FMO DATABASE

FMODB ID: PKR33

Calculation Name: 4M91-A-Xray13

Preferred Name: Protein cereblon

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4M91

Chain ID: A

ChEMBL ID: CHEMBL3763008

UniProt ID: Q96SW2

Base Structure: X-ray

Registration Date: 2018-02-14

Reference:

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water	No
Procedure	Auto-FMO protocol ver. 1.20181228

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	155
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-1632084.841489
FMO2-HF: Nuclear repulsion	1567922.958619
FMO2-HF: Total energy	-64161.88287
FMO2-MP2: Total energy	-64346.768092

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(A:1:ACE)

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

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.
0.48	0.172	2.962	-0.98	-1.675	-0.015

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.022

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	LYS	1	0.986	1.005	3.837	1.562	2.274	-0.011	-0.359	-0.342	0.001
4	A	4	LYS	1	0.986	0.968	6.958	0.979	0.979	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.872	-0.938	2.418	-3.759	-4.986	2.974	-0.603	-1.144	-0.016
6	A	6	ASN	0	0.018	0.004	3.915	0.482	0.689	-0.001	-0.018	-0.189	0.000
7	A	7	LEU	0	0.022	0.007	7.038	0.103	0.103	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.084	-0.047	9.245	0.073	0.073	0.000	0.000	0.000	0.000
9	A	9	ALA	0	0.022	0.009	8.777	0.048	0.048	0.000	0.000	0.000	0.000
10	A	10	GLU	-1	-0.844	-0.917	10.655	-0.016	-0.016	0.000	0.000	0.000	0.000
11	A	11	LYS	1	0.800	0.906	13.123	0.196	0.196	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.030	-0.028	13.805	0.010	0.010	0.000	0.000	0.000	0.000
13	A	13	GLU	-1	-0.883	-0.936	14.303	0.146	0.146	0.000	0.000	0.000	0.000
14	A	14	GLN	0	-0.020	-0.014	16.682	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	15	LEU	0	-0.045	-0.009	18.306	0.001	0.001	0.000	0.000	0.000	0.000
16	A	16	MET	0	0.007	0.012	18.470	-0.002	-0.002	0.000	0.000	0.000	0.000
17	A	17	GLU	-1	-0.762	-0.855	20.809	0.014	0.014	0.000	0.000	0.000	0.000
18	A	18	TRP	0	-0.022	0.005	22.798	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	19	SER	0	0.007	-0.015	23.344	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.066	-0.036	25.312	0.002	0.002	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.814	0.887	26.073	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.888	0.945	28.677	0.002	0.002	0.000	0.000	0.000	0.000
23	A	23	SER	0	0.056	0.024	28.543	0.003	0.003	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.003	0.015	29.337	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	25	PHE	0	-0.076	-0.037	23.283	0.001	0.001	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.819	0.870	28.750	0.016	0.016	0.000	0.000	0.000	0.000
27	A	27	MET	0	-0.057	-0.026	24.665	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	28	ASN	0	0.129	0.078	29.785	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.084	0.014	29.544	-0.004	-0.004	0.000	0.000	0.000	0.000
30	A	30	ASP	-1	-0.872	-0.932	27.247	-0.074	-0.074	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.899	0.946	24.495	0.037	0.037	0.000	0.000	0.000	0.000
