FMO DATABASE

FMODB ID: ZY75N

Calculation Name: 1DKG-B-Xray372

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: 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	151
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1092966.108055
FMO2-HF: Nuclear repulsion	1033171.881045
FMO2-HF: Total energy	-59794.22701
FMO2-MP2: Total energy	-59966.107224

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:38:ASP)

Summations of interaction energy for fragment #1(B:38:ASP)

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.
13.328	11.817	17.64	-8.927	-7.201	-0.037

Interaction energy analysis for fragmet #1(B:38:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.900 / q_NPA : -0.973

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	40	ARG	1	0.891	0.924	3.097	-38.905	-37.007	0.009	-0.874	-1.033	0.004
4	B	41	ASP	-1	-0.798	-0.867	1.778	35.903	29.969	17.456	-6.973	-4.549	-0.051
5	B	42	GLU	-1	-0.893	-0.941	2.995	42.165	44.563	0.176	-1.061	-1.512	0.010
6	B	43	LYS	1	0.896	0.944	4.776	-33.930	-33.803	-0.001	-0.019	-0.107	0.000
7	B	44	VAL	0	-0.024	-0.030	6.607	-3.942	-3.942	0.000	0.000	0.000	0.000
8	B	45	ALA	0	0.060	0.042	7.458	-3.004	-3.004	0.000	0.000	0.000	0.000
9	B	46	ASN	0	-0.017	-0.012	9.218	-3.879	-3.879	0.000	0.000	0.000	0.000
10	B	47	LEU	0	-0.046	-0.014	10.971	-2.331	-2.331	0.000	0.000	0.000	0.000
11	B	48	GLU	-1	-0.875	-0.937	12.211	21.067	21.067	0.000	0.000	0.000	0.000
12	B	49	ALA	0	-0.010	-0.004	13.568	-1.532	-1.532	0.000	0.000	0.000	0.000
13	B	50	GLN	0	-0.060	-0.041	14.378	-2.475	-2.475	0.000	0.000	0.000	0.000
14	B	51	LEU	0	-0.015	-0.002	16.781	-1.176	-1.176	0.000	0.000	0.000	0.000
15	B	52	ALA	0	0.033	0.010	18.217	-0.992	-0.992	0.000	0.000	0.000	0.000
16	B	53	GLU	-1	-0.868	-0.898	19.550	13.592	13.592	0.000	0.000	0.000	0.000
17	B	54	ALA	0	-0.015	-0.017	21.353	-0.794	-0.794	0.000	0.000	0.000	0.000
18	B	55	GLN	0	-0.009	0.023	22.646	-0.315	-0.315	0.000	0.000	0.000	0.000
19	B	56	THR	0	-0.049	-0.047	23.532	-0.723	-0.723	0.000	0.000	0.000	0.000
20	B	57	ARG	1	0.876	0.919	22.598	-13.615	-13.615	0.000	0.000	0.000	0.000
21	B	58	GLU	-1	-0.936	-0.959	26.974	10.366	10.366	0.000	0.000	0.000	0.000
22	B	59	ARG	1	0.812	0.872	27.265	-11.364	-11.364	0.000	0.000	0.000	0.000
23	B	60	ASP	-1	-0.790	-0.880	28.833	10.284	10.284	0.000	0.000	0.000	0.000
24	B	61	GLY	0	0.017	0.010	30.836	-0.374	-0.374	0.000	0.000	0.000	0.000
