FMO DATABASE

FMODB ID: LRZK9

Calculation Name: 7S3D-O-Other547

Preferred Name:

Target Type:

Ligand 3-letter code: F6C | CLA | CL0 | BCR | LMG | LHG | LMT | PQN | SF4 | FES | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7S3D

Chain ID: O

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	143
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1118413.15284
FMO2-HF: Nuclear repulsion	1062987.79446
FMO2-HF: Total energy	-55425.358381
FMO2-MP2: Total energy	-55586.076769

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-31.168	-29.285	0.03	-1.048	-0.865	-0.004

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.854 / q_NPA : 0.917

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	4	THR	0	-0.011	-0.007	3.259	-9.307	-7.508	0.031	-1.035	-0.795	-0.004
92	A	93	THR	0	-0.037	-0.029	4.520	-1.112	-1.028	-0.001	-0.013	-0.070	0.000
4	A	5	GLY	0	0.066	0.025	5.665	3.567	3.567	0.000	0.000	0.000	0.000
5	A	6	SER	0	-0.039	-0.015	8.365	-2.011	-2.011	0.000	0.000	0.000	0.000
6	A	7	MET	0	0.030	0.010	11.008	1.267	1.267	0.000	0.000	0.000	0.000
7	A	8	PRO	0	-0.029	-0.010	12.409	1.328	1.328	0.000	0.000	0.000	0.000
8	A	9	LYS	1	0.935	0.971	16.027	18.180	18.180	0.000	0.000	0.000	0.000
9	A	10	PHE	0	0.027	0.000	18.500	0.771	0.771	0.000	0.000	0.000	0.000
10	A	11	GLY	0	0.015	0.013	20.030	-0.260	-0.260	0.000	0.000	0.000	0.000
11	A	12	GLY	0	-0.001	0.014	20.159	0.021	0.021	0.000	0.000	0.000	0.000
12	A	13	SER	0	-0.040	-0.031	21.080	0.456	0.456	0.000	0.000	0.000	0.000
13	A	14	THR	0	0.026	0.000	22.271	-0.523	-0.523	0.000	0.000	0.000	0.000
14	A	15	GLY	0	-0.001	0.019	23.615	0.047	0.047	0.000	0.000	0.000	0.000
15	A	16	GLY	0	-0.018	-0.010	19.463	-0.362	-0.362	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.024	-0.010	13.307	0.371	0.371	0.000	0.000	0.000	0.000
17	A	18	LEU	0	0.039	0.021	17.956	0.494	0.494	0.000	0.000	0.000	0.000
18	A	19	THR	0	0.040	-0.003	18.478	-0.821	-0.821	0.000	0.000	0.000	0.000
19	A	20	ALA	0	0.081	0.050	18.304	-0.720	-0.720	0.000	0.000	0.000	0.000
20	A	21	ALA	0	-0.025	-0.004	14.797	-0.508	-0.508	0.000	0.000	0.000	0.000
21	A	22	PHE	0	-0.050	-0.034	12.564	-1.779	-1.779	0.000	0.000	0.000	0.000
22	A	23	VAL	0	-0.022	-0.007	14.888	-0.424	-0.424	0.000	0.000	0.000	0.000
23	A	24	GLU	-1	-0.918	-0.957	17.056	-13.761	-13.761	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.852	-0.910	13.871	-17.943	-17.943	0.000	0.000	0.000	0.000
25	A	26	ARG	1	0.851	0.920	8.815	29.041	29.041	0.000	0.000	0.000	0.000
26	A	27	TYR	0	-0.033	-0.043	11.799	-0.225	-0.225	0.000	0.000	0.000	0.000
27	A	28	ALA	0	0.032	0.020	8.464	-0.597	-0.597	0.000	0.000	0.000	0.000
28	A	29	ILE	0	-0.053	-0.026	10.534	0.899	0.899	0.000	0.000	0.000	0.000
29	A	30	THR	0	-0.018	-0.014	8.412	-0.692	-0.692	0.000	0.000	0.000	0.000
