FMO DATABASE

FMODB ID: 4365N

Calculation Name: 2DBO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DBO

Chain ID: A

ChEMBL ID:

UniProt ID: O66742

Base Structure: X-ray

Registration Date: 2023-03-13

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	148
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1442814.127207
FMO2-HF: Nuclear repulsion	1384086.770203
FMO2-HF: Total energy	-58727.357004
FMO2-MP2: Total energy	-58901.195592

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:1:MET)

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

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.
-33.689	-26.583	46.836	-20.692	-33.249	-0.099

Interaction energy analysis for fragmet #1(A:1:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.063 / q_NPA : -0.038

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	3	ALA	0	0.028	0.002	3.859	-1.282	0.397	-0.016	-0.794	-0.869	0.003
4	A	4	VAL	0	-0.046	-0.021	5.778	0.105	0.105	0.000	0.000	0.000	0.000
5	A	5	ILE	0	0.002	0.004	9.103	0.063	0.063	0.000	0.000	0.000	0.000
6	A	6	GLN	0	-0.009	-0.004	11.447	-0.052	-0.052	0.000	0.000	0.000	0.000
7	A	7	ARG	1	0.815	0.888	15.184	-0.099	-0.099	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.059	-0.022	17.714	-0.016	-0.016	0.000	0.000	0.000	0.000
9	A	9	LYS	1	0.914	0.940	20.014	-0.099	-0.099	0.000	0.000	0.000	0.000
10	A	10	LYS	1	0.934	0.982	22.406	-0.127	-0.127	0.000	0.000	0.000	0.000
11	A	11	SER	0	-0.051	-0.037	17.860	0.011	0.011	0.000	0.000	0.000	0.000
12	A	12	TRP	0	-0.009	-0.018	19.615	0.010	0.010	0.000	0.000	0.000	0.000
13	A	13	VAL	0	0.019	0.019	15.702	0.000	0.000	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.860	-0.934	19.138	0.091	0.091	0.000	0.000	0.000	0.000
15	A	15	VAL	0	0.016	0.004	20.066	0.001	0.001	0.000	0.000	0.000	0.000
16	A	16	ASP	-1	-0.867	-0.921	22.871	0.049	0.049	0.000	0.000	0.000	0.000
17	A	17	GLY	0	0.025	0.031	25.890	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.797	0.889	24.635	-0.066	-0.066	0.000	0.000	0.000	0.000
19	A	19	VAL	0	-0.006	-0.019	22.533	0.005	0.005	0.000	0.000	0.000	0.000
20	A	20	VAL	0	-0.056	-0.036	18.744	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	21	GLY	0	0.043	0.036	18.605	0.015	0.015	0.000	0.000	0.000	0.000
22	A	22	SER	0	-0.042	-0.050	19.687	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	23	ILE	0	-0.068	-0.007	16.849	0.001	0.001	0.000	0.000	0.000	0.000
24	A	24	ASN	0	-0.063	-0.050	20.792	-0.022	-0.022	0.000	0.000	0.000	0.000
25	A	25	GLU	-1	-0.905	-0.958	21.452	0.137	0.137	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.030	0.009	18.583	0.008	0.008	0.000	0.000	0.000	0.000
27	A	27	LEU	0	-0.036	-0.010	12.949	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	28	ASN	0	0.005	0.002	13.428	0.052	0.052	0.000	0.000	0.000	0.000
29	A	29	VAL	0	0.004	-0.013	7.545	-0.026	-0.026	0.000	0.000	0.000	0.000
30	A	30	PHE	0	0.050	0.028	8.994	0.106	0.106	0.000	0.000	0.000	0.000
31	A	31	LEU	0	0.016	0.003	2.487	-1.789	-0.955	1.415	-0.419	-1.830	0.001