25	B	62	ILE	0	-0.022	-0.011	32.702	-0.447	-0.447	0.000	0.000	0.000	0.000
26	B	63	LEU	0	-0.009	-0.008	33.703	-0.357	-0.357	0.000	0.000	0.000	0.000
27	B	64	ARG	1	0.840	0.910	35.285	-8.494	-8.494	0.000	0.000	0.000	0.000
28	B	65	VAL	0	0.079	0.013	36.994	-0.278	-0.278	0.000	0.000	0.000	0.000
29	B	66	LYS	1	0.941	0.969	38.012	-8.473	-8.473	0.000	0.000	0.000	0.000
30	B	67	ALA	0	-0.020	-0.005	40.124	-0.213	-0.213	0.000	0.000	0.000	0.000
31	B	68	GLU	-1	-0.895	-0.911	40.392	7.710	7.710	0.000	0.000	0.000	0.000
32	B	69	MET	0	-0.023	-0.022	42.629	-0.165	-0.165	0.000	0.000	0.000	0.000
33	B	70	GLU	-1	-0.833	-0.908	44.669	6.426	6.426	0.000	0.000	0.000	0.000
34	B	71	ASN	0	0.024	0.022	44.390	-0.238	-0.238	0.000	0.000	0.000	0.000
35	B	72	LEU	0	-0.025	-0.009	47.120	-0.143	-0.143	0.000	0.000	0.000	0.000
36	B	73	ARG	1	0.970	0.992	48.069	-6.646	-6.646	0.000	0.000	0.000	0.000
37	B	74	ARG	1	0.878	0.920	46.824	-6.765	-6.765	0.000	0.000	0.000	0.000
38	B	75	ARG	1	0.935	0.968	48.122	-6.579	-6.579	0.000	0.000	0.000	0.000
39	B	76	THR	0	-0.012	-0.020	53.053	-0.103	-0.103	0.000	0.000	0.000	0.000
40	B	77	GLU	-1	-0.916	-0.938	55.159	5.391	5.391	0.000	0.000	0.000	0.000
41	B	78	LEU	0	0.009	0.004	56.080	-0.119	-0.119	0.000	0.000	0.000	0.000
42	B	79	ASP	-1	-0.888	-0.970	56.062	5.623	5.623	0.000	0.000	0.000	0.000
43	B	80	ILE	0	-0.027	0.000	58.543	-0.082	-0.082	0.000	0.000	0.000	0.000
44	B	81	GLU	-1	-0.821	-0.911	60.897	4.884	4.884	0.000	0.000	0.000	0.000
45	B	82	LYS	1	0.793	0.907	58.371	-5.582	-5.582	0.000	0.000	0.000	0.000
46	B	83	ALA	0	-0.001	-0.008	63.376	-0.093	-0.093	0.000	0.000	0.000	0.000
47	B	84	HIS	0	0.027	0.033	65.292	-0.087	-0.087	0.000	0.000	0.000	0.000
48	B	85	LYS	1	0.898	0.942	65.789	-4.964	-4.964	0.000	0.000	0.000	0.000
49	B	86	PHE	0	-0.014	-0.012	67.765	-0.075	-0.075	0.000	0.000	0.000	0.000
50	B	87	ALA	0	0.012	0.006	69.352	-0.074	-0.074	0.000	0.000	0.000	0.000
51	B	88	LEU	0	-0.021	-0.014	70.986	-0.080	-0.080	0.000	0.000	0.000	0.000
52	B	89	GLU	-1	-0.809	-0.882	71.646	4.459	4.459	0.000	0.000	0.000	0.000
53	B	90	LYS	1	0.939	0.984	73.869	-4.351	-4.351	0.000	0.000	0.000	0.000
54	B	91	PHE	0	-0.031	-0.017	75.402	-0.070	-0.070	0.000	0.000	0.000	0.000
55	B	92	ILE	0	0.018	0.002	76.644	-0.065	-0.065	0.000	0.000	0.000	0.000
56	B	93	ASN	0	0.020	0.006	78.313	-0.080	-0.080	0.000	0.000	0.000	0.000
