FMO DATABASE

FMODB ID: LR4K9

Calculation Name: 1LL8-A-Other549

Preferred Name: PAS domain-containing serine/threonine-protein kinase

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1LL8

Chain ID: A

ChEMBL ID: CHEMBL6054

UniProt ID: Q96RG2

Base Structure: SolutionNMR

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	114
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-898221.640791
FMO2-HF: Nuclear repulsion	852864.258507
FMO2-HF: Total energy	-45357.382283
FMO2-MP2: Total energy	-45486.069957

3D Structure Molmil

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(A:1:GLY)

Summations of interaction energy for fragment #1(A:1:GLY)

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.
-177.93	-173.972	16.284	-11.568	-8.676	-0.135

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.755 / q_NPA : 0.864

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	A	3	MET	0	0.031	0.025	3.576	8.785	11.400	-0.020	-1.281	-1.314	-0.006
6	A	6	GLU	-1	-0.785	-0.890	1.889	-133.075	-132.446	16.274	-9.986	-6.918	-0.128
7	A	7	PHE	0	-0.075	-0.025	3.488	-4.616	-3.934	0.028	-0.279	-0.432	-0.001
8	A	8	ASN	0	0.022	-0.010	4.050	2.935	2.967	0.002	-0.022	-0.012	0.000
4	A	4	ASP	-1	-0.704	-0.854	5.545	-34.479	-34.479	0.000	0.000	0.000	0.000
5	A	5	PRO	0	-0.110	-0.083	6.119	-0.828	-0.828	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.980	1.028	7.433	27.727	27.727	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.041	0.019	9.495	0.199	0.199	0.000	0.000	0.000	0.000
11	A	11	ILE	0	-0.057	-0.026	11.012	1.145	1.145	0.000	0.000	0.000	0.000
12	A	12	PHE	0	0.058	0.019	14.476	0.100	0.100	0.000	0.000	0.000	0.000
13	A	13	THR	0	-0.012	-0.015	18.115	0.024	0.024	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.013	0.005	20.452	0.304	0.304	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.818	-0.926	24.208	-10.372	-10.372	0.000	0.000	0.000	0.000
16	A	16	ALA	0	-0.045	-0.027	27.609	0.012	0.012	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.897	0.955	28.961	9.181	9.181	0.000	0.000	0.000	0.000
18	A	18	THR	0	-0.049	-0.041	31.341	0.463	0.463	0.000	0.000	0.000	0.000
19	A	19	THR	0	0.023	0.025	26.464	0.092	0.092	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.899	-0.949	27.525	-11.222	-11.222	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.034	-0.009	21.037	-0.310	-0.310	0.000	0.000	0.000	0.000
22	A	22	LEU	0	-0.011	0.000	22.773	0.004	0.004	0.000	0.000	0.000	0.000
23	A	23	VAL	0	0.020	0.001	18.505	-0.056	-0.056	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.036	0.016	16.624	0.009	0.009	0.000	0.000	0.000	0.000
25	A	25	ASN	0	0.060	0.032	10.419	1.278	1.278	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.864	-0.949	10.587	-22.583	-22.583	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.711	0.872	5.718	38.042	38.042	0.000	0.000	0.000	0.000
28	A	28	ALA	0	0.060	0.020	10.421	0.730	0.730	0.000	0.000	0.000	0.000
29	A	29	CYS	0	-0.066	-0.021	13.793	0.637	0.637	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.028	0.007	12.456	0.920	0.920	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.051	-0.005	13.412	0.523	0.523	0.000	0.000	0.000	0.000
