FMO DATABASE

FMODB ID: YY5Y2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-674159.432292
FMO2-HF: Nuclear repulsion	636538.911546
FMO2-HF: Total energy	-37620.520746
FMO2-MP2: Total energy	-37731.79749

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.
-13.194	-7.25	4.792	-4.145	-6.589	0.033

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 : 0.056 / q_NPA : 0.021

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	0.070	0.056	2.691	-1.277	1.732	0.359	-1.535	-1.833	0.008
4	C	6	ILE	0	-0.004	0.002	2.126	-7.220	-5.065	4.423	-2.401	-4.176	0.024
5	C	7	SER	0	-0.066	-0.033	3.990	-1.643	-1.093	0.012	-0.181	-0.381	0.001
6	C	8	TYR	0	0.085	0.028	5.962	0.138	0.138	0.000	0.000	0.000	0.000
7	C	9	GLU	-1	-0.754	-0.874	6.811	-0.006	-0.006	0.000	0.000	0.000	0.000
8	C	10	SER	0	-0.094	-0.058	6.875	-0.023	-0.023	0.000	0.000	0.000	0.000
9	C	11	ASP	-1	-0.868	-0.907	9.464	-0.197	-0.197	0.000	0.000	0.000	0.000
10	C	12	PHE	0	0.030	0.007	11.566	0.030	0.030	0.000	0.000	0.000	0.000
11	C	13	LYS	1	0.849	0.905	9.378	-0.198	-0.198	0.000	0.000	0.000	0.000
12	C	14	THR	0	-0.036	-0.023	13.128	0.011	0.011	0.000	0.000	0.000	0.000
13	C	15	THR	0	0.012	-0.015	15.620	0.013	0.013	0.000	0.000	0.000	0.000
14	C	16	LEU	0	-0.009	0.006	17.074	0.003	0.003	0.000	0.000	0.000	0.000
15	C	17	GLU	-1	-0.846	-0.914	18.358	-0.009	-0.009	0.000	0.000	0.000	0.000
16	C	18	GLN	0	-0.006	0.012	18.791	-0.003	-0.003	0.000	0.000	0.000	0.000
17	C	19	ALA	0	0.045	0.045	21.523	0.003	0.003	0.000	0.000	0.000	0.000
18	C	20	LYS	1	0.844	0.889	21.604	0.021	0.021	0.000	0.000	0.000	0.000
19	C	21	ALA	0	-0.024	-0.003	24.341	0.003	0.003	0.000	0.000	0.000	0.000
20	C	22	SER	0	-0.002	-0.017	25.284	0.001	0.001	0.000	0.000	0.000	0.000
21	C	23	LEU	0	-0.037	-0.018	27.446	0.001	0.001	0.000	0.000	0.000	0.000
22	C	24	ALA	0	-0.027	-0.009	28.954	0.001	0.001	0.000	0.000	0.000	0.000
23	C	25	GLU	-1	-0.891	-0.930	29.639	-0.016	-0.016	0.000	0.000	0.000	0.000
24	C	26	ALA	0	0.014	0.022	31.856	0.001	0.001	0.000	0.000	0.000	0.000
25	C	27	PRO	0	-0.037	-0.024	33.678	0.000	0.000	0.000	0.000	0.000	0.000
26	C	28	SER	0	-0.098	-0.060	35.457	0.002	0.002	0.000	0.000	0.000	0.000
27	C	29	GLN	0	0.034	0.038	31.485	-0.001	-0.001	0.000	0.000	0.000	0.000
28	C	30	PRO	0	0.023	0.012	37.237	-0.001	-0.001	0.000	0.000	0.000	0.000
29	C	31	LEU	0	0.023	0.009	38.689	-0.001	-0.001	0.000	0.000	0.000	0.000