32	A	32	PHE	0	0.094	0.042	24.595	-0.008	-0.008	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.860	0.916	24.643	0.067	0.067	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.904	0.972	18.871	0.080	0.080	0.000	0.000	0.000	0.000
35	A	35	PHE	0	0.005	-0.019	19.229	-0.017	-0.017	0.000	0.000	0.000	0.000
36	A	36	ILE	0	0.023	0.036	20.750	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.890	0.955	22.111	0.098	0.098	0.000	0.000	0.000	0.000
38	A	38	ALA	0	-0.001	0.013	18.962	-0.014	-0.014	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.035	0.000	15.508	0.002	0.002	0.000	0.000	0.000	0.000
40	A	40	PRO	0	0.010	0.012	11.378	0.005	0.005	0.000	0.000	0.000	0.000
41	A	41	ARG	1	0.893	0.938	13.730	0.187	0.187	0.000	0.000	0.000	0.000
42	A	42	ASN	0	-0.029	-0.033	11.483	-0.019	-0.019	0.000	0.000	0.000	0.000
43	A	43	TYR	0	0.003	-0.002	14.645	0.011	0.011	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.003	-0.032	18.052	-0.018	-0.018	0.000	0.000	0.000	0.000
45	A	45	MET	0	-0.052	0.016	21.662	0.010	0.010	0.000	0.000	0.000	0.000
46	A	46	ILE	0	0.031	0.028	24.142	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.032	-0.023	27.664	0.001	0.001	0.000	0.000	0.000	0.000
48	A	48	MET	0	-0.008	0.021	30.054	0.001	0.001	0.000	0.000	0.000	0.000
49	A	49	PHE	0	-0.007	-0.015	30.675	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	50	THR	0	0.036	-0.006	35.502	0.002	0.002	0.000	0.000	0.000	0.000
51	A	51	ALA	0	0.066	0.015	38.617	-0.002	-0.002	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.052	-0.028	39.229	0.002	0.002	0.000	0.000	0.000	0.000
53	A	53	GLN	0	0.017	0.029	41.956	0.002	0.002	0.000	0.000	0.000	0.000
54	A	54	PRO	0	0.024	0.012	44.773	0.000	0.000	0.000	0.000	0.000	0.000
55	A	55	GLN	0	0.035	0.007	46.389	0.001	0.001	0.000	0.000	0.000	0.000
56	A	56	ARG	1	0.799	0.862	44.437	0.024	0.024	0.000	0.000	0.000	0.000
57	A	57	GLN	0	-0.009	0.016	48.772	0.000	0.000	0.000	0.000	0.000	0.000
58	A	58	CYS	0	0.004	0.008	44.774	0.000	0.000	0.000	0.000	0.000	0.000
59	A	59	SER	0	0.013	-0.007	46.222	0.000	0.000	0.000	0.000	0.000	0.000
60	A	60	VAL	0	0.055	0.027	43.871	0.001	0.001	0.000	0.000	0.000	0.000
61	A	61	SER	0	0.024	0.008	41.985	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	62	ARG	1	0.965	0.985	42.019	0.009	0.009	0.000	0.000	0.000	0.000
63	A	63	GLN	0	0.042	0.029	43.443	0.000	0.000	0.000	0.000	0.000	0.000
64	A	64	ALA	0	0.014	0.002	40.010	0.001	0.001	0.000	0.000	0.000	0.000
65	A	65	ASN	0	0.053	0.007	38.014	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	66	GLU	-1	-0.928	-0.959	38.957	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.793	-0.887	39.842	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	68	TYR	0	-0.027	-0.037	30.712	0.001	0.001	0.000	0.000	0.000	0.000
69	A	69	GLN	0	-0.050	-0.037	34.986	0.003	0.003	0.000	0.000	0.000	0.000
70	A	70	ILE	0	0.023	0.028	35.993	0.002	0.002	0.000	0.000	0.000	0.000
71	A	71	LEU	0	-0.019	0.000	32.548	0.002	0.002	0.000	0.000	0.000	0.000
72	A	72	ALA	0	0.006	-0.002	31.236	0.002	0.002	0.000	0.000	0.000	0.000
73	A	73	ASN	0	-0.037	-0.021	31.451	0.004	0.004	0.000	0.000	0.000	0.000
74	A	74	SER	0	0.003	-0.008	33.272	0.004	0.004	0.000	0.000	0.000	0.000
