FMO DATABASE

FMODB ID: JLY49

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1446181.138539
FMO2-HF: Nuclear repulsion	1386779.867086
FMO2-HF: Total energy	-59401.271453
FMO2-MP2: Total energy	-59572.115733

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.
-9.561	-4.708	0.629	-1.916	-3.566	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 : -0.057 / q_NPA : -0.045

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	-0.063	-0.021	2.992	-2.807	-0.233	0.439	-1.119	-1.894	0.009
4	A	16	THR	0	0.001	0.009	4.804	-0.656	-0.582	-0.001	-0.012	-0.060	0.000
5	A	17	LEU	0	-0.040	-0.009	8.467	0.240	0.240	0.000	0.000	0.000	0.000
6	A	18	PRO	0	0.037	0.020	11.082	-0.151	-0.151	0.000	0.000	0.000	0.000
7	A	19	TYR	0	-0.026	-0.010	4.117	0.333	0.530	-0.001	-0.023	-0.173	0.000
8	A	20	LYS	1	0.837	0.904	9.578	-0.871	-0.871	0.000	0.000	0.000	0.000
9	A	21	ARG	1	0.888	0.960	4.520	-4.098	-3.904	-0.001	-0.006	-0.186	0.000
10	A	22	PRO	0	0.038	0.015	9.434	-0.158	-0.158	0.000	0.000	0.000	0.000
11	A	23	ILE	0	-0.010	-0.004	10.431	0.295	0.295	0.000	0.000	0.000	0.000
12	A	24	PRO	0	-0.057	-0.031	8.225	-0.148	-0.148	0.000	0.000	0.000	0.000
13	A	25	GLY	0	0.026	0.017	11.485	-0.079	-0.079	0.000	0.000	0.000	0.000
14	A	26	GLY	0	-0.024	0.002	14.680	-0.083	-0.083	0.000	0.000	0.000	0.000
15	A	27	LEU	0	0.007	-0.001	15.557	0.015	0.015	0.000	0.000	0.000	0.000
16	A	28	SER	0	0.006	-0.040	17.281	-0.065	-0.065	0.000	0.000	0.000	0.000
17	A	29	VAL	0	0.024	-0.010	19.026	0.011	0.011	0.000	0.000	0.000	0.000
18	A	30	GLY	0	-0.019	-0.006	20.104	-0.014	-0.014	0.000	0.000	0.000	0.000
19	A	31	MET	0	-0.064	0.029	13.430	-0.029	-0.029	0.000	0.000	0.000	0.000
20	A	32	SER	0	-0.023	-0.019	14.414	-0.034	-0.034	0.000	0.000	0.000	0.000
21	A	33	VAL	0	-0.031	-0.016	11.837	0.063	0.063	0.000	0.000	0.000	0.000
22	A	34	TYR	0	-0.070	-0.059	9.531	-0.086	-0.086	0.000	0.000	0.000	0.000
23	A	35	ILE	0	-0.005	-0.018	8.943	0.268	0.268	0.000	0.000	0.000	0.000
24	A	36	GLN	0	-0.003	0.013	7.585	-0.431	-0.431	0.000	0.000	0.000	0.000
25	A	37	GLY	0	0.058	0.014	7.855	0.332	0.332	0.000	0.000	0.000	0.000
26	A	38	MET	0	-0.007	0.013	10.024	-0.144	-0.144	0.000	0.000	0.000	0.000
27	A	39	ALA	0	0.015	0.020	13.186	0.069	0.069	0.000	0.000	0.000	0.000
28	A	40	LYS	1	0.939	0.993	14.699	-0.311	-0.311	0.000	0.000	0.000	0.000
29	A	41	GLU	-1	-0.888	-0.960	17.708	-0.041	-0.041	0.000	0.000	0.000	0.000
30	A	42	ASN	0	-0.048	-0.023	20.923	0.004	0.004	0.000	0.000	0.000	0.000
31	A	43	MET	0	-0.045	0.000	19.289	0.009	0.009	0.000	0.000	0.000	0.000
32	A	44	ARG	1	0.896	0.943	21.098	-0.134	-0.134	0.000	0.000	0.000	0.000
33	A	45	ARG	1	0.803	0.888	21.257	-0.212	-0.212	0.000	0.000	0.000	0.000
34	A	46	PHE	0	0.026	0.025	15.513	0.005	0.005	0.000	0.000	0.000	0.000
35	A	47	HIS	0	-0.033	-0.010	16.772	-0.099	-0.099	0.000	0.000	0.000	0.000
