FMO DATABASE

FMODB ID: 3JQVL

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	OptH
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	-713730.3543
FMO2-HF: Nuclear repulsion	672564.194293
FMO2-HF: Total energy	-41166.160007
FMO2-MP2: Total energy	-41285.151912

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.
-13.518	-5.97	17.632	-6.211	-18.971	-0.075

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 : -0.073 / 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

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	0.036	0.013	2.646	-3.590	-0.492	3.417	-1.844	-4.671	-0.010
4	A	4	SER	0	-0.026	-0.023	4.951	0.190	0.215	-0.001	-0.003	-0.021	0.000
5	A	5	THR	0	0.057	0.031	8.603	0.098	0.098	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.030	-0.006	11.704	0.021	0.021	0.000	0.000	0.000	0.000
7	A	7	PRO	0	0.064	0.024	11.849	0.056	0.056	0.000	0.000	0.000	0.000
8	A	8	THR	0	0.002	-0.009	12.751	0.049	0.049	0.000	0.000	0.000	0.000
9	A	9	LEU	0	0.032	0.016	7.880	-0.023	-0.023	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.872	-0.936	12.397	0.249	0.249	0.000	0.000	0.000	0.000
11	A	11	GLY	0	-0.091	-0.035	14.019	0.043	0.043	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.027	-0.031	8.948	0.024	0.024	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.029	-0.024	13.079	-0.102	-0.102	0.000	0.000	0.000	0.000
14	A	14	ILE	0	0.030	0.018	10.323	0.076	0.076	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.091	-0.052	11.432	-0.076	-0.076	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.897	-0.962	10.391	-0.087	-0.087	0.000	0.000	0.000	0.000
17	A	17	TYR	0	0.000	0.005	9.831	0.069	0.069	0.000	0.000	0.000	0.000
18	A	18	CYS	0	-0.028	-0.024	7.534	-0.064	-0.064	0.000	0.000	0.000	0.000
19	A	19	GLY	0	0.031	0.027	9.642	-0.063	-0.063	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.024	-0.019	9.637	0.080	0.080	0.000	0.000	0.000	0.000
21	A	21	VAL	0	-0.032	-0.006	6.483	-0.048	-0.048	0.000	0.000	0.000	0.000
22	A	22	THR	0	-0.013	-0.044	9.808	0.040	0.040	0.000	0.000	0.000	0.000
23	A	23	GLY	0	0.008	0.010	10.030	-0.048	-0.048	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.938	-0.972	10.929	-0.148	-0.148	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.009	0.002	14.003	-0.024	-0.024	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.011	-0.003	16.364	0.021	0.021	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.033	-0.001	20.096	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.040	0.003	22.262	0.012	0.012	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.060	0.005	25.640	0.002	0.002	0.000	0.000	0.000	0.000
30	A	30	ASN	0	-0.056	-0.029	27.600	0.001	0.001	0.000	0.000	0.000	0.000
31	A	31	ILE	0	0.068	0.052	23.932	0.005	0.005	0.000	0.000	0.000	0.000
32	A	32	PHE	0	0.063	0.028	26.487	0.003	0.003	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.911	0.934	28.499	0.087	0.087	0.000	0.000	0.000	0.000
34	A	34	ASP	-1	-0.914	-0.943	29.655	-0.088	-0.088	0.000	0.000	0.000	0.000
35	A	35	PHE	0	-0.070	-0.041	27.123	0.002	0.002	0.000	0.000	0.000	0.000
36	A	36	PHE	0	-0.015	-0.017	23.391	0.000	0.000	0.000	0.000	0.000	0.000
37	A	37	ALA	0	0.000	-0.006	29.597	0.006	0.006	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.000	0.010	33.157	0.005	0.005	0.000	0.000	0.000	0.000
39	A	39	ILE	0	-0.079	-0.026	29.149	0.003	0.003	0.000	0.000	0.000	0.000
40	A	40	ARG	1	0.949	0.979	33.604	0.055	0.055	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.922	-0.960	35.122	-0.043	-0.043	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.006	-0.001	30.833	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.011	0.021	28.588	0.000	0.000	0.000	0.000	0.000	0.000
44	A	44	GLY	0	0.034	0.021	26.758	-0.004	-0.004	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.073	0.016	22.901	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	46	ARG	1	0.932	0.954	23.486	0.062	0.062	0.000	0.000	0.000	0.000
47	A	47	SER	0	-0.002	-0.004	24.826	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	48	GLY	0	-0.010	0.010	26.986	0.002	0.002	0.000	0.000	0.000	0.000
49	A	49	ALA	0	-0.004	-0.013	25.509	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	50	TYR	0	0.060	0.016	23.601	-0.012	-0.012	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.816	-0.896	19.088	-0.210	-0.210	0.000	0.000	0.000	0.000
52	A	52	LYS	1	0.836	0.909	20.218	0.114	0.114	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.880	-0.934	19.852	-0.194	-0.194	0.000	0.000	0.000	0.000
