FMO DATABASE

FMODB ID: 53ZZZ

Calculation Name: 3A98-A-Xray317

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: 2021-09-07

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	161
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1494547.598936
FMO2-HF: Nuclear repulsion	1430345.289276
FMO2-HF: Total energy	-64202.30966
FMO2-MP2: Total energy	-64389.897414

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:-1:ACE )

Summations of interaction energy for fragment #1(A:-1: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.
1.692	2.472	-0.005	-0.35	-0.425	0

Interaction energy analysis for fragmet #1(A:-1:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / 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].
3	A	1	MET	0	-0.033	0.001	3.838	1.131	1.911	-0.005	-0.350	-0.425
4	A	2	ALA	0	0.011	-0.003	6.870	-0.033	-0.033	0.000	0.000	0.000
5	A	3	PRO	0	0.005	0.013	10.240	0.075	0.075	0.000	0.000	0.000
6	A	4	TRP	0	0.021	0.007	12.349	0.067	0.067	0.000	0.000	0.000
7	A	5	ARG	1	0.937	0.969	16.004	0.252	0.252	0.000	0.000	0.000
8	A	6	LYS	1	0.986	0.981	18.292	0.168	0.168	0.000	0.000	0.000
9	A	7	ALA	0	0.000	0.013	21.712	-0.010	-0.010	0.000	0.000	0.000
10	A	8	ASP	-1	-0.875	-0.940	23.750	-0.143	-0.143	0.000	0.000	0.000
11	A	9	LYS	1	0.917	0.938	25.714	0.124	0.124	0.000	0.000	0.000
12	A	10	GLU	-1	-0.882	-0.924	23.478	-0.135	-0.135	0.000	0.000	0.000
13	A	11	ARG	1	0.957	0.983	27.434	0.093	0.093	0.000	0.000	0.000
14	A	12	HIS	0	0.051	0.011	29.842	-0.001	-0.001	0.000	0.000	0.000
15	A	13	GLY	0	0.061	0.034	30.970	-0.001	-0.001	0.000	0.000	0.000
16	A	14	VAL	0	-0.079	-0.025	31.981	0.002	0.002	0.000	0.000	0.000
17	A	15	ALA	0	0.042	0.025	31.870	-0.002	-0.002	0.000	0.000	0.000
18	A	16	ILE	0	0.006	0.001	30.639	0.004	0.004	0.000	0.000	0.000
19	A	17	TYR	0	0.006	-0.009	31.856	0.005	0.005	0.000	0.000	0.000
20	A	18	ASN	0	-0.005	0.014	32.846	-0.005	-0.005	0.000	0.000	0.000
21	A	19	PHE	0	-0.014	-0.012	24.540	0.001	0.001	0.000	0.000	0.000
22	A	20	GLN	0	-0.005	-0.018	30.014	-0.002	-0.002	0.000	0.000	0.000
23	A	21	GLY	0	0.032	0.011	26.681	0.001	0.001	0.000	0.000	0.000
24	A	22	SER	0	-0.048	-0.025	24.216	0.005	0.005	0.000	0.000	0.000
25	A	23	GLY	0	0.056	0.032	26.727	0.003	0.003	0.000	0.000	0.000
26	A	24	ALA	0	0.012	0.012	25.405	-0.005	-0.005	0.000	0.000	0.000
27	A	25	PRO	0	0.016	-0.004	20.460	0.004	0.004	0.000	0.000	0.000
28	A	26	GLN	0	-0.002	0.007	21.330	-0.003	-0.003	0.000	0.000	0.000
29	A	27	LEU	0	-0.036	-0.008	24.721	0.006	0.006	0.000	0.000	0.000
30	A	28	SER	0	0.014	0.001	27.964	-0.002	-0.002	0.000	0.000	0.000
31	A	29	LEU	0	-0.062	-0.021	28.748	-0.002	-0.002	0.000	0.000	0.000
32	A	30	GLN	0	0.007	0.008	32.219	0.006	0.006	0.000	0.000	0.000
33	A	31	ILE	0	0.016	0.002	35.489	-0.003	-0.003	0.000	0.000	0.000
34	A	32	GLY	0	-0.011	-0.012	36.166	0.002	0.002	0.000	0.000	0.000
