FMO DATABASE

FMODB ID: R5QG8

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	OptAll
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	-1091464.544731
FMO2-HF: Nuclear repulsion	1031669.078457
FMO2-HF: Total energy	-59795.466273
FMO2-MP2: Total energy	-59967.112619

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.
8.877	8.61	13.453	-7.137	-6.048	-0.038

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 : -0.956

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	0.819	0.899	3.030	-43.813	-41.349	0.009	-1.279	-1.194	0.006
4	B	41	ASP	-1	-0.791	-0.885	1.826	34.754	30.804	13.431	-5.437	-4.044	-0.046
5	B	42	GLU	-1	-0.893	-0.937	3.335	41.692	42.819	0.014	-0.416	-0.725	0.002
6	B	43	LYS	1	0.929	0.954	5.327	-32.558	-32.466	-0.001	-0.005	-0.085	0.000
7	B	44	VAL	0	-0.002	-0.002	7.081	-3.686	-3.686	0.000	0.000	0.000	0.000
8	B	45	ALA	0	0.083	0.051	7.862	-2.795	-2.795	0.000	0.000	0.000	0.000
9	B	46	ASN	0	-0.038	-0.017	9.421	-3.697	-3.697	0.000	0.000	0.000	0.000
10	B	47	LEU	0	-0.035	-0.023	11.328	-2.281	-2.281	0.000	0.000	0.000	0.000
11	B	48	GLU	-1	-0.910	-0.953	11.979	20.924	20.924	0.000	0.000	0.000	0.000
12	B	49	ALA	0	-0.013	-0.003	13.716	-1.520	-1.520	0.000	0.000	0.000	0.000
13	B	50	GLN	0	-0.046	-0.041	14.716	-2.319	-2.319	0.000	0.000	0.000	0.000
14	B	51	LEU	0	0.001	0.016	17.091	-1.095	-1.095	0.000	0.000	0.000	0.000
15	B	52	ALA	0	0.024	0.008	18.371	-0.975	-0.975	0.000	0.000	0.000	0.000
16	B	53	GLU	-1	-0.804	-0.859	19.659	13.359	13.359	0.000	0.000	0.000	0.000
17	B	54	ALA	0	-0.034	-0.015	21.357	-0.799	-0.799	0.000	0.000	0.000	0.000
18	B	55	GLN	0	-0.028	-0.025	22.916	-0.344	-0.344	0.000	0.000	0.000	0.000
19	B	56	THR	0	-0.079	-0.056	23.589	-0.691	-0.691	0.000	0.000	0.000	0.000
20	B	57	ARG	1	0.851	0.902	23.125	-13.538	-13.538	0.000	0.000	0.000	0.000
21	B	58	GLU	-1	-0.894	-0.930	27.262	10.485	10.485	0.000	0.000	0.000	0.000
22	B	59	ARG	1	0.811	0.874	27.543	-11.300	-11.300	0.000	0.000	0.000	0.000
23	B	60	ASP	-1	-0.780	-0.875	29.074	10.215	10.215	0.000	0.000	0.000	0.000
24	B	61	GLY	0	0.018	0.015	31.302	-0.346	-0.346	0.000	0.000	0.000	0.000
25	B	62	ILE	0	-0.012	-0.011	33.165	-0.443	-0.443	0.000	0.000	0.000	0.000
26	B	63	LEU	0	-0.037	-0.019	33.406	-0.372	-0.372	0.000	0.000	0.000	0.000
27	B	64	ARG	1	0.813	0.883	35.314	-8.483	-8.483	0.000	0.000	0.000	0.000
28	B	65	VAL	0	0.054	0.016	37.155	-0.287	-0.287	0.000	0.000	0.000	0.000
29	B	66	LYS	1	0.945	0.968	38.302	-8.414	-8.414	0.000	0.000	0.000	0.000
30	B	67	ALA	0	0.021	0.006	40.283	-0.233	-0.233	0.000	0.000	0.000	0.000
31	B	68	GLU	-1	-0.859	-0.886	41.272	7.561	7.561	0.000	0.000	0.000	0.000
32	B	69	MET	0	-0.026	-0.018	43.197	-0.168	-0.168	0.000	0.000	0.000	0.000
33	B	70	GLU	-1	-0.827	-0.901	44.996	6.398	6.398	0.000	0.000	0.000	0.000
34	B	71	ASN	0	0.039	0.018	44.295	-0.259	-0.259	0.000	0.000	0.000	0.000
