FMO DATABASE

FMODB ID: K3KL3

Calculation Name: 1DKG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DKG

Chain ID: A

ChEMBL ID:

UniProt ID: P0A6Y8

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	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	164
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1223371.847875
FMO2-HF: Nuclear repulsion	1158982.709737
FMO2-HF: Total energy	-64389.138138
FMO2-MP2: Total energy	-64574.628461

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:34:ALA)

Summations of interaction energy for fragment #1(A:34:ALA)

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.
-2.682	-1.53	-0.011	-0.463	-0.679	0.001

Interaction energy analysis for fragmet #1(A:34:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.059 / q_NPA : -0.048

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	36	GLN	0	0.012	0.002	3.822	-1.555	-0.403	-0.011	-0.463	-0.679	0.001
4	A	37	VAL	0	0.051	0.033	6.432	0.399	0.399	0.000	0.000	0.000	0.000
5	A	38	ASP	-1	-0.802	-0.859	9.419	-0.232	-0.232	0.000	0.000	0.000	0.000
6	A	39	PRO	0	0.080	0.045	10.957	-0.102	-0.102	0.000	0.000	0.000	0.000
7	A	40	ARG	1	0.717	0.807	13.009	0.347	0.347	0.000	0.000	0.000	0.000
8	A	41	ASP	-1	-0.884	-0.954	7.583	-0.971	-0.971	0.000	0.000	0.000	0.000
9	A	42	GLU	-1	-0.891	-0.948	9.141	-0.823	-0.823	0.000	0.000	0.000	0.000
10	A	43	LYS	1	0.878	0.948	10.472	0.455	0.455	0.000	0.000	0.000	0.000
11	A	44	VAL	0	-0.035	-0.022	9.599	0.082	0.082	0.000	0.000	0.000	0.000
12	A	45	ALA	0	0.059	0.040	8.358	0.064	0.064	0.000	0.000	0.000	0.000
13	A	46	ASN	0	-0.018	0.010	10.229	0.060	0.060	0.000	0.000	0.000	0.000
14	A	47	LEU	0	-0.074	-0.031	13.499	0.060	0.060	0.000	0.000	0.000	0.000
15	A	48	GLU	-1	-0.900	-0.959	9.712	-0.730	-0.730	0.000	0.000	0.000	0.000
16	A	49	ALA	0	0.008	0.006	12.734	0.039	0.039	0.000	0.000	0.000	0.000
17	A	50	GLN	0	0.015	-0.006	14.359	0.058	0.058	0.000	0.000	0.000	0.000
18	A	51	LEU	0	-0.013	0.005	17.186	0.037	0.037	0.000	0.000	0.000	0.000
19	A	52	ALA	0	0.065	0.036	15.429	0.034	0.034	0.000	0.000	0.000	0.000
20	A	53	GLU	-1	-0.917	-0.953	17.534	-0.241	-0.241	0.000	0.000	0.000	0.000
21	A	54	ALA	0	-0.144	-0.067	19.907	0.030	0.030	0.000	0.000	0.000	0.000
22	A	55	GLN	0	0.036	0.003	19.431	0.014	0.014	0.000	0.000	0.000	0.000
23	A	56	THR	0	-0.065	-0.030	20.219	0.020	0.020	0.000	0.000	0.000	0.000
24	A	57	ARG	1	0.953	0.965	22.889	0.209	0.209	0.000	0.000	0.000	0.000
25	A	58	GLU	-1	-0.951	-0.963	25.752	-0.140	-0.140	0.000	0.000	0.000	0.000
26	A	59	ARG	1	0.992	0.996	21.877	0.184	0.184	0.000	0.000	0.000	0.000
