FMO DATABASE

FMODB ID: K3LG3

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

Total energy (hartree)

FMO2-HF: Electronic energy	-745640.38087
FMO2-HF: Nuclear repulsion	702210.061021
FMO2-HF: Total energy	-43430.319849
FMO2-MP2: Total energy	-43558.047529

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.
-13.271	-7.167	3.714	-4.247	-5.57	-0.005

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 : -0.003 / q_NPA : -0.012

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	0.947	0.979	3.428	-9.740	-5.978	0.096	-1.811	-2.047	0.008
4	O	12	HIS	0	-0.021	-0.011	2.566	-2.622	-0.637	3.617	-2.387	-3.215	-0.013
5	O	13	ARG	1	0.905	0.953	3.718	-0.296	0.061	0.001	-0.049	-0.308	0.000
6	O	14	VAL	0	0.018	0.009	5.728	0.193	0.193	0.000	0.000	0.000	0.000
7	O	15	HIS	0	0.022	0.024	6.047	-0.021	-0.021	0.000	0.000	0.000	0.000
8	O	16	LEU	0	0.055	0.037	10.609	0.073	0.073	0.000	0.000	0.000	0.000
9	O	25	VAL	0	0.006	-0.006	27.778	0.000	0.000	0.000	0.000	0.000	0.000
10	O	26	PRO	0	0.000	0.000	30.208	0.000	0.000	0.000	0.000	0.000	0.000
11	O	27	ALA	0	0.008	0.011	30.288	0.004	0.004	0.000	0.000	0.000	0.000
12	O	28	THR	0	-0.033	-0.015	32.278	-0.002	-0.002	0.000	0.000	0.000	0.000
13	O	29	LEU	0	0.015	0.006	28.864	0.004	0.004	0.000	0.000	0.000	0.000
14	O	30	HIS	0	0.047	0.019	33.614	-0.003	-0.003	0.000	0.000	0.000	0.000
15	O	31	LEU	0	0.006	0.018	31.875	0.004	0.004	0.000	0.000	0.000	0.000
16	O	32	LEU	0	0.016	-0.005	34.856	-0.003	-0.003	0.000	0.000	0.000	0.000
17	O	33	PRO	0	-0.016	0.004	36.491	0.003	0.003	0.000	0.000	0.000	0.000
18	O	34	CYS	0	-0.053	-0.035	37.871	0.000	0.000	0.000	0.000	0.000	0.000
19	O	35	GLU	-1	-0.904	-0.939	33.455	0.073	0.073	0.000	0.000	0.000	0.000
20	O	36	VAL	0	-0.070	-0.047	34.579	-0.002	-0.002	0.000	0.000	0.000	0.000
21	O	37	ALA	0	0.022	0.002	34.168	0.003	0.003	0.000	0.000	0.000	0.000
22	O	38	VAL	0	-0.072	-0.028	33.190	0.005	0.005	0.000	0.000	0.000	0.000
23	O	39	ASP	-1	-0.854	-0.927	27.781	0.094	0.094	0.000	0.000	0.000	0.000
24	O	40	GLY	0	0.002	0.006	30.883	0.005	0.005	0.000	0.000	0.000	0.000
25	O	41	PRO	0	-0.044	-0.017	31.798	-0.006	-0.006	0.000	0.000	0.000	0.000
26	O	42	ALA	0	0.071	0.022	34.668	0.002	0.002	0.000	0.000	0.000	0.000
27	O	43	PRO	0	-0.053	-0.014	37.724	-0.004	-0.004	0.000	0.000	0.000	0.000
28	O	44	VAL	0	0.049	0.009	36.911	-0.002	-0.002	0.000	0.000	0.000	0.000
29	O	45	GLY	0	0.047	0.023	40.193	-0.002	-0.002	0.000	0.000	0.000	0.000
30	O	46	ARG	1	0.918	0.954	41.970	-0.027	-0.027	0.000	0.000	0.000	0.000
31	O	47	PHE	0	-0.016	-0.012	43.775	-0.001	-0.001	0.000	0.000	0.000	0.000
32	O	48	PHE	0	0.018	0.009	40.822	-0.001	-0.001	0.000	0.000	0.000	0.000
33	O	49	THR	0	0.074	0.017	40.885	-0.001	-0.001	0.000	0.000	0.000	0.000
34	O	50	PRO	0	-0.066	-0.023	43.751	-0.002	-0.002	0.000	0.000	0.000	0.000
35	O	51	ALA	0	0.000	0.015	46.870	-0.001	-0.001	0.000	0.000	0.000	0.000
36	O	52	ILE	0	-0.055	-0.019	42.616	0.000	0.000	0.000	0.000	0.000	0.000
