FMO DATABASE

FMODB ID: NN4KQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1481513.461257
FMO2-HF: Nuclear repulsion	1417652.0059
FMO2-HF: Total energy	-63861.455357
FMO2-MP2: Total energy	-64047.905289

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.
0.588	1.511	-0.012	-0.44	-0.471	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 : 0.013 / 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	0.023	-0.002	3.824	-0.136	0.787	-0.012	-0.440	-0.471	0.002
4	A	3	PRO	0	0.014	0.022	6.332	0.369	0.369	0.000	0.000	0.000	0.000
5	A	4	TRP	0	0.010	-0.002	8.285	-0.055	-0.055	0.000	0.000	0.000	0.000
6	A	5	ARG	1	0.871	0.936	12.042	0.347	0.347	0.000	0.000	0.000	0.000
7	A	6	LYS	1	1.001	0.985	14.156	0.072	0.072	0.000	0.000	0.000	0.000
8	A	7	ALA	0	0.004	0.015	17.631	-0.027	-0.027	0.000	0.000	0.000	0.000
9	A	8	ASP	-1	-0.845	-0.906	19.127	-0.174	-0.174	0.000	0.000	0.000	0.000
10	A	9	LYS	1	0.926	0.930	20.470	0.206	0.206	0.000	0.000	0.000	0.000
11	A	10	GLU	-1	-0.867	-0.896	19.322	-0.223	-0.223	0.000	0.000	0.000	0.000
12	A	11	ARG	1	0.955	0.983	23.512	0.082	0.082	0.000	0.000	0.000	0.000
13	A	12	HIS	0	0.077	0.026	25.882	0.003	0.003	0.000	0.000	0.000	0.000
14	A	13	GLY	0	0.064	0.036	27.420	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	14	VAL	0	-0.084	-0.031	28.400	0.010	0.010	0.000	0.000	0.000	0.000
16	A	15	ALA	0	0.050	0.031	28.854	-0.009	-0.009	0.000	0.000	0.000	0.000
17	A	16	ILE	0	0.011	0.002	28.058	0.008	0.008	0.000	0.000	0.000	0.000
18	A	17	TYR	0	0.006	-0.008	29.450	0.003	0.003	0.000	0.000	0.000	0.000
19	A	18	ASN	0	0.001	0.015	30.291	0.001	0.001	0.000	0.000	0.000	0.000
20	A	19	PHE	0	-0.023	-0.012	22.758	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	20	GLN	0	0.003	-0.010	28.027	0.006	0.006	0.000	0.000	0.000	0.000
22	A	21	GLY	0	0.034	0.015	24.950	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	22	SER	0	-0.017	-0.022	23.225	0.003	0.003	0.000	0.000	0.000	0.000
24	A	23	GLY	0	0.028	0.021	25.491	0.011	0.011	0.000	0.000	0.000	0.000
25	A	24	ALA	0	0.014	0.013	23.752	-0.005	-0.005	0.000	0.000	0.000	0.000
26	A	25	PRO	0	0.019	-0.004	18.543	0.009	0.009	0.000	0.000	0.000	0.000
27	A	26	GLN	0	-0.009	0.009	19.965	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	27	LEU	0	-0.038	-0.008	22.581	0.011	0.011	0.000	0.000	0.000	0.000
29	A	28	SER	0	0.019	0.002	25.516	-0.010	-0.010	0.000	0.000	0.000	0.000
30	A	29	LEU	0	-0.063	-0.021	26.115	0.002	0.002	0.000	0.000	0.000	0.000
31	A	30	GLN	0	-0.002	0.010	29.682	0.001	0.001	0.000	0.000	0.000	0.000
32	A	31	ILE	0	0.019	-0.004	32.749	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	32	GLY	0	-0.013	-0.010	33.254	0.005	0.005	0.000	0.000	0.000	0.000
34	A	33	ASP	-1	-0.868	-0.930	31.478	-0.045	-0.045	0.000	0.000	0.000	0.000
35	A	34	VAL	0	-0.036	-0.021	31.397	-0.007	-0.007	0.000	0.000	0.000	0.000
36	A	35	VAL	0	-0.014	-0.012	26.291	0.007	0.007	0.000	0.000	0.000	0.000
37	A	36	ARG	1	0.840	0.935	25.037	0.066	0.066	0.000	0.000	0.000	0.000