35	A	33	ASP	-1	-0.872	-0.924	34.233	-0.043	-0.043	0.000	0.000	0.000
36	A	34	VAL	0	-0.032	-0.022	34.554	-0.003	-0.003	0.000	0.000	0.000
37	A	35	VAL	0	-0.017	-0.014	29.608	0.000	0.000	0.000	0.000	0.000
38	A	36	ARG	1	0.867	0.953	29.063	0.094	0.094	0.000	0.000	0.000
39	A	37	ILE	0	-0.007	-0.016	25.045	-0.001	-0.001	0.000	0.000	0.000
40	A	38	GLN	0	-0.110	-0.086	25.498	0.003	0.003	0.000	0.000	0.000
41	A	39	GLU	-1	-0.853	-0.945	20.125	-0.203	-0.203	0.000	0.000	0.000
42	A	40	THR	0	-0.041	-0.028	18.789	0.016	0.016	0.000	0.000	0.000
43	A	41	CYS	0	0.042	0.016	14.007	-0.043	-0.043	0.000	0.000	0.000
44	A	42	GLY	0	-0.001	0.020	14.923	0.015	0.015	0.000	0.000	0.000
45	A	43	ASP	-1	-0.952	-0.968	15.457	-0.112	-0.112	0.000	0.000	0.000
46	A	44	TRP	0	0.008	0.007	17.128	0.030	0.030	0.000	0.000	0.000
47	A	45	TYR	0	-0.018	-0.001	19.818	-0.018	-0.018	0.000	0.000	0.000
48	A	46	ARG	1	0.934	0.970	21.527	0.144	0.144	0.000	0.000	0.000
49	A	47	GLY	0	-0.011	-0.022	23.411	-0.004	-0.004	0.000	0.000	0.000
50	A	48	TYR	0	0.017	0.013	27.130	0.006	0.006	0.000	0.000	0.000
51	A	49	LEU	0	0.078	0.051	30.532	0.000	0.000	0.000	0.000	0.000
52	A	50	ILE	0	0.008	0.008	33.815	0.001	0.001	0.000	0.000	0.000
53	A	51	LYS	1	0.926	0.959	36.204	0.039	0.039	0.000	0.000	0.000
54	A	52	HIS	1	0.887	0.929	36.436	0.043	0.043	0.000	0.000	0.000
55	A	53	LYS	1	0.999	1.004	34.275	0.057	0.057	0.000	0.000	0.000
56	A	54	MET	0	-0.001	0.018	33.288	-0.004	-0.004	0.000	0.000	0.000
57	A	55	LEU	0	-0.027	0.001	32.494	0.000	0.000	0.000	0.000	0.000
58	A	56	GLN	0	0.032	-0.002	26.962	-0.011	-0.011	0.000	0.000	0.000
59	A	57	GLY	0	-0.007	0.005	25.226	0.004	0.004	0.000	0.000	0.000
60	A	58	ILE	0	-0.031	-0.022	19.771	-0.005	-0.005	0.000	0.000	0.000
61	A	59	PHE	0	0.023	0.015	23.458	0.011	0.011	0.000	0.000	0.000
62	A	60	PRO	0	0.032	0.023	22.347	-0.013	-0.013	0.000	0.000	0.000
63	A	61	LYS	1	0.996	0.994	19.860	0.133	0.133	0.000	0.000	0.000
64	A	62	SER	0	-0.007	-0.015	23.839	0.004	0.004	0.000	0.000	0.000
65	A	63	PHE	0	0.007	0.006	25.635	0.007	0.007	0.000	0.000	0.000
66	A	64	ILE	0	-0.031	-0.003	27.482	0.003	0.003	0.000	0.000	0.000
67	A	65	HIS	0	0.004	0.024	28.929	-0.001	-0.001	0.000	0.000	0.000
68	A	66	ILE	0	-0.004	-0.015	27.341	0.001	0.001	0.000	0.000	0.000
69	A	67	LYS	1	0.906	0.953	31.016	0.053	0.053	0.000	0.000	0.000
70	A	68	GLU	-1	-0.862	-0.922	33.843	-0.075	-0.075	0.000	0.000	0.000
71	A	69	VAL	0	-0.095	-0.078	36.263	0.004	0.004	0.000	0.000	0.000
72	A	70	NME	0	0.019	0.035	38.527	-0.001	-0.001	0.000	0.000	0.000
73	A	80	ACE	0	0.013	-0.006	43.755	0.000	0.000	0.000	0.000	0.000
74	A	81	ILE	0	-0.005	-0.012	42.825	-0.002	-0.002	0.000	0.000	0.000
75	A	82	PRO	0	-0.010	0.025	44.406	0.002	0.002	0.000	0.000	0.000
76	A	83	ALA	0	0.093	0.014	47.376	0.000	0.000	0.000	0.000	0.000
77	A	84	GLU	-1	-0.799	-0.923	48.337	-0.032	-0.032	0.000	0.000	0.000