37	O	53	ARG	1	0.812	0.904	47.247	-0.015	-0.015	0.000	0.000	0.000	0.000
38	O	54	GLN	0	-0.024	-0.023	48.831	0.000	0.000	0.000	0.000	0.000	0.000
39	O	55	GLY	0	0.058	0.039	50.754	0.000	0.000	0.000	0.000	0.000	0.000
40	O	56	PRO	0	-0.032	-0.024	51.960	-0.001	-0.001	0.000	0.000	0.000	0.000
41	O	57	GLU	-1	-0.880	-0.933	51.172	0.009	0.009	0.000	0.000	0.000	0.000
42	O	58	GLY	0	-0.001	-0.011	47.946	0.000	0.000	0.000	0.000	0.000	0.000
43	O	59	LEU	0	-0.021	0.009	43.658	0.000	0.000	0.000	0.000	0.000	0.000
44	O	60	GLU	-1	-0.836	-0.918	47.100	0.013	0.013	0.000	0.000	0.000	0.000
45	O	61	VAL	0	0.025	0.018	43.909	-0.001	-0.001	0.000	0.000	0.000	0.000
46	O	62	SER	0	-0.006	0.005	47.042	0.000	0.000	0.000	0.000	0.000	0.000
47	O	63	PHE	0	0.004	0.002	40.196	0.000	0.000	0.000	0.000	0.000	0.000
48	O	64	ARG	1	0.934	0.951	41.949	-0.044	-0.044	0.000	0.000	0.000	0.000
49	O	65	GLY	0	0.029	0.020	46.453	0.001	0.001	0.000	0.000	0.000	0.000
50	O	66	ARG	1	0.816	0.899	46.337	-0.030	-0.030	0.000	0.000	0.000	0.000
51	O	67	CYS	0	0.011	0.006	47.388	0.000	0.000	0.000	0.000	0.000	0.000
52	O	68	LEU	0	-0.014	-0.005	42.005	0.001	0.001	0.000	0.000	0.000	0.000
53	O	69	ARG	1	0.937	0.957	45.388	-0.012	-0.012	0.000	0.000	0.000	0.000
54	O	70	GLY	0	0.028	-0.006	42.604	0.001	0.001	0.000	0.000	0.000	0.000
55	O	71	GLU	-1	-0.813	-0.872	40.626	0.000	0.000	0.000	0.000	0.000	0.000
56	O	72	GLU	-1	-0.846	-0.915	38.607	-0.007	-0.007	0.000	0.000	0.000	0.000
57	O	73	VAL	0	-0.016	0.001	35.143	-0.002	-0.002	0.000	0.000	0.000	0.000
58	O	74	ALA	0	-0.028	-0.025	35.222	0.000	0.000	0.000	0.000	0.000	0.000
59	O	75	VAL	0	-0.005	0.000	28.799	0.002	0.002	0.000	0.000	0.000	0.000
60	O	76	PRO	0	-0.004	-0.001	29.873	-0.003	-0.003	0.000	0.000	0.000	0.000
61	O	77	PRO	0	0.017	0.006	30.513	-0.004	-0.004	0.000	0.000	0.000	0.000
62	O	78	GLY	0	0.012	0.006	28.823	-0.001	-0.001	0.000	0.000	0.000	0.000
63	O	79	LEU	0	-0.022	-0.008	25.257	-0.006	-0.006	0.000	0.000	0.000	0.000
64	O	80	VAL	0	-0.023	-0.013	24.240	0.003	0.003	0.000	0.000	0.000	0.000
65	O	81	GLY	0	0.017	0.030	24.546	0.000	0.000	0.000	0.000	0.000	0.000
66	O	82	TYR	0	0.012	-0.017	21.968	-0.004	-0.004	0.000	0.000	0.000	0.000
67	O	83	VAL	0	0.014	0.014	23.844	0.009	0.009	0.000	0.000	0.000	0.000
68	O	84	MET	0	-0.029	-0.016	18.048	-0.007	-0.007	0.000	0.000	0.000	0.000
69	O	85	VAL	0	0.035	0.032	20.856	0.016	0.016	0.000	0.000	0.000	0.000
70	O	86	THR	0	-0.003	-0.003	17.672	-0.019	-0.019	0.000	0.000	0.000	0.000
71	O	118	ARG	1	0.892	0.927	7.907	-0.626	-0.626	0.000	0.000	0.000	0.000
72	O	119	PHE	0	-0.054	-0.049	10.493	-0.128	-0.128	0.000	0.000	0.000	0.000
73	O	120	ILE	0	0.019	0.017	13.138	0.051	0.051	0.000	0.000	0.000	0.000
74	O	121	GLY	0	0.057	0.033	15.888	-0.044	-0.044	0.000	0.000	0.000	0.000
75	O	122	ALA	0	-0.032	-0.020	18.653	0.019	0.019	0.000	0.000	0.000	0.000
76	O	123	THR	0	-0.017	-0.009	21.565	0.000	0.000	0.000	0.000	0.000	0.000
77	O	124	ALA	0	0.000	-0.006	25.026	-0.003	-0.003	0.000	0.000	0.000	0.000
