FMO DATABASE

FMODB ID: 3QLML

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	OptHSide
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	-1451937.909282
FMO2-HF: Nuclear repulsion	1390472.182195
FMO2-HF: Total energy	-61465.727087
FMO2-MP2: Total energy	-61645.783896

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.
-16.455	-3.501	6.01	-5.098	-13.864	-0.005

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 : -0.017 / q_NPA : -0.008

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	0.004	-0.004	2.642	-3.811	0.091	0.721	-1.549	-3.075	-0.004
4	B	50	ASN	0	0.017	0.006	4.377	0.159	0.248	0.000	-0.022	-0.067	0.000
5	B	51	HIS	0	0.056	-0.003	5.266	0.210	0.210	0.000	0.000	0.000	0.000
6	B	52	GLY	0	0.044	0.043	8.236	0.041	0.041	0.000	0.000	0.000	0.000
7	B	53	LYS	1	0.943	0.960	10.355	0.113	0.113	0.000	0.000	0.000	0.000
8	B	54	LEU	0	-0.008	0.003	5.646	0.035	0.035	0.000	0.000	0.000	0.000
9	B	55	THR	0	0.042	0.016	10.082	0.030	0.030	0.000	0.000	0.000	0.000
10	B	56	ASN	0	0.011	0.007	12.819	0.020	0.020	0.000	0.000	0.000	0.000
11	B	57	GLN	0	-0.008	-0.001	11.785	0.004	0.004	0.000	0.000	0.000	0.000
12	B	58	LEU	0	-0.024	-0.007	12.762	0.017	0.017	0.000	0.000	0.000	0.000
13	B	59	LEU	0	0.056	0.011	14.864	0.023	0.023	0.000	0.000	0.000	0.000
14	B	60	GLN	0	-0.031	-0.014	17.661	0.014	0.014	0.000	0.000	0.000	0.000
15	B	61	ALA	0	-0.089	-0.052	17.492	0.018	0.018	0.000	0.000	0.000	0.000
16	B	62	VAL	0	0.028	0.027	18.710	0.012	0.012	0.000	0.000	0.000	0.000
17	B	63	ALA	0	0.002	0.005	21.063	0.013	0.013	0.000	0.000	0.000	0.000
18	B	64	LYS	1	0.881	0.940	19.673	0.135	0.135	0.000	0.000	0.000	0.000
19	B	65	GLN	0	-0.009	0.004	22.678	-0.004	-0.004	0.000	0.000	0.000	0.000
20	B	66	THR	0	0.005	0.015	26.298	0.008	0.008	0.000	0.000	0.000	0.000
21	B	67	ARG	1	1.008	0.987	29.099	0.062	0.062	0.000	0.000	0.000	0.000
22	B	68	ASN	0	-0.059	-0.029	30.201	0.003	0.003	0.000	0.000	0.000	0.000
23	B	69	GLY	0	0.027	0.021	26.169	0.000	0.000	0.000	0.000	0.000	0.000
24	B	70	ASP	-1	-0.811	-0.908	25.384	-0.119	-0.119	0.000	0.000	0.000	0.000
25	B	71	THR	0	-0.018	-0.020	21.601	-0.008	-0.008	0.000	0.000	0.000	0.000
26	B	72	GLN	0	-0.017	-0.008	23.282	-0.011	-0.011	0.000	0.000	0.000	0.000
27	B	73	GLN	0	0.011	0.005	25.525	-0.005	-0.005	0.000	0.000	0.000	0.000
28	B	74	TRP	0	0.005	-0.007	16.381	-0.005	-0.005	0.000	0.000	0.000	0.000
29	B	75	PHE	0	0.003	0.006	19.588	-0.015	-0.015	0.000	0.000	0.000	0.000
30	B	76	GLN	0	0.027	0.002	21.977	-0.008	-0.008	0.000	0.000	0.000	0.000
31	B	77	GLN	0	0.007	0.002	23.628	-0.010	-0.010	0.000	0.000	0.000	0.000
32	B	78	GLU	-1	-0.678	-0.764	16.298	-0.344	-0.344	0.000	0.000	0.000	0.000
33	B	79	GLN	0	0.011	0.009	19.434	-0.030	-0.030	0.000	0.000	0.000	0.000
34	B	80	THR	0	0.015	0.014	20.695	-0.014	-0.014	0.000	0.000	0.000	0.000
35	B	81	THR	0	-0.002	0.007	19.455	0.001	0.001	0.000	0.000	0.000	0.000
