FMO DATABASE

FMODB ID: 892VY

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	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	-859237.379325
FMO2-HF: Nuclear repulsion	815720.548717
FMO2-HF: Total energy	-43516.830608
FMO2-MP2: Total energy	-43645.283259

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.
-2.187	-0.241	5.073	-3.154	-3.863	-0.012

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 : -0.036 / q_NPA : -0.035

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	-0.877	-0.932	3.203	-3.772	-1.851	0.111	-0.814	-1.218	-0.001
4	A	7	ILE	0	-0.044	-0.038	4.886	0.521	0.564	-0.001	-0.002	-0.040	0.000
5	A	8	GLY	0	0.017	0.006	7.803	0.073	0.073	0.000	0.000	0.000	0.000
6	A	9	GLU	-1	-0.918	-0.943	7.368	-0.410	-0.410	0.000	0.000	0.000	0.000
7	A	10	ILE	0	0.039	0.027	9.732	0.044	0.044	0.000	0.000	0.000	0.000
8	A	11	VAL	0	0.017	0.002	8.108	0.039	0.039	0.000	0.000	0.000	0.000
9	A	12	THR	0	-0.076	-0.045	11.240	0.080	0.080	0.000	0.000	0.000	0.000
10	A	13	GLY	0	0.045	0.020	11.491	-0.024	-0.024	0.000	0.000	0.000	0.000
11	A	14	ILE	0	-0.056	-0.023	13.394	0.010	0.010	0.000	0.000	0.000	0.000
12	A	15	TYR	0	0.064	0.016	15.261	0.013	0.013	0.000	0.000	0.000	0.000
13	A	16	LYS	1	0.949	0.974	17.570	0.002	0.002	0.000	0.000	0.000	0.000
14	A	17	THR	0	-0.002	0.002	20.353	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	18	GLY	0	0.029	0.032	21.052	0.005	0.005	0.000	0.000	0.000	0.000
16	A	19	LYS	1	0.935	0.959	15.707	-0.037	-0.037	0.000	0.000	0.000	0.000
17	A	20	TYR	0	0.041	0.041	16.774	0.005	0.005	0.000	0.000	0.000	0.000
18	A	21	ILE	0	0.045	0.025	15.840	-0.001	-0.001	0.000	0.000	0.000	0.000
19	A	22	GLY	0	0.024	-0.008	14.642	0.017	0.017	0.000	0.000	0.000	0.000
20	A	23	GLU	-1	-0.905	-0.937	12.343	-0.480	-0.480	0.000	0.000	0.000	0.000
21	A	24	VAL	0	-0.014	0.004	6.220	0.102	0.102	0.000	0.000	0.000	0.000
22	A	25	THR	0	-0.016	-0.027	9.689	-0.034	-0.034	0.000	0.000	0.000	0.000
23	A	26	ASN	0	0.009	-0.008	8.698	-0.083	-0.083	0.000	0.000	0.000	0.000
24	A	27	SER	0	0.017	0.017	2.706	-0.091	0.315	0.074	-0.144	-0.335	0.001
25	A	28	ARG	1	0.955	0.980	5.931	0.070	0.070	0.000	0.000	0.000	0.000
26	A	29	PRO	0	0.047	0.012	6.521	0.233	0.233	0.000	0.000	0.000	0.000
27	A	30	GLY	0	0.036	0.029	7.067	-0.179	-0.179	0.000	0.000	0.000	0.000
28	A	31	SER	0	-0.096	-0.074	7.218	-0.096	-0.096	0.000	0.000	0.000	0.000
29	A	32	TYR	0	0.069	0.053	2.235	-1.307	-1.905	4.890	-2.183	-2.109	-0.012
30	A	33	VAL	0	-0.054	-0.017	8.037	0.130	0.130	0.000	0.000	0.000	0.000
31	A	34	VAL	0	0.016	0.006	10.395	-0.114	-0.114	0.000	0.000	0.000	0.000
32	A	35	LYS	1	0.915	0.972	12.554	0.424	0.424	0.000	0.000	0.000	0.000
33	A	36	VAL	0	-0.007	-0.005	15.628	-0.011	-0.011	0.000	0.000	0.000	0.000
34	A	37	LEU	0	-0.003	-0.012	17.002	0.008	0.008	0.000	0.000	0.000	0.000
