FMO DATABASE

FMODB ID: QV72Y

Calculation Name: 2PYT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PYT

Chain ID: A

ChEMBL ID:

UniProt ID: Q9ZFV5

Base Structure: X-ray

Registration Date: 2023-09-20

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	128
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1049921.032371
FMO2-HF: Nuclear repulsion	999814.326525
FMO2-HF: Total energy	-50106.705846
FMO2-MP2: Total energy	-50249.809436

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:100:LEU)

Summations of interaction energy for fragment #1(A:100:LEU)

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.
-7.842	-1.78	5.02	-3.585	-7.5	-0.013

Interaction energy analysis for fragmet #1(A:100:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.009

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	102	LEU	0	-0.023	-0.009	2.064	-1.566	0.327	2.268	-1.560	-2.601	0.004
4	A	103	GLY	0	-0.005	-0.007	2.575	-0.656	0.970	1.030	-0.852	-1.804	-0.002
5	A	104	THR	0	-0.046	-0.028	3.342	-0.495	-0.436	0.009	0.388	-0.457	-0.001
6	A	105	MET	0	-0.007	0.017	2.475	-5.870	-3.597	1.715	-1.516	-2.473	-0.014
7	A	106	GLN	0	-0.021	-0.007	4.357	0.625	0.724	-0.001	-0.024	-0.075	0.000
8	A	107	PRO	0	0.038	0.037	7.717	0.208	0.208	0.000	0.000	0.000	0.000
9	A	108	SER	0	-0.035	-0.025	10.240	0.077	0.077	0.000	0.000	0.000	0.000
10	A	109	PHE	0	0.044	0.023	11.808	0.059	0.059	0.000	0.000	0.000	0.000
11	A	110	THR	0	-0.025	-0.014	14.470	0.010	0.010	0.000	0.000	0.000	0.000
12	A	111	SER	0	0.019	0.005	17.804	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	112	VAL	0	-0.042	-0.013	21.093	0.000	0.000	0.000	0.000	0.000	0.000
14	A	113	THR	0	0.033	0.014	24.894	-0.010	-0.010	0.000	0.000	0.000	0.000
15	A	114	GLY	0	-0.010	0.004	27.575	0.003	0.003	0.000	0.000	0.000	0.000
16	A	115	LYS	1	0.930	0.935	31.230	-0.028	-0.028	0.000	0.000	0.000	0.000
17	A	116	GLY	0	-0.006	0.002	33.957	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	117	GLY	0	0.042	0.029	30.613	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	118	VAL	0	-0.015	-0.010	29.329	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	119	LYS	1	0.840	0.911	20.945	0.041	0.041	0.000	0.000	0.000	0.000
21	A	120	VAL	0	-0.009	-0.002	23.497	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	121	ILE	0	0.029	-0.005	17.567	0.006	0.006	0.000	0.000	0.000	0.000
23	A	122	ASP	-1	-0.826	-0.870	17.326	0.297	0.297	0.000	0.000	0.000	0.000
24	A	123	GLY	0	0.064	0.037	16.075	0.012	0.012	0.000	0.000	0.000	0.000
25	A	124	SER	0	-0.049	-0.041	13.899	0.036	0.036	0.000	0.000	0.000	0.000
