FMO DATABASE

FMODB ID: 39ZKL

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1445506.714669
FMO2-HF: Nuclear repulsion	1386105.162429
FMO2-HF: Total energy	-59401.55224
FMO2-MP2: Total energy	-59572.419244

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.
-14.044	-7.316	1.459	-2.891	-5.295	0.009

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 : -0.048 / q_NPA : -0.048

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	-0.056	-0.007	2.537	-3.206	-0.862	1.106	-1.139	-2.311	0.007
4	A	16	THR	0	0.029	0.016	4.690	-0.164	-0.062	-0.001	-0.013	-0.088	0.000
5	A	17	LEU	0	-0.060	-0.022	8.121	0.480	0.480	0.000	0.000	0.000	0.000
6	A	18	PRO	0	0.052	0.021	10.911	-0.144	-0.144	0.000	0.000	0.000	0.000
7	A	19	TYR	0	-0.019	-0.006	4.203	0.767	0.937	-0.001	-0.011	-0.158	0.000
8	A	20	LYS	1	0.785	0.855	8.701	-0.725	-0.725	0.000	0.000	0.000	0.000
9	A	21	ARG	1	0.864	0.948	3.101	-8.754	-7.257	0.048	-0.617	-0.928	0.006
10	A	22	PRO	0	0.048	0.019	9.149	-0.118	-0.118	0.000	0.000	0.000	0.000
11	A	23	ILE	0	-0.018	-0.003	9.876	0.356	0.356	0.000	0.000	0.000	0.000
12	A	24	PRO	0	-0.052	-0.030	7.746	-0.163	-0.163	0.000	0.000	0.000	0.000
13	A	25	GLY	0	0.039	0.027	10.981	-0.079	-0.079	0.000	0.000	0.000	0.000
14	A	26	GLY	0	-0.024	0.003	14.235	-0.094	-0.094	0.000	0.000	0.000	0.000
15	A	27	LEU	0	0.002	-0.012	14.853	0.062	0.062	0.000	0.000	0.000	0.000
16	A	28	SER	0	0.019	-0.033	17.004	-0.076	-0.076	0.000	0.000	0.000	0.000
17	A	29	VAL	0	0.026	0.001	18.852	0.023	0.023	0.000	0.000	0.000	0.000
18	A	30	GLY	0	-0.015	0.003	19.831	-0.019	-0.019	0.000	0.000	0.000	0.000
19	A	31	MET	0	-0.073	0.023	13.288	-0.029	-0.029	0.000	0.000	0.000	0.000
20	A	32	SER	0	-0.021	-0.023	14.165	-0.056	-0.056	0.000	0.000	0.000	0.000
21	A	33	VAL	0	-0.025	-0.006	11.417	0.084	0.084	0.000	0.000	0.000	0.000
22	A	34	TYR	0	-0.048	-0.051	9.277	-0.163	-0.163	0.000	0.000	0.000	0.000
23	A	35	ILE	0	-0.022	-0.011	8.881	0.403	0.403	0.000	0.000	0.000	0.000
24	A	36	GLN	0	-0.011	-0.002	7.581	-0.489	-0.489	0.000	0.000	0.000	0.000
25	A	37	GLY	0	0.031	0.007	7.770	0.528	0.528	0.000	0.000	0.000	0.000
26	A	38	MET	0	-0.007	0.018	9.869	-0.197	-0.197	0.000	0.000	0.000	0.000
27	A	39	ALA	0	0.032	0.024	13.052	0.066	0.066	0.000	0.000	0.000	0.000
28	A	40	LYS	1	0.918	0.972	14.457	-0.338	-0.338	0.000	0.000	0.000	0.000
29	A	41	GLU	-1	-0.889	-0.957	17.999	0.008	0.008	0.000	0.000	0.000	0.000
30	A	42	ASN	0	-0.038	-0.018	21.096	0.002	0.002	0.000	0.000	0.000	0.000
31	A	43	MET	0	-0.048	0.006	19.659	0.008	0.008	0.000	0.000	0.000	0.000
32	A	44	ARG	1	0.894	0.933	21.601	-0.146	-0.146	0.000	0.000	0.000	0.000
33	A	45	ARG	1	0.783	0.854	21.198	-0.222	-0.222	0.000	0.000	0.000	0.000
34	A	46	PHE	0	0.050	0.040	15.708	0.006	0.006	0.000	0.000	0.000	0.000
