FMO DATABASE

FMODB ID: 89LRY

Calculation Name: 3A98-A-Xray372

Preferred Name: Dedicator of cytokinesis protein 2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3A98

Chain ID: A

ChEMBL ID: CHEMBL4105810

UniProt ID: Q92608

Base Structure: X-ray

Registration Date: 2023-09-24

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	157
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1481565.48116
FMO2-HF: Nuclear repulsion	1417705.08522
FMO2-HF: Total energy	-63860.39594
FMO2-MP2: Total energy	-64046.915427

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:0:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

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.
0.693	1.585	-0.011	-0.415	-0.465	0.002

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.002

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	2	ALA	0	0.009	-0.005	3.828	-0.008	0.884	-0.011	-0.415	-0.465	0.002
4	A	3	PRO	0	0.003	0.012	6.216	0.367	0.367	0.000	0.000	0.000	0.000
5	A	4	TRP	0	0.022	0.008	8.284	-0.060	-0.060	0.000	0.000	0.000	0.000
6	A	5	ARG	1	0.938	0.970	11.950	0.428	0.428	0.000	0.000	0.000	0.000
7	A	6	LYS	1	0.985	0.981	14.155	0.074	0.074	0.000	0.000	0.000	0.000
8	A	7	ALA	0	-0.001	0.013	17.632	-0.026	-0.026	0.000	0.000	0.000	0.000
9	A	8	ASP	-1	-0.876	-0.940	19.723	-0.172	-0.172	0.000	0.000	0.000	0.000
10	A	9	LYS	1	0.918	0.939	21.542	0.199	0.199	0.000	0.000	0.000	0.000
11	A	10	GLU	-1	-0.881	-0.924	19.510	-0.230	-0.230	0.000	0.000	0.000	0.000
12	A	11	ARG	1	0.954	0.982	23.513	0.082	0.082	0.000	0.000	0.000	0.000
13	A	12	HIS	0	0.051	0.010	25.883	0.004	0.004	0.000	0.000	0.000	0.000
14	A	13	GLY	0	0.060	0.034	27.422	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	14	VAL	0	-0.081	-0.024	28.401	0.010	0.010	0.000	0.000	0.000	0.000
16	A	15	ALA	0	0.047	0.026	28.860	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	16	ILE	0	0.005	0.000	28.014	0.009	0.009	0.000	0.000	0.000	0.000
18	A	17	TYR	0	0.005	-0.009	29.463	0.003	0.003	0.000	0.000	0.000	0.000
19	A	18	ASN	0	-0.002	0.014	30.291	0.002	0.002	0.000	0.000	0.000	0.000
20	A	19	PHE	0	-0.013	-0.012	22.569	-0.007	-0.007	0.000	0.000	0.000	0.000
21	A	20	GLN	0	-0.004	-0.017	28.027	0.007	0.007	0.000	0.000	0.000	0.000
22	A	21	GLY	0	0.030	0.010	24.953	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	22	SER	0	-0.047	-0.025	22.939	0.010	0.010	0.000	0.000	0.000	0.000
24	A	23	GLY	0	0.055	0.032	25.491	0.011	0.011	0.000	0.000	0.000	0.000
25	A	24	ALA	0	0.013	0.012	23.749	-0.006	-0.006	0.000	0.000	0.000	0.000
26	A	25	PRO	0	0.014	-0.004	18.513	0.009	0.009	0.000	0.000	0.000	0.000
27	A	26	GLN	0	-0.002	0.007	19.790	-0.014	-0.014	0.000	0.000	0.000	0.000
28	A	27	LEU	0	-0.038	-0.008	22.579	0.013	0.013	0.000	0.000	0.000	0.000
29	A	28	SER	0	0.014	0.001	25.514	-0.011	-0.011	0.000	0.000	0.000	0.000
30	A	29	LEU	0	-0.055	-0.019	25.887	0.002	0.002	0.000	0.000	0.000	0.000
31	A	30	GLN	0	0.004	0.008	29.682	0.001	0.001	0.000	0.000	0.000	0.000
32	A	31	ILE	0	0.013	0.000	32.758	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	32	GLY	0	-0.012	-0.012	33.251	0.005	0.005	0.000	0.000	0.000	0.000
