FMO DATABASE

FMODB ID: 5312Z

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

Total energy (hartree)

FMO2-HF: Electronic energy	-670420.807434
FMO2-HF: Nuclear repulsion	632800.446243
FMO2-HF: Total energy	-37620.361191
FMO2-MP2: Total energy	-37731.647839

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.
-10.952	-5.728	4.985	-3.904	-6.304	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 : 0.033 / q_NPA : 0.013

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	0.082	0.069	3.085	-1.505	1.527	0.112	-1.467	-1.677	0.006
4	C	6	ILE	0	0.007	0.003	2.243	-8.477	-6.925	4.857	-2.262	-4.147	0.020
5	C	7	SER	0	-0.053	-0.026	3.886	-1.548	-1.003	0.017	-0.173	-0.388	0.001
6	C	8	TYR	0	0.091	0.027	5.659	0.156	0.156	0.000	0.000	0.000	0.000
7	C	9	GLU	-1	-0.746	-0.874	6.379	0.672	0.672	0.000	0.000	0.000	0.000
8	C	10	SER	0	-0.100	-0.064	6.951	-0.087	-0.087	0.000	0.000	0.000	0.000
9	C	11	ASP	-1	-0.846	-0.914	9.545	-0.345	-0.345	0.000	0.000	0.000	0.000
10	C	12	PHE	0	0.004	0.005	11.414	0.064	0.064	0.000	0.000	0.000	0.000
11	C	13	LYS	1	0.853	0.911	8.992	-0.174	-0.174	0.000	0.000	0.000	0.000
12	C	14	THR	0	-0.028	-0.022	12.866	0.009	0.009	0.000	0.000	0.000	0.000
13	C	15	THR	0	0.022	0.011	15.473	0.019	0.019	0.000	0.000	0.000	0.000
14	C	16	LEU	0	-0.029	-0.011	17.007	0.020	0.020	0.000	0.000	0.000	0.000
15	C	17	GLU	-1	-0.872	-0.923	17.964	-0.027	-0.027	0.000	0.000	0.000	0.000
16	C	18	GLN	0	0.008	0.018	18.529	0.015	0.015	0.000	0.000	0.000	0.000
17	C	19	ALA	0	0.054	0.045	21.589	0.010	0.010	0.000	0.000	0.000	0.000
18	C	20	LYS	1	0.859	0.897	21.137	0.028	0.028	0.000	0.000	0.000	0.000
19	C	21	ALA	0	-0.028	-0.003	24.302	0.006	0.006	0.000	0.000	0.000	0.000
20	C	22	SER	0	0.006	-0.013	25.375	0.003	0.003	0.000	0.000	0.000	0.000
21	C	23	LEU	0	-0.036	-0.023	27.169	0.005	0.005	0.000	0.000	0.000	0.000
22	C	24	ALA	0	-0.047	-0.023	29.034	0.005	0.005	0.000	0.000	0.000	0.000
23	C	25	GLU	-1	-0.934	-0.962	29.143	-0.073	-0.073	0.000	0.000	0.000	0.000
24	C	26	ALA	0	0.000	0.009	31.819	0.002	0.002	0.000	0.000	0.000	0.000
25	C	27	PRO	0	-0.026	-0.018	33.551	0.001	0.001	0.000	0.000	0.000	0.000
26	C	28	SER	0	-0.092	-0.040	35.595	0.001	0.001	0.000	0.000	0.000	0.000
27	C	29	GLN	0	0.063	0.058	31.660	0.000	0.000	0.000	0.000	0.000	0.000
28	C	30	PRO	0	0.021	0.009	37.512	0.004	0.004	0.000	0.000	0.000	0.000
29	C	31	LEU	0	0.040	0.013	38.750	-0.003	-0.003	0.000	0.000	0.000	0.000