35	A	47	HIS	0	-0.036	-0.012	16.053	-0.120	-0.120	0.000	0.000	0.000	0.000
36	A	48	VAL	0	-0.006	0.003	13.428	0.111	0.111	0.000	0.000	0.000	0.000
37	A	49	ASN	0	0.020	0.018	15.151	-0.164	-0.164	0.000	0.000	0.000	0.000
38	A	50	PHE	0	0.042	0.006	15.625	0.132	0.132	0.000	0.000	0.000	0.000
39	A	51	ALA	0	0.024	0.009	16.560	-0.094	-0.094	0.000	0.000	0.000	0.000
40	A	52	VAL	0	0.036	0.003	18.025	0.044	0.044	0.000	0.000	0.000	0.000
41	A	53	GLY	0	0.005	0.014	19.391	-0.027	-0.027	0.000	0.000	0.000	0.000
42	A	54	GLN	0	-0.002	-0.002	15.209	0.008	0.008	0.000	0.000	0.000	0.000
43	A	55	ASP	-1	-0.812	-0.898	16.723	0.391	0.391	0.000	0.000	0.000	0.000
44	A	56	ASP	-1	-0.903	-0.956	16.735	0.561	0.561	0.000	0.000	0.000	0.000
45	A	57	GLY	0	-0.026	-0.004	19.564	-0.015	-0.015	0.000	0.000	0.000	0.000
46	A	58	ALA	0	-0.053	-0.006	20.397	-0.018	-0.018	0.000	0.000	0.000	0.000
47	A	59	ASP	-1	-0.754	-0.866	22.080	0.309	0.309	0.000	0.000	0.000	0.000
48	A	60	VAL	0	-0.048	-0.028	19.654	0.058	0.058	0.000	0.000	0.000	0.000
49	A	61	ALA	0	0.054	0.034	21.340	-0.039	-0.039	0.000	0.000	0.000	0.000
50	A	62	PHE	0	-0.032	-0.005	19.835	-0.045	-0.045	0.000	0.000	0.000	0.000
51	A	63	HIS	0	-0.051	-0.016	19.689	0.034	0.034	0.000	0.000	0.000	0.000
52	A	64	PHE	0	0.040	0.013	17.574	-0.061	-0.061	0.000	0.000	0.000	0.000
53	A	65	ASN	0	0.029	-0.007	18.867	0.016	0.016	0.000	0.000	0.000	0.000
54	A	66	PRO	0	0.022	0.014	18.921	-0.055	-0.055	0.000	0.000	0.000	0.000
55	A	67	ARG	1	0.802	0.882	21.892	-0.256	-0.256	0.000	0.000	0.000	0.000
56	A	68	PHE	0	0.006	-0.002	22.176	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	69	ASP	-1	-0.716	-0.853	25.835	0.151	0.151	0.000	0.000	0.000	0.000
58	A	70	GLY	0	-0.012	0.016	29.336	0.004	0.004	0.000	0.000	0.000	0.000
59	A	71	TRP	0	0.026	-0.031	31.484	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	72	ASP	-1	-0.877	-0.934	27.043	0.151	0.151	0.000	0.000	0.000	0.000
61	A	73	LYS	1	0.802	0.921	26.999	-0.206	-0.206	0.000	0.000	0.000	0.000
62	A	74	VAL	0	0.011	0.014	22.115	0.018	0.018	0.000	0.000	0.000	0.000
63	A	75	VAL	0	-0.057	-0.030	24.054	-0.030	-0.030	0.000	0.000	0.000	0.000
64	A	76	PHE	0	0.027	0.005	23.096	0.037	0.037	0.000	0.000	0.000	0.000
65	A	77	ASN	0	-0.030	-0.024	24.284	-0.035	-0.035	0.000	0.000	0.000	0.000
66	A	78	THR	0	0.017	0.006	24.304	0.027	0.027	0.000	0.000	0.000	0.000
67	A	79	MET	0	-0.045	0.001	24.452	-0.021	-0.021	0.000	0.000	0.000	0.000
68	A	80	GLN	0	0.025	-0.002	25.832	0.021	0.021	0.000	0.000	0.000	0.000
69	A	81	SER	0	-0.051	-0.039	28.528	-0.024	-0.024	0.000	0.000	0.000	0.000
70	A	82	GLY	0	0.034	0.018	27.493	-0.016	-0.016	0.000	0.000	0.000	0.000
71	A	83	GLN	0	-0.027	-0.011	28.564	-0.003	-0.003	0.000	0.000	0.000	0.000
72	A	84	TRP	0	-0.007	-0.003	22.771	0.017	0.017	0.000	0.000	0.000	0.000
73	A	85	GLY	0	0.039	0.028	29.112	-0.018	-0.018	0.000	0.000	0.000	0.000