32	A	32	LEU	0	-0.013	-0.010	14.678	1.021	1.021	0.000	0.000	0.000	0.000
33	A	33	GLY	0	-0.004	-0.008	17.225	0.872	0.872	0.000	0.000	0.000	0.000
34	A	34	TYR	0	-0.018	-0.002	18.426	0.796	0.796	0.000	0.000	0.000	0.000
35	A	35	SER	0	0.046	-0.024	17.463	-1.067	-1.067	0.000	0.000	0.000	0.000
36	A	36	SER	0	-0.017	-0.009	17.937	0.884	0.884	0.000	0.000	0.000	0.000
37	A	37	GLN	0	-0.040	-0.028	19.639	0.668	0.668	0.000	0.000	0.000	0.000
38	A	38	ASP	-1	-0.849	-0.885	21.184	-13.645	-13.645	0.000	0.000	0.000	0.000
39	A	39	LEU	0	-0.035	-0.024	19.026	0.292	0.292	0.000	0.000	0.000	0.000
40	A	40	ILE	0	0.005	0.017	23.498	0.249	0.249	0.000	0.000	0.000	0.000
41	A	41	GLY	0	-0.017	-0.001	25.045	0.336	0.336	0.000	0.000	0.000	0.000
42	A	42	GLN	0	-0.021	-0.002	26.051	0.165	0.165	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.946	0.948	26.640	9.811	9.811	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.049	0.027	21.638	0.068	0.068	0.000	0.000	0.000	0.000
45	A	45	THR	0	-0.005	-0.011	23.931	-0.306	-0.306	0.000	0.000	0.000	0.000
46	A	46	GLN	0	-0.026	-0.008	26.148	0.072	0.072	0.000	0.000	0.000	0.000
47	A	47	PHE	0	-0.061	-0.033	21.731	0.085	0.085	0.000	0.000	0.000	0.000
48	A	48	PHE	0	0.000	-0.012	19.701	-0.758	-0.758	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.039	0.009	24.610	0.285	0.285	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.850	0.929	27.530	9.399	9.399	0.000	0.000	0.000	0.000
51	A	51	SER	0	0.053	0.026	28.945	0.015	0.015	0.000	0.000	0.000	0.000
52	A	52	ASP	-1	-0.955	-0.969	30.443	-8.816	-8.816	0.000	0.000	0.000	0.000
53	A	53	SER	0	-0.007	-0.016	34.257	0.065	0.065	0.000	0.000	0.000	0.000
54	A	54	ASP	-1	-0.764	-0.891	31.217	-9.460	-9.460	0.000	0.000	0.000	0.000
55	A	55	VAL	0	-0.041	-0.001	29.454	-0.148	-0.148	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.057	-0.040	30.602	-0.179	-0.179	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.904	-0.942	33.571	-8.394	-8.394	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.009	-0.010	28.813	-0.061	-0.061	0.000	0.000	0.000	0.000
59	A	59	LEU	0	-0.113	-0.062	27.667	-0.342	-0.342	0.000	0.000	0.000	0.000
60	A	60	SER	0	-0.045	-0.032	31.293	0.065	0.065	0.000	0.000	0.000	0.000
61	A	61	GLU	-1	-0.939	-0.972	33.662	-8.443	-8.443	0.000	0.000	0.000	0.000
62	A	62	GLU	-1	-0.915	-0.941	28.812	-11.103	-11.103	0.000	0.000	0.000	0.000
63	A	63	HIS	0	-0.030	-0.017	30.472	0.128	0.128	0.000	0.000	0.000	0.000
64	A	64	MET	0	-0.017	-0.010	31.470	-0.255	-0.255	0.000	0.000	0.000	0.000
65	A	65	GLU	-1	-0.825	-0.886	33.774	-8.329	-8.329	0.000	0.000	0.000	0.000
66	A	66	ALA	0	-0.068	-0.046	36.161	0.186	0.186	0.000	0.000	0.000	0.000
67	A	67	ASP	-1	-0.916	-0.961	37.050	-8.205	-8.205	0.000	0.000	0.000	0.000
68	A	68	GLY	0	-0.026	-0.012	36.951	0.148	0.148	0.000	0.000	0.000	0.000
69	A	69	HIS	0	-0.049	-0.023	36.520	-0.012	-0.012	0.000	0.000	0.000	0.000
70	A	70	ALA	0	0.014	-0.014	33.335	-0.248	-0.248	0.000	0.000	0.000	0.000
71	A	71	ALA	0	-0.058	-0.009	33.430	-0.136	-0.136	0.000	0.000	0.000	0.000
72	A	72	VAL	0	0.043	0.022	31.982	-0.174	-0.174	0.000	0.000	0.000	0.000
