FMO DATABASE

FMODB ID: 1NL4Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-546986.711837
FMO2-HF: Nuclear repulsion	513658.758386
FMO2-HF: Total energy	-33327.953451
FMO2-MP2: Total energy	-33426.744498

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.
-7.02	0.156	4.908	-4.362	-7.722	-0.018

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 : -0.024 / q_NPA : -0.021

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	0.004	-0.002	3.254	-2.460	-0.063	0.065	-1.134	-1.329	0.002
4	A	10	PHE	0	0.077	0.032	2.593	-0.891	-0.235	1.563	-0.653	-1.567	-0.009
5	A	11	GLU	-1	-0.922	-0.966	4.730	0.111	0.220	-0.001	-0.006	-0.101	0.000
6	A	12	ASP	-1	-0.783	-0.865	2.438	1.539	3.386	1.875	-1.754	-1.968	-0.009
7	A	13	LEU	0	0.048	0.032	2.523	-1.950	-0.110	1.390	-0.780	-2.449	-0.002
8	A	14	PHE	0	0.027	0.022	3.872	-0.043	0.118	0.017	-0.029	-0.150	0.000
9	A	15	ALA	0	-0.020	-0.016	6.823	0.032	0.032	0.000	0.000	0.000	0.000
10	A	16	GLU	-1	-0.856	-0.910	4.762	-0.355	-0.189	-0.001	-0.006	-0.158	0.000
11	A	17	LEU	0	-0.024	-0.011	6.904	0.003	0.003	0.000	0.000	0.000	0.000
12	A	18	GLY	0	0.023	0.005	9.061	0.022	0.022	0.000	0.000	0.000	0.000
13	A	19	ASP	-1	-0.842	-0.909	10.048	0.267	0.267	0.000	0.000	0.000	0.000
14	A	20	ARG	1	0.795	0.881	8.032	-0.153	-0.153	0.000	0.000	0.000	0.000
15	A	21	ALA	0	0.005	0.007	12.388	-0.009	-0.009	0.000	0.000	0.000	0.000
16	A	22	ARG	1	0.796	0.899	12.408	-0.213	-0.213	0.000	0.000	0.000	0.000
17	A	23	THR	0	-0.048	-0.049	13.459	-0.026	-0.026	0.000	0.000	0.000	0.000
18	A	24	ARG	1	0.757	0.854	15.931	0.047	0.047	0.000	0.000	0.000	0.000
19	A	25	PRO	0	0.012	0.014	13.490	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	26	ALA	0	-0.011	-0.033	16.072	-0.027	-0.027	0.000	0.000	0.000	0.000
21	A	27	ASP	-1	-0.938	-0.954	12.402	-0.197	-0.197	0.000	0.000	0.000	0.000
22	A	28	SER	0	0.017	0.014	10.948	-0.044	-0.044	0.000	0.000	0.000	0.000
23	A	29	THR	0	0.062	0.024	12.212	0.026	0.026	0.000	0.000	0.000	0.000
24	A	30	THR	0	0.040	0.021	10.479	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	31	VAL	0	-0.034	0.000	13.096	0.026	0.026	0.000	0.000	0.000	0.000
26	A	32	ALA	0	0.047	0.019	16.311	0.009	0.009	0.000	0.000	0.000	0.000
27	A	33	ALA	0	-0.010	0.003	15.103	0.008	0.008	0.000	0.000	0.000	0.000
28	A	34	LEU	0	-0.044	-0.023	14.684	0.009	0.009	0.000	0.000	0.000	0.000
29	A	35	ASP	-1	-0.830	-0.874	18.068	-0.068	-0.068	0.000	0.000	0.000	0.000
30	A	36	GLY	0	-0.025	-0.001	20.488	0.010	0.010	0.000	0.000	0.000	0.000
31	A	37	GLY	0	-0.008	0.004	21.323	0.003	0.003	0.000	0.000	0.000	0.000
32	A	38	VAL	0	0.024	-0.011	21.008	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	39	HIS	0	0.007	0.004	21.790	-0.015	-0.015	0.000	0.000	0.000	0.000
34	A	40	ALA	0	0.019	0.012	21.334	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	41	LEU	0	0.038	0.022	16.014	-0.017	-0.017	0.000	0.000	0.000	0.000
36	A	42	GLY	0	0.004	0.003	18.213	-0.024	-0.024	0.000	0.000	0.000	0.000
37	A	43	LYS	1	0.867	0.932	20.393	0.145	0.145	0.000	0.000	0.000	0.000
38	A	44	LYS	1	0.835	0.905	15.601	0.372	0.372	0.000	0.000	0.000	0.000
39	A	45	LEU	0	0.008	0.002	14.313	-0.018	-0.018	0.000	0.000	0.000	0.000
40	A	46	LEU	0	-0.049	-0.024	17.217	-0.009	-0.009	0.000	0.000	0.000	0.000
41	A	47	GLU	-1	-0.874	-0.926	19.533	-0.281	-0.281	0.000	0.000	0.000	0.000
42	A	48	GLU	-1	-0.776	-0.899	13.645	-0.518	-0.518	0.000	0.000	0.000	0.000
