0.046	0.000	0.000	0.000	0.000
10	A	16	GLU	-1	-0.862	-0.917	4.449	-0.404	-0.197	-0.001	-0.013	-0.193	0.000
11	A	17	LEU	0	0.000	-0.001	6.857	0.027	0.027	0.000	0.000	0.000	0.000
12	A	18	GLY	0	0.026	0.010	9.082	0.028	0.028	0.000	0.000	0.000	0.000
13	A	19	ASP	-1	-0.877	-0.950	10.163	0.273	0.273	0.000	0.000	0.000	0.000
14	A	20	ARG	1	0.814	0.907	7.763	-0.161	-0.161	0.000	0.000	0.000	0.000
15	A	21	ALA	0	0.000	0.006	12.375	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	22	ARG	1	0.811	0.911	12.465	-0.173	-0.173	0.000	0.000	0.000	0.000
17	A	23	THR	0	-0.038	-0.031	14.141	-0.011	-0.011	0.000	0.000	0.000	0.000
18	A	24	ARG	1	0.746	0.842	16.094	0.049	0.049	0.000	0.000	0.000	0.000
19	A	25	PRO	0	0.002	0.012	13.512	0.002	0.002	0.000	0.000	0.000	0.000
20	A	26	ALA	0	-0.010	-0.033	16.722	-0.026	-0.026	0.000	0.000	0.000	0.000
21	A	27	ASP	-1	-0.940	-0.967	12.698	-0.148	-0.148	0.000	0.000	0.000	0.000
22	A	28	SER	0	-0.004	0.018	11.537	-0.048	-0.048	0.000	0.000	0.000	0.000
23	A	29	THR	0	0.071	0.024	11.991	0.023	0.023	0.000	0.000	0.000	0.000
24	A	30	THR	0	0.031	0.013	10.393	-0.011	-0.011	0.000	0.000	0.000	0.000
25	A	31	VAL	0	-0.011	0.013	13.210	0.022	0.022	0.000	0.000	0.000	0.000
26	A	32	ALA	0	0.041	0.025	16.376	0.011	0.011	0.000	0.000	0.000	0.000
27	A	33	ALA	0	-0.004	-0.001	15.367	0.010	0.010	0.000	0.000	0.000	0.000
28	A	34	LEU	0	-0.060	-0.032	14.798	0.010	0.010	0.000	0.000	0.000	0.000
29	A	35	ASP	-1	-0.826	-0.868	18.193	-0.068	-0.068	0.000	0.000	0.000	0.000
30	A	36	GLY	0	-0.023	0.003	20.592	0.011	0.011	0.000	0.000	0.000	0.000
31	A	37	GLY	0	-0.017	0.002	21.698	0.004	0.004	0.000	0.000	0.000	0.000
32	A	38	VAL	0	0.034	-0.006	21.023	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	39	HIS	0	0.001	-0.002	21.929	-0.016	-0.016	0.000	0.000	0.000	0.000
34	A	40	ALA	0	0.029	0.005	21.734	-0.007	-0.007	0.000	0.000	0.000	0.000
35	A	41	LEU	0	0.052	0.034	16.257	-0.017	-0.017	0.000	0.000	0.000	0.000
36	A	42	GLY	0	-0.013	-0.004	18.471	-0.025	-0.025	0.000	0.000	0.000	0.000
37	A	43	LYS	1	0.873	0.932	20.657	0.151	0.151	0.000	0.000	0.000	0.000
38	A	44	LYS	1	0.826	0.901	15.681	0.375	0.375	0.000	0.000	0.000	0.000
39	A	45	LEU	0	0.014	0.013	14.572	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	46	LEU	0	-0.046	-0.024	17.244	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	47	GLU	-1	-0.871	-0.929	19.516	-0.290	-0.290	0.000	0.000	0.000	0.000
42	A	48	GLU	-1	-0.775	-0.885	14.701	-0.501	-0.501	0.000	0.000	0.000	0.000
43	A	49	ALA	0	-0.039	-0.013	17.015	-0.017	-0.017	0.000	0.000	0.000	0.000
44	A	50	GLY	0	-0.041	-0.017	18.218	0.008	0.008	0.000	0.000	0.000	0.000
45	A	51	GLU	-1	-0.854	-0.934	17.695	-0.284	-0.284	0.000	0.000	0.000	0.000
46	A	52	VAL	0	-0.027	-0.016	14.545	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	53	TRP	0	-0.163	-0.081	17.456	0.018	0.018	0.000	0.000	0.000	0.000
48	A	54	LEU	0	0.019	0.000	20.930	0.017	0.017	0.000	0.000	0.000	0.000
