FMO DATABASE

FMODB ID: KRNY3

Calculation Name: 1DKG-A-Xray307

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: 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	165
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1225506.339605
FMO2-HF: Nuclear repulsion	1160968.5975
FMO2-HF: Total energy	-64537.742105
FMO2-MP2: Total energy	-64723.916365

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:33:ACE )

Summations of interaction energy for fragment #1(A:33: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.
-0.782	0.361	-0.004	-0.463	-0.677	-0.002

Interaction energy analysis for fragmet #1(A:33:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.021

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	35	GLU	-1	-0.966	-0.968	3.827	-0.356	0.787	-0.004	-0.463	-0.677	-0.002
4	A	36	GLN	0	0.030	0.001	6.134	0.121	0.121	0.000	0.000	0.000	0.000
5	A	37	VAL	0	0.050	0.033	9.315	0.136	0.136	0.000	0.000	0.000	0.000
6	A	38	ASP	-1	-0.839	-0.906	11.693	-0.209	-0.209	0.000	0.000	0.000	0.000
7	A	39	PRO	0	0.092	0.051	14.331	-0.018	-0.018	0.000	0.000	0.000	0.000
8	A	40	ARG	1	0.756	0.846	16.664	0.222	0.222	0.000	0.000	0.000	0.000
9	A	41	ASP	-1	-0.867	-0.943	12.100	-0.566	-0.566	0.000	0.000	0.000	0.000
10	A	42	GLU	-1	-0.899	-0.956	12.088	-0.235	-0.235	0.000	0.000	0.000	0.000
11	A	43	LYS	1	0.886	0.951	13.917	0.208	0.208	0.000	0.000	0.000	0.000
12	A	44	VAL	0	-0.035	-0.019	14.290	0.039	0.039	0.000	0.000	0.000	0.000
13	A	45	ALA	0	0.059	0.037	12.271	0.019	0.019	0.000	0.000	0.000	0.000
14	A	46	ASN	0	-0.018	0.014	14.145	0.044	0.044	0.000	0.000	0.000	0.000
15	A	47	LEU	0	-0.064	-0.026	17.008	0.021	0.021	0.000	0.000	0.000	0.000
16	A	48	GLU	-1	-0.913	-0.966	14.060	-0.355	-0.355	0.000	0.000	0.000	0.000
17	A	49	ALA	0	0.012	0.011	15.918	0.016	0.016	0.000	0.000	0.000	0.000
18	A	50	GLN	0	-0.001	-0.016	17.619	0.019	0.019	0.000	0.000	0.000	0.000
19	A	51	LEU	0	-0.004	0.004	20.966	0.014	0.014	0.000	0.000	0.000	0.000
20	A	52	ALA	0	0.076	0.051	18.597	0.010	0.010	0.000	0.000	0.000	0.000
21	A	53	GLU	-1	-0.937	-0.945	20.675	-0.035	-0.035	0.000	0.000	0.000	0.000
22	A	54	ALA	0	-0.139	-0.066	22.720	0.011	0.011	0.000	0.000	0.000	0.000
23	A	55	GLN	0	0.056	0.007	22.476	0.005	0.005	0.000	0.000	0.000	0.000
24	A	56	THR	0	-0.069	-0.046	22.893	0.008	0.008	0.000	0.000	0.000	0.000
25	A	57	ARG	1	0.928	0.954	25.481	0.054	0.054	0.000	0.000	0.000	0.000
26	A	58	GLU	-1	-0.920	-0.950	28.437	-0.054	-0.054	0.000	0.000	0.000	0.000
27	A	59	ARG	1	0.965	0.989	24.730	0.059	0.059	0.000	0.000	0.000	0.000
