FMO DATABASE

FMODB ID: N98ZQ

Calculation Name: 2DYC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DYC

Chain ID: A

ChEMBL ID:

UniProt ID: Q8K419

Base Structure: X-ray

Registration Date: 2023-06-22

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	147
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1445494.931132
FMO2-HF: Nuclear repulsion	1386094.313508
FMO2-HF: Total energy	-59400.617624
FMO2-MP2: Total energy	-59571.43158

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:13:TYR)

Summations of interaction energy for fragment #1(A:13:TYR)

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.
-7.919	-3.987	1.559	-1.784	-3.706	0.005

Interaction energy analysis for fragmet #1(A:13:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.055 / q_NPA : -0.042

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	15	PRO	0	-0.076	-0.039	2.756	-3.479	-1.230	1.391	-1.050	-2.589	0.009
4	A	16	THR	0	0.013	0.022	4.804	-0.628	-0.542	-0.001	-0.016	-0.070	0.000
5	A	17	LEU	0	-0.049	-0.020	8.467	0.253	0.253	0.000	0.000	0.000	0.000
6	A	18	PRO	0	0.056	0.031	11.081	-0.145	-0.145	0.000	0.000	0.000	0.000
7	A	19	TYR	0	-0.031	-0.007	4.252	0.790	1.018	-0.001	-0.022	-0.204	0.000
8	A	20	LYS	1	0.938	0.966	9.578	-0.907	-0.907	0.000	0.000	0.000	0.000
9	A	21	ARG	1	0.900	0.964	5.342	-3.267	-3.267	0.000	0.000	0.000	0.000
10	A	22	PRO	0	0.029	0.012	9.248	-0.138	-0.138	0.000	0.000	0.000	0.000
11	A	23	ILE	0	0.001	0.000	10.041	0.268	0.268	0.000	0.000	0.000	0.000
12	A	24	PRO	0	-0.061	-0.033	8.275	-0.150	-0.150	0.000	0.000	0.000	0.000
13	A	25	GLY	0	0.036	0.023	11.583	-0.068	-0.068	0.000	0.000	0.000	0.000
14	A	26	GLY	0	-0.029	0.000	14.800	-0.077	-0.077	0.000	0.000	0.000	0.000
15	A	27	LEU	0	0.003	-0.003	15.847	0.016	0.016	0.000	0.000	0.000	0.000
16	A	28	SER	0	0.016	-0.037	17.512	-0.063	-0.063	0.000	0.000	0.000	0.000
17	A	29	VAL	0	0.021	-0.011	19.364	0.014	0.014	0.000	0.000	0.000	0.000
18	A	30	GLY	0	-0.024	-0.011	20.488	-0.015	-0.015	0.000	0.000	0.000	0.000
19	A	31	MET	0	-0.064	0.025	13.670	-0.024	-0.024	0.000	0.000	0.000	0.000
20	A	32	SER	0	-0.014	-0.015	14.831	-0.033	-0.033	0.000	0.000	0.000	0.000
21	A	33	VAL	0	-0.033	-0.013	11.807	0.064	0.064	0.000	0.000	0.000	0.000
22	A	34	TYR	0	-0.028	-0.021	10.313	-0.109	-0.109	0.000	0.000	0.000	0.000
23	A	35	ILE	0	-0.003	-0.011	8.965	0.289	0.289	0.000	0.000	0.000	0.000
24	A	36	GLN	0	-0.008	0.017	7.554	-0.360	-0.360	0.000	0.000	0.000	0.000
25	A	37	GLY	0	0.060	0.014	7.867	0.347	0.347	0.000	0.000	0.000	0.000
26	A	38	MET	0	-0.011	0.009	10.033	-0.150	-0.150	0.000	0.000	0.000	0.000
27	A	39	ALA	0	0.022	0.025	13.191	0.067	0.067	0.000	0.000	0.000	0.000
28	A	40	LYS	1	0.985	1.009	15.326	-0.264	-0.264	0.000	0.000	0.000	0.000
29	A	41	GLU	-1	-0.884	-0.957	17.722	-0.028	-0.028	0.000	0.000	0.000	0.000
30	A	42	ASN	0	-0.042	-0.021	20.960	-0.001	-0.001	0.000	0.000	0.000	0.000
