FMO DATABASE

FMODB ID: J3NV9

Calculation Name: 3GCG-B-Xray372

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: 2023-06-19

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	152
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1451493.736057
FMO2-HF: Nuclear repulsion	1390029.196587
FMO2-HF: Total energy	-61464.539471
FMO2-MP2: Total energy	-61644.695482

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:47:PHE)

Summations of interaction energy for fragment #1(B:47:PHE)

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.
-16.24	-4.152	6.328	-4.893	-13.519	-0.008

Interaction energy analysis for fragmet #1(B:47:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / q_NPA : 0.004

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	B	49	ILE	0	-0.003	-0.009	2.779	-2.806	0.675	0.457	-1.247	-2.691	-0.002
4	B	50	ASN	0	0.023	0.014	4.310	0.090	0.173	0.000	-0.019	-0.064	0.000
5	B	51	HIS	0	0.039	-0.020	4.878	0.467	0.467	0.000	0.000	0.000	0.000
6	B	52	GLY	0	0.044	0.034	8.199	0.067	0.067	0.000	0.000	0.000	0.000
7	B	53	LYS	1	0.934	0.956	10.445	0.141	0.141	0.000	0.000	0.000	0.000
8	B	54	LEU	0	-0.001	0.005	5.933	0.051	0.051	0.000	0.000	0.000	0.000
9	B	55	THR	0	0.058	0.031	10.247	0.039	0.039	0.000	0.000	0.000	0.000
10	B	56	ASN	0	0.010	0.006	12.900	0.020	0.020	0.000	0.000	0.000	0.000
11	B	57	GLN	0	-0.013	-0.006	12.493	0.025	0.025	0.000	0.000	0.000	0.000
12	B	58	LEU	0	-0.013	0.000	13.169	0.023	0.023	0.000	0.000	0.000	0.000
13	B	59	LEU	0	0.043	0.006	15.045	0.028	0.028	0.000	0.000	0.000	0.000
14	B	60	GLN	0	-0.041	-0.018	17.849	0.017	0.017	0.000	0.000	0.000	0.000
15	B	61	ALA	0	-0.091	-0.064	17.733	0.022	0.022	0.000	0.000	0.000	0.000
16	B	62	VAL	0	0.017	0.026	18.870	0.013	0.013	0.000	0.000	0.000	0.000
17	B	63	ALA	0	-0.002	0.001	21.243	0.014	0.014	0.000	0.000	0.000	0.000
18	B	64	LYS	1	0.907	0.957	19.815	0.155	0.155	0.000	0.000	0.000	0.000
19	B	65	GLN	0	-0.016	0.003	22.750	-0.006	-0.006	0.000	0.000	0.000	0.000
20	B	66	THR	0	0.000	0.016	26.511	0.009	0.009	0.000	0.000	0.000	0.000
21	B	67	ARG	1	1.013	0.987	29.289	0.075	0.075	0.000	0.000	0.000	0.000
22	B	68	ASN	0	-0.046	-0.023	30.390	0.005	0.005	0.000	0.000	0.000	0.000
23	B	69	GLY	0	0.015	0.016	26.339	-0.001	-0.001	0.000	0.000	0.000	0.000
24	B	70	ASP	-1	-0.849	-0.929	25.510	-0.145	-0.145	0.000	0.000	0.000	0.000
