FMO DATABASE

FMODB ID: JQ1N9

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1483607.631769
FMO2-HF: Nuclear repulsion	1419745.823866
FMO2-HF: Total energy	-63861.807903
FMO2-MP2: Total energy	-64048.237437

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.
-0.017	0.788	-0.004	-0.383	-0.418	0.001

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 : 0.015 / q_NPA : -0.003

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	0.026	0.010	3.848	-0.484	0.321	-0.004	-0.383	-0.418	0.001
4	A	3	PRO	0	0.011	0.011	5.944	0.431	0.431	0.000	0.000	0.000	0.000
5	A	4	TRP	0	0.015	0.007	8.269	-0.141	-0.141	0.000	0.000	0.000	0.000
6	A	5	ARG	1	0.841	0.905	12.070	0.210	0.210	0.000	0.000	0.000	0.000
7	A	6	LYS	1	1.005	0.995	14.121	-0.021	-0.021	0.000	0.000	0.000	0.000
8	A	7	ALA	0	-0.013	0.003	17.814	-0.022	-0.022	0.000	0.000	0.000	0.000
9	A	8	ASP	-1	-0.830	-0.881	19.633	-0.089	-0.089	0.000	0.000	0.000	0.000
10	A	9	LYS	1	0.893	0.909	19.944	0.138	0.138	0.000	0.000	0.000	0.000
11	A	10	GLU	-1	-0.784	-0.843	19.420	-0.148	-0.148	0.000	0.000	0.000	0.000
12	A	11	ARG	1	0.916	0.949	23.326	0.035	0.035	0.000	0.000	0.000	0.000
13	A	12	HIS	0	0.079	0.025	25.579	0.008	0.008	0.000	0.000	0.000	0.000
14	A	13	GLY	0	0.061	0.030	27.468	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	14	VAL	0	-0.082	-0.031	28.424	0.009	0.009	0.000	0.000	0.000	0.000
16	A	15	ALA	0	0.051	0.033	28.827	-0.008	-0.008	0.000	0.000	0.000	0.000
17	A	16	ILE	0	0.013	0.003	27.680	0.006	0.006	0.000	0.000	0.000	0.000
18	A	17	TYR	0	-0.003	-0.010	29.423	0.001	0.001	0.000	0.000	0.000	0.000
19	A	18	ASN	0	0.013	0.013	30.145	0.004	0.004	0.000	0.000	0.000	0.000
20	A	19	PHE	0	-0.004	0.016	22.945	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	20	GLN	0	0.003	-0.011	27.975	0.008	0.008	0.000	0.000	0.000	0.000
22	A	21	GLY	0	0.042	0.013	24.784	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	22	SER	0	-0.017	-0.023	22.950	0.001	0.001	0.000	0.000	0.000	0.000
24	A	23	GLY	0	0.019	0.022	25.258	0.008	0.008	0.000	0.000	0.000	0.000
25	A	24	ALA	0	0.009	0.011	24.097	-0.002	-0.002	0.000	0.000	0.000	0.000
26	A	25	PRO	0	0.022	0.004	19.097	0.006	0.006	0.000	0.000	0.000	0.000
27	A	26	GLN	0	0.004	0.003	19.861	-0.016	-0.016	0.000	0.000	0.000	0.000
28	A	27	LEU	0	-0.046	-0.018	22.837	0.008	0.008	0.000	0.000	0.000	0.000
29	A	28	SER	0	0.023	0.001	25.802	-0.009	-0.009	0.000	0.000	0.000	0.000
30	A	29	LEU	0	-0.078	-0.026	26.399	0.004	0.004	0.000	0.000	0.000	0.000
31	A	30	GLN	0	-0.022	-0.021	29.921	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	31	ILE	0	-0.004	-0.008	32.727	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	32	GLY	0	0.003	0.002	33.397	0.004	0.004	0.000	0.000	0.000	0.000
34	A	33	ASP	-1	-0.850	-0.912	31.731	-0.019	-0.019	0.000	0.000	0.000	0.000
35	A	34	VAL	0	-0.038	-0.021	31.576	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	35	VAL	0	-0.009	-0.002	26.432	0.007	0.007	0.000	0.000	0.000	0.000
37	A	36	ARG	1	0.845	0.930	24.967	0.009	0.009	0.000	0.000	0.000	0.000
