FMO DATABASE

FMODB ID: 76MYK

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	OptH
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	-1278875.873961
FMO2-HF: Nuclear repulsion	1220726.738988
FMO2-HF: Total energy	-58149.134973
FMO2-MP2: Total energy	-58322.411684

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.
82.241	85.378	2.885	-2.47	-3.552	-0.026

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 : 0.988 / q_NPA : 0.981

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	-0.761	-0.865	2.296	-52.222	-49.944	2.827	-2.183	-2.922	-0.023
4	A	9	ARG	1	1.018	0.980	4.780	28.414	28.526	-0.001	-0.006	-0.105	0.000
5	A	10	VAL	0	-0.007	0.001	6.188	1.676	1.676	0.000	0.000	0.000	0.000
6	A	11	ASP	-1	-0.741	-0.863	6.624	-29.170	-29.170	0.000	0.000	0.000	0.000
7	A	12	MET	0	-0.008	-0.005	3.652	-4.854	-4.107	0.059	-0.281	-0.525	-0.003
8	A	13	GLN	0	0.012	0.001	6.720	1.484	1.484	0.000	0.000	0.000	0.000
9	A	14	LEU	0	-0.004	0.000	9.764	2.619	2.619	0.000	0.000	0.000	0.000
10	A	15	VAL	0	0.012	0.003	8.488	2.056	2.056	0.000	0.000	0.000	0.000
11	A	16	LYS	1	0.929	0.971	8.813	29.274	29.274	0.000	0.000	0.000	0.000
12	A	17	ILE	0	0.019	0.021	11.823	1.528	1.528	0.000	0.000	0.000	0.000
13	A	18	LEU	0	-0.040	-0.029	14.500	1.295	1.295	0.000	0.000	0.000	0.000
14	A	19	SER	0	-0.063	-0.038	13.375	0.826	0.826	0.000	0.000	0.000	0.000
15	A	20	GLU	-1	-0.975	-0.962	15.883	-14.995	-14.995	0.000	0.000	0.000	0.000
16	A	21	ASN	0	0.050	0.016	18.212	1.131	1.131	0.000	0.000	0.000	0.000
17	A	22	SER	0	-0.021	-0.015	19.333	-0.128	-0.128	0.000	0.000	0.000	0.000
18	A	23	ARG	1	0.923	0.961	20.266	11.597	11.597	0.000	0.000	0.000	0.000
19	A	24	LEU	0	0.018	0.033	19.272	0.430	0.430	0.000	0.000	0.000	0.000
20	A	25	THR	0	-0.006	-0.006	22.268	-0.210	-0.210	0.000	0.000	0.000	0.000
21	A	26	TYR	0	0.060	-0.009	20.184	-0.295	-0.295	0.000	0.000	0.000	0.000
22	A	27	ARG	1	0.955	0.945	21.710	10.647	10.647	0.000	0.000	0.000	0.000
23	A	28	GLU	-1	-0.800	-0.881	23.031	-12.802	-12.802	0.000	0.000	0.000	0.000
24	A	29	LEU	0	-0.008	0.005	17.308	-0.552	-0.552	0.000	0.000	0.000	0.000
25	A	30	ALA	0	-0.069	-0.050	18.267	-0.869	-0.869	0.000	0.000	0.000	0.000
26	A	31	ASP	-1	-0.878	-0.930	19.583	-13.454	-13.454	0.000	0.000	0.000	0.000
27	A	32	ILE	0	-0.016	0.008	16.568	-0.389	-0.389	0.000	0.000	0.000	0.000
28	A	33	LEU	0	-0.086	-0.055	12.848	-0.833	-0.833	0.000	0.000	0.000	0.000
29	A	34	ASN	0	-0.007	0.015	16.057	0.141	0.141	0.000	0.000	0.000	0.000
30	A	35	THR	0	-0.004	-0.009	16.544	0.033	0.033	0.000	0.000	0.000	0.000
31	A	36	THR	0	0.056	0.023	18.972	0.503	0.503	0.000	0.000	0.000	0.000
32	A	37	ARG	1	1.007	0.994	19.916	11.171	11.171	0.000	0.000	0.000	0.000
33	A	38	GLN	0	0.022	0.025	21.074	-0.141	-0.141	0.000	0.000	0.000	0.000
