FMO DATABASE

FMODB ID: 4J1NN

Calculation Name: 4M91-A-Xray372

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: 2023-09-23

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	OptAll
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	153
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1626925.61003
FMO2-HF: Nuclear repulsion	1562934.038185
FMO2-HF: Total energy	-63991.571846
FMO2-MP2: Total energy	-64176.002116

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:2:SER)

Summations of interaction energy for fragment #1(A:2: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.
-36.401	-31.472	15.632	-9.969	-10.593	-0.043

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.058 / q_NPA : 0.030

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	LYS	1	0.963	0.975	2.335	-11.700	-7.361	1.835	-2.819	-3.354	0.029
4	A	5	GLU	-1	-0.851	-0.926	1.923	-26.027	-26.475	13.779	-6.790	-6.542	-0.073
5	A	6	ASN	0	-0.009	-0.006	3.410	-0.633	0.405	0.018	-0.360	-0.697	0.001
6	A	7	LEU	0	-0.006	-0.003	6.125	-0.132	-0.132	0.000	0.000	0.000	0.000
7	A	8	LEU	0	-0.072	-0.033	6.921	-0.186	-0.186	0.000	0.000	0.000	0.000
8	A	9	ALA	0	0.027	0.021	8.117	-0.014	-0.014	0.000	0.000	0.000	0.000
9	A	10	GLU	-1	-0.694	-0.838	9.189	1.331	1.331	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.742	0.880	11.430	-0.208	-0.208	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.016	-0.019	12.532	-0.035	-0.035	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.892	-0.945	13.858	0.147	0.147	0.000	0.000	0.000	0.000
13	A	14	GLN	0	0.011	0.004	14.685	-0.019	-0.019	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.030	-0.001	16.066	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	16	MET	0	0.014	0.023	18.063	-0.027	-0.027	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.770	-0.841	20.053	0.109	0.109	0.000	0.000	0.000	0.000
17	A	18	TRP	0	-0.004	0.014	21.827	-0.003	-0.003	0.000	0.000	0.000	0.000
18	A	19	SER	0	-0.014	-0.035	22.254	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	20	SER	0	-0.037	-0.017	24.653	-0.007	-0.007	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.834	0.876	25.020	-0.097	-0.097	0.000	0.000	0.000	0.000
21	A	22	ARG	1	0.880	0.940	27.622	-0.035	-0.035	0.000	0.000	0.000	0.000
22	A	23	SER	0	0.067	0.037	27.663	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	24	ILE	0	-0.004	0.008	27.819	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	25	PHE	0	-0.057	-0.030	21.635	0.014	0.014	0.000	0.000	0.000	0.000
25	A	26	ARG	1	0.836	0.874	26.696	-0.046	-0.046	0.000	0.000	0.000	0.000
26	A	27	MET	0	-0.099	-0.037	21.633	0.019	0.019	0.000	0.000	0.000	0.000
27	A	28	ASN	0	0.084	0.033	26.434	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.078	0.023	26.085	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.814	-0.884	23.265	0.165	0.165	0.000	0.000	0.000	0.000
30	A	31	LYS	1	0.893	0.957	21.666	-0.137	-0.137	0.000	0.000	0.000	0.000
31	A	32	PHE	0	0.101	0.036	21.264	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	33	ARG	1	0.793	0.869	20.317	-0.149	-0.149	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.863	0.939	15.940	-0.333	-0.333	0.000	0.000	0.000	0.000
