FMO DATABASE

FMODB ID: R8N78

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1049922.471995
FMO2-HF: Nuclear repulsion	999815.871013
FMO2-HF: Total energy	-50106.600982
FMO2-MP2: Total energy	-50249.633249

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.
-4.13	-0.564	6.024	-2.96	-6.628	-0.001

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 : 0.014 / q_NPA : 0.004

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	-0.029	-0.012	1.867	-1.229	0.036	3.861	-2.062	-3.064	0.006
4	A	103	GLY	0	-0.025	-0.012	2.268	-0.608	0.727	2.038	-1.209	-2.164	-0.002
5	A	104	THR	0	-0.031	-0.021	3.134	0.042	-0.517	-0.001	0.939	-0.379	-0.001
6	A	105	MET	0	-0.008	0.014	3.110	-2.678	-1.311	0.128	-0.608	-0.887	-0.004
7	A	106	GLN	0	-0.022	-0.006	4.903	0.519	0.585	-0.001	-0.004	-0.060	0.000
8	A	107	PRO	0	0.030	0.031	8.071	0.171	0.171	0.000	0.000	0.000	0.000
9	A	108	SER	0	-0.043	-0.034	10.247	0.113	0.113	0.000	0.000	0.000	0.000
10	A	109	PHE	0	0.036	0.014	11.962	0.033	0.033	0.000	0.000	0.000	0.000
11	A	110	THR	0	0.018	0.020	14.646	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	111	SER	0	-0.028	-0.025	17.784	-0.017	-0.017	0.000	0.000	0.000	0.000
13	A	112	VAL	0	-0.009	0.000	21.086	0.006	0.006	0.000	0.000	0.000	0.000
14	A	113	THR	0	0.037	0.017	24.844	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	114	GLY	0	-0.021	-0.001	27.526	0.004	0.004	0.000	0.000	0.000	0.000
16	A	115	LYS	1	0.945	0.942	31.144	-0.025	-0.025	0.000	0.000	0.000	0.000
17	A	116	GLY	0	-0.026	-0.022	34.159	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	117	GLY	0	0.051	0.045	30.875	-0.004	-0.004	0.000	0.000	0.000	0.000
19	A	118	VAL	0	-0.022	0.002	29.160	-0.004	-0.004	0.000	0.000	0.000	0.000
20	A	119	LYS	1	0.842	0.902	21.401	0.051	0.051	0.000	0.000	0.000	0.000
21	A	120	VAL	0	-0.007	-0.004	23.164	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	121	ILE	0	0.043	0.008	17.478	0.009	0.009	0.000	0.000	0.000	0.000
23	A	122	ASP	-1	-0.847	-0.885	17.699	0.252	0.252	0.000	0.000	0.000	0.000
24	A	123	GLY	0	0.051	0.023	16.103	0.013	0.013	0.000	0.000	0.000	0.000
25	A	124	SER	0	-0.054	-0.054	14.166	0.024	0.024	0.000	0.000	0.000	0.000
26	A	125	SER	0	-0.053	-0.032	13.133	0.086	0.086	0.000	0.000	0.000	0.000
27	A	126	VAL	0	-0.024	-0.012	10.744	0.032	0.032	0.000	0.000	0.000	0.000
28	A	127	LYS	1	0.846	0.937	7.215	-0.456	-0.456	0.000	0.000	0.000	0.000
29	A	128	PHE	0	0.029	0.022	6.081	-0.055	-0.055	0.000	0.000	0.000	0.000
30	A	129	GLY	0	0.017	0.008	6.216	-0.386	-0.386	0.000	0.000	0.000	0.000
31	A	130	ARG	1	0.901	0.935	4.759	3.200	3.292	-0.001	-0.016	-0.074	0.000
32	A	131	PHE	0	0.009	0.008	8.959	0.188	0.188	0.000	0.000	0.000	0.000
33	A	132	ASP	-1	-0.870	-0.949	12.415	-0.738	-0.738	0.000	0.000	0.000	0.000
34	A	133	GLY	0	-0.067	-0.033	14.629	0.033	0.033	0.000	0.000	0.000	0.000
35	A	134	ALA	0	-0.016	0.003	13.393	0.053	0.053	0.000	0.000	0.000	0.000
36	A	135	GLU	-1	-0.914	-0.950	11.837	-1.075	-1.075	0.000	0.000	0.000	0.000
37	A	136	PRO	0	-0.102	-0.063	14.179	0.100	0.100	0.000	0.000	0.000	0.000
38	A	137	HIS	0	-0.044	-0.009	12.002	-0.106	-0.106	0.000	0.000	0.000	0.000
39	A	138	CYS	0	0.011	0.018	6.591	-0.470	-0.470	0.000	0.000	0.000	0.000
40	A	139	VAL	0	0.005	0.004	9.016	0.010	0.010	0.000	0.000	0.000	0.000
41	A	140	GLY	0	0.009	0.008	8.034	-0.142	-0.142	0.000	0.000	0.000	0.000