34	A	39	ARG	1	0.937	0.959	16.597	15.956	15.956	0.000	0.000	0.000	0.000
35	A	40	ILE	0	0.006	0.022	16.020	-1.031	-1.031	0.000	0.000	0.000	0.000
36	A	41	ALA	0	0.015	0.007	16.891	-0.587	-0.587	0.000	0.000	0.000	0.000
37	A	42	ARG	1	0.922	0.958	16.292	14.974	14.974	0.000	0.000	0.000	0.000
38	A	43	ARG	1	0.814	0.905	9.064	27.151	27.151	0.000	0.000	0.000	0.000
39	A	44	ILE	0	0.069	0.032	13.168	-0.791	-0.791	0.000	0.000	0.000	0.000
40	A	45	ASP	-1	-0.889	-0.941	15.082	-15.227	-15.227	0.000	0.000	0.000	0.000
41	A	46	LYS	1	0.877	0.925	8.028	28.132	28.132	0.000	0.000	0.000	0.000
42	A	47	LEU	0	-0.022	-0.020	9.116	-0.272	-0.272	0.000	0.000	0.000	0.000
43	A	48	LYS	1	0.947	0.977	11.517	15.206	15.206	0.000	0.000	0.000	0.000
44	A	49	LYS	1	0.859	0.937	14.377	15.141	15.141	0.000	0.000	0.000	0.000
45	A	50	LEU	0	-0.039	-0.020	7.725	0.231	0.231	0.000	0.000	0.000	0.000
46	A	51	GLY	0	0.031	0.030	11.175	-0.147	-0.147	0.000	0.000	0.000	0.000
47	A	52	ILE	0	-0.057	-0.028	6.591	-0.679	-0.679	0.000	0.000	0.000	0.000
48	A	53	ILE	0	-0.025	-0.003	10.178	-0.283	-0.283	0.000	0.000	0.000	0.000
49	A	54	ARG	1	0.981	0.978	13.487	17.782	17.782	0.000	0.000	0.000	0.000
50	A	55	LYS	1	0.944	0.954	16.169	14.226	14.226	0.000	0.000	0.000	0.000
51	A	56	PHE	0	0.005	0.026	17.623	-0.759	-0.759	0.000	0.000	0.000	0.000
52	A	57	THR	0	0.013	-0.005	20.624	0.866	0.866	0.000	0.000	0.000	0.000
53	A	58	ILE	0	0.011	0.004	22.787	-0.262	-0.262	0.000	0.000	0.000	0.000
54	A	59	ILE	0	0.004	0.004	21.474	-0.113	-0.113	0.000	0.000	0.000	0.000
55	A	60	PRO	0	-0.023	-0.003	25.074	0.144	0.144	0.000	0.000	0.000	0.000
56	A	61	ASP	-1	-0.823	-0.929	28.754	-9.905	-9.905	0.000	0.000	0.000	0.000
57	A	62	ILE	0	-0.004	-0.021	29.605	0.273	0.273	0.000	0.000	0.000	0.000
58	A	63	ASP	-1	-0.811	-0.891	32.301	-8.268	-8.268	0.000	0.000	0.000	0.000
59	A	64	LYS	1	0.868	0.934	34.483	9.189	9.189	0.000	0.000	0.000	0.000
60	A	65	LEU	0	-0.078	-0.030	32.463	0.152	0.152	0.000	0.000	0.000	0.000
61	A	66	GLY	0	0.007	0.016	36.466	0.161	0.161	0.000	0.000	0.000	0.000
62	A	67	TYR	0	-0.024	-0.020	34.003	0.046	0.046	0.000	0.000	0.000	0.000
63	A	68	MET	0	0.013	-0.003	34.476	0.019	0.019	0.000	0.000	0.000	0.000
64	A	69	TYR	0	-0.023	-0.020	27.103	-0.174	-0.174	0.000	0.000	0.000	0.000
65	A	70	ALA	0	0.044	0.024	31.819	0.252	0.252	0.000	0.000	0.000	0.000
66	A	71	ILE	0	-0.039	-0.017	27.149	-0.355	-0.355	0.000	0.000	0.000	0.000
67	A	72	VAL	0	0.010	0.001	30.358	0.317	0.317	0.000	0.000	0.000	0.000
68	A	73	LEU	0	-0.036	-0.014	28.570	-0.483	-0.483	0.000	0.000	0.000	0.000
69	A	74	ILE	0	0.046	0.020	30.155	0.405	0.405	0.000	0.000	0.000	0.000
70	A	75	LYS	1	0.899	0.958	30.362	9.382	9.382	0.000	0.000	0.000	0.000
71	A	76	SER	0	0.031	0.006	31.113	0.216	0.216	0.000	0.000	0.000	0.000
72	A	77	LYS	1	0.878	0.935	33.078	7.635	7.635	0.000	0.000	0.000	0.000