30	A	31	TRP	0	-0.004	-0.048	11.682	1.627	1.627	0.000	0.000	0.000	0.000
31	A	32	THR	0	0.053	0.030	14.553	-0.720	-0.720	0.000	0.000	0.000	0.000
32	A	33	SER	0	-0.084	-0.063	16.162	1.472	1.472	0.000	0.000	0.000	0.000
33	A	34	SER	0	0.016	0.007	19.108	-0.295	-0.295	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.889	0.939	21.618	13.042	13.042	0.000	0.000	0.000	0.000
35	A	36	GLU	-1	-0.924	-0.936	20.943	-14.863	-14.863	0.000	0.000	0.000	0.000
36	A	37	GLN	0	-0.028	-0.043	21.973	1.514	1.514	0.000	0.000	0.000	0.000
37	A	38	VAL	0	0.010	0.012	22.408	-0.633	-0.633	0.000	0.000	0.000	0.000
38	A	39	PHE	0	-0.024	-0.020	17.720	0.107	0.107	0.000	0.000	0.000	0.000
39	A	40	GLU	-1	-0.924	-0.958	23.617	-11.471	-11.471	0.000	0.000	0.000	0.000
40	A	41	MET	0	0.000	0.004	17.694	-0.827	-0.827	0.000	0.000	0.000	0.000
41	A	42	PRO	0	-0.021	-0.019	19.720	0.544	0.544	0.000	0.000	0.000	0.000
42	A	43	THR	0	-0.022	0.001	19.288	0.093	0.093	0.000	0.000	0.000	0.000
43	A	44	GLY	0	0.016	0.018	22.489	0.367	0.367	0.000	0.000	0.000	0.000
44	A	45	GLY	0	0.029	0.005	24.123	-0.388	-0.388	0.000	0.000	0.000	0.000
45	A	46	ALA	0	-0.008	-0.010	24.323	-0.087	-0.087	0.000	0.000	0.000	0.000
46	A	47	ALA	0	0.008	0.012	19.441	-0.071	-0.071	0.000	0.000	0.000	0.000
47	A	48	THR	0	-0.007	-0.006	20.657	0.609	0.609	0.000	0.000	0.000	0.000
48	A	49	MET	0	-0.072	0.021	17.735	-0.983	-0.983	0.000	0.000	0.000	0.000
49	A	50	ASN	0	0.042	0.001	14.762	1.872	1.872	0.000	0.000	0.000	0.000
50	A	51	GLU	-1	-0.928	-0.947	17.575	-16.660	-16.660	0.000	0.000	0.000	0.000
51	A	52	GLY	0	0.072	0.049	15.473	-0.906	-0.906	0.000	0.000	0.000	0.000
52	A	53	GLU	-1	-0.874	-0.935	9.705	-27.471	-27.471	0.000	0.000	0.000	0.000
53	A	54	ASN	0	-0.037	-0.014	12.073	-0.456	-0.456	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.010	-0.003	5.840	-1.095	-1.095	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.021	-0.014	10.165	1.114	1.114	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.847	-0.907	8.169	-33.044	-33.044	0.000	0.000	0.000	0.000
57	A	58	LEU	0	-0.041	-0.042	11.848	1.996	1.996	0.000	0.000	0.000	0.000
58	A	59	ALA	0	0.085	0.035	14.463	-0.791	-0.791	0.000	0.000	0.000	0.000
59	A	60	ARG	1	0.858	0.915	17.081	13.675	13.675	0.000	0.000	0.000	0.000
60	A	61	LYS	1	1.013	1.013	16.577	15.878	15.878	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.850	-0.905	17.815	-12.459	-12.459	0.000	0.000	0.000	0.000
62	A	63	GLN	0	0.044	0.019	18.697	-0.382	-0.382	0.000	0.000	0.000	0.000
63	A	64	CYS	0	0.000	0.018	15.263	-0.428	-0.428	0.000	0.000	0.000	0.000
64	A	65	LEU	0	0.031	0.004	17.460	0.027	0.027	0.000	0.000	0.000	0.000
65	A	66	ALA	0	-0.021	0.008	20.289	0.483	0.483	0.000	0.000	0.000	0.000
66	A	67	LEU	0	0.018	0.014	16.898	0.506	0.506	0.000	0.000	0.000	0.000
67	A	68	GLY	0	0.056	0.013	19.622	0.193	0.193	0.000	0.000	0.000	0.000