74	A	86	LYS	1	0.970	0.975	31.030	-0.155	-0.155	0.000	0.000	0.000	0.000
75	A	87	GLU	-1	-0.742	-0.852	28.585	0.217	0.217	0.000	0.000	0.000	0.000
76	A	88	GLU	-1	-0.738	-0.826	28.658	0.212	0.212	0.000	0.000	0.000	0.000
77	A	89	LYS	1	0.768	0.857	28.108	-0.168	-0.168	0.000	0.000	0.000	0.000
78	A	90	LYS	1	0.881	0.950	27.038	-0.202	-0.202	0.000	0.000	0.000	0.000
79	A	91	LYS	1	0.871	0.958	28.103	-0.110	-0.110	0.000	0.000	0.000	0.000
80	A	92	SER	0	-0.005	-0.008	27.575	-0.011	-0.011	0.000	0.000	0.000	0.000
81	A	93	MET	0	0.044	0.026	22.903	0.034	0.034	0.000	0.000	0.000	0.000
82	A	94	PRO	0	-0.026	0.007	20.792	-0.019	-0.019	0.000	0.000	0.000	0.000
83	A	95	PHE	0	0.010	0.000	16.116	0.006	0.006	0.000	0.000	0.000	0.000
84	A	96	GLN	0	0.014	-0.008	19.568	-0.034	-0.034	0.000	0.000	0.000	0.000
85	A	97	LYS	1	0.841	0.931	19.601	-0.128	-0.128	0.000	0.000	0.000	0.000
86	A	98	GLY	0	0.052	0.026	18.693	-0.024	-0.024	0.000	0.000	0.000	0.000
87	A	99	LYS	1	0.844	0.929	17.794	-0.069	-0.069	0.000	0.000	0.000	0.000
88	A	100	HIS	0	-0.017	-0.010	10.377	-0.006	-0.006	0.000	0.000	0.000	0.000
89	A	101	PHE	0	-0.037	-0.025	12.642	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	102	GLU	-1	-0.759	-0.846	12.263	0.200	0.200	0.000	0.000	0.000	0.000
91	A	103	LEU	0	-0.067	-0.032	12.847	-0.081	-0.081	0.000	0.000	0.000	0.000
92	A	104	VAL	0	0.009	0.011	13.364	0.157	0.157	0.000	0.000	0.000	0.000
93	A	105	PHE	0	0.011	-0.006	14.546	-0.072	-0.072	0.000	0.000	0.000	0.000
94	A	106	MET	0	0.015	0.016	16.361	0.025	0.025	0.000	0.000	0.000	0.000
95	A	107	VAL	0	0.006	0.002	17.486	-0.014	-0.014	0.000	0.000	0.000	0.000
96	A	108	MET	0	0.013	0.015	20.174	-0.033	-0.033	0.000	0.000	0.000	0.000
97	A	109	PRO	0	0.019	-0.014	23.597	0.018	0.018	0.000	0.000	0.000	0.000
98	A	110	GLU	-1	-0.922	-0.944	26.366	0.174	0.174	0.000	0.000	0.000	0.000
99	A	111	HIS	0	-0.023	-0.025	25.211	0.002	0.002	0.000	0.000	0.000	0.000
100	A	112	TYR	0	0.010	0.007	19.501	0.033	0.033	0.000	0.000	0.000	0.000
101	A	113	LYS	1	0.851	0.912	21.912	-0.208	-0.208	0.000	0.000	0.000	0.000
102	A	114	VAL	0	-0.034	-0.014	19.275	0.029	0.029	0.000	0.000	0.000	0.000
103	A	115	VAL	0	0.006	-0.008	18.568	-0.055	-0.055	0.000	0.000	0.000	0.000
104	A	116	VAL	0	-0.003	-0.006	17.397	0.060	0.060	0.000	0.000	0.000	0.000
105	A	117	ASN	0	0.009	0.002	16.952	-0.025	-0.025	0.000	0.000	0.000	0.000
106	A	118	GLY	0	0.056	0.041	18.530	-0.036	-0.036	0.000	0.000	0.000	0.000
107	A	119	ASN	0	-0.047	-0.021	20.333	-0.024	-0.024	0.000	0.000	0.000	0.000
108	A	120	SER	0	0.016	0.002	22.381	0.035	0.035	0.000	0.000	0.000	0.000
109	A	121	PHE	0	-0.031	-0.017	22.651	-0.018	-0.018	0.000	0.000	0.000	0.000
110	A	122	TYR	0	-0.034	-0.056	24.228	-0.023	-0.023	0.000	0.000	0.000	0.000
