FMO DATABASE

FMODB ID: QV28Y

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	OptH
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	-1625902.52843
FMO2-HF: Nuclear repulsion	1561911.627884
FMO2-HF: Total energy	-63990.900546
FMO2-MP2: Total energy	-64175.242947

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.
-35.759	-35.187	21.977	-10.539	-12.012	-0.024

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 : 0.043 / q_NPA : 0.019

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	0.983	0.967	2.427	-11.138	-7.223	1.770	-2.482	-3.204	0.027
4	A	5	GLU	-1	-0.869	-0.930	1.961	-24.838	-29.330	20.181	-7.814	-7.876	-0.052
5	A	6	ASN	0	0.027	0.009	3.504	-1.642	-0.628	0.027	-0.236	-0.806	0.001
6	A	7	LEU	0	0.021	0.006	5.365	-0.016	0.119	-0.001	-0.007	-0.126	0.000
7	A	8	LEU	0	-0.086	-0.049	6.696	-0.126	-0.126	0.000	0.000	0.000	0.000
8	A	9	ALA	0	0.023	0.010	7.684	0.032	0.032	0.000	0.000	0.000	0.000
9	A	10	GLU	-1	-0.843	-0.917	9.351	0.712	0.712	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.800	0.906	11.267	-0.094	-0.094	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.030	-0.028	12.077	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	13	GLU	-1	-0.883	-0.936	13.365	-0.085	-0.085	0.000	0.000	0.000	0.000
13	A	14	GLN	0	-0.020	-0.014	15.306	0.015	0.015	0.000	0.000	0.000	0.000
14	A	15	LEU	0	-0.045	-0.009	16.239	0.010	0.010	0.000	0.000	0.000	0.000
15	A	16	MET	0	0.007	0.013	17.559	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	17	GLU	-1	-0.762	-0.855	19.600	0.034	0.034	0.000	0.000	0.000	0.000
17	A	18	TRP	0	-0.022	0.005	21.543	0.011	0.011	0.000	0.000	0.000	0.000
18	A	19	SER	0	0.007	-0.015	22.167	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	20	SER	0	-0.066	-0.036	24.260	0.000	0.000	0.000	0.000	0.000	0.000
20	A	21	ARG	1	0.814	0.887	24.596	-0.020	-0.020	0.000	0.000	0.000	0.000
21	A	22	ARG	1	0.888	0.945	27.306	0.005	0.005	0.000	0.000	0.000	0.000
22	A	23	SER	0	0.057	0.025	27.268	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	24	ILE	0	-0.003	0.015	27.719	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	25	PHE	0	-0.076	-0.037	21.375	0.014	0.014	0.000	0.000	0.000	0.000
25	A	26	ARG	1	0.818	0.869	26.517	-0.022	-0.022	0.000	0.000	0.000	0.000
26	A	27	MET	0	-0.057	-0.026	21.862	0.015	0.015	0.000	0.000	0.000	0.000
27	A	28	ASN	0	0.129	0.078	26.431	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	29	GLY	0	0.085	0.013	26.092	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	30	ASP	-1	-0.873	-0.932	23.407	0.170	0.170	0.000	0.000	0.000	0.000
30	A	31	LYS	1	0.899	0.947	21.780	-0.112	-0.112	0.000	0.000	0.000	0.000
31	A	32	PHE	0	0.094	0.042	21.293	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	33	ARG	1	0.860	0.916	20.396	-0.147	-0.147	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.903	0.972	16.117	-0.272	-0.272	0.000	0.000	0.000	0.000
34	A	35	PHE	0	0.005	-0.019	16.422	0.025	0.025	0.000	0.000	0.000	0.000
