FMO DATABASE

FMODB ID: 2NL4R

Calculation Name: 2DBB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2DBB

Chain ID: A

ChEMBL ID:

UniProt ID: O57802

Base Structure: X-ray

Registration Date: 2023-09-22

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1280091.333629
FMO2-HF: Nuclear repulsion	1221941.03987
FMO2-HF: Total energy	-58150.293759
FMO2-MP2: Total energy	-58323.51926

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:6:LYS)

Summations of interaction energy for fragment #1(A:6:LYS)

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.
66.692	69.958	9.111	-5.874	-6.502	-0.059

Interaction energy analysis for fragmet #1(A:6:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.989 / q_NPA : 0.994

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	8	ASP	-1	-0.765	-0.868	1.874	-78.557	-76.387	8.507	-5.427	-5.250	-0.054
4	A	9	ARG	1	1.020	0.990	4.294	29.826	30.037	-0.001	-0.018	-0.192	0.000
5	A	10	VAL	0	0.010	0.008	5.380	2.450	2.504	-0.001	0.000	-0.053	0.000
6	A	11	ASP	-1	-0.738	-0.845	5.970	-33.320	-33.320	0.000	0.000	0.000	0.000
7	A	12	MET	0	-0.029	-0.011	3.222	-6.686	-5.855	0.606	-0.429	-1.007	-0.005
8	A	13	GLN	0	0.027	0.007	5.733	3.123	3.123	0.000	0.000	0.000	0.000
9	A	14	LEU	0	-0.007	-0.001	8.605	3.245	3.245	0.000	0.000	0.000	0.000
10	A	15	VAL	0	0.021	0.008	8.665	2.507	2.507	0.000	0.000	0.000	0.000
11	A	16	LYS	1	0.911	0.975	8.782	27.592	27.592	0.000	0.000	0.000	0.000
12	A	17	ILE	0	0.022	0.018	11.431	1.839	1.839	0.000	0.000	0.000	0.000
13	A	18	LEU	0	-0.031	-0.023	13.977	1.458	1.458	0.000	0.000	0.000	0.000
14	A	19	SER	0	-0.075	-0.054	13.088	0.804	0.804	0.000	0.000	0.000	0.000
15	A	20	GLU	-1	-0.970	-0.960	15.598	-15.474	-15.474	0.000	0.000	0.000	0.000
16	A	21	ASN	0	0.038	0.003	17.967	1.252	1.252	0.000	0.000	0.000	0.000
17	A	22	SER	0	-0.016	-0.004	18.917	-0.222	-0.222	0.000	0.000	0.000	0.000
18	A	23	ARG	1	0.922	0.957	19.879	12.066	12.066	0.000	0.000	0.000	0.000
19	A	24	LEU	0	-0.002	0.025	18.431	0.455	0.455	0.000	0.000	0.000	0.000
20	A	25	THR	0	-0.004	-0.041	21.399	-0.283	-0.283	0.000	0.000	0.000	0.000
21	A	26	TYR	0	0.041	-0.021	19.975	-0.666	-0.666	0.000	0.000	0.000	0.000
22	A	27	ARG	1	0.850	0.906	20.616	11.544	11.544	0.000	0.000	0.000	0.000
23	A	28	GLU	-1	-0.733	-0.824	21.693	-13.456	-13.456	0.000	0.000	0.000	0.000
24	A	29	LEU	0	-0.004	0.001	16.089	-0.641	-0.641	0.000	0.000	0.000	0.000
25	A	30	ALA	0	-0.083	-0.049	17.073	-0.991	-0.991	0.000	0.000	0.000	0.000
26	A	31	ASP	-1	-0.813	-0.895	18.510	-14.024	-14.024	0.000	0.000	0.000	0.000
27	A	32	ILE	0	0.005	0.017	15.231	-0.401	-0.401	0.000	0.000	0.000	0.000
28	A	33	LEU	0	-0.078	-0.052	11.667	-0.948	-0.948	0.000	0.000	0.000	0.000
29	A	34	ASN	0	-0.037	0.002	14.994	0.058	0.058	0.000	0.000	0.000	0.000
30	A	35	THR	0	-0.003	-0.016	15.338	-0.284	-0.284	0.000	0.000	0.000	0.000
