FMO DATABASE

FMODB ID: Q891Y

Calculation Name: 3GCG-B-Xray312

Preferred Name: Cell division control protein 42 homolog

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3GCG

Chain ID: B

ChEMBL ID: CHEMBL6088

UniProt ID: P60953

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	154
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1458865.983243
FMO2-HF: Nuclear repulsion	1397230.524886
FMO2-HF: Total energy	-61635.458356
FMO2-MP2: Total energy	-61816.145769

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(B:46:ACE )

Summations of interaction energy for fragment #1(B:46: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.
0.666	1.214	-0.002	-0.424	-0.122	0

Interaction energy analysis for fragmet #1(B:46:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.010

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].
3	B	48	VAL	0	0.057	0.031	3.849	1.292	1.993	-0.005	-0.359	-0.337
4	B	49	ILE	0	-0.004	-0.009	7.230	0.028	0.028	0.000	0.000	0.000
5	B	50	ASN	0	0.023	0.013	10.222	0.122	0.122	0.000	0.000	0.000
6	B	51	HIS	0	0.039	-0.020	9.911	0.011	0.011	0.000	0.000	0.000
7	B	52	GLY	0	0.046	0.035	14.576	0.027	0.027	0.000	0.000	0.000
8	B	53	LYS	1	0.935	0.956	16.967	0.245	0.245	0.000	0.000	0.000
9	B	54	LEU	0	-0.007	0.004	13.232	0.010	0.010	0.000	0.000	0.000
10	B	55	THR	0	0.064	0.033	17.445	0.021	0.021	0.000	0.000	0.000
11	B	56	ASN	0	0.011	0.007	19.916	0.013	0.013	0.000	0.000	0.000
12	B	57	GLN	0	-0.014	-0.006	19.248	0.004	0.004	0.000	0.000	0.000
13	B	58	LEU	0	-0.014	0.000	20.357	0.006	0.006	0.000	0.000	0.000
14	B	59	LEU	0	0.038	0.005	22.290	0.010	0.010	0.000	0.000	0.000
15	B	60	GLN	0	-0.037	-0.017	25.119	-0.002	-0.002	0.000	0.000	0.000
16	B	61	ALA	0	-0.090	-0.063	24.938	0.005	0.005	0.000	0.000	0.000
17	B	62	VAL	0	0.017	0.026	25.967	0.005	0.005	0.000	0.000	0.000
18	B	63	ALA	0	-0.004	0.001	28.405	0.005	0.005	0.000	0.000	0.000
19	B	64	LYS	1	0.908	0.957	26.900	0.085	0.085	0.000	0.000	0.000
20	B	65	GLN	0	-0.020	0.001	29.678	-0.001	-0.001	0.000	0.000	0.000
21	B	66	THR	0	0.002	0.017	33.636	0.003	0.003	0.000	0.000	0.000
22	B	67	ARG	1	1.013	0.986	36.476	0.033	0.033	0.000	0.000	0.000
23	B	68	ASN	0	-0.046	-0.023	37.622	-0.002	-0.002	0.000	0.000	0.000
24	B	69	GLY	0	0.018	0.018	33.582	-0.001	-0.001	0.000	0.000	0.000
25	B	70	ASP	-1	-0.852	-0.930	32.646	-0.027	-0.027	0.000	0.000	0.000
26	B	71	THR	0	-0.005	-0.013	28.751	-0.001	-0.001	0.000	0.000	0.000
27	B	72	GLN	0	0.010	0.007	30.011	0.002	0.002	0.000	0.000	0.000
28	B	73	GLN	0	0.031	0.014	31.912	0.003	0.003	0.000	0.000	0.000
29	B	74	TRP	0	0.002	-0.007	23.089	0.002	0.002	0.000	0.000	0.000
30	B	75	PHE	0	0.011	0.007	25.220	0.002	0.002	0.000	0.000	0.000
31	B	76	GLN	0	-0.001	-0.009	28.062	0.003	0.003	0.000	0.000	0.000
