FMO DATABASE

FMODB ID: JQ399

Calculation Name: 1Y71-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Y71

Chain ID: A

ChEMBL ID:

UniProt ID: Q816F1

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
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-862239.148469
FMO2-HF: Nuclear repulsion	818721.356737
FMO2-HF: Total energy	-43517.791732
FMO2-MP2: Total energy	-43646.200486

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:4:THR)

Summations of interaction energy for fragment #1(A:4:THR)

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.
-9.769	-5.146	3.868	-3.458	-5.032	-0.022

Interaction energy analysis for fragmet #1(A:4:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.025

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	6	GLU	-1	-0.868	-0.935	3.163	-4.384	-2.389	0.094	-0.924	-1.165	-0.003
4	A	7	ILE	0	-0.049	-0.031	4.989	0.536	0.600	-0.001	-0.002	-0.061	0.000
5	A	8	GLY	0	0.010	0.005	7.671	0.168	0.168	0.000	0.000	0.000	0.000
6	A	9	GLU	-1	-0.852	-0.900	7.219	-0.320	-0.320	0.000	0.000	0.000	0.000
7	A	10	ILE	0	0.014	0.014	9.443	0.026	0.026	0.000	0.000	0.000	0.000
8	A	11	VAL	0	0.008	-0.003	8.302	0.105	0.105	0.000	0.000	0.000	0.000
9	A	12	THR	0	-0.053	-0.031	11.504	0.041	0.041	0.000	0.000	0.000	0.000
10	A	13	GLY	0	0.028	0.011	11.669	-0.010	-0.010	0.000	0.000	0.000	0.000
11	A	14	ILE	0	-0.043	-0.019	13.412	0.028	0.028	0.000	0.000	0.000	0.000
12	A	15	TYR	0	0.070	0.018	15.341	-0.021	-0.021	0.000	0.000	0.000	0.000
13	A	16	LYS	1	0.927	0.969	17.663	0.198	0.198	0.000	0.000	0.000	0.000
14	A	17	THR	0	0.030	0.020	20.349	0.014	0.014	0.000	0.000	0.000	0.000
15	A	18	GLY	0	0.039	0.041	21.184	0.018	0.018	0.000	0.000	0.000	0.000
16	A	19	LYS	1	0.912	0.944	15.705	-0.058	-0.058	0.000	0.000	0.000	0.000
17	A	20	TYR	0	0.041	0.024	16.933	0.011	0.011	0.000	0.000	0.000	0.000
18	A	21	ILE	0	0.051	0.025	15.887	0.013	0.013	0.000	0.000	0.000	0.000
19	A	22	GLY	0	0.019	-0.004	14.827	0.007	0.007	0.000	0.000	0.000	0.000
20	A	23	GLU	-1	-0.782	-0.857	12.069	-0.562	-0.562	0.000	0.000	0.000	0.000
21	A	24	VAL	0	-0.023	-0.008	5.661	0.095	0.095	0.000	0.000	0.000	0.000
22	A	25	THR	0	0.001	-0.020	9.156	-0.065	-0.065	0.000	0.000	0.000	0.000
23	A	26	ASN	0	0.000	-0.009	8.152	-0.058	-0.058	0.000	0.000	0.000	0.000
24	A	27	SER	0	0.007	0.008	3.271	-0.899	-0.175	0.110	-0.316	-0.517	-0.002
25	A	28	ARG	1	0.912	0.958	5.441	1.152	1.152	0.000	0.000	0.000	0.000
26	A	29	PRO	0	0.040	0.020	5.473	-0.387	-0.387	0.000	0.000	0.000	0.000
27	A	30	GLY	0	0.044	0.031	5.900	0.329	0.329	0.000	0.000	0.000	0.000
28	A	31	SER	0	-0.142	-0.092	6.338	0.358	0.358	0.000	0.000	0.000	0.000
29	A	32	TYR	0	0.019	-0.008	2.383	-1.935	-1.053	3.642	-1.783	-2.742	-0.014
30	A	33	VAL	0	-0.043	-0.015	7.582	0.310	0.310	0.000	0.000	0.000	0.000
31	A	34	VAL	0	0.015	-0.003	10.001	-0.132	-0.132	0.000	0.000	0.000	0.000
32	A	35	LYS	1	0.795	0.887	12.141	0.615	0.615	0.000	0.000	0.000	0.000