75	A	75	TRP	0	-0.007	-0.005	23.610	0.003	0.003	0.000	0.000	0.000	0.000
76	A	76	ARG	1	0.838	0.931	28.740	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	77	TYR	0	-0.016	-0.018	29.496	0.005	0.005	0.000	0.000	0.000	0.000
78	A	78	SER	0	-0.039	0.017	29.171	0.003	0.003	0.000	0.000	0.000	0.000
79	A	79	SER	0	0.031	-0.003	28.674	0.002	0.002	0.000	0.000	0.000	0.000
80	A	80	ALA	0	-0.023	-0.013	26.297	0.004	0.004	0.000	0.000	0.000	0.000
81	A	81	PHE	0	-0.030	0.006	23.434	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	82	SER	0	0.040	0.009	20.198	0.006	0.006	0.000	0.000	0.000	0.000
83	A	83	ASN	0	0.020	-0.002	15.194	-0.016	-0.016	0.000	0.000	0.000	0.000
84	A	84	LYS	1	0.928	0.951	13.339	-0.004	-0.004	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.017	0.016	19.083	-0.015	-0.015	0.000	0.000	0.000	0.000
86	A	86	PHE	0	-0.006	-0.004	18.827	0.006	0.006	0.000	0.000	0.000	0.000
87	A	87	PHE	0	0.077	0.038	24.191	-0.006	-0.006	0.000	0.000	0.000	0.000
88	A	88	SER	0	0.011	-0.029	26.204	0.002	0.002	0.000	0.000	0.000	0.000
89	A	89	MET	0	-0.010	0.003	28.896	0.001	0.001	0.000	0.000	0.000	0.000
90	A	90	VAL	0	-0.010	-0.002	30.907	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	91	ASP	-1	-0.755	-0.879	33.412	-0.024	-0.024	0.000	0.000	0.000	0.000
92	A	92	TYR	0	0.013	-0.003	36.922	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	93	ASP	-1	-0.762	-0.850	38.989	-0.027	-0.027	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.848	-0.871	35.535	-0.025	-0.025	0.000	0.000	0.000	0.000
95	A	95	GLY	0	-0.029	-0.027	34.268	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	96	THR	0	-0.004	-0.013	34.983	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	97	ASP	-1	-0.766	-0.886	32.796	-0.058	-0.058	0.000	0.000	0.000	0.000
98	A	98	VAL	0	-0.060	-0.033	30.700	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	99	PHE	0	-0.012	-0.009	33.104	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	100	GLN	0	0.021	0.023	36.217	0.000	0.000	0.000	0.000	0.000	0.000
101	A	101	GLN	0	-0.077	-0.031	30.718	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	102	LEU	0	-0.090	-0.060	30.575	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	103	ASN	0	-0.032	-0.001	34.424	0.003	0.003	0.000	0.000	0.000	0.000
104	A	104	MET	0	-0.033	-0.003	34.193	0.002	0.002	0.000	0.000	0.000	0.000
105	A	105	ASN	0	0.033	0.009	39.155	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	106	SER	0	-0.002	-0.009	41.560	0.003	0.003	0.000	0.000	0.000	0.000
107	A	107	ALA	0	-0.021	0.014	40.416	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	108	PRO	0	-0.033	-0.014	39.075	0.002	0.002	0.000	0.000	0.000	0.000
109	A	109	THR	0	0.013	-0.003	35.320	0.000	0.000	0.000	0.000	0.000	0.000
110	A	110	PHE	0	0.015	0.013	33.774	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	111	MET	0	-0.022	-0.011	30.196	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	112	HIS	0	0.038	0.040	24.558	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	113	PHE	0	-0.019	-0.032	24.089	-0.006	-0.006	0.000	0.000	0.000	0.000
114	A	114	PRO	0	0.026	0.028	22.045	0.000	0.000	0.000	0.000	0.000	0.000