35	A	36	ILE	0	0.023	0.036	17.659	-0.052	-0.052	0.000	0.000	0.000	0.000
36	A	37	LYS	1	0.890	0.955	18.440	-0.058	-0.058	0.000	0.000	0.000	0.000
37	A	38	ALA	0	-0.001	0.013	14.390	-0.007	-0.007	0.000	0.000	0.000	0.000
38	A	39	PRO	0	-0.036	0.000	10.478	-0.084	-0.084	0.000	0.000	0.000	0.000
39	A	40	PRO	0	0.009	0.011	7.691	0.065	0.065	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.893	0.938	9.869	0.135	0.135	0.000	0.000	0.000	0.000
41	A	42	ASN	0	-0.029	-0.034	10.407	0.046	0.046	0.000	0.000	0.000	0.000
42	A	43	TYR	0	0.003	-0.002	12.580	-0.017	-0.017	0.000	0.000	0.000	0.000
43	A	44	SER	0	-0.003	-0.032	16.123	0.007	0.007	0.000	0.000	0.000	0.000
44	A	45	MET	0	-0.052	0.016	19.483	0.012	0.012	0.000	0.000	0.000	0.000
45	A	46	ILE	0	0.031	0.028	21.674	0.002	0.002	0.000	0.000	0.000	0.000
46	A	47	VAL	0	-0.032	-0.023	24.775	0.012	0.012	0.000	0.000	0.000	0.000
47	A	48	MET	0	-0.007	0.021	27.308	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	49	PHE	0	-0.007	-0.014	27.235	0.008	0.008	0.000	0.000	0.000	0.000
49	A	50	THR	0	0.042	-0.002	32.426	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	51	ALA	0	0.051	0.006	35.635	0.006	0.006	0.000	0.000	0.000	0.000
51	A	52	LEU	0	-0.050	-0.027	36.643	-0.003	-0.003	0.000	0.000	0.000	0.000
52	A	53	GLN	0	0.019	0.030	39.091	0.001	0.001	0.000	0.000	0.000	0.000
53	A	54	PRO	0	0.024	0.012	41.867	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	55	GLN	0	0.035	0.006	43.308	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	56	ARG	1	0.797	0.860	40.929	-0.015	-0.015	0.000	0.000	0.000	0.000
56	A	57	GLN	0	-0.019	0.010	45.643	-0.004	-0.004	0.000	0.000	0.000	0.000
57	A	58	CYS	0	0.008	0.012	41.670	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	59	SER	0	0.032	0.001	43.459	-0.002	-0.002	0.000	0.000	0.000	0.000
59	A	60	VAL	0	0.049	0.025	41.169	-0.002	-0.002	0.000	0.000	0.000	0.000
60	A	61	SER	0	0.020	0.003	39.219	-0.005	-0.005	0.000	0.000	0.000	0.000
61	A	62	ARG	1	0.968	0.989	39.493	0.015	0.015	0.000	0.000	0.000	0.000
62	A	63	GLN	0	0.040	0.028	41.175	0.000	0.000	0.000	0.000	0.000	0.000
63	A	64	ALA	0	0.014	0.002	37.578	-0.005	-0.005	0.000	0.000	0.000	0.000
64	A	65	ASN	0	0.053	0.006	35.793	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.929	-0.960	36.958	-0.038	-0.038	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.793	-0.887	38.029	-0.068	-0.068	0.000	0.000	0.000	0.000
67	A	68	TYR	0	-0.026	-0.037	28.347	-0.013	-0.013	0.000	0.000	0.000	0.000
68	A	69	GLN	0	-0.050	-0.037	33.282	-0.009	-0.009	0.000	0.000	0.000	0.000
69	A	70	ILE	0	0.022	0.028	34.618	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	71	LEU	0	-0.019	0.001	30.839	-0.007	-0.007	0.000	0.000	0.000	0.000
71	A	72	ALA	0	0.006	-0.002	29.757	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	73	ASN	0	-0.037	-0.021	30.388	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	74	SER	0	0.004	-0.007	32.603	-0.004	-0.004	0.000	0.000	0.000	0.000