27	A	60	ASP	-1	-0.874	-0.942	25.937	-0.131	-0.131	0.000	0.000	0.000	0.000
28	A	61	GLY	0	-0.085	-0.053	28.780	0.010	0.010	0.000	0.000	0.000	0.000
29	A	62	ILE	0	-0.008	-0.010	30.524	0.010	0.010	0.000	0.000	0.000	0.000
30	A	63	LEU	0	-0.003	-0.002	30.780	0.008	0.008	0.000	0.000	0.000	0.000
31	A	64	ARG	1	0.896	0.924	33.117	0.093	0.093	0.000	0.000	0.000	0.000
32	A	65	VAL	0	0.029	0.019	35.175	0.005	0.005	0.000	0.000	0.000	0.000
33	A	66	LYS	1	0.934	0.985	34.573	0.085	0.085	0.000	0.000	0.000	0.000
34	A	67	ALA	0	0.003	-0.010	37.098	0.005	0.005	0.000	0.000	0.000	0.000
35	A	68	GLU	-1	-0.901	-0.926	38.649	-0.069	-0.069	0.000	0.000	0.000	0.000
36	A	69	MET	0	-0.026	-0.011	40.598	0.004	0.004	0.000	0.000	0.000	0.000
37	A	70	GLU	-1	-0.810	-0.896	41.566	-0.051	-0.051	0.000	0.000	0.000	0.000
38	A	71	ASN	0	0.004	-0.012	41.674	0.005	0.005	0.000	0.000	0.000	0.000
39	A	72	LEU	0	-0.083	-0.041	45.079	0.002	0.002	0.000	0.000	0.000	0.000
40	A	73	ARG	1	0.952	0.977	43.502	0.054	0.054	0.000	0.000	0.000	0.000
41	A	74	ARG	1	0.991	1.003	47.667	0.043	0.043	0.000	0.000	0.000	0.000
42	A	75	ARG	1	0.875	0.926	45.717	0.051	0.051	0.000	0.000	0.000	0.000
43	A	76	THR	0	0.054	0.027	51.201	0.001	0.001	0.000	0.000	0.000	0.000
44	A	77	GLU	-1	-0.927	-0.949	51.564	-0.037	-0.037	0.000	0.000	0.000	0.000
45	A	78	LEU	0	-0.016	-0.004	52.575	0.002	0.002	0.000	0.000	0.000	0.000
46	A	79	ASP	-1	-0.921	-0.974	54.358	-0.036	-0.036	0.000	0.000	0.000	0.000
47	A	80	ILE	0	-0.006	-0.004	56.291	0.001	0.001	0.000	0.000	0.000	0.000
48	A	81	GLU	-1	-0.806	-0.893	58.448	-0.026	-0.026	0.000	0.000	0.000	0.000
49	A	82	LYS	1	0.814	0.905	57.414	0.034	0.034	0.000	0.000	0.000	0.000
50	A	83	ALA	0	-0.021	-0.017	61.278	0.001	0.001	0.000	0.000	0.000	0.000
51	A	84	HIS	0	-0.012	0.008	63.017	0.001	0.001	0.000	0.000	0.000	0.000
52	A	85	LYS	1	0.858	0.921	63.251	0.026	0.026	0.000	0.000	0.000	0.000
53	A	86	PHE	0	-0.005	-0.019	63.390	0.000	0.000	0.000	0.000	0.000	0.000
54	A	87	ALA	0	0.009	0.033	67.411	0.000	0.000	0.000	0.000	0.000	0.000
55	A	88	LEU	0	0.019	-0.016	68.244	0.000	0.000	0.000	0.000	0.000	0.000
56	A	89	GLU	-1	-0.800	-0.878	68.755	-0.023	-0.023	0.000	0.000	0.000	0.000
57	A	90	LYS	1	0.839	0.888	70.819	0.022	0.022	0.000	0.000	0.000	0.000
58	A	91	PHE	0	0.050	0.032	72.519	0.000	0.000	0.000	0.000	0.000	0.000
59	A	92	ILE	0	-0.012	-0.004	74.259	0.001	0.001	0.000	0.000	0.000	0.000
60	A	93	ASN	0	0.027	0.000	72.746	0.001	0.001	0.000	0.000	0.000	0.000
61	A	94	GLU	-1	-0.885	-0.932	76.277	-0.020	-0.020	0.000	0.000	0.000	0.000
62	A	95	LEU	0	0.000	0.000	78.636	0.000	0.000	0.000	0.000	0.000	0.000
