FMO DATABASE

FMODB ID: 6Z2RZ

Calculation Name: 1UNL-D-Xray547

Preferred Name: Cyclin-dependent kinase 5 regulatory subunit 1

Target Type: SINGLE PROTEIN

Ligand Name: r-roscovitine

Ligand 3-letter code: RRC

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1UNL

Chain ID: D

ChEMBL ID: CHEMBL2783

UniProt ID: Q15078

Base Structure: X-ray

Registration Date: 2025-10-03

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	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1514685.926923
FMO2-HF: Nuclear repulsion	1452812.232617
FMO2-HF: Total energy	-61873.694305
FMO2-MP2: Total energy	-62048.524627

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:145:GLN)

Summations of interaction energy for fragment #1(A:145:GLN)

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.
-86.42	-88.296	37.842	-15.395	-20.57	-0.042

Interaction energy analysis for fragmet #1(A:145:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.864 / q_NPA : 0.926

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	147	SER	0	0.026	0.023	3.573	8.981	11.833	-0.016	-1.482	-1.354	-0.003
4	A	148	THR	0	0.078	0.031	5.086	-2.375	-2.227	-0.001	-0.003	-0.143	0.000
6	A	150	GLU	-1	-0.866	-0.899	1.903	-70.654	-68.107	7.776	-5.417	-4.906	-0.043
7	A	151	LEU	0	0.004	0.008	3.193	1.119	2.629	0.119	-0.495	-1.134	0.003
8	A	152	LEU	0	-0.001	-0.003	5.085	2.662	2.675	-0.001	-0.005	-0.006	0.000
9	A	153	ARG	1	0.811	0.894	4.710	40.963	41.022	-0.001	-0.009	-0.049	0.000
10	A	154	CYS	0	-0.002	0.001	1.835	0.596	-9.499	17.494	-4.047	-3.352	0.022
11	A	155	LEU	0	0.035	0.021	5.502	1.268	1.282	-0.001	0.000	-0.013	0.000
145	A	289	LEU	0	-0.001	0.003	4.602	-1.059	-1.026	-0.001	-0.007	-0.025	0.000
146	A	290	LYS	1	0.843	0.918	2.110	47.380	47.792	8.996	-3.291	-6.117	0.017
147	A	291	ASN	0	-0.061	-0.024	2.117	-18.020	-18.535	3.435	-0.073	-2.847	-0.032
149	A	293	SER	-1	-0.927	-0.948	3.090	-38.118	-36.972	0.043	-0.566	-0.624	-0.006
5	A	149	SER	0	0.012	-0.007	7.575	1.991	1.991	0.000	0.000	0.000	0.000
12	A	156	GLY	0	0.025	0.010	8.504	1.399	1.399	0.000	0.000	0.000	0.000
13	A	157	GLU	-1	-0.844	-0.923	8.190	-25.461	-25.461	0.000	0.000	0.000	0.000
14	A	158	PHE	0	-0.013	0.002	9.117	1.255	1.255	0.000	0.000	0.000	0.000
15	A	159	LEU	0	-0.025	-0.017	10.710	1.248	1.248	0.000	0.000	0.000	0.000
16	A	160	CYS	0	-0.028	-0.004	13.351	1.023	1.023	0.000	0.000	0.000	0.000
