FMO DATABASE

FMODB ID: LJYV9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1455211.999357
FMO2-HF: Nuclear repulsion	1393745.89892
FMO2-HF: Total energy	-61466.100437
FMO2-MP2: Total energy	-61646.068933

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.
-20.911	-7.029	9.267	-6.28	-16.867	-0.023

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 : -0.019 / q_NPA : -0.012

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	-0.014	-0.009	2.409	-3.132	0.127	1.213	-1.284	-3.189	-0.002
4	B	50	ASN	0	0.011	0.008	4.194	0.079	0.187	0.000	-0.027	-0.082	0.000
5	B	51	HIS	0	0.073	0.004	4.941	0.199	0.199	0.000	0.000	0.000	0.000
6	B	52	GLY	0	0.052	0.058	8.003	0.040	0.040	0.000	0.000	0.000	0.000
7	B	53	LYS	1	0.940	0.959	10.256	0.043	0.043	0.000	0.000	0.000	0.000
8	B	54	LEU	0	-0.014	0.000	5.480	0.029	0.029	0.000	0.000	0.000	0.000
9	B	55	THR	0	0.041	0.010	10.021	0.014	0.014	0.000	0.000	0.000	0.000
10	B	56	ASN	0	0.007	-0.001	12.638	0.013	0.013	0.000	0.000	0.000	0.000
11	B	57	GLN	0	0.002	-0.001	11.633	0.003	0.003	0.000	0.000	0.000	0.000
12	B	58	LEU	0	-0.007	0.015	12.627	0.015	0.015	0.000	0.000	0.000	0.000
13	B	59	LEU	0	0.053	0.021	15.071	0.016	0.016	0.000	0.000	0.000	0.000
14	B	60	GLN	0	-0.018	-0.018	17.792	0.011	0.011	0.000	0.000	0.000	0.000
15	B	61	ALA	0	-0.092	-0.046	17.286	0.013	0.013	0.000	0.000	0.000	0.000
16	B	62	VAL	0	0.037	0.023	18.687	0.008	0.008	0.000	0.000	0.000	0.000
17	B	63	ALA	0	0.005	0.008	21.035	0.008	0.008	0.000	0.000	0.000	0.000
18	B	64	LYS	1	0.878	0.936	19.998	0.075	0.075	0.000	0.000	0.000	0.000
19	B	65	GLN	0	-0.002	0.007	22.544	-0.003	-0.003	0.000	0.000	0.000	0.000
20	B	66	THR	0	-0.025	0.002	26.369	0.003	0.003	0.000	0.000	0.000	0.000
21	B	67	ARG	1	0.973	0.967	29.018	0.041	0.041	0.000	0.000	0.000	0.000
22	B	68	ASN	0	-0.034	-0.022	29.953	0.005	0.005	0.000	0.000	0.000	0.000
23	B	69	GLY	0	0.019	0.020	25.778	0.000	0.000	0.000	0.000	0.000	0.000
24	B	70	ASP	-1	-0.792	-0.890	25.242	-0.093	-0.093	0.000	0.000	0.000	0.000
25	B	71	THR	0	-0.010	-0.016	21.057	-0.006	-0.006	0.000	0.000	0.000	0.000
26	B	72	GLN	0	-0.009	-0.001	22.805	-0.011	-0.011	0.000	0.000	0.000	0.000
27	B	73	GLN	0	-0.006	-0.011	25.086	-0.005	-0.005	0.000	0.000	0.000	0.000
28	B	74	TRP	0	-0.004	-0.010	16.096	-0.003	-0.003	0.000	0.000	0.000	0.000
29	B	75	PHE	0	0.006	0.010	18.935	-0.012	-0.012	0.000	0.000	0.000	0.000
30	B	76	GLN	0	0.031	0.003	21.682	-0.008	-0.008	0.000	0.000	0.000	0.000
31	B	77	GLN	0	0.020	0.017	23.329	-0.008	-0.008	0.000	0.000	0.000	0.000
32	B	78	GLU	-1	-0.701	-0.787	15.750	-0.284	-0.284	0.000	0.000	0.000	0.000
33	B	79	GLN	0	-0.014	-0.014	19.048	-0.029	-0.029	0.000	0.000	0.000	0.000
34	B	80	THR	0	0.049	0.024	20.629	-0.008	-0.008	0.000	0.000	0.000	0.000
35	B	81	THR	0	-0.064	-0.026	19.345	-0.001	-0.001	0.000	0.000	0.000	0.000
36	B	82	TYR	0	-0.007	-0.013	10.928	-0.002	-0.002	0.000	0.000	0.000	0.000
