FMO DATABASE

FMODB ID: 5353Z

Calculation Name: 3BCY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BCY

Chain ID: A

ChEMBL ID:

UniProt ID: P40043

Base Structure: X-ray

Registration Date: 2023-03-14

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	146
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1459639.776357
FMO2-HF: Nuclear repulsion	1399492.654293
FMO2-HF: Total energy	-60147.122065
FMO2-MP2: Total energy	-60324.876313

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:16:THR)

Summations of interaction energy for fragment #1(A:16:THR)

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.
-6.845	-1.296	4.834	-3.509	-6.872	-0.014

Interaction energy analysis for fragmet #1(A:16:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.025 / q_NPA : -0.013

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	18	ASP	-1	-0.892	-0.961	3.807	-4.982	-2.670	-0.014	-1.169	-1.129	0.005
4	A	19	GLY	0	-0.055	-0.017	6.013	0.552	0.552	0.000	0.000	0.000	0.000
5	A	20	GLU	-1	-1.016	-1.023	8.851	-0.609	-0.609	0.000	0.000	0.000	0.000
6	A	21	THR	0	0.021	0.012	10.458	0.035	0.035	0.000	0.000	0.000	0.000
7	A	22	VAL	0	-0.075	-0.019	8.187	0.269	0.269	0.000	0.000	0.000	0.000
8	A	23	LYS	1	1.001	1.023	4.040	-1.099	-0.876	0.000	-0.031	-0.190	0.000
9	A	24	VAL	0	-0.043	-0.039	3.588	1.150	1.532	0.001	-0.076	-0.307	0.000
10	A	25	PHE	0	-0.012	-0.011	2.275	-5.068	-2.885	4.764	-2.394	-4.553	-0.019
11	A	26	GLU	-1	-0.870	-0.947	2.816	-0.292	-0.027	0.086	0.188	-0.539	0.000
12	A	27	ASP	-1	-0.905	-0.951	4.640	3.228	3.342	-0.001	-0.013	-0.101	0.000
13	A	28	LEU	0	-0.003	-0.022	6.358	0.228	0.228	0.000	0.000	0.000	0.000
14	A	29	GLN	0	-0.004	0.017	8.420	-0.209	-0.209	0.000	0.000	0.000	0.000
15	A	30	GLY	0	0.017	0.017	4.274	-0.156	-0.097	-0.001	-0.012	-0.046	0.000
16	A	31	PHE	0	0.013	-0.003	5.260	-0.204	-0.193	-0.001	-0.002	-0.007	0.000
17	A	32	GLU	-1	-0.901	-0.946	6.703	0.726	0.726	0.000	0.000	0.000	0.000
18	A	33	THR	0	0.012	-0.016	7.870	-0.227	-0.227	0.000	0.000	0.000	0.000
19	A	34	PHE	0	-0.034	-0.015	6.326	-0.139	-0.139	0.000	0.000	0.000	0.000
20	A	35	ILE	0	0.012	0.005	8.367	-0.311	-0.311	0.000	0.000	0.000	0.000
21	A	36	ALA	0	0.001	0.016	11.514	-0.161	-0.161	0.000	0.000	0.000	0.000
22	A	37	ASN	0	-0.034	-0.033	10.936	-0.168	-0.168	0.000	0.000	0.000	0.000
23	A	38	GLU	-1	-0.826	-0.923	10.699	0.428	0.428	0.000	0.000	0.000	0.000
24	A	39	THR	0	-0.089	-0.052	13.859	-0.139	-0.139	0.000	0.000	0.000	0.000
25	A	40	GLU	-1	-0.927	-0.947	16.320	0.330	0.330	0.000	0.000	0.000	0.000
26	A	41	ASP	-1	-0.969	-0.972	14.822	0.444	0.444	0.000	0.000	0.000	0.000
27	A	42	ASP	-1	-0.895	-0.937	17.790	0.105	0.105	0.000	0.000	0.000	0.000
28	A	43	ASP	-1	-0.811	-0.904	15.702	0.093	0.093	0.000	0.000	0.000	0.000
29	A	44	PHE	0	-0.033	-0.028	16.824	-0.020	-0.020	0.000	0.000	0.000	0.000
30	A	45	ASP	-1	-0.882	-0.894	17.874	0.083	0.083	0.000	0.000	0.000	0.000