30	C	32	SER	0	0.018	0.006	38.803	-0.001	-0.001	0.000	0.000	0.000	0.000
31	C	33	GLN	0	0.027	0.010	33.280	0.000	0.000	0.000	0.000	0.000	0.000
32	C	34	ARG	1	0.904	0.955	34.543	0.033	0.033	0.000	0.000	0.000	0.000
33	C	35	ASN	0	0.000	-0.010	34.286	0.000	0.000	0.000	0.000	0.000	0.000
34	C	36	THR	0	-0.016	0.002	31.286	-0.001	-0.001	0.000	0.000	0.000	0.000
35	C	37	THR	0	-0.023	-0.029	29.643	-0.007	-0.007	0.000	0.000	0.000	0.000
36	C	38	LEU	0	0.017	0.004	29.385	-0.003	-0.003	0.000	0.000	0.000	0.000
37	C	39	LYS	1	0.966	0.989	29.886	0.072	0.072	0.000	0.000	0.000	0.000
38	C	40	HIS	0	0.003	0.006	23.116	0.003	0.003	0.000	0.000	0.000	0.000
39	C	41	VAL	0	0.030	0.005	25.454	-0.005	-0.005	0.000	0.000	0.000	0.000
40	C	42	GLU	-1	-0.993	-0.997	25.290	-0.038	-0.038	0.000	0.000	0.000	0.000
41	C	43	GLN	0	-0.069	-0.038	22.560	0.014	0.014	0.000	0.000	0.000	0.000
42	C	44	GLN	0	0.030	0.006	20.132	0.013	0.013	0.000	0.000	0.000	0.000
43	C	45	GLN	0	-0.036	-0.028	20.723	0.015	0.015	0.000	0.000	0.000	0.000
44	C	46	ASP	-1	-0.894	-0.941	21.576	-0.026	-0.026	0.000	0.000	0.000	0.000
45	C	47	GLU	-1	-0.825	-0.904	18.124	-0.156	-0.156	0.000	0.000	0.000	0.000
46	C	48	LEU	0	-0.046	-0.023	16.464	0.011	0.011	0.000	0.000	0.000	0.000
47	C	49	PHE	0	-0.057	-0.052	16.840	0.041	0.041	0.000	0.000	0.000	0.000
48	C	50	ASP	-1	-0.852	-0.910	17.394	-0.030	-0.030	0.000	0.000	0.000	0.000
49	C	51	LEU	0	-0.022	-0.014	11.670	0.035	0.035	0.000	0.000	0.000	0.000
50	C	52	LEU	0	-0.064	-0.026	12.674	0.096	0.096	0.000	0.000	0.000	0.000
51	C	53	ASP	-1	-0.903	-0.936	14.080	0.147	0.147	0.000	0.000	0.000	0.000
52	C	54	GLN	0	-0.039	-0.026	11.443	0.027	0.027	0.000	0.000	0.000	0.000
53	C	55	MET	0	-0.030	-0.014	8.706	0.060	0.060	0.000	0.000	0.000	0.000
54	C	56	ASP	-1	-0.790	-0.870	9.976	0.491	0.491	0.000	0.000	0.000	0.000
55	C	57	VAL	0	-0.015	-0.014	11.682	0.035	0.035	0.000	0.000	0.000	0.000
56	C	58	GLU	-1	-0.887	-0.957	5.014	0.125	0.220	-0.001	-0.002	-0.092	0.000
57	C	59	VAL	0	-0.061	-0.013	7.679	0.151	0.151	0.000	0.000	0.000	0.000
58	C	60	ASN	0	-0.099	-0.061	9.068	0.006	0.006	0.000	0.000	0.000	0.000
59	C	61	ASN	0	-0.017	0.003	9.203	-0.030	-0.030	0.000	0.000	0.000	0.000
60	C	62	SER	0	-0.042	-0.025	5.302	0.145	0.145	0.000	0.000	0.000	0.000
61	C	63	ILE	0	-0.016	0.014	6.027	0.032	0.032	0.000	0.000	0.000	0.000
62	C	64	GLY	0	0.061	0.028	9.105	-0.128	-0.128	0.000	0.000	0.000	0.000