37	B	83	ILE	0	0.032	0.028	17.520	-0.021	-0.021	0.000	0.000	0.000	0.000
38	B	84	SER	0	0.026	0.005	19.667	0.003	0.003	0.000	0.000	0.000	0.000
39	B	85	ARG	1	0.804	0.893	12.428	0.413	0.413	0.000	0.000	0.000	0.000
40	B	86	THR	0	-0.043	-0.020	16.641	-0.029	-0.029	0.000	0.000	0.000	0.000
41	B	87	VAL	0	0.018	0.026	18.095	0.000	0.000	0.000	0.000	0.000	0.000
42	B	88	ASN	0	0.007	-0.011	21.315	0.017	0.017	0.000	0.000	0.000	0.000
43	B	89	ARG	1	0.904	0.949	13.616	0.414	0.414	0.000	0.000	0.000	0.000
44	B	90	THR	0	-0.048	-0.037	19.366	-0.008	-0.008	0.000	0.000	0.000	0.000
45	B	91	LEU	0	0.043	0.017	21.080	0.014	0.014	0.000	0.000	0.000	0.000
46	B	92	ASP	-1	-0.908	-0.949	20.992	-0.208	-0.208	0.000	0.000	0.000	0.000
47	B	93	ASP	-1	-0.859	-0.934	18.439	-0.305	-0.305	0.000	0.000	0.000	0.000
48	B	94	TYR	0	0.015	0.033	21.629	0.010	0.010	0.000	0.000	0.000	0.000
49	B	95	CYS	0	-0.019	-0.018	25.115	0.014	0.014	0.000	0.000	0.000	0.000
50	B	96	ARG	1	0.803	0.894	19.054	0.256	0.256	0.000	0.000	0.000	0.000
51	B	97	SER	0	-0.064	-0.051	23.722	0.010	0.010	0.000	0.000	0.000	0.000
52	B	98	ASN	0	-0.036	-0.018	25.582	0.016	0.016	0.000	0.000	0.000	0.000
53	B	99	ASN	0	-0.047	-0.017	28.729	0.008	0.008	0.000	0.000	0.000	0.000
54	B	100	SER	0	0.014	0.017	30.288	0.007	0.007	0.000	0.000	0.000	0.000
55	B	101	VAL	0	-0.008	-0.008	30.623	-0.007	-0.007	0.000	0.000	0.000	0.000
56	B	102	ILE	0	0.006	0.016	29.389	0.005	0.005	0.000	0.000	0.000	0.000
57	B	103	SER	0	-0.002	-0.001	32.657	-0.001	-0.001	0.000	0.000	0.000	0.000
58	B	104	LYS	1	0.986	0.959	31.371	0.103	0.103	0.000	0.000	0.000	0.000
59	B	105	GLU	-1	-0.852	-0.900	33.887	-0.076	-0.076	0.000	0.000	0.000	0.000
60	B	106	THR	0	0.057	0.030	33.711	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	107	LYS	1	0.825	0.920	25.952	0.144	0.144	0.000	0.000	0.000	0.000
62	B	108	GLY	0	0.015	0.000	30.495	-0.006	-0.006	0.000	0.000	0.000	0.000
63	B	109	HIS	0	-0.032	-0.020	32.477	-0.004	-0.004	0.000	0.000	0.000	0.000
64	B	110	ILE	0	0.019	0.016	27.742	-0.002	-0.002	0.000	0.000	0.000	0.000
65	B	111	PHE	0	-0.004	-0.011	24.146	-0.005	-0.005	0.000	0.000	0.000	0.000
66	B	112	ARG	1	0.843	0.893	28.927	0.090	0.090	0.000	0.000	0.000	0.000
67	B	113	ALA	0	0.003	0.014	30.808	0.002	0.002	0.000	0.000	0.000	0.000
68	B	114	VAL	0	0.006	-0.008	24.338	0.000	0.000	0.000	0.000	0.000	0.000
69	B	115	GLU	-1	-0.842	-0.894	27.476	-0.105	-0.105	0.000	0.000	0.000	0.000
70	B	116	ASN	0	-0.021	-0.012	28.802	0.004	0.004	0.000	0.000	0.000	0.000
71	B	117	ALA	0	-0.007	0.007	28.047	0.004	0.004	0.000	0.000	0.000	0.000
72	B	118	LEU	0	-0.036	-0.021	23.000	-0.003	-0.003	0.000	0.000	0.000	0.000
73	B	119	GLN	0	-0.083	-0.042	26.616	0.003	0.003	0.000	0.000	0.000	0.000
74	B	120	GLN	0	-0.011	0.005	23.809	-0.001	-0.001	0.000	0.000	0.000	0.000
75	B	121	PRO	0	0.023	0.016	27.203	-0.003	-0.003	0.000	0.000	0.000	0.000