68	A	69	ALA	0	-0.055	-0.032	20.268	0.503	0.503	0.000	0.000	0.000	0.000
69	A	70	GLN	0	-0.004	0.006	23.052	0.580	0.580	0.000	0.000	0.000	0.000
70	A	71	LEU	0	0.027	0.022	17.974	0.607	0.607	0.000	0.000	0.000	0.000
71	A	72	ARG	1	0.902	0.952	22.600	13.171	13.171	0.000	0.000	0.000	0.000
72	A	73	THR	0	-0.111	-0.086	24.985	0.724	0.724	0.000	0.000	0.000	0.000
73	A	74	LYS	1	0.938	0.961	26.705	11.055	11.055	0.000	0.000	0.000	0.000
74	A	75	PHE	0	0.026	0.038	23.933	0.152	0.152	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.935	0.968	27.273	10.091	10.091	0.000	0.000	0.000	0.000
76	A	77	PRO	0	0.032	0.005	25.364	0.248	0.248	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.844	0.922	25.733	11.056	11.056	0.000	0.000	0.000	0.000
78	A	79	ILE	0	0.025	0.030	19.158	-0.051	-0.051	0.000	0.000	0.000	0.000
79	A	80	THR	0	-0.033	-0.044	21.395	-0.039	-0.039	0.000	0.000	0.000	0.000
80	A	81	ASP	-1	-0.814	-0.889	16.334	-18.946	-18.946	0.000	0.000	0.000	0.000
81	A	82	TYR	0	0.004	0.014	15.516	-1.131	-1.131	0.000	0.000	0.000	0.000
82	A	83	LYS	1	0.887	0.949	11.592	23.439	23.439	0.000	0.000	0.000	0.000
83	A	84	ILE	0	-0.042	-0.028	12.227	-0.996	-0.996	0.000	0.000	0.000	0.000
84	A	85	TYR	0	0.007	-0.009	7.788	-0.306	-0.306	0.000	0.000	0.000	0.000
85	A	86	ARG	1	0.862	0.926	10.159	19.905	19.905	0.000	0.000	0.000	0.000
86	A	87	ILE	0	-0.031	-0.016	6.431	-1.909	-1.909	0.000	0.000	0.000	0.000
87	A	88	PHE	0	0.038	0.016	8.855	2.675	2.675	0.000	0.000	0.000	0.000
88	A	89	PRO	0	0.015	0.005	10.171	-2.125	-2.125	0.000	0.000	0.000	0.000
89	A	90	ASN	0	-0.009	0.002	10.860	-1.143	-1.143	0.000	0.000	0.000	0.000
90	A	91	GLY	0	-0.001	0.005	7.558	-0.962	-0.962	0.000	0.000	0.000	0.000
91	A	92	GLU	-1	-0.953	-0.968	5.786	-29.408	-29.408	0.000	0.000	0.000	0.000
93	A	94	THR	0	0.013	0.013	6.463	0.657	0.657	0.000	0.000	0.000	0.000
94	A	95	PHE	0	0.000	-0.008	9.041	-0.493	-0.493	0.000	0.000	0.000	0.000
95	A	96	ILE	0	-0.034	-0.020	10.247	1.965	1.965	0.000	0.000	0.000	0.000
96	A	97	HIS	0	-0.046	-0.012	13.745	1.763	1.763	0.000	0.000	0.000	0.000
97	A	98	PRO	0	0.043	0.004	14.699	-1.198	-1.198	0.000	0.000	0.000	0.000
98	A	99	ALA	0	-0.007	-0.007	16.161	-0.466	-0.466	0.000	0.000	0.000	0.000
99	A	100	ASP	-1	-0.828	-0.876	17.326	-13.481	-13.481	0.000	0.000	0.000	0.000
100	A	101	GLY	0	0.065	0.016	17.295	-0.557	-0.557	0.000	0.000	0.000	0.000
101	A	102	VAL	0	-0.036	-0.002	18.317	-0.086	-0.086	0.000	0.000	0.000	0.000
102	A	103	PHE	0	0.007	-0.005	19.637	-0.500	-0.500	0.000	0.000	0.000	0.000
103	A	104	PRO	0	-0.004	0.001	21.291	0.515	0.515	0.000	0.000	0.000	0.000
104	A	105	GLU	-1	-0.823	-0.905	24.245	-12.226	-12.226	0.000	0.000	0.000	0.000
105	A	106	LYS	1	0.857	0.931	26.134	11.399	11.399	0.000	0.000	0.000	0.000
106	A	107	VAL	0	0.036	0.024	26.728	-0.382	-0.382	0.000	0.000	0.000	0.000
