FMO DATABASE

FMODB ID: 43VJN

Calculation Name: 3PUF-O-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PUF

Chain ID: O

ChEMBL ID:

UniProt ID: O75792

Base Structure: X-ray

Registration Date: 2023-06-19

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	116
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-747773.373038
FMO2-HF: Nuclear repulsion	704342.794793
FMO2-HF: Total energy	-43430.578246
FMO2-MP2: Total energy	-43558.323963

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(O:9:ILE)

Summations of interaction energy for fragment #1(O:9:ILE)

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.
-15.568	-7.744	3.874	-4.901	-6.795	0.004

Interaction energy analysis for fragmet #1(O:9:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.044 / q_NPA : 0.007

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	O	11	ARG	1	0.934	0.976	2.963	-13.116	-8.273	0.616	-2.368	-3.091	0.018
4	O	12	HIS	0	-0.034	-0.020	2.660	-1.511	0.880	3.246	-2.437	-3.200	-0.014
5	O	13	ARG	1	0.887	0.951	3.381	-0.459	0.115	0.013	-0.091	-0.495	0.000
6	O	14	VAL	0	0.016	0.003	5.214	0.295	0.311	-0.001	-0.005	-0.009	0.000
7	O	15	HIS	0	-0.029	-0.007	5.972	-0.107	-0.107	0.000	0.000	0.000	0.000
8	O	16	LEU	0	0.051	0.030	10.263	0.073	0.073	0.000	0.000	0.000	0.000
9	O	25	VAL	0	-0.001	-0.005	27.315	0.000	0.000	0.000	0.000	0.000	0.000
10	O	26	PRO	0	0.009	0.000	29.821	0.001	0.001	0.000	0.000	0.000	0.000
11	O	27	ALA	0	0.020	0.018	30.229	0.004	0.004	0.000	0.000	0.000	0.000
12	O	28	THR	0	-0.024	-0.013	32.263	-0.002	-0.002	0.000	0.000	0.000	0.000
13	O	29	LEU	0	0.019	0.013	28.474	0.005	0.005	0.000	0.000	0.000	0.000
14	O	30	HIS	0	0.025	0.011	33.168	-0.001	-0.001	0.000	0.000	0.000	0.000
15	O	31	LEU	0	0.001	0.009	31.822	0.003	0.003	0.000	0.000	0.000	0.000
16	O	32	LEU	0	0.020	0.005	34.771	-0.002	-0.002	0.000	0.000	0.000	0.000
17	O	33	PRO	0	-0.015	0.006	36.165	0.002	0.002	0.000	0.000	0.000	0.000
18	O	34	CYS	0	-0.059	-0.044	37.441	0.000	0.000	0.000	0.000	0.000	0.000
19	O	35	GLU	-1	-0.893	-0.928	32.857	0.065	0.065	0.000	0.000	0.000	0.000
20	O	36	VAL	0	-0.047	-0.040	34.165	-0.003	-0.003	0.000	0.000	0.000	0.000
21	O	37	ALA	0	-0.010	0.003	33.741	0.003	0.003	0.000	0.000	0.000	0.000
22	O	38	VAL	0	-0.066	-0.038	33.484	0.004	0.004	0.000	0.000	0.000	0.000
23	O	39	ASP	-1	-0.859	-0.930	27.145	0.076	0.076	0.000	0.000	0.000	0.000
24	O	40	GLY	0	0.010	0.020	30.219	0.004	0.004	0.000	0.000	0.000	0.000
25	O	41	PRO	0	-0.051	-0.022	31.074	-0.006	-0.006	0.000	0.000	0.000	0.000
26	O	42	ALA	0	0.078	0.026	34.019	0.002	0.002	0.000	0.000	0.000	0.000
27	O	43	PRO	0	-0.038	-0.009	37.153	-0.004	-0.004	0.000	0.000	0.000	0.000
28	O	44	VAL	0	0.051	0.008	36.571	-0.002	-0.002	0.000	0.000	0.000	0.000
29	O	45	GLY	0	0.050	0.017	39.810	-0.002	-0.002	0.000	0.000	0.000	0.000
30	O	46	ARG	1	0.922	0.951	41.476	-0.022	-0.022	0.000	0.000	0.000	0.000
31	O	47	PHE	0	-0.036	-0.012	43.442	0.000	0.000	0.000	0.000	0.000	0.000
32	O	48	PHE	0	0.001	0.009	40.587	0.000	0.000	0.000	0.000	0.000	0.000
33	O	49	THR	0	0.074	0.014	40.699	-0.001	-0.001	0.000	0.000	0.000	0.000