17	A	161	ARG	1	0.819	0.910	8.538	22.361	22.361	0.000	0.000	0.000	0.000
18	A	162	ARG	1	0.802	0.896	14.585	14.890	14.890	0.000	0.000	0.000	0.000
19	A	163	CYS	0	-0.016	-0.008	16.489	0.880	0.880	0.000	0.000	0.000	0.000
20	A	164	TYR	0	-0.026	-0.036	19.129	0.268	0.268	0.000	0.000	0.000	0.000
21	A	165	ARG	1	0.865	0.935	20.662	10.270	10.270	0.000	0.000	0.000	0.000
22	A	166	LEU	0	-0.038	-0.007	20.208	0.390	0.390	0.000	0.000	0.000	0.000
23	A	167	LYS	1	0.827	0.900	21.222	10.780	10.780	0.000	0.000	0.000	0.000
24	A	168	HIS	0	0.001	-0.005	22.752	-0.254	-0.254	0.000	0.000	0.000	0.000
25	A	169	LEU	0	0.021	0.038	16.899	-0.114	-0.114	0.000	0.000	0.000	0.000
26	A	170	SER	0	0.035	0.034	16.869	-0.885	-0.885	0.000	0.000	0.000	0.000
27	A	171	PRO	0	0.044	0.007	11.529	0.021	0.021	0.000	0.000	0.000	0.000
28	A	172	THR	0	-0.071	-0.064	12.490	-0.751	-0.751	0.000	0.000	0.000	0.000
29	A	173	ASP	-1	-0.817	-0.903	14.551	-13.854	-13.854	0.000	0.000	0.000	0.000
30	A	174	PRO	0	0.014	0.004	13.252	0.159	0.159	0.000	0.000	0.000	0.000
31	A	175	VAL	0	-0.026	-0.008	11.113	0.008	0.008	0.000	0.000	0.000	0.000
32	A	176	LEU	0	0.012	0.005	13.803	0.171	0.171	0.000	0.000	0.000	0.000
33	A	177	TRP	0	0.023	-0.006	17.512	0.409	0.409	0.000	0.000	0.000	0.000
34	A	178	LEU	0	0.024	0.010	13.088	0.421	0.421	0.000	0.000	0.000	0.000
35	A	179	ARG	1	0.910	0.953	11.235	21.352	21.352	0.000	0.000	0.000	0.000
36	A	180	SER	0	-0.047	-0.010	17.180	0.536	0.536	0.000	0.000	0.000	0.000
37	A	181	VAL	0	0.033	0.021	20.185	0.459	0.459	0.000	0.000	0.000	0.000
38	A	182	ASP	-1	-0.741	-0.837	17.547	-15.195	-15.195	0.000	0.000	0.000	0.000
39	A	183	ARG	1	0.942	0.967	20.132	13.035	13.035	0.000	0.000	0.000	0.000
40	A	184	SER	0	-0.057	-0.031	21.916	0.459	0.459	0.000	0.000	0.000	0.000
41	A	185	LEU	0	0.012	-0.004	22.301	0.472	0.472	0.000	0.000	0.000	0.000
42	A	186	LEU	0	-0.014	0.007	20.952	0.252	0.252	0.000	0.000	0.000	0.000
43	A	187	LEU	0	-0.038	-0.020	24.666	0.375	0.375	0.000	0.000	0.000	0.000
44	A	188	GLN	0	-0.075	-0.028	27.093	0.202	0.202	0.000	0.000	0.000	0.000
45	A	189	GLY	0	0.005	0.014	28.527	0.309	0.309	0.000	0.000	0.000	0.000
46	A	190	TRP	0	-0.040	-0.034	27.170	0.308	0.308	0.000	0.000	0.000	0.000
47	A	191	GLN	0	0.001	-0.020	20.853	-0.109	-0.109	0.000	0.000	0.000	0.000
48	A	192	ASP	-1	-0.897	-0.928	25.539	-11.052	-11.052	0.000	0.000	0.000	0.000
49	A	193	GLN	0	-0.096	-0.058	20.229	-0.677	-0.677	0.000	0.000	0.000	0.000