34	A	35	PHE	0	0.033	0.000	16.302	0.036	0.036	0.000	0.000	0.000	0.000
35	A	36	ILE	0	0.000	0.030	17.702	-0.048	-0.048	0.000	0.000	0.000	0.000
36	A	37	LYS	1	0.918	0.966	18.830	-0.047	-0.047	0.000	0.000	0.000	0.000
37	A	38	ALA	0	0.011	0.016	14.629	-0.031	-0.031	0.000	0.000	0.000	0.000
38	A	39	PRO	0	-0.011	0.010	10.254	-0.068	-0.068	0.000	0.000	0.000	0.000
39	A	40	PRO	0	0.013	0.005	7.842	0.061	0.061	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.858	0.921	10.122	0.198	0.198	0.000	0.000	0.000	0.000
41	A	42	ASN	0	0.002	-0.014	10.443	-0.017	-0.017	0.000	0.000	0.000	0.000
42	A	43	TYR	0	0.022	0.007	12.956	-0.007	-0.007	0.000	0.000	0.000	0.000
43	A	44	SER	0	0.027	0.004	16.577	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	45	MET	0	-0.051	0.016	19.865	0.019	0.019	0.000	0.000	0.000	0.000
45	A	46	ILE	0	0.026	0.026	21.900	-0.002	-0.002	0.000	0.000	0.000	0.000
46	A	47	VAL	0	-0.028	-0.024	24.896	0.016	0.016	0.000	0.000	0.000	0.000
47	A	48	MET	0	-0.004	0.021	27.525	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	49	PHE	0	0.005	-0.005	27.309	0.010	0.010	0.000	0.000	0.000	0.000
49	A	50	THR	0	0.027	-0.012	32.541	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.038	0.002	35.807	0.005	0.005	0.000	0.000	0.000	0.000
51	A	52	LEU	0	-0.058	-0.034	36.747	-0.004	-0.004	0.000	0.000	0.000	0.000
52	A	53	GLN	0	0.031	0.027	38.770	0.000	0.000	0.000	0.000	0.000	0.000
53	A	54	PRO	0	0.022	0.024	41.866	-0.003	-0.003	0.000	0.000	0.000	0.000
54	A	55	GLN	0	0.040	0.008	43.551	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	56	ARG	1	0.792	0.850	40.895	-0.022	-0.022	0.000	0.000	0.000	0.000
56	A	57	GLN	0	-0.028	-0.005	45.951	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	58	CYS	0	-0.003	0.015	41.902	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	59	SER	0	0.027	0.002	43.585	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	60	VAL	0	0.033	0.019	41.747	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	61	SER	0	0.027	0.008	39.322	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	62	ARG	1	0.866	0.909	39.514	0.006	0.006	0.000	0.000	0.000	0.000
62	A	63	GLN	0	0.043	0.019	41.086	0.000	0.000	0.000	0.000	0.000	0.000
63	A	64	ALA	0	-0.007	0.000	38.024	-0.004	-0.004	0.000	0.000	0.000	0.000
64	A	65	ASN	0	0.056	0.008	36.231	-0.004	-0.004	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.853	-0.898	37.101	-0.015	-0.015	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.721	-0.816	38.497	-0.050	-0.050	0.000	0.000	0.000	0.000
67	A	68	TYR	0	-0.022	-0.036	28.835	-0.010	-0.010	0.000	0.000	0.000	0.000
68	A	69	GLN	0	-0.044	-0.030	33.603	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	70	ILE	0	0.013	0.021	34.943	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.025	0.011	31.554	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	72	ALA	0	0.011	0.005	30.409	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	73	ASN	0	-0.033	-0.025	30.794	0.001	0.001	0.000	0.000	0.000	0.000