38	A	37	ILE	0	-0.008	-0.016	21.401	0.006	0.006	0.000	0.000	0.000	0.000
39	A	38	GLN	0	-0.059	-0.049	21.640	0.008	0.008	0.000	0.000	0.000	0.000
40	A	39	GLU	-1	-0.849	-0.929	16.290	-0.061	-0.061	0.000	0.000	0.000	0.000
41	A	40	THR	0	-0.027	-0.023	15.049	-0.008	-0.008	0.000	0.000	0.000	0.000
42	A	41	CYS	0	0.011	0.015	9.959	-0.010	-0.010	0.000	0.000	0.000	0.000
43	A	42	GLY	0	0.036	0.030	11.713	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.874	-0.932	12.240	-0.407	-0.407	0.000	0.000	0.000	0.000
45	A	44	TRP	0	0.009	0.009	14.811	0.084	0.084	0.000	0.000	0.000	0.000
46	A	45	TYR	0	-0.022	-0.026	16.467	-0.024	-0.024	0.000	0.000	0.000	0.000
47	A	46	ARG	1	0.888	0.936	18.177	0.039	0.039	0.000	0.000	0.000	0.000
48	A	47	GLY	0	-0.011	-0.021	20.025	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	48	TYR	0	0.011	0.007	23.644	0.008	0.008	0.000	0.000	0.000	0.000
50	A	49	LEU	0	0.063	0.046	27.184	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	50	ILE	0	0.011	0.008	30.556	0.006	0.006	0.000	0.000	0.000	0.000
52	A	51	LYS	1	0.923	0.969	32.687	0.040	0.040	0.000	0.000	0.000	0.000
53	A	52	HIS	1	0.894	0.937	33.377	0.026	0.026	0.000	0.000	0.000	0.000
54	A	53	LYS	1	0.990	0.993	30.864	0.028	0.028	0.000	0.000	0.000	0.000
55	A	54	MET	0	-0.004	0.015	29.944	0.001	0.001	0.000	0.000	0.000	0.000
56	A	55	LEU	0	-0.020	0.004	29.649	0.003	0.003	0.000	0.000	0.000	0.000
57	A	56	GLN	0	0.006	-0.020	23.471	-0.006	-0.006	0.000	0.000	0.000	0.000
58	A	57	GLY	0	0.018	0.015	22.374	0.010	0.010	0.000	0.000	0.000	0.000
59	A	58	ILE	0	-0.038	-0.026	17.218	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	59	PHE	0	0.029	0.018	20.623	0.013	0.013	0.000	0.000	0.000	0.000
61	A	60	PRO	0	0.035	0.023	19.659	-0.019	-0.019	0.000	0.000	0.000	0.000
62	A	61	LYS	1	0.877	0.925	15.956	0.394	0.394	0.000	0.000	0.000	0.000
63	A	62	SER	0	0.017	-0.006	20.809	0.013	0.013	0.000	0.000	0.000	0.000
64	A	63	PHE	0	-0.017	-0.003	22.981	0.013	0.013	0.000	0.000	0.000	0.000
65	A	64	ILE	0	-0.042	-0.013	24.183	0.016	0.016	0.000	0.000	0.000	0.000
66	A	65	HIS	0	0.020	0.035	25.785	-0.013	-0.013	0.000	0.000	0.000	0.000
67	A	66	ILE	0	-0.010	-0.018	23.619	0.010	0.010	0.000	0.000	0.000	0.000
68	A	67	LYS	1	0.907	0.957	27.406	0.071	0.071	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.866	-0.931	29.963	-0.085	-0.085	0.000	0.000	0.000	0.000
70	A	69	VAL	0	-0.073	-0.036	32.419	0.005	0.005	0.000	0.000	0.000	0.000
71	A	81	ILE	0	-0.011	-0.017	38.307	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	82	PRO	0	0.022	0.020	40.454	0.003	0.003	0.000	0.000	0.000	0.000
73	A	83	ALA	0	0.081	0.024	43.342	0.000	0.000	0.000	0.000	0.000	0.000
74	A	84	GLU	-1	-0.775	-0.892	44.505	-0.039	-0.039	0.000	0.000	0.000	0.000
75	A	85	ILE	0	-0.015	0.004	38.837	0.000	0.000	0.000	0.000	0.000	0.000
76	A	86	PRO	0	0.005	0.004	41.805	0.000	0.000	0.000	0.000	0.000	0.000
77	A	87	LEU	0	0.042	0.032	42.769	0.001	0.001	0.000	0.000	0.000	0.000
78	A	88	ALA	0	0.026	0.007	42.471	0.001	0.001	0.000	0.000	0.000	0.000