36	A	48	VAL	0	0.001	0.008	13.666	0.104	0.104	0.000	0.000	0.000	0.000
37	A	49	ASN	0	0.003	0.002	15.369	-0.160	-0.160	0.000	0.000	0.000	0.000
38	A	50	PHE	0	0.046	0.036	15.690	0.146	0.146	0.000	0.000	0.000	0.000
39	A	51	ALA	0	0.024	-0.008	16.884	-0.090	-0.090	0.000	0.000	0.000	0.000
40	A	52	VAL	0	0.018	0.000	18.336	0.045	0.045	0.000	0.000	0.000	0.000
41	A	53	GLY	0	0.028	0.020	19.392	-0.039	-0.039	0.000	0.000	0.000	0.000
42	A	54	GLN	0	-0.019	-0.008	15.707	0.001	0.001	0.000	0.000	0.000	0.000
43	A	55	ASP	-1	-0.837	-0.922	17.169	0.477	0.477	0.000	0.000	0.000	0.000
44	A	56	ASP	-1	-0.895	-0.969	17.460	0.623	0.623	0.000	0.000	0.000	0.000
45	A	57	GLY	0	-0.040	0.002	20.084	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	58	ALA	0	-0.044	0.001	20.391	-0.025	-0.025	0.000	0.000	0.000	0.000
47	A	59	ASP	-1	-0.756	-0.866	22.538	0.304	0.304	0.000	0.000	0.000	0.000
48	A	60	VAL	0	-0.049	-0.035	20.206	0.058	0.058	0.000	0.000	0.000	0.000
49	A	61	ALA	0	0.032	0.021	21.638	-0.043	-0.043	0.000	0.000	0.000	0.000
50	A	62	PHE	0	-0.040	-0.017	20.221	-0.047	-0.047	0.000	0.000	0.000	0.000
51	A	63	HIS	0	-0.029	-0.008	20.038	0.026	0.026	0.000	0.000	0.000	0.000
52	A	64	PHE	0	0.024	0.005	17.600	-0.062	-0.062	0.000	0.000	0.000	0.000
53	A	65	ASN	0	0.034	-0.006	19.148	0.011	0.011	0.000	0.000	0.000	0.000
54	A	66	PRO	0	0.033	0.020	18.813	-0.049	-0.049	0.000	0.000	0.000	0.000
55	A	67	ARG	1	0.802	0.883	21.823	-0.230	-0.230	0.000	0.000	0.000	0.000
56	A	68	PHE	0	-0.011	-0.029	21.722	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	69	ASP	-1	-0.776	-0.886	25.784	0.131	0.131	0.000	0.000	0.000	0.000
58	A	70	GLY	0	-0.024	0.005	29.286	0.004	0.004	0.000	0.000	0.000	0.000
59	A	71	TRP	0	0.012	-0.014	31.939	-0.006	-0.006	0.000	0.000	0.000	0.000
60	A	72	ASP	-1	-0.836	-0.919	26.906	0.111	0.111	0.000	0.000	0.000	0.000
61	A	73	LYS	1	0.834	0.925	26.851	-0.172	-0.172	0.000	0.000	0.000	0.000
62	A	74	VAL	0	0.002	0.009	22.275	0.015	0.015	0.000	0.000	0.000	0.000
63	A	75	VAL	0	-0.072	-0.031	24.375	-0.022	-0.022	0.000	0.000	0.000	0.000
64	A	76	PHE	0	0.028	0.012	23.011	0.030	0.030	0.000	0.000	0.000	0.000
65	A	77	ASN	0	-0.014	-0.015	24.813	-0.029	-0.029	0.000	0.000	0.000	0.000
66	A	78	THR	0	-0.001	0.004	24.849	0.022	0.022	0.000	0.000	0.000	0.000
67	A	79	MET	0	-0.037	-0.001	24.904	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	80	GLN	0	0.018	-0.001	26.278	0.020	0.020	0.000	0.000	0.000	0.000
69	A	81	SER	0	-0.038	-0.041	28.772	-0.024	-0.024	0.000	0.000	0.000	0.000
70	A	82	GLY	0	0.025	0.016	28.311	-0.017	-0.017	0.000	0.000	0.000	0.000
71	A	83	GLN	0	-0.022	-0.007	29.338	-0.004	-0.004	0.000	0.000	0.000	0.000
72	A	84	TRP	0	-0.007	0.005	22.940	0.010	0.010	0.000	0.000	0.000	0.000
73	A	85	GLY	0	0.031	0.021	29.669	-0.018	-0.018	0.000	0.000	0.000	0.000
