FMO DATABASE

FMODB ID: Q8QRY

Calculation Name: 1DKG-B-Xray307

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DKG

Chain ID: B

ChEMBL ID:

UniProt ID: P0A6Y8

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	155
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1102795.100772
FMO2-HF: Nuclear repulsion	1042661.158961
FMO2-HF: Total energy	-60133.941811
FMO2-MP2: Total energy	-60307.204961

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(B:37:ACE )

Summations of interaction energy for fragment #1(B:37:ACE )

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.
-3.324	-1.025	1.576	-1.806	-2.067	-0.017

Interaction energy analysis for fragmet #1(B:37:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.052 / q_NPA : -0.032

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	B	39	PRO	0	0.008	0.010	3.278	0.933	2.110	0.056	-0.554	-0.678	-0.001
4	B	40	ARG	1	0.884	0.923	4.524	0.321	0.403	0.000	-0.011	-0.071	0.000
5	B	41	ASP	-1	-0.812	-0.883	2.598	-5.162	-4.122	1.520	-1.241	-1.318	-0.016
6	B	42	GLU	-1	-0.881	-0.938	5.554	-0.339	-0.339	0.000	0.000	0.000	0.000
7	B	43	LYS	1	0.884	0.942	7.958	0.540	0.540	0.000	0.000	0.000	0.000
8	B	44	VAL	0	-0.026	-0.033	8.033	0.158	0.158	0.000	0.000	0.000	0.000
9	B	45	ALA	0	0.058	0.043	9.790	0.106	0.106	0.000	0.000	0.000	0.000
10	B	46	ASN	0	-0.021	-0.023	11.750	0.124	0.124	0.000	0.000	0.000	0.000
11	B	47	LEU	0	-0.048	-0.015	12.654	0.068	0.068	0.000	0.000	0.000	0.000
12	B	48	GLU	-1	-0.883	-0.942	12.694	-0.255	-0.255	0.000	0.000	0.000	0.000
13	B	49	ALA	0	-0.001	0.000	15.888	0.033	0.033	0.000	0.000	0.000	0.000
14	B	50	GLN	0	-0.058	-0.032	17.097	0.056	0.056	0.000	0.000	0.000	0.000
15	B	51	LEU	0	-0.023	0.001	18.824	0.024	0.024	0.000	0.000	0.000	0.000
16	B	52	ALA	0	0.033	0.010	20.338	0.018	0.018	0.000	0.000	0.000	0.000
17	B	53	GLU	-1	-0.932	-0.952	22.081	-0.122	-0.122	0.000	0.000	0.000	0.000
18	B	54	ALA	0	-0.015	-0.021	23.750	0.013	0.013	0.000	0.000	0.000	0.000
19	B	55	GLN	0	0.013	0.027	24.326	0.007	0.007	0.000	0.000	0.000	0.000
20	B	56	THR	0	-0.045	-0.050	26.076	0.009	0.009	0.000	0.000	0.000	0.000
21	B	57	ARG	1	0.946	0.983	25.738	0.106	0.106	0.000	0.000	0.000	0.000
22	B	58	GLU	-1	-0.951	-0.962	29.343	-0.044	-0.044	0.000	0.000	0.000	0.000
23	B	59	ARG	1	0.901	0.938	29.479	0.080	0.080	0.000	0.000	0.000	0.000
24	B	60	ASP	-1	-0.871	-0.944	32.058	-0.070	-0.070	0.000	0.000	0.000	0.000