34	A	33	ASP	-1	-0.870	-0.923	31.310	-0.053	-0.053	0.000	0.000	0.000	0.000
35	A	34	VAL	0	-0.031	-0.021	31.397	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	35	VAL	0	-0.019	-0.015	26.313	0.007	0.007	0.000	0.000	0.000	0.000
37	A	36	ARG	1	0.870	0.953	25.009	0.067	0.067	0.000	0.000	0.000	0.000
38	A	37	ILE	0	-0.008	-0.016	21.356	0.006	0.006	0.000	0.000	0.000	0.000
39	A	38	GLN	0	-0.111	-0.087	21.661	0.011	0.011	0.000	0.000	0.000	0.000
40	A	39	GLU	-1	-0.854	-0.945	16.259	-0.066	-0.066	0.000	0.000	0.000	0.000
41	A	40	THR	0	-0.036	-0.025	14.864	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	41	CYS	0	0.040	0.014	10.699	-0.056	-0.056	0.000	0.000	0.000	0.000
43	A	42	GLY	0	0.001	0.022	11.717	-0.014	-0.014	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.950	-0.968	12.240	-0.460	-0.460	0.000	0.000	0.000	0.000
45	A	44	TRP	0	0.007	0.007	14.525	0.097	0.097	0.000	0.000	0.000	0.000
46	A	45	TYR	0	-0.018	-0.001	16.467	-0.022	-0.022	0.000	0.000	0.000	0.000
47	A	46	ARG	1	0.932	0.969	18.122	0.044	0.044	0.000	0.000	0.000	0.000
48	A	47	GLY	0	-0.014	-0.023	20.023	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	48	TYR	0	0.023	0.016	23.643	0.009	0.009	0.000	0.000	0.000	0.000
50	A	49	LEU	0	0.077	0.051	27.183	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	50	ILE	0	0.007	0.007	30.554	0.007	0.007	0.000	0.000	0.000	0.000
52	A	51	LYS	1	0.926	0.958	32.685	0.045	0.045	0.000	0.000	0.000	0.000
53	A	52	HIS	1	0.887	0.930	33.369	0.030	0.030	0.000	0.000	0.000	0.000
54	A	53	LYS	1	0.997	1.003	30.860	0.032	0.032	0.000	0.000	0.000	0.000
55	A	54	MET	0	0.000	0.019	29.942	0.002	0.002	0.000	0.000	0.000	0.000
56	A	55	LEU	0	-0.023	0.002	29.653	0.003	0.003	0.000	0.000	0.000	0.000
57	A	56	GLN	0	0.027	-0.005	23.782	-0.014	-0.014	0.000	0.000	0.000	0.000
58	A	57	GLY	0	-0.005	0.005	22.374	0.010	0.010	0.000	0.000	0.000	0.000
59	A	58	ILE	0	-0.028	-0.020	17.387	-0.009	-0.009	0.000	0.000	0.000	0.000
60	A	59	PHE	0	0.021	0.014	20.629	0.013	0.013	0.000	0.000	0.000	0.000
61	A	60	PRO	0	0.036	0.025	19.660	-0.020	-0.020	0.000	0.000	0.000	0.000
62	A	61	LYS	1	0.998	0.995	16.750	0.376	0.376	0.000	0.000	0.000	0.000
63	A	62	SER	0	0.003	-0.011	20.809	0.012	0.012	0.000	0.000	0.000	0.000
64	A	63	PHE	0	-0.009	-0.001	22.981	0.013	0.013	0.000	0.000	0.000	0.000
65	A	64	ILE	0	-0.030	-0.003	24.237	0.017	0.017	0.000	0.000	0.000	0.000
66	A	65	HIS	0	0.004	0.025	25.787	-0.015	-0.015	0.000	0.000	0.000	0.000
67	A	66	ILE	0	-0.007	-0.016	23.741	0.011	0.011	0.000	0.000	0.000	0.000
68	A	67	LYS	1	0.909	0.954	27.408	0.076	0.076	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.860	-0.919	29.964	-0.093	-0.093	0.000	0.000	0.000	0.000
70	A	69	VAL	0	-0.069	-0.039	32.408	0.005	0.005	0.000	0.000	0.000	0.000
71	A	81	ILE	0	0.006	-0.011	38.719	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	82	PRO	0	-0.008	0.019	40.372	0.003	0.003	0.000	0.000	0.000	0.000
73	A	83	ALA	0	0.088	0.012	43.343	0.000	0.000	0.000	0.000	0.000	0.000
74	A	84	GLU	-1	-0.796	-0.923	44.451	-0.042	-0.042	0.000	0.000	0.000	0.000
75	A	85	ILE	0	-0.016	0.003	38.865	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	86	PRO	0	-0.015	-0.002	41.874	0.000	0.000	0.000	0.000	0.000	0.000