34	O	50	PRO	0	-0.063	-0.024	43.550	-0.002	-0.002	0.000	0.000	0.000	0.000
35	O	51	ALA	0	0.009	0.017	46.507	0.000	0.000	0.000	0.000	0.000	0.000
36	O	52	ILE	0	-0.051	-0.018	42.071	0.000	0.000	0.000	0.000	0.000	0.000
37	O	53	ARG	1	0.784	0.896	46.692	-0.011	-0.011	0.000	0.000	0.000	0.000
38	O	54	GLN	0	-0.018	-0.016	48.600	0.000	0.000	0.000	0.000	0.000	0.000
39	O	55	GLY	0	0.056	0.035	50.621	0.000	0.000	0.000	0.000	0.000	0.000
40	O	56	PRO	0	-0.014	-0.017	51.921	-0.001	-0.001	0.000	0.000	0.000	0.000
41	O	57	GLU	-1	-0.877	-0.930	50.880	0.005	0.005	0.000	0.000	0.000	0.000
42	O	58	GLY	0	0.003	0.009	47.607	0.000	0.000	0.000	0.000	0.000	0.000
43	O	59	LEU	0	0.000	0.012	43.166	0.000	0.000	0.000	0.000	0.000	0.000
44	O	60	GLU	-1	-0.864	-0.929	46.530	0.009	0.009	0.000	0.000	0.000	0.000
45	O	61	VAL	0	0.038	0.016	43.312	-0.001	-0.001	0.000	0.000	0.000	0.000
46	O	62	SER	0	-0.018	-0.011	46.635	0.000	0.000	0.000	0.000	0.000	0.000
47	O	63	PHE	0	0.018	0.013	39.765	0.000	0.000	0.000	0.000	0.000	0.000
48	O	64	ARG	1	0.926	0.955	41.454	-0.039	-0.039	0.000	0.000	0.000	0.000
49	O	65	GLY	0	0.040	0.026	46.043	0.001	0.001	0.000	0.000	0.000	0.000
50	O	66	ARG	1	0.790	0.871	45.924	-0.025	-0.025	0.000	0.000	0.000	0.000
51	O	67	CYS	0	0.022	0.014	47.416	-0.001	-0.001	0.000	0.000	0.000	0.000
52	O	68	LEU	0	-0.025	-0.011	41.641	0.001	0.001	0.000	0.000	0.000	0.000
53	O	69	ARG	1	0.912	0.933	45.093	-0.008	-0.008	0.000	0.000	0.000	0.000
54	O	70	GLY	0	0.019	-0.014	42.511	0.002	0.002	0.000	0.000	0.000	0.000
55	O	71	GLU	-1	-0.805	-0.856	40.038	-0.006	-0.006	0.000	0.000	0.000	0.000
56	O	72	GLU	-1	-0.828	-0.898	38.244	-0.014	-0.014	0.000	0.000	0.000	0.000
57	O	73	VAL	0	-0.010	0.009	34.663	-0.002	-0.002	0.000	0.000	0.000	0.000
58	O	74	ALA	0	-0.005	-0.017	34.902	0.000	0.000	0.000	0.000	0.000	0.000
59	O	75	VAL	0	-0.026	-0.014	28.324	0.002	0.002	0.000	0.000	0.000	0.000
60	O	76	PRO	0	0.010	0.006	29.247	-0.002	-0.002	0.000	0.000	0.000	0.000
61	O	77	PRO	0	0.008	0.002	29.911	-0.005	-0.005	0.000	0.000	0.000	0.000
62	O	78	GLY	0	0.027	0.011	28.420	-0.001	-0.001	0.000	0.000	0.000	0.000
63	O	79	LEU	0	-0.048	-0.012	24.758	-0.009	-0.009	0.000	0.000	0.000	0.000
64	O	80	VAL	0	-0.013	-0.015	24.414	0.004	0.004	0.000	0.000	0.000	0.000
65	O	81	GLY	0	0.013	0.023	24.581	-0.002	-0.002	0.000	0.000	0.000	0.000
66	O	82	TYR	0	0.002	-0.017	22.161	-0.004	-0.004	0.000	0.000	0.000	0.000
67	O	83	VAL	0	0.001	0.007	23.993	0.008	0.008	0.000	0.000	0.000	0.000
68	O	84	MET	0	-0.001	-0.016	18.124	-0.012	-0.012	0.000	0.000	0.000	0.000
69	O	85	VAL	0	0.019	0.024	20.278	0.015	0.015	0.000	0.000	0.000	0.000
70	O	86	THR	0	0.024	0.011	17.001	-0.023	-0.023	0.000	0.000	0.000	0.000
71	O	118	ARG	1	0.893	0.927	7.719	-0.471	-0.471	0.000	0.000	0.000	0.000
72	O	119	PHE	0	-0.039	-0.034	9.977	-0.147	-0.147	0.000	0.000	0.000	0.000
73	O	120	ILE	0	0.010	0.013	12.704	0.059	0.059	0.000	0.000	0.000	0.000
74	O	121	GLY	0	0.038	0.022	15.626	-0.042	-0.042	0.000	0.000	0.000	0.000
75	O	122	ALA	0	-0.020	-0.008	18.428	0.016	0.016	0.000	0.000	0.000	0.000
