FMO DATABASE

FMODB ID: 4319N

Calculation Name: 3ONL-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ONL

Chain ID: C

ChEMBL ID:

UniProt ID: P47160

Base Structure: X-ray

Registration Date: 2023-06-20

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	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	95
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-669823.22563
FMO2-HF: Nuclear repulsion	632203.580105
FMO2-HF: Total energy	-37619.645525
FMO2-MP2: Total energy	-37730.939778

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(C:3:SER)

Summations of interaction energy for fragment #1(C:3:SER)

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.
-9.587	-8.8	12.459	-5.748	-7.498	0.027

Interaction energy analysis for fragmet #1(C:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / 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	C	5	LEU	0	0.072	0.077	3.008	-2.114	1.225	0.380	-1.668	-2.050	0.008
4	C	6	ILE	0	0.007	0.001	1.744	-7.916	-11.043	12.055	-3.939	-4.990	0.018
5	C	7	SER	0	-0.071	-0.054	3.521	-1.298	-0.723	0.024	-0.141	-0.458	0.001
6	C	8	TYR	0	0.101	0.033	5.521	0.169	0.169	0.000	0.000	0.000	0.000
7	C	9	GLU	-1	-0.821	-0.947	6.665	0.838	0.838	0.000	0.000	0.000	0.000
8	C	10	SER	0	-0.114	-0.060	7.032	-0.034	-0.034	0.000	0.000	0.000	0.000
9	C	11	ASP	-1	-0.848	-0.918	9.432	-0.300	-0.300	0.000	0.000	0.000	0.000
10	C	12	PHE	0	0.004	0.006	11.208	0.057	0.057	0.000	0.000	0.000	0.000
11	C	13	LYS	1	0.907	0.945	8.684	0.011	0.011	0.000	0.000	0.000	0.000
12	C	14	THR	0	-0.028	-0.010	12.810	0.006	0.006	0.000	0.000	0.000	0.000
13	C	15	THR	0	0.022	0.007	15.341	0.018	0.018	0.000	0.000	0.000	0.000
14	C	16	LEU	0	-0.037	-0.014	16.712	0.021	0.021	0.000	0.000	0.000	0.000
15	C	17	GLU	-1	-0.852	-0.922	18.028	-0.037	-0.037	0.000	0.000	0.000	0.000
16	C	18	GLN	0	-0.024	-0.011	18.636	0.016	0.016	0.000	0.000	0.000	0.000
17	C	19	ALA	0	0.068	0.050	21.371	0.009	0.009	0.000	0.000	0.000	0.000
18	C	20	LYS	1	0.859	0.906	21.034	0.027	0.027	0.000	0.000	0.000	0.000
19	C	21	ALA	0	-0.030	-0.002	24.068	0.006	0.006	0.000	0.000	0.000	0.000
20	C	22	SER	0	0.015	-0.004	25.456	0.003	0.003	0.000	0.000	0.000	0.000
21	C	23	LEU	0	-0.033	-0.019	26.385	0.005	0.005	0.000	0.000	0.000	0.000
22	C	24	ALA	0	-0.052	-0.023	28.691	0.005	0.005	0.000	0.000	0.000	0.000
23	C	25	GLU	-1	-0.945	-0.972	28.893	-0.075	-0.075	0.000	0.000	0.000	0.000
24	C	26	ALA	0	0.009	0.009	31.657	0.002	0.002	0.000	0.000	0.000	0.000
25	C	27	PRO	0	-0.031	-0.019	33.439	0.001	0.001	0.000	0.000	0.000	0.000