76	B	122	LEU	0	-0.033	-0.028	23.697	-0.014	-0.014	0.000	0.000	0.000	0.000
77	B	123	ASP	-1	-0.787	-0.889	25.625	-0.119	-0.119	0.000	0.000	0.000	0.000
78	B	124	MET	0	0.008	0.013	25.532	-0.011	-0.011	0.000	0.000	0.000	0.000
79	B	125	ASN	0	-0.107	-0.071	26.405	-0.004	-0.004	0.000	0.000	0.000	0.000
80	B	126	GLY	0	0.016	0.021	23.031	-0.005	-0.005	0.000	0.000	0.000	0.000
81	B	127	ALA	0	0.043	0.014	20.006	-0.012	-0.012	0.000	0.000	0.000	0.000
82	B	128	GLN	0	-0.010	-0.013	16.903	-0.050	-0.050	0.000	0.000	0.000	0.000
83	B	129	SER	0	0.001	0.001	13.855	0.001	0.001	0.000	0.000	0.000	0.000
84	B	130	SER	0	-0.005	-0.044	15.194	-0.003	-0.003	0.000	0.000	0.000	0.000
85	B	131	ILE	0	-0.015	-0.004	10.581	0.010	0.010	0.000	0.000	0.000	0.000
86	B	132	GLY	0	0.015	0.002	10.606	-0.016	-0.016	0.000	0.000	0.000	0.000
87	B	133	HIS	0	-0.005	-0.024	11.646	0.033	0.033	0.000	0.000	0.000	0.000
88	B	134	PHE	0	0.004	0.007	11.102	0.044	0.044	0.000	0.000	0.000	0.000
89	B	135	LEU	0	-0.029	-0.025	6.888	0.039	0.039	0.000	0.000	0.000	0.000
90	B	136	GLN	0	-0.033	-0.019	10.160	0.094	0.094	0.000	0.000	0.000	0.000
91	B	137	SER	0	0.027	0.026	12.139	0.046	0.046	0.000	0.000	0.000	0.000
92	B	138	ASN	0	-0.057	-0.008	9.969	0.064	0.064	0.000	0.000	0.000	0.000
93	B	139	LYS	1	1.006	0.987	10.772	0.039	0.039	0.000	0.000	0.000	0.000
94	B	140	TYR	0	-0.021	0.001	7.164	0.016	0.016	0.000	0.000	0.000	0.000
95	B	141	PHE	0	0.049	0.005	4.496	0.027	0.240	-0.001	-0.010	-0.202	0.000
96	B	142	ASN	0	0.012	-0.003	6.561	0.389	0.389	0.000	0.000	0.000	0.000
97	B	143	GLN	0	-0.024	-0.009	7.846	-0.007	-0.007	0.000	0.000	0.000	0.000
98	B	144	LYS	1	0.826	0.889	2.685	-1.997	-0.496	0.466	-0.464	-1.503	0.002
99	B	145	VAL	0	-0.002	-0.005	4.129	-0.312	0.134	0.001	-0.046	-0.401	0.000
100	B	146	ASP	-1	-0.807	-0.881	6.448	-0.236	-0.236	0.000	0.000	0.000	0.000
101	B	147	GLU	-1	-0.808	-0.872	4.620	0.430	0.557	-0.001	-0.010	-0.115	0.000
102	B	148	GLN	0	0.021	0.016	2.361	-8.920	-4.929	3.479	-2.496	-4.973	-0.030
103	B	149	CYS	0	-0.093	-0.047	4.415	-0.118	-0.045	-0.001	-0.015	-0.056	0.000
104	B	150	GLY	0	0.044	0.014	8.181	0.013	0.013	0.000	0.000	0.000	0.000
105	B	151	LYS	1	0.915	0.952	9.540	-0.093	-0.093	0.000	0.000	0.000	0.000
106	B	152	ARG	1	0.855	0.943	7.381	0.532	0.532	0.000	0.000	0.000	0.000
107	B	153	VAL	0	0.040	0.013	12.208	-0.034	-0.034	0.000	0.000	0.000	0.000
108	B	154	ASP	-1	-0.736	-0.821	14.553	-0.127	-0.127	0.000	0.000	0.000	0.000
109	B	155	PRO	0	0.018	0.002	15.599	-0.022	-0.022	0.000	0.000	0.000	0.000
110	B	156	ILE	0	0.020	0.011	16.091	-0.017	-0.017	0.000	0.000	0.000	0.000
111	B	157	THR	0	-0.034	-0.050	12.236	-0.048	-0.048	0.000	0.000	0.000	0.000
112	B	158	ARG	1	0.787	0.885	11.000	-0.141	-0.141	0.000	0.000	0.000	0.000
113	B	159	PHE	0	0.045	0.021	11.153	-0.018	-0.018	0.000	0.000	0.000	0.000
114	B	160	ASN	0	0.014	0.004	11.752	-0.040	-0.040	0.000	0.000	0.000	0.000