78	A	85	ILE	0	-0.016	0.003	42.833	0.000	0.000	0.000	0.000	0.000
79	A	86	PRO	0	-0.013	-0.002	45.836	0.000	0.000	0.000	0.000	0.000
80	A	87	LEU	0	0.045	0.033	46.748	0.001	0.001	0.000	0.000	0.000
81	A	88	ALA	0	0.018	0.001	46.179	0.001	0.001	0.000	0.000	0.000
82	A	89	GLN	0	-0.073	-0.057	41.359	0.001	0.001	0.000	0.000	0.000
83	A	90	GLU	-1	-0.811	-0.909	45.811	-0.030	-0.030	0.000	0.000	0.000
84	A	91	VAL	0	0.027	0.032	48.927	0.001	0.001	0.000	0.000	0.000
85	A	92	THR	0	-0.089	-0.039	43.620	0.000	0.000	0.000	0.000	0.000
86	A	93	THR	0	-0.031	-0.027	45.933	0.000	0.000	0.000	0.000	0.000
87	A	94	THR	0	0.069	0.037	47.380	0.001	0.001	0.000	0.000	0.000
88	A	95	LEU	0	-0.042	-0.026	49.103	0.001	0.001	0.000	0.000	0.000
89	A	96	TRP	0	-0.066	-0.040	43.298	0.000	0.000	0.000	0.000	0.000
90	A	97	GLU	-1	-0.916	-0.949	48.651	-0.028	-0.028	0.000	0.000	0.000
91	A	98	TRP	0	-0.023	-0.016	51.258	0.002	0.002	0.000	0.000	0.000
92	A	99	GLY	0	0.038	0.017	51.425	0.001	0.001	0.000	0.000	0.000
93	A	100	SER	0	-0.103	-0.049	50.649	0.001	0.001	0.000	0.000	0.000
94	A	101	ILE	0	0.127	0.059	52.381	0.001	0.001	0.000	0.000	0.000
95	A	102	TRP	0	-0.027	-0.019	53.931	0.001	0.001	0.000	0.000	0.000
96	A	103	LYS	1	0.968	0.970	49.371	0.022	0.022	0.000	0.000	0.000
97	A	104	GLN	0	0.029	0.018	55.867	0.001	0.001	0.000	0.000	0.000
98	A	105	LEU	0	-0.059	-0.024	58.135	0.001	0.001	0.000	0.000	0.000
99	A	106	TYR	0	-0.029	-0.010	58.169	0.001	0.001	0.000	0.000	0.000
100	A	107	VAL	0	-0.015	-0.004	57.519	0.001	0.001	0.000	0.000	0.000
101	A	108	ALA	0	-0.038	-0.006	60.629	0.001	0.001	0.000	0.000	0.000
102	A	109	SER	0	-0.001	0.001	63.372	0.001	0.001	0.000	0.000	0.000
103	A	110	LYS	1	0.946	0.988	64.227	0.014	0.014	0.000	0.000	0.000
104	A	111	LYS	1	0.980	0.972	65.063	0.010	0.010	0.000	0.000	0.000
105	A	112	GLU	-1	-0.875	-0.943	65.902	-0.012	-0.012	0.000	0.000	0.000
106	A	113	ARG	1	0.975	0.990	63.562	0.015	0.015	0.000	0.000	0.000
107	A	114	PHE	0	0.018	0.019	58.182	-0.001	-0.001	0.000	0.000	0.000
108	A	115	LEU	0	0.023	0.010	61.201	-0.001	-0.001	0.000	0.000	0.000
109	A	116	GLN	0	0.022	0.002	62.522	0.000	0.000	0.000	0.000	0.000
110	A	117	VAL	0	0.037	0.000	57.561	-0.001	-0.001	0.000	0.000	0.000
111	A	118	GLN	0	-0.032	-0.005	57.947	-0.001	-0.001	0.000	0.000	0.000
112	A	119	SER	0	-0.009	-0.008	58.131	0.000	0.000	0.000	0.000	0.000
113	A	120	MET	0	-0.058	-0.009	59.140	0.000	0.000	0.000	0.000	0.000
114	A	121	MET	0	0.010	0.009	54.047	-0.001	-0.001	0.000	0.000	0.000
115	A	122	TYR	0	-0.007	-0.015	54.457	-0.001	-0.001	0.000	0.000	0.000
116	A	123	ASP	-1	-0.865	-0.928	55.390	-0.018	-0.018	0.000	0.000	0.000
117	A	124	LEU	0	-0.014	0.001	53.520	-0.001	-0.001	0.000	0.000	0.000
118	A	125	MET	0	-0.062	-0.030	49.777	-0.001	-0.001	0.000	0.000	0.000
119	A	126	GLU	-1	-0.842	-0.907	51.194	-0.021	-0.021	0.000	0.000	0.000
120	A	127	TRP	0	0.022	-0.016	53.139	-0.001	-0.001	0.000	0.000	0.000