115	A	115	PRO	0	0.014	0.009	16.857	-0.014	-0.014	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.921	0.955	12.553	0.250	0.250	0.000	0.000	0.000	0.000
117	A	117	GLY	0	0.001	0.010	18.955	0.017	0.017	0.000	0.000	0.000	0.000
118	A	118	ARG	1	0.958	0.979	22.037	0.106	0.106	0.000	0.000	0.000	0.000
119	A	119	PRO	0	0.056	0.018	25.273	0.000	0.000	0.000	0.000	0.000	0.000
120	A	120	LYS	1	0.857	0.924	24.646	0.091	0.091	0.000	0.000	0.000	0.000
121	A	121	ARG	1	1.039	1.012	29.973	0.043	0.043	0.000	0.000	0.000	0.000
122	A	122	ALA	0	0.029	0.012	32.313	0.002	0.002	0.000	0.000	0.000	0.000
123	A	123	ASP	-1	-0.778	-0.853	27.944	-0.059	-0.059	0.000	0.000	0.000	0.000
124	A	124	THR	0	0.003	0.004	30.938	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	125	PHE	0	-0.011	0.011	34.041	0.001	0.001	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.810	-0.911	35.968	-0.027	-0.027	0.000	0.000	0.000	0.000
127	A	127	LEU	0	0.004	-0.005	39.563	0.002	0.002	0.000	0.000	0.000	0.000
128	A	128	GLN	0	0.012	-0.010	41.252	0.001	0.001	0.000	0.000	0.000	0.000
129	A	129	ARG	1	0.888	0.959	40.345	0.023	0.023	0.000	0.000	0.000	0.000
130	A	130	ILE	0	-0.079	-0.035	39.659	0.001	0.001	0.000	0.000	0.000	0.000
131	A	131	GLY	0	0.027	0.036	43.485	0.002	0.002	0.000	0.000	0.000	0.000
132	A	132	PHE	0	-0.015	-0.044	40.283	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	133	ALA	0	0.032	0.031	40.467	0.001	0.001	0.000	0.000	0.000	0.000
134	A	134	ALA	0	0.026	0.007	37.565	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	135	GLU	-1	-0.772	-0.878	37.029	-0.004	-0.004	0.000	0.000	0.000	0.000
136	A	136	GLN	0	-0.026	-0.023	37.789	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	137	LEU	0	-0.018	-0.001	34.756	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	138	ALA	0	0.019	0.005	33.120	-0.002	-0.002	0.000	0.000	0.000	0.000
139	A	139	LYS	1	0.914	0.961	32.922	0.007	0.007	0.000	0.000	0.000	0.000
140	A	140	TRP	0	-0.002	0.012	31.408	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	141	ILE	0	0.021	-0.002	28.084	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	142	ALA	0	-0.017	0.011	28.783	-0.003	-0.003	0.000	0.000	0.000	0.000
143	A	143	ASP	-1	-0.908	-0.950	29.323	-0.022	-0.022	0.000	0.000	0.000	0.000
144	A	144	ARG	1	0.738	0.855	28.085	0.043	0.043	0.000	0.000	0.000	0.000
145	A	145	THR	0	-0.095	-0.071	24.378	-0.005	-0.005	0.000	0.000	0.000	0.000
146	A	146	ASP	-1	-0.890	-0.934	24.250	-0.010	-0.010	0.000	0.000	0.000	0.000
147	A	147	VAL	0	-0.059	-0.009	23.889	0.007	0.007	0.000	0.000	0.000	0.000
148	A	148	HIS	0	-0.013	-0.013	26.622	-0.001	-0.001	0.000	0.000	0.000	0.000
149	A	149	ILE	0	-0.032	-0.011	28.711	0.004	0.004	0.000	0.000	0.000	0.000
150	A	150	ARG	1	0.926	0.953	31.627	-0.006	-0.006	0.000	0.000	0.000	0.000
151	A	151	VAL	0	0.017	0.001	34.962	0.002	0.002	0.000	0.000	0.000	0.000
152	A	152	PHE	0	0.016	0.017	37.080	0.001	0.001	0.000	0.000	0.000	0.000
153	A	153	ARG	1	0.772	0.844	38.942	0.001	0.001	0.000	0.000	0.000	0.000
154	A	154	LEU	0	-0.002	0.005	42.155	0.001	0.001	0.000	0.000	0.000	0.000
155	A	155	NME	0	0.037	0.029	44.038	-0.001	-0.001	0.000	0.000	0.000	0.000

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