25	B	71	THR	0	-0.004	-0.012	21.700	-0.005	-0.005	0.000	0.000	0.000	0.000
26	B	72	GLN	0	0.009	0.007	23.330	-0.015	-0.015	0.000	0.000	0.000	0.000
27	B	73	GLN	0	0.031	0.014	25.540	-0.008	-0.008	0.000	0.000	0.000	0.000
28	B	74	TRP	0	-0.001	-0.008	16.533	-0.006	-0.006	0.000	0.000	0.000	0.000
29	B	75	PHE	0	0.014	0.008	19.340	-0.014	-0.014	0.000	0.000	0.000	0.000
30	B	76	GLN	0	-0.004	-0.010	22.096	-0.010	-0.010	0.000	0.000	0.000	0.000
31	B	77	GLN	0	-0.003	-0.008	23.565	-0.012	-0.012	0.000	0.000	0.000	0.000
32	B	78	GLU	-1	-0.684	-0.782	16.325	-0.408	-0.408	0.000	0.000	0.000	0.000
33	B	79	GLN	0	0.013	0.012	19.525	-0.037	-0.037	0.000	0.000	0.000	0.000
34	B	80	THR	0	-0.017	0.007	20.779	-0.017	-0.017	0.000	0.000	0.000	0.000
35	B	81	THR	0	0.020	0.031	19.234	0.001	0.001	0.000	0.000	0.000	0.000
36	B	82	TYR	0	-0.020	-0.029	11.623	-0.005	-0.005	0.000	0.000	0.000	0.000
37	B	83	ILE	0	0.027	0.020	17.805	-0.027	-0.027	0.000	0.000	0.000	0.000
38	B	84	SER	0	0.034	0.006	19.930	0.008	0.008	0.000	0.000	0.000	0.000
39	B	85	ARG	1	0.855	0.964	12.553	0.578	0.578	0.000	0.000	0.000	0.000
40	B	86	THR	0	-0.071	-0.032	16.767	-0.030	-0.030	0.000	0.000	0.000	0.000
41	B	87	VAL	0	0.024	0.018	18.222	0.001	0.001	0.000	0.000	0.000	0.000
42	B	88	ASN	0	-0.028	-0.054	21.788	0.023	0.023	0.000	0.000	0.000	0.000
43	B	89	ARG	1	0.929	0.980	13.583	0.557	0.557	0.000	0.000	0.000	0.000
44	B	90	THR	0	-0.018	-0.011	19.612	-0.004	-0.004	0.000	0.000	0.000	0.000
45	B	91	LEU	0	0.005	0.000	21.237	0.019	0.019	0.000	0.000	0.000	0.000
46	B	92	ASP	-1	-0.937	-0.964	21.308	-0.255	-0.255	0.000	0.000	0.000	0.000
47	B	93	ASP	-1	-0.965	-0.997	18.667	-0.363	-0.363	0.000	0.000	0.000	0.000
48	B	94	TYR	0	-0.002	0.002	22.025	0.016	0.016	0.000	0.000	0.000	0.000
49	B	95	CYS	0	-0.009	-0.006	25.381	0.020	0.020	0.000	0.000	0.000	0.000
50	B	96	ARG	1	0.901	0.968	20.203	0.296	0.296	0.000	0.000	0.000	0.000
51	B	97	SER	0	-0.066	-0.032	24.204	0.016	0.016	0.000	0.000	0.000	0.000
52	B	98	ASN	0	-0.027	-0.016	26.016	0.018	0.018	0.000	0.000	0.000	0.000
53	B	99	ASN	0	-0.052	-0.016	28.857	0.008	0.008	0.000	0.000	0.000	0.000
54	B	100	SER	0	-0.005	0.006	30.407	0.011	0.011	0.000	0.000	0.000	0.000
55	B	101	VAL	0	0.005	-0.003	31.100	-0.008	-0.008	0.000	0.000	0.000	0.000
56	B	102	ILE	0	0.010	0.028	29.795	0.007	0.007	0.000	0.000	0.000	0.000
57	B	103	SER	0	0.015	0.012	32.824	-0.005	-0.005	0.000	0.000	0.000	0.000