26	A	125	SER	0	-0.003	-0.026	12.681	0.108	0.108	0.000	0.000	0.000	0.000
27	A	126	VAL	0	-0.022	0.009	10.847	0.053	0.053	0.000	0.000	0.000	0.000
28	A	127	LYS	1	0.774	0.889	7.217	-0.572	-0.572	0.000	0.000	0.000	0.000
29	A	128	PHE	0	0.054	0.023	5.863	-0.075	-0.075	0.000	0.000	0.000	0.000
30	A	129	GLY	0	0.007	0.011	5.811	-0.458	-0.458	0.000	0.000	0.000	0.000
31	A	130	ARG	1	0.881	0.924	4.636	3.579	3.691	-0.001	-0.021	-0.090	0.000
32	A	131	PHE	0	0.012	0.013	8.461	0.209	0.209	0.000	0.000	0.000	0.000
33	A	132	ASP	-1	-0.867	-0.949	12.124	-0.729	-0.729	0.000	0.000	0.000	0.000
34	A	133	GLY	0	-0.067	-0.028	14.630	0.045	0.045	0.000	0.000	0.000	0.000
35	A	134	ALA	0	-0.026	-0.009	13.708	0.061	0.061	0.000	0.000	0.000	0.000
36	A	135	GLU	-1	-0.871	-0.927	11.064	-1.257	-1.257	0.000	0.000	0.000	0.000
37	A	136	PRO	0	-0.107	-0.057	13.629	0.109	0.109	0.000	0.000	0.000	0.000
38	A	137	HIS	0	-0.008	-0.002	11.918	-0.099	-0.099	0.000	0.000	0.000	0.000
39	A	138	CYS	0	-0.022	0.017	6.342	-0.523	-0.523	0.000	0.000	0.000	0.000
40	A	139	VAL	0	-0.011	0.001	8.350	-0.041	-0.041	0.000	0.000	0.000	0.000
41	A	140	GLY	0	0.014	0.004	7.817	-0.195	-0.195	0.000	0.000	0.000	0.000
42	A	141	LEU	0	-0.007	-0.014	8.487	0.242	0.242	0.000	0.000	0.000	0.000
43	A	142	THR	0	-0.036	-0.052	10.333	-0.149	-0.149	0.000	0.000	0.000	0.000
44	A	143	ASP	-1	-0.821	-0.868	12.642	-0.186	-0.186	0.000	0.000	0.000	0.000
45	A	144	LEU	0	-0.076	-0.045	14.528	0.024	0.024	0.000	0.000	0.000	0.000
46	A	145	VAL	0	-0.060	-0.028	18.146	0.027	0.027	0.000	0.000	0.000	0.000
47	A	146	THR	0	0.023	-0.001	20.853	-0.019	-0.019	0.000	0.000	0.000	0.000
48	A	147	GLU	-1	-0.841	-0.940	23.562	-0.110	-0.110	0.000	0.000	0.000	0.000
49	A	148	GLN	0	-0.028	-0.013	24.395	0.011	0.011	0.000	0.000	0.000	0.000
50	A	149	ASP	-1	-0.829	-0.876	23.214	-0.046	-0.046	0.000	0.000	0.000	0.000
51	A	150	GLY	0	-0.033	-0.018	26.559	0.010	0.010	0.000	0.000	0.000	0.000
52	A	151	SER	0	-0.066	-0.041	26.396	0.007	0.007	0.000	0.000	0.000	0.000
53	A	152	SER	0	-0.003	-0.014	28.356	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	153	MET	0	-0.035	-0.020	26.473	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	154	ALA	0	0.030	0.050	21.687	0.008	0.008	0.000	0.000	0.000	0.000
56	A	155	ALA	0	0.022	0.004	21.017	0.006	0.006	0.000	0.000	0.000	0.000
57	A	156	GLY	0	0.044	0.023	16.861	0.002	0.002	0.000	0.000	0.000	0.000
58	A	157	PHE	0	-0.041	-0.006	13.228	0.045	0.045	0.000	0.000	0.000	0.000
59	A	158	MET	0	0.030	0.021	12.011	-0.060	-0.060	0.000	0.000	0.000	0.000
60	A	159	GLN	0	0.013	-0.002	8.780	0.156	0.156	0.000	0.000	0.000	0.000