32	B	77	GLN	0	-0.002	-0.008	29.867	0.003	0.003	0.000	0.000	0.000
33	B	78	GLU	-1	-0.687	-0.783	22.482	-0.011	-0.011	0.000	0.000	0.000
34	B	79	GLN	0	0.011	0.011	25.413	0.008	0.008	0.000	0.000	0.000
35	B	80	THR	0	-0.013	0.009	26.344	0.006	0.006	0.000	0.000	0.000
36	B	81	THR	0	0.023	0.032	25.123	0.006	0.006	0.000	0.000	0.000
37	B	82	TYR	0	-0.023	-0.031	16.752	0.010	0.010	0.000	0.000	0.000
38	B	83	ILE	0	0.026	0.020	22.925	0.011	0.011	0.000	0.000	0.000
39	B	84	SER	0	0.036	0.007	24.909	0.008	0.008	0.000	0.000	0.000
40	B	85	ARG	1	0.857	0.964	17.680	-0.036	-0.036	0.000	0.000	0.000
41	B	86	THR	0	-0.076	-0.033	20.886	0.012	0.012	0.000	0.000	0.000
42	B	87	VAL	0	0.025	0.019	22.573	0.010	0.010	0.000	0.000	0.000
43	B	88	ASN	0	-0.027	-0.054	25.947	0.006	0.006	0.000	0.000	0.000
44	B	89	ARG	1	0.927	0.979	16.965	-0.096	-0.096	0.000	0.000	0.000
45	B	90	THR	0	-0.017	-0.011	23.296	0.013	0.013	0.000	0.000	0.000
46	B	91	LEU	0	0.005	0.000	24.235	0.002	0.002	0.000	0.000	0.000
47	B	92	ASP	-1	-0.938	-0.964	24.498	0.060	0.060	0.000	0.000	0.000
48	B	93	ASP	-1	-0.967	-0.998	20.998	0.131	0.131	0.000	0.000	0.000
49	B	94	TYR	0	0.005	0.004	24.307	0.004	0.004	0.000	0.000	0.000
50	B	95	CYS	0	-0.008	-0.005	27.444	-0.003	-0.003	0.000	0.000	0.000
51	B	96	ARG	1	0.902	0.967	22.755	-0.097	-0.097	0.000	0.000	0.000
52	B	97	SER	0	-0.066	-0.031	25.637	-0.002	-0.002	0.000	0.000	0.000
53	B	98	ASN	0	-0.014	-0.009	27.566	-0.001	-0.001	0.000	0.000	0.000
54	B	99	ASN	0	-0.050	-0.019	30.747	-0.005	-0.005	0.000	0.000	0.000
55	B	100	SER	0	-0.032	-0.003	32.423	-0.005	-0.005	0.000	0.000	0.000
56	B	101	VAL	0	0.010	-0.004	33.531	0.000	0.000	0.000	0.000	0.000
57	B	102	ILE	0	0.015	0.030	32.952	-0.001	-0.001	0.000	0.000	0.000
58	B	103	SER	0	0.014	0.011	36.093	-0.001	-0.001	0.000	0.000	0.000
59	B	104	LYS	1	1.005	0.966	34.852	-0.026	-0.026	0.000	0.000	0.000
60	B	105	GLU	-1	-0.883	-0.919	38.134	0.025	0.025	0.000	0.000	0.000
61	B	106	THR	0	0.059	0.016	36.614	0.000	0.000	0.000	0.000	0.000
62	B	107	LYS	1	0.887	0.943	31.501	-0.033	-0.033	0.000	0.000	0.000
63	B	108	GLY	0	0.026	-0.009	34.745	0.001	0.001	0.000	0.000	0.000
64	B	109	HIS	0	0.001	0.006	36.940	0.000	0.000	0.000	0.000	0.000
65	B	110	ILE	0	0.007	0.007	31.560	0.001	0.001	0.000	0.000	0.000
66	B	111	PHE	0	0.004	-0.006	29.185	0.002	0.002	0.000	0.000	0.000
67	B	112	ARG	1	0.951	0.982	33.484	-0.023	-0.023	0.000	0.000	0.000
68	B	113	ALA	0	0.006	0.014	34.588	-0.001	-0.001	0.000	0.000	0.000
69	B	114	VAL	0	-0.008	-0.015	28.805	0.001	0.001	0.000	0.000	0.000
70	B	115	GLU	-1	-0.872	-0.922	31.687	0.022	0.022	0.000	0.000	0.000
71	B	116	ASN	0	-0.034	-0.029	33.603	-0.004	-0.004	0.000	0.000	0.000
72	B	117	ALA	0	-0.031	-0.008	31.981	-0.001	-0.001	0.000	0.000	0.000
73	B	118	LEU	0	-0.039	-0.017	27.590	0.001	0.001	0.000	0.000	0.000