74	A	86	LYS	1	0.952	0.967	31.737	-0.140	-0.140	0.000	0.000	0.000	0.000
75	A	87	GLU	-1	-0.764	-0.867	29.139	0.193	0.193	0.000	0.000	0.000	0.000
76	A	88	GLU	-1	-0.813	-0.863	28.854	0.181	0.181	0.000	0.000	0.000	0.000
77	A	89	LYS	1	0.826	0.878	28.221	-0.138	-0.138	0.000	0.000	0.000	0.000
78	A	90	LYS	1	0.881	0.958	26.921	-0.141	-0.141	0.000	0.000	0.000	0.000
79	A	91	LYS	1	0.850	0.945	28.096	-0.087	-0.087	0.000	0.000	0.000	0.000
80	A	92	SER	0	0.006	-0.006	27.668	-0.012	-0.012	0.000	0.000	0.000	0.000
81	A	93	MET	0	0.038	0.021	22.965	0.027	0.027	0.000	0.000	0.000	0.000
82	A	94	PRO	0	-0.028	0.003	20.921	-0.017	-0.017	0.000	0.000	0.000	0.000
83	A	95	PHE	0	0.010	0.006	16.184	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	96	GLN	0	0.028	-0.003	19.566	-0.024	-0.024	0.000	0.000	0.000	0.000
85	A	97	LYS	1	0.887	0.945	19.560	-0.097	-0.097	0.000	0.000	0.000	0.000
86	A	98	GLY	0	0.051	0.020	18.346	-0.020	-0.020	0.000	0.000	0.000	0.000
87	A	99	LYS	1	0.881	0.964	17.948	0.023	0.023	0.000	0.000	0.000	0.000
88	A	100	HIS	0	-0.025	-0.013	10.283	0.007	0.007	0.000	0.000	0.000	0.000
89	A	101	PHE	0	-0.040	-0.027	12.780	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	102	GLU	-1	-0.779	-0.869	12.618	-0.114	-0.114	0.000	0.000	0.000	0.000
91	A	103	LEU	0	-0.065	-0.027	12.886	-0.038	-0.038	0.000	0.000	0.000	0.000
92	A	104	VAL	0	0.027	0.021	13.351	0.095	0.095	0.000	0.000	0.000	0.000
93	A	105	PHE	0	0.016	0.003	14.669	-0.042	-0.042	0.000	0.000	0.000	0.000
94	A	106	MET	0	0.006	0.007	16.457	0.010	0.010	0.000	0.000	0.000	0.000
95	A	107	VAL	0	0.013	0.006	18.026	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	108	MET	0	0.018	0.021	20.651	-0.031	-0.031	0.000	0.000	0.000	0.000
97	A	109	PRO	0	0.002	-0.019	24.048	0.019	0.019	0.000	0.000	0.000	0.000
98	A	110	GLU	-1	-0.916	-0.947	26.807	0.137	0.137	0.000	0.000	0.000	0.000
99	A	111	HIS	0	-0.007	-0.023	25.474	0.007	0.007	0.000	0.000	0.000	0.000
100	A	112	TYR	0	-0.005	0.013	19.940	0.023	0.023	0.000	0.000	0.000	0.000
101	A	113	LYS	1	0.871	0.915	21.823	-0.143	-0.143	0.000	0.000	0.000	0.000
102	A	114	VAL	0	-0.046	-0.022	18.877	0.026	0.026	0.000	0.000	0.000	0.000
103	A	115	VAL	0	0.004	-0.002	19.203	-0.041	-0.041	0.000	0.000	0.000	0.000
104	A	116	VAL	0	0.002	0.001	17.578	0.031	0.031	0.000	0.000	0.000	0.000
105	A	117	ASN	0	0.035	0.009	17.207	-0.018	-0.018	0.000	0.000	0.000	0.000
106	A	118	GLY	0	0.044	0.031	18.668	-0.026	-0.026	0.000	0.000	0.000	0.000
107	A	119	ASN	0	-0.041	-0.016	20.670	-0.011	-0.011	0.000	0.000	0.000	0.000
108	A	120	SER	0	0.001	-0.008	22.663	0.029	0.029	0.000	0.000	0.000	0.000
109	A	121	PHE	0	-0.028	-0.027	22.534	-0.009	-0.009	0.000	0.000	0.000	0.000
110	A	122	TYR	0	-0.048	-0.058	24.044	-0.017	-0.017	0.000	0.000	0.000	0.000