31	A	43	MET	0	-0.069	-0.016	19.263	0.009	0.009	0.000	0.000	0.000	0.000
32	A	44	ARG	1	0.922	0.964	21.101	-0.142	-0.142	0.000	0.000	0.000	0.000
33	A	45	ARG	1	0.894	0.946	21.290	-0.238	-0.238	0.000	0.000	0.000	0.000
34	A	46	PHE	0	0.023	0.026	15.278	0.003	0.003	0.000	0.000	0.000	0.000
35	A	47	HIS	0	-0.032	-0.009	16.775	-0.077	-0.077	0.000	0.000	0.000	0.000
36	A	48	VAL	0	0.021	0.017	13.694	0.103	0.103	0.000	0.000	0.000	0.000
37	A	49	ASN	0	0.021	0.026	15.363	-0.140	-0.140	0.000	0.000	0.000	0.000
38	A	50	PHE	0	0.036	0.032	15.677	0.141	0.141	0.000	0.000	0.000	0.000
39	A	51	ALA	0	0.007	-0.019	16.873	-0.084	-0.084	0.000	0.000	0.000	0.000
40	A	52	VAL	0	0.035	0.010	18.324	0.046	0.046	0.000	0.000	0.000	0.000
41	A	53	GLY	0	0.015	0.015	19.394	-0.037	-0.037	0.000	0.000	0.000	0.000
42	A	54	GLN	0	-0.041	-0.029	15.676	0.010	0.010	0.000	0.000	0.000	0.000
43	A	55	ASP	-1	-0.879	-0.945	17.160	0.456	0.456	0.000	0.000	0.000	0.000
44	A	56	ASP	-1	-0.923	-0.979	17.965	0.543	0.543	0.000	0.000	0.000	0.000
45	A	57	GLY	0	-0.051	-0.011	20.082	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	58	ALA	0	-0.045	0.001	20.391	-0.022	-0.022	0.000	0.000	0.000	0.000
47	A	59	ASP	-1	-0.803	-0.899	22.527	0.304	0.304	0.000	0.000	0.000	0.000
48	A	60	VAL	0	-0.051	-0.038	20.100	0.058	0.058	0.000	0.000	0.000	0.000
49	A	61	ALA	0	0.043	0.024	21.625	-0.040	-0.040	0.000	0.000	0.000	0.000
50	A	62	PHE	0	-0.035	-0.014	20.325	-0.042	-0.042	0.000	0.000	0.000	0.000
51	A	63	HIS	0	-0.035	-0.023	20.023	0.028	0.028	0.000	0.000	0.000	0.000
52	A	64	PHE	0	0.039	0.011	17.498	-0.061	-0.061	0.000	0.000	0.000	0.000
53	A	65	ASN	0	0.023	-0.007	19.181	0.013	0.013	0.000	0.000	0.000	0.000
54	A	66	PRO	0	0.035	0.017	18.701	-0.054	-0.054	0.000	0.000	0.000	0.000
55	A	67	ARG	1	0.810	0.885	21.850	-0.234	-0.234	0.000	0.000	0.000	0.000
56	A	68	PHE	0	-0.014	-0.027	21.561	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	69	ASP	-1	-0.861	-0.939	25.807	0.138	0.138	0.000	0.000	0.000	0.000
58	A	70	GLY	0	-0.023	0.000	29.310	0.004	0.004	0.000	0.000	0.000	0.000
59	A	71	TRP	0	-0.025	-0.023	31.962	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	72	ASP	-1	-0.845	-0.922	26.943	0.119	0.119	0.000	0.000	0.000	0.000
61	A	73	LYS	1	0.847	0.923	26.868	-0.167	-0.167	0.000	0.000	0.000	0.000
62	A	74	VAL	0	0.012	0.017	22.450	0.015	0.015	0.000	0.000	0.000	0.000
63	A	75	VAL	0	-0.064	-0.027	24.400	-0.022	-0.022	0.000	0.000	0.000	0.000
64	A	76	PHE	0	0.010	0.009	22.832	0.032	0.032	0.000	0.000	0.000	0.000
65	A	77	ASN	0	-0.001	-0.003	24.847	-0.027	-0.027	0.000	0.000	0.000	0.000
66	A	78	THR	0	0.006	0.002	24.835	0.023	0.023	0.000	0.000	0.000	0.000
67	A	79	MET	0	-0.044	-0.002	24.891	-0.017	-0.017	0.000	0.000	0.000	0.000
68	A	80	GLN	0	0.026	0.000	26.279	0.022	0.022	0.000	0.000	0.000	0.000
69	A	81	SER	0	-0.017	-0.015	28.766	-0.022	-0.022	0.000	0.000	0.000	0.000