36	B	82	TYR	0	-0.026	-0.030	11.386	-0.001	-0.001	0.000	0.000	0.000	0.000
37	B	83	ILE	0	0.034	0.022	17.781	-0.023	-0.023	0.000	0.000	0.000	0.000
38	B	84	SER	0	0.048	0.017	19.909	0.007	0.007	0.000	0.000	0.000	0.000
39	B	85	ARG	1	0.828	0.939	12.455	0.497	0.497	0.000	0.000	0.000	0.000
40	B	86	THR	0	-0.070	-0.035	16.746	-0.025	-0.025	0.000	0.000	0.000	0.000
41	B	87	VAL	0	0.023	0.018	18.246	0.002	0.002	0.000	0.000	0.000	0.000
42	B	88	ASN	0	0.000	-0.035	21.766	0.022	0.022	0.000	0.000	0.000	0.000
43	B	89	ARG	1	0.885	0.949	13.366	0.481	0.481	0.000	0.000	0.000	0.000
44	B	90	THR	0	-0.050	-0.032	19.666	-0.005	-0.005	0.000	0.000	0.000	0.000
45	B	91	LEU	0	0.035	0.014	21.322	0.015	0.015	0.000	0.000	0.000	0.000
46	B	92	ASP	-1	-0.914	-0.950	21.346	-0.225	-0.225	0.000	0.000	0.000	0.000
47	B	93	ASP	-1	-0.898	-0.959	18.719	-0.318	-0.318	0.000	0.000	0.000	0.000
48	B	94	TYR	0	0.008	0.013	21.989	0.012	0.012	0.000	0.000	0.000	0.000
49	B	95	CYS	0	-0.010	-0.013	25.332	0.016	0.016	0.000	0.000	0.000	0.000
50	B	96	ARG	1	0.829	0.914	19.537	0.268	0.268	0.000	0.000	0.000	0.000
51	B	97	SER	0	-0.052	-0.029	24.233	0.013	0.013	0.000	0.000	0.000	0.000
52	B	98	ASN	0	-0.036	-0.022	26.017	0.017	0.017	0.000	0.000	0.000	0.000
53	B	99	ASN	0	-0.057	-0.017	28.858	0.008	0.008	0.000	0.000	0.000	0.000
54	B	100	SER	0	0.007	0.015	30.406	0.009	0.009	0.000	0.000	0.000	0.000
55	B	101	VAL	0	-0.008	-0.013	31.081	-0.007	-0.007	0.000	0.000	0.000	0.000
56	B	102	ILE	0	0.008	0.024	29.749	0.006	0.006	0.000	0.000	0.000	0.000
57	B	103	SER	0	0.030	0.021	32.876	-0.005	-0.005	0.000	0.000	0.000	0.000
58	B	104	LYS	1	1.009	0.970	31.061	0.121	0.121	0.000	0.000	0.000	0.000
59	B	105	GLU	-1	-0.878	-0.908	34.140	-0.083	-0.083	0.000	0.000	0.000	0.000
60	B	106	THR	0	0.066	0.017	33.794	-0.001	-0.001	0.000	0.000	0.000	0.000
61	B	107	LYS	1	0.803	0.910	26.314	0.161	0.161	0.000	0.000	0.000	0.000
62	B	108	GLY	0	0.024	-0.001	30.758	-0.007	-0.007	0.000	0.000	0.000	0.000
63	B	109	HIS	0	-0.016	-0.014	32.756	-0.004	-0.004	0.000	0.000	0.000	0.000
64	B	110	ILE	0	0.011	0.008	28.038	-0.002	-0.002	0.000	0.000	0.000	0.000
65	B	111	PHE	0	0.000	-0.014	24.459	-0.006	-0.006	0.000	0.000	0.000	0.000
66	B	112	ARG	1	0.852	0.904	29.284	0.101	0.101	0.000	0.000	0.000	0.000
67	B	113	ALA	0	-0.001	0.017	31.201	0.002	0.002	0.000	0.000	0.000	0.000
68	B	114	VAL	0	-0.006	-0.017	24.739	0.000	0.000	0.000	0.000	0.000	0.000
69	B	115	GLU	-1	-0.817	-0.883	27.666	-0.120	-0.120	0.000	0.000	0.000	0.000
70	B	116	ASN	0	-0.033	-0.022	29.224	0.003	0.003	0.000	0.000	0.000	0.000
71	B	117	ALA	0	-0.009	0.004	28.506	0.004	0.004	0.000	0.000	0.000	0.000
72	B	118	LEU	0	-0.031	-0.011	23.515	-0.003	-0.003	0.000	0.000	0.000	0.000
73	B	119	GLN	0	-0.096	-0.042	27.205	0.003	0.003	0.000	0.000	0.000	0.000
74	B	120	GLN	0	-0.016	-0.011	24.203	-0.003	-0.003	0.000	0.000	0.000	0.000
75	B	121	PRO	0	0.017	0.020	27.640	-0.001	-0.001	0.000	0.000	0.000	0.000
