FMO DATABASE

FMODB ID: R84N8

Calculation Name: 3ON0-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ON0

Chain ID: D

ChEMBL ID:

UniProt ID: P33788

Base Structure: X-ray

Registration Date: 2023-09-23

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	107
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-623954.748575
FMO2-HF: Nuclear repulsion	580169.686619
FMO2-HF: Total energy	-43785.061956
FMO2-MP2: Total energy	-43910.087191

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(D:2:PRO)

Summations of interaction energy for fragment #1(D:2:PRO)

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.
-1.412	0.87	-0.034	-0.978	-1.27	0.006

Interaction energy analysis for fragmet #1(D:2:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / 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

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	D	4	ILE	0	0.052	0.018	3.761	-1.079	1.203	-0.034	-0.978	-1.270	0.006
4	D	5	GLN	0	-0.070	-0.036	6.211	0.259	0.259	0.000	0.000	0.000	0.000
5	D	6	THR	0	0.047	0.021	9.897	0.074	0.074	0.000	0.000	0.000	0.000
6	D	7	TYR	0	-0.033	-0.012	12.263	0.029	0.029	0.000	0.000	0.000	0.000
7	D	8	VAL	0	0.013	0.020	15.253	0.005	0.005	0.000	0.000	0.000	0.000
8	D	9	ASN	0	0.021	0.014	17.784	0.025	0.025	0.000	0.000	0.000	0.000
9	D	10	ASN	0	0.077	-0.004	21.093	-0.025	-0.025	0.000	0.000	0.000	0.000
10	D	11	ASN	0	0.042	0.039	23.568	0.005	0.005	0.000	0.000	0.000	0.000
11	D	12	VAL	0	0.014	0.005	17.486	-0.007	-0.007	0.000	0.000	0.000	0.000
12	D	13	TYR	0	-0.010	-0.012	17.403	-0.014	-0.014	0.000	0.000	0.000	0.000
13	D	14	GLU	-1	-0.858	-0.927	20.141	-0.184	-0.184	0.000	0.000	0.000	0.000
14	D	15	GLN	0	0.020	0.010	21.320	-0.006	-0.006	0.000	0.000	0.000	0.000
15	D	16	ILE	0	-0.035	-0.011	15.795	-0.015	-0.015	0.000	0.000	0.000	0.000
16	D	17	THR	0	-0.077	-0.040	19.135	0.007	0.007	0.000	0.000	0.000	0.000
17	D	18	ASP	-1	-0.870	-0.938	20.365	-0.184	-0.184	0.000	0.000	0.000	0.000
18	D	19	LEU	0	-0.017	-0.015	19.424	0.006	0.006	0.000	0.000	0.000	0.000
19	D	20	VAL	0	-0.087	-0.043	17.167	0.004	0.004	0.000	0.000	0.000	0.000
20	D	21	THR	0	-0.004	-0.002	19.637	0.021	0.021	0.000	0.000	0.000	0.000
21	D	22	ILE	0	-0.035	-0.013	23.224	0.014	0.014	0.000	0.000	0.000	0.000
22	D	23	ARG	1	0.965	0.982	17.392	0.357	0.357	0.000	0.000	0.000	0.000
23	D	24	LYS	1	0.946	0.994	19.520	0.201	0.201	0.000	0.000	0.000	0.000
24	D	25	GLN	0	-0.052	-0.019	22.871	0.013	0.013	0.000	0.000	0.000	0.000
25	D	26	GLU	-1	-0.963	-0.987	24.203	-0.198	-0.198	0.000	0.000	0.000	0.000
26	D	27	GLY	0	-0.038	-0.017	25.299	0.000	0.000	0.000	0.000	0.000	0.000
27	D	28	ILE	0	-0.030	-0.012	18.797	0.000	0.000	0.000	0.000	0.000	0.000
28	D	29	GLU	-1	-0.902	-0.950	20.085	-0.113	-0.113	0.000	0.000	0.000	0.000
29	D	30	GLU	-1	-0.986	-0.996	15.637	-0.215	-0.215	0.000	0.000	0.000	0.000