31	A	46	HIS	0	-0.034	-0.024	17.771	-0.071	-0.071	0.000	0.000	0.000	0.000
32	A	47	LEU	0	0.031	0.046	12.965	-0.006	-0.006	0.000	0.000	0.000	0.000
33	A	48	HIS	0	-0.013	-0.043	12.135	-0.089	-0.089	0.000	0.000	0.000	0.000
34	A	49	CYS	0	-0.062	0.011	7.248	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	50	LYS	1	0.896	0.915	7.040	0.533	0.533	0.000	0.000	0.000	0.000
36	A	51	LEU	0	-0.020	0.007	6.433	0.203	0.203	0.000	0.000	0.000	0.000
37	A	52	ASN	0	0.006	0.004	7.127	-0.042	-0.042	0.000	0.000	0.000	0.000
38	A	53	TYR	0	0.025	-0.005	7.917	0.155	0.155	0.000	0.000	0.000	0.000
39	A	54	TYR	0	0.025	0.015	10.268	-0.095	-0.095	0.000	0.000	0.000	0.000
40	A	55	PRO	0	-0.014	0.002	13.509	0.094	0.094	0.000	0.000	0.000	0.000
41	A	56	PRO	0	0.055	0.007	14.947	-0.034	-0.034	0.000	0.000	0.000	0.000
42	A	57	PHE	0	-0.034	-0.026	16.982	-0.022	-0.022	0.000	0.000	0.000	0.000
43	A	58	VAL	0	0.050	0.030	17.476	-0.020	-0.020	0.000	0.000	0.000	0.000
44	A	59	LEU	0	0.044	0.038	13.881	-0.026	-0.026	0.000	0.000	0.000	0.000
45	A	60	HIS	1	0.796	0.860	18.549	-0.401	-0.401	0.000	0.000	0.000	0.000
46	A	61	GLU	-1	-0.919	-0.951	21.388	0.138	0.138	0.000	0.000	0.000	0.000
47	A	62	SER	0	-0.017	-0.009	20.799	-0.036	-0.036	0.000	0.000	0.000	0.000
48	A	63	HIS	0	-0.060	-0.035	21.874	0.004	0.004	0.000	0.000	0.000	0.000
49	A	64	GLU	-1	-0.856	-0.900	18.233	0.372	0.372	0.000	0.000	0.000	0.000
50	A	65	ASP	-1	-0.791	-0.881	17.933	0.166	0.166	0.000	0.000	0.000	0.000
51	A	66	PRO	0	0.043	0.005	14.359	-0.022	-0.022	0.000	0.000	0.000	0.000
52	A	67	GLU	-1	-0.938	-0.956	17.413	-0.052	-0.052	0.000	0.000	0.000	0.000
53	A	68	LYS	1	0.756	0.864	19.991	-0.146	-0.146	0.000	0.000	0.000	0.000
54	A	69	ILE	0	-0.050	-0.008	17.445	0.013	0.013	0.000	0.000	0.000	0.000
55	A	70	SER	0	-0.032	-0.012	21.921	-0.028	-0.028	0.000	0.000	0.000	0.000
56	A	71	ASP	-1	-0.800	-0.907	23.925	-0.028	-0.028	0.000	0.000	0.000	0.000
57	A	72	ALA	0	-0.098	-0.048	25.424	-0.008	-0.008	0.000	0.000	0.000	0.000
58	A	73	ALA	0	-0.078	-0.038	22.411	0.006	0.006	0.000	0.000	0.000	0.000
59	A	74	ASN	0	0.114	0.062	22.070	-0.007	-0.007	0.000	0.000	0.000	0.000
60	A	75	SER	0	0.018	-0.011	22.946	0.018	0.018	0.000	0.000	0.000	0.000
61	A	76	HIS	1	0.786	0.878	24.316	0.045	0.045	0.000	0.000	0.000	0.000
62	A	77	SER	0	-0.018	0.021	26.138	0.006	0.006	0.000	0.000	0.000	0.000
63	A	78	LYS	1	0.933	0.948	26.884	-0.013	-0.013	0.000	0.000	0.000	0.000
64	A	79	LYS	1	0.833	0.905	26.886	-0.128	-0.128	0.000	0.000	0.000	0.000
65	A	80	PHE	0	0.039	0.027	18.818	0.018	0.018	0.000	0.000	0.000	0.000
66	A	81	VAL	0	0.055	0.029	23.074	0.019	0.019	0.000	0.000	0.000	0.000
67	A	82	ARG	1	0.914	0.964	24.003	-0.088	-0.088	0.000	0.000	0.000	0.000
68	A	83	HIS	0	-0.033	-0.020	23.183	0.004	0.004	0.000	0.000	0.000	0.000
69	A	84	LEU	0	0.050	0.040	17.334	0.033	0.033	0.000	0.000	0.000	0.000