63	A	96	LEU	0	0.027	0.039	77.275	0.001	0.001	0.000	0.000	0.000	0.000
64	A	97	PRO	0	0.019	0.014	81.114	0.000	0.000	0.000	0.000	0.000	0.000
65	A	98	VAL	0	-0.067	-0.039	84.004	0.000	0.000	0.000	0.000	0.000	0.000
66	A	99	ILE	0	-0.017	-0.009	82.153	0.000	0.000	0.000	0.000	0.000	0.000
67	A	100	ASP	-1	-0.780	-0.897	84.053	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	101	SER	0	-0.102	-0.058	87.155	0.000	0.000	0.000	0.000	0.000	0.000
69	A	102	LEU	0	-0.004	0.013	89.429	0.000	0.000	0.000	0.000	0.000	0.000
70	A	103	ASP	-1	-0.754	-0.877	88.283	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	104	ARG	1	0.982	1.006	88.676	0.014	0.014	0.000	0.000	0.000	0.000
72	A	105	ALA	0	-0.068	-0.040	92.569	0.000	0.000	0.000	0.000	0.000	0.000
73	A	106	LEU	0	-0.043	-0.019	93.192	0.000	0.000	0.000	0.000	0.000	0.000
74	A	107	GLU	-1	-0.953	-0.961	92.984	-0.012	-0.012	0.000	0.000	0.000	0.000
75	A	108	VAL	0	-0.034	-0.022	96.195	0.000	0.000	0.000	0.000	0.000	0.000
76	A	109	ALA	0	-0.031	0.009	98.732	0.000	0.000	0.000	0.000	0.000	0.000
77	A	110	ASP	-1	-0.949	-0.979	99.334	-0.010	-0.010	0.000	0.000	0.000	0.000
78	A	111	LYS	1	0.855	0.912	101.333	0.010	0.010	0.000	0.000	0.000	0.000
79	A	112	ALA	0	-0.026	0.005	104.858	0.000	0.000	0.000	0.000	0.000	0.000
80	A	113	ASN	0	-0.056	-0.055	106.623	0.000	0.000	0.000	0.000	0.000	0.000
81	A	114	PRO	0	0.030	0.010	107.736	0.000	0.000	0.000	0.000	0.000	0.000
82	A	115	ASP	-1	-0.837	-0.874	109.498	-0.009	-0.009	0.000	0.000	0.000	0.000
83	A	116	MET	0	-0.060	-0.037	102.846	0.000	0.000	0.000	0.000	0.000	0.000
84	A	117	SER	0	-0.024	-0.031	104.630	0.000	0.000	0.000	0.000	0.000	0.000
85	A	118	ALA	0	0.069	0.037	103.144	0.000	0.000	0.000	0.000	0.000	0.000
86	A	119	MET	0	0.035	0.014	100.395	0.000	0.000	0.000	0.000	0.000	0.000
87	A	120	VAL	0	0.008	0.003	99.119	0.000	0.000	0.000	0.000	0.000	0.000
88	A	121	GLU	-1	-0.903	-0.957	98.083	-0.011	-0.011	0.000	0.000	0.000	0.000
89	A	122	ASP	-1	-0.937	-0.963	97.485	-0.011	-0.011	0.000	0.000	0.000	0.000
90	A	123	ILE	0	-0.097	-0.072	94.160	0.000	0.000	0.000	0.000	0.000	0.000
91	A	124	GLU	-1	-0.879	-0.930	93.205	-0.012	-0.012	0.000	0.000	0.000	0.000
92	A	125	LEU	0	0.004	0.006	92.796	0.000	0.000	0.000	0.000	0.000	0.000
93	A	126	THR	0	-0.042	-0.026	90.398	0.000	0.000	0.000	0.000	0.000	0.000
94	A	127	LEU	0	0.016	0.009	87.716	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	128	LYS	1	0.926	0.944	87.831	0.013	0.013	0.000	0.000	0.000	0.000
96	A	129	SER	0	-0.063	-0.039	87.229	0.000	0.000	0.000	0.000	0.000	0.000