77	A	87	LEU	0	0.046	0.032	42.770	0.001	0.001	0.000	0.000	0.000	0.000
78	A	88	ALA	0	0.015	0.001	42.369	0.001	0.001	0.000	0.000	0.000	0.000
79	A	89	GLN	0	-0.079	-0.063	37.401	0.002	0.002	0.000	0.000	0.000	0.000
80	A	90	GLU	-1	-0.814	-0.910	42.018	-0.028	-0.028	0.000	0.000	0.000	0.000
81	A	91	VAL	0	0.026	0.032	45.168	0.002	0.002	0.000	0.000	0.000	0.000
82	A	92	THR	0	-0.088	-0.039	40.166	0.000	0.000	0.000	0.000	0.000	0.000
83	A	93	THR	0	-0.029	-0.027	42.260	0.000	0.000	0.000	0.000	0.000	0.000
84	A	94	THR	0	0.071	0.037	43.813	0.002	0.002	0.000	0.000	0.000	0.000
85	A	95	LEU	0	-0.044	-0.026	45.772	0.001	0.001	0.000	0.000	0.000	0.000
86	A	96	TRP	0	-0.065	-0.040	40.229	0.001	0.001	0.000	0.000	0.000	0.000
87	A	97	GLU	-1	-0.917	-0.949	45.388	-0.021	-0.021	0.000	0.000	0.000	0.000
88	A	98	TRP	0	-0.022	-0.016	47.906	0.001	0.001	0.000	0.000	0.000	0.000
89	A	99	GLY	0	0.037	0.016	48.371	0.001	0.001	0.000	0.000	0.000	0.000
90	A	100	SER	0	-0.101	-0.048	47.570	0.001	0.001	0.000	0.000	0.000	0.000
91	A	101	ILE	0	0.127	0.059	49.353	0.001	0.001	0.000	0.000	0.000	0.000
92	A	102	TRP	0	-0.028	-0.019	51.131	0.001	0.001	0.000	0.000	0.000	0.000
93	A	103	LYS	1	0.968	0.970	46.606	0.023	0.023	0.000	0.000	0.000	0.000
94	A	104	GLN	0	0.030	0.018	52.988	0.000	0.000	0.000	0.000	0.000	0.000
95	A	105	LEU	0	-0.057	-0.024	55.311	0.001	0.001	0.000	0.000	0.000	0.000
96	A	106	TYR	0	-0.029	-0.010	55.605	0.000	0.000	0.000	0.000	0.000	0.000
97	A	107	VAL	0	-0.015	-0.004	54.974	0.001	0.001	0.000	0.000	0.000	0.000
98	A	108	ALA	0	-0.038	-0.006	58.065	0.001	0.001	0.000	0.000	0.000	0.000
99	A	109	SER	0	-0.001	0.001	60.726	0.000	0.000	0.000	0.000	0.000	0.000
100	A	110	LYS	1	0.947	0.988	61.305	0.011	0.011	0.000	0.000	0.000	0.000
101	A	111	LYS	1	0.980	0.972	62.162	0.013	0.013	0.000	0.000	0.000	0.000
102	A	112	GLU	-1	-0.876	-0.942	62.988	-0.014	-0.014	0.000	0.000	0.000	0.000
103	A	113	ARG	1	0.974	0.990	60.374	0.014	0.014	0.000	0.000	0.000	0.000
104	A	114	PHE	0	0.018	0.019	55.399	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	115	LEU	0	0.020	0.008	58.201	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	116	GLN	0	0.026	0.003	59.432	-0.001	-0.001	0.000	0.000	0.000	0.000
107	A	117	VAL	0	0.037	0.000	54.443	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	118	GLN	0	-0.033	-0.006	54.886	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	119	SER	0	-0.010	-0.008	55.005	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	120	MET	0	-0.057	-0.008	55.786	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	121	MET	0	0.008	0.009	50.835	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	122	TYR	0	-0.007	-0.014	51.151	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	123	ASP	-1	-0.864	-0.927	52.103	-0.028	-0.028	0.000	0.000	0.000	0.000
114	A	124	LEU	0	-0.019	-0.001	50.033	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	125	MET	0	-0.054	-0.028	46.490	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	126	GLU	-1	-0.846	-0.908	47.806	-0.041	-0.041	0.000	0.000	0.000	0.000