73	A	73	VAL	0	0.017	0.014	28.208	0.045	0.045	0.000	0.000	0.000	0.000
74	A	74	PHE	0	-0.006	-0.016	22.420	-0.462	-0.462	0.000	0.000	0.000	0.000
75	A	75	GLY	0	-0.008	-0.001	24.265	-0.259	-0.259	0.000	0.000	0.000	0.000
76	A	76	THR	0	-0.032	-0.020	24.164	0.257	0.257	0.000	0.000	0.000	0.000
77	A	77	VAL	0	-0.009	-0.005	21.009	-0.309	-0.309	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.004	0.008	22.638	0.617	0.617	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.879	-0.936	22.818	-12.593	-12.593	0.000	0.000	0.000	0.000
80	A	80	ILE	0	-0.055	-0.020	18.782	0.403	0.403	0.000	0.000	0.000	0.000
81	A	81	ILE	0	-0.045	-0.027	23.360	-0.054	-0.054	0.000	0.000	0.000	0.000
82	A	82	SER	0	0.045	0.038	20.733	0.267	0.267	0.000	0.000	0.000	0.000
83	A	83	ARG	1	0.932	0.971	21.335	14.229	14.229	0.000	0.000	0.000	0.000
84	A	84	SER	0	-0.081	-0.049	22.460	0.274	0.274	0.000	0.000	0.000	0.000
85	A	85	GLY	0	-0.013	0.003	24.694	0.380	0.380	0.000	0.000	0.000	0.000
86	A	86	GLU	-1	-0.908	-0.957	20.175	-13.808	-13.808	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.880	0.937	23.367	10.977	10.977	0.000	0.000	0.000	0.000
88	A	88	ILE	0	0.032	0.026	18.530	-0.014	-0.014	0.000	0.000	0.000	0.000
89	A	89	PRO	0	0.045	0.027	21.658	-0.178	-0.178	0.000	0.000	0.000	0.000
90	A	90	VAL	0	-0.030	-0.014	17.421	-0.948	-0.948	0.000	0.000	0.000	0.000
91	A	91	SER	0	0.034	0.007	17.357	1.278	1.278	0.000	0.000	0.000	0.000
92	A	92	VAL	0	0.005	0.020	17.975	-0.970	-0.970	0.000	0.000	0.000	0.000
93	A	93	TRP	0	0.002	-0.018	14.696	0.644	0.644	0.000	0.000	0.000	0.000
94	A	94	MET	0	0.057	0.033	20.121	-0.614	-0.614	0.000	0.000	0.000	0.000
95	A	95	LYS	1	0.899	0.947	19.829	14.996	14.996	0.000	0.000	0.000	0.000
96	A	96	ARG	1	0.880	0.929	23.134	10.530	10.530	0.000	0.000	0.000	0.000
97	A	97	MET	0	-0.018	0.006	17.538	0.099	0.099	0.000	0.000	0.000	0.000
98	A	98	ARG	1	0.878	0.935	23.385	11.434	11.434	0.000	0.000	0.000	0.000
99	A	99	GLN	0	0.036	0.007	19.325	-1.059	-1.059	0.000	0.000	0.000	0.000
100	A	100	GLU	-1	-0.844	-0.921	23.290	-12.896	-12.896	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.897	0.935	26.522	10.030	10.030	0.000	0.000	0.000	0.000
102	A	102	ARG	1	0.945	0.996	27.002	11.441	11.441	0.000	0.000	0.000	0.000
103	A	103	LEU	0	0.009	-0.008	27.627	-0.453	-0.453	0.000	0.000	0.000	0.000
104	A	104	CYS	0	-0.031	0.028	22.747	0.004	0.004	0.000	0.000	0.000	0.000
105	A	105	CYS	0	-0.001	-0.004	24.277	-0.064	-0.064	0.000	0.000	0.000	0.000
106	A	106	VAL	0	0.004	-0.006	17.397	-0.222	-0.222	0.000	0.000	0.000	0.000
107	A	107	VAL	0	0.015	0.012	18.949	0.405	0.405	0.000	0.000	0.000	0.000
108	A	108	VAL	0	-0.069	-0.038	13.520	-1.051	-1.051	0.000	0.000	0.000	0.000
109	A	109	LEU	0	0.002	0.006	15.219	0.751	0.751	0.000	0.000	0.000	0.000
110	A	110	GLU	-1	-0.948	-0.981	12.303	-22.784	-22.784	0.000	0.000	0.000	0.000
111	A	111	PRO	0	-0.016	-0.019	12.735	1.320	1.320	0.000	0.000	0.000	0.000
112	A	112	VAL	0	0.010	0.017	15.378	-0.555	-0.555	0.000	0.000	0.000	0.000
113	A	113	GLU	-1	-1.000	-1.009	17.253	-14.514	-14.514	0.000	0.000	0.000	0.000
114	A	114	ARG	0	0.001	0.024	11.523	-5.602	-5.602	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:GLY)