35	B	72	LEU	0	-0.038	-0.010	47.529	-0.133	-0.133	0.000	0.000	0.000	0.000
36	B	73	ARG	1	0.947	0.987	48.275	-6.618	-6.618	0.000	0.000	0.000	0.000
37	B	74	ARG	1	0.852	0.900	46.797	-6.784	-6.784	0.000	0.000	0.000	0.000
38	B	75	ARG	1	0.913	0.980	48.778	-6.502	-6.502	0.000	0.000	0.000	0.000
39	B	76	THR	0	0.002	-0.025	53.292	-0.122	-0.122	0.000	0.000	0.000	0.000
40	B	77	GLU	-1	-0.901	-0.937	55.443	5.372	5.372	0.000	0.000	0.000	0.000
41	B	78	LEU	0	0.007	0.007	56.370	-0.115	-0.115	0.000	0.000	0.000	0.000
42	B	79	ASP	-1	-0.884	-0.961	56.237	5.626	5.626	0.000	0.000	0.000	0.000
43	B	80	ILE	0	0.002	0.009	58.902	-0.107	-0.107	0.000	0.000	0.000	0.000
44	B	81	GLU	-1	-0.777	-0.880	61.320	4.871	4.871	0.000	0.000	0.000	0.000
45	B	82	LYS	1	0.811	0.901	58.439	-5.601	-5.601	0.000	0.000	0.000	0.000
46	B	83	ALA	0	-0.002	0.003	63.628	-0.092	-0.092	0.000	0.000	0.000	0.000
47	B	84	HIS	0	-0.003	0.004	65.454	-0.099	-0.099	0.000	0.000	0.000	0.000
48	B	85	LYS	1	0.853	0.908	66.098	-4.957	-4.957	0.000	0.000	0.000	0.000
49	B	86	PHE	0	0.000	0.004	68.088	-0.081	-0.081	0.000	0.000	0.000	0.000
50	B	87	ALA	0	0.007	0.001	69.625	-0.081	-0.081	0.000	0.000	0.000	0.000
51	B	88	LEU	0	-0.010	0.004	71.363	-0.081	-0.081	0.000	0.000	0.000	0.000
52	B	89	GLU	-1	-0.785	-0.865	72.254	4.412	4.412	0.000	0.000	0.000	0.000
53	B	90	LYS	1	0.785	0.889	73.998	-4.297	-4.297	0.000	0.000	0.000	0.000
54	B	91	PHE	0	-0.005	-0.010	75.610	-0.067	-0.067	0.000	0.000	0.000	0.000
55	B	92	ILE	0	0.014	-0.001	77.140	-0.068	-0.068	0.000	0.000	0.000	0.000
56	B	93	ASN	0	-0.027	-0.030	77.544	-0.101	-0.101	0.000	0.000	0.000	0.000
57	B	94	GLU	-1	-0.829	-0.901	79.518	4.070	4.070	0.000	0.000	0.000	0.000
58	B	95	LEU	0	-0.020	0.001	81.362	-0.056	-0.056	0.000	0.000	0.000	0.000
59	B	96	LEU	0	0.016	0.014	82.838	-0.054	-0.054	0.000	0.000	0.000	0.000
60	B	97	PRO	0	0.023	0.018	85.257	-0.052	-0.052	0.000	0.000	0.000	0.000
61	B	98	VAL	0	-0.035	-0.006	86.379	-0.058	-0.058	0.000	0.000	0.000	0.000
62	B	99	ILE	0	0.018	0.000	84.969	-0.042	-0.042	0.000	0.000	0.000	0.000
63	B	100	ASP	-1	-0.768	-0.864	89.383	3.619	3.619	0.000	0.000	0.000	0.000
64	B	101	SER	0	-0.070	-0.052	91.589	-0.065	-0.065	0.000	0.000	0.000	0.000
65	B	102	LEU	0	-0.022	0.003	90.702	-0.039	-0.039	0.000	0.000	0.000	0.000
66	B	103	ASP	-1	-0.758	-0.869	92.755	3.472	3.472	0.000	0.000	0.000	0.000
67	B	104	ARG	1	0.872	0.930	94.068	-3.460	-3.460	0.000	0.000	0.000	0.000
68	B	105	ALA	0	-0.048	-0.024	97.229	-0.038	-0.038	0.000	0.000	0.000	0.000
69	B	106	LEU	0	-0.015	-0.002	97.268	-0.030	-0.030	0.000	0.000	0.000	0.000
70	B	107	GLU	-1	-0.948	-0.964	99.093	3.230	3.230	0.000	0.000	0.000	0.000
71	B	108	VAL	0	-0.116	-0.046	101.579	-0.038	-0.038	0.000	0.000	0.000	0.000
72	B	116	MET	0	0.002	-0.019	107.104	-0.003	-0.003	0.000	0.000	0.000	0.000