97	A	130	MET	0	-0.033	-0.012	84.248	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	131	LEU	0	0.014	0.007	83.199	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	132	ASP	-1	-0.766	-0.862	82.190	-0.015	-0.015	0.000	0.000	0.000	0.000
100	A	133	VAL	0	-0.039	-0.006	81.223	0.000	0.000	0.000	0.000	0.000	0.000
101	A	134	VAL	0	-0.028	-0.019	78.583	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	135	ARG	1	0.878	0.915	77.499	0.014	0.014	0.000	0.000	0.000	0.000
103	A	136	LYS	1	0.793	0.903	75.832	0.018	0.018	0.000	0.000	0.000	0.000
104	A	137	PHE	0	-0.084	-0.043	73.990	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	138	GLY	0	0.028	0.007	72.697	0.000	0.000	0.000	0.000	0.000	0.000
106	A	139	VAL	0	-0.029	-0.007	73.544	0.000	0.000	0.000	0.000	0.000	0.000
107	A	140	GLU	-1	-0.774	-0.850	75.943	-0.015	-0.015	0.000	0.000	0.000	0.000
108	A	141	VAL	0	-0.054	-0.061	77.662	0.000	0.000	0.000	0.000	0.000	0.000
109	A	142	ILE	0	-0.041	-0.020	76.020	0.000	0.000	0.000	0.000	0.000	0.000
110	A	143	ALA	0	0.003	-0.044	79.969	0.000	0.000	0.000	0.000	0.000	0.000
111	A	144	GLU	-1	-0.933	-0.948	81.390	-0.013	-0.013	0.000	0.000	0.000	0.000
112	A	145	THR	0	0.015	-0.014	83.134	0.000	0.000	0.000	0.000	0.000	0.000
113	A	146	ASN	0	-0.051	-0.029	84.823	0.000	0.000	0.000	0.000	0.000	0.000
114	A	147	VAL	0	0.053	0.050	80.102	0.000	0.000	0.000	0.000	0.000	0.000
115	A	148	PRO	0	-0.013	-0.009	77.895	0.000	0.000	0.000	0.000	0.000	0.000
116	A	149	LEU	0	-0.001	0.002	77.473	0.000	0.000	0.000	0.000	0.000	0.000
117	A	150	ASP	-1	-0.770	-0.894	72.855	-0.017	-0.017	0.000	0.000	0.000	0.000
118	A	151	PRO	0	-0.052	-0.034	71.941	0.000	0.000	0.000	0.000	0.000	0.000
119	A	152	ASN	0	-0.111	-0.056	68.796	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	153	VAL	0	-0.052	-0.034	71.750	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	154	HIS	0	0.069	0.045	74.793	0.000	0.000	0.000	0.000	0.000	0.000
122	A	155	GLN	0	-0.006	-0.005	76.727	0.000	0.000	0.000	0.000	0.000	0.000
123	A	156	ALA	0	-0.009	-0.004	78.951	0.000	0.000	0.000	0.000	0.000	0.000
124	A	157	ILE	0	-0.012	-0.004	81.337	0.000	0.000	0.000	0.000	0.000	0.000
125	A	158	ALA	0	-0.028	-0.022	83.759	0.000	0.000	0.000	0.000	0.000	0.000
126	A	159	MET	0	-0.058	-0.007	84.073	0.000	0.000	0.000	0.000	0.000	0.000
127	A	160	VAL	0	0.034	0.011	87.091	0.000	0.000	0.000	0.000	0.000	0.000
128	A	161	GLU	-1	-0.885	-0.938	90.220	-0.010	-0.010	0.000	0.000	0.000	0.000
129	A	162	SER	0	-0.029	-0.045	91.512	0.000	0.000	0.000	0.000	0.000	0.000
130	A	163	ASP	-1	-0.822	-0.926	91.545	-0.009	-0.009	0.000	0.000	0.000	0.000
