FMO DATABASE

FMODB ID: N3RQQ

Calculation Name: 1Y96-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y96

Chain ID: A

ChEMBL ID:

UniProt ID: Q8WXD5

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	86
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-597045.299716
FMO2-HF: Nuclear repulsion	561290.020165
FMO2-HF: Total energy	-35755.279551
FMO2-MP2: Total energy	-35856.155318

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:1:MET )

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

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.
-2.989	2.505	2.767	-2.343	-5.918	-0.005

Interaction energy analysis for fragmet #1(A:1:MET )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / 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	3	GLU	-1	-0.904	-0.971	3.459	-4.249	-2.328	0.015	-0.931	-1.006	-0.001
4	A	4	TRP	0	0.002	0.002	6.176	-0.160	-0.160	0.000	0.000	0.000	0.000
5	A	5	MET	0	-0.002	-0.017	2.280	-1.577	-0.004	1.269	-0.656	-2.186	-0.005
6	A	6	LYS	1	0.882	0.950	2.240	2.917	4.711	1.475	-0.724	-2.545	0.001
7	A	7	LYS	1	0.940	1.001	3.819	1.503	1.709	0.008	-0.032	-0.181	0.000
8	A	8	GLY	0	0.033	0.033	7.378	0.029	0.029	0.000	0.000	0.000	0.000
9	A	9	PRO	0	0.031	-0.014	9.398	0.116	0.116	0.000	0.000	0.000	0.000
10	A	10	LEU	0	-0.006	-0.008	11.811	0.070	0.070	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.900	-0.944	10.970	-1.084	-1.084	0.000	0.000	0.000	0.000
12	A	12	TRP	0	-0.024	-0.017	6.769	0.145	0.145	0.000	0.000	0.000	0.000
13	A	13	GLN	0	-0.016	-0.013	13.129	0.064	0.064	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.884	-0.932	16.500	-0.379	-0.379	0.000	0.000	0.000	0.000
15	A	15	TYR	0	-0.059	-0.040	13.201	-0.019	-0.019	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.010	0.001	17.959	0.040	0.040	0.000	0.000	0.000	0.000
17	A	17	TYR	0	-0.040	-0.040	20.063	0.009	0.009	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.893	0.976	20.341	0.351	0.351	0.000	0.000	0.000	0.000
19	A	19	GLU	-1	-0.951	-0.978	21.723	-0.141	-0.141	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.002	-0.006	17.131	-0.021	-0.021	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.948	0.971	19.257	0.225	0.225	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.008	-0.010	13.677	-0.053	-0.053	0.000	0.000	0.000	0.000
23	A	23	THR	0	0.017	0.020	15.011	0.051	0.051	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.019	-0.004	12.951	-0.074	-0.074	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.014	-0.021	11.624	0.011	0.011	0.000	0.000	0.000	0.000
26	A	26	GLU	-1	-0.980	-0.989	13.808	0.237	0.237	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.911	0.953	16.854	-0.083	-0.083	0.000	0.000	0.000	0.000
28	A	28	ASN	0	-0.005	0.022	17.404	-0.022	-0.022	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.922	-0.967	17.659	-0.127	-0.127	0.000	0.000	0.000	0.000
30	A	30	TYR	0	-0.005	-0.004	16.930	0.025	0.025	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.963	0.979	20.018	0.097	0.097	0.000	0.000	0.000	0.000
32	A	32	GLY	0	0.020	0.031	21.535	0.026	0.026	0.000	0.000	0.000	0.000
33	A	33	TRP	0	0.001	0.002	21.611	-0.030	-0.030	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.010	0.003	17.032	0.016	0.016	0.000	0.000	0.000	0.000
35	A	35	LEU	0	0.030	0.028	19.927	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	36	THR	0	0.006	-0.012	16.764	-0.023	-0.023	0.000	0.000	0.000	0.000
37	A	37	THR	0	0.005	-0.005	11.029	-0.016	-0.016	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.819	-0.886	12.670	0.041	0.041	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.020	-0.008	9.965	-0.006	-0.006	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.052	-0.007	8.694	-0.031	-0.031	0.000	0.000	0.000	0.000