74	A	75	TRP	0	-0.007	-0.005	22.813	-0.006	-0.006	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.838	0.931	28.023	0.067	0.067	0.000	0.000	0.000	0.000
76	A	77	TYR	0	-0.016	-0.018	29.136	-0.003	-0.003	0.000	0.000	0.000	0.000
77	A	78	SER	0	-0.039	0.017	28.948	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	79	SER	0	0.032	-0.003	28.657	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	80	ALA	0	-0.023	-0.013	26.496	-0.016	-0.016	0.000	0.000	0.000	0.000
80	A	81	PHE	0	-0.030	0.006	23.017	-0.025	-0.025	0.000	0.000	0.000	0.000
81	A	82	SER	0	0.040	0.009	20.143	-0.033	-0.033	0.000	0.000	0.000	0.000
82	A	83	ASN	0	0.021	-0.002	14.990	0.002	0.002	0.000	0.000	0.000	0.000
83	A	84	LYS	1	0.928	0.951	13.097	0.760	0.760	0.000	0.000	0.000	0.000
84	A	85	LEU	0	0.017	0.016	18.076	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	86	PHE	0	-0.006	-0.004	17.237	0.013	0.013	0.000	0.000	0.000	0.000
86	A	87	PHE	0	0.077	0.038	22.425	0.001	0.001	0.000	0.000	0.000	0.000
87	A	88	SER	0	0.011	-0.029	23.720	0.018	0.018	0.000	0.000	0.000	0.000
88	A	89	MET	0	-0.010	0.003	26.424	-0.006	-0.006	0.000	0.000	0.000	0.000
89	A	90	VAL	0	-0.009	-0.001	27.639	0.010	0.010	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.755	-0.879	30.315	0.002	0.002	0.000	0.000	0.000	0.000
91	A	92	TYR	0	0.013	-0.003	33.619	0.008	0.008	0.000	0.000	0.000	0.000
92	A	93	ASP	-1	-0.761	-0.849	35.527	0.027	0.027	0.000	0.000	0.000	0.000
93	A	94	GLU	-1	-0.848	-0.871	32.349	0.034	0.034	0.000	0.000	0.000	0.000
94	A	95	GLY	0	-0.029	-0.027	30.705	0.011	0.011	0.000	0.000	0.000	0.000
95	A	96	THR	0	-0.004	-0.013	31.327	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	97	ASP	-1	-0.766	-0.886	28.421	0.079	0.079	0.000	0.000	0.000	0.000
97	A	98	VAL	0	-0.060	-0.033	26.614	0.000	0.000	0.000	0.000	0.000	0.000
98	A	99	PHE	0	-0.012	-0.009	28.892	-0.009	-0.009	0.000	0.000	0.000	0.000
99	A	100	GLN	0	0.021	0.023	32.071	-0.003	-0.003	0.000	0.000	0.000	0.000
100	A	101	GLN	0	-0.077	-0.031	25.871	0.006	0.006	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.090	-0.060	26.319	-0.007	-0.007	0.000	0.000	0.000	0.000
102	A	103	ASN	0	-0.032	0.000	29.941	-0.005	-0.005	0.000	0.000	0.000	0.000
103	A	104	MET	0	-0.033	-0.003	30.637	-0.004	-0.004	0.000	0.000	0.000	0.000
104	A	105	ASN	0	0.033	0.009	35.001	0.003	0.003	0.000	0.000	0.000	0.000
105	A	106	SER	0	-0.002	-0.009	37.741	0.001	0.001	0.000	0.000	0.000	0.000
106	A	107	ALA	0	-0.030	0.009	37.143	0.000	0.000	0.000	0.000	0.000	0.000
107	A	108	PRO	0	-0.019	-0.006	36.290	0.001	0.001	0.000	0.000	0.000	0.000
108	A	109	THR	0	0.011	-0.005	32.238	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	110	PHE	0	0.015	0.013	31.154	0.002	0.002	0.000	0.000	0.000	0.000
110	A	111	MET	0	-0.022	-0.011	26.700	0.001	0.001	0.000	0.000	0.000	0.000
111	A	112	HIS	0	0.038	0.040	22.255	-0.021	-0.021	0.000	0.000	0.000	0.000
112	A	113	PHE	0	-0.020	-0.033	20.856	0.009	0.009	0.000	0.000	0.000	0.000
113	A	114	PRO	0	0.026	0.028	19.338	-0.018	-0.018	0.000	0.000	0.000	0.000
114	A	115	PRO	0	0.014	0.009	14.312	0.026	0.026	0.000	0.000	0.000	0.000