78	O	125	ASN	0	0.010	0.013	25.923	-0.003	-0.003	0.000	0.000	0.000	0.000
79	O	126	PHE	0	-0.015	-0.020	26.405	0.004	0.004	0.000	0.000	0.000	0.000
80	O	127	SER	0	0.014	0.010	29.825	-0.002	-0.002	0.000	0.000	0.000	0.000
81	O	128	ARG	1	0.847	0.901	32.486	0.013	0.013	0.000	0.000	0.000	0.000
82	O	129	PHE	0	-0.019	0.004	31.775	0.002	0.002	0.000	0.000	0.000	0.000
83	O	130	THR	0	0.027	0.019	34.619	-0.003	-0.003	0.000	0.000	0.000	0.000
84	O	131	LEU	0	-0.027	-0.002	35.920	0.004	0.004	0.000	0.000	0.000	0.000
85	O	132	TRP	0	-0.027	-0.035	37.939	-0.002	-0.002	0.000	0.000	0.000	0.000
86	O	133	GLY	0	0.031	0.011	39.778	0.002	0.002	0.000	0.000	0.000	0.000
87	O	134	LEU	0	-0.027	-0.007	42.479	-0.001	-0.001	0.000	0.000	0.000	0.000
88	O	135	GLU	-1	-0.776	-0.874	45.027	0.024	0.024	0.000	0.000	0.000	0.000
89	O	136	THR	0	-0.054	-0.029	46.851	-0.002	-0.002	0.000	0.000	0.000	0.000
90	O	137	ILE	0	0.013	0.023	42.975	0.002	0.002	0.000	0.000	0.000	0.000
91	O	138	PRO	0	-0.026	-0.013	39.646	0.000	0.000	0.000	0.000	0.000	0.000
92	O	139	GLY	0	0.110	0.068	42.114	-0.003	-0.003	0.000	0.000	0.000	0.000
93	O	140	PRO	0	0.004	-0.025	41.179	0.000	0.000	0.000	0.000	0.000	0.000
94	O	141	ASP	-1	-0.903	-0.946	39.792	0.014	0.014	0.000	0.000	0.000	0.000
95	O	142	ALA	0	-0.014	0.004	37.787	0.003	0.003	0.000	0.000	0.000	0.000
96	O	143	LYS	1	1.007	0.977	33.136	-0.036	-0.036	0.000	0.000	0.000	0.000
97	O	144	VAL	0	0.007	0.007	31.929	-0.002	-0.002	0.000	0.000	0.000	0.000
98	O	145	ARG	1	0.747	0.843	32.575	-0.009	-0.009	0.000	0.000	0.000	0.000
99	O	146	GLY	0	0.043	0.030	33.904	-0.004	-0.004	0.000	0.000	0.000	0.000
100	O	147	ALA	0	-0.026	-0.015	28.666	-0.003	-0.003	0.000	0.000	0.000	0.000
101	O	148	LEU	0	-0.003	-0.011	28.908	-0.005	-0.005	0.000	0.000	0.000	0.000
102	O	149	THR	0	-0.025	-0.008	30.636	-0.006	-0.006	0.000	0.000	0.000	0.000
103	O	150	TRP	0	0.031	0.024	23.217	-0.006	-0.006	0.000	0.000	0.000	0.000
104	O	151	PRO	0	0.023	0.007	25.284	-0.005	-0.005	0.000	0.000	0.000	0.000
105	O	152	SER	0	-0.038	-0.019	26.552	-0.008	-0.008	0.000	0.000	0.000	0.000
106	O	153	LEU	0	0.021	0.015	29.372	-0.004	-0.004	0.000	0.000	0.000	0.000
107	O	154	ALA	0	-0.007	-0.012	23.850	-0.004	-0.004	0.000	0.000	0.000	0.000
108	O	155	ALA	0	-0.010	-0.013	24.637	-0.008	-0.008	0.000	0.000	0.000	0.000
109	O	156	ALA	0	-0.020	-0.002	25.678	-0.007	-0.007	0.000	0.000	0.000	0.000
110	O	157	ILE	0	-0.040	-0.019	25.523	-0.001	-0.001	0.000	0.000	0.000	0.000
111	O	158	HIS	0	-0.043	-0.026	21.501	-0.008	-0.008	0.000	0.000	0.000	0.000
112	O	159	ALA	0	-0.014	0.018	22.688	-0.015	-0.015	0.000	0.000	0.000	0.000
113	O	160	GLN	0	-0.016	-0.023	22.412	0.004	0.004	0.000	0.000	0.000	0.000
114	O	161	VAL	0	0.016	0.014	25.198	0.005	0.005	0.000	0.000	0.000	0.000
115	O	162	PRO	0	-0.061	-0.021	27.898	-0.007	-0.007	0.000	0.000	0.000	0.000
116	O	163	GLU	-1	-0.954	-0.974	28.100	-0.089	-0.089	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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