32	A	32	GLY	0	0.006	0.002	4.256	0.042	0.239	-0.001	-0.032	-0.164	0.000
33	A	33	VAL	0	-0.013	0.002	2.283	-3.737	-0.722	2.155	-1.941	-3.230	-0.009
34	A	34	ARG	1	0.812	0.890	2.888	-1.156	0.045	0.207	-0.174	-1.234	0.000
35	A	35	LYS	1	0.804	0.875	4.462	-1.080	-0.989	-0.001	-0.005	-0.085	0.000
36	A	36	GLY	0	-0.009	0.007	6.382	0.406	0.406	0.000	0.000	0.000	0.000
37	A	37	ASP	-1	-0.707	-0.824	1.735	-16.854	-23.183	22.683	-8.158	-8.196	-0.080
38	A	38	THR	0	-0.058	-0.059	3.693	1.256	1.611	0.002	-0.109	-0.249	0.000
39	A	39	GLU	-1	-0.763	-0.878	3.685	-1.806	-1.452	0.010	-0.120	-0.244	-0.001
40	A	40	GLU	-1	-0.857	-0.917	6.209	-0.445	-0.445	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.808	-0.861	2.655	-4.834	-3.628	0.553	-0.478	-1.282	0.001
42	A	42	ILE	0	0.042	0.030	2.402	0.106	1.222	2.454	-0.816	-2.753	-0.003
43	A	43	GLU	-1	-0.825	-0.904	4.439	0.331	0.337	0.008	0.157	-0.171	0.000
44	A	44	LYS	1	0.744	0.853	5.609	1.536	1.536	0.000	0.000	0.000	0.000
45	A	45	LEU	0	-0.015	-0.003	2.567	-1.464	-0.373	1.295	-0.483	-1.904	-0.002
46	A	46	VAL	0	0.035	0.011	5.696	-0.230	-0.230	0.000	0.000	0.000	0.000
47	A	47	ASN	0	0.029	0.018	8.063	-0.236	-0.236	0.000	0.000	0.000	0.000
48	A	48	LYS	1	0.918	0.966	9.107	-0.087	-0.087	0.000	0.000	0.000	0.000
49	A	49	ILE	0	-0.009	-0.014	7.606	-0.083	-0.083	0.000	0.000	0.000	0.000
50	A	50	LEU	0	0.005	0.003	10.959	-0.059	-0.059	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.024	-0.019	13.802	-0.068	-0.068	0.000	0.000	0.000	0.000
52	A	52	LEU	0	-0.025	-0.016	12.004	-0.045	-0.045	0.000	0.000	0.000	0.000
53	A	53	ARG	1	0.805	0.900	15.670	-0.103	-0.103	0.000	0.000	0.000	0.000
54	A	54	ILE	0	0.009	0.006	15.471	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	55	PHE	0	0.017	0.011	17.470	-0.004	-0.004	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.831	-0.892	22.016	0.083	0.083	0.000	0.000	0.000	0.000
57	A	57	ASP	-1	-0.730	-0.847	25.770	0.077	0.077	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.894	-0.941	29.408	0.062	0.062	0.000	0.000	0.000	0.000
59	A	59	ARG	1	0.809	0.901	31.622	-0.060	-0.060	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.017	0.005	29.583	-0.004	-0.004	0.000	0.000	0.000	0.000
61	A	61	LYS	1	0.846	0.896	25.347	-0.077	-0.077	0.000	0.000	0.000	0.000
62	A	62	PHE	0	-0.040	-0.022	20.019	-0.004	-0.004	0.000	0.000	0.000	0.000
63	A	63	GLN	0	0.017	0.032	23.111	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	64	TYR	0	-0.067	-0.040	22.740	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	65	SER	0	-0.025	-0.037	17.409	0.010	0.010	0.000	0.000	0.000	0.000
66	A	66	VAL	0	0.029	0.005	14.910	-0.013	-0.013	0.000	0.000	0.000	0.000
67	A	67	LEU	0	0.068	0.035	16.538	-0.006	-0.006	0.000	0.000	0.000	0.000
68	A	68	ASP	-1	-0.825	-0.861	19.397	0.113	0.113	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.009	0.006	20.604	-0.010	-0.010	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.793	0.891	21.343	-0.136	-0.136	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.031	0.031	20.379	-0.008	-0.008	0.000	0.000	0.000	0.000