115	A	116	LYS	1	0.921	0.955	9.873	0.881	0.881	0.000	0.000	0.000	0.000
116	A	117	GLY	0	0.001	0.010	15.566	0.017	0.017	0.000	0.000	0.000	0.000
117	A	118	ARG	1	0.958	0.979	17.962	0.078	0.078	0.000	0.000	0.000	0.000
118	A	119	PRO	0	0.056	0.018	21.163	-0.025	-0.025	0.000	0.000	0.000	0.000
119	A	120	LYS	1	0.857	0.924	21.177	0.230	0.230	0.000	0.000	0.000	0.000
120	A	121	ARG	1	1.039	1.012	26.539	0.106	0.106	0.000	0.000	0.000	0.000
121	A	122	ALA	0	0.029	0.012	29.815	0.007	0.007	0.000	0.000	0.000	0.000
122	A	123	ASP	-1	-0.778	-0.853	25.053	-0.190	-0.190	0.000	0.000	0.000	0.000
123	A	124	THR	0	0.002	0.004	28.177	0.009	0.009	0.000	0.000	0.000	0.000
124	A	125	PHE	0	-0.011	0.011	31.107	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	126	ASP	-1	-0.810	-0.911	33.403	-0.067	-0.067	0.000	0.000	0.000	0.000
126	A	127	LEU	0	0.005	-0.005	36.966	0.001	0.001	0.000	0.000	0.000	0.000
127	A	128	GLN	0	0.012	-0.009	38.670	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	129	ARG	1	0.887	0.959	38.117	0.087	0.087	0.000	0.000	0.000	0.000
129	A	130	ILE	0	-0.079	-0.035	37.428	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	131	GLY	0	0.027	0.036	41.291	0.001	0.001	0.000	0.000	0.000	0.000
131	A	132	PHE	0	-0.014	-0.043	38.068	-0.005	-0.005	0.000	0.000	0.000	0.000
132	A	133	ALA	0	0.032	0.030	38.500	0.000	0.000	0.000	0.000	0.000	0.000
133	A	134	ALA	0	0.026	0.007	36.162	-0.007	-0.007	0.000	0.000	0.000	0.000
134	A	135	GLU	-1	-0.772	-0.878	35.555	-0.091	-0.091	0.000	0.000	0.000	0.000
135	A	136	GLN	0	-0.026	-0.022	36.436	-0.012	-0.012	0.000	0.000	0.000	0.000
136	A	137	LEU	0	-0.018	-0.001	32.876	-0.007	-0.007	0.000	0.000	0.000	0.000
137	A	138	ALA	0	0.019	0.005	31.709	-0.010	-0.010	0.000	0.000	0.000	0.000
138	A	139	LYS	1	0.914	0.961	31.597	0.099	0.099	0.000	0.000	0.000	0.000
139	A	140	TRP	0	-0.002	0.012	28.912	-0.009	-0.009	0.000	0.000	0.000	0.000
140	A	141	ILE	0	0.021	-0.002	26.468	-0.010	-0.010	0.000	0.000	0.000	0.000
141	A	142	ALA	0	-0.017	0.011	27.259	-0.021	-0.021	0.000	0.000	0.000	0.000
142	A	143	ASP	-1	-0.908	-0.950	28.098	-0.178	-0.178	0.000	0.000	0.000	0.000
143	A	144	ARG	1	0.738	0.855	25.939	0.179	0.179	0.000	0.000	0.000	0.000
144	A	145	THR	0	-0.095	-0.072	22.895	-0.021	-0.021	0.000	0.000	0.000	0.000
145	A	146	ASP	-1	-0.890	-0.934	23.110	-0.335	-0.335	0.000	0.000	0.000	0.000
146	A	147	VAL	0	-0.059	-0.009	22.913	-0.010	-0.010	0.000	0.000	0.000	0.000
147	A	148	HIS	0	-0.013	-0.013	25.838	0.038	0.038	0.000	0.000	0.000	0.000
148	A	149	ILE	0	-0.032	-0.011	27.547	0.001	0.001	0.000	0.000	0.000	0.000
149	A	150	ARG	1	0.926	0.953	30.909	0.163	0.163	0.000	0.000	0.000	0.000
150	A	151	VAL	0	0.017	0.001	34.449	0.001	0.001	0.000	0.000	0.000	0.000
151	A	152	PHE	0	0.018	0.019	36.308	0.001	0.001	0.000	0.000	0.000	0.000
152	A	153	ARG	1	0.769	0.845	38.380	0.074	0.074	0.000	0.000	0.000	0.000
153	A	154	LEU	0	0.036	0.031	41.424	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:2:SER)