73	A	74	SER	0	-0.001	-0.017	33.011	-0.002	-0.002	0.000	0.000	0.000	0.000
74	A	75	TRP	0	-0.038	-0.018	23.254	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.812	0.896	28.255	0.014	0.014	0.000	0.000	0.000	0.000
76	A	77	TYR	0	-0.005	0.000	29.800	0.001	0.001	0.000	0.000	0.000	0.000
77	A	78	SER	0	-0.010	0.020	29.038	-0.004	-0.004	0.000	0.000	0.000	0.000
78	A	79	SER	0	0.015	-0.007	28.900	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	80	ALA	0	0.004	0.008	26.423	-0.012	-0.012	0.000	0.000	0.000	0.000
80	A	81	PHE	0	-0.019	-0.003	24.240	-0.020	-0.020	0.000	0.000	0.000	0.000
81	A	82	SER	0	0.029	0.009	20.396	-0.019	-0.019	0.000	0.000	0.000	0.000
82	A	83	ASN	0	0.038	0.009	15.208	-0.030	-0.030	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.797	0.881	14.205	0.432	0.432	0.000	0.000	0.000	0.000
84	A	85	LEU	0	0.019	0.023	18.589	-0.015	-0.015	0.000	0.000	0.000	0.000
85	A	86	PHE	0	0.018	0.012	17.260	0.019	0.019	0.000	0.000	0.000	0.000
86	A	87	PHE	0	0.088	0.034	22.552	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	88	SER	0	0.018	-0.024	24.035	0.022	0.022	0.000	0.000	0.000	0.000
88	A	89	MET	0	-0.029	-0.003	26.686	-0.009	-0.009	0.000	0.000	0.000	0.000
89	A	90	VAL	0	0.004	0.006	27.858	0.012	0.012	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.732	-0.867	30.694	0.013	0.013	0.000	0.000	0.000	0.000
91	A	92	TYR	0	0.027	0.012	33.834	0.008	0.008	0.000	0.000	0.000	0.000
92	A	93	ASP	-1	-0.772	-0.850	35.903	0.035	0.035	0.000	0.000	0.000	0.000
93	A	94	GLU	-1	-0.848	-0.876	32.827	0.054	0.054	0.000	0.000	0.000	0.000
94	A	95	GLY	0	-0.010	-0.020	30.609	0.011	0.011	0.000	0.000	0.000	0.000
95	A	96	THR	0	0.009	-0.006	31.260	-0.004	-0.004	0.000	0.000	0.000	0.000
96	A	97	ASP	-1	-0.751	-0.868	28.053	0.081	0.081	0.000	0.000	0.000	0.000
97	A	98	VAL	0	-0.033	-0.015	26.764	-0.003	-0.003	0.000	0.000	0.000	0.000
98	A	99	PHE	0	-0.017	-0.010	28.981	-0.011	-0.011	0.000	0.000	0.000	0.000
99	A	100	GLN	0	0.014	0.018	32.051	-0.004	-0.004	0.000	0.000	0.000	0.000
100	A	101	GLN	0	-0.104	-0.057	25.284	0.004	0.004	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.065	-0.034	26.544	-0.010	-0.010	0.000	0.000	0.000	0.000
102	A	103	ASN	0	-0.025	-0.001	30.238	-0.004	-0.004	0.000	0.000	0.000	0.000
103	A	104	MET	0	-0.037	-0.003	31.101	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	105	ASN	0	0.023	-0.003	35.223	0.004	0.004	0.000	0.000	0.000	0.000
105	A	106	SER	0	-0.002	0.000	38.164	0.002	0.002	0.000	0.000	0.000	0.000
106	A	107	ALA	0	-0.016	0.008	37.691	0.000	0.000	0.000	0.000	0.000	0.000
107	A	108	PRO	0	0.002	0.014	36.737	0.001	0.001	0.000	0.000	0.000	0.000
108	A	109	THR	0	-0.005	-0.024	32.590	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	110	PHE	0	0.002	0.011	31.422	0.004	0.004	0.000	0.000	0.000	0.000
110	A	111	MET	0	-0.026	-0.010	27.367	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	112	HIS	0	0.035	0.024	22.360	-0.011	-0.011	0.000	0.000	0.000	0.000
112	A	113	PHE	0	-0.003	-0.023	20.933	0.000	0.000	0.000	0.000	0.000	0.000
113	A	114	PRO	0	0.039	0.033	19.340	-0.010	-0.010	0.000	0.000	0.000	0.000