74	B	119	GLN	0	-0.084	-0.025	31.234	-0.005	-0.005	0.000	0.000	0.000
75	B	120	GLN	0	0.001	-0.005	28.372	-0.005	-0.005	0.000	0.000	0.000
76	B	121	PRO	0	-0.043	-0.006	32.536	0.002	0.002	0.000	0.000	0.000
77	B	122	LEU	0	-0.027	-0.041	29.096	0.001	0.001	0.000	0.000	0.000
78	B	123	ASP	-1	-0.814	-0.910	31.076	0.011	0.011	0.000	0.000	0.000
79	B	124	MET	0	-0.011	0.005	30.906	0.002	0.002	0.000	0.000	0.000
80	B	125	ASN	0	-0.047	-0.021	31.569	0.005	0.005	0.000	0.000	0.000
81	B	126	GLY	0	-0.031	-0.007	28.262	-0.002	-0.002	0.000	0.000	0.000
82	B	127	ALA	0	0.038	-0.024	25.186	0.006	0.006	0.000	0.000	0.000
83	B	128	GLN	0	-0.024	-0.011	23.158	-0.004	-0.004	0.000	0.000	0.000
84	B	129	SER	0	-0.010	-0.039	20.470	-0.005	-0.005	0.000	0.000	0.000
85	B	130	SER	0	-0.005	-0.020	21.818	-0.009	-0.009	0.000	0.000	0.000
86	B	131	ILE	0	0.009	0.016	17.422	-0.015	-0.015	0.000	0.000	0.000
87	B	132	GLY	0	0.006	-0.011	17.060	-0.018	-0.018	0.000	0.000	0.000
88	B	133	HIS	0	-0.002	-0.023	18.064	-0.022	-0.022	0.000	0.000	0.000
89	B	134	PHE	0	-0.026	0.000	18.906	-0.015	-0.015	0.000	0.000	0.000
90	B	135	LEU	0	-0.033	-0.027	13.689	-0.018	-0.018	0.000	0.000	0.000
91	B	136	GLN	0	0.041	0.028	16.825	-0.025	-0.025	0.000	0.000	0.000
92	B	137	SER	0	-0.011	0.018	18.046	-0.012	-0.012	0.000	0.000	0.000
93	B	138	ASN	0	-0.031	-0.005	17.041	-0.033	-0.033	0.000	0.000	0.000
94	B	139	LYS	1	0.996	0.983	17.218	0.128	0.128	0.000	0.000	0.000
95	B	140	TYR	0	0.012	0.015	13.284	-0.040	-0.040	0.000	0.000	0.000
96	B	141	PHE	0	0.060	0.006	10.781	-0.084	-0.084	0.000	0.000	0.000
97	B	142	ASN	0	-0.010	-0.038	12.200	-0.069	-0.069	0.000	0.000	0.000
98	B	143	GLN	0	-0.013	0.023	13.697	0.031	0.031	0.000	0.000	0.000
99	B	144	LYS	1	0.888	0.940	8.817	0.886	0.886	0.000	0.000	0.000
100	B	145	VAL	0	-0.006	-0.002	8.975	-0.179	-0.179	0.000	0.000	0.000
101	B	146	ASP	-1	-0.847	-0.920	10.452	-0.334	-0.334	0.000	0.000	0.000
102	B	147	GLU	-1	-0.902	-0.960	9.190	-0.921	-0.921	0.000	0.000	0.000
103	B	148	GLN	0	-0.011	-0.001	3.954	-1.071	-1.224	0.003	-0.065	0.215
104	B	149	CYS	0	-0.151	-0.051	7.375	0.230	0.230	0.000	0.000	0.000
105	B	150	GLY	0	0.032	0.021	10.046	0.094	0.094	0.000	0.000	0.000
106	B	151	LYS	1	0.923	0.946	10.793	0.183	0.183	0.000	0.000	0.000
107	B	152	ARG	1	0.923	0.966	7.623	0.100	0.100	0.000	0.000	0.000
108	B	153	VAL	0	0.047	0.008	14.008	-0.037	-0.037	0.000	0.000	0.000
109	B	154	ASP	-1	-0.805	-0.857	16.725	-0.017	-0.017	0.000	0.000	0.000
110	B	155	PRO	0	0.015	-0.028	17.803	-0.004	-0.004	0.000	0.000	0.000
111	B	156	ILE	0	0.042	0.028	18.665	-0.006	-0.006	0.000	0.000	0.000
112	B	157	THR	0	-0.025	-0.011	13.246	0.012	0.012	0.000	0.000	0.000
113	B	158	ARG	1	0.891	0.927	13.651	0.243	0.243	0.000	0.000	0.000
114	B	159	PHE	0	0.020	0.019	13.864	-0.022	-0.022	0.000	0.000	0.000