70	A	82	GLY	0	0.031	0.019	28.312	-0.016	-0.016	0.000	0.000	0.000	0.000
71	A	83	GLN	0	-0.027	-0.009	29.338	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	84	TRP	0	-0.001	0.004	22.957	0.012	0.012	0.000	0.000	0.000	0.000
73	A	85	GLY	0	0.024	0.017	29.669	-0.018	-0.018	0.000	0.000	0.000	0.000
74	A	86	LYS	1	0.941	0.959	31.737	-0.143	-0.143	0.000	0.000	0.000	0.000
75	A	87	GLU	-1	-0.922	-0.950	29.117	0.205	0.205	0.000	0.000	0.000	0.000
76	A	88	GLU	-1	-0.813	-0.872	28.896	0.188	0.188	0.000	0.000	0.000	0.000
77	A	89	LYS	1	0.933	0.940	28.250	-0.128	-0.128	0.000	0.000	0.000	0.000
78	A	90	LYS	1	0.927	0.992	26.923	-0.154	-0.154	0.000	0.000	0.000	0.000
79	A	91	LYS	1	0.858	0.934	28.120	-0.097	-0.097	0.000	0.000	0.000	0.000
80	A	92	SER	0	0.011	-0.003	27.654	-0.013	-0.013	0.000	0.000	0.000	0.000
81	A	93	MET	0	0.028	0.017	22.919	0.028	0.028	0.000	0.000	0.000	0.000
82	A	94	PRO	0	-0.019	0.006	20.991	-0.017	-0.017	0.000	0.000	0.000	0.000
83	A	95	PHE	0	0.016	0.010	16.300	0.000	0.000	0.000	0.000	0.000	0.000
84	A	96	GLN	0	0.028	-0.003	19.573	-0.025	-0.025	0.000	0.000	0.000	0.000
85	A	97	LYS	1	0.934	0.971	19.569	-0.095	-0.095	0.000	0.000	0.000	0.000
86	A	98	GLY	0	0.049	0.019	18.350	-0.021	-0.021	0.000	0.000	0.000	0.000
87	A	99	LYS	1	0.891	0.967	17.936	0.015	0.015	0.000	0.000	0.000	0.000
88	A	100	HIS	0	-0.014	-0.005	10.143	0.025	0.025	0.000	0.000	0.000	0.000
89	A	101	PHE	0	-0.061	-0.034	12.690	-0.010	-0.010	0.000	0.000	0.000	0.000
90	A	102	GLU	-1	-0.845	-0.933	12.611	-0.010	-0.010	0.000	0.000	0.000	0.000
91	A	103	LEU	0	-0.059	-0.024	12.896	-0.051	-0.051	0.000	0.000	0.000	0.000
92	A	104	VAL	0	0.027	0.020	13.367	0.106	0.106	0.000	0.000	0.000	0.000
93	A	105	PHE	0	0.004	-0.002	14.567	-0.052	-0.052	0.000	0.000	0.000	0.000
94	A	106	MET	0	0.005	0.007	17.223	0.011	0.011	0.000	0.000	0.000	0.000
95	A	107	VAL	0	0.014	0.009	18.445	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	108	MET	0	0.002	0.010	21.050	-0.031	-0.031	0.000	0.000	0.000	0.000
97	A	109	PRO	0	-0.005	-0.023	24.457	0.017	0.017	0.000	0.000	0.000	0.000
98	A	110	GLU	-1	-0.901	-0.942	27.185	0.142	0.142	0.000	0.000	0.000	0.000
99	A	111	HIS	0	0.023	0.000	26.011	0.007	0.007	0.000	0.000	0.000	0.000
100	A	112	TYR	0	-0.020	0.010	19.922	0.002	0.002	0.000	0.000	0.000	0.000
101	A	113	LYS	1	0.971	0.983	22.266	-0.152	-0.152	0.000	0.000	0.000	0.000
102	A	114	VAL	0	-0.039	-0.023	18.983	0.028	0.028	0.000	0.000	0.000	0.000
103	A	115	VAL	0	-0.002	-0.006	19.218	-0.045	-0.045	0.000	0.000	0.000	0.000
104	A	116	VAL	0	0.000	0.000	17.730	0.037	0.037	0.000	0.000	0.000	0.000
105	A	117	ASN	0	0.030	0.007	17.058	-0.026	-0.026	0.000	0.000	0.000	0.000
106	A	118	GLY	0	0.043	0.030	18.671	-0.029	-0.029	0.000	0.000	0.000	0.000
107	A	119	ASN	0	-0.016	-0.003	20.796	-0.017	-0.017	0.000	0.000	0.000	0.000
108	A	120	SER	0	-0.024	-0.022	22.672	0.029	0.029	0.000	0.000	0.000	0.000
109	A	121	PHE	0	-0.029	-0.026	22.551	-0.013	-0.013	0.000	0.000	0.000	0.000