38	A	37	ILE	0	-0.001	0.000	21.591	0.006	0.006	0.000	0.000	0.000	0.000
39	A	38	GLN	0	-0.060	-0.044	21.765	0.001	0.001	0.000	0.000	0.000	0.000
40	A	39	GLU	-1	-0.845	-0.925	16.454	0.072	0.072	0.000	0.000	0.000	0.000
41	A	40	THR	0	-0.043	-0.032	14.977	-0.014	-0.014	0.000	0.000	0.000	0.000
42	A	41	CYS	0	0.008	0.008	10.018	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	42	GLY	0	0.052	0.029	11.565	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.850	-0.908	12.214	-0.351	-0.351	0.000	0.000	0.000	0.000
45	A	44	TRP	0	0.000	0.013	15.132	0.068	0.068	0.000	0.000	0.000	0.000
46	A	45	TYR	0	-0.022	-0.023	16.578	-0.014	-0.014	0.000	0.000	0.000	0.000
47	A	46	ARG	1	0.880	0.932	18.602	-0.057	-0.057	0.000	0.000	0.000	0.000
48	A	47	GLY	0	0.016	-0.013	20.339	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	48	TYR	0	-0.004	0.001	24.014	0.006	0.006	0.000	0.000	0.000	0.000
50	A	49	LEU	0	0.067	0.047	27.601	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	50	ILE	0	-0.008	-0.003	30.868	0.006	0.006	0.000	0.000	0.000	0.000
52	A	51	LYS	1	0.936	0.980	33.017	0.019	0.019	0.000	0.000	0.000	0.000
53	A	52	HIS	1	0.857	0.923	33.828	0.002	0.002	0.000	0.000	0.000	0.000
54	A	53	LYS	1	0.984	0.987	31.329	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	54	MET	0	0.023	0.022	30.262	0.004	0.004	0.000	0.000	0.000	0.000
56	A	55	LEU	0	-0.010	0.006	30.070	0.004	0.004	0.000	0.000	0.000	0.000
57	A	56	GLN	0	0.015	-0.007	23.914	0.000	0.000	0.000	0.000	0.000	0.000
58	A	57	GLY	0	0.021	0.015	22.891	0.008	0.008	0.000	0.000	0.000	0.000
59	A	58	ILE	0	-0.040	-0.020	17.466	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	59	PHE	0	0.041	0.019	20.885	0.005	0.005	0.000	0.000	0.000	0.000
61	A	60	PRO	0	0.022	0.021	19.576	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	61	LYS	1	0.837	0.888	15.907	0.322	0.322	0.000	0.000	0.000	0.000
63	A	62	SER	0	0.010	-0.005	20.580	0.012	0.012	0.000	0.000	0.000	0.000
64	A	63	PHE	0	0.000	0.004	22.703	0.009	0.009	0.000	0.000	0.000	0.000
65	A	64	ILE	0	-0.052	-0.018	24.167	0.015	0.015	0.000	0.000	0.000	0.000
66	A	65	HIS	0	0.018	0.028	25.814	-0.012	-0.012	0.000	0.000	0.000	0.000
67	A	66	ILE	0	-0.006	-0.019	23.429	0.010	0.010	0.000	0.000	0.000	0.000
68	A	67	LYS	1	0.892	0.950	27.296	0.044	0.044	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.857	-0.923	29.996	-0.041	-0.041	0.000	0.000	0.000	0.000
70	A	69	VAL	0	-0.079	-0.040	32.064	0.002	0.002	0.000	0.000	0.000	0.000
71	A	81	ILE	0	-0.002	-0.013	38.212	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	82	PRO	0	0.003	0.018	40.784	0.002	0.002	0.000	0.000	0.000	0.000
73	A	83	ALA	0	0.087	0.021	43.418	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	84	GLU	-1	-0.753	-0.881	44.585	-0.022	-0.022	0.000	0.000	0.000	0.000
75	A	85	ILE	0	-0.018	0.006	38.747	0.000	0.000	0.000	0.000	0.000	0.000
76	A	86	PRO	0	0.004	0.004	41.722	0.000	0.000	0.000	0.000	0.000	0.000
77	A	87	LEU	0	0.069	0.044	42.730	0.001	0.001	0.000	0.000	0.000	0.000
78	A	88	ALA	0	0.051	0.025	42.589	0.001	0.001	0.000	0.000	0.000	0.000