63	C	65	ASP	-1	-0.826	-0.906	12.137	0.327	0.327	0.000	0.000	0.000	0.000
64	C	66	ALA	0	0.009	-0.012	13.898	0.036	0.036	0.000	0.000	0.000	0.000
65	C	67	SER	0	0.008	0.004	16.648	-0.025	-0.025	0.000	0.000	0.000	0.000
66	C	68	GLU	-1	-0.907	-0.962	9.123	0.920	0.920	0.000	0.000	0.000	0.000
67	C	69	ARG	1	0.855	0.908	12.460	-0.381	-0.381	0.000	0.000	0.000	0.000
68	C	70	ALA	0	-0.025	-0.009	13.453	-0.012	-0.012	0.000	0.000	0.000	0.000
69	C	71	THR	0	-0.037	-0.018	13.598	-0.039	-0.039	0.000	0.000	0.000	0.000
70	C	72	TYR	0	-0.005	-0.005	6.966	0.083	0.083	0.000	0.000	0.000	0.000
71	C	73	LYS	1	0.810	0.885	12.442	-0.399	-0.399	0.000	0.000	0.000	0.000
72	C	74	ALA	0	-0.038	-0.011	15.454	-0.045	-0.045	0.000	0.000	0.000	0.000
73	C	75	LYS	1	0.856	0.936	9.497	-0.782	-0.782	0.000	0.000	0.000	0.000
74	C	76	LEU	0	0.053	0.033	11.691	-0.049	-0.049	0.000	0.000	0.000	0.000
75	C	77	ARG	1	0.914	0.957	15.306	-0.250	-0.250	0.000	0.000	0.000	0.000
76	C	78	GLU	-1	-0.802	-0.883	18.406	0.081	0.081	0.000	0.000	0.000	0.000
77	C	79	TRP	0	0.043	0.012	10.957	-0.016	-0.016	0.000	0.000	0.000	0.000
78	C	80	LYS	1	0.995	1.005	17.901	-0.117	-0.117	0.000	0.000	0.000	0.000
79	C	81	LYS	1	0.722	0.837	20.117	-0.120	-0.120	0.000	0.000	0.000	0.000
80	C	82	THR	0	0.030	0.012	20.153	-0.012	-0.012	0.000	0.000	0.000	0.000
81	C	83	ILE	0	0.042	0.042	18.158	-0.014	-0.014	0.000	0.000	0.000	0.000
82	C	84	GLN	0	-0.058	-0.038	22.209	-0.009	-0.009	0.000	0.000	0.000	0.000
83	C	85	SER	0	-0.094	-0.078	25.365	-0.005	-0.005	0.000	0.000	0.000	0.000
84	C	86	ASP	-1	-0.860	-0.921	23.832	0.018	0.018	0.000	0.000	0.000	0.000
85	C	87	ILE	0	-0.007	0.002	22.226	-0.009	-0.009	0.000	0.000	0.000	0.000
86	C	88	LYS	1	0.878	0.929	25.672	0.005	0.005	0.000	0.000	0.000	0.000
87	C	89	ARG	1	0.946	0.974	27.510	-0.026	-0.026	0.000	0.000	0.000	0.000
88	C	90	PRO	0	-0.007	-0.009	28.551	-0.002	-0.002	0.000	0.000	0.000	0.000
89	C	91	LEU	0	0.046	0.041	27.911	-0.002	-0.002	0.000	0.000	0.000	0.000
90	C	92	GLN	0	0.016	0.011	30.882	0.000	0.000	0.000	0.000	0.000	0.000
91	C	93	SER	0	-0.002	0.014	33.204	-0.001	-0.001	0.000	0.000	0.000	0.000
92	C	94	LEU	0	0.007	-0.013	32.856	-0.001	-0.001	0.000	0.000	0.000	0.000
93	C	95	VAL	0	-0.068	-0.026	33.423	-0.002	-0.002	0.000	0.000	0.000	0.000
94	C	96	ASP	-1	-0.927	-0.952	36.279	-0.012	-0.012	0.000	0.000	0.000	0.000
95	C	97	SER	0	-0.179	-0.085	38.499	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)