76	B	122	LEU	0	-0.022	-0.023	23.977	-0.016	-0.016	0.000	0.000	0.000	0.000
77	B	123	ASP	-1	-0.781	-0.889	25.821	-0.140	-0.140	0.000	0.000	0.000	0.000
78	B	124	MET	0	0.002	0.011	25.689	-0.013	-0.013	0.000	0.000	0.000	0.000
79	B	125	ASN	0	-0.089	-0.054	26.452	-0.003	-0.003	0.000	0.000	0.000	0.000
80	B	126	GLY	0	-0.008	0.005	22.833	-0.008	-0.008	0.000	0.000	0.000	0.000
81	B	127	ALA	0	0.029	-0.016	20.031	-0.008	-0.008	0.000	0.000	0.000	0.000
82	B	128	GLN	0	-0.010	-0.007	17.230	-0.051	-0.051	0.000	0.000	0.000	0.000
83	B	129	SER	0	-0.001	-0.006	14.393	0.000	0.000	0.000	0.000	0.000	0.000
84	B	130	SER	0	-0.003	-0.051	15.450	-0.014	-0.014	0.000	0.000	0.000	0.000
85	B	131	ILE	0	-0.013	0.000	10.880	-0.003	-0.003	0.000	0.000	0.000	0.000
86	B	132	GLY	0	0.007	-0.006	10.571	-0.047	-0.047	0.000	0.000	0.000	0.000
87	B	133	HIS	0	-0.018	-0.031	11.634	0.014	0.014	0.000	0.000	0.000	0.000
88	B	134	PHE	0	-0.021	0.004	11.376	0.038	0.038	0.000	0.000	0.000	0.000
89	B	135	LEU	0	-0.030	-0.028	6.985	0.033	0.033	0.000	0.000	0.000	0.000
90	B	136	GLN	0	0.007	0.012	10.319	0.081	0.081	0.000	0.000	0.000	0.000
91	B	137	SER	0	0.012	0.023	12.056	0.057	0.057	0.000	0.000	0.000	0.000
92	B	138	ASN	0	-0.051	-0.013	10.104	0.044	0.044	0.000	0.000	0.000	0.000
93	B	139	LYS	1	1.003	0.982	10.697	0.081	0.081	0.000	0.000	0.000	0.000
94	B	140	TYR	0	0.011	0.014	7.170	0.000	0.000	0.000	0.000	0.000	0.000
95	B	141	PHE	0	0.052	0.004	4.305	0.017	0.210	-0.001	-0.009	-0.182	0.000
96	B	142	ASN	0	0.024	0.000	6.318	0.350	0.350	0.000	0.000	0.000	0.000
97	B	143	GLN	0	-0.042	-0.005	8.295	0.036	0.036	0.000	0.000	0.000	0.000
98	B	144	LYS	1	0.816	0.886	2.503	-1.537	-0.153	0.392	-0.463	-1.314	0.003
99	B	145	VAL	0	0.006	-0.002	4.983	0.235	0.489	-0.001	-0.005	-0.248	0.000
100	B	146	ASP	-1	-0.814	-0.885	7.151	-0.064	-0.064	0.000	0.000	0.000	0.000
101	B	147	GLU	-1	-0.795	-0.873	5.075	0.339	0.451	-0.001	-0.004	-0.106	0.000
102	B	148	GLN	0	-0.010	0.000	2.736	-4.874	-1.697	0.985	-1.254	-2.907	-0.012
103	B	149	CYS	0	-0.146	-0.071	4.937	-0.430	-0.369	-0.001	-0.003	-0.057	0.000
104	B	150	GLY	0	0.040	0.023	8.145	-0.040	-0.040	0.000	0.000	0.000	0.000
105	B	151	LYS	1	0.936	0.953	9.549	-0.114	-0.114	0.000	0.000	0.000	0.000
106	B	152	ARG	1	0.885	0.955	7.765	0.347	0.347	0.000	0.000	0.000	0.000
107	B	153	VAL	0	0.045	0.007	12.657	0.004	0.004	0.000	0.000	0.000	0.000
108	B	154	ASP	-1	-0.751	-0.810	15.260	-0.126	-0.126	0.000	0.000	0.000	0.000
109	B	155	PRO	0	0.019	-0.026	16.271	-0.020	-0.020	0.000	0.000	0.000	0.000
110	B	156	ILE	0	0.016	0.015	16.123	-0.019	-0.019	0.000	0.000	0.000	0.000
111	B	157	THR	0	-0.032	-0.040	12.412	-0.047	-0.047	0.000	0.000	0.000	0.000
112	B	158	ARG	1	0.808	0.899	11.211	-0.109	-0.109	0.000	0.000	0.000	0.000
113	B	159	PHE	0	0.052	0.026	11.010	-0.019	-0.019	0.000	0.000	0.000	0.000
114	B	160	ASN	0	0.029	0.006	11.668	-0.056	-0.056	0.000	0.000	0.000	0.000