33	A	36	VAL	0	-0.008	-0.001	15.152	0.008	0.008	0.000	0.000	0.000	0.000
34	A	37	LEU	0	-0.030	-0.027	16.798	0.013	0.013	0.000	0.000	0.000	0.000
35	A	38	ALA	0	0.035	0.025	19.615	0.024	0.024	0.000	0.000	0.000	0.000
36	A	39	VAL	0	-0.010	-0.014	20.165	-0.015	-0.015	0.000	0.000	0.000	0.000
37	A	40	LEU	0	0.009	0.002	18.287	0.016	0.016	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.830	0.902	22.048	0.051	0.051	0.000	0.000	0.000	0.000
39	A	42	HIS	0	0.114	0.087	22.935	-0.024	-0.024	0.000	0.000	0.000	0.000
40	A	43	PRO	0	-0.016	-0.004	23.892	0.014	0.014	0.000	0.000	0.000	0.000
41	A	44	VAL	0	0.003	0.011	25.308	0.005	0.005	0.000	0.000	0.000	0.000
42	A	45	GLN	0	-0.042	-0.066	27.854	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	61	GLU	-1	-0.740	-0.815	31.197	-0.058	-0.058	0.000	0.000	0.000	0.000
44	A	62	ARG	1	0.853	0.931	24.583	0.064	0.064	0.000	0.000	0.000	0.000
45	A	63	ARG	1	0.938	0.954	27.856	0.114	0.114	0.000	0.000	0.000	0.000
46	A	64	ALA	0	-0.023	-0.009	24.405	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	65	LEU	0	-0.048	-0.010	18.282	0.002	0.002	0.000	0.000	0.000	0.000
48	A	66	ALA	0	0.024	0.030	22.424	0.011	0.011	0.000	0.000	0.000	0.000
49	A	67	PHE	0	0.037	0.018	21.647	-0.027	-0.027	0.000	0.000	0.000	0.000
50	A	68	ARG	1	0.880	0.934	19.230	0.244	0.244	0.000	0.000	0.000	0.000
51	A	69	GLU	-1	-0.838	-0.899	19.425	-0.276	-0.276	0.000	0.000	0.000	0.000
52	A	70	GLN	0	0.016	0.014	14.913	-0.088	-0.088	0.000	0.000	0.000	0.000
53	A	71	THR	0	0.012	0.007	15.740	-0.012	-0.012	0.000	0.000	0.000	0.000
54	A	72	ASN	0	0.004	0.005	11.770	-0.146	-0.146	0.000	0.000	0.000	0.000
55	A	73	ILE	0	-0.007	-0.002	11.221	0.122	0.122	0.000	0.000	0.000	0.000
56	A	74	PRO	0	0.015	0.012	9.881	-0.170	-0.170	0.000	0.000	0.000	0.000
57	A	75	GLU	-1	-0.806	-0.884	3.603	-4.965	-4.007	0.023	-0.433	-0.547	-0.003
58	A	76	GLN	0	0.029	0.009	7.461	0.270	0.270	0.000	0.000	0.000	0.000
59	A	77	MET	0	-0.065	-0.027	9.930	0.174	0.174	0.000	0.000	0.000	0.000
60	A	78	VAL	0	0.009	0.013	7.634	-0.030	-0.030	0.000	0.000	0.000	0.000
61	A	79	LYS	1	0.870	0.916	8.262	-0.264	-0.264	0.000	0.000	0.000	0.000
62	A	80	LYS	1	0.881	0.953	8.457	-0.044	-0.044	0.000	0.000	0.000	0.000
63	A	81	TYR	0	-0.123	-0.079	9.884	0.097	0.097	0.000	0.000	0.000	0.000
64	A	82	GLU	-1	-0.892	-0.956	12.825	0.100	0.100	0.000	0.000	0.000	0.000
65	A	83	GLY	0	0.005	0.020	16.106	0.013	0.013	0.000	0.000	0.000	0.000
66	A	84	GLU	-1	-0.911	-0.958	19.166	-0.089	-0.089	0.000	0.000	0.000	0.000
67	A	85	ILE	0	-0.038	-0.018	17.501	0.002	0.002	0.000	0.000	0.000	0.000
68	A	86	PRO	0	-0.003	0.011	21.338	-0.001	-0.001	0.000	0.000	0.000	0.000
69	A	87	ASP	-1	-0.698	-0.857	23.907	-0.141	-0.141	0.000	0.000	0.000	0.000
70	A	88	TYR	0	-0.031	-0.019	22.863	0.011	0.011	0.000	0.000	0.000	0.000
71	A	89	THR	0	-0.039	-0.035	25.380	0.005	0.005	0.000	0.000	0.000	0.000