49	A	55	ALA	0	0.049	0.018	17.945	0.013	0.013	0.000	0.000	0.000	0.000
50	A	56	ALA	0	-0.072	-0.039	19.017	0.005	0.005	0.000	0.000	0.000	0.000
51	A	57	GLU	-1	-0.948	-0.958	20.320	-0.185	-0.185	0.000	0.000	0.000	0.000
52	A	58	HIS	0	-0.090	-0.050	23.202	0.016	0.016	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.935	-0.940	20.286	-0.242	-0.242	0.000	0.000	0.000	0.000
54	A	60	SER	0	-0.034	-0.013	18.704	-0.014	-0.014	0.000	0.000	0.000	0.000
55	A	61	ASN	0	0.013	-0.019	16.234	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	62	ASP	-1	-0.970	-0.980	13.613	-0.580	-0.580	0.000	0.000	0.000	0.000
57	A	63	ALA	0	0.071	0.043	13.791	-0.073	-0.073	0.000	0.000	0.000	0.000
58	A	64	LEU	0	0.027	0.016	15.060	-0.039	-0.039	0.000	0.000	0.000	0.000
59	A	65	ALA	0	-0.058	-0.035	10.555	-0.053	-0.053	0.000	0.000	0.000	0.000
60	A	66	GLU	-1	-0.858	-0.914	10.397	-1.085	-1.085	0.000	0.000	0.000	0.000
61	A	67	GLU	-1	-0.834	-0.914	11.284	-0.576	-0.576	0.000	0.000	0.000	0.000
62	A	68	ILE	0	-0.044	-0.032	9.597	-0.019	-0.019	0.000	0.000	0.000	0.000
63	A	69	SER	0	-0.093	-0.050	6.728	-0.109	-0.109	0.000	0.000	0.000	0.000
64	A	70	GLN	0	0.013	0.005	7.919	-0.078	-0.078	0.000	0.000	0.000	0.000
65	A	71	LEU	0	0.010	0.010	10.526	0.062	0.062	0.000	0.000	0.000	0.000
66	A	72	LEU	0	-0.058	-0.023	6.793	0.067	0.067	0.000	0.000	0.000	0.000
67	A	73	TYR	0	0.021	-0.007	7.106	0.086	0.086	0.000	0.000	0.000	0.000
68	A	74	TRP	0	0.052	0.005	8.527	0.169	0.169	0.000	0.000	0.000	0.000
69	A	75	THR	0	-0.061	-0.042	10.944	0.112	0.112	0.000	0.000	0.000	0.000
70	A	76	GLN	0	-0.034	-0.030	5.738	0.072	0.072	0.000	0.000	0.000	0.000
71	A	77	VAL	0	0.009	0.013	10.663	0.101	0.101	0.000	0.000	0.000	0.000
72	A	78	LEU	0	-0.016	-0.002	12.890	0.072	0.072	0.000	0.000	0.000	0.000
73	A	79	MET	0	-0.069	-0.030	12.604	0.023	0.023	0.000	0.000	0.000	0.000
74	A	80	ILE	0	0.013	0.012	11.087	0.047	0.047	0.000	0.000	0.000	0.000
75	A	81	SER	0	-0.047	-0.012	15.422	0.035	0.035	0.000	0.000	0.000	0.000
76	A	82	ARG	1	0.874	0.927	18.358	0.150	0.150	0.000	0.000	0.000	0.000
77	A	83	GLY	0	-0.009	0.009	18.572	0.015	0.015	0.000	0.000	0.000	0.000
78	A	84	LEU	0	-0.079	-0.029	16.433	0.015	0.015	0.000	0.000	0.000	0.000
79	A	85	SER	0	-0.002	-0.034	14.715	-0.006	-0.006	0.000	0.000	0.000	0.000
80	A	86	LEU	0	0.038	0.004	8.792	-0.030	-0.030	0.000	0.000	0.000	0.000
81	A	87	ASP	-1	-0.871	-0.927	12.846	-0.041	-0.041	0.000	0.000	0.000	0.000
82	A	88	ASP	-1	-0.851	-0.897	16.002	-0.082	-0.082	0.000	0.000	0.000	0.000
83	A	89	VAL	0	-0.017	-0.011	14.076	0.001	0.001	0.000	0.000	0.000	0.000
84	A	90	TYR	0	0.049	0.002	8.937	-0.044	-0.044	0.000	0.000	0.000	0.000
85	A	91	ARG	1	0.838	0.914	15.700	0.072	0.072	0.000	0.000	0.000	0.000
86	A	92	LYS	1	0.871	0.943	18.752	0.132	0.132	0.000	0.000	0.000	0.000
87	A	93	LEU	0	-0.018	0.017	14.284	-0.004	-0.004	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:VAL)