41	A	41	SER	0	-0.069	-0.064	8.111	0.233	0.233	0.000	0.000	0.000	0.000
42	A	42	ALA	0	0.028	0.008	6.962	0.085	0.085	0.000	0.000	0.000	0.000
43	A	43	ASN	0	0.028	0.007	8.921	-0.066	-0.066	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.009	0.012	11.348	-0.052	-0.052	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.009	0.004	14.011	0.056	0.056	0.000	0.000	0.000	0.000
46	A	46	LEU	0	-0.033	-0.018	17.713	-0.031	-0.031	0.000	0.000	0.000	0.000
47	A	47	VAL	0	0.037	0.023	20.290	0.026	0.026	0.000	0.000	0.000	0.000
48	A	48	ASN	0	-0.055	-0.054	23.910	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	49	PHE	0	-0.003	-0.010	26.437	0.010	0.010	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.007	0.001	27.956	-0.004	-0.004	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.928	-0.975	31.431	-0.032	-0.032	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.899	-0.929	34.541	-0.019	-0.019	0.000	0.000	0.000	0.000
53	A	53	GLY	0	-0.051	-0.020	35.393	0.002	0.002	0.000	0.000	0.000	0.000
54	A	54	SER	0	-0.087	-0.038	33.193	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	55	MET	0	-0.005	-0.019	28.509	-0.009	-0.009	0.000	0.000	0.000	0.000
56	A	56	SER	0	-0.013	0.003	26.070	0.005	0.005	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.029	0.004	22.167	-0.014	-0.014	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.008	-0.002	19.027	0.026	0.026	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.007	0.014	17.129	-0.028	-0.028	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.026	-0.009	12.797	0.035	0.035	0.000	0.000	0.000	0.000
61	A	61	MET	0	0.012	-0.006	11.074	-0.037	-0.037	0.000	0.000	0.000	0.000
62	A	62	GLY	0	0.072	0.042	8.055	-0.049	-0.049	0.000	0.000	0.000	0.000
63	A	63	HIS	0	-0.024	-0.037	6.020	-0.244	-0.244	0.000	0.000	0.000	0.000
64	A	64	ALA	0	-0.071	-0.026	7.055	0.026	0.026	0.000	0.000	0.000	0.000
65	A	65	VAL	0	-0.001	0.015	8.565	-0.027	-0.027	0.000	0.000	0.000	0.000
66	A	66	GLN	0	-0.068	-0.032	8.399	-0.185	-0.185	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.011	-0.013	10.458	-0.168	-0.168	0.000	0.000	0.000	0.000
68	A	68	VAL	0	0.034	0.015	11.877	0.079	0.079	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.927	-0.957	14.400	-0.319	-0.319	0.000	0.000	0.000	0.000
70	A	70	THR	0	-0.017	-0.020	17.813	0.027	0.027	0.000	0.000	0.000	0.000
71	A	71	MET	0	-0.056	-0.014	20.400	0.009	0.009	0.000	0.000	0.000	0.000
72	A	72	ASN	0	-0.006	-0.015	23.814	0.017	0.017	0.000	0.000	0.000	0.000
73	A	73	GLU	-1	-0.862	-0.934	24.022	-0.283	-0.283	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.023	0.019	26.173	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	75	ASP	-1	-0.918	-0.969	28.304	-0.117	-0.117	0.000	0.000	0.000	0.000
76	A	76	HIS	0	-0.002	-0.018	30.909	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.952	0.972	32.962	0.084	0.084	0.000	0.000	0.000	0.000
78	A	78	VAL	0	0.005	0.009	28.719	0.007	0.007	0.000	0.000	0.000	0.000
79	A	79	ARG	1	0.951	0.987	26.078	0.181	0.181	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.894	-0.952	29.298	-0.101	-0.101	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.878	0.940	31.334	0.085	0.085	0.000	0.000	0.000	0.000
82	A	82	LEU	0	-0.015	-0.011	25.172	0.005	0.005	0.000	0.000	0.000	0.000
83	A	83	MET	0	-0.028	-0.004	27.341	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	84	HIS	0	-0.035	-0.014	28.656	0.004	0.004	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.082	-0.028	26.279	0.010	0.010	0.000	0.000	0.000	0.000
86	A	86	PHE	-1	-0.948	-0.961	24.293	-0.065	-0.065	0.000	0.000	0.000	0.000

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