131	A	164	ASP	-1	-0.929	-0.926	92.530	-0.010	-0.010	0.000	0.000	0.000	0.000
132	A	165	VAL	0	-0.027	-0.023	87.565	0.000	0.000	0.000	0.000	0.000	0.000
133	A	166	ALA	0	-0.014	0.005	85.454	0.000	0.000	0.000	0.000	0.000	0.000
134	A	167	PRO	0	0.018	-0.013	85.261	0.000	0.000	0.000	0.000	0.000	0.000
135	A	168	GLY	0	-0.034	-0.020	82.061	0.000	0.000	0.000	0.000	0.000	0.000
136	A	169	ASN	0	-0.052	-0.032	81.526	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	170	VAL	0	-0.039	-0.007	81.387	0.000	0.000	0.000	0.000	0.000	0.000
138	A	171	LEU	0	0.014	-0.010	84.175	0.000	0.000	0.000	0.000	0.000	0.000
139	A	172	GLY	0	0.023	0.005	87.224	0.000	0.000	0.000	0.000	0.000	0.000
140	A	173	ILE	0	-0.087	-0.029	84.418	0.000	0.000	0.000	0.000	0.000	0.000
141	A	174	MET	0	0.011	0.011	86.344	0.000	0.000	0.000	0.000	0.000	0.000
142	A	175	GLN	0	-0.030	-0.030	83.573	0.000	0.000	0.000	0.000	0.000	0.000
143	A	176	LYS	1	0.878	0.934	83.141	0.013	0.013	0.000	0.000	0.000	0.000
144	A	177	GLY	0	0.043	0.023	79.302	0.000	0.000	0.000	0.000	0.000	0.000
145	A	178	TYR	0	0.022	0.020	77.552	0.000	0.000	0.000	0.000	0.000	0.000
146	A	179	THR	0	-0.007	-0.006	72.521	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	180	LEU	0	0.027	0.027	70.317	0.000	0.000	0.000	0.000	0.000	0.000
148	A	181	ASN	0	-0.061	-0.053	67.927	0.000	0.000	0.000	0.000	0.000	0.000
149	A	182	GLY	0	0.010	0.006	67.538	-0.001	-0.001	0.000	0.000	0.000	0.000
150	A	183	ARG	1	0.790	0.914	64.314	0.025	0.025	0.000	0.000	0.000	0.000
151	A	184	THR	0	0.011	-0.013	68.441	0.000	0.000	0.000	0.000	0.000	0.000
152	A	185	ILE	0	-0.079	-0.034	71.213	-0.001	-0.001	0.000	0.000	0.000	0.000
153	A	186	ARG	1	0.841	0.919	73.367	0.016	0.016	0.000	0.000	0.000	0.000
154	A	187	ALA	0	0.019	0.025	75.128	0.000	0.000	0.000	0.000	0.000	0.000
155	A	188	ALA	0	0.044	0.032	76.777	0.000	0.000	0.000	0.000	0.000	0.000
156	A	189	MET	0	-0.043	-0.010	80.068	0.000	0.000	0.000	0.000	0.000	0.000
157	A	190	VAL	0	-0.005	-0.006	81.335	0.000	0.000	0.000	0.000	0.000	0.000
158	A	191	THR	0	0.053	0.029	83.882	0.000	0.000	0.000	0.000	0.000	0.000
159	A	192	VAL	0	0.019	0.027	81.659	0.000	0.000	0.000	0.000	0.000	0.000
160	A	193	ALA	0	0.055	0.046	84.981	0.000	0.000	0.000	0.000	0.000	0.000
161	A	194	LYS	1	0.807	0.891	86.264	0.010	0.010	0.000	0.000	0.000	0.000
162	A	195	ALA	0	0.028	-0.007	88.232	0.000	0.000	0.000	0.000	0.000	0.000
163	A	196	LYS	1	0.929	0.985	90.291	0.008	0.008	0.000	0.000	0.000	0.000
164	A	197	ALA	0	-0.041	-0.002	93.367	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:34:ALA)