72	A	90	GLU	-1	-0.943	-0.968	28.725	-0.067	-0.067	0.000	0.000	0.000	0.000
73	A	91	SER	0	-0.044	-0.034	24.477	0.006	0.006	0.000	0.000	0.000	0.000
74	A	92	LEU	0	-0.009	-0.005	26.502	0.009	0.009	0.000	0.000	0.000	0.000
75	A	93	LYS	1	0.866	0.916	27.342	0.058	0.058	0.000	0.000	0.000	0.000
76	A	94	LEU	0	0.034	0.021	27.779	0.007	0.007	0.000	0.000	0.000	0.000
77	A	95	ALA	0	-0.001	0.008	25.699	0.010	0.010	0.000	0.000	0.000	0.000
78	A	96	LEU	0	-0.021	-0.014	27.657	0.007	0.007	0.000	0.000	0.000	0.000
79	A	97	GLU	-1	-0.810	-0.882	30.375	-0.039	-0.039	0.000	0.000	0.000	0.000
80	A	98	THR	0	-0.023	-0.023	28.799	0.008	0.008	0.000	0.000	0.000	0.000
81	A	99	GLN	0	-0.014	-0.014	28.762	0.000	0.000	0.000	0.000	0.000	0.000
82	A	100	MET	0	-0.033	-0.004	30.938	0.003	0.003	0.000	0.000	0.000	0.000
83	A	101	ASN	0	0.021	0.001	34.332	0.003	0.003	0.000	0.000	0.000	0.000
84	A	102	SER	0	-0.110	-0.064	31.660	0.005	0.005	0.000	0.000	0.000	0.000
85	A	103	PHE	0	-0.003	-0.002	32.876	0.002	0.002	0.000	0.000	0.000	0.000
86	A	104	SER	0	0.009	0.005	36.623	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	105	GLU	-1	-1.008	-1.006	39.197	0.012	0.012	0.000	0.000	0.000	0.000
88	A	106	ASP	-1	-0.847	-0.887	37.353	0.001	0.001	0.000	0.000	0.000	0.000
89	A	107	ASP	-1	-0.923	-0.959	40.385	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	108	SER	0	-0.057	-0.050	39.017	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	109	PRO	0	0.025	-0.016	40.840	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	110	PHE	0	-0.046	-0.016	31.684	-0.004	-0.004	0.000	0.000	0.000	0.000
93	A	111	ALA	0	0.048	0.039	36.666	-0.005	-0.005	0.000	0.000	0.000	0.000
94	A	112	GLU	-1	-0.933	-0.958	37.708	-0.025	-0.025	0.000	0.000	0.000	0.000
95	A	113	ARG	1	0.949	0.954	34.199	0.039	0.039	0.000	0.000	0.000	0.000
96	A	114	SER	0	-0.085	-0.042	34.132	-0.007	-0.007	0.000	0.000	0.000	0.000
97	A	115	LEU	0	-0.020	-0.007	35.564	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	116	GLU	-1	-0.892	-0.936	37.855	-0.037	-0.037	0.000	0.000	0.000	0.000
99	A	117	THR	0	-0.081	-0.059	33.706	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	118	LEU	0	-0.025	-0.020	30.908	-0.007	-0.007	0.000	0.000	0.000	0.000
101	A	119	GLN	0	0.035	0.010	34.515	-0.005	-0.005	0.000	0.000	0.000	0.000
102	A	120	GLN	0	-0.047	-0.011	37.108	0.003	0.003	0.000	0.000	0.000	0.000
103	A	121	LEU	0	0.005	-0.004	30.451	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	122	LYS	1	0.898	0.945	33.827	0.043	0.043	0.000	0.000	0.000	0.000
105	A	123	LYS	1	0.874	0.929	35.201	0.047	0.047	0.000	0.000	0.000	0.000
106	A	124	ASP	-1	-0.865	-0.910	33.539	-0.083	-0.083	0.000	0.000	0.000	0.000
107	A	125	TYR	0	-0.069	-0.064	28.758	-0.012	-0.012	0.000	0.000	0.000	0.000
108	A	126	LYS	1	0.915	0.967	32.877	0.088	0.088	0.000	0.000	0.000	0.000
109	A	127	LEU	0	-0.037	-0.010	33.643	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:THR)