57	B	94	GLU	-1	-0.945	-0.978	79.191	4.059	4.059	0.000	0.000	0.000	0.000
58	B	95	LEU	0	-0.014	0.000	81.231	-0.057	-0.057	0.000	0.000	0.000	0.000
59	B	96	LEU	0	0.020	0.008	82.513	-0.056	-0.056	0.000	0.000	0.000	0.000
60	B	97	PRO	0	0.014	0.013	84.794	-0.051	-0.051	0.000	0.000	0.000	0.000
61	B	98	VAL	0	-0.032	-0.016	86.323	-0.058	-0.058	0.000	0.000	0.000	0.000
62	B	99	ILE	0	0.011	-0.002	84.831	-0.040	-0.040	0.000	0.000	0.000	0.000
63	B	100	ASP	-1	-0.753	-0.847	89.107	3.617	3.617	0.000	0.000	0.000	0.000
64	B	101	SER	0	-0.083	-0.042	91.320	-0.066	-0.066	0.000	0.000	0.000	0.000
65	B	102	LEU	0	-0.006	-0.001	90.702	-0.042	-0.042	0.000	0.000	0.000	0.000
66	B	103	ASP	-1	-0.768	-0.861	92.493	3.485	3.485	0.000	0.000	0.000	0.000
67	B	104	ARG	1	0.922	0.957	94.310	-3.446	-3.446	0.000	0.000	0.000	0.000
68	B	105	ALA	0	-0.071	-0.040	97.060	-0.039	-0.039	0.000	0.000	0.000	0.000
69	B	106	LEU	0	-0.037	-0.018	96.733	-0.032	-0.032	0.000	0.000	0.000	0.000
70	B	107	GLU	-1	-0.955	-0.966	98.526	3.239	3.239	0.000	0.000	0.000	0.000
71	B	108	VAL	0	-0.118	-0.042	101.096	-0.040	-0.040	0.000	0.000	0.000	0.000
72	B	116	MET	0	-0.008	-0.025	106.387	-0.003	-0.003	0.000	0.000	0.000	0.000
73	B	117	SER	0	0.025	0.000	105.441	0.027	0.027	0.000	0.000	0.000	0.000
74	B	118	ALA	0	0.070	0.039	104.337	0.014	0.014	0.000	0.000	0.000	0.000
75	B	119	MET	0	-0.025	0.008	100.205	0.028	0.028	0.000	0.000	0.000	0.000
76	B	120	VAL	0	0.050	0.011	100.766	0.037	0.037	0.000	0.000	0.000	0.000
77	B	121	GLU	-1	-0.918	-0.946	99.764	3.224	3.224	0.000	0.000	0.000	0.000
78	B	122	ASP	-1	-0.894	-0.946	97.647	3.326	3.326	0.000	0.000	0.000	0.000
79	B	123	ILE	0	-0.077	-0.040	96.172	0.055	0.055	0.000	0.000	0.000	0.000
80	B	124	GLU	-1	-0.846	-0.929	95.370	3.321	3.321	0.000	0.000	0.000	0.000
81	B	125	LEU	0	-0.028	-0.010	93.243	0.049	0.049	0.000	0.000	0.000	0.000
82	B	126	THR	0	-0.087	-0.051	91.465	0.058	0.058	0.000	0.000	0.000	0.000
83	B	127	LEU	0	0.019	0.014	90.449	0.061	0.061	0.000	0.000	0.000	0.000
84	B	128	LYS	1	0.901	0.952	89.196	-3.579	-3.579	0.000	0.000	0.000	0.000
85	B	129	SER	0	-0.033	-0.024	87.543	0.054	0.054	0.000	0.000	0.000	0.000
86	B	130	MET	0	0.002	0.015	85.840	0.080	0.080	0.000	0.000	0.000	0.000
87	B	131	LEU	0	0.039	0.009	84.949	0.062	0.062	0.000	0.000	0.000	0.000
88	B	132	ASP	-1	-0.885	-0.934	84.194	3.793	3.793	0.000	0.000	0.000	0.000