25	B	61	GLY	0	0.016	0.007	33.407	0.004	0.004	0.000	0.000	0.000	0.000
26	B	62	ILE	0	-0.030	-0.009	34.768	0.005	0.005	0.000	0.000	0.000	0.000
27	B	63	LEU	0	-0.003	-0.009	36.569	0.004	0.004	0.000	0.000	0.000	0.000
28	B	64	ARG	1	0.892	0.956	38.031	0.047	0.047	0.000	0.000	0.000	0.000
29	B	65	VAL	0	0.111	0.025	39.684	0.003	0.003	0.000	0.000	0.000	0.000
30	B	66	LYS	1	0.919	0.961	39.514	0.039	0.039	0.000	0.000	0.000	0.000
31	B	67	ALA	0	-0.021	-0.009	42.664	0.002	0.002	0.000	0.000	0.000	0.000
32	B	68	GLU	-1	-0.971	-0.962	42.823	-0.039	-0.039	0.000	0.000	0.000	0.000
33	B	69	MET	0	-0.013	-0.022	45.467	0.002	0.002	0.000	0.000	0.000	0.000
34	B	70	GLU	-1	-0.889	-0.951	47.143	-0.026	-0.026	0.000	0.000	0.000	0.000
35	B	71	ASN	0	0.006	0.012	47.951	0.002	0.002	0.000	0.000	0.000	0.000
36	B	72	LEU	0	-0.029	-0.004	49.914	0.001	0.001	0.000	0.000	0.000	0.000
37	B	73	ARG	1	0.983	0.989	49.570	0.024	0.024	0.000	0.000	0.000	0.000
38	B	74	ARG	1	0.943	0.974	49.533	0.030	0.030	0.000	0.000	0.000	0.000
39	B	75	ARG	1	0.927	0.956	50.761	0.029	0.029	0.000	0.000	0.000	0.000
40	B	76	THR	0	-0.030	-0.012	55.624	0.001	0.001	0.000	0.000	0.000	0.000
41	B	77	GLU	-1	-0.892	-0.937	57.813	-0.018	-0.018	0.000	0.000	0.000	0.000
42	B	78	LEU	0	0.009	0.006	59.190	0.001	0.001	0.000	0.000	0.000	0.000
43	B	79	ASP	-1	-0.887	-0.976	59.057	-0.022	-0.022	0.000	0.000	0.000	0.000
44	B	80	ILE	0	-0.008	0.008	61.161	0.001	0.001	0.000	0.000	0.000	0.000
45	B	81	GLU	-1	-0.921	-0.966	63.661	-0.016	-0.016	0.000	0.000	0.000	0.000
46	B	82	LYS	1	0.778	0.906	61.546	0.021	0.021	0.000	0.000	0.000	0.000
47	B	83	ALA	0	-0.001	-0.010	66.405	0.001	0.001	0.000	0.000	0.000	0.000
48	B	84	HIS	0	0.039	0.034	68.172	0.001	0.001	0.000	0.000	0.000	0.000
49	B	85	LYS	1	0.978	1.000	69.173	0.017	0.017	0.000	0.000	0.000	0.000
50	B	86	PHE	0	-0.007	-0.011	70.825	0.000	0.000	0.000	0.000	0.000	0.000
51	B	87	ALA	0	0.003	-0.002	72.319	0.000	0.000	0.000	0.000	0.000	0.000
52	B	88	LEU	0	-0.020	-0.015	73.839	0.001	0.001	0.000	0.000	0.000	0.000
53	B	89	GLU	-1	-0.912	-0.972	74.602	-0.014	-0.014	0.000	0.000	0.000	0.000
54	B	90	LYS	1	0.965	0.989	76.956	0.013	0.013	0.000	0.000	0.000	0.000
55	B	91	PHE	0	-0.018	-0.008	78.350	0.000	0.000	0.000	0.000	0.000	0.000
56	B	92	ILE	0	0.011	-0.001	78.968	0.000	0.000	0.000	0.000	0.000	0.000
57	B	93	ASN	0	-0.003	-0.004	81.410	0.000	0.000	0.000	0.000	0.000	0.000