107	A	108	ASN	0	-0.030	-0.044	23.129	0.247	0.247	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.923	-0.951	27.048	-9.739	-9.739	0.000	0.000	0.000	0.000
109	A	110	GLY	0	0.030	0.004	25.752	-0.173	-0.173	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.748	0.885	23.631	12.218	12.218	0.000	0.000	0.000	0.000
111	A	112	GLY	0	0.046	0.036	25.508	-0.099	-0.099	0.000	0.000	0.000	0.000
112	A	113	TYR	0	-0.029	-0.031	28.241	-0.110	-0.110	0.000	0.000	0.000	0.000
113	A	114	SER	0	0.045	0.011	26.766	-0.101	-0.101	0.000	0.000	0.000	0.000
114	A	115	GLY	0	0.017	0.007	28.808	-0.084	-0.084	0.000	0.000	0.000	0.000
115	A	116	LYS	1	0.791	0.897	31.738	8.464	8.464	0.000	0.000	0.000	0.000
116	A	117	LYS	1	0.884	0.939	34.732	8.143	8.143	0.000	0.000	0.000	0.000
117	A	118	ASP	-1	-0.807	-0.869	38.082	-7.879	-7.879	0.000	0.000	0.000	0.000
118	A	119	ARG	1	0.766	0.867	41.044	7.520	7.520	0.000	0.000	0.000	0.000
119	A	120	ARG	1	0.947	0.969	43.220	6.301	6.301	0.000	0.000	0.000	0.000
120	A	121	ILE	0	0.017	0.004	41.318	0.148	0.148	0.000	0.000	0.000	0.000
121	A	122	GLY	0	0.006	0.011	44.079	-0.005	-0.005	0.000	0.000	0.000	0.000
122	A	123	GLU	-1	-0.806	-0.907	46.368	-6.509	-6.509	0.000	0.000	0.000	0.000
123	A	124	ASN	0	0.023	0.028	42.616	-0.161	-0.161	0.000	0.000	0.000	0.000
124	A	125	PRO	0	0.009	0.022	44.403	0.126	0.126	0.000	0.000	0.000	0.000
125	A	126	ASN	0	0.069	0.021	46.695	-0.122	-0.122	0.000	0.000	0.000	0.000
126	A	127	PRO	0	0.030	0.014	46.874	0.028	0.028	0.000	0.000	0.000	0.000
127	A	128	ALA	0	-0.062	-0.040	48.723	0.082	0.082	0.000	0.000	0.000	0.000
128	A	129	THR	0	-0.011	-0.007	49.673	-0.003	-0.003	0.000	0.000	0.000	0.000
129	A	130	ILE	0	0.025	0.022	44.172	0.026	0.026	0.000	0.000	0.000	0.000
130	A	131	LYS	1	0.917	0.982	46.178	6.017	6.017	0.000	0.000	0.000	0.000
131	A	132	PHE	0	0.005	-0.008	46.912	-0.051	-0.051	0.000	0.000	0.000	0.000
132	A	133	SER	0	-0.002	-0.013	44.541	-0.040	-0.040	0.000	0.000	0.000	0.000
133	A	134	GLY	0	0.013	0.014	41.157	-0.107	-0.107	0.000	0.000	0.000	0.000
134	A	135	GLN	0	0.014	0.011	39.723	-0.018	-0.018	0.000	0.000	0.000	0.000
135	A	136	ASN	0	0.017	-0.005	36.923	0.245	0.245	0.000	0.000	0.000	0.000
136	A	137	THR	0	0.017	0.013	40.701	-0.099	-0.099	0.000	0.000	0.000	0.000
137	A	138	PHE	0	-0.032	-0.029	35.763	0.128	0.128	0.000	0.000	0.000	0.000
138	A	139	GLU	-1	-0.892	-0.935	35.274	-8.830	-8.830	0.000	0.000	0.000	0.000
139	A	140	THR	0	-0.015	0.005	37.948	0.125	0.125	0.000	0.000	0.000	0.000
140	A	141	ASP	-1	-0.865	-0.938	39.257	-7.957	-7.957	0.000	0.000	0.000	0.000
141	A	142	MET	0	-0.025	0.000	41.875	0.014	0.014	0.000	0.000	0.000	0.000
142	A	143	LYS	1	0.788	0.866	44.770	6.652	6.652	0.000	0.000	0.000	0.000
143	A	144	SER	-1	-0.902	-0.942	47.270	-6.151	-6.151	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)