79	A	89	GLN	0	-0.058	-0.045	37.787	0.000	0.000	0.000	0.000	0.000	0.000
80	A	90	GLU	-1	-0.830	-0.914	42.017	-0.026	-0.026	0.000	0.000	0.000	0.000
81	A	91	VAL	0	0.036	0.036	45.169	0.002	0.002	0.000	0.000	0.000	0.000
82	A	92	THR	0	-0.086	-0.042	40.173	0.000	0.000	0.000	0.000	0.000	0.000
83	A	93	THR	0	-0.028	-0.028	42.383	0.000	0.000	0.000	0.000	0.000	0.000
84	A	94	THR	0	0.057	0.030	43.814	0.002	0.002	0.000	0.000	0.000	0.000
85	A	95	LEU	0	-0.040	-0.022	45.811	0.001	0.001	0.000	0.000	0.000	0.000
86	A	96	TRP	0	-0.057	-0.044	40.682	0.001	0.001	0.000	0.000	0.000	0.000
87	A	97	GLU	-1	-0.913	-0.943	45.390	-0.018	-0.018	0.000	0.000	0.000	0.000
88	A	98	TRP	0	-0.030	-0.027	47.908	0.001	0.001	0.000	0.000	0.000	0.000
89	A	99	GLY	0	0.042	0.019	48.372	0.001	0.001	0.000	0.000	0.000	0.000
90	A	100	SER	0	-0.067	-0.042	47.600	0.001	0.001	0.000	0.000	0.000	0.000
91	A	101	ILE	0	0.085	0.046	49.354	0.001	0.001	0.000	0.000	0.000	0.000
92	A	102	TRP	0	-0.029	-0.018	51.331	0.001	0.001	0.000	0.000	0.000	0.000
93	A	103	LYS	1	0.953	0.969	46.758	0.019	0.019	0.000	0.000	0.000	0.000
94	A	104	GLN	0	0.019	0.011	52.954	0.000	0.000	0.000	0.000	0.000	0.000
95	A	105	LEU	0	-0.039	-0.018	55.313	0.001	0.001	0.000	0.000	0.000	0.000
96	A	106	TYR	0	-0.026	-0.009	55.621	0.000	0.000	0.000	0.000	0.000	0.000
97	A	107	VAL	0	-0.004	0.000	55.034	0.001	0.001	0.000	0.000	0.000	0.000
98	A	108	ALA	0	-0.043	-0.011	58.067	0.001	0.001	0.000	0.000	0.000	0.000
99	A	109	SER	0	-0.009	-0.002	60.725	0.000	0.000	0.000	0.000	0.000	0.000
100	A	110	LYS	1	0.941	0.989	61.307	0.009	0.009	0.000	0.000	0.000	0.000
101	A	111	LYS	1	0.913	0.915	62.164	0.011	0.011	0.000	0.000	0.000	0.000
102	A	112	GLU	-1	-0.814	-0.887	62.988	-0.012	-0.012	0.000	0.000	0.000	0.000
103	A	113	ARG	1	0.943	0.971	59.824	0.012	0.012	0.000	0.000	0.000	0.000
104	A	114	PHE	0	0.026	0.018	55.581	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	115	LEU	0	0.032	0.017	58.201	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	116	GLN	0	0.049	0.025	59.432	0.000	0.000	0.000	0.000	0.000	0.000
107	A	117	VAL	0	0.037	-0.001	54.445	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	118	GLN	0	-0.018	0.013	54.883	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	119	SER	0	-0.012	-0.013	55.005	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	120	MET	0	-0.054	0.001	55.811	-0.001	-0.001	0.000	0.000	0.000	0.000
111	A	121	MET	0	0.008	0.005	50.951	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	122	TYR	0	-0.015	-0.031	51.197	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	123	ASP	-1	-0.807	-0.883	52.102	-0.025	-0.025	0.000	0.000	0.000	0.000
114	A	124	LEU	0	-0.007	0.004	50.050	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	125	MET	0	-0.058	-0.029	46.756	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	126	GLU	-1	-0.839	-0.900	47.809	-0.038	-0.038	0.000	0.000	0.000	0.000
117	A	127	TRP	0	0.023	-0.015	49.720	-0.001	-0.001	0.000	0.000	0.000	0.000
118	A	128	ARG	1	0.907	0.964	40.347	0.042	0.042	0.000	0.000	0.000	0.000