35	A	38	ALA	0	0.028	0.016	19.552	0.017	0.017	0.000	0.000	0.000	0.000
36	A	39	VAL	0	-0.008	-0.008	20.089	-0.008	-0.008	0.000	0.000	0.000	0.000
37	A	40	LEU	0	-0.008	-0.012	17.755	0.008	0.008	0.000	0.000	0.000	0.000
38	A	41	LYS	1	0.905	0.959	21.761	-0.013	-0.013	0.000	0.000	0.000	0.000
39	A	42	HIS	0	0.106	0.098	22.928	-0.014	-0.014	0.000	0.000	0.000	0.000
40	A	43	PRO	0	-0.048	-0.016	23.768	0.010	0.010	0.000	0.000	0.000	0.000
41	A	44	VAL	0	0.007	-0.003	25.162	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	45	GLN	0	-0.050	-0.077	27.796	0.000	0.000	0.000	0.000	0.000	0.000
43	A	61	GLU	-1	-0.851	-0.886	31.656	-0.001	-0.001	0.000	0.000	0.000	0.000
44	A	62	ARG	1	0.896	0.954	24.132	-0.012	-0.012	0.000	0.000	0.000	0.000
45	A	63	ARG	1	0.994	0.990	27.864	0.056	0.056	0.000	0.000	0.000	0.000
46	A	64	ALA	0	-0.020	-0.013	24.410	0.000	0.000	0.000	0.000	0.000	0.000
47	A	65	LEU	0	-0.043	-0.023	18.348	0.000	0.000	0.000	0.000	0.000	0.000
48	A	66	ALA	0	0.022	0.021	22.523	0.003	0.003	0.000	0.000	0.000	0.000
49	A	67	PHE	0	0.031	0.015	22.109	-0.018	-0.018	0.000	0.000	0.000	0.000
50	A	68	ARG	1	0.890	0.939	20.101	0.167	0.167	0.000	0.000	0.000	0.000
51	A	69	GLU	-1	-0.898	-0.928	20.045	-0.128	-0.128	0.000	0.000	0.000	0.000
52	A	70	GLN	0	0.020	0.009	15.073	-0.059	-0.059	0.000	0.000	0.000	0.000
53	A	71	THR	0	0.016	0.000	15.405	0.023	0.023	0.000	0.000	0.000	0.000
54	A	72	ASN	0	-0.014	0.008	11.541	-0.025	-0.025	0.000	0.000	0.000	0.000
55	A	73	ILE	0	-0.044	-0.015	11.367	0.052	0.052	0.000	0.000	0.000	0.000
56	A	74	PRO	0	0.030	0.014	10.140	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	75	GLU	-1	-0.877	-0.954	4.457	2.886	3.060	-0.001	-0.011	-0.161	0.000
58	A	76	GLN	0	0.024	0.012	7.631	-0.105	-0.105	0.000	0.000	0.000	0.000
59	A	77	MET	0	-0.104	-0.046	9.920	-0.022	-0.022	0.000	0.000	0.000	0.000
60	A	78	VAL	0	-0.014	-0.001	7.505	-0.062	-0.062	0.000	0.000	0.000	0.000
61	A	79	LYS	1	0.927	0.966	7.725	-0.201	-0.201	0.000	0.000	0.000	0.000
62	A	80	LYS	1	0.942	0.974	7.454	0.017	0.017	0.000	0.000	0.000	0.000
63	A	81	TYR	0	-0.115	-0.083	8.996	0.108	0.108	0.000	0.000	0.000	0.000
64	A	82	GLU	-1	-0.889	-0.962	12.790	0.057	0.057	0.000	0.000	0.000	0.000
65	A	83	GLY	0	-0.025	0.018	15.095	0.010	0.010	0.000	0.000	0.000	0.000
66	A	84	GLU	-1	-0.912	-0.955	18.318	-0.070	-0.070	0.000	0.000	0.000	0.000
67	A	85	ILE	0	-0.027	-0.020	17.584	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	86	PRO	0	-0.010	0.016	20.904	0.003	0.003	0.000	0.000	0.000	0.000
69	A	87	ASP	-1	-0.767	-0.901	23.777	-0.094	-0.094	0.000	0.000	0.000	0.000
70	A	88	TYR	0	-0.019	-0.024	22.863	0.010	0.010	0.000	0.000	0.000	0.000
71	A	89	THR	0	0.012	0.013	25.400	0.008	0.008	0.000	0.000	0.000	0.000
72	A	90	GLU	-1	-0.920	-0.959	28.827	-0.043	-0.043	0.000	0.000	0.000	0.000
73	A	91	SER	0	-0.063	-0.034	24.457	0.005	0.005	0.000	0.000	0.000	0.000