58	B	104	LYS	1	1.006	0.966	30.630	0.142	0.142	0.000	0.000	0.000	0.000
59	B	105	GLU	-1	-0.882	-0.919	34.117	-0.100	-0.100	0.000	0.000	0.000	0.000
60	B	106	THR	0	0.058	0.016	33.398	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	107	LYS	1	0.886	0.943	27.171	0.183	0.183	0.000	0.000	0.000	0.000
62	B	108	GLY	0	0.026	-0.009	30.729	-0.009	-0.009	0.000	0.000	0.000	0.000
63	B	109	HIS	0	0.000	0.005	32.738	-0.005	-0.005	0.000	0.000	0.000	0.000
64	B	110	ILE	0	0.009	0.008	28.008	-0.003	-0.003	0.000	0.000	0.000	0.000
65	B	111	PHE	0	0.002	-0.006	24.619	-0.008	-0.008	0.000	0.000	0.000	0.000
66	B	112	ARG	1	0.950	0.982	29.265	0.124	0.124	0.000	0.000	0.000	0.000
67	B	113	ALA	0	0.006	0.014	31.061	0.002	0.002	0.000	0.000	0.000	0.000
68	B	114	VAL	0	-0.006	-0.014	24.792	-0.001	-0.001	0.000	0.000	0.000	0.000
69	B	115	GLU	-1	-0.872	-0.922	27.647	-0.157	-0.157	0.000	0.000	0.000	0.000
70	B	116	ASN	0	-0.035	-0.031	29.222	0.002	0.002	0.000	0.000	0.000	0.000
71	B	117	ALA	0	-0.030	-0.008	28.434	0.004	0.004	0.000	0.000	0.000	0.000
72	B	118	LEU	0	-0.038	-0.016	23.461	-0.004	-0.004	0.000	0.000	0.000	0.000
73	B	119	GLN	0	-0.083	-0.026	27.196	0.003	0.003	0.000	0.000	0.000	0.000
74	B	120	GLN	0	-0.002	-0.006	23.536	0.009	0.009	0.000	0.000	0.000	0.000
75	B	121	PRO	0	-0.042	-0.005	27.665	0.000	0.000	0.000	0.000	0.000	0.000
76	B	122	LEU	0	-0.027	-0.041	24.175	-0.020	-0.020	0.000	0.000	0.000	0.000
77	B	123	ASP	-1	-0.816	-0.910	25.855	-0.166	-0.166	0.000	0.000	0.000	0.000
78	B	124	MET	0	-0.009	0.006	25.723	-0.014	-0.014	0.000	0.000	0.000	0.000
79	B	125	ASN	0	-0.048	-0.022	26.492	-0.005	-0.005	0.000	0.000	0.000	0.000
80	B	126	GLY	0	-0.030	-0.007	22.881	-0.009	-0.009	0.000	0.000	0.000	0.000
81	B	127	ALA	0	0.038	-0.024	20.067	-0.011	-0.011	0.000	0.000	0.000	0.000
82	B	128	GLN	0	-0.024	-0.011	17.489	-0.047	-0.047	0.000	0.000	0.000	0.000
83	B	129	SER	0	-0.011	-0.038	14.489	0.000	0.000	0.000	0.000	0.000	0.000
84	B	130	SER	0	-0.005	-0.020	15.576	-0.012	-0.012	0.000	0.000	0.000	0.000
85	B	131	ILE	0	0.009	0.015	10.984	0.001	0.001	0.000	0.000	0.000	0.000
86	B	132	GLY	0	0.005	-0.012	10.713	-0.046	-0.046	0.000	0.000	0.000	0.000
87	B	133	HIS	0	0.001	-0.022	11.771	0.010	0.010	0.000	0.000	0.000	0.000
88	B	134	PHE	0	-0.029	-0.002	11.662	0.045	0.045	0.000	0.000	0.000	0.000
89	B	135	LEU	0	-0.033	-0.028	7.176	0.042	0.042	0.000	0.000	0.000	0.000