70	A	85	HIS	0	-0.058	-0.034	20.331	0.020	0.020	0.000	0.000	0.000	0.000
71	A	86	GLN	0	-0.034	-0.031	22.441	0.019	0.019	0.000	0.000	0.000	0.000
72	A	87	HIS	0	0.013	0.026	15.342	0.042	0.042	0.000	0.000	0.000	0.000
73	A	88	ILE	0	0.065	0.023	17.622	0.045	0.045	0.000	0.000	0.000	0.000
74	A	89	GLU	-1	-0.795	-0.877	19.056	0.205	0.205	0.000	0.000	0.000	0.000
75	A	90	LYS	1	0.847	0.937	21.414	-0.238	-0.238	0.000	0.000	0.000	0.000
76	A	91	HIS	0	-0.025	-0.023	16.616	0.040	0.040	0.000	0.000	0.000	0.000
77	A	92	LEU	0	0.085	0.067	12.833	0.027	0.027	0.000	0.000	0.000	0.000
78	A	93	LEU	0	0.015	-0.004	15.616	0.032	0.032	0.000	0.000	0.000	0.000
79	A	94	LYS	1	0.770	0.889	16.497	-0.589	-0.589	0.000	0.000	0.000	0.000
80	A	95	ASP	-1	-0.793	-0.902	13.414	0.730	0.730	0.000	0.000	0.000	0.000
81	A	96	ILE	0	0.040	0.028	13.678	0.016	0.016	0.000	0.000	0.000	0.000
82	A	97	LYS	1	0.855	0.932	15.512	-0.279	-0.279	0.000	0.000	0.000	0.000
83	A	98	GLN	0	-0.119	-0.070	15.553	-0.094	-0.094	0.000	0.000	0.000	0.000
84	A	99	ALA	0	0.037	0.032	13.609	-0.027	-0.027	0.000	0.000	0.000	0.000
85	A	100	VAL	0	-0.016	-0.010	15.552	-0.025	-0.025	0.000	0.000	0.000	0.000
86	A	101	ARG	1	0.792	0.888	17.642	-0.499	-0.499	0.000	0.000	0.000	0.000
87	A	102	LYS	1	0.820	0.902	20.804	-0.255	-0.255	0.000	0.000	0.000	0.000
88	A	103	PRO	0	0.051	0.025	22.374	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	104	GLU	-1	-0.907	-0.970	23.326	0.205	0.205	0.000	0.000	0.000	0.000
90	A	105	LEU	0	-0.021	0.016	21.927	-0.023	-0.023	0.000	0.000	0.000	0.000
91	A	106	LYS	1	0.799	0.887	24.954	-0.177	-0.177	0.000	0.000	0.000	0.000
92	A	107	PHE	0	0.069	0.040	19.483	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	108	HIS	0	-0.067	-0.059	25.410	-0.009	-0.009	0.000	0.000	0.000	0.000
94	A	109	GLU	-1	-0.833	-0.876	26.048	0.025	0.025	0.000	0.000	0.000	0.000
95	A	110	LYS	1	0.891	0.927	25.544	-0.111	-0.111	0.000	0.000	0.000	0.000
96	A	111	SER	0	-0.032	-0.006	25.555	-0.015	-0.015	0.000	0.000	0.000	0.000
97	A	112	LYS	1	0.877	0.927	25.226	-0.027	-0.027	0.000	0.000	0.000	0.000
98	A	113	GLU	-1	-0.873	-0.905	25.362	-0.082	-0.082	0.000	0.000	0.000	0.000
99	A	114	GLU	-1	-0.866	-0.946	25.666	0.014	0.014	0.000	0.000	0.000	0.000
100	A	115	THR	0	-0.009	-0.004	25.978	-0.009	-0.009	0.000	0.000	0.000	0.000
101	A	116	PHE	0	-0.016	-0.015	27.938	0.014	0.014	0.000	0.000	0.000	0.000
102	A	117	ASP	-1	-0.805	-0.902	24.510	-0.114	-0.114	0.000	0.000	0.000	0.000
103	A	118	LYS	1	0.848	0.928	21.564	0.111	0.111	0.000	0.000	0.000	0.000
104	A	119	ILE	0	-0.059	-0.026	22.508	0.011	0.011	0.000	0.000	0.000	0.000
105	A	120	THR	0	0.016	0.018	20.168	-0.012	-0.012	0.000	0.000	0.000	0.000
106	A	121	TRP	0	-0.006	-0.015	20.510	0.002	0.002	0.000	0.000	0.000	0.000
107	A	122	HIS	0	-0.058	-0.031	20.409	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	123	TYR	0	-0.079	-0.068	20.267	0.007	0.007	0.000	0.000	0.000	0.000