74	A	92	LEU	0	-0.003	-0.007	26.505	0.008	0.008	0.000	0.000	0.000	0.000
75	A	93	LYS	1	0.913	0.961	27.656	0.034	0.034	0.000	0.000	0.000	0.000
76	A	94	LEU	0	0.054	0.036	27.128	0.005	0.005	0.000	0.000	0.000	0.000
77	A	95	ALA	0	-0.019	-0.013	25.823	0.008	0.008	0.000	0.000	0.000	0.000
78	A	96	LEU	0	-0.018	-0.017	27.753	0.007	0.007	0.000	0.000	0.000	0.000
79	A	97	GLU	-1	-0.892	-0.963	30.745	-0.013	-0.013	0.000	0.000	0.000	0.000
80	A	98	THR	0	-0.048	-0.018	28.109	0.006	0.006	0.000	0.000	0.000	0.000
81	A	99	GLN	0	-0.010	-0.011	29.216	0.001	0.001	0.000	0.000	0.000	0.000
82	A	100	MET	0	-0.047	-0.004	30.919	0.003	0.003	0.000	0.000	0.000	0.000
83	A	101	ASN	0	0.023	-0.004	34.162	0.001	0.001	0.000	0.000	0.000	0.000
84	A	102	SER	0	-0.115	-0.065	31.620	0.004	0.004	0.000	0.000	0.000	0.000
85	A	103	PHE	0	-0.006	-0.005	33.026	0.003	0.003	0.000	0.000	0.000	0.000
86	A	104	SER	0	0.025	0.016	36.704	-0.001	-0.001	0.000	0.000	0.000	0.000
87	A	105	GLU	-1	-1.018	-1.016	39.064	0.026	0.026	0.000	0.000	0.000	0.000
88	A	106	ASP	-1	-0.838	-0.895	37.237	0.026	0.026	0.000	0.000	0.000	0.000
89	A	107	ASP	-1	-0.957	-0.974	40.335	0.018	0.018	0.000	0.000	0.000	0.000
90	A	108	SER	0	-0.058	-0.040	39.053	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	109	PRO	0	0.055	-0.002	41.305	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	110	PHE	0	-0.049	-0.017	31.789	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	111	ALA	0	0.061	0.049	36.975	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	112	GLU	-1	-0.907	-0.951	37.992	0.002	0.002	0.000	0.000	0.000	0.000
95	A	113	ARG	1	0.990	1.002	34.161	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	114	SER	0	-0.112	-0.073	34.105	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	115	LEU	0	0.004	0.000	35.650	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	116	GLU	-1	-0.904	-0.929	37.708	-0.005	-0.005	0.000	0.000	0.000	0.000
99	A	117	THR	0	-0.068	-0.044	33.699	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	118	LEU	0	-0.033	-0.022	31.189	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	119	GLN	0	-0.002	0.000	34.739	-0.004	-0.004	0.000	0.000	0.000	0.000
102	A	120	GLN	0	-0.079	-0.024	37.235	0.000	0.000	0.000	0.000	0.000	0.000
103	A	121	LEU	0	0.021	0.001	30.823	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	122	LYS	1	0.966	0.995	33.985	0.015	0.015	0.000	0.000	0.000	0.000
105	A	123	LYS	1	0.938	0.961	35.347	0.014	0.014	0.000	0.000	0.000	0.000
106	A	124	ASP	-1	-0.866	-0.929	34.094	-0.034	-0.034	0.000	0.000	0.000	0.000
107	A	125	TYR	0	-0.115	-0.103	28.720	-0.007	-0.007	0.000	0.000	0.000	0.000
108	A	126	LYS	1	0.890	0.952	33.199	0.047	0.047	0.000	0.000	0.000	0.000
109	A	127	LEU	0	-0.032	-0.004	33.228	0.000	0.000	0.000	0.000	0.000	0.000

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