115	B	161	THR	0	-0.048	-0.032	6.660	-0.189	-0.189	0.000	0.000	0.000	0.000
116	B	162	GLN	0	-0.024	-0.025	6.890	-0.158	-0.158	0.000	0.000	0.000	0.000
117	B	163	THR	0	-0.009	-0.011	7.734	-0.149	-0.149	0.000	0.000	0.000	0.000
118	B	164	LYS	1	0.944	0.965	6.674	0.664	0.664	0.000	0.000	0.000	0.000
119	B	165	MET	0	-0.012	0.016	2.709	-3.706	-2.043	3.304	-1.061	-3.905	0.014
120	B	166	ILE	0	-0.018	0.009	4.321	-0.669	-0.508	-0.001	-0.029	-0.130	0.000
121	B	167	GLU	-1	-0.827	-0.879	6.953	-0.678	-0.678	0.000	0.000	0.000	0.000
122	B	168	GLN	0	-0.029	-0.023	3.139	-2.707	-1.522	0.066	-0.434	-0.818	-0.004
123	B	169	VAL	0	0.036	0.010	2.529	-0.681	0.068	0.548	-0.261	-1.036	-0.002
124	B	170	SER	0	-0.015	-0.015	5.153	0.381	0.405	-0.001	-0.004	-0.019	0.000
125	B	171	GLN	0	-0.022	-0.004	8.453	0.110	0.110	0.000	0.000	0.000	0.000
126	B	172	GLU	-1	-0.800	-0.886	5.323	-0.947	-0.947	0.000	0.000	0.000	0.000
127	B	173	ILE	0	-0.082	-0.052	7.861	0.145	0.145	0.000	0.000	0.000	0.000
128	B	174	PHE	0	0.010	0.010	10.623	0.099	0.099	0.000	0.000	0.000	0.000
129	B	175	GLU	-1	-0.761	-0.884	12.257	-0.401	-0.401	0.000	0.000	0.000	0.000
130	B	176	ARG	1	0.813	0.912	8.694	0.499	0.499	0.000	0.000	0.000	0.000
131	B	177	ASN	0	-0.076	-0.044	13.371	0.075	0.075	0.000	0.000	0.000	0.000
132	B	178	PHE	0	-0.024	-0.009	15.823	0.021	0.021	0.000	0.000	0.000	0.000
133	B	179	SER	0	-0.030	0.005	17.792	0.000	0.000	0.000	0.000	0.000	0.000
134	B	180	GLY	0	-0.020	-0.004	19.712	0.022	0.022	0.000	0.000	0.000	0.000
135	B	181	PHE	0	0.016	-0.024	20.394	0.017	0.017	0.000	0.000	0.000	0.000
136	B	182	LYS	1	0.868	0.939	16.441	0.154	0.154	0.000	0.000	0.000	0.000
137	B	183	VAL	0	0.028	0.001	13.678	0.021	0.021	0.000	0.000	0.000	0.000
138	B	184	SER	0	-0.003	-0.003	16.244	0.009	0.009	0.000	0.000	0.000	0.000
139	B	185	GLU	-1	-0.829	-0.898	17.662	-0.159	-0.159	0.000	0.000	0.000	0.000
140	B	186	ILE	0	0.044	0.023	18.248	0.013	0.013	0.000	0.000	0.000	0.000
141	B	187	LYS	1	0.897	0.966	16.271	0.373	0.373	0.000	0.000	0.000	0.000
142	B	188	ALA	0	0.035	0.027	20.614	0.016	0.016	0.000	0.000	0.000	0.000
143	B	189	ILE	0	0.011	0.000	23.320	0.014	0.014	0.000	0.000	0.000	0.000
144	B	190	THR	0	-0.002	-0.023	23.173	0.010	0.010	0.000	0.000	0.000	0.000
145	B	191	GLN	0	-0.048	-0.027	22.521	0.006	0.006	0.000	0.000	0.000	0.000
146	B	192	ASN	0	0.003	0.006	26.059	0.012	0.012	0.000	0.000	0.000	0.000
147	B	193	ALA	0	0.028	0.026	28.362	0.009	0.009	0.000	0.000	0.000	0.000
148	B	194	ILE	0	-0.014	-0.026	25.792	0.006	0.006	0.000	0.000	0.000	0.000
149	B	195	LEU	0	-0.055	-0.028	29.993	0.007	0.007	0.000	0.000	0.000	0.000
150	B	196	GLU	-1	-0.924	-0.942	32.028	-0.086	-0.086	0.000	0.000	0.000	0.000
151	B	197	HIS	0	-0.087	-0.053	33.301	0.005	0.005	0.000	0.000	0.000	0.000
152	B	198	VAL	0	-0.099	-0.037	31.148	0.006	0.006	0.000	0.000	0.000	0.000

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