43	A	49	ALA	0	-0.037	-0.017	16.789	-0.017	-0.017	0.000	0.000	0.000	0.000
44	A	50	GLY	0	-0.035	-0.009	18.101	0.009	0.009	0.000	0.000	0.000	0.000
45	A	51	GLU	-1	-0.856	-0.932	17.653	-0.274	-0.274	0.000	0.000	0.000	0.000
46	A	52	VAL	0	-0.015	-0.011	14.069	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	53	TRP	0	-0.153	-0.076	16.997	0.016	0.016	0.000	0.000	0.000	0.000
48	A	54	LEU	0	0.015	-0.004	20.482	0.015	0.015	0.000	0.000	0.000	0.000
49	A	55	ALA	0	0.026	0.006	17.574	0.012	0.012	0.000	0.000	0.000	0.000
50	A	56	ALA	0	-0.051	-0.033	18.653	0.003	0.003	0.000	0.000	0.000	0.000
51	A	57	GLU	-1	-0.954	-0.955	20.082	-0.179	-0.179	0.000	0.000	0.000	0.000
52	A	58	HIS	0	-0.095	-0.054	23.050	0.015	0.015	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.912	-0.934	20.213	-0.248	-0.248	0.000	0.000	0.000	0.000
54	A	60	SER	0	-0.034	-0.011	18.653	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	61	ASN	0	-0.005	-0.026	16.413	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	62	ASP	-1	-0.967	-0.973	13.903	-0.564	-0.564	0.000	0.000	0.000	0.000
57	A	63	ALA	0	0.074	0.040	13.610	-0.078	-0.078	0.000	0.000	0.000	0.000
58	A	64	LEU	0	0.015	0.006	14.585	-0.046	-0.046	0.000	0.000	0.000	0.000
59	A	65	ALA	0	-0.047	-0.026	10.473	-0.047	-0.047	0.000	0.000	0.000	0.000
60	A	66	GLU	-1	-0.859	-0.906	9.871	-1.110	-1.110	0.000	0.000	0.000	0.000
61	A	67	GLU	-1	-0.848	-0.923	10.520	-0.587	-0.587	0.000	0.000	0.000	0.000
62	A	68	ILE	0	-0.041	-0.027	9.330	-0.008	-0.008	0.000	0.000	0.000	0.000
63	A	69	SER	0	-0.096	-0.056	6.107	-0.111	-0.111	0.000	0.000	0.000	0.000
64	A	70	GLN	0	-0.014	-0.009	7.443	-0.062	-0.062	0.000	0.000	0.000	0.000
65	A	71	LEU	0	0.043	0.023	10.036	0.049	0.049	0.000	0.000	0.000	0.000
66	A	72	LEU	0	-0.056	-0.017	6.896	0.083	0.083	0.000	0.000	0.000	0.000
67	A	73	TYR	0	0.024	-0.011	6.968	0.095	0.095	0.000	0.000	0.000	0.000
68	A	74	TRP	0	0.024	-0.002	8.208	0.181	0.181	0.000	0.000	0.000	0.000
69	A	75	THR	0	-0.060	-0.045	10.708	0.110	0.110	0.000	0.000	0.000	0.000
70	A	76	GLN	0	-0.037	-0.031	5.558	0.053	0.053	0.000	0.000	0.000	0.000
71	A	77	VAL	0	0.009	0.009	10.665	0.095	0.095	0.000	0.000	0.000	0.000
72	A	78	LEU	0	-0.008	0.000	13.076	0.067	0.067	0.000	0.000	0.000	0.000
73	A	79	MET	0	-0.068	-0.033	12.542	0.021	0.021	0.000	0.000	0.000	0.000
74	A	80	ILE	0	0.014	0.016	11.097	0.044	0.044	0.000	0.000	0.000	0.000
75	A	81	SER	0	-0.036	-0.010	15.330	0.031	0.031	0.000	0.000	0.000	0.000
76	A	82	ARG	1	0.859	0.924	18.117	0.131	0.131	0.000	0.000	0.000	0.000
77	A	83	GLY	0	-0.010	0.004	18.493	0.013	0.013	0.000	0.000	0.000	0.000
78	A	84	LEU	0	-0.085	-0.030	16.314	0.017	0.017	0.000	0.000	0.000	0.000
79	A	85	SER	0	0.009	-0.032	14.725	-0.007	-0.007	0.000	0.000	0.000	0.000
80	A	86	LEU	0	0.040	0.010	8.845	-0.033	-0.033	0.000	0.000	0.000	0.000
81	A	87	ASP	-1	-0.859	-0.924	12.874	-0.006	-0.006	0.000	0.000	0.000	0.000
82	A	88	ASP	-1	-0.833	-0.881	16.134	-0.056	-0.056	0.000	0.000	0.000	0.000
83	A	89	VAL	0	-0.010	-0.006	14.178	-0.004	-0.004	0.000	0.000	0.000	0.000
84	A	90	TYR	0	0.068	0.010	9.172	-0.044	-0.044	0.000	0.000	0.000	0.000
85	A	91	ARG	1	0.796	0.887	15.713	0.043	0.043	0.000	0.000	0.000	0.000
86	A	92	LYS	1	0.856	0.936	18.644	0.113	0.113	0.000	0.000	0.000	0.000
87	A	93	LEU	0	-0.018	0.016	14.175	-0.008	-0.008	0.000	0.000	0.000	0.000

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