58	B	94	GLU	-1	-0.962	-0.981	82.607	-0.011	-0.011	0.000	0.000	0.000	0.000
59	B	95	LEU	0	-0.021	-0.003	83.629	0.000	0.000	0.000	0.000	0.000	0.000
60	B	96	LEU	0	0.016	0.002	85.758	0.000	0.000	0.000	0.000	0.000	0.000
61	B	97	PRO	0	-0.006	0.011	87.773	0.000	0.000	0.000	0.000	0.000	0.000
62	B	98	VAL	0	-0.005	-0.006	89.206	0.000	0.000	0.000	0.000	0.000	0.000
63	B	99	ILE	0	-0.004	-0.005	87.704	0.000	0.000	0.000	0.000	0.000	0.000
64	B	100	ASP	-1	-0.754	-0.878	91.844	-0.009	-0.009	0.000	0.000	0.000	0.000
65	B	101	SER	0	-0.146	-0.098	94.177	0.000	0.000	0.000	0.000	0.000	0.000
66	B	102	LEU	0	0.015	-0.003	93.274	0.000	0.000	0.000	0.000	0.000	0.000
67	B	103	ASP	-1	-0.813	-0.904	95.141	-0.008	-0.008	0.000	0.000	0.000	0.000
68	B	104	ARG	1	0.907	0.985	98.034	0.008	0.008	0.000	0.000	0.000	0.000
69	B	105	ALA	0	-0.066	-0.038	99.814	0.000	0.000	0.000	0.000	0.000	0.000
70	B	106	LEU	0	-0.020	-0.016	99.303	0.000	0.000	0.000	0.000	0.000	0.000
71	B	107	GLU	-1	-0.963	-0.964	101.425	-0.007	-0.007	0.000	0.000	0.000	0.000
72	B	108	VAL	0	-0.073	-0.037	103.867	0.000	0.000	0.000	0.000	0.000	0.000
73	B	109	NME	0	-0.047	-0.010	106.707	0.000	0.000	0.000	0.000	0.000	0.000
74	B	115	ACE	0	-0.005	-0.015	111.173	0.000	0.000	0.000	0.000	0.000	0.000
75	B	116	MET	0	0.012	-0.020	108.615	0.000	0.000	0.000	0.000	0.000	0.000
76	B	117	SER	0	0.014	0.006	107.642	0.000	0.000	0.000	0.000	0.000	0.000
77	B	118	ALA	0	0.061	0.038	106.287	0.000	0.000	0.000	0.000	0.000	0.000
78	B	119	MET	0	-0.023	0.017	102.417	0.000	0.000	0.000	0.000	0.000	0.000
79	B	120	VAL	0	0.053	0.011	102.878	0.000	0.000	0.000	0.000	0.000	0.000
80	B	121	GLU	-1	-0.925	-0.948	101.967	-0.006	-0.006	0.000	0.000	0.000	0.000
81	B	122	ASP	-1	-0.882	-0.945	99.839	-0.006	-0.006	0.000	0.000	0.000	0.000
82	B	123	ILE	0	-0.065	-0.029	98.260	0.000	0.000	0.000	0.000	0.000	0.000
83	B	124	GLU	-1	-0.859	-0.937	97.681	-0.007	-0.007	0.000	0.000	0.000	0.000
84	B	125	LEU	0	-0.032	-0.012	95.106	0.000	0.000	0.000	0.000	0.000	0.000
85	B	126	THR	0	-0.084	-0.046	93.594	0.000	0.000	0.000	0.000	0.000	0.000
86	B	127	LEU	0	0.015	0.008	92.661	0.000	0.000	0.000	0.000	0.000	0.000
87	B	128	LYS	1	0.924	0.978	91.479	0.007	0.007	0.000	0.000	0.000	0.000
88	B	129	SER	0	-0.016	-0.028	89.677	0.000	0.000	0.000	0.000	0.000	0.000
89	B	130	MET	0	-0.014	0.009	88.125	0.000	0.000	0.000	0.000	0.000	0.000
90	B	131	LEU	0	0.010	-0.003	87.315	0.000	0.000	0.000	0.000	0.000	0.000