79	A	89	GLN	0	-0.039	-0.009	37.713	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	90	GLU	-1	-0.846	-0.923	41.877	-0.010	-0.010	0.000	0.000	0.000	0.000
81	A	91	VAL	0	0.036	0.027	45.194	0.001	0.001	0.000	0.000	0.000	0.000
82	A	92	THR	0	-0.111	-0.078	39.949	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	93	THR	0	-0.061	-0.028	42.701	0.001	0.001	0.000	0.000	0.000	0.000
84	A	94	THR	0	0.052	0.018	43.978	0.001	0.001	0.000	0.000	0.000	0.000
85	A	95	LEU	0	-0.015	-0.006	45.948	0.001	0.001	0.000	0.000	0.000	0.000
86	A	96	TRP	0	-0.023	-0.027	40.417	0.001	0.001	0.000	0.000	0.000	0.000
87	A	97	GLU	-1	-0.903	-0.942	45.703	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	98	TRP	0	-0.033	-0.027	48.258	0.000	0.000	0.000	0.000	0.000	0.000
89	A	99	GLY	0	0.054	0.017	48.668	0.000	0.000	0.000	0.000	0.000	0.000
90	A	100	SER	0	-0.095	-0.055	47.559	0.000	0.000	0.000	0.000	0.000	0.000
91	A	101	ILE	0	0.090	0.044	49.280	0.000	0.000	0.000	0.000	0.000	0.000
92	A	102	TRP	0	-0.037	-0.018	51.517	0.000	0.000	0.000	0.000	0.000	0.000
93	A	103	LYS	1	0.939	0.973	46.870	0.006	0.006	0.000	0.000	0.000	0.000
94	A	104	GLN	0	0.015	0.008	53.010	0.000	0.000	0.000	0.000	0.000	0.000
95	A	105	LEU	0	-0.017	-0.011	55.426	0.000	0.000	0.000	0.000	0.000	0.000
96	A	106	TYR	0	-0.016	0.002	55.689	0.000	0.000	0.000	0.000	0.000	0.000
97	A	107	VAL	0	0.018	0.015	55.284	0.000	0.000	0.000	0.000	0.000	0.000
98	A	108	ALA	0	-0.030	-0.006	58.266	0.000	0.000	0.000	0.000	0.000	0.000
99	A	109	SER	0	0.023	0.010	60.951	0.000	0.000	0.000	0.000	0.000	0.000
100	A	110	LYS	1	0.867	0.937	61.186	0.002	0.002	0.000	0.000	0.000	0.000
101	A	111	LYS	1	0.896	0.914	62.359	0.006	0.006	0.000	0.000	0.000	0.000
102	A	112	GLU	-1	-0.797	-0.876	62.951	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	113	ARG	1	0.898	0.949	59.517	0.004	0.004	0.000	0.000	0.000	0.000
104	A	114	PHE	0	0.022	0.009	55.964	0.000	0.000	0.000	0.000	0.000	0.000
105	A	115	LEU	0	0.035	0.019	58.239	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	116	GLN	0	0.041	0.032	59.616	0.000	0.000	0.000	0.000	0.000	0.000
107	A	117	VAL	0	0.040	0.004	54.364	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	118	GLN	0	-0.007	0.019	54.869	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	119	SER	0	-0.012	-0.018	54.984	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	120	MET	0	-0.039	0.001	55.857	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	121	MET	0	-0.006	0.000	51.030	0.000	0.000	0.000	0.000	0.000	0.000
112	A	122	TYR	0	-0.016	-0.034	51.232	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	123	ASP	-1	-0.814	-0.883	52.289	-0.015	-0.015	0.000	0.000	0.000	0.000
114	A	124	LEU	0	-0.008	-0.003	50.051	-0.001	-0.001	0.000	0.000	0.000	0.000
115	A	125	MET	0	-0.061	-0.029	46.961	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	126	GLU	-1	-0.820	-0.892	47.864	-0.026	-0.026	0.000	0.000	0.000	0.000
117	A	127	TRP	0	0.003	-0.018	49.864	0.000	0.000	0.000	0.000	0.000	0.000
118	A	128	ARG	1	0.886	0.940	40.527	0.025	0.025	0.000	0.000	0.000	0.000
