FMO DATABASE

FMODB ID: 98GV2

Calculation Name: 1Y2I-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y2I

Chain ID: A

ChEMBL ID:

UniProt ID: Q83LS2

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	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	109
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-714767.382055
FMO2-HF: Nuclear repulsion	673600.264018
FMO2-HF: Total energy	-41167.118038
FMO2-MP2: Total energy	-41286.06939

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.
-14.839	-10.658	25.364	-5.842	-23.703	-0.088

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 : -0.053 / q_NPA : 0.014

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	3	PHE	0	0.055	0.009	2.832	-5.389	-0.251	2.833	-2.678	-5.293	-0.016
4	A	4	SER	0	-0.031	-0.037	4.798	0.195	0.223	-0.001	-0.005	-0.022	0.000
5	A	5	THR	0	0.058	0.035	8.527	0.166	0.166	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.016	0.011	11.579	0.056	0.056	0.000	0.000	0.000	0.000
7	A	7	PRO	0	0.045	0.017	11.587	0.024	0.024	0.000	0.000	0.000	0.000
8	A	8	THR	0	-0.010	-0.007	12.833	0.070	0.070	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.015	0.015	7.782	-0.072	-0.072	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.894	-0.942	12.451	-0.160	-0.160	0.000	0.000	0.000	0.000
11	A	11	GLY	0	-0.061	-0.033	14.292	-0.054	-0.054	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.028	-0.010	9.236	0.016	0.016	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.028	-0.018	13.492	0.005	0.005	0.000	0.000	0.000	0.000
14	A	14	ILE	0	0.029	0.022	10.165	0.011	0.011	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.079	-0.054	11.324	-0.052	-0.052	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.795	-0.873	9.776	0.218	0.218	0.000	0.000	0.000	0.000
17	A	17	TYR	0	0.022	0.000	9.710	0.079	0.079	0.000	0.000	0.000	0.000
18	A	18	CYS	0	-0.045	-0.024	7.099	-0.055	-0.055	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.044	0.029	9.197	-0.056	-0.056	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.045	-0.022	9.454	0.126	0.126	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.035	-0.015	6.446	0.021	0.021	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.036	-0.062	9.799	-0.018	-0.018	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.011	0.011	9.191	0.038	0.038	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.878	-0.931	10.485	-0.027	-0.027	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.008	0.007	13.790	0.012	0.012	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.012	-0.020	16.238	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.032	0.004	20.048	0.005	0.005	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.047	0.008	22.215	0.007	0.007	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.053	0.005	25.489	-0.005	-0.005	0.000	0.000	0.000	0.000
30	A	30	ASN	0	-0.072	-0.025	27.556	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	31	ILE	0	0.078	0.042	24.025	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	32	PHE	0	0.053	0.033	26.433	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.933	0.958	28.328	0.038	0.038	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.913	-0.964	29.781	-0.053	-0.053	0.000	0.000	0.000	0.000
35	A	35	PHE	0	-0.048	-0.030	26.326	-0.004	-0.004	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.010	-0.020	23.385	-0.009	-0.009	0.000	0.000	0.000	0.000
37	A	37	ALA	0	-0.008	-0.001	29.697	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.025	0.027	33.139	0.004	0.004	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.088	-0.038	28.990	0.000	0.000	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.920	0.963	33.600	0.072	0.072	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.916	-0.958	34.933	-0.076	-0.076	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.017	0.007	31.248	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.011	0.018	29.229	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.054	0.045	26.975	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.056	0.006	23.293	0.004	0.004	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.945	0.961	23.053	0.202	0.202	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.006	0.012	24.748	0.001	0.001	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.044	0.022	27.102	0.008	0.008	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.001	-0.005	25.543	-0.013	-0.013	0.000	0.000	0.000	0.000