50	A	194	GLY	0	-0.008	0.004	18.359	0.238	0.238	0.000	0.000	0.000	0.000
51	A	195	PHE	0	0.044	0.017	16.984	-0.705	-0.705	0.000	0.000	0.000	0.000
52	A	196	ILE	0	-0.053	-0.023	12.483	-1.030	-1.030	0.000	0.000	0.000	0.000
53	A	197	THR	0	0.011	-0.002	11.975	-1.387	-1.387	0.000	0.000	0.000	0.000
54	A	198	PRO	0	-0.004	-0.023	7.531	0.446	0.446	0.000	0.000	0.000	0.000
55	A	199	ALA	0	0.050	0.025	9.132	0.045	0.045	0.000	0.000	0.000	0.000
56	A	200	ASN	0	0.026	0.017	11.758	0.606	0.606	0.000	0.000	0.000	0.000
57	A	201	VAL	0	-0.030	-0.013	8.271	0.799	0.799	0.000	0.000	0.000	0.000
58	A	202	VAL	0	-0.008	0.001	7.979	0.271	0.271	0.000	0.000	0.000	0.000
59	A	203	PHE	0	0.020	0.008	10.167	0.896	0.896	0.000	0.000	0.000	0.000
60	A	204	LEU	0	0.026	0.014	12.634	0.740	0.740	0.000	0.000	0.000	0.000
61	A	205	TYR	0	-0.030	-0.038	9.529	0.786	0.786	0.000	0.000	0.000	0.000
62	A	206	MET	0	-0.027	0.005	11.588	0.874	0.874	0.000	0.000	0.000	0.000
63	A	207	LEU	0	0.019	0.008	14.035	0.791	0.791	0.000	0.000	0.000	0.000
64	A	208	CYS	0	-0.042	-0.036	13.402	0.593	0.593	0.000	0.000	0.000	0.000
65	A	209	ARG	1	0.820	0.896	11.252	18.227	18.227	0.000	0.000	0.000	0.000
66	A	210	ASP	-1	-0.817	-0.896	14.955	-13.413	-13.413	0.000	0.000	0.000	0.000
67	A	211	VAL	0	-0.022	-0.011	18.558	0.584	0.584	0.000	0.000	0.000	0.000
68	A	212	ILE	0	-0.036	-0.007	16.253	0.494	0.494	0.000	0.000	0.000	0.000
69	A	213	SER	0	0.026	0.017	18.969	-0.375	-0.375	0.000	0.000	0.000	0.000
70	A	214	SER	0	0.048	-0.013	20.290	-0.323	-0.323	0.000	0.000	0.000	0.000
71	A	215	GLU	-1	-0.873	-0.894	21.200	-10.677	-10.677	0.000	0.000	0.000	0.000
72	A	216	VAL	0	-0.010	0.016	21.706	0.402	0.402	0.000	0.000	0.000	0.000
73	A	217	GLY	0	-0.006	-0.013	24.230	-0.068	-0.068	0.000	0.000	0.000	0.000
74	A	218	SER	0	-0.030	-0.026	25.652	0.130	0.130	0.000	0.000	0.000	0.000
75	A	219	ASP	-1	-0.796	-0.913	22.143	-12.085	-12.085	0.000	0.000	0.000	0.000
76	A	220	HIS	0	-0.054	-0.030	22.568	-0.283	-0.283	0.000	0.000	0.000	0.000
77	A	221	GLU	-1	-0.850	-0.923	24.881	-10.255	-10.255	0.000	0.000	0.000	0.000
78	A	222	LEU	0	0.027	0.002	17.338	-0.146	-0.146	0.000	0.000	0.000	0.000
79	A	223	GLN	0	-0.036	-0.014	20.439	0.008	0.008	0.000	0.000	0.000	0.000
80	A	224	ALA	0	0.024	0.017	21.585	-0.187	-0.187	0.000	0.000	0.000	0.000
81	A	225	VAL	0	0.005	0.015	20.672	-0.027	-0.027	0.000	0.000	0.000	0.000
82	A	226	LEU	0	0.031	0.022	14.947	-0.238	-0.238	0.000	0.000	0.000	0.000