109	A	124	GLY	0	0.033	0.019	21.177	0.003	0.003	0.000	0.000	0.000	0.000
110	A	125	GLU	-1	-0.834	-0.927	23.205	0.127	0.127	0.000	0.000	0.000	0.000
111	A	126	GLU	-1	-0.926	-0.948	23.907	0.040	0.040	0.000	0.000	0.000	0.000
112	A	127	THR	0	-0.015	-0.015	23.075	0.016	0.016	0.000	0.000	0.000	0.000
113	A	128	GLU	-1	-0.921	-0.962	25.910	0.094	0.094	0.000	0.000	0.000	0.000
114	A	129	TYR	0	-0.022	0.004	21.660	0.024	0.024	0.000	0.000	0.000	0.000
115	A	130	HIS	0	0.027	0.022	23.727	-0.023	-0.023	0.000	0.000	0.000	0.000
116	A	131	GLY	0	0.001	0.012	26.706	-0.012	-0.012	0.000	0.000	0.000	0.000
117	A	132	ARG	1	0.731	0.818	21.820	-0.133	-0.133	0.000	0.000	0.000	0.000
118	A	133	PRO	0	0.023	0.008	25.945	0.018	0.018	0.000	0.000	0.000	0.000
119	A	134	PHE	0	-0.012	-0.024	19.620	-0.010	-0.010	0.000	0.000	0.000	0.000
120	A	135	LYS	1	0.764	0.864	22.613	-0.028	-0.028	0.000	0.000	0.000	0.000
121	A	136	ILE	0	0.003	0.004	17.922	0.001	0.001	0.000	0.000	0.000	0.000
122	A	137	ASP	-1	-0.800	-0.902	18.729	0.010	0.010	0.000	0.000	0.000	0.000
123	A	138	VAL	0	0.006	0.001	15.446	0.010	0.010	0.000	0.000	0.000	0.000
124	A	139	GLN	0	-0.017	-0.011	16.211	-0.044	-0.044	0.000	0.000	0.000	0.000
125	A	140	VAL	0	-0.002	-0.004	15.624	0.018	0.018	0.000	0.000	0.000	0.000
126	A	141	VAL	0	0.007	0.001	16.235	-0.009	-0.009	0.000	0.000	0.000	0.000
127	A	142	CYS	0	-0.033	0.002	16.893	0.019	0.019	0.000	0.000	0.000	0.000
128	A	143	THR	0	0.046	-0.022	18.520	0.000	0.000	0.000	0.000	0.000	0.000
129	A	144	HIS	0	-0.033	-0.006	21.141	0.025	0.025	0.000	0.000	0.000	0.000
130	A	145	GLU	-1	-0.853	-0.927	20.166	-0.149	-0.149	0.000	0.000	0.000	0.000
131	A	146	ASP	-1	-0.799	-0.904	16.730	-0.106	-0.106	0.000	0.000	0.000	0.000
132	A	147	ALA	0	-0.021	0.001	18.297	0.012	0.012	0.000	0.000	0.000	0.000
133	A	148	MET	0	-0.033	-0.007	10.982	0.022	0.022	0.000	0.000	0.000	0.000
134	A	149	VAL	0	-0.092	-0.051	13.576	-0.022	-0.022	0.000	0.000	0.000	0.000
135	A	150	PHE	0	0.015	-0.001	11.817	0.028	0.028	0.000	0.000	0.000	0.000
136	A	151	VAL	0	-0.009	-0.010	11.320	0.003	0.003	0.000	0.000	0.000	0.000
137	A	152	ASP	-1	-0.839	-0.889	10.960	-0.329	-0.329	0.000	0.000	0.000	0.000
138	A	153	TYR	0	0.041	0.015	11.810	0.053	0.053	0.000	0.000	0.000	0.000
139	A	154	LYS	1	0.925	0.944	12.887	0.202	0.202	0.000	0.000	0.000	0.000
140	A	155	THR	0	-0.044	-0.036	15.564	0.011	0.011	0.000	0.000	0.000	0.000
141	A	156	HIS	1	0.867	0.952	18.306	-0.029	-0.029	0.000	0.000	0.000	0.000
142	A	157	PRO	0	0.061	0.033	21.147	0.017	0.017	0.000	0.000	0.000	0.000
143	A	158	VAL	0	-0.046	-0.011	24.527	-0.017	-0.017	0.000	0.000	0.000	0.000
144	A	159	GLY	0	-0.005	-0.004	27.566	0.004	0.004	0.000	0.000	0.000	0.000
145	A	160	ALA	0	-0.006	0.006	27.936	0.002	0.002	0.000	0.000	0.000	0.000
146	A	161	ASN	0	-0.030	-0.014	29.909	-0.011	-0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:16:THR)