119	A	129	SER	0	-0.023	-0.010	45.111	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	130	GLN	0	-0.012	-0.026	46.075	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	131	LEU	0	-0.059	-0.014	46.621	-0.001	-0.001	0.000	0.000	0.000	0.000
122	A	132	LEU	0	-0.081	-0.049	40.893	-0.002	-0.002	0.000	0.000	0.000	0.000
123	A	133	SER	0	-0.027	-0.016	42.735	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	134	GLY	0	-0.019	-0.001	44.677	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	135	THR	0	-0.045	-0.032	45.616	-0.001	-0.001	0.000	0.000	0.000	0.000
126	A	136	LEU	0	0.007	0.014	48.658	0.001	0.001	0.000	0.000	0.000	0.000
127	A	137	PRO	0	0.011	0.023	51.024	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	138	LYS	1	0.859	0.893	52.740	0.031	0.031	0.000	0.000	0.000	0.000
129	A	139	ASP	-1	-0.837	-0.918	53.696	-0.029	-0.029	0.000	0.000	0.000	0.000
130	A	140	GLU	-1	-0.852	-0.924	55.264	-0.030	-0.030	0.000	0.000	0.000	0.000
131	A	141	LEU	0	0.003	0.010	48.588	0.001	0.001	0.000	0.000	0.000	0.000
132	A	142	LYS	1	0.921	0.962	53.046	0.026	0.026	0.000	0.000	0.000	0.000
133	A	143	GLU	-1	-0.823	-0.916	54.838	-0.023	-0.023	0.000	0.000	0.000	0.000
134	A	144	LEU	0	-0.030	-0.011	51.275	0.001	0.001	0.000	0.000	0.000	0.000
135	A	145	LYS	1	0.853	0.899	48.525	0.036	0.036	0.000	0.000	0.000	0.000
136	A	146	GLN	0	0.002	0.014	52.871	0.000	0.000	0.000	0.000	0.000	0.000
137	A	147	LYS	1	0.896	0.965	56.209	0.026	0.026	0.000	0.000	0.000	0.000
138	A	148	VAL	0	0.004	-0.005	49.976	0.001	0.001	0.000	0.000	0.000	0.000
139	A	149	THR	0	0.054	0.016	51.910	0.000	0.000	0.000	0.000	0.000	0.000
140	A	150	SER	0	-0.023	-0.009	53.914	0.001	0.001	0.000	0.000	0.000	0.000
141	A	151	LYS	1	0.796	0.900	55.020	0.023	0.023	0.000	0.000	0.000	0.000
142	A	152	ILE	0	-0.005	0.006	49.743	0.001	0.001	0.000	0.000	0.000	0.000
143	A	153	ASP	-1	-0.834	-0.917	53.632	-0.019	-0.019	0.000	0.000	0.000	0.000
144	A	154	TYR	0	-0.062	-0.042	56.033	0.001	0.001	0.000	0.000	0.000	0.000
145	A	155	GLY	0	0.001	-0.029	55.875	0.001	0.001	0.000	0.000	0.000	0.000
146	A	156	ASN	0	0.073	0.023	51.294	0.001	0.001	0.000	0.000	0.000	0.000
147	A	157	LYS	1	0.977	1.015	55.250	0.014	0.014	0.000	0.000	0.000	0.000
148	A	158	ILE	0	-0.083	-0.046	58.818	0.001	0.001	0.000	0.000	0.000	0.000
149	A	159	LEU	0	-0.092	-0.043	54.391	0.001	0.001	0.000	0.000	0.000	0.000
150	A	160	GLU	-1	-0.999	-0.987	56.717	-0.009	-0.009	0.000	0.000	0.000	0.000
151	A	161	LEU	0	-0.048	-0.028	51.415	0.000	0.000	0.000	0.000	0.000	0.000
152	A	162	ASP	-1	-0.913	-0.969	51.186	-0.014	-0.014	0.000	0.000	0.000	0.000
153	A	163	LEU	0	-0.079	-0.034	53.041	-0.001	-0.001	0.000	0.000	0.000	0.000
154	A	164	ILE	0	0.018	0.020	49.355	0.000	0.000	0.000	0.000	0.000	0.000
155	A	165	VAL	0	-0.003	-0.004	51.829	0.001	0.001	0.000	0.000	0.000	0.000
156	A	166	ARG	1	0.897	0.943	51.497	0.021	0.021	0.000	0.000	0.000	0.000
157	A	167	ASP	-1	-0.929	-0.951	46.744	-0.027	-0.027	0.000	0.000	0.000	0.000

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