31	A	36	THR	0	0.057	0.024	18.149	0.599	0.599	0.000	0.000	0.000	0.000
32	A	37	ARG	1	1.032	1.004	19.118	11.609	11.609	0.000	0.000	0.000	0.000
33	A	38	GLN	0	0.008	0.015	20.406	-0.379	-0.379	0.000	0.000	0.000	0.000
34	A	39	ARG	1	0.966	0.976	16.043	17.082	17.082	0.000	0.000	0.000	0.000
35	A	40	ILE	0	0.002	0.023	15.114	-1.219	-1.219	0.000	0.000	0.000	0.000
36	A	41	ALA	0	0.004	0.001	16.308	-0.656	-0.656	0.000	0.000	0.000	0.000
37	A	42	ARG	1	0.861	0.914	16.201	16.599	16.599	0.000	0.000	0.000	0.000
38	A	43	ARG	1	0.808	0.876	8.578	31.229	31.229	0.000	0.000	0.000	0.000
39	A	44	ILE	0	0.067	0.032	13.013	-1.002	-1.002	0.000	0.000	0.000	0.000
40	A	45	ASP	-1	-0.844	-0.891	14.994	-16.168	-16.168	0.000	0.000	0.000	0.000
41	A	46	LYS	1	0.880	0.924	7.884	32.586	32.586	0.000	0.000	0.000	0.000
42	A	47	LEU	0	-0.008	-0.013	8.815	-0.360	-0.360	0.000	0.000	0.000	0.000
43	A	48	LYS	1	0.940	0.979	11.469	16.455	16.455	0.000	0.000	0.000	0.000
44	A	49	LYS	1	0.851	0.913	13.796	16.245	16.245	0.000	0.000	0.000	0.000
45	A	50	LEU	0	-0.034	-0.017	6.952	0.261	0.261	0.000	0.000	0.000	0.000
46	A	51	GLY	0	0.033	0.031	10.638	-0.072	-0.072	0.000	0.000	0.000	0.000
47	A	52	ILE	0	-0.065	-0.029	6.560	-0.603	-0.603	0.000	0.000	0.000	0.000
48	A	53	ILE	0	-0.031	-0.006	10.146	-0.049	-0.049	0.000	0.000	0.000	0.000
49	A	54	ARG	1	0.986	0.980	13.461	18.407	18.407	0.000	0.000	0.000	0.000
50	A	55	LYS	1	0.951	0.964	16.139	14.283	14.283	0.000	0.000	0.000	0.000
51	A	56	PHE	0	0.001	0.020	17.314	-0.867	-0.867	0.000	0.000	0.000	0.000
52	A	57	THR	0	0.013	-0.012	20.622	0.882	0.882	0.000	0.000	0.000	0.000
53	A	58	ILE	0	0.011	0.007	22.615	-0.291	-0.291	0.000	0.000	0.000	0.000
54	A	59	ILE	0	0.006	0.005	21.128	-0.087	-0.087	0.000	0.000	0.000	0.000
55	A	60	PRO	0	-0.012	0.007	25.009	0.139	0.139	0.000	0.000	0.000	0.000
56	A	61	ASP	-1	-0.802	-0.897	28.745	-9.784	-9.784	0.000	0.000	0.000	0.000
57	A	62	ILE	0	-0.001	-0.022	29.091	0.271	0.271	0.000	0.000	0.000	0.000
58	A	63	ASP	-1	-0.786	-0.864	32.367	-8.229	-8.229	0.000	0.000	0.000	0.000
59	A	64	LYS	1	0.847	0.899	34.426	9.401	9.401	0.000	0.000	0.000	0.000
60	A	65	LEU	0	-0.073	-0.027	32.465	0.138	0.138	0.000	0.000	0.000	0.000
61	A	66	GLY	0	0.002	0.013	36.479	0.156	0.156	0.000	0.000	0.000	0.000
62	A	67	TYR	0	-0.026	-0.021	34.518	0.079	0.079	0.000	0.000	0.000	0.000
63	A	68	MET	0	0.003	-0.005	34.654	0.019	0.019	0.000	0.000	0.000	0.000
64	A	69	TYR	0	-0.021	-0.021	26.897	-0.183	-0.183	0.000	0.000	0.000	0.000
65	A	70	ALA	0	0.038	0.023	32.138	0.256	0.256	0.000	0.000	0.000	0.000
66	A	71	ILE	0	-0.040	-0.015	27.677	-0.353	-0.353	0.000	0.000	0.000	0.000
67	A	72	VAL	0	0.007	0.000	30.701	0.316	0.316	0.000	0.000	0.000	0.000
68	A	73	LEU	0	-0.031	-0.010	29.309	-0.450	-0.450	0.000	0.000	0.000	0.000
69	A	74	ILE	0	0.050	0.016	30.365	0.388	0.388	0.000	0.000	0.000	0.000
70	A	75	LYS	1	0.886	0.954	30.458	8.995	8.995	0.000	0.000	0.000	0.000