30	D	31	ALA	0	-0.004	0.009	15.442	-0.058	-0.058	0.000	0.000	0.000	0.000
31	D	32	SER	0	-0.034	-0.048	12.219	0.000	0.000	0.000	0.000	0.000	0.000
32	D	33	LEU	0	0.096	0.034	13.584	-0.065	-0.065	0.000	0.000	0.000	0.000
33	D	34	SER	0	-0.005	0.024	8.040	0.024	0.024	0.000	0.000	0.000	0.000
34	D	35	ASN	0	0.021	0.030	10.272	-0.096	-0.096	0.000	0.000	0.000	0.000
35	D	36	VAL	0	0.050	0.021	11.273	-0.071	-0.071	0.000	0.000	0.000	0.000
36	D	37	SER	0	-0.004	-0.045	11.134	0.023	0.023	0.000	0.000	0.000	0.000
37	D	38	SER	0	-0.016	0.004	8.209	-0.177	-0.177	0.000	0.000	0.000	0.000
38	D	39	MET	0	0.001	0.019	9.686	0.033	0.033	0.000	0.000	0.000	0.000
39	D	40	LEU	0	0.012	-0.014	12.527	0.057	0.057	0.000	0.000	0.000	0.000
40	D	41	LEU	0	-0.048	-0.017	8.044	0.053	0.053	0.000	0.000	0.000	0.000
41	D	42	GLU	-1	-0.935	-0.966	9.557	-1.039	-1.039	0.000	0.000	0.000	0.000
42	D	43	LEU	0	-0.095	-0.051	11.809	0.102	0.102	0.000	0.000	0.000	0.000
43	D	44	GLY	0	0.011	-0.007	14.926	0.062	0.062	0.000	0.000	0.000	0.000
44	D	45	LEU	0	-0.034	-0.021	9.822	0.046	0.046	0.000	0.000	0.000	0.000
45	D	46	ARG	1	0.895	0.965	14.402	0.519	0.519	0.000	0.000	0.000	0.000
46	D	47	VAL	0	-0.026	0.003	16.881	0.066	0.066	0.000	0.000	0.000	0.000
47	D	59	PHE	0	0.033	0.001	22.745	0.003	0.003	0.000	0.000	0.000	0.000
48	D	60	ASN	0	0.007	-0.004	22.044	-0.010	-0.010	0.000	0.000	0.000	0.000
49	D	61	GLN	0	0.084	0.048	24.163	0.012	0.012	0.000	0.000	0.000	0.000
50	D	62	MET	0	0.024	0.023	25.824	0.016	0.016	0.000	0.000	0.000	0.000
51	D	63	GLU	-1	-0.892	-0.947	26.385	-0.166	-0.166	0.000	0.000	0.000	0.000
52	D	64	TYR	0	-0.020	-0.016	28.135	0.013	0.013	0.000	0.000	0.000	0.000
53	D	65	ASN	0	0.016	-0.014	29.999	0.016	0.016	0.000	0.000	0.000	0.000
54	D	66	LYS	1	0.941	0.983	31.317	0.149	0.149	0.000	0.000	0.000	0.000
55	D	67	LEU	0	0.028	0.013	32.445	0.008	0.008	0.000	0.000	0.000	0.000
56	D	68	MET	0	0.000	0.001	34.113	0.009	0.009	0.000	0.000	0.000	0.000
57	D	69	LEU	0	0.010	0.015	35.909	0.007	0.007	0.000	0.000	0.000	0.000
58	D	70	GLU	-1	-0.867	-0.926	37.128	-0.091	-0.091	0.000	0.000	0.000	0.000
59	D	71	ASN	0	0.023	0.002	37.799	0.006	0.006	0.000	0.000	0.000	0.000
60	D	72	VAL	0	0.017	0.014	40.121	0.005	0.005	0.000	0.000	0.000	0.000
61	D	73	SER	0	-0.020	-0.014	41.628	0.006	0.006	0.000	0.000	0.000	0.000
62	D	74	ARG	1	0.857	0.919	40.548	0.085	0.085	0.000	0.000	0.000	0.000
63	D	75	VAL	0	0.017	0.006	44.183	0.004	0.004	0.000	0.000	0.000	0.000
64	D	76	ARG	1	0.980	0.996	46.073	0.060	0.060	0.000	0.000	0.000	0.000
65	D	77	ALA	0	-0.021	-0.004	47.573	0.003	0.003	0.000	0.000	0.000	0.000
66	D	78	MET	0	0.020	0.002	46.192	0.003	0.003	0.000	0.000	0.000	0.000
67	D	79	CYS	0	0.012	0.000	49.730	0.003	0.003	0.000	0.000	0.000	0.000
68	D	80	THR	0	-0.056	-0.019	51.904	0.003	0.003	0.000	0.000	0.000	0.000
69	D	81	GLU	-1	-0.880	-0.946	53.639	-0.044	-0.044	0.000	0.000	0.000	0.000