54	A	54	LEU	0	0.014	0.013	18.909	-0.019	-0.019	0.000	0.000	0.000	0.000
55	A	55	ARG	1	0.892	0.959	15.928	0.195	0.195	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.931	0.970	14.836	0.172	0.172	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.023	0.014	14.941	-0.032	-0.032	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.893	0.933	12.494	0.268	0.268	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.952	-0.965	9.669	-0.833	-0.833	0.000	0.000	0.000	0.000
60	A	60	ILE	0	0.023	0.017	9.841	-0.089	-0.089	0.000	0.000	0.000	0.000
61	A	61	ALA	0	0.003	0.018	10.483	-0.033	-0.033	0.000	0.000	0.000	0.000
62	A	62	PHE	0	-0.014	-0.032	5.965	0.070	0.070	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.942	-0.967	5.516	-0.911	-0.911	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.921	-0.952	6.520	-0.438	-0.438	0.000	0.000	0.000	0.000
65	A	65	LEU	0	0.004	0.028	5.412	-0.018	-0.018	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.013	-0.013	2.673	-0.403	0.217	0.815	-0.584	-0.851	0.001
67	A	67	SER	0	-0.114	-0.054	2.849	-2.717	-1.644	0.277	-0.201	-1.149	-0.012
68	A	68	GLN	0	0.070	0.034	5.481	-0.035	-0.035	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.019	0.001	2.632	-0.589	-0.254	1.242	-0.385	-1.193	-0.001
70	A	70	ARG	1	0.933	0.957	3.020	-1.017	0.829	0.272	-0.506	-1.613	0.000
71	A	71	ALA	0	-0.043	-0.011	3.751	0.393	0.460	0.014	0.033	-0.113	0.000
72	A	72	LEU	0	-0.028	-0.002	6.156	0.214	0.214	0.000	0.000	0.000	0.000
73	A	73	GLY	0	-0.043	-0.008	5.912	0.255	0.255	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.043	-0.018	3.269	0.138	0.495	0.015	-0.084	-0.288	0.000
75	A	75	ASP	-1	-0.869	-0.909	2.549	-2.728	-1.353	2.015	-1.308	-2.082	-0.015
76	A	76	ALA	0	0.013	-0.007	2.366	-0.050	1.136	6.579	-3.265	-4.500	-0.033
77	A	77	VAL	0	0.016	-0.001	2.829	0.317	-2.110	2.987	1.957	-2.518	-0.005
78	A	78	VAL	0	-0.031	-0.008	5.024	-0.825	-0.832	0.000	-0.021	0.028	0.000
79	A	79	GLY	0	-0.048	-0.026	8.591	-0.023	-0.023	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.071	-0.038	6.060	-0.059	-0.059	0.000	0.000	0.000	0.000
81	A	81	ASP	-1	-0.877	-0.932	10.661	-0.029	-0.029	0.000	0.000	0.000	0.000
82	A	82	ILE	0	-0.096	-0.064	11.837	-0.039	-0.039	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.903	-0.929	14.341	-0.057	-0.057	0.000	0.000	0.000	0.000
84	A	84	TYR	0	-0.011	-0.023	17.147	-0.035	-0.035	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.812	-0.911	20.188	-0.095	-0.095	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.084	-0.026	23.179	-0.007	-0.007	0.000	0.000	0.000	0.000
87	A	87	VAL	0	0.031	0.012	24.455	0.007	0.007	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.000	-0.014	27.217	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	89	GLN	0	-0.025	-0.033	30.206	0.005	0.005	0.000	0.000	0.000	0.000
90	A	90	ASN	0	-0.010	-0.003	32.841	0.007	0.007	0.000	0.000	0.000	0.000
91	A	91	GLY	0	0.037	0.032	30.461	0.000	0.000	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.015	-0.022	29.689	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	93	MET	0	-0.069	-0.028	25.421	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	94	LEU	0	-0.017	0.003	21.672	0.008	0.008	0.000	0.000	0.000	0.000
95	A	95	MET	0	-0.003	0.004	18.742	-0.011	-0.011	0.000	0.000	0.000	0.000
96	A	96	VAL	0	-0.031	-0.027	14.676	0.005	0.005	0.000	0.000	0.000	0.000
97	A	97	SER	0	0.069	0.035	14.866	-0.027	-0.027	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.047	-0.004	9.201	0.005	0.005	0.000	0.000	0.000	0.000
99	A	99	SER	0	0.020	0.007	11.258	0.025	0.025	0.000	0.000	0.000	0.000
100	A	100	GLY	0	0.079	0.035	9.163	-0.018	-0.018	0.000	0.000	0.000	0.000
101	A	101	THR	0	-0.065	-0.020	9.144	-0.072	-0.072	0.000	0.000	0.000	0.000
102	A	102	ALA	0	0.032	0.028	5.115	0.329	0.329	0.000	0.000	0.000	0.000
103	A	103	VAL	0	-0.022	-0.018	5.365	-0.380	-0.380	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.955	0.999	5.408	0.205	0.205	0.000	0.000	0.000	0.000
105	A	105	THR	0	-0.074	-0.079	6.936	-0.060	-0.060	0.000	0.000	0.000	0.000
106	A	106	ARG	1	0.962	0.981	9.622	-0.366	-0.366	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.933	0.974	12.149	-0.577	-0.577	0.000	0.000	0.000	0.000
108	A	108	ASN	0	-0.005	0.001	13.244	-0.057	-0.057	0.000	0.000	0.000	0.000
109	A	109	ILE	0	0.000	0.017	16.296	-0.012	-0.012	0.000	0.000	0.000	0.000

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