89	B	133	VAL	0	-0.119	-0.074	80.849	0.069	0.069	0.000	0.000	0.000	0.000
90	B	134	VAL	0	0.040	0.018	80.273	0.070	0.070	0.000	0.000	0.000	0.000
91	B	135	ARG	1	0.880	0.936	79.469	-3.796	-3.796	0.000	0.000	0.000	0.000
92	B	136	LYS	1	0.849	0.925	77.319	-3.954	-3.954	0.000	0.000	0.000	0.000
93	B	137	PHE	0	-0.070	-0.039	73.827	0.074	0.074	0.000	0.000	0.000	0.000
94	B	138	GLY	0	0.007	-0.001	75.349	0.049	0.049	0.000	0.000	0.000	0.000
95	B	139	VAL	0	-0.087	0.001	76.853	-0.008	-0.008	0.000	0.000	0.000	0.000
96	B	140	GLU	-1	-0.753	-0.853	79.996	3.864	3.864	0.000	0.000	0.000	0.000
97	B	141	VAL	0	-0.035	-0.029	82.741	0.000	0.000	0.000	0.000	0.000	0.000
98	B	142	ILE	0	-0.044	0.010	84.118	-0.006	-0.006	0.000	0.000	0.000	0.000
99	B	143	ALA	0	0.013	-0.020	87.714	-0.021	-0.021	0.000	0.000	0.000	0.000
100	B	144	GLU	-1	-0.934	-0.938	90.004	3.571	3.571	0.000	0.000	0.000	0.000
101	B	145	THR	0	-0.007	-0.023	92.311	0.002	0.002	0.000	0.000	0.000	0.000
102	B	146	ASN	0	-0.019	-0.022	95.077	-0.002	-0.002	0.000	0.000	0.000	0.000
103	B	147	VAL	0	0.011	0.030	90.946	0.007	0.007	0.000	0.000	0.000	0.000
104	B	148	PRO	0	0.003	0.003	91.430	-0.010	-0.010	0.000	0.000	0.000	0.000
105	B	149	LEU	0	-0.022	-0.007	90.902	0.033	0.033	0.000	0.000	0.000	0.000
106	B	150	ASP	-1	-0.754	-0.882	85.129	3.871	3.871	0.000	0.000	0.000	0.000
107	B	151	PRO	0	-0.059	-0.017	85.656	0.011	0.011	0.000	0.000	0.000	0.000
108	B	152	ASN	0	-0.109	-0.047	80.954	0.074	0.074	0.000	0.000	0.000	0.000
109	B	153	VAL	0	0.003	0.003	83.123	0.040	0.040	0.000	0.000	0.000	0.000
110	B	154	HIS	0	0.045	0.002	85.593	-0.013	-0.013	0.000	0.000	0.000	0.000
111	B	155	GLN	0	0.006	0.005	87.776	-0.004	-0.004	0.000	0.000	0.000	0.000
112	B	156	ALA	0	-0.008	0.008	90.310	-0.029	-0.029	0.000	0.000	0.000	0.000
113	B	157	ILE	0	-0.015	-0.014	93.692	0.011	0.011	0.000	0.000	0.000	0.000
114	B	158	ALA	0	-0.034	-0.023	95.936	-0.031	-0.031	0.000	0.000	0.000	0.000
115	B	159	MET	0	-0.042	-0.019	98.794	0.027	0.027	0.000	0.000	0.000	0.000
116	B	160	VAL	0	-0.025	-0.020	101.032	-0.027	-0.027	0.000	0.000	0.000	0.000
117	B	161	GLU	-1	-0.762	-0.859	104.251	3.068	3.068	0.000	0.000	0.000	0.000
118	B	162	SER	0	-0.002	-0.020	104.831	-0.014	-0.014	0.000	0.000	0.000	0.000
119	B	163	ASP	-1	-0.902	-0.943	106.289	2.996	2.996	0.000	0.000	0.000	0.000
120	B	164	ASP	-1	-0.966	-0.979	104.290	3.090	3.090	0.000	0.000	0.000	0.000