110	A	122	TYR	0	-0.075	-0.069	24.058	-0.020	-0.020	0.000	0.000	0.000	0.000
111	A	123	GLU	-1	-0.861	-0.923	24.515	0.167	0.167	0.000	0.000	0.000	0.000
112	A	124	TYR	0	-0.033	-0.022	24.520	-0.015	-0.015	0.000	0.000	0.000	0.000
113	A	125	GLY	0	0.068	0.030	26.230	0.013	0.013	0.000	0.000	0.000	0.000
114	A	126	HIS	0	-0.060	-0.023	23.729	0.025	0.025	0.000	0.000	0.000	0.000
115	A	127	ARG	1	0.802	0.883	27.369	-0.246	-0.246	0.000	0.000	0.000	0.000
116	A	128	LEU	0	0.025	0.012	24.891	-0.009	-0.009	0.000	0.000	0.000	0.000
117	A	129	PRO	0	-0.008	-0.010	26.273	0.009	0.009	0.000	0.000	0.000	0.000
118	A	130	VAL	0	0.067	0.031	21.123	0.025	0.025	0.000	0.000	0.000	0.000
119	A	131	GLN	0	0.006	-0.013	21.527	0.046	0.046	0.000	0.000	0.000	0.000
120	A	132	MET	0	-0.028	0.007	22.045	0.001	0.001	0.000	0.000	0.000	0.000
121	A	133	VAL	0	-0.049	-0.012	17.214	0.027	0.027	0.000	0.000	0.000	0.000
122	A	134	THR	0	0.003	0.018	16.860	0.039	0.039	0.000	0.000	0.000	0.000
123	A	135	HIS	0	-0.032	-0.040	13.284	0.140	0.140	0.000	0.000	0.000	0.000
124	A	136	LEU	0	0.019	0.023	10.392	-0.103	-0.103	0.000	0.000	0.000	0.000
125	A	137	GLN	0	-0.036	-0.031	11.451	0.166	0.166	0.000	0.000	0.000	0.000
126	A	138	VAL	0	0.002	0.002	10.433	-0.114	-0.114	0.000	0.000	0.000	0.000
127	A	139	ASP	-1	-0.824	-0.927	12.240	0.667	0.667	0.000	0.000	0.000	0.000
128	A	140	GLY	0	0.030	0.017	14.370	-0.055	-0.055	0.000	0.000	0.000	0.000
129	A	141	ASP	-1	-0.822	-0.923	15.619	0.258	0.258	0.000	0.000	0.000	0.000
130	A	142	LEU	0	-0.059	-0.044	11.201	-0.042	-0.042	0.000	0.000	0.000	0.000
131	A	143	GLU	-1	-0.910	-0.946	10.473	-0.043	-0.043	0.000	0.000	0.000	0.000
132	A	144	LEU	0	-0.034	-0.023	5.964	-0.043	-0.043	0.000	0.000	0.000	0.000
133	A	145	GLN	0	0.065	0.032	5.142	0.071	0.071	0.000	0.000	0.000	0.000
134	A	146	SER	0	-0.035	-0.039	3.160	-1.389	-0.125	0.170	-0.672	-0.763	-0.004
135	A	147	ILE	0	0.039	0.022	4.187	-1.297	-1.192	0.000	-0.024	-0.080	0.000
136	A	148	ASN	0	0.000	0.004	5.168	1.582	1.582	0.000	0.000	0.000	0.000
137	A	149	PHE	0	0.015	0.000	7.914	-0.038	-0.038	0.000	0.000	0.000	0.000
138	A	150	LEU	0	0.019	0.011	9.463	-0.213	-0.213	0.000	0.000	0.000	0.000
139	A	151	GLY	0	0.044	0.024	12.202	0.050	0.050	0.000	0.000	0.000	0.000
140	A	152	GLY	0	0.039	0.011	14.033	0.058	0.058	0.000	0.000	0.000	0.000
141	A	153	GLN	0	0.019	0.007	15.456	-0.006	-0.006	0.000	0.000	0.000	0.000
142	A	154	PRO	0	0.028	0.017	10.625	0.053	0.053	0.000	0.000	0.000	0.000
143	A	155	ALA	0	0.020	0.000	11.676	0.121	0.121	0.000	0.000	0.000	0.000
144	A	156	ALA	0	-0.028	-0.013	11.978	-0.050	-0.050	0.000	0.000	0.000	0.000
145	A	157	ALA	0	-0.051	-0.015	7.183	0.109	0.109	0.000	0.000	0.000	0.000
146	A	158	PRO	0	0.005	0.009	5.741	-0.204	-0.204	0.000	0.000	0.000	0.000
147	A	159	TYR	0	0.003	-0.001	6.176	-0.154	-0.154	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:13:TYR)