72	A	72	GLU	-1	-0.764	-0.879	18.670	0.198	0.198	0.000	0.000	0.000	0.000
73	A	73	ILE	0	-0.006	-0.012	11.988	0.016	0.016	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.006	0.009	13.988	-0.014	-0.014	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.006	0.016	8.000	0.002	0.002	0.000	0.000	0.000	0.000
76	A	76	VAL	0	0.035	0.006	9.753	-0.103	-0.103	0.000	0.000	0.000	0.000
77	A	77	SER	0	-0.013	0.003	8.490	0.033	0.033	0.000	0.000	0.000	0.000
78	A	78	GLN	0	0.010	0.016	7.971	-0.083	-0.083	0.000	0.000	0.000	0.000
79	A	79	PHE	0	0.062	0.018	7.732	-0.059	-0.059	0.000	0.000	0.000	0.000
80	A	80	THR	0	-0.059	-0.045	8.653	0.071	0.071	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.022	0.025	6.365	0.054	0.054	0.000	0.000	0.000	0.000
82	A	82	TYR	0	-0.086	-0.051	2.454	0.633	1.689	1.099	-0.746	-1.409	0.003
83	A	83	ALA	0	-0.019	-0.006	8.041	-0.081	-0.081	0.000	0.000	0.000	0.000
84	A	84	ASN	0	-0.060	-0.050	11.882	0.047	0.047	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.064	0.001	14.355	-0.040	-0.040	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.926	0.967	15.180	-0.282	-0.282	0.000	0.000	0.000	0.000
87	A	87	LYS	1	0.842	0.921	17.082	-0.140	-0.140	0.000	0.000	0.000	0.000
88	A	88	GLY	0	0.005	0.008	21.509	-0.013	-0.013	0.000	0.000	0.000	0.000
89	A	89	ARG	1	0.962	0.977	21.611	-0.041	-0.041	0.000	0.000	0.000	0.000
90	A	90	ARG	1	0.937	0.985	18.110	-0.035	-0.035	0.000	0.000	0.000	0.000
91	A	91	PRO	0	0.030	0.023	15.813	0.001	0.001	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.059	-0.039	16.117	-0.030	-0.030	0.000	0.000	0.000	0.000
93	A	93	PHE	0	0.066	0.013	11.519	0.028	0.028	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.729	-0.826	11.644	0.126	0.126	0.000	0.000	0.000	0.000
95	A	95	GLU	-1	-0.799	-0.881	7.628	1.100	1.100	0.000	0.000	0.000	0.000
96	A	96	ALA	0	0.030	0.031	7.034	-0.005	-0.005	0.000	0.000	0.000	0.000
97	A	97	GLU	-1	-0.818	-0.911	5.991	-1.239	-1.239	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.834	-0.904	8.317	-0.214	-0.214	0.000	0.000	0.000	0.000
99	A	99	PRO	0	0.021	-0.002	9.641	-0.109	-0.109	0.000	0.000	0.000	0.000
100	A	100	LYS	1	0.880	0.929	10.733	0.285	0.285	0.000	0.000	0.000	0.000
101	A	101	ARG	1	0.862	0.918	6.535	1.790	1.790	0.000	0.000	0.000	0.000
102	A	102	ALA	0	-0.019	-0.013	5.823	-0.265	-0.265	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.811	0.894	6.448	0.203	0.203	0.000	0.000	0.000	0.000
104	A	104	GLU	-1	-0.807	-0.902	7.194	-1.044	-1.044	0.000	0.000	0.000	0.000
105	A	105	LEU	0	0.020	-0.007	2.599	-0.949	-0.136	0.912	-0.267	-1.457	0.001
106	A	106	TYR	0	-0.018	-0.004	3.897	0.524	0.921	0.003	-0.098	-0.302	0.000
107	A	107	GLU	-1	-0.820	-0.904	6.032	0.354	0.354	0.000	0.000	0.000	0.000
108	A	108	LYS	1	0.852	0.917	5.389	0.786	0.786	0.000	0.000	0.000	0.000
109	A	109	PHE	0	0.006	-0.005	3.143	-1.116	-0.110	0.982	-0.467	-1.520	-0.001