83	A	227	LEU	0	-0.017	-0.015	18.928	-0.371	-0.371	0.000	0.000	0.000	0.000
84	A	228	THR	0	-0.004	-0.003	21.145	0.299	0.299	0.000	0.000	0.000	0.000
85	A	229	CYS	0	-0.025	-0.009	17.755	0.053	0.053	0.000	0.000	0.000	0.000
86	A	230	LEU	0	0.000	0.013	16.631	-0.296	-0.296	0.000	0.000	0.000	0.000
87	A	231	TYR	0	-0.018	-0.002	18.979	0.046	0.046	0.000	0.000	0.000	0.000
88	A	232	LEU	0	0.012	0.008	21.611	0.194	0.194	0.000	0.000	0.000	0.000
89	A	233	SER	0	-0.015	-0.026	17.525	-0.270	-0.270	0.000	0.000	0.000	0.000
90	A	234	TYR	0	-0.072	-0.065	19.519	-0.156	-0.156	0.000	0.000	0.000	0.000
91	A	235	SER	0	-0.054	-0.047	21.567	0.306	0.306	0.000	0.000	0.000	0.000
92	A	236	TYR	0	-0.037	-0.014	21.444	0.314	0.314	0.000	0.000	0.000	0.000
93	A	237	MET	0	-0.020	0.012	17.056	0.158	0.158	0.000	0.000	0.000	0.000
94	A	238	GLY	0	-0.026	-0.004	20.340	-0.517	-0.517	0.000	0.000	0.000	0.000
95	A	239	ASN	0	-0.034	-0.021	21.924	0.182	0.182	0.000	0.000	0.000	0.000
96	A	240	GLU	-1	-0.864	-0.927	24.445	-10.865	-10.865	0.000	0.000	0.000	0.000
97	A	241	ILE	0	-0.039	-0.024	26.988	-0.038	-0.038	0.000	0.000	0.000	0.000
98	A	242	SER	0	-0.036	-0.020	29.073	0.277	0.277	0.000	0.000	0.000	0.000
99	A	243	TYR	0	0.082	0.047	23.159	-0.093	-0.093	0.000	0.000	0.000	0.000
100	A	244	PRO	0	-0.029	-0.001	27.393	0.257	0.257	0.000	0.000	0.000	0.000
101	A	245	LEU	0	0.044	0.000	28.135	-0.215	-0.215	0.000	0.000	0.000	0.000
102	A	246	LYS	1	0.916	0.953	28.558	8.769	8.769	0.000	0.000	0.000	0.000
103	A	247	PRO	0	0.028	0.011	24.953	0.100	0.100	0.000	0.000	0.000	0.000
104	A	248	PHE	0	0.021	0.015	21.639	-0.321	-0.321	0.000	0.000	0.000	0.000
105	A	249	LEU	0	-0.035	-0.010	25.328	0.001	0.001	0.000	0.000	0.000	0.000
106	A	250	VAL	0	0.051	0.026	25.191	0.154	0.154	0.000	0.000	0.000	0.000
107	A	251	GLU	-1	-0.792	-0.852	28.158	-9.623	-9.623	0.000	0.000	0.000	0.000
108	A	252	SER	0	-0.006	-0.013	30.809	0.049	0.049	0.000	0.000	0.000	0.000
109	A	253	CYS	0	-0.010	0.001	33.938	0.211	0.211	0.000	0.000	0.000	0.000
110	A	254	LYS	1	0.969	0.967	33.154	7.995	7.995	0.000	0.000	0.000	0.000
111	A	255	GLU	-1	-0.915	-0.949	33.261	-7.674	-7.674	0.000	0.000	0.000	0.000
112	A	256	ALA	0	0.087	0.038	31.578	-0.120	-0.120	0.000	0.000	0.000	0.000
113	A	257	PHE	0	-0.006	0.000	25.613	-0.236	-0.236	0.000	0.000	0.000	0.000
114	A	258	TRP	0	0.006	0.000	28.781	-0.292	-0.292	0.000	0.000	0.000	0.000