73	A	78	VAL	0	-0.004	0.005	33.584	-0.022	-0.022	0.000	0.000	0.000	0.000
74	A	79	PRO	0	0.010	-0.013	28.235	-0.096	-0.096	0.000	0.000	0.000	0.000
75	A	80	SER	0	0.015	0.005	29.043	-0.176	-0.176	0.000	0.000	0.000	0.000
76	A	81	ASP	-1	-0.837	-0.929	30.379	-8.794	-8.794	0.000	0.000	0.000	0.000
77	A	82	ALA	0	-0.028	-0.024	27.254	0.020	0.020	0.000	0.000	0.000	0.000
78	A	83	ASP	-1	-0.848	-0.905	25.064	-11.719	-11.719	0.000	0.000	0.000	0.000
79	A	84	LYS	1	0.936	0.974	27.682	8.678	8.678	0.000	0.000	0.000	0.000
80	A	85	VAL	0	0.033	0.020	30.470	0.095	0.095	0.000	0.000	0.000	0.000
81	A	86	ILE	0	0.020	0.001	24.172	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	87	SER	0	-0.018	0.010	27.937	-0.085	-0.085	0.000	0.000	0.000	0.000
83	A	88	GLU	-1	-0.927	-0.948	29.054	-8.416	-8.416	0.000	0.000	0.000	0.000
84	A	89	ILE	0	-0.038	-0.032	28.628	0.152	0.152	0.000	0.000	0.000	0.000
85	A	90	SER	0	-0.087	-0.077	26.176	-0.213	-0.213	0.000	0.000	0.000	0.000
86	A	91	ASP	-1	-0.918	-0.948	27.789	-10.181	-10.181	0.000	0.000	0.000	0.000
87	A	92	ILE	0	-0.083	-0.018	30.191	0.203	0.203	0.000	0.000	0.000	0.000
88	A	93	GLU	-1	-0.862	-0.938	30.907	-9.247	-9.247	0.000	0.000	0.000	0.000
89	A	94	TYR	0	0.013	0.007	31.209	-0.441	-0.441	0.000	0.000	0.000	0.000
90	A	95	VAL	0	0.002	0.004	27.728	-0.151	-0.151	0.000	0.000	0.000	0.000
91	A	96	LYS	1	0.784	0.889	26.605	10.236	10.236	0.000	0.000	0.000	0.000
92	A	97	SER	0	-0.045	-0.032	22.821	-0.394	-0.394	0.000	0.000	0.000	0.000
93	A	98	VAL	0	0.056	0.031	23.243	0.452	0.452	0.000	0.000	0.000	0.000
94	A	99	GLU	-1	-0.982	-0.979	19.838	-15.641	-15.641	0.000	0.000	0.000	0.000
95	A	100	LYS	1	0.876	0.922	21.286	13.123	13.123	0.000	0.000	0.000	0.000
96	A	101	GLY	0	-0.020	-0.022	21.220	-0.722	-0.722	0.000	0.000	0.000	0.000
97	A	102	VAL	0	-0.016	-0.018	21.234	0.534	0.534	0.000	0.000	0.000	0.000
98	A	103	GLY	0	0.041	0.015	23.352	-0.332	-0.332	0.000	0.000	0.000	0.000
99	A	104	ARG	1	0.842	0.929	26.050	9.618	9.618	0.000	0.000	0.000	0.000
100	A	105	TYR	0	0.041	0.010	27.782	0.457	0.457	0.000	0.000	0.000	0.000
101	A	106	ASN	0	-0.011	-0.005	26.177	-0.179	-0.179	0.000	0.000	0.000	0.000
102	A	107	ILE	0	0.032	0.028	25.760	-0.425	-0.425	0.000	0.000	0.000	0.000
103	A	108	ILE	0	-0.007	0.014	23.912	0.411	0.411	0.000	0.000	0.000	0.000
104	A	109	VAL	0	0.033	0.019	25.808	-0.376	-0.376	0.000	0.000	0.000	0.000
105	A	110	ARG	1	0.923	0.993	24.394	12.325	12.325	0.000	0.000	0.000	0.000
106	A	111	LEU	0	0.008	0.004	28.358	-0.076	-0.076	0.000	0.000	0.000	0.000
107	A	112	LEU	0	-0.053	-0.031	30.970	-0.173	-0.173	0.000	0.000	0.000	0.000
108	A	113	LEU	0	0.016	0.006	32.597	0.151	0.151	0.000	0.000	0.000	0.000
109	A	114	PRO	0	0.065	0.041	36.298	-0.152	-0.152	0.000	0.000	0.000	0.000
110	A	115	LYS	1	0.871	0.921	38.501	8.180	8.180	0.000	0.000	0.000	0.000