115	B	161	THR	0	-0.063	-0.041	6.622	-0.190	-0.190	0.000	0.000	0.000	0.000
116	B	162	GLN	0	-0.022	-0.020	6.911	-0.128	-0.128	0.000	0.000	0.000	0.000
117	B	163	THR	0	0.017	-0.011	8.037	-0.088	-0.088	0.000	0.000	0.000	0.000
118	B	164	LYS	1	0.932	0.972	6.699	0.648	0.648	0.000	0.000	0.000	0.000
119	B	165	MET	0	0.006	0.019	2.712	-4.296	-2.256	3.104	-1.086	-4.058	0.014
120	B	166	ILE	0	-0.012	0.016	4.582	-0.445	-0.322	-0.001	-0.010	-0.113	0.000
121	B	167	GLU	-1	-0.794	-0.850	7.363	-0.593	-0.593	0.000	0.000	0.000	0.000
122	B	168	GLN	0	-0.008	-0.006	3.189	-2.549	-1.318	0.059	-0.479	-0.811	-0.005
123	B	169	VAL	0	0.012	-0.002	2.492	-0.830	-0.124	0.951	-0.347	-1.309	-0.002
124	B	170	SER	0	-0.035	-0.037	4.971	0.333	0.366	-0.001	-0.006	-0.025	0.000
125	B	171	GLN	0	-0.027	-0.009	8.193	0.073	0.073	0.000	0.000	0.000	0.000
126	B	172	GLU	-1	-0.804	-0.880	5.155	-0.842	-0.811	-0.001	0.000	-0.030	0.000
127	B	173	ILE	0	-0.066	-0.042	7.553	0.142	0.142	0.000	0.000	0.000	0.000
128	B	174	PHE	0	0.044	0.033	10.269	0.088	0.088	0.000	0.000	0.000	0.000
129	B	175	GLU	-1	-0.754	-0.878	11.763	-0.398	-0.398	0.000	0.000	0.000	0.000
130	B	176	ARG	1	0.791	0.888	8.233	0.461	0.461	0.000	0.000	0.000	0.000
131	B	177	ASN	0	-0.085	-0.049	12.976	0.066	0.066	0.000	0.000	0.000	0.000
132	B	178	PHE	0	-0.021	-0.007	15.457	0.024	0.024	0.000	0.000	0.000	0.000
133	B	179	SER	0	-0.024	-0.012	16.888	0.002	0.002	0.000	0.000	0.000	0.000
134	B	180	GLY	0	-0.042	-0.014	19.002	0.019	0.019	0.000	0.000	0.000	0.000
135	B	181	PHE	0	0.011	-0.012	20.151	0.013	0.013	0.000	0.000	0.000	0.000
136	B	182	LYS	1	0.829	0.913	16.099	0.159	0.159	0.000	0.000	0.000	0.000
137	B	183	VAL	0	0.026	-0.002	13.177	0.018	0.018	0.000	0.000	0.000	0.000
138	B	184	SER	0	-0.007	-0.009	15.636	0.014	0.014	0.000	0.000	0.000	0.000
139	B	185	GLU	-1	-0.768	-0.865	17.014	-0.154	-0.154	0.000	0.000	0.000	0.000
140	B	186	ILE	0	0.041	0.021	18.000	0.014	0.014	0.000	0.000	0.000	0.000
141	B	187	LYS	1	0.856	0.953	16.087	0.355	0.355	0.000	0.000	0.000	0.000
142	B	188	ALA	0	0.039	0.022	20.188	0.017	0.017	0.000	0.000	0.000	0.000
143	B	189	ILE	0	0.010	0.002	22.812	0.014	0.014	0.000	0.000	0.000	0.000
144	B	190	THR	0	-0.011	-0.024	22.743	0.012	0.012	0.000	0.000	0.000	0.000
145	B	191	GLN	0	-0.040	-0.033	22.008	-0.001	-0.001	0.000	0.000	0.000	0.000
146	B	192	ASN	0	-0.012	0.011	25.668	0.011	0.011	0.000	0.000	0.000	0.000
147	B	193	ALA	0	0.029	0.015	28.133	0.008	0.008	0.000	0.000	0.000	0.000
148	B	194	ILE	0	-0.001	-0.020	25.398	0.005	0.005	0.000	0.000	0.000	0.000
149	B	195	LEU	0	-0.037	-0.014	29.478	0.006	0.006	0.000	0.000	0.000	0.000
150	B	196	GLU	-1	-0.919	-0.953	31.727	-0.085	-0.085	0.000	0.000	0.000	0.000
151	B	197	HIS	0	-0.069	-0.038	32.812	0.006	0.006	0.000	0.000	0.000	0.000
152	B	198	VAL	0	-0.110	-0.044	31.295	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)