111	A	123	GLU	-1	-0.793	-0.879	24.429	0.221	0.221	0.000	0.000	0.000	0.000
112	A	124	TYR	0	-0.011	-0.012	24.094	-0.025	-0.025	0.000	0.000	0.000	0.000
113	A	125	GLY	0	0.064	0.033	25.584	0.017	0.017	0.000	0.000	0.000	0.000
114	A	126	HIS	0	-0.026	-0.027	22.923	0.026	0.026	0.000	0.000	0.000	0.000
115	A	127	ARG	1	0.754	0.860	27.239	-0.265	-0.265	0.000	0.000	0.000	0.000
116	A	128	LEU	0	0.001	0.008	24.442	-0.012	-0.012	0.000	0.000	0.000	0.000
117	A	129	PRO	0	0.000	-0.003	25.628	0.018	0.018	0.000	0.000	0.000	0.000
118	A	130	VAL	0	0.038	0.030	20.281	0.022	0.022	0.000	0.000	0.000	0.000
119	A	131	GLN	0	0.020	0.002	20.763	0.052	0.052	0.000	0.000	0.000	0.000
120	A	132	MET	0	-0.025	-0.001	21.675	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	133	VAL	0	-0.046	-0.015	16.808	0.020	0.020	0.000	0.000	0.000	0.000
122	A	134	THR	0	-0.026	-0.010	16.695	0.031	0.031	0.000	0.000	0.000	0.000
123	A	135	HIS	0	-0.021	-0.024	13.063	0.128	0.128	0.000	0.000	0.000	0.000
124	A	136	LEU	0	0.000	0.013	10.694	-0.083	-0.083	0.000	0.000	0.000	0.000
125	A	137	GLN	0	0.029	0.013	11.469	0.154	0.154	0.000	0.000	0.000	0.000
126	A	138	VAL	0	-0.017	-0.012	10.287	-0.060	-0.060	0.000	0.000	0.000	0.000
127	A	139	ASP	-1	-0.808	-0.913	11.894	0.559	0.559	0.000	0.000	0.000	0.000
128	A	140	GLY	0	0.024	0.011	14.077	-0.021	-0.021	0.000	0.000	0.000	0.000
129	A	141	ASP	-1	-0.787	-0.893	15.615	0.240	0.240	0.000	0.000	0.000	0.000
130	A	142	LEU	0	-0.053	-0.031	11.081	-0.035	-0.035	0.000	0.000	0.000	0.000
131	A	143	GLU	-1	-0.891	-0.954	10.461	0.044	0.044	0.000	0.000	0.000	0.000
132	A	144	LEU	0	-0.021	-0.011	5.989	0.001	0.001	0.000	0.000	0.000	0.000
133	A	145	GLN	0	0.045	0.012	5.111	0.045	0.045	0.000	0.000	0.000	0.000
134	A	146	SER	0	0.017	-0.010	2.899	-1.971	-0.133	0.296	-0.957	-1.177	-0.004
135	A	147	ILE	0	0.001	0.010	4.153	-2.316	-2.159	0.001	-0.035	-0.123	0.000
136	A	148	ASN	0	-0.014	-0.003	3.791	1.296	1.916	0.010	-0.119	-0.510	0.000
137	A	149	PHE	0	0.037	0.004	6.707	-0.075	-0.075	0.000	0.000	0.000	0.000
138	A	150	LEU	0	0.003	0.009	8.653	-0.228	-0.228	0.000	0.000	0.000	0.000
139	A	151	GLY	0	0.064	0.033	11.462	0.050	0.050	0.000	0.000	0.000	0.000
140	A	152	GLY	0	0.025	0.005	13.342	0.070	0.070	0.000	0.000	0.000	0.000
141	A	153	GLN	0	0.028	-0.001	14.838	-0.017	-0.017	0.000	0.000	0.000	0.000
142	A	154	PRO	0	0.024	0.022	9.991	0.041	0.041	0.000	0.000	0.000	0.000
143	A	155	ALA	0	0.019	0.003	11.269	0.143	0.143	0.000	0.000	0.000	0.000
144	A	156	ALA	0	-0.025	-0.014	11.963	-0.089	-0.089	0.000	0.000	0.000	0.000
145	A	157	ALA	0	-0.048	-0.010	6.619	0.078	0.078	0.000	0.000	0.000	0.000
146	A	158	PRO	0	0.009	0.006	6.323	-0.203	-0.203	0.000	0.000	0.000	0.000
147	A	159	TYR	0	-0.015	-0.007	6.056	-0.005	-0.005	0.000	0.000	0.000	0.000

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