28	A	60	ASP	-1	-0.867	-0.944	28.114	-0.021	-0.021	0.000	0.000	0.000	0.000
29	A	61	GLY	0	-0.095	-0.054	31.155	0.003	0.003	0.000	0.000	0.000	0.000
30	A	62	ILE	0	-0.016	-0.003	33.145	0.002	0.002	0.000	0.000	0.000	0.000
31	A	63	LEU	0	-0.003	-0.010	32.671	0.002	0.002	0.000	0.000	0.000	0.000
32	A	64	ARG	1	0.991	0.984	35.515	0.016	0.016	0.000	0.000	0.000	0.000
33	A	65	VAL	0	0.033	0.027	37.325	0.002	0.002	0.000	0.000	0.000	0.000
34	A	66	LYS	1	0.922	0.971	37.447	0.026	0.026	0.000	0.000	0.000	0.000
35	A	67	ALA	0	-0.002	-0.008	39.196	0.001	0.001	0.000	0.000	0.000	0.000
36	A	68	GLU	-1	-0.973	-0.981	40.824	-0.012	-0.012	0.000	0.000	0.000	0.000
37	A	69	MET	0	-0.004	-0.005	42.759	0.001	0.001	0.000	0.000	0.000	0.000
38	A	70	GLU	-1	-0.894	-0.930	43.642	-0.011	-0.011	0.000	0.000	0.000	0.000
39	A	71	ASN	0	0.004	-0.015	43.632	0.001	0.001	0.000	0.000	0.000	0.000
40	A	72	LEU	0	-0.084	-0.044	47.019	0.001	0.001	0.000	0.000	0.000	0.000
41	A	73	ARG	1	1.006	1.008	46.997	0.014	0.014	0.000	0.000	0.000	0.000
42	A	74	ARG	1	1.015	1.017	49.574	0.003	0.003	0.000	0.000	0.000	0.000
43	A	75	ARG	1	0.874	0.916	47.927	0.007	0.007	0.000	0.000	0.000	0.000
44	A	76	THR	0	0.070	0.030	53.344	0.000	0.000	0.000	0.000	0.000	0.000
45	A	77	GLU	-1	-0.946	-0.954	53.642	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	78	LEU	0	-0.017	-0.004	54.270	0.001	0.001	0.000	0.000	0.000	0.000
47	A	79	ASP	-1	-0.970	-0.993	56.736	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	80	ILE	0	-0.022	-0.014	59.104	0.000	0.000	0.000	0.000	0.000	0.000
49	A	81	GLU	-1	-0.905	-0.954	60.430	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	82	LYS	1	0.882	0.940	60.762	0.003	0.003	0.000	0.000	0.000	0.000
51	A	83	ALA	0	-0.028	-0.023	63.268	0.000	0.000	0.000	0.000	0.000	0.000
52	A	84	HIS	0	0.005	0.020	64.991	0.000	0.000	0.000	0.000	0.000	0.000
53	A	85	LYS	1	0.911	0.960	64.788	0.002	0.002	0.000	0.000	0.000	0.000
54	A	86	PHE	0	-0.028	-0.034	65.592	0.000	0.000	0.000	0.000	0.000	0.000
55	A	87	ALA	0	0.015	0.037	69.267	0.000	0.000	0.000	0.000	0.000	0.000
56	A	88	LEU	0	0.019	-0.016	70.291	0.000	0.000	0.000	0.000	0.000	0.000
57	A	89	GLU	-1	-0.814	-0.897	70.349	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	90	LYS	1	0.989	0.980	72.765	0.003	0.003	0.000	0.000	0.000	0.000
59	A	91	PHE	0	0.025	0.018	74.416	0.000	0.000	0.000	0.000	0.000	0.000
60	A	92	ILE	0	-0.029	-0.001	75.929	0.000	0.000	0.000	0.000	0.000	0.000
61	A	93	ASN	0	0.018	-0.005	74.330	0.000	0.000	0.000	0.000	0.000	0.000
62	A	94	GLU	-1	-0.995	-1.007	78.094	-0.002	-0.002	0.000	0.000	0.000	0.000