73	B	117	SER	0	0.020	0.013	105.748	0.028	0.028	0.000	0.000	0.000	0.000
74	B	118	ALA	0	0.076	0.036	104.239	0.023	0.023	0.000	0.000	0.000	0.000
75	B	119	MET	0	0.003	0.009	100.170	0.029	0.029	0.000	0.000	0.000	0.000
76	B	120	VAL	0	0.026	0.007	101.017	0.034	0.034	0.000	0.000	0.000	0.000
77	B	121	GLU	-1	-0.910	-0.947	100.167	3.228	3.228	0.000	0.000	0.000	0.000
78	B	122	ASP	-1	-0.900	-0.950	97.923	3.328	3.328	0.000	0.000	0.000	0.000
79	B	123	ILE	0	-0.052	-0.015	96.369	0.058	0.058	0.000	0.000	0.000	0.000
80	B	124	GLU	-1	-0.882	-0.942	95.599	3.324	3.324	0.000	0.000	0.000	0.000
81	B	125	LEU	0	-0.021	-0.004	93.109	0.056	0.056	0.000	0.000	0.000	0.000
82	B	126	THR	0	-0.047	-0.029	91.868	0.064	0.064	0.000	0.000	0.000	0.000
83	B	127	LEU	0	-0.009	-0.001	90.868	0.062	0.062	0.000	0.000	0.000	0.000
84	B	128	LYS	1	0.884	0.923	89.077	-3.578	-3.578	0.000	0.000	0.000	0.000
85	B	129	SER	0	-0.076	-0.045	88.162	0.051	0.051	0.000	0.000	0.000	0.000
86	B	130	MET	0	-0.014	-0.002	85.936	0.076	0.076	0.000	0.000	0.000	0.000
87	B	131	LEU	0	0.049	0.016	85.269	0.063	0.063	0.000	0.000	0.000	0.000
88	B	132	ASP	-1	-0.824	-0.900	84.574	3.803	3.803	0.000	0.000	0.000	0.000
89	B	133	VAL	0	-0.107	-0.043	80.946	0.066	0.066	0.000	0.000	0.000	0.000
90	B	134	VAL	0	0.032	0.010	80.574	0.066	0.066	0.000	0.000	0.000	0.000
91	B	135	ARG	1	0.865	0.905	79.956	-3.781	-3.781	0.000	0.000	0.000	0.000
92	B	136	LYS	1	0.821	0.906	77.513	-3.946	-3.946	0.000	0.000	0.000	0.000
93	B	137	PHE	0	-0.055	-0.023	74.283	0.076	0.076	0.000	0.000	0.000	0.000
94	B	138	GLY	0	0.010	0.010	75.724	0.043	0.043	0.000	0.000	0.000	0.000
95	B	139	VAL	0	-0.035	-0.011	77.041	-0.004	-0.004	0.000	0.000	0.000	0.000
96	B	140	GLU	-1	-0.790	-0.874	79.965	3.839	3.839	0.000	0.000	0.000	0.000
97	B	141	VAL	0	-0.034	-0.011	83.018	0.005	0.005	0.000	0.000	0.000	0.000
98	B	142	ILE	0	-0.053	-0.002	84.352	-0.001	-0.001	0.000	0.000	0.000	0.000
99	B	143	ALA	0	0.018	-0.021	88.190	-0.022	-0.022	0.000	0.000	0.000	0.000
100	B	144	GLU	-1	-0.920	-0.947	90.163	3.566	3.566	0.000	0.000	0.000	0.000
101	B	145	THR	0	0.008	-0.002	92.690	-0.001	-0.001	0.000	0.000	0.000	0.000
102	B	146	ASN	0	-0.025	-0.032	95.704	-0.006	-0.006	0.000	0.000	0.000	0.000
103	B	147	VAL	0	0.015	0.035	90.953	0.001	0.001	0.000	0.000	0.000	0.000
104	B	148	PRO	0	0.014	-0.009	91.570	-0.021	-0.021	0.000	0.000	0.000	0.000
105	B	149	LEU	0	-0.023	0.000	91.225	0.031	0.031	0.000	0.000	0.000	0.000
106	B	150	ASP	-1	-0.772	-0.881	85.060	3.867	3.867	0.000	0.000	0.000	0.000
107	B	151	PRO	0	-0.030	-0.016	85.781	0.009	0.009	0.000	0.000	0.000	0.000
108	B	152	ASN	0	-0.099	-0.046	80.847	0.074	0.074	0.000	0.000	0.000	0.000
109	B	153	VAL	0	-0.023	0.004	83.203	0.042	0.042	0.000	0.000	0.000	0.000
110	B	154	HIS	0	0.041	0.009	85.839	-0.009	-0.009	0.000	0.000	0.000	0.000