76	O	123	THR	0	-0.034	-0.023	21.292	0.005	0.005	0.000	0.000	0.000	0.000
77	O	124	ALA	0	0.005	-0.001	24.775	0.001	0.001	0.000	0.000	0.000	0.000
78	O	125	ASN	0	0.016	0.012	25.581	-0.008	-0.008	0.000	0.000	0.000	0.000
79	O	126	PHE	0	-0.043	-0.024	26.412	0.005	0.005	0.000	0.000	0.000	0.000
80	O	127	SER	0	0.042	0.013	29.264	-0.004	-0.004	0.000	0.000	0.000	0.000
81	O	128	ARG	1	0.836	0.895	31.957	0.021	0.021	0.000	0.000	0.000	0.000
82	O	129	PHE	0	-0.029	-0.002	31.336	0.001	0.001	0.000	0.000	0.000	0.000
83	O	130	THR	0	0.021	0.018	34.481	-0.002	-0.002	0.000	0.000	0.000	0.000
84	O	131	LEU	0	-0.035	-0.011	35.666	0.003	0.003	0.000	0.000	0.000	0.000
85	O	132	TRP	0	-0.011	-0.021	37.875	-0.001	-0.001	0.000	0.000	0.000	0.000
86	O	133	GLY	0	0.026	-0.003	39.503	0.002	0.002	0.000	0.000	0.000	0.000
87	O	134	LEU	0	-0.030	-0.006	42.180	0.000	0.000	0.000	0.000	0.000	0.000
88	O	135	GLU	-1	-0.753	-0.860	44.815	0.019	0.019	0.000	0.000	0.000	0.000
89	O	136	THR	0	-0.046	-0.017	46.454	-0.002	-0.002	0.000	0.000	0.000	0.000
90	O	137	ILE	0	0.002	0.012	42.721	0.001	0.001	0.000	0.000	0.000	0.000
91	O	138	PRO	0	-0.005	0.001	39.324	0.000	0.000	0.000	0.000	0.000	0.000
92	O	139	GLY	0	0.100	0.066	41.772	-0.003	-0.003	0.000	0.000	0.000	0.000
93	O	140	PRO	0	0.005	-0.018	40.794	0.000	0.000	0.000	0.000	0.000	0.000
94	O	141	ASP	-1	-0.891	-0.942	39.471	0.008	0.008	0.000	0.000	0.000	0.000
95	O	142	ALA	0	-0.009	0.005	37.576	0.003	0.003	0.000	0.000	0.000	0.000
96	O	143	LYS	1	0.987	0.970	32.840	-0.026	-0.026	0.000	0.000	0.000	0.000
97	O	144	VAL	0	0.014	0.017	31.723	-0.002	-0.002	0.000	0.000	0.000	0.000
98	O	145	ARG	1	0.751	0.831	32.263	-0.003	-0.003	0.000	0.000	0.000	0.000
99	O	146	GLY	0	0.040	0.025	33.373	-0.004	-0.004	0.000	0.000	0.000	0.000
100	O	147	ALA	0	-0.009	-0.007	28.255	-0.005	-0.005	0.000	0.000	0.000	0.000
101	O	148	LEU	0	-0.003	-0.004	28.546	-0.006	-0.006	0.000	0.000	0.000	0.000
102	O	149	THR	0	-0.035	-0.017	30.455	-0.006	-0.006	0.000	0.000	0.000	0.000
103	O	150	TRP	0	0.023	0.024	23.278	-0.006	-0.006	0.000	0.000	0.000	0.000
104	O	151	PRO	0	0.031	0.009	24.814	-0.005	-0.005	0.000	0.000	0.000	0.000
105	O	152	SER	0	-0.043	-0.027	26.111	-0.008	-0.008	0.000	0.000	0.000	0.000
106	O	153	LEU	0	0.018	0.011	28.801	-0.004	-0.004	0.000	0.000	0.000	0.000
107	O	154	ALA	0	-0.008	-0.008	23.400	-0.004	-0.004	0.000	0.000	0.000	0.000
108	O	155	ALA	0	-0.005	-0.009	24.324	-0.009	-0.009	0.000	0.000	0.000	0.000
109	O	156	ALA	0	-0.024	-0.005	25.346	-0.006	-0.006	0.000	0.000	0.000	0.000
110	O	157	ILE	0	-0.047	-0.027	24.846	-0.001	-0.001	0.000	0.000	0.000	0.000
111	O	158	HIS	0	-0.036	-0.016	21.340	-0.007	-0.007	0.000	0.000	0.000	0.000
112	O	159	ALA	0	-0.015	0.008	22.799	-0.015	-0.015	0.000	0.000	0.000	0.000
113	O	160	GLN	0	-0.024	-0.019	22.075	0.003	0.003	0.000	0.000	0.000	0.000
114	O	161	VAL	0	0.031	0.015	24.938	0.005	0.005	0.000	0.000	0.000	0.000
115	O	162	PRO	0	-0.065	-0.020	27.606	-0.008	-0.008	0.000	0.000	0.000	0.000
116	O	163	GLU	-1	-0.962	-0.977	28.137	-0.093	-0.093	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(O:9:ILE)