63	A	95	LEU	0	0.002	0.003	80.467	0.000	0.000	0.000	0.000	0.000	0.000
64	A	96	LEU	0	0.021	0.038	79.316	0.000	0.000	0.000	0.000	0.000	0.000
65	A	97	PRO	0	0.009	0.007	82.619	0.000	0.000	0.000	0.000	0.000	0.000
66	A	98	VAL	0	-0.039	-0.029	85.691	0.000	0.000	0.000	0.000	0.000	0.000
67	A	99	ILE	0	-0.048	-0.025	84.043	0.000	0.000	0.000	0.000	0.000	0.000
68	A	100	ASP	-1	-0.819	-0.910	85.719	0.000	0.000	0.000	0.000	0.000	0.000
69	A	101	SER	0	-0.107	-0.057	88.674	0.000	0.000	0.000	0.000	0.000	0.000
70	A	102	LEU	0	0.008	0.010	90.981	0.000	0.000	0.000	0.000	0.000	0.000
71	A	103	ASP	-1	-0.749	-0.907	89.674	0.000	0.000	0.000	0.000	0.000	0.000
72	A	104	ARG	1	0.945	0.995	90.077	0.000	0.000	0.000	0.000	0.000	0.000
73	A	105	ALA	0	-0.068	-0.042	94.000	0.000	0.000	0.000	0.000	0.000	0.000
74	A	106	LEU	0	-0.039	-0.017	94.783	0.000	0.000	0.000	0.000	0.000	0.000
75	A	107	GLU	-1	-0.960	-0.970	93.554	0.001	0.001	0.000	0.000	0.000	0.000
76	A	108	VAL	0	-0.051	-0.025	97.499	0.000	0.000	0.000	0.000	0.000	0.000
77	A	109	ALA	0	-0.045	0.001	100.136	0.000	0.000	0.000	0.000	0.000	0.000
78	A	110	ASP	-1	-0.921	-0.967	101.226	0.001	0.001	0.000	0.000	0.000	0.000
79	A	111	LYS	1	0.851	0.920	103.032	0.000	0.000	0.000	0.000	0.000	0.000
80	A	112	ALA	0	0.046	0.033	104.969	0.000	0.000	0.000	0.000	0.000	0.000
81	A	113	ASN	0	-0.062	-0.041	107.025	0.000	0.000	0.000	0.000	0.000	0.000
82	A	114	PRO	0	0.042	0.001	109.288	0.000	0.000	0.000	0.000	0.000	0.000
83	A	115	ASP	-1	-0.919	-0.935	110.636	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	116	MET	0	-0.066	-0.032	104.536	0.000	0.000	0.000	0.000	0.000	0.000
85	A	117	SER	0	-0.011	-0.017	106.249	0.000	0.000	0.000	0.000	0.000	0.000
86	A	118	ALA	0	0.068	0.037	104.754	0.000	0.000	0.000	0.000	0.000	0.000
87	A	119	MET	0	0.039	0.016	101.822	0.000	0.000	0.000	0.000	0.000	0.000
88	A	120	VAL	0	0.022	0.007	100.420	0.000	0.000	0.000	0.000	0.000	0.000
89	A	121	GLU	-1	-0.900	-0.959	99.694	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	122	ASP	-1	-0.952	-0.963	99.172	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	123	ILE	0	-0.113	-0.077	95.656	0.000	0.000	0.000	0.000	0.000	0.000
92	A	124	GLU	-1	-0.889	-0.936	95.086	0.000	0.000	0.000	0.000	0.000	0.000
93	A	125	LEU	0	-0.012	-0.004	94.405	0.000	0.000	0.000	0.000	0.000	0.000
94	A	126	THR	0	-0.010	-0.009	92.020	0.000	0.000	0.000	0.000	0.000	0.000
95	A	127	LEU	0	0.004	0.001	89.107	0.000	0.000	0.000	0.000	0.000	0.000
96	A	128	LYS	1	0.971	0.994	89.468	0.002	0.002	0.000	0.000	0.000	0.000