90	B	136	GLN	0	0.046	0.029	10.581	0.082	0.082	0.000	0.000	0.000	0.000
91	B	137	SER	0	-0.013	0.017	12.237	0.062	0.062	0.000	0.000	0.000	0.000
92	B	138	ASN	0	-0.031	-0.004	10.147	0.039	0.039	0.000	0.000	0.000	0.000
93	B	139	LYS	1	0.996	0.983	11.094	0.079	0.079	0.000	0.000	0.000	0.000
94	B	140	TYR	0	0.013	0.015	7.084	-0.011	-0.011	0.000	0.000	0.000	0.000
95	B	141	PHE	0	0.059	0.006	4.498	0.070	0.233	-0.001	-0.006	-0.155	0.000
96	B	142	ASN	0	-0.006	-0.036	6.736	0.314	0.314	0.000	0.000	0.000	0.000
97	B	143	GLN	0	-0.020	0.021	8.433	0.004	0.004	0.000	0.000	0.000	0.000
98	B	144	LYS	1	0.896	0.942	3.094	-1.156	-0.038	0.077	-0.285	-0.910	0.002
99	B	145	VAL	0	-0.006	-0.002	4.994	0.101	0.339	-0.001	-0.005	-0.231	0.000
100	B	146	ASP	-1	-0.847	-0.920	7.316	-0.049	-0.049	0.000	0.000	0.000	0.000
101	B	147	GLU	-1	-0.907	-0.962	5.139	0.739	0.739	0.000	0.000	0.000	0.000
102	B	148	GLN	0	-0.017	-0.005	2.665	-5.575	-2.141	1.246	-1.592	-3.088	-0.018
103	B	149	CYS	0	-0.146	-0.048	4.936	-0.352	-0.286	-0.001	-0.002	-0.063	0.000
104	B	150	GLY	0	0.032	0.020	8.140	-0.004	-0.004	0.000	0.000	0.000	0.000
105	B	151	LYS	1	0.925	0.947	9.544	-0.304	-0.304	0.000	0.000	0.000	0.000
106	B	152	ARG	1	0.925	0.966	8.147	0.294	0.294	0.000	0.000	0.000	0.000
107	B	153	VAL	0	0.047	0.008	12.660	-0.004	-0.004	0.000	0.000	0.000	0.000
108	B	154	ASP	-1	-0.806	-0.857	15.263	-0.108	-0.108	0.000	0.000	0.000	0.000
109	B	155	PRO	0	0.015	-0.028	16.061	-0.028	-0.028	0.000	0.000	0.000	0.000
110	B	156	ILE	0	0.043	0.028	15.942	-0.026	-0.026	0.000	0.000	0.000	0.000
111	B	157	THR	0	-0.027	-0.012	12.130	-0.055	-0.055	0.000	0.000	0.000	0.000
112	B	158	ARG	1	0.888	0.926	11.423	-0.081	-0.081	0.000	0.000	0.000	0.000
113	B	159	PHE	0	0.025	0.020	10.837	-0.043	-0.043	0.000	0.000	0.000	0.000
114	B	160	ASN	0	0.036	0.009	11.538	-0.063	-0.063	0.000	0.000	0.000	0.000
115	B	161	THR	0	-0.040	-0.011	6.209	-0.227	-0.227	0.000	0.000	0.000	0.000
116	B	162	GLN	0	-0.012	-0.014	6.753	-0.208	-0.208	0.000	0.000	0.000	0.000
117	B	163	THR	0	-0.030	-0.020	7.806	-0.160	-0.160	0.000	0.000	0.000	0.000
118	B	164	LYS	1	0.951	0.967	6.560	0.799	0.799	0.000	0.000	0.000	0.000
119	B	165	MET	0	-0.006	0.007	2.515	-4.079	-2.619	4.278	-1.173	-4.565	0.015
120	B	166	ILE	0	-0.015	0.016	4.396	-0.601	-0.456	-0.001	-0.022	-0.122	0.000
121	B	167	GLU	-1	-0.932	-0.959	7.048	-0.828	-0.828	0.000	0.000	0.000	0.000