61	A	160	TRP	0	-0.073	-0.022	8.952	-0.244	-0.244	0.000	0.000	0.000	0.000
62	A	161	ASP	-1	-0.821	-0.921	9.587	0.165	0.165	0.000	0.000	0.000	0.000
63	A	162	ASN	0	-0.107	-0.063	11.309	-0.089	-0.089	0.000	0.000	0.000	0.000
64	A	163	ALA	0	0.038	0.036	12.828	-0.042	-0.042	0.000	0.000	0.000	0.000
65	A	164	PHE	0	0.001	-0.009	14.904	0.042	0.042	0.000	0.000	0.000	0.000
66	A	165	PHE	0	0.014	0.004	15.457	-0.035	-0.035	0.000	0.000	0.000	0.000
67	A	166	PRO	0	0.012	0.017	18.695	0.024	0.024	0.000	0.000	0.000	0.000
68	A	167	TRP	0	0.002	-0.009	20.148	-0.043	-0.043	0.000	0.000	0.000	0.000
69	A	168	THR	0	-0.024	-0.021	22.304	0.030	0.030	0.000	0.000	0.000	0.000
70	A	169	LEU	0	0.017	0.052	23.683	-0.011	-0.011	0.000	0.000	0.000	0.000
71	A	170	ASN	0	-0.027	-0.016	25.929	0.023	0.023	0.000	0.000	0.000	0.000
72	A	171	TYR	0	-0.078	-0.069	21.659	0.007	0.007	0.000	0.000	0.000	0.000
73	A	172	ASP	-1	-0.829	-0.912	27.552	-0.095	-0.095	0.000	0.000	0.000	0.000
74	A	173	GLU	-1	-0.798	-0.908	21.178	-0.195	-0.195	0.000	0.000	0.000	0.000
75	A	174	ILE	0	-0.050	-0.026	24.524	0.010	0.010	0.000	0.000	0.000	0.000
76	A	175	ASP	-1	-0.848	-0.919	20.743	-0.144	-0.144	0.000	0.000	0.000	0.000
77	A	176	MET	0	-0.048	-0.037	21.054	0.016	0.016	0.000	0.000	0.000	0.000
78	A	177	VAL	0	0.004	0.004	18.485	0.002	0.002	0.000	0.000	0.000	0.000
79	A	178	LEU	0	-0.057	-0.020	16.480	0.020	0.020	0.000	0.000	0.000	0.000
80	A	179	GLU	-1	-0.900	-0.970	14.296	0.306	0.306	0.000	0.000	0.000	0.000
81	A	180	GLY	0	0.023	0.016	16.601	-0.030	-0.030	0.000	0.000	0.000	0.000
82	A	181	GLU	-1	-0.854	-0.922	17.628	-0.028	-0.028	0.000	0.000	0.000	0.000
83	A	182	LEU	0	0.012	0.036	17.521	-0.023	-0.023	0.000	0.000	0.000	0.000
84	A	183	HIS	0	-0.078	-0.065	19.607	0.012	0.012	0.000	0.000	0.000	0.000
85	A	184	VAL	0	0.043	0.007	21.084	-0.026	-0.026	0.000	0.000	0.000	0.000
86	A	185	ARG	1	0.781	0.885	23.727	0.187	0.187	0.000	0.000	0.000	0.000
87	A	186	HIS	0	0.050	0.003	26.358	-0.019	-0.019	0.000	0.000	0.000	0.000
88	A	187	GLU	-1	-0.916	-0.957	29.182	-0.080	-0.080	0.000	0.000	0.000	0.000
89	A	188	GLY	0	-0.067	-0.036	31.158	0.003	0.003	0.000	0.000	0.000	0.000
90	A	189	GLU	-1	-0.964	-0.966	30.893	-0.069	-0.069	0.000	0.000	0.000	0.000
91	A	190	THR	0	-0.022	-0.032	25.281	-0.012	-0.012	0.000	0.000	0.000	0.000
92	A	191	MET	0	0.020	0.029	26.882	0.013	0.013	0.000	0.000	0.000	0.000
93	A	192	ILE	0	-0.032	-0.034	23.578	-0.010	-0.010	0.000	0.000	0.000	0.000
94	A	193	ALA	0	-0.011	0.009	22.916	0.009	0.009	0.000	0.000	0.000	0.000
95	A	194	LYS	1	0.867	0.901	21.846	0.013	0.013	0.000	0.000	0.000	0.000