97	A	129	SER	0	-0.047	-0.034	88.922	0.000	0.000	0.000	0.000	0.000	0.000
98	A	130	MET	0	-0.027	-0.007	85.832	0.000	0.000	0.000	0.000	0.000	0.000
99	A	131	LEU	0	0.011	-0.001	84.460	0.000	0.000	0.000	0.000	0.000	0.000
100	A	132	ASP	-1	-0.864	-0.942	83.852	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	133	VAL	0	-0.058	-0.011	82.939	0.000	0.000	0.000	0.000	0.000	0.000
102	A	134	VAL	0	-0.032	-0.020	80.326	0.000	0.000	0.000	0.000	0.000	0.000
103	A	135	ARG	1	0.943	0.958	79.243	0.001	0.001	0.000	0.000	0.000	0.000
104	A	136	LYS	1	0.794	0.911	77.981	0.003	0.003	0.000	0.000	0.000	0.000
105	A	137	PHE	0	-0.078	-0.045	76.254	0.000	0.000	0.000	0.000	0.000	0.000
106	A	138	GLY	0	0.021	0.008	74.385	0.000	0.000	0.000	0.000	0.000	0.000
107	A	139	VAL	0	-0.015	-0.005	75.107	0.000	0.000	0.000	0.000	0.000	0.000
108	A	140	GLU	-1	-0.791	-0.873	77.386	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	141	VAL	0	-0.060	-0.052	79.058	0.000	0.000	0.000	0.000	0.000	0.000
110	A	142	ILE	0	-0.047	-0.007	77.317	0.000	0.000	0.000	0.000	0.000	0.000
111	A	143	ALA	0	0.012	-0.065	81.081	0.000	0.000	0.000	0.000	0.000	0.000
112	A	144	GLU	-1	-0.935	-0.949	82.155	0.001	0.001	0.000	0.000	0.000	0.000
113	A	145	THR	0	-0.010	-0.045	83.918	0.000	0.000	0.000	0.000	0.000	0.000
114	A	146	ASN	0	-0.003	-0.011	85.492	0.000	0.000	0.000	0.000	0.000	0.000
115	A	147	VAL	0	0.050	0.046	80.755	0.000	0.000	0.000	0.000	0.000	0.000
116	A	148	PRO	0	-0.025	-0.015	78.313	0.000	0.000	0.000	0.000	0.000	0.000
117	A	149	LEU	0	-0.019	-0.005	77.585	0.000	0.000	0.000	0.000	0.000	0.000
118	A	150	ASP	-1	-0.795	-0.920	73.532	0.003	0.003	0.000	0.000	0.000	0.000
119	A	151	PRO	0	-0.048	-0.039	72.625	0.000	0.000	0.000	0.000	0.000	0.000
120	A	152	ASN	0	-0.066	-0.025	68.927	0.000	0.000	0.000	0.000	0.000	0.000
121	A	153	VAL	0	-0.039	-0.023	72.549	0.000	0.000	0.000	0.000	0.000	0.000
122	A	154	HIS	0	0.070	0.057	75.716	0.000	0.000	0.000	0.000	0.000	0.000
123	A	155	GLN	0	-0.007	-0.015	77.490	0.000	0.000	0.000	0.000	0.000	0.000
124	A	156	ALA	0	0.002	-0.006	79.729	0.000	0.000	0.000	0.000	0.000	0.000
125	A	157	ILE	0	0.009	0.010	81.951	0.000	0.000	0.000	0.000	0.000	0.000
126	A	158	ALA	0	-0.052	-0.040	84.441	0.000	0.000	0.000	0.000	0.000	0.000
127	A	159	MET	0	-0.051	-0.004	84.047	0.000	0.000	0.000	0.000	0.000	0.000
128	A	160	VAL	0	0.028	0.009	87.449	0.000	0.000	0.000	0.000	0.000	0.000
129	A	161	GLU	-1	-0.941	-0.985	90.504	0.004	0.004	0.000	0.000	0.000	0.000
130	A	162	SER	0	-0.007	-0.008	91.734	0.000	0.000	0.000	0.000	0.000	0.000
131	A	163	ASP	-1	-0.845	-0.925	91.733	0.004	0.004	0.000	0.000	0.000	0.000