122	B	168	GLN	0	-0.040	-0.031	3.119	-2.716	-1.609	0.080	-0.358	-0.828	-0.004
123	B	169	VAL	0	0.040	0.019	2.885	-0.481	0.246	0.196	-0.180	-0.743	-0.001
124	B	170	SER	0	-0.028	-0.021	5.252	0.412	0.433	-0.001	-0.002	-0.018	0.000
125	B	171	GLN	0	0.044	0.033	8.495	0.146	0.146	0.000	0.000	0.000	0.000
126	B	172	GLU	-1	-0.871	-0.926	4.880	-2.101	-2.056	-0.001	-0.002	-0.041	0.000
127	B	173	ILE	0	-0.066	-0.043	8.171	0.174	0.174	0.000	0.000	0.000	0.000
128	B	174	PHE	0	0.010	0.015	10.514	0.118	0.118	0.000	0.000	0.000	0.000
129	B	175	GLU	-1	-0.826	-0.931	12.479	-0.522	-0.522	0.000	0.000	0.000	0.000
130	B	176	ARG	1	0.874	0.946	9.337	0.691	0.691	0.000	0.000	0.000	0.000
131	B	177	ASN	0	-0.077	-0.050	13.280	0.092	0.092	0.000	0.000	0.000	0.000
132	B	178	PHE	0	-0.009	-0.003	16.059	0.033	0.033	0.000	0.000	0.000	0.000
133	B	179	SER	0	-0.036	0.002	17.841	-0.002	-0.002	0.000	0.000	0.000	0.000
134	B	180	GLY	0	-0.015	-0.001	19.746	0.026	0.026	0.000	0.000	0.000	0.000
135	B	181	PHE	0	0.030	-0.014	20.406	0.021	0.021	0.000	0.000	0.000	0.000
136	B	182	LYS	1	0.925	0.976	16.663	0.259	0.259	0.000	0.000	0.000	0.000
137	B	183	VAL	0	0.039	0.019	13.642	0.032	0.032	0.000	0.000	0.000	0.000
138	B	184	SER	0	-0.018	-0.019	16.189	0.015	0.015	0.000	0.000	0.000	0.000
139	B	185	GLU	-1	-0.855	-0.923	17.560	-0.217	-0.217	0.000	0.000	0.000	0.000
140	B	186	ILE	0	0.037	0.022	18.089	0.018	0.018	0.000	0.000	0.000	0.000
141	B	187	LYS	1	0.930	0.971	14.741	0.529	0.529	0.000	0.000	0.000	0.000
142	B	188	ALA	0	0.033	0.028	20.523	0.020	0.020	0.000	0.000	0.000	0.000
143	B	189	ILE	0	0.016	0.003	23.210	0.019	0.019	0.000	0.000	0.000	0.000
144	B	190	THR	0	-0.005	-0.020	23.125	0.014	0.014	0.000	0.000	0.000	0.000
145	B	191	GLN	0	-0.054	-0.030	22.943	0.011	0.011	0.000	0.000	0.000	0.000
146	B	192	ASN	0	0.019	0.008	25.950	0.013	0.013	0.000	0.000	0.000	0.000
147	B	193	ALA	0	0.018	0.025	28.274	0.011	0.011	0.000	0.000	0.000	0.000
148	B	194	ILE	0	-0.032	-0.035	25.699	0.008	0.008	0.000	0.000	0.000	0.000
149	B	195	LEU	0	-0.042	-0.022	29.899	0.009	0.009	0.000	0.000	0.000	0.000
150	B	196	GLU	-1	-0.984	-0.974	31.914	-0.108	-0.108	0.000	0.000	0.000	0.000
151	B	197	HIS	0	-0.034	-0.021	32.700	0.008	0.008	0.000	0.000	0.000	0.000
152	B	198	VAL	0	-0.090	-0.033	31.088	0.005	0.005	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:47:PHE)