111	A	116	ASP	-1	-0.852	-0.907	40.412	-6.834	-6.834	0.000	0.000	0.000	0.000
112	A	117	ILE	0	0.037	0.004	42.268	-0.071	-0.071	0.000	0.000	0.000	0.000
113	A	118	LYS	1	0.955	0.990	43.926	6.442	6.442	0.000	0.000	0.000	0.000
114	A	119	ASP	-1	-0.897	-0.957	43.336	-7.045	-7.045	0.000	0.000	0.000	0.000
115	A	120	ALA	0	-0.051	-0.030	39.607	-0.139	-0.139	0.000	0.000	0.000	0.000
116	A	121	GLU	-1	-0.880	-0.921	40.471	-7.215	-7.215	0.000	0.000	0.000	0.000
117	A	122	ASN	0	0.007	0.016	42.741	-0.111	-0.111	0.000	0.000	0.000	0.000
118	A	123	LEU	0	0.031	0.017	37.629	-0.068	-0.068	0.000	0.000	0.000	0.000
119	A	124	ILE	0	-0.034	-0.020	37.453	-0.204	-0.204	0.000	0.000	0.000	0.000
120	A	125	SER	0	-0.047	-0.062	39.071	-0.141	-0.141	0.000	0.000	0.000	0.000
121	A	126	GLU	-1	-0.937	-0.954	38.587	-7.893	-7.893	0.000	0.000	0.000	0.000
122	A	127	PHE	0	-0.039	-0.033	31.864	-0.134	-0.134	0.000	0.000	0.000	0.000
123	A	128	LEU	0	-0.007	-0.024	36.604	-0.123	-0.123	0.000	0.000	0.000	0.000
124	A	129	GLN	0	-0.003	0.027	38.362	-0.051	-0.051	0.000	0.000	0.000	0.000
125	A	130	ARG	1	0.872	0.924	34.961	8.531	8.531	0.000	0.000	0.000	0.000
126	A	131	ILE	0	-0.040	-0.001	33.792	-0.214	-0.214	0.000	0.000	0.000	0.000
127	A	132	LYS	1	0.901	0.948	36.425	7.906	7.906	0.000	0.000	0.000	0.000
128	A	133	ASN	0	0.039	0.029	37.285	0.011	0.011	0.000	0.000	0.000	0.000
129	A	134	ALA	0	0.038	0.026	35.808	-0.138	-0.138	0.000	0.000	0.000	0.000
130	A	135	GLU	-1	-0.952	-0.980	35.960	-7.858	-7.858	0.000	0.000	0.000	0.000
131	A	136	ASN	0	-0.013	-0.022	34.922	-0.084	-0.084	0.000	0.000	0.000	0.000
132	A	137	VAL	0	0.041	0.012	34.998	-0.282	-0.282	0.000	0.000	0.000	0.000
133	A	138	GLU	-1	-0.928	-0.945	33.833	-8.334	-8.334	0.000	0.000	0.000	0.000
134	A	139	VAL	0	0.017	0.009	34.107	-0.323	-0.323	0.000	0.000	0.000	0.000
135	A	140	ILE	0	-0.005	0.001	31.568	0.171	0.171	0.000	0.000	0.000	0.000
136	A	141	LEU	0	0.030	0.012	33.706	-0.263	-0.263	0.000	0.000	0.000	0.000
137	A	142	ILE	0	-0.060	-0.034	30.455	-0.086	-0.086	0.000	0.000	0.000	0.000
138	A	143	SER	0	0.025	0.014	33.632	0.067	0.067	0.000	0.000	0.000	0.000
139	A	144	GLU	-1	-0.932	-0.981	32.571	-9.163	-9.163	0.000	0.000	0.000	0.000
140	A	145	VAL	0	-0.017	0.005	27.315	-0.325	-0.325	0.000	0.000	0.000	0.000
141	A	146	ARG	1	0.951	0.977	28.207	10.021	10.021	0.000	0.000	0.000	0.000
142	A	147	LYS	1	0.965	0.974	19.441	15.157	15.157	0.000	0.000	0.000	0.000
143	A	148	PHE	0	-0.023	-0.014	22.986	-0.029	-0.029	0.000	0.000	0.000	0.000
144	A	149	GLU	-1	-0.908	-0.948	18.411	-16.128	-16.128	0.000	0.000	0.000	0.000
145	A	150	ILE	0	-0.017	-0.008	15.834	0.010	0.010	0.000	0.000	0.000	0.000
146	A	151	ILE	0	-0.011	0.001	10.823	-1.870	-1.870	0.000	0.000	0.000	0.000

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