119	A	129	SER	0	-0.020	-0.003	45.502	-0.002	-0.002	0.000	0.000	0.000	0.000
120	A	130	GLN	0	-0.018	-0.033	46.315	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	131	LEU	0	-0.044	-0.007	46.545	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	132	LEU	0	-0.061	-0.038	40.881	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	133	SER	0	-0.029	-0.018	43.041	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	134	GLY	0	-0.025	0.000	44.809	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	135	THR	0	-0.036	-0.027	45.704	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	136	LEU	0	0.001	0.014	48.825	0.001	0.001	0.000	0.000	0.000	0.000
127	A	137	PRO	0	0.024	0.022	51.249	0.000	0.000	0.000	0.000	0.000	0.000
128	A	138	LYS	1	0.850	0.887	52.647	0.019	0.019	0.000	0.000	0.000	0.000
129	A	139	ASP	-1	-0.834	-0.900	53.629	-0.017	-0.017	0.000	0.000	0.000	0.000
130	A	140	GLU	-1	-0.858	-0.933	55.720	-0.020	-0.020	0.000	0.000	0.000	0.000
131	A	141	LEU	0	0.008	0.013	48.638	0.001	0.001	0.000	0.000	0.000	0.000
132	A	142	LYS	1	0.908	0.955	52.711	0.014	0.014	0.000	0.000	0.000	0.000
133	A	143	GLU	-1	-0.815	-0.918	54.558	-0.013	-0.013	0.000	0.000	0.000	0.000
134	A	144	LEU	0	-0.029	0.001	50.932	0.001	0.001	0.000	0.000	0.000	0.000
135	A	145	LYS	1	0.824	0.896	48.713	0.021	0.021	0.000	0.000	0.000	0.000
136	A	146	GLN	0	-0.010	-0.003	52.730	0.001	0.001	0.000	0.000	0.000	0.000
137	A	147	LYS	1	0.891	0.957	56.201	0.015	0.015	0.000	0.000	0.000	0.000
138	A	148	VAL	0	0.008	-0.004	49.930	0.001	0.001	0.000	0.000	0.000	0.000
139	A	149	THR	0	0.048	0.018	51.765	0.000	0.000	0.000	0.000	0.000	0.000
140	A	150	SER	0	-0.012	-0.009	53.811	0.001	0.001	0.000	0.000	0.000	0.000
141	A	151	LYS	1	0.781	0.887	54.965	0.013	0.013	0.000	0.000	0.000	0.000
142	A	152	ILE	0	0.003	0.002	49.641	0.000	0.000	0.000	0.000	0.000	0.000
143	A	153	ASP	-1	-0.856	-0.927	53.631	-0.006	-0.006	0.000	0.000	0.000	0.000
144	A	154	TYR	0	-0.049	-0.036	56.130	0.001	0.001	0.000	0.000	0.000	0.000
145	A	155	GLY	0	0.011	-0.022	55.863	0.001	0.001	0.000	0.000	0.000	0.000
146	A	156	ASN	0	0.033	0.002	51.168	0.000	0.000	0.000	0.000	0.000	0.000
147	A	157	LYS	1	0.994	1.008	55.290	0.004	0.004	0.000	0.000	0.000	0.000
148	A	158	ILE	0	-0.090	-0.040	58.923	0.001	0.001	0.000	0.000	0.000	0.000
149	A	159	LEU	0	-0.076	-0.046	54.556	0.000	0.000	0.000	0.000	0.000	0.000
150	A	160	GLU	-1	-0.969	-0.972	56.555	0.001	0.001	0.000	0.000	0.000	0.000
151	A	161	LEU	0	-0.047	-0.006	51.366	0.001	0.001	0.000	0.000	0.000	0.000
152	A	162	ASP	-1	-0.874	-0.945	51.349	0.000	0.000	0.000	0.000	0.000	0.000
153	A	163	LEU	0	-0.080	-0.036	53.475	-0.001	-0.001	0.000	0.000	0.000	0.000
154	A	164	ILE	0	0.009	0.013	49.551	0.001	0.001	0.000	0.000	0.000	0.000
155	A	165	VAL	0	0.011	0.005	51.776	0.000	0.000	0.000	0.000	0.000	0.000
156	A	166	ARG	1	0.884	0.938	51.303	0.008	0.008	0.000	0.000	0.000	0.000
157	A	167	ASP	-1	-0.925	-0.949	46.214	-0.008	-0.008	0.000	0.000	0.000	0.000

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