111	A	123	GLU	-1	-0.771	-0.857	24.495	0.150	0.150	0.000	0.000	0.000	0.000
112	A	124	TYR	0	-0.026	-0.023	24.481	-0.015	-0.015	0.000	0.000	0.000	0.000
113	A	125	GLY	0	0.060	0.030	26.202	0.013	0.013	0.000	0.000	0.000	0.000
114	A	126	HIS	0	-0.056	-0.026	23.453	0.029	0.029	0.000	0.000	0.000	0.000
115	A	127	ARG	1	0.794	0.878	27.382	-0.241	-0.241	0.000	0.000	0.000	0.000
116	A	128	LEU	0	0.027	0.016	24.906	-0.009	-0.009	0.000	0.000	0.000	0.000
117	A	129	PRO	0	-0.006	-0.011	26.286	0.008	0.008	0.000	0.000	0.000	0.000
118	A	130	VAL	0	0.048	0.023	20.929	0.026	0.026	0.000	0.000	0.000	0.000
119	A	131	GLN	0	0.015	-0.007	21.303	0.047	0.047	0.000	0.000	0.000	0.000
120	A	132	MET	0	-0.023	0.007	21.883	0.003	0.003	0.000	0.000	0.000	0.000
121	A	133	VAL	0	-0.046	-0.014	17.237	0.028	0.028	0.000	0.000	0.000	0.000
122	A	134	THR	0	-0.006	0.004	17.094	0.035	0.035	0.000	0.000	0.000	0.000
123	A	135	HIS	0	-0.029	-0.025	13.068	0.169	0.169	0.000	0.000	0.000	0.000
124	A	136	LEU	0	0.016	0.021	10.737	-0.112	-0.112	0.000	0.000	0.000	0.000
125	A	137	GLN	0	-0.006	-0.007	11.464	0.170	0.170	0.000	0.000	0.000	0.000
126	A	138	VAL	0	-0.004	0.000	10.429	-0.126	-0.126	0.000	0.000	0.000	0.000
127	A	139	ASP	-1	-0.792	-0.917	12.240	0.675	0.675	0.000	0.000	0.000	0.000
128	A	140	GLY	0	0.034	0.020	14.370	-0.058	-0.058	0.000	0.000	0.000	0.000
129	A	141	ASP	-1	-0.781	-0.899	15.612	0.241	0.241	0.000	0.000	0.000	0.000
130	A	142	LEU	0	-0.054	-0.042	11.352	-0.042	-0.042	0.000	0.000	0.000	0.000
131	A	143	GLU	-1	-0.904	-0.948	10.567	-0.022	-0.022	0.000	0.000	0.000	0.000
132	A	144	LEU	0	-0.033	-0.021	5.959	-0.040	-0.040	0.000	0.000	0.000	0.000
133	A	145	GLN	0	0.027	0.009	5.201	-0.026	-0.026	0.000	0.000	0.000	0.000
134	A	146	SER	0	0.026	-0.013	3.137	-1.576	-0.220	0.194	-0.711	-0.839	-0.004
135	A	147	ILE	0	0.009	0.015	4.169	-1.257	-1.142	0.000	-0.024	-0.092	0.000
136	A	148	ASN	0	-0.022	-0.009	4.303	0.901	1.244	-0.001	-0.021	-0.322	0.000
137	A	149	PHE	0	0.032	0.010	7.124	0.004	0.004	0.000	0.000	0.000	0.000
138	A	150	LEU	0	0.016	0.013	9.052	-0.247	-0.247	0.000	0.000	0.000	0.000
139	A	151	GLY	0	0.052	0.026	11.792	0.062	0.062	0.000	0.000	0.000	0.000
140	A	152	GLY	0	0.040	0.011	13.710	0.061	0.061	0.000	0.000	0.000	0.000
141	A	153	GLN	0	0.013	-0.003	15.194	-0.009	-0.009	0.000	0.000	0.000	0.000
142	A	154	PRO	0	0.031	0.018	10.504	0.054	0.054	0.000	0.000	0.000	0.000
143	A	155	ALA	0	0.013	0.000	11.609	0.134	0.134	0.000	0.000	0.000	0.000
144	A	156	ALA	0	-0.022	-0.006	12.070	-0.050	-0.050	0.000	0.000	0.000	0.000
145	A	157	ALA	0	-0.045	-0.013	7.142	0.106	0.106	0.000	0.000	0.000	0.000
146	A	158	PRO	0	0.010	0.009	6.041	-0.214	-0.214	0.000	0.000	0.000	0.000
147	A	159	TYR	0	-0.004	-0.003	6.151	-0.118	-0.118	0.000	0.000	0.000	0.000

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