26	C	28	SER	0	-0.090	-0.034	35.664	0.001	0.001	0.000	0.000	0.000	0.000
27	C	29	GLN	0	0.065	0.065	31.658	0.000	0.000	0.000	0.000	0.000	0.000
28	C	30	PRO	0	0.020	0.006	37.403	0.004	0.004	0.000	0.000	0.000	0.000
29	C	31	LEU	0	0.021	0.006	38.623	-0.003	-0.003	0.000	0.000	0.000	0.000
30	C	32	SER	0	0.009	0.003	38.669	-0.001	-0.001	0.000	0.000	0.000	0.000
31	C	33	GLN	0	0.049	0.018	33.462	0.003	0.003	0.000	0.000	0.000	0.000
32	C	34	ARG	1	0.918	0.963	34.404	0.030	0.030	0.000	0.000	0.000	0.000
33	C	35	ASN	0	-0.007	-0.011	34.163	0.000	0.000	0.000	0.000	0.000	0.000
34	C	36	THR	0	-0.013	0.004	31.089	0.000	0.000	0.000	0.000	0.000	0.000
35	C	37	THR	0	-0.028	-0.039	29.436	-0.007	-0.007	0.000	0.000	0.000	0.000
36	C	38	LEU	0	0.018	0.005	29.259	-0.002	-0.002	0.000	0.000	0.000	0.000
37	C	39	LYS	1	0.974	0.994	29.644	0.063	0.063	0.000	0.000	0.000	0.000
38	C	40	HIS	0	-0.001	0.002	22.963	0.006	0.006	0.000	0.000	0.000	0.000
39	C	41	VAL	0	0.029	0.005	25.319	-0.004	-0.004	0.000	0.000	0.000	0.000
40	C	42	GLU	-1	-0.981	-0.997	25.046	-0.022	-0.022	0.000	0.000	0.000	0.000
41	C	43	GLN	0	-0.016	0.006	22.566	0.017	0.017	0.000	0.000	0.000	0.000
42	C	44	GLN	0	0.027	0.001	20.424	0.015	0.015	0.000	0.000	0.000	0.000
43	C	45	GLN	0	-0.019	-0.020	20.465	0.015	0.015	0.000	0.000	0.000	0.000
44	C	46	ASP	-1	-0.928	-0.966	21.303	0.003	0.003	0.000	0.000	0.000	0.000
45	C	47	GLU	-1	-0.885	-0.945	17.817	-0.133	-0.133	0.000	0.000	0.000	0.000
46	C	48	LEU	0	-0.049	-0.025	16.302	0.022	0.022	0.000	0.000	0.000	0.000
47	C	49	PHE	0	-0.065	-0.056	16.565	0.046	0.046	0.000	0.000	0.000	0.000
48	C	50	ASP	-1	-0.837	-0.902	17.240	0.043	0.043	0.000	0.000	0.000	0.000
49	C	51	LEU	0	-0.012	-0.011	11.378	0.057	0.057	0.000	0.000	0.000	0.000
50	C	52	LEU	0	-0.088	-0.034	12.372	0.125	0.125	0.000	0.000	0.000	0.000
51	C	53	ASP	-1	-0.903	-0.933	13.790	0.232	0.232	0.000	0.000	0.000	0.000
52	C	54	GLN	0	-0.031	-0.028	11.267	0.045	0.045	0.000	0.000	0.000	0.000
53	C	55	MET	0	-0.042	-0.020	8.527	0.094	0.094	0.000	0.000	0.000	0.000
54	C	56	ASP	-1	-0.876	-0.940	9.899	0.616	0.616	0.000	0.000	0.000	0.000
55	C	57	VAL	0	-0.021	-0.010	11.698	0.034	0.034	0.000	0.000	0.000	0.000
56	C	58	GLU	-1	-0.907	-0.967	5.552	0.894	0.894	0.000	0.000	0.000	0.000
57	C	59	VAL	0	-0.062	-0.021	7.799	0.183	0.183	0.000	0.000	0.000	0.000
58	C	60	ASN	0	-0.085	-0.052	9.198	-0.031	-0.031	0.000	0.000	0.000	0.000
59	C	61	ASN	0	-0.022	-0.004	9.506	-0.079	-0.079	0.000	0.000	0.000	0.000
60	C	62	SER	0	-0.048	-0.016	5.342	0.145	0.145	0.000	0.000	0.000	0.000