115	B	160	ASN	0	0.038	0.010	14.612	-0.005	-0.005	0.000	0.000	0.000
116	B	161	THR	0	-0.038	-0.010	8.756	0.051	0.051	0.000	0.000	0.000
117	B	162	GLN	0	-0.007	-0.012	10.418	0.003	0.003	0.000	0.000	0.000
118	B	163	THR	0	-0.040	-0.024	12.563	0.012	0.012	0.000	0.000	0.000
119	B	164	LYS	1	0.955	0.968	9.682	-0.276	-0.276	0.000	0.000	0.000
120	B	165	MET	0	-0.006	0.006	6.686	0.076	0.076	0.000	0.000	0.000
121	B	166	ILE	0	-0.014	0.016	9.375	-0.015	-0.015	0.000	0.000	0.000
122	B	167	GLU	-1	-0.932	-0.958	12.393	0.094	0.094	0.000	0.000	0.000
123	B	168	GLN	0	-0.040	-0.031	6.281	-0.091	-0.091	0.000	0.000	0.000
124	B	169	VAL	0	0.036	0.017	9.255	-0.014	-0.014	0.000	0.000	0.000
125	B	170	SER	0	-0.030	-0.022	11.379	0.004	0.004	0.000	0.000	0.000
126	B	171	GLN	0	0.045	0.034	13.358	0.004	0.004	0.000	0.000	0.000
127	B	172	GLU	-1	-0.871	-0.926	9.241	-0.006	-0.006	0.000	0.000	0.000
128	B	173	ILE	0	-0.064	-0.043	13.738	-0.015	-0.015	0.000	0.000	0.000
129	B	174	PHE	0	0.008	0.014	16.373	-0.002	-0.002	0.000	0.000	0.000
130	B	175	GLU	-1	-0.825	-0.930	15.861	0.112	0.112	0.000	0.000	0.000
131	B	176	ARG	1	0.872	0.946	12.752	0.053	0.053	0.000	0.000	0.000
132	B	177	ASN	0	-0.078	-0.050	19.153	-0.008	-0.008	0.000	0.000	0.000
133	B	178	PHE	0	-0.008	-0.004	21.670	-0.004	-0.004	0.000	0.000	0.000
134	B	179	SER	0	-0.035	0.003	21.968	0.011	0.011	0.000	0.000	0.000
135	B	180	GLY	0	-0.012	-0.001	24.004	-0.001	-0.001	0.000	0.000	0.000
136	B	181	PHE	0	0.028	-0.014	24.627	0.003	0.003	0.000	0.000	0.000
137	B	182	LYS	1	0.926	0.975	19.300	-0.092	-0.092	0.000	0.000	0.000
138	B	183	VAL	0	0.037	0.018	17.445	0.001	0.001	0.000	0.000	0.000
139	B	184	SER	0	-0.019	-0.019	18.213	0.003	0.003	0.000	0.000	0.000
140	B	185	GLU	-1	-0.854	-0.922	19.897	0.074	0.074	0.000	0.000	0.000
141	B	186	ILE	0	0.035	0.021	22.259	-0.003	-0.003	0.000	0.000	0.000
142	B	187	LYS	1	0.933	0.972	17.187	-0.175	-0.175	0.000	0.000	0.000
143	B	188	ALA	0	0.033	0.028	23.303	-0.003	-0.003	0.000	0.000	0.000
144	B	189	ILE	0	0.017	0.003	25.312	-0.005	-0.005	0.000	0.000	0.000
145	B	190	THR	0	-0.009	-0.021	26.313	-0.007	-0.007	0.000	0.000	0.000
146	B	191	GLN	0	-0.050	-0.029	24.100	-0.001	-0.001	0.000	0.000	0.000
147	B	192	ASN	0	0.017	0.009	28.155	0.001	0.001	0.000	0.000	0.000
148	B	193	ALA	0	0.019	0.024	30.916	-0.004	-0.004	0.000	0.000	0.000
149	B	194	ILE	0	-0.029	-0.032	28.464	-0.003	-0.003	0.000	0.000	0.000
150	B	195	LEU	0	-0.035	-0.021	32.107	-0.002	-0.002	0.000	0.000	0.000
151	B	196	GLU	-1	-0.981	-0.974	33.854	0.042	0.042	0.000	0.000	0.000
152	B	197	HIS	0	-0.034	-0.026	35.798	-0.004	-0.004	0.000	0.000	0.000
153	B	198	VAL	0	-0.100	-0.040	33.744	-0.002	-0.002	0.000	0.000	0.000
154	B	199	NME	0	-0.013	0.005	35.757	-0.002	-0.002	0.000	0.000	0.000

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