132	A	164	ASP	-1	-0.952	-0.965	93.022	0.002	0.002	0.000	0.000	0.000	0.000
133	A	165	VAL	0	-0.043	-0.032	87.943	0.000	0.000	0.000	0.000	0.000	0.000
134	A	166	ALA	0	-0.025	-0.003	85.568	0.000	0.000	0.000	0.000	0.000	0.000
135	A	167	PRO	0	0.017	-0.012	85.216	0.000	0.000	0.000	0.000	0.000	0.000
136	A	168	GLY	0	-0.037	-0.022	82.245	0.000	0.000	0.000	0.000	0.000	0.000
137	A	169	ASN	0	-0.010	-0.005	81.858	0.000	0.000	0.000	0.000	0.000	0.000
138	A	170	VAL	0	-0.080	0.010	82.168	0.000	0.000	0.000	0.000	0.000	0.000
139	A	171	LEU	0	0.030	-0.008	84.738	0.000	0.000	0.000	0.000	0.000	0.000
140	A	172	GLY	0	0.023	-0.017	87.860	0.000	0.000	0.000	0.000	0.000	0.000
141	A	173	ILE	0	-0.081	-0.016	85.345	0.000	0.000	0.000	0.000	0.000	0.000
142	A	174	MET	0	0.016	0.016	87.243	0.000	0.000	0.000	0.000	0.000	0.000
143	A	175	GLN	0	0.010	-0.009	84.325	0.000	0.000	0.000	0.000	0.000	0.000
144	A	176	LYS	1	0.925	0.984	84.357	0.000	0.000	0.000	0.000	0.000	0.000
145	A	177	GLY	0	0.038	0.026	80.445	0.000	0.000	0.000	0.000	0.000	0.000
146	A	178	TYR	0	0.032	0.025	78.921	0.000	0.000	0.000	0.000	0.000	0.000
147	A	179	THR	0	0.020	0.005	73.809	0.000	0.000	0.000	0.000	0.000	0.000
148	A	180	LEU	0	0.031	0.039	72.216	0.000	0.000	0.000	0.000	0.000	0.000
149	A	181	ASN	0	-0.073	-0.054	69.329	0.000	0.000	0.000	0.000	0.000	0.000
150	A	182	GLY	0	0.010	-0.001	68.955	0.000	0.000	0.000	0.000	0.000	0.000
151	A	183	ARG	1	0.847	0.937	65.601	0.002	0.002	0.000	0.000	0.000	0.000
152	A	184	THR	0	0.002	-0.015	69.755	0.000	0.000	0.000	0.000	0.000	0.000
153	A	185	ILE	0	-0.079	-0.031	72.525	0.000	0.000	0.000	0.000	0.000	0.000
154	A	186	ARG	1	0.817	0.892	74.776	0.000	0.000	0.000	0.000	0.000	0.000
155	A	187	ALA	0	0.028	0.028	76.200	0.000	0.000	0.000	0.000	0.000	0.000
156	A	188	ALA	0	0.040	0.028	77.851	0.000	0.000	0.000	0.000	0.000	0.000
157	A	189	MET	0	-0.042	-0.003	80.992	0.000	0.000	0.000	0.000	0.000	0.000
158	A	190	VAL	0	-0.005	-0.005	82.048	0.000	0.000	0.000	0.000	0.000	0.000
159	A	191	THR	0	0.015	0.031	84.658	0.000	0.000	0.000	0.000	0.000	0.000
160	A	192	VAL	0	0.027	0.025	82.248	0.000	0.000	0.000	0.000	0.000	0.000
161	A	193	ALA	0	0.056	0.038	85.434	0.000	0.000	0.000	0.000	0.000	0.000
162	A	194	LYS	1	0.802	0.924	86.468	-0.004	-0.004	0.000	0.000	0.000	0.000
163	A	195	ALA	0	0.022	-0.016	88.366	0.000	0.000	0.000	0.000	0.000	0.000
164	A	196	LYS	1	0.920	0.968	90.286	-0.004	-0.004	0.000	0.000	0.000	0.000
165	A	197	ALA	-1	-0.912	-0.933	93.297	0.004	0.004	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:33:ACE )