30	C	32	SER	0	0.029	0.010	38.817	-0.002	-0.002	0.000	0.000	0.000	0.000
31	C	33	GLN	0	0.016	0.011	33.253	-0.001	-0.001	0.000	0.000	0.000	0.000
32	C	34	ARG	1	0.918	0.965	34.484	0.020	0.020	0.000	0.000	0.000	0.000
33	C	35	ASN	0	0.006	-0.008	34.337	-0.001	-0.001	0.000	0.000	0.000	0.000
34	C	36	THR	0	-0.035	-0.011	31.472	-0.004	-0.004	0.000	0.000	0.000	0.000
35	C	37	THR	0	-0.020	-0.037	29.559	-0.005	-0.005	0.000	0.000	0.000	0.000
36	C	38	LEU	0	0.001	0.005	29.409	-0.003	-0.003	0.000	0.000	0.000	0.000
37	C	39	LYS	1	0.986	0.994	29.677	0.055	0.055	0.000	0.000	0.000	0.000
38	C	40	HIS	0	-0.014	0.002	23.369	-0.006	-0.006	0.000	0.000	0.000	0.000
39	C	41	VAL	0	0.011	-0.005	25.407	-0.006	-0.006	0.000	0.000	0.000	0.000
40	C	42	GLU	-1	-0.987	-0.997	25.223	-0.065	-0.065	0.000	0.000	0.000	0.000
41	C	43	GLN	0	-0.086	-0.046	22.532	0.003	0.003	0.000	0.000	0.000	0.000
42	C	44	GLN	0	0.055	0.008	20.174	0.001	0.001	0.000	0.000	0.000	0.000
43	C	45	GLN	0	-0.034	-0.026	20.561	0.001	0.001	0.000	0.000	0.000	0.000
44	C	46	ASP	-1	-0.886	-0.925	21.271	-0.100	-0.100	0.000	0.000	0.000	0.000
45	C	47	GLU	-1	-0.841	-0.917	18.116	-0.133	-0.133	0.000	0.000	0.000	0.000
46	C	48	LEU	0	-0.024	-0.005	16.122	-0.015	-0.015	0.000	0.000	0.000	0.000
47	C	49	PHE	0	-0.048	-0.045	16.467	-0.003	-0.003	0.000	0.000	0.000	0.000
48	C	50	ASP	-1	-0.868	-0.924	17.191	-0.213	-0.213	0.000	0.000	0.000	0.000
49	C	51	LEU	0	0.019	0.004	11.583	-0.026	-0.026	0.000	0.000	0.000	0.000
50	C	52	LEU	0	-0.049	-0.023	12.275	-0.014	-0.014	0.000	0.000	0.000	0.000
51	C	53	ASP	-1	-0.911	-0.945	13.257	-0.218	-0.218	0.000	0.000	0.000	0.000
52	C	54	GLN	0	-0.082	-0.046	11.480	-0.079	-0.079	0.000	0.000	0.000	0.000
53	C	55	MET	0	-0.026	-0.010	8.392	-0.055	-0.055	0.000	0.000	0.000	0.000
54	C	56	ASP	-1	-0.780	-0.869	9.142	-0.413	-0.413	0.000	0.000	0.000	0.000
55	C	57	VAL	0	-0.018	-0.009	11.109	-0.056	-0.056	0.000	0.000	0.000	0.000
56	C	58	GLU	-1	-0.831	-0.929	4.233	-1.706	-1.535	-0.001	-0.027	-0.143	0.000
57	C	59	VAL	0	-0.054	-0.012	7.310	-0.277	-0.277	0.000	0.000	0.000	0.000
58	C	60	ASN	0	-0.094	-0.061	8.346	-0.032	-0.032	0.000	0.000	0.000	0.000
59	C	61	ASN	0	-0.020	0.001	8.489	0.116	0.116	0.000	0.000	0.000	0.000
60	C	62	SER	0	-0.040	-0.021	4.979	-0.246	-0.246	0.000	0.000	0.000	0.000
61	C	63	ILE	0	-0.034	0.008	4.799	-0.029	0.030	-0.001	-0.001	-0.056	0.000
62	C	64	GLY	0	0.051	0.026	8.355	0.227	0.227	0.000	0.000	0.000	0.000