91	B	132	ASP	-1	-0.940	-0.972	86.574	-0.009	-0.009	0.000	0.000	0.000	0.000
92	B	133	VAL	0	-0.088	-0.053	82.944	0.000	0.000	0.000	0.000	0.000	0.000
93	B	134	VAL	0	0.054	0.014	82.515	0.000	0.000	0.000	0.000	0.000	0.000
94	B	135	ARG	1	1.004	1.028	81.955	0.009	0.009	0.000	0.000	0.000	0.000
95	B	136	LYS	1	0.877	0.949	79.239	0.009	0.009	0.000	0.000	0.000	0.000
96	B	137	PHE	0	-0.083	-0.044	76.242	0.000	0.000	0.000	0.000	0.000	0.000
97	B	138	GLY	0	0.011	0.002	78.002	0.000	0.000	0.000	0.000	0.000	0.000
98	B	139	VAL	0	-0.081	0.011	79.517	0.000	0.000	0.000	0.000	0.000	0.000
99	B	140	GLU	-1	-0.875	-0.961	82.765	-0.010	-0.010	0.000	0.000	0.000	0.000
100	B	141	VAL	0	-0.032	-0.028	85.537	0.000	0.000	0.000	0.000	0.000	0.000
101	B	142	ILE	0	-0.038	0.010	87.422	0.000	0.000	0.000	0.000	0.000	0.000
102	B	143	ALA	0	0.005	-0.030	90.814	0.000	0.000	0.000	0.000	0.000	0.000
103	B	144	GLU	-1	-0.942	-0.939	93.404	-0.009	-0.009	0.000	0.000	0.000	0.000
104	B	145	THR	0	0.026	-0.021	95.352	0.000	0.000	0.000	0.000	0.000	0.000
105	B	146	ASN	0	-0.052	-0.036	98.214	0.000	0.000	0.000	0.000	0.000	0.000
106	B	147	VAL	0	0.005	0.043	94.152	0.000	0.000	0.000	0.000	0.000	0.000
107	B	148	PRO	0	-0.002	-0.003	95.069	0.000	0.000	0.000	0.000	0.000	0.000
108	B	149	LEU	0	-0.026	-0.009	94.663	0.000	0.000	0.000	0.000	0.000	0.000
109	B	150	ASP	-1	-0.793	-0.897	88.981	-0.012	-0.012	0.000	0.000	0.000	0.000
110	B	151	PRO	0	-0.033	-0.026	89.586	0.000	0.000	0.000	0.000	0.000	0.000
111	B	152	ASN	0	-0.067	-0.017	84.635	0.000	0.000	0.000	0.000	0.000	0.000
112	B	153	VAL	0	-0.020	-0.005	86.718	0.000	0.000	0.000	0.000	0.000	0.000
113	B	154	HIS	0	0.032	-0.004	89.100	0.000	0.000	0.000	0.000	0.000	0.000
114	B	155	GLN	0	0.003	0.004	92.021	0.000	0.000	0.000	0.000	0.000	0.000
115	B	156	ALA	0	-0.014	0.006	94.039	0.000	0.000	0.000	0.000	0.000	0.000
116	B	157	ILE	0	-0.006	-0.004	97.555	0.000	0.000	0.000	0.000	0.000	0.000
117	B	158	ALA	0	-0.040	-0.033	99.733	0.000	0.000	0.000	0.000	0.000	0.000
118	B	159	MET	0	-0.030	-0.013	102.760	0.000	0.000	0.000	0.000	0.000	0.000
119	B	160	VAL	0	-0.021	-0.018	104.833	0.000	0.000	0.000	0.000	0.000	0.000
120	B	161	GLU	-1	-0.781	-0.906	107.951	-0.007	-0.007	0.000	0.000	0.000	0.000
121	B	162	SER	0	-0.003	-0.010	108.391	0.000	0.000	0.000	0.000	0.000	0.000
122	B	163	ASP	-1	-0.897	-0.937	109.839	-0.007	-0.007	0.000	0.000	0.000	0.000
123	B	164	ASP	-1	-0.996	-0.992	107.439	-0.007	-0.007	0.000	0.000	0.000	0.000