71	A	76	SER	0	0.035	0.009	31.231	0.209	0.209	0.000	0.000	0.000	0.000
72	A	77	LYS	1	0.897	0.956	33.078	7.492	7.492	0.000	0.000	0.000	0.000
73	A	78	VAL	0	0.012	0.005	33.612	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	79	PRO	0	0.025	-0.005	28.161	-0.083	-0.083	0.000	0.000	0.000	0.000
75	A	80	SER	0	0.029	0.014	29.035	-0.152	-0.152	0.000	0.000	0.000	0.000
76	A	81	ASP	-1	-0.837	-0.918	30.367	-8.561	-8.561	0.000	0.000	0.000	0.000
77	A	82	ALA	0	-0.015	-0.007	27.302	0.017	0.017	0.000	0.000	0.000	0.000
78	A	83	ASP	-1	-0.801	-0.884	24.881	-11.522	-11.522	0.000	0.000	0.000	0.000
79	A	84	LYS	1	0.872	0.934	27.665	8.559	8.559	0.000	0.000	0.000	0.000
80	A	85	VAL	0	0.022	0.010	30.574	0.075	0.075	0.000	0.000	0.000	0.000
81	A	86	ILE	0	0.020	0.003	24.257	-0.014	-0.014	0.000	0.000	0.000	0.000
82	A	87	SER	0	-0.020	0.008	27.921	-0.128	-0.128	0.000	0.000	0.000	0.000
83	A	88	GLU	-1	-0.888	-0.929	29.030	-8.211	-8.211	0.000	0.000	0.000	0.000
84	A	89	ILE	0	-0.025	-0.023	28.976	0.167	0.167	0.000	0.000	0.000	0.000
85	A	90	SER	0	-0.063	-0.056	26.110	-0.211	-0.211	0.000	0.000	0.000	0.000
86	A	91	ASP	-1	-0.925	-0.949	27.766	-10.189	-10.189	0.000	0.000	0.000	0.000
87	A	92	ILE	0	-0.086	-0.023	30.166	0.196	0.196	0.000	0.000	0.000	0.000
88	A	93	GLU	-1	-0.803	-0.922	30.888	-9.539	-9.539	0.000	0.000	0.000	0.000
89	A	94	TYR	0	-0.037	-0.031	31.192	-0.466	-0.466	0.000	0.000	0.000	0.000
90	A	95	VAL	0	0.001	-0.001	27.742	-0.117	-0.117	0.000	0.000	0.000	0.000
91	A	96	LYS	1	0.723	0.860	26.665	10.015	10.015	0.000	0.000	0.000	0.000
92	A	97	SER	0	-0.106	-0.064	22.702	-0.377	-0.377	0.000	0.000	0.000	0.000
93	A	98	VAL	0	0.069	0.033	23.223	0.489	0.489	0.000	0.000	0.000	0.000
94	A	99	GLU	-1	-0.933	-0.943	20.114	-14.548	-14.548	0.000	0.000	0.000	0.000
95	A	100	LYS	1	0.824	0.889	21.293	12.618	12.618	0.000	0.000	0.000	0.000
96	A	101	GLY	0	-0.018	-0.018	21.223	-0.664	-0.664	0.000	0.000	0.000	0.000
97	A	102	VAL	0	-0.017	-0.020	21.732	0.480	0.480	0.000	0.000	0.000	0.000
98	A	103	GLY	0	0.041	0.016	24.026	-0.291	-0.291	0.000	0.000	0.000	0.000
99	A	104	ARG	1	0.837	0.913	26.726	9.287	9.287	0.000	0.000	0.000	0.000
100	A	105	TYR	0	-0.041	-0.049	28.524	0.260	0.260	0.000	0.000	0.000	0.000
101	A	106	ASN	0	-0.011	-0.005	26.355	-0.102	-0.102	0.000	0.000	0.000	0.000
102	A	107	ILE	0	0.020	0.014	25.762	-0.404	-0.404	0.000	0.000	0.000	0.000
103	A	108	ILE	0	-0.010	0.016	24.685	0.390	0.390	0.000	0.000	0.000	0.000
104	A	109	VAL	0	0.032	0.016	25.808	-0.355	-0.355	0.000	0.000	0.000	0.000
105	A	110	ARG	1	0.938	1.003	24.538	12.292	12.292	0.000	0.000	0.000	0.000
106	A	111	LEU	0	0.012	0.006	28.640	-0.083	-0.083	0.000	0.000	0.000	0.000
107	A	112	LEU	0	-0.053	-0.033	31.159	-0.146	-0.146	0.000	0.000	0.000	0.000
108	A	113	LEU	0	0.022	0.011	32.867	0.149	0.149	0.000	0.000	0.000	0.000