63	C	65	ASP	-1	-0.832	-0.904	11.153	-0.151	-0.151	0.000	0.000	0.000	0.000
64	C	66	ALA	0	0.017	-0.012	12.590	-0.047	-0.047	0.000	0.000	0.000	0.000
65	C	67	SER	0	0.020	0.013	15.292	0.014	0.014	0.000	0.000	0.000	0.000
66	C	68	GLU	-1	-0.873	-0.926	7.709	-0.814	-0.814	0.000	0.000	0.000	0.000
67	C	69	ARG	1	0.874	0.925	10.896	0.405	0.405	0.000	0.000	0.000	0.000
68	C	70	ALA	0	-0.032	-0.014	11.842	0.026	0.026	0.000	0.000	0.000	0.000
69	C	71	THR	0	-0.035	-0.027	12.492	0.040	0.040	0.000	0.000	0.000	0.000
70	C	72	TYR	0	-0.028	-0.035	6.080	0.024	0.024	0.000	0.000	0.000	0.000
71	C	73	LYS	1	0.810	0.876	11.273	0.373	0.373	0.000	0.000	0.000	0.000
72	C	74	ALA	0	-0.063	-0.025	14.347	0.031	0.031	0.000	0.000	0.000	0.000
73	C	75	LYS	1	0.843	0.921	8.605	0.147	0.147	0.000	0.000	0.000	0.000
74	C	76	LEU	0	0.044	0.025	10.848	0.028	0.028	0.000	0.000	0.000	0.000
75	C	77	ARG	1	0.921	0.966	14.442	0.162	0.162	0.000	0.000	0.000	0.000
76	C	78	GLU	-1	-0.795	-0.871	17.748	-0.051	-0.051	0.000	0.000	0.000	0.000
77	C	79	TRP	0	0.029	0.019	10.545	0.010	0.010	0.000	0.000	0.000	0.000
78	C	80	LYS	1	1.002	1.006	17.397	0.119	0.119	0.000	0.000	0.000	0.000
79	C	81	LYS	1	0.723	0.833	19.492	0.068	0.068	0.000	0.000	0.000	0.000
80	C	82	THR	0	0.029	0.006	19.705	0.007	0.007	0.000	0.000	0.000	0.000
81	C	83	ILE	0	0.039	0.039	18.039	0.006	0.006	0.000	0.000	0.000	0.000
82	C	84	GLN	0	-0.044	-0.032	22.097	-0.003	-0.003	0.000	0.000	0.000	0.000
83	C	85	SER	0	-0.115	-0.085	24.904	0.002	0.002	0.000	0.000	0.000	0.000
84	C	86	ASP	-1	-0.849	-0.915	23.591	-0.030	-0.030	0.000	0.000	0.000	0.000
85	C	87	ILE	0	-0.002	0.007	22.154	0.002	0.002	0.000	0.000	0.000	0.000
86	C	88	LYS	1	0.890	0.924	25.532	0.069	0.069	0.000	0.000	0.000	0.000
87	C	89	ARG	1	0.937	0.979	27.509	0.047	0.047	0.000	0.000	0.000	0.000
88	C	90	PRO	0	-0.016	-0.014	28.614	0.002	0.002	0.000	0.000	0.000	0.000
89	C	91	LEU	0	0.041	0.035	27.858	0.003	0.003	0.000	0.000	0.000	0.000
90	C	92	GLN	0	0.010	0.013	30.842	-0.002	-0.002	0.000	0.000	0.000	0.000
91	C	93	SER	0	0.003	0.019	33.167	0.003	0.003	0.000	0.000	0.000	0.000
92	C	94	LEU	0	-0.002	-0.003	33.018	0.003	0.003	0.000	0.000	0.000	0.000
93	C	95	VAL	0	-0.059	-0.017	33.245	0.001	0.001	0.000	0.000	0.000	0.000
94	C	96	ASP	-1	-0.909	-0.956	36.165	-0.040	-0.040	0.000	0.000	0.000	0.000
95	C	97	SER	0	-0.173	-0.099	38.599	0.004	0.004	0.000	0.000	0.000	0.000

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