42	A	141	LEU	0	0.006	-0.008	8.619	0.226	0.226	0.000	0.000	0.000	0.000
43	A	142	THR	0	-0.041	-0.045	10.439	-0.132	-0.132	0.000	0.000	0.000	0.000
44	A	143	ASP	-1	-0.833	-0.878	12.757	-0.212	-0.212	0.000	0.000	0.000	0.000
45	A	144	LEU	0	-0.074	-0.041	14.704	0.028	0.028	0.000	0.000	0.000	0.000
46	A	145	VAL	0	-0.056	-0.024	18.270	0.027	0.027	0.000	0.000	0.000	0.000
47	A	146	THR	0	0.028	0.014	20.780	-0.019	-0.019	0.000	0.000	0.000	0.000
48	A	147	GLU	-1	-0.830	-0.932	23.515	-0.108	-0.108	0.000	0.000	0.000	0.000
49	A	148	GLN	0	-0.029	-0.013	24.561	0.011	0.011	0.000	0.000	0.000	0.000
50	A	149	ASP	-1	-0.825	-0.888	23.644	-0.052	-0.052	0.000	0.000	0.000	0.000
51	A	150	GLY	0	-0.059	-0.031	27.021	0.009	0.009	0.000	0.000	0.000	0.000
52	A	151	SER	0	-0.072	-0.040	26.551	0.009	0.009	0.000	0.000	0.000	0.000
53	A	152	SER	0	0.009	-0.010	28.679	-0.008	-0.008	0.000	0.000	0.000	0.000
54	A	153	MET	0	-0.042	-0.026	26.560	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	154	ALA	0	0.010	0.035	21.998	0.007	0.007	0.000	0.000	0.000	0.000
56	A	155	ALA	0	0.019	0.006	21.001	0.005	0.005	0.000	0.000	0.000	0.000
57	A	156	GLY	0	0.059	0.025	16.834	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	157	PHE	0	-0.061	-0.008	13.215	0.045	0.045	0.000	0.000	0.000	0.000
59	A	158	MET	0	0.040	0.021	12.203	-0.057	-0.057	0.000	0.000	0.000	0.000
60	A	159	GLN	0	0.012	0.002	8.608	0.151	0.151	0.000	0.000	0.000	0.000
61	A	160	TRP	0	-0.079	-0.029	8.894	-0.259	-0.259	0.000	0.000	0.000	0.000
62	A	161	ASP	-1	-0.825	-0.928	9.205	0.028	0.028	0.000	0.000	0.000	0.000
63	A	162	ASN	0	-0.116	-0.063	11.028	-0.083	-0.083	0.000	0.000	0.000	0.000
64	A	163	ALA	0	0.052	0.035	12.886	-0.049	-0.049	0.000	0.000	0.000	0.000
65	A	164	PHE	0	-0.013	-0.009	14.952	0.038	0.038	0.000	0.000	0.000	0.000
66	A	165	PHE	0	0.009	-0.001	15.242	-0.033	-0.033	0.000	0.000	0.000	0.000
67	A	166	PRO	0	0.034	0.029	18.742	0.024	0.024	0.000	0.000	0.000	0.000
68	A	167	TRP	0	-0.020	-0.022	20.321	-0.042	-0.042	0.000	0.000	0.000	0.000
69	A	168	THR	0	0.015	0.008	22.354	0.022	0.022	0.000	0.000	0.000	0.000
70	A	169	LEU	0	0.019	0.047	23.492	-0.010	-0.010	0.000	0.000	0.000	0.000
71	A	170	ASN	0	-0.042	-0.024	25.858	0.022	0.022	0.000	0.000	0.000	0.000
72	A	171	TYR	0	-0.043	-0.039	21.382	0.007	0.007	0.000	0.000	0.000	0.000
73	A	172	ASP	-1	-0.846	-0.915	27.402	-0.102	-0.102	0.000	0.000	0.000	0.000
74	A	173	GLU	-1	-0.831	-0.944	21.209	-0.212	-0.212	0.000	0.000	0.000	0.000
75	A	174	ILE	0	-0.041	-0.014	24.830	0.010	0.010	0.000	0.000	0.000	0.000
76	A	175	ASP	-1	-0.827	-0.920	20.837	-0.171	-0.171	0.000	0.000	0.000	0.000
77	A	176	MET	0	-0.066	-0.037	21.165	0.016	0.016	0.000	0.000	0.000	0.000
78	A	177	VAL	0	0.003	0.001	18.724	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	178	LEU	0	-0.068	-0.034	16.376	0.024	0.024	0.000	0.000	0.000	0.000
80	A	179	GLU	-1	-0.931	-0.989	13.664	0.219	0.219	0.000	0.000	0.000	0.000
81	A	180	GLY	0	0.006	0.014	16.767	-0.033	-0.033	0.000	0.000	0.000	0.000
82	A	181	GLU	-1	-0.843	-0.915	17.747	-0.054	-0.054	0.000	0.000	0.000	0.000
83	A	182	LEU	0	0.012	0.033	17.704	-0.027	-0.027	0.000	0.000	0.000	0.000
84	A	183	HIS	0	-0.076	-0.058	19.830	0.016	0.016	0.000	0.000	0.000	0.000
85	A	184	VAL	0	0.043	0.016	21.255	-0.025	-0.025	0.000	0.000	0.000	0.000