109	A	114	PRO	0	0.072	0.040	36.565	-0.148	-0.148	0.000	0.000	0.000	0.000
110	A	115	LYS	1	0.838	0.892	38.025	8.214	8.214	0.000	0.000	0.000	0.000
111	A	116	ASP	-1	-0.821	-0.891	40.611	-6.803	-6.803	0.000	0.000	0.000	0.000
112	A	117	ILE	0	0.032	0.006	42.545	-0.072	-0.072	0.000	0.000	0.000	0.000
113	A	118	LYS	1	0.837	0.908	44.219	6.668	6.668	0.000	0.000	0.000	0.000
114	A	119	ASP	-1	-0.833	-0.914	43.440	-6.973	-6.973	0.000	0.000	0.000	0.000
115	A	120	ALA	0	-0.053	-0.025	39.947	-0.134	-0.134	0.000	0.000	0.000	0.000
116	A	121	GLU	-1	-0.895	-0.932	40.618	-7.119	-7.119	0.000	0.000	0.000	0.000
117	A	122	ASN	0	0.009	0.018	42.735	-0.087	-0.087	0.000	0.000	0.000	0.000
118	A	123	LEU	0	0.015	0.003	37.768	-0.062	-0.062	0.000	0.000	0.000	0.000
119	A	124	ILE	0	-0.022	-0.013	37.552	-0.185	-0.185	0.000	0.000	0.000	0.000
120	A	125	SER	0	-0.026	-0.045	39.064	-0.126	-0.126	0.000	0.000	0.000	0.000
121	A	126	GLU	-1	-0.897	-0.907	38.528	-7.914	-7.914	0.000	0.000	0.000	0.000
122	A	127	PHE	0	-0.003	-0.017	31.735	-0.141	-0.141	0.000	0.000	0.000	0.000
123	A	128	LEU	0	-0.014	-0.026	36.717	-0.118	-0.118	0.000	0.000	0.000	0.000
124	A	129	GLN	0	-0.006	0.023	38.354	-0.002	-0.002	0.000	0.000	0.000	0.000
125	A	130	ARG	1	0.894	0.923	34.616	8.564	8.564	0.000	0.000	0.000	0.000
126	A	131	ILE	0	-0.055	-0.016	33.707	-0.210	-0.210	0.000	0.000	0.000	0.000
127	A	132	LYS	1	0.849	0.936	36.414	8.086	8.086	0.000	0.000	0.000	0.000
128	A	133	ASN	0	-0.002	-0.002	37.275	-0.019	-0.019	0.000	0.000	0.000	0.000
129	A	134	ALA	0	0.041	0.031	35.784	-0.128	-0.128	0.000	0.000	0.000	0.000
130	A	135	GLU	-1	-0.920	-0.971	36.128	-7.600	-7.600	0.000	0.000	0.000	0.000
131	A	136	ASN	0	-0.024	-0.012	35.528	-0.059	-0.059	0.000	0.000	0.000	0.000
132	A	137	VAL	0	0.046	0.019	35.172	-0.273	-0.273	0.000	0.000	0.000	0.000
133	A	138	GLU	-1	-0.822	-0.876	34.706	-8.297	-8.297	0.000	0.000	0.000	0.000
134	A	139	VAL	0	0.003	0.004	34.697	-0.308	-0.308	0.000	0.000	0.000	0.000
135	A	140	ILE	0	-0.007	0.001	32.261	0.179	0.179	0.000	0.000	0.000	0.000
136	A	141	LEU	0	0.035	0.018	34.108	-0.262	-0.262	0.000	0.000	0.000	0.000
137	A	142	ILE	0	-0.056	-0.033	30.666	-0.064	-0.064	0.000	0.000	0.000	0.000
138	A	143	SER	0	0.030	0.018	33.927	0.063	0.063	0.000	0.000	0.000	0.000
139	A	144	GLU	-1	-0.852	-0.926	33.016	-9.166	-9.166	0.000	0.000	0.000	0.000
140	A	145	VAL	0	-0.025	-0.003	27.515	-0.290	-0.290	0.000	0.000	0.000	0.000
141	A	146	ARG	1	0.865	0.924	28.450	9.669	9.669	0.000	0.000	0.000	0.000
142	A	147	LYS	1	0.843	0.890	20.088	14.755	14.755	0.000	0.000	0.000	0.000
143	A	148	PHE	0	-0.013	-0.011	23.055	0.003	0.003	0.000	0.000	0.000	0.000
144	A	149	GLU	-1	-0.793	-0.869	18.409	-15.465	-15.465	0.000	0.000	0.000	0.000
145	A	150	ILE	0	-0.008	-0.005	16.006	0.021	0.021	0.000	0.000	0.000	0.000
146	A	151	ILE	0	0.011	0.012	10.790	-1.940	-1.940	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:LYS)