61	C	63	ILE	0	0.004	0.021	5.979	-0.026	-0.026	0.000	0.000	0.000	0.000
62	C	64	GLY	0	0.054	0.024	9.109	-0.141	-0.141	0.000	0.000	0.000	0.000
63	C	65	ASP	-1	-0.840	-0.926	12.097	0.346	0.346	0.000	0.000	0.000	0.000
64	C	66	ALA	0	-0.002	-0.011	13.902	0.041	0.041	0.000	0.000	0.000	0.000
65	C	67	SER	0	-0.031	-0.010	16.655	-0.013	-0.013	0.000	0.000	0.000	0.000
66	C	68	GLU	-1	-0.865	-0.931	9.360	0.827	0.827	0.000	0.000	0.000	0.000
67	C	69	ARG	1	0.851	0.906	12.389	-0.463	-0.463	0.000	0.000	0.000	0.000
68	C	70	ALA	0	-0.032	-0.013	13.394	-0.010	-0.010	0.000	0.000	0.000	0.000
69	C	71	THR	0	-0.025	-0.013	13.491	-0.042	-0.042	0.000	0.000	0.000	0.000
70	C	72	TYR	0	-0.016	-0.008	6.070	-0.062	-0.062	0.000	0.000	0.000	0.000
71	C	73	LYS	1	0.886	0.948	12.356	-0.449	-0.449	0.000	0.000	0.000	0.000
72	C	74	ALA	0	-0.033	-0.010	15.315	-0.047	-0.047	0.000	0.000	0.000	0.000
73	C	75	LYS	1	0.915	0.982	9.204	-0.711	-0.711	0.000	0.000	0.000	0.000
74	C	76	LEU	0	0.062	0.037	11.741	-0.058	-0.058	0.000	0.000	0.000	0.000
75	C	77	ARG	1	0.912	0.953	15.124	-0.290	-0.290	0.000	0.000	0.000	0.000
76	C	78	GLU	-1	-0.897	-0.954	18.104	0.093	0.093	0.000	0.000	0.000	0.000
77	C	79	TRP	0	0.069	0.021	10.641	-0.006	-0.006	0.000	0.000	0.000	0.000
78	C	80	LYS	1	0.989	1.003	17.730	-0.156	-0.156	0.000	0.000	0.000	0.000
79	C	81	LYS	1	0.803	0.893	19.903	-0.134	-0.134	0.000	0.000	0.000	0.000
80	C	82	THR	0	0.036	0.028	19.916	-0.015	-0.015	0.000	0.000	0.000	0.000
81	C	83	ILE	0	0.044	0.042	17.937	-0.016	-0.016	0.000	0.000	0.000	0.000
82	C	84	GLN	0	-0.080	-0.046	22.000	-0.010	-0.010	0.000	0.000	0.000	0.000
83	C	85	SER	0	-0.105	-0.080	25.173	-0.006	-0.006	0.000	0.000	0.000	0.000
84	C	86	ASP	-1	-0.828	-0.910	23.589	0.025	0.025	0.000	0.000	0.000	0.000
85	C	87	ILE	0	-0.009	0.002	22.109	-0.010	-0.010	0.000	0.000	0.000	0.000
86	C	88	LYS	1	0.962	0.986	25.468	-0.025	-0.025	0.000	0.000	0.000	0.000
87	C	89	ARG	1	0.907	0.961	27.277	-0.039	-0.039	0.000	0.000	0.000	0.000
88	C	90	PRO	0	-0.008	-0.012	28.333	-0.002	-0.002	0.000	0.000	0.000	0.000
89	C	91	LEU	0	0.054	0.044	27.834	-0.004	-0.004	0.000	0.000	0.000	0.000
90	C	92	GLN	0	0.014	-0.002	30.660	-0.005	-0.005	0.000	0.000	0.000	0.000
91	C	93	SER	0	-0.034	-0.011	32.965	-0.002	-0.002	0.000	0.000	0.000	0.000
92	C	94	LEU	0	-0.016	-0.011	32.515	-0.002	-0.002	0.000	0.000	0.000	0.000
93	C	95	VAL	0	-0.067	-0.030	33.217	-0.003	-0.003	0.000	0.000	0.000	0.000
94	C	96	ASP	-1	-0.923	-0.949	36.039	-0.003	-0.003	0.000	0.000	0.000	0.000
95	C	97	SER	0	-0.148	-0.066	38.562	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:3:SER)