117	A	127	TRP	0	0.024	-0.014	49.722	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	128	ARG	1	0.936	0.981	40.159	0.047	0.047	0.000	0.000	0.000	0.000
119	A	129	SER	0	-0.034	-0.016	45.115	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	130	GLN	0	-0.001	-0.018	46.077	-0.002	-0.002	0.000	0.000	0.000	0.000
121	A	131	LEU	0	-0.057	-0.020	46.610	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	132	LEU	0	-0.086	-0.053	40.779	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	133	SER	0	-0.020	-0.005	42.737	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	134	GLY	0	-0.021	-0.004	44.679	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	135	THR	0	-0.038	-0.024	45.618	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	136	LEU	0	-0.001	0.009	48.659	0.001	0.001	0.000	0.000	0.000	0.000
127	A	137	PRO	0	0.014	0.021	51.026	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	138	LYS	1	0.962	0.953	52.742	0.036	0.036	0.000	0.000	0.000	0.000
129	A	139	ASP	-1	-0.913	-0.957	53.698	-0.030	-0.030	0.000	0.000	0.000	0.000
130	A	140	GLU	-1	-0.873	-0.936	55.269	-0.033	-0.033	0.000	0.000	0.000	0.000
131	A	141	LEU	0	-0.001	0.009	48.772	0.001	0.001	0.000	0.000	0.000	0.000
132	A	142	LYS	1	0.922	0.957	53.048	0.029	0.029	0.000	0.000	0.000	0.000
133	A	143	GLU	-1	-0.869	-0.936	54.839	-0.024	-0.024	0.000	0.000	0.000	0.000
134	A	144	LEU	0	-0.052	-0.022	51.148	0.001	0.001	0.000	0.000	0.000	0.000
135	A	145	LYS	1	0.891	0.937	48.750	0.037	0.037	0.000	0.000	0.000	0.000
136	A	146	GLN	0	0.017	0.013	52.872	0.000	0.000	0.000	0.000	0.000	0.000
137	A	147	LYS	1	0.963	1.019	56.082	0.028	0.028	0.000	0.000	0.000	0.000
138	A	148	VAL	0	-0.008	-0.009	49.983	0.001	0.001	0.000	0.000	0.000	0.000
139	A	149	THR	0	0.004	-0.003	51.962	0.001	0.001	0.000	0.000	0.000	0.000
140	A	150	SER	0	0.027	0.002	53.916	0.001	0.001	0.000	0.000	0.000	0.000
141	A	151	LYS	1	0.861	0.947	54.982	0.025	0.025	0.000	0.000	0.000	0.000
142	A	152	ILE	0	-0.004	0.010	49.616	0.001	0.001	0.000	0.000	0.000	0.000
143	A	153	ASP	-1	-0.821	-0.914	53.631	-0.020	-0.020	0.000	0.000	0.000	0.000
144	A	154	TYR	0	-0.072	-0.045	56.032	0.001	0.001	0.000	0.000	0.000	0.000
145	A	155	GLY	0	-0.001	-0.035	55.887	0.001	0.001	0.000	0.000	0.000	0.000
146	A	156	ASN	0	0.086	0.027	51.340	0.001	0.001	0.000	0.000	0.000	0.000
147	A	157	LYS	1	0.962	1.010	55.249	0.015	0.015	0.000	0.000	0.000	0.000
148	A	158	ILE	0	-0.113	-0.057	58.817	0.001	0.001	0.000	0.000	0.000	0.000
149	A	159	LEU	0	-0.069	-0.035	54.356	0.001	0.001	0.000	0.000	0.000	0.000
150	A	160	GLU	-1	-0.996	-0.983	56.716	-0.010	-0.010	0.000	0.000	0.000	0.000
151	A	161	LEU	0	-0.050	-0.031	51.377	0.000	0.000	0.000	0.000	0.000	0.000
152	A	162	ASP	-1	-0.928	-0.973	51.208	-0.014	-0.014	0.000	0.000	0.000	0.000
153	A	163	LEU	0	-0.082	-0.041	53.040	-0.001	-0.001	0.000	0.000	0.000	0.000
154	A	164	ILE	0	0.045	0.036	49.243	0.001	0.001	0.000	0.000	0.000	0.000
155	A	165	VAL	0	-0.016	-0.011	51.813	0.001	0.001	0.000	0.000	0.000	0.000
156	A	166	ARG	1	0.921	0.956	51.497	0.022	0.022	0.000	0.000	0.000	0.000
157	A	167	ASP	-1	-0.948	-0.961	47.395	-0.025	-0.025	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)