124	B	165	VAL	0	-0.056	-0.030	103.236	0.000	0.000	0.000	0.000	0.000	0.000
125	B	166	ALA	0	-0.024	0.002	103.544	0.000	0.000	0.000	0.000	0.000	0.000
126	B	167	PRO	0	0.033	-0.006	104.093	0.000	0.000	0.000	0.000	0.000	0.000
127	B	168	GLY	0	-0.048	-0.016	101.117	0.000	0.000	0.000	0.000	0.000	0.000
128	B	169	ASN	0	0.001	-0.005	99.081	0.000	0.000	0.000	0.000	0.000	0.000
129	B	170	VAL	0	-0.024	-0.013	96.063	0.000	0.000	0.000	0.000	0.000	0.000
130	B	171	LEU	0	0.077	0.024	99.401	0.000	0.000	0.000	0.000	0.000	0.000
131	B	172	GLY	0	0.056	0.065	102.113	0.000	0.000	0.000	0.000	0.000	0.000
132	B	173	ILE	0	-0.016	-0.014	96.292	0.000	0.000	0.000	0.000	0.000	0.000
133	B	174	MET	0	-0.016	0.000	99.072	0.000	0.000	0.000	0.000	0.000	0.000
134	B	175	GLN	0	0.008	-0.010	93.688	0.000	0.000	0.000	0.000	0.000	0.000
135	B	176	LYS	1	0.951	0.983	92.710	0.008	0.008	0.000	0.000	0.000	0.000
136	B	177	GLY	0	0.024	-0.003	90.417	0.000	0.000	0.000	0.000	0.000	0.000
137	B	178	TYR	0	0.004	-0.003	85.987	0.000	0.000	0.000	0.000	0.000	0.000
138	B	179	THR	0	0.008	-0.003	83.004	0.000	0.000	0.000	0.000	0.000	0.000
139	B	180	LEU	0	0.015	0.010	77.385	0.000	0.000	0.000	0.000	0.000	0.000
140	B	181	ASN	0	-0.055	-0.047	75.989	0.000	0.000	0.000	0.000	0.000	0.000
141	B	182	GLY	0	0.030	0.027	78.824	0.000	0.000	0.000	0.000	0.000	0.000
142	B	183	ARG	1	0.928	0.960	75.333	0.014	0.014	0.000	0.000	0.000	0.000
143	B	184	THR	0	-0.004	-0.021	80.183	0.000	0.000	0.000	0.000	0.000	0.000
144	B	185	ILE	0	-0.095	-0.024	80.974	0.000	0.000	0.000	0.000	0.000	0.000
145	B	186	ARG	1	0.813	0.889	83.455	0.010	0.010	0.000	0.000	0.000	0.000
146	B	187	ALA	0	0.023	0.017	87.147	0.000	0.000	0.000	0.000	0.000	0.000
147	B	188	ALA	0	0.005	0.009	89.756	0.000	0.000	0.000	0.000	0.000	0.000
148	B	189	MET	0	-0.024	0.002	92.968	0.000	0.000	0.000	0.000	0.000	0.000
149	B	190	VAL	0	-0.021	-0.010	95.667	0.000	0.000	0.000	0.000	0.000	0.000
150	B	191	THR	0	-0.078	-0.063	98.318	0.000	0.000	0.000	0.000	0.000	0.000
151	B	192	VAL	0	0.049	0.018	99.131	0.000	0.000	0.000	0.000	0.000	0.000
152	B	193	ALA	0	0.054	0.044	101.758	0.000	0.000	0.000	0.000	0.000	0.000
153	B	194	LYS	1	0.760	0.859	104.860	0.008	0.008	0.000	0.000	0.000	0.000
154	B	195	ALA	0	0.036	0.042	106.987	0.000	0.000	0.000	0.000	0.000	0.000
155	B	196	NME	0	-0.013	0.011	109.776	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:37:ACE )