121	A	128	ARG	1	0.939	0.982	43.676	0.032	0.032	0.000	0.000	0.000
122	A	129	SER	0	-0.035	-0.016	48.558	-0.002	-0.002	0.000	0.000	0.000
123	A	130	GLN	0	0.000	-0.018	49.531	-0.001	-0.001	0.000	0.000	0.000
124	A	131	LEU	0	-0.055	-0.019	50.365	-0.001	-0.001	0.000	0.000	0.000
125	A	132	LEU	0	-0.091	-0.055	44.378	-0.002	-0.002	0.000	0.000	0.000
126	A	133	SER	0	-0.020	-0.005	46.285	-0.001	-0.001	0.000	0.000	0.000
127	A	134	GLY	0	-0.019	-0.002	48.138	0.000	0.000	0.000	0.000	0.000
128	A	135	THR	0	-0.040	-0.024	49.196	0.001	0.001	0.000	0.000	0.000
129	A	136	LEU	0	-0.001	0.008	52.114	0.001	0.001	0.000	0.000	0.000
130	A	137	PRO	0	0.013	0.021	54.680	-0.001	-0.001	0.000	0.000	0.000
131	A	138	LYS	1	0.962	0.953	56.553	0.024	0.024	0.000	0.000	0.000
132	A	139	ASP	-1	-0.913	-0.957	57.494	-0.020	-0.020	0.000	0.000	0.000
133	A	140	GLU	-1	-0.873	-0.936	58.923	-0.019	-0.019	0.000	0.000	0.000
134	A	141	LEU	0	0.001	0.010	52.622	0.000	0.000	0.000	0.000	0.000
135	A	142	LYS	1	0.922	0.957	56.830	0.023	0.023	0.000	0.000	0.000
136	A	143	GLU	-1	-0.869	-0.937	58.740	-0.019	-0.019	0.000	0.000	0.000
137	A	144	LEU	0	-0.052	-0.022	54.786	0.000	0.000	0.000	0.000	0.000
138	A	145	LYS	1	0.893	0.938	52.731	0.029	0.029	0.000	0.000	0.000
139	A	146	GLN	0	0.016	0.013	56.748	-0.001	-0.001	0.000	0.000	0.000
140	A	147	LYS	1	0.962	1.019	59.813	0.019	0.019	0.000	0.000	0.000
141	A	148	VAL	0	-0.007	-0.009	53.782	0.000	0.000	0.000	0.000	0.000
142	A	149	THR	0	0.004	-0.003	55.873	0.000	0.000	0.000	0.000	0.000
143	A	150	SER	0	0.024	0.001	57.770	0.000	0.000	0.000	0.000	0.000
144	A	151	LYS	1	0.863	0.948	58.596	0.019	0.019	0.000	0.000	0.000
145	A	152	ILE	0	-0.004	0.010	53.327	0.001	0.001	0.000	0.000	0.000
146	A	153	ASP	-1	-0.821	-0.913	57.279	-0.024	-0.024	0.000	0.000	0.000
147	A	154	TYR	0	-0.074	-0.046	59.780	0.001	0.001	0.000	0.000	0.000
148	A	155	GLY	0	-0.001	-0.035	59.389	0.001	0.001	0.000	0.000	0.000
149	A	156	ASN	0	0.088	0.029	55.047	0.001	0.001	0.000	0.000	0.000
150	A	157	LYS	1	0.962	1.011	58.861	0.018	0.018	0.000	0.000	0.000
151	A	158	ILE	0	-0.115	-0.059	62.464	0.001	0.001	0.000	0.000	0.000
152	A	159	LEU	0	-0.073	-0.036	57.698	0.001	0.001	0.000	0.000	0.000
153	A	160	GLU	-1	-0.993	-0.982	60.148	-0.018	-0.018	0.000	0.000	0.000
154	A	161	LEU	0	-0.048	-0.031	54.893	0.000	0.000	0.000	0.000	0.000
155	A	162	ASP	-1	-0.930	-0.973	55.001	-0.026	-0.026	0.000	0.000	0.000
156	A	163	LEU	0	-0.081	-0.041	56.827	0.000	0.000	0.000	0.000	0.000
157	A	164	ILE	0	0.044	0.036	53.153	-0.001	-0.001	0.000	0.000	0.000
158	A	165	VAL	0	-0.015	-0.011	55.829	0.001	0.001	0.000	0.000	0.000
159	A	166	ARG	1	0.907	0.950	55.521	0.026	0.026	0.000	0.000	0.000
160	A	167	ASP	-1	-0.841	-0.903	51.413	-0.034	-0.034	0.000	0.000	0.000
161	A	168	NME	0	-0.097	-0.055	51.321	0.001	0.001	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-1:ACE )