96	A	195	ALA	0	-0.015	-0.003	20.220	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	196	GLY	0	-0.033	-0.013	21.770	0.008	0.008	0.000	0.000	0.000	0.000
98	A	197	ASP	-1	-0.865	-0.913	24.399	-0.014	-0.014	0.000	0.000	0.000	0.000
99	A	198	VAL	0	-0.046	-0.040	24.066	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	199	MET	0	-0.032	-0.012	23.695	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	200	PHE	0	-0.030	-0.028	26.223	0.001	0.001	0.000	0.000	0.000	0.000
102	A	201	ILE	0	0.023	0.020	23.320	0.001	0.001	0.000	0.000	0.000	0.000
103	A	202	PRO	0	0.004	0.010	27.509	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	203	LYS	1	0.924	0.984	29.497	0.092	0.092	0.000	0.000	0.000	0.000
105	A	204	GLY	0	-0.060	-0.031	29.749	0.009	0.009	0.000	0.000	0.000	0.000
106	A	205	SER	0	-0.046	-0.027	27.758	0.001	0.001	0.000	0.000	0.000	0.000
107	A	206	SER	0	-0.038	-0.034	27.170	-0.010	-0.010	0.000	0.000	0.000	0.000
108	A	207	ILE	0	-0.033	-0.020	22.179	0.012	0.012	0.000	0.000	0.000	0.000
109	A	208	GLU	-1	-0.878	-0.918	21.340	-0.243	-0.243	0.000	0.000	0.000	0.000
110	A	209	PHE	0	0.055	0.039	17.982	0.022	0.022	0.000	0.000	0.000	0.000
111	A	210	GLY	0	0.028	-0.012	17.114	-0.033	-0.033	0.000	0.000	0.000	0.000
112	A	211	THR	0	-0.020	-0.006	14.476	0.040	0.040	0.000	0.000	0.000	0.000
113	A	212	PRO	0	-0.025	0.000	16.873	-0.028	-0.028	0.000	0.000	0.000	0.000
114	A	213	THR	0	-0.064	-0.039	16.061	0.011	0.011	0.000	0.000	0.000	0.000
115	A	214	SER	0	0.049	0.034	13.016	0.002	0.002	0.000	0.000	0.000	0.000
116	A	215	VAL	0	-0.034	-0.004	13.085	0.030	0.030	0.000	0.000	0.000	0.000
117	A	216	ARG	1	0.868	0.933	11.180	-0.293	-0.293	0.000	0.000	0.000	0.000
118	A	217	PHE	0	-0.006	-0.003	13.963	0.036	0.036	0.000	0.000	0.000	0.000
119	A	218	LEU	0	-0.027	0.002	15.864	-0.021	-0.021	0.000	0.000	0.000	0.000
120	A	219	TYR	0	0.016	-0.011	15.288	-0.007	-0.007	0.000	0.000	0.000	0.000
121	A	220	VAL	0	-0.024	-0.031	20.037	0.009	0.009	0.000	0.000	0.000	0.000
122	A	221	ALA	0	0.047	0.031	22.829	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	222	TRP	0	-0.052	-0.007	24.666	0.007	0.007	0.000	0.000	0.000	0.000
124	A	223	PRO	0	-0.017	-0.023	28.168	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	224	ALA	0	0.038	-0.012	25.513	-0.011	-0.011	0.000	0.000	0.000	0.000
126	A	225	ASN	0	-0.020	0.003	24.804	-0.014	-0.014	0.000	0.000	0.000	0.000
127	A	226	TRP	0	-0.024	-0.009	20.108	-0.005	-0.005	0.000	0.000	0.000	0.000
128	A	227	GLN	0	-0.036	0.002	19.140	-0.019	-0.019	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:100:LEU)