121	B	165	VAL	0	-0.046	-0.033	99.752	0.030	0.030	0.000	0.000	0.000	0.000
122	B	166	ALA	0	-0.021	0.011	100.100	-0.013	-0.013	0.000	0.000	0.000	0.000
123	B	167	PRO	0	0.037	-0.003	100.562	0.021	0.021	0.000	0.000	0.000	0.000
124	B	168	GLY	0	-0.048	-0.016	97.382	0.021	0.021	0.000	0.000	0.000	0.000
125	B	169	ASN	0	-0.032	-0.026	95.788	0.068	0.068	0.000	0.000	0.000	0.000
126	B	170	VAL	0	-0.020	-0.012	92.634	-0.037	-0.037	0.000	0.000	0.000	0.000
127	B	171	LEU	0	0.036	0.020	95.934	-0.008	-0.008	0.000	0.000	0.000	0.000
128	B	172	GLY	0	0.048	0.047	98.869	-0.011	-0.011	0.000	0.000	0.000	0.000
129	B	173	ILE	0	-0.024	-0.023	93.275	0.030	0.030	0.000	0.000	0.000	0.000
130	B	174	MET	0	0.001	0.009	95.688	-0.016	-0.016	0.000	0.000	0.000	0.000
131	B	175	GLN	0	0.007	-0.011	90.343	0.030	0.030	0.000	0.000	0.000	0.000
132	B	176	LYS	1	0.855	0.924	89.834	-3.522	-3.522	0.000	0.000	0.000	0.000
133	B	177	GLY	0	0.034	-0.008	87.165	0.019	0.019	0.000	0.000	0.000	0.000
134	B	178	TYR	0	0.009	-0.003	83.001	-0.005	-0.005	0.000	0.000	0.000	0.000
135	B	179	THR	0	0.000	0.005	79.917	0.033	0.033	0.000	0.000	0.000	0.000
136	B	180	LEU	0	0.056	0.010	74.638	-0.009	-0.009	0.000	0.000	0.000	0.000
137	B	181	ASN	0	-0.074	-0.050	73.629	0.052	0.052	0.000	0.000	0.000	0.000
138	B	182	GLY	0	0.029	0.026	75.774	0.037	0.037	0.000	0.000	0.000	0.000
139	B	183	ARG	1	0.820	0.871	72.105	-4.464	-4.464	0.000	0.000	0.000	0.000
140	B	184	THR	0	-0.010	-0.019	76.833	0.001	0.001	0.000	0.000	0.000	0.000
141	B	185	ILE	0	-0.089	-0.035	76.973	0.035	0.035	0.000	0.000	0.000	0.000
142	B	186	ARG	1	0.762	0.850	80.076	-3.721	-3.721	0.000	0.000	0.000	0.000
143	B	187	ALA	0	0.027	0.014	83.725	-0.018	-0.018	0.000	0.000	0.000	0.000
144	B	188	ALA	0	0.015	0.016	86.253	-0.023	-0.023	0.000	0.000	0.000	0.000
145	B	189	MET	0	-0.019	0.001	89.580	-0.017	-0.017	0.000	0.000	0.000	0.000
146	B	190	VAL	0	-0.031	-0.019	92.185	-0.024	-0.024	0.000	0.000	0.000	0.000
147	B	191	THR	0	-0.016	-0.031	94.803	-0.009	-0.009	0.000	0.000	0.000	0.000
148	B	192	VAL	0	0.001	0.007	95.295	-0.005	-0.005	0.000	0.000	0.000	0.000
149	B	193	ALA	0	0.054	0.042	98.100	-0.031	-0.031	0.000	0.000	0.000	0.000
150	B	194	LYS	1	0.758	0.857	101.160	-3.066	-3.066	0.000	0.000	0.000	0.000
151	B	195	ALA	0	0.011	0.015	103.205	-0.038	-0.038	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(B:38:ASP)