114	A	115	PRO	0	0.015	0.008	14.380	0.020	0.020	0.000	0.000	0.000	0.000
115	A	116	LYS	1	0.916	0.938	10.098	0.901	0.901	0.000	0.000	0.000	0.000
116	A	117	GLY	0	0.003	0.012	15.915	0.027	0.027	0.000	0.000	0.000	0.000
117	A	118	ARG	1	0.961	0.983	18.200	0.132	0.132	0.000	0.000	0.000	0.000
118	A	119	PRO	0	0.068	0.027	21.398	-0.029	-0.029	0.000	0.000	0.000	0.000
119	A	120	LYS	1	0.867	0.928	21.813	0.243	0.243	0.000	0.000	0.000	0.000
120	A	121	ARG	1	1.016	0.996	27.087	0.111	0.111	0.000	0.000	0.000	0.000
121	A	122	ALA	0	0.058	0.036	29.658	0.008	0.008	0.000	0.000	0.000	0.000
122	A	123	ASP	-1	-0.815	-0.855	25.791	-0.191	-0.191	0.000	0.000	0.000	0.000
123	A	124	THR	0	0.016	-0.001	28.156	0.011	0.011	0.000	0.000	0.000	0.000
124	A	125	PHE	0	0.011	0.013	31.141	-0.004	-0.004	0.000	0.000	0.000	0.000
125	A	126	ASP	-1	-0.788	-0.875	33.590	-0.066	-0.066	0.000	0.000	0.000	0.000
126	A	127	LEU	0	0.002	-0.013	37.153	0.001	0.001	0.000	0.000	0.000	0.000
127	A	128	GLN	0	0.014	-0.008	38.797	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	129	ARG	1	0.835	0.915	38.602	0.082	0.082	0.000	0.000	0.000	0.000
129	A	130	ILE	0	-0.068	-0.024	37.375	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	131	GLY	0	0.034	0.038	41.273	0.001	0.001	0.000	0.000	0.000	0.000
131	A	132	PHE	0	-0.021	-0.044	38.516	-0.005	-0.005	0.000	0.000	0.000	0.000
132	A	133	ALA	0	0.032	0.027	38.784	0.001	0.001	0.000	0.000	0.000	0.000
133	A	134	ALA	0	0.034	0.007	36.527	-0.006	-0.006	0.000	0.000	0.000	0.000
134	A	135	GLU	-1	-0.771	-0.877	35.732	-0.072	-0.072	0.000	0.000	0.000	0.000
135	A	136	GLN	0	-0.010	-0.006	36.543	-0.014	-0.014	0.000	0.000	0.000	0.000
136	A	137	LEU	0	-0.027	-0.006	33.218	-0.008	-0.008	0.000	0.000	0.000	0.000
137	A	138	ALA	0	0.007	-0.001	31.907	-0.009	-0.009	0.000	0.000	0.000	0.000
138	A	139	LYS	1	0.921	0.970	31.732	0.090	0.090	0.000	0.000	0.000	0.000
139	A	140	TRP	0	0.001	0.014	29.216	-0.009	-0.009	0.000	0.000	0.000	0.000
140	A	141	ILE	0	0.009	-0.012	26.764	-0.011	-0.011	0.000	0.000	0.000	0.000
141	A	142	ALA	0	-0.005	0.032	27.443	-0.020	-0.020	0.000	0.000	0.000	0.000
142	A	143	ASP	-1	-0.865	-0.937	28.200	-0.162	-0.162	0.000	0.000	0.000	0.000
143	A	144	ARG	1	0.697	0.818	26.043	0.184	0.184	0.000	0.000	0.000	0.000
144	A	145	THR	0	-0.103	-0.081	23.194	-0.018	-0.018	0.000	0.000	0.000	0.000
145	A	146	ASP	-1	-0.848	-0.899	23.520	-0.275	-0.275	0.000	0.000	0.000	0.000
146	A	147	VAL	0	-0.043	-0.012	23.165	0.000	0.000	0.000	0.000	0.000	0.000
147	A	148	HIS	0	-0.010	-0.014	26.144	0.039	0.039	0.000	0.000	0.000	0.000
148	A	149	ILE	0	-0.031	-0.011	27.974	0.008	0.008	0.000	0.000	0.000	0.000
149	A	150	ARG	1	0.866	0.920	31.007	0.135	0.135	0.000	0.000	0.000	0.000
150	A	151	VAL	0	0.002	0.000	34.708	0.002	0.002	0.000	0.000	0.000	0.000
151	A	152	PHE	0	0.014	0.012	36.796	0.000	0.000	0.000	0.000	0.000	0.000
152	A	153	ARG	1	0.721	0.785	38.825	0.055	0.055	0.000	0.000	0.000	0.000
153	A	154	LEU	0	0.032	0.030	41.853	0.000	0.000	0.000	0.000	0.000	0.000

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Support

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