86	A	185	ARG	1	0.771	0.883	23.743	0.194	0.194	0.000	0.000	0.000	0.000
87	A	186	HIS	0	0.046	0.003	26.357	-0.017	-0.017	0.000	0.000	0.000	0.000
88	A	187	GLU	-1	-0.934	-0.970	29.077	-0.086	-0.086	0.000	0.000	0.000	0.000
89	A	188	GLY	0	-0.050	-0.022	30.935	0.007	0.007	0.000	0.000	0.000	0.000
90	A	189	GLU	-1	-0.962	-0.971	30.965	-0.078	-0.078	0.000	0.000	0.000	0.000
91	A	190	THR	0	-0.025	-0.025	25.263	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	191	MET	0	-0.010	0.007	26.934	0.015	0.015	0.000	0.000	0.000	0.000
93	A	192	ILE	0	-0.031	-0.033	23.475	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	193	ALA	0	-0.009	0.017	23.036	0.012	0.012	0.000	0.000	0.000	0.000
95	A	194	LYS	1	0.865	0.900	22.097	0.033	0.033	0.000	0.000	0.000	0.000
96	A	195	ALA	0	0.001	-0.003	20.378	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	196	GLY	0	-0.030	-0.019	21.944	0.008	0.008	0.000	0.000	0.000	0.000
98	A	197	ASP	-1	-0.865	-0.910	24.276	-0.030	-0.030	0.000	0.000	0.000	0.000
99	A	198	VAL	0	-0.050	-0.047	24.245	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	199	MET	0	-0.024	-0.007	23.515	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	200	PHE	0	-0.036	-0.029	26.296	0.002	0.002	0.000	0.000	0.000	0.000
102	A	201	ILE	0	0.025	0.021	23.332	0.003	0.003	0.000	0.000	0.000	0.000
103	A	202	PRO	0	0.002	0.008	27.644	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	203	LYS	1	0.961	0.990	29.435	0.094	0.094	0.000	0.000	0.000	0.000
105	A	204	GLY	0	-0.075	-0.039	29.664	0.008	0.008	0.000	0.000	0.000	0.000
106	A	205	SER	0	-0.028	-0.015	27.928	0.001	0.001	0.000	0.000	0.000	0.000
107	A	206	SER	0	-0.043	-0.032	27.038	-0.010	-0.010	0.000	0.000	0.000	0.000
108	A	207	ILE	0	-0.024	-0.020	22.302	0.015	0.015	0.000	0.000	0.000	0.000
109	A	208	GLU	-1	-0.878	-0.916	21.460	-0.252	-0.252	0.000	0.000	0.000	0.000
110	A	209	PHE	0	0.058	0.024	17.936	0.019	0.019	0.000	0.000	0.000	0.000
111	A	210	GLY	0	0.026	-0.012	17.302	-0.034	-0.034	0.000	0.000	0.000	0.000
112	A	211	THR	0	-0.024	-0.011	14.409	0.041	0.041	0.000	0.000	0.000	0.000
113	A	212	PRO	0	-0.002	0.010	16.415	-0.032	-0.032	0.000	0.000	0.000	0.000
114	A	213	THR	0	-0.058	-0.034	15.753	0.007	0.007	0.000	0.000	0.000	0.000
115	A	214	SER	0	0.038	0.034	12.408	-0.014	-0.014	0.000	0.000	0.000	0.000
116	A	215	VAL	0	-0.022	-0.002	13.004	0.041	0.041	0.000	0.000	0.000	0.000
117	A	216	ARG	1	0.914	0.968	11.067	-0.212	-0.212	0.000	0.000	0.000	0.000
118	A	217	PHE	0	-0.029	-0.011	14.053	0.039	0.039	0.000	0.000	0.000	0.000
119	A	218	LEU	0	-0.024	-0.003	15.901	-0.025	-0.025	0.000	0.000	0.000	0.000
120	A	219	TYR	0	0.040	0.013	15.425	-0.003	-0.003	0.000	0.000	0.000	0.000
121	A	220	VAL	0	-0.024	-0.034	20.204	0.010	0.010	0.000	0.000	0.000	0.000
122	A	221	ALA	0	0.022	0.013	23.262	0.000	0.000	0.000	0.000	0.000	0.000
123	A	222	TRP	0	-0.028	0.007	24.949	0.009	0.009	0.000	0.000	0.000	0.000
124	A	223	PRO	0	-0.017	-0.022	28.405	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	224	ALA	0	0.034	0.000	25.801	-0.011	-0.011	0.000	0.000	0.000	0.000
126	A	225	ASN	0	-0.029	-0.006	25.182	-0.012	-0.012	0.000	0.000	0.000	0.000
127	A	226	TRP	0	0.010	0.004	20.380	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	227	GLN	0	-0.034	0.007	19.701	-0.009	-0.009	0.000	0.000	0.000	0.000

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