110	A	110	VAL	0	-0.027	-0.026	5.534	-0.174	-0.174	0.000	0.000	0.000	0.000
111	A	111	ASP	-1	-0.906	-0.960	9.148	0.150	0.150	0.000	0.000	0.000	0.000
112	A	112	LYS	1	0.752	0.863	7.732	-0.308	-0.308	0.000	0.000	0.000	0.000
113	A	113	ILE	0	-0.004	-0.006	8.775	-0.088	-0.088	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.871	0.948	10.551	-0.503	-0.503	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.855	-0.902	12.843	0.160	0.160	0.000	0.000	0.000	0.000
116	A	116	SER	0	-0.072	-0.044	14.298	-0.064	-0.064	0.000	0.000	0.000	0.000
117	A	117	GLY	0	-0.020	-0.004	15.982	-0.035	-0.035	0.000	0.000	0.000	0.000
118	A	118	LEU	0	-0.051	-0.012	15.912	-0.027	-0.027	0.000	0.000	0.000	0.000
119	A	119	LYS	1	0.821	0.912	17.360	-0.171	-0.171	0.000	0.000	0.000	0.000
120	A	120	VAL	0	-0.008	-0.007	12.075	0.015	0.015	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.808	-0.904	15.360	0.209	0.209	0.000	0.000	0.000	0.000
122	A	122	THR	0	-0.030	-0.026	12.040	0.083	0.083	0.000	0.000	0.000	0.000
123	A	123	GLY	0	0.022	0.011	13.441	-0.064	-0.064	0.000	0.000	0.000	0.000
124	A	124	ILE	0	0.016	0.001	14.248	0.022	0.022	0.000	0.000	0.000	0.000
125	A	125	PHE	0	0.021	-0.005	8.341	0.011	0.011	0.000	0.000	0.000	0.000
126	A	126	GLY	0	-0.034	-0.015	13.772	-0.029	-0.029	0.000	0.000	0.000	0.000
127	A	127	ALA	0	-0.023	-0.006	15.470	-0.013	-0.013	0.000	0.000	0.000	0.000
128	A	128	MET	0	-0.026	-0.020	16.737	0.014	0.014	0.000	0.000	0.000	0.000
129	A	129	MET	0	-0.025	-0.001	13.473	0.016	0.016	0.000	0.000	0.000	0.000
130	A	130	ASP	-1	-0.900	-0.918	19.077	0.084	0.084	0.000	0.000	0.000	0.000
131	A	131	VAL	0	-0.030	-0.037	15.384	0.013	0.013	0.000	0.000	0.000	0.000
132	A	132	PHE	0	0.025	0.033	18.750	-0.007	-0.007	0.000	0.000	0.000	0.000
133	A	133	ILE	0	-0.021	-0.008	15.709	0.017	0.017	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.861	-0.908	19.795	0.095	0.095	0.000	0.000	0.000	0.000
135	A	135	ASN	0	-0.010	-0.029	18.223	0.000	0.000	0.000	0.000	0.000	0.000
136	A	136	TRP	0	0.008	0.003	20.917	-0.011	-0.011	0.000	0.000	0.000	0.000
137	A	137	GLY	0	0.003	0.010	22.610	0.003	0.003	0.000	0.000	0.000	0.000
138	A	138	PRO	0	-0.011	-0.010	20.814	-0.007	-0.007	0.000	0.000	0.000	0.000
139	A	139	VAL	0	-0.021	-0.015	18.081	-0.006	-0.006	0.000	0.000	0.000	0.000
140	A	140	THR	0	-0.003	-0.005	14.434	0.016	0.016	0.000	0.000	0.000	0.000
141	A	141	ILE	0	-0.012	0.004	12.130	-0.010	-0.010	0.000	0.000	0.000	0.000
142	A	142	ILE	0	0.001	-0.002	9.571	0.012	0.012	0.000	0.000	0.000	0.000
143	A	143	ILE	0	-0.012	0.000	6.546	0.063	0.063	0.000	0.000	0.000	0.000
144	A	144	ASP	-1	-0.670	-0.820	4.011	3.482	3.826	0.012	-0.138	-0.218	0.000
145	A	145	SER	0	-0.057	-0.047	1.868	-3.007	-7.421	12.207	-3.851	-3.941	-0.022
146	A	146	ARG	1	0.788	0.863	2.454	-2.795	0.208	0.858	-1.751	-2.110	0.010
147	A	147	GLU	-1	-0.933	-0.950	5.201	0.292	0.377	-0.001	-0.002	-0.081	0.000
148	A	148	ILE	0	-0.082	-0.022	6.128	0.059	0.059	0.000	0.000	0.000	0.000

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