50	A	50	TYR	0	0.063	0.002	24.006	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.761	-0.831	18.899	-0.300	-0.300	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.764	0.883	20.069	0.129	0.129	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.813	-0.882	20.077	-0.130	-0.130	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.019	0.012	19.141	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.919	0.963	15.765	0.258	0.258	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.803	0.888	14.676	0.104	0.104	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.022	0.011	15.088	0.003	0.003	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.848	0.878	12.698	0.377	0.377	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.936	-0.959	9.478	-0.769	-0.769	0.000	0.000	0.000	0.000
60	A	60	ILE	0	0.009	0.005	9.846	-0.021	-0.021	0.000	0.000	0.000	0.000
61	A	61	ALA	0	0.038	0.034	10.341	0.035	0.035	0.000	0.000	0.000	0.000
62	A	62	PHE	0	0.014	-0.012	5.816	0.087	0.087	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.988	-0.989	5.346	-0.096	-0.096	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.916	-0.940	6.464	0.184	0.184	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.046	0.048	5.173	0.071	0.071	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.004	-0.013	2.181	-0.340	-0.052	1.906	-1.155	-1.040	-0.001
67	A	67	SER	0	-0.134	-0.080	2.720	-1.511	-0.661	0.480	0.154	-1.483	-0.018
68	A	68	GLN	0	0.048	0.025	5.468	-0.006	-0.006	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.037	0.011	2.373	-0.309	-0.394	2.328	-0.615	-1.628	-0.001
70	A	70	ARG	1	0.927	0.955	2.239	-5.972	-4.160	2.325	-0.990	-3.147	0.001
71	A	71	ALA	0	-0.028	-0.001	3.624	0.278	0.296	0.033	0.099	-0.150	0.000
72	A	72	LEU	0	-0.036	-0.006	5.812	0.071	0.071	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.040	-0.020	6.021	0.061	0.061	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.039	-0.019	2.521	-0.186	0.320	0.296	-0.143	-0.659	0.000
75	A	75	ASP	-1	-0.860	-0.903	2.551	-1.896	-0.637	1.984	-1.080	-2.164	-0.013
76	A	76	ALA	0	0.002	-0.022	2.430	-1.596	-1.870	8.045	-3.279	-4.492	-0.028
77	A	77	VAL	0	0.026	0.005	2.769	3.639	-1.868	5.134	3.877	-3.503	-0.012
78	A	78	VAL	0	-0.043	-0.022	4.804	-1.328	-1.323	0.002	-0.021	0.014	0.000
79	A	79	GLY	0	-0.013	-0.014	8.451	0.094	0.094	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.089	-0.040	5.765	-0.018	-0.018	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.856	-0.928	10.343	-0.181	-0.181	0.000	0.000	0.000	0.000
82	A	82	ILE	0	-0.095	-0.062	11.299	-0.021	-0.021	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.896	-0.934	14.271	-0.096	-0.096	0.000	0.000	0.000	0.000
84	A	84	TYR	0	-0.025	-0.032	17.292	-0.027	-0.027	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.784	-0.867	19.054	-0.076	-0.076	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.037	-0.021	22.655	0.001	0.001	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.005	0.003	24.474	0.008	0.008	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.021	0.001	27.151	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	89	GLN	0	-0.034	-0.039	30.066	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	90	ASN	0	-0.013	-0.002	32.840	0.001	0.001	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.026	0.032	30.464	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.030	-0.031	29.747	-0.006	-0.006	0.000	0.000	0.000	0.000
93	A	93	MET	0	-0.053	-0.030	25.292	0.004	0.004	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.023	0.001	21.553	0.001	0.001	0.000	0.000	0.000	0.000
95	A	95	MET	0	-0.026	0.007	18.496	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.030	-0.028	14.772	-0.015	-0.015	0.000	0.000	0.000	0.000
97	A	97	SER	0	0.025	-0.004	14.467	0.002	0.002	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.048	-0.018	9.118	-0.044	-0.044	0.000	0.000	0.000	0.000
99	A	99	SER	0	-0.002	0.009	10.453	0.073	0.073	0.000	0.000	0.000	0.000
100	A	100	GLY	0	0.078	0.032	9.116	-0.108	-0.108	0.000	0.000	0.000	0.000
101	A	101	THR	0	-0.056	-0.019	9.258	0.024	0.024	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.035	0.026	4.939	0.335	0.335	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.044	-0.035	5.263	-0.634	-0.634	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.867	0.940	5.190	-0.156	-0.013	-0.001	-0.006	-0.136	0.000
105	A	105	THR	0	-0.077	-0.071	7.105	-0.247	-0.247	0.000	0.000	0.000	0.000
106	A	106	ARG	1	0.945	0.964	9.662	-0.090	-0.090	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.974	0.992	12.194	0.167	0.167	0.000	0.000	0.000	0.000
108	A	108	ASN	0	-0.041	-0.014	13.484	0.049	0.049	0.000	0.000	0.000	0.000
109	A	109	ILE	0	-0.001	0.003	16.226	-0.010	-0.010	0.000	0.000	0.000	0.000

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