115	A	259	ASP	-1	-0.852	-0.922	30.712	-8.368	-8.368	0.000	0.000	0.000	0.000
116	A	260	ARG	1	0.740	0.828	24.690	10.111	10.111	0.000	0.000	0.000	0.000
117	A	261	CYS	0	-0.056	-0.031	26.257	-0.377	-0.377	0.000	0.000	0.000	0.000
118	A	262	LEU	0	0.014	0.003	27.132	-0.186	-0.186	0.000	0.000	0.000	0.000
119	A	263	SER	0	-0.022	-0.003	28.009	-0.091	-0.091	0.000	0.000	0.000	0.000
120	A	264	VAL	0	0.019	0.004	21.940	-0.126	-0.126	0.000	0.000	0.000	0.000
121	A	265	ILE	0	0.014	0.008	24.517	-0.251	-0.251	0.000	0.000	0.000	0.000
122	A	266	ASN	0	-0.045	-0.025	26.476	0.080	0.080	0.000	0.000	0.000	0.000
123	A	267	LEU	0	-0.033	-0.005	23.109	0.033	0.033	0.000	0.000	0.000	0.000
124	A	268	MET	0	-0.022	-0.005	18.616	-0.065	-0.065	0.000	0.000	0.000	0.000
125	A	269	SER	0	0.009	0.000	22.457	-0.346	-0.346	0.000	0.000	0.000	0.000
126	A	270	SER	0	-0.025	-0.008	24.313	-0.293	-0.293	0.000	0.000	0.000	0.000
127	A	271	LYS	1	0.924	0.943	19.197	12.610	12.610	0.000	0.000	0.000	0.000
128	A	272	MET	0	-0.040	-0.005	19.728	-0.474	-0.474	0.000	0.000	0.000	0.000
129	A	273	LEU	0	0.057	0.038	20.826	-0.339	-0.339	0.000	0.000	0.000	0.000
130	A	274	GLN	0	-0.038	-0.019	20.319	-0.088	-0.088	0.000	0.000	0.000	0.000
131	A	275	ILE	0	-0.052	-0.033	13.496	-0.368	-0.368	0.000	0.000	0.000	0.000
132	A	276	ASN	0	-0.045	-0.039	17.023	-0.998	-0.998	0.000	0.000	0.000	0.000
133	A	277	ALA	0	-0.020	-0.005	19.631	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	278	ASP	-1	-0.828	-0.921	19.363	-14.125	-14.125	0.000	0.000	0.000	0.000
135	A	279	PRO	0	0.027	-0.001	16.357	-0.767	-0.767	0.000	0.000	0.000	0.000
136	A	280	HIS	0	-0.008	0.014	14.919	-1.950	-1.950	0.000	0.000	0.000	0.000
137	A	281	TYR	0	-0.007	0.006	14.933	-0.975	-0.975	0.000	0.000	0.000	0.000
138	A	282	PHE	0	0.014	0.009	10.427	-1.105	-1.105	0.000	0.000	0.000	0.000
139	A	283	THR	0	-0.045	-0.046	10.607	-2.003	-2.003	0.000	0.000	0.000	0.000
140	A	284	GLN	0	-0.041	-0.013	10.111	-1.547	-1.547	0.000	0.000	0.000	0.000
141	A	285	VAL	0	0.042	0.028	10.626	-1.248	-1.248	0.000	0.000	0.000	0.000
142	A	286	PHE	0	0.009	-0.010	5.050	-3.332	-3.332	0.000	0.000	0.000	0.000
143	A	287	SER	0	-0.061	-0.036	6.111	-3.850	-3.850	0.000	0.000	0.000	0.000
144	A	288	ASP	-1	-0.809	-0.889	6.517	-22.097	-22.097	0.000	0.000	0.000	0.000
148	A	292	GLU	-1	-0.847	-0.894	4.955	-17.986	-17.986	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:145:GLN)