70	D	82	ILE	0	0.018	0.005	52.590	0.002	0.002	0.000	0.000	0.000	0.000
71	D	83	LEU	0	-0.019	-0.001	56.130	0.002	0.002	0.000	0.000	0.000	0.000
72	D	84	LYS	1	0.865	0.930	56.888	0.046	0.046	0.000	0.000	0.000	0.000
73	D	85	MET	0	0.013	0.003	57.013	0.002	0.002	0.000	0.000	0.000	0.000
74	D	86	SER	0	-0.007	-0.006	59.470	0.001	0.001	0.000	0.000	0.000	0.000
75	D	87	VAL	0	-0.030	-0.007	62.026	0.001	0.001	0.000	0.000	0.000	0.000
76	D	88	LEU	0	-0.043	-0.021	64.113	0.001	0.001	0.000	0.000	0.000	0.000
77	D	89	ASN	0	-0.023	0.012	64.855	0.001	0.001	0.000	0.000	0.000	0.000
78	D	90	GLN	0	0.013	0.005	66.796	0.001	0.001	0.000	0.000	0.000	0.000
79	D	91	GLU	-1	-0.870	-0.950	68.276	-0.026	-0.026	0.000	0.000	0.000	0.000
80	D	92	SER	0	-0.054	-0.038	65.258	0.001	0.001	0.000	0.000	0.000	0.000
81	D	93	ILE	0	0.009	0.005	68.112	0.001	0.001	0.000	0.000	0.000	0.000
82	D	94	ALA	0	-0.030	-0.016	70.748	0.001	0.001	0.000	0.000	0.000	0.000
83	D	95	SER	0	-0.077	-0.030	69.463	0.000	0.000	0.000	0.000	0.000	0.000
84	D	96	GLY	0	0.021	0.016	71.743	0.000	0.000	0.000	0.000	0.000	0.000
85	D	97	ASN	0	-0.028	-0.012	67.914	0.000	0.000	0.000	0.000	0.000	0.000
86	D	98	PHE	0	-0.078	-0.057	63.332	-0.001	-0.001	0.000	0.000	0.000	0.000
87	D	99	ASP	-1	-0.774	-0.878	66.337	-0.029	-0.029	0.000	0.000	0.000	0.000
88	D	100	TYR	0	0.030	-0.006	59.130	-0.001	-0.001	0.000	0.000	0.000	0.000
89	D	101	ALA	0	-0.008	-0.008	63.449	-0.001	-0.001	0.000	0.000	0.000	0.000
90	D	102	VAL	0	-0.014	-0.006	65.257	0.000	0.000	0.000	0.000	0.000	0.000
91	D	103	ILE	0	0.033	0.015	60.126	-0.001	-0.001	0.000	0.000	0.000	0.000
92	D	104	LYS	1	0.821	0.929	55.317	0.042	0.042	0.000	0.000	0.000	0.000
93	D	105	PRO	0	0.045	0.024	58.745	-0.001	-0.001	0.000	0.000	0.000	0.000
94	D	106	ALA	0	0.007	0.008	59.370	-0.001	-0.001	0.000	0.000	0.000	0.000
95	D	107	ILE	0	0.003	-0.008	54.776	-0.001	-0.001	0.000	0.000	0.000	0.000
96	D	108	ASP	-1	-0.873	-0.926	54.888	-0.044	-0.044	0.000	0.000	0.000	0.000
97	D	109	LYS	1	0.857	0.914	54.943	0.030	0.030	0.000	0.000	0.000	0.000
98	D	110	PHE	0	0.038	0.024	51.551	0.000	0.000	0.000	0.000	0.000	0.000
99	D	111	ALA	0	0.006	-0.003	50.798	-0.001	-0.001	0.000	0.000	0.000	0.000
100	D	112	ARG	1	0.938	0.967	50.909	0.039	0.039	0.000	0.000	0.000	0.000
101	D	113	GLU	-1	-0.895	-0.941	51.948	-0.034	-0.034	0.000	0.000	0.000	0.000
102	D	114	GLN	0	0.008	0.012	49.323	0.001	0.001	0.000	0.000	0.000	0.000
103	D	115	VAL	0	-0.028	-0.010	46.593	-0.001	-0.001	0.000	0.000	0.000	0.000
104	D	116	SER	0	-0.081	-0.058	47.614	-0.001	-0.001	0.000	0.000	0.000	0.000
105	D	117	ILE	0	-0.016	0.010	47.750	0.001	0.001	0.000	0.000	0.000	0.000
106	D	118	PHE	0	-0.025	-0.020	43.378	0.001	0.001	0.000	0.000	0.000	0.000
107	D	119	PHE	0	-0.064	-0.011	40.936	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(D:2:PRO)