111	B	155	GLN	0	-0.014	-0.015	88.182	0.001	0.001	0.000	0.000	0.000	0.000
112	B	156	ALA	0	0.022	0.011	90.797	-0.028	-0.028	0.000	0.000	0.000	0.000
113	B	157	ILE	0	-0.028	-0.011	94.003	0.003	0.003	0.000	0.000	0.000	0.000
114	B	158	ALA	0	-0.030	-0.013	96.123	-0.031	-0.031	0.000	0.000	0.000	0.000
115	B	159	MET	0	-0.037	-0.025	98.956	0.033	0.033	0.000	0.000	0.000	0.000
116	B	160	VAL	0	-0.009	-0.001	101.332	-0.025	-0.025	0.000	0.000	0.000	0.000
117	B	161	GLU	-1	-0.784	-0.856	104.688	3.064	3.064	0.000	0.000	0.000	0.000
118	B	162	SER	0	-0.040	-0.047	105.446	-0.021	-0.021	0.000	0.000	0.000	0.000
119	B	163	ASP	-1	-0.912	-0.946	106.186	3.003	3.003	0.000	0.000	0.000	0.000
120	B	164	ASP	-1	-0.929	-0.935	104.298	3.088	3.088	0.000	0.000	0.000	0.000
121	B	165	VAL	0	-0.052	-0.030	99.932	0.027	0.027	0.000	0.000	0.000	0.000
122	B	166	ALA	0	-0.006	0.010	99.783	-0.023	-0.023	0.000	0.000	0.000	0.000
123	B	167	PRO	0	-0.008	-0.020	100.247	0.029	0.029	0.000	0.000	0.000	0.000
124	B	168	GLY	0	-0.013	0.002	97.599	0.018	0.018	0.000	0.000	0.000	0.000
125	B	169	ASN	0	-0.049	-0.028	95.991	0.066	0.066	0.000	0.000	0.000	0.000
126	B	170	VAL	0	0.002	-0.003	92.968	-0.037	-0.037	0.000	0.000	0.000	0.000
127	B	171	LEU	0	0.005	0.005	96.356	-0.008	-0.008	0.000	0.000	0.000	0.000
128	B	172	GLY	0	0.052	0.046	98.724	-0.020	-0.020	0.000	0.000	0.000	0.000
129	B	173	ILE	0	-0.035	-0.029	93.319	0.030	0.030	0.000	0.000	0.000	0.000
130	B	174	MET	0	0.010	0.009	96.064	-0.014	-0.014	0.000	0.000	0.000	0.000
131	B	175	GLN	0	-0.002	-0.016	90.818	0.025	0.025	0.000	0.000	0.000	0.000
132	B	176	LYS	1	0.859	0.927	90.046	-3.508	-3.508	0.000	0.000	0.000	0.000
133	B	177	GLY	0	0.056	0.010	87.525	0.019	0.019	0.000	0.000	0.000	0.000
134	B	178	TYR	0	-0.020	-0.021	83.210	-0.005	-0.005	0.000	0.000	0.000	0.000
135	B	179	THR	0	0.005	0.008	80.056	0.038	0.038	0.000	0.000	0.000	0.000
136	B	180	LEU	0	0.036	-0.002	74.866	-0.006	-0.006	0.000	0.000	0.000	0.000
137	B	181	ASN	0	-0.057	-0.038	73.823	0.045	0.045	0.000	0.000	0.000	0.000
138	B	182	GLY	0	0.021	0.025	75.679	0.039	0.039	0.000	0.000	0.000	0.000
139	B	183	ARG	1	0.804	0.873	72.776	-4.430	-4.430	0.000	0.000	0.000	0.000
140	B	184	THR	0	0.000	-0.021	77.266	-0.001	-0.001	0.000	0.000	0.000	0.000
141	B	185	ILE	0	-0.092	-0.039	77.122	0.053	0.053	0.000	0.000	0.000	0.000
142	B	186	ARG	1	0.766	0.866	80.338	-3.708	-3.708	0.000	0.000	0.000	0.000
143	B	187	ALA	0	0.045	0.031	84.117	-0.021	-0.021	0.000	0.000	0.000	0.000
144	B	188	ALA	0	0.032	0.016	86.253	-0.021	-0.021	0.000	0.000	0.000	0.000
145	B	189	MET	0	-0.040	0.000	89.696	-0.013	-0.013	0.000	0.000	0.000	0.000
146	B	190	VAL	0	-0.033	-0.018	92.599	-0.022	-0.022	0.000	0.000	0.000	0.000
147	B	191	THR	0	-0.005	-0.014	95.199	-0.006	-0.006	0.000	0.000	0.000	0.000
148	B	192	VAL	0	-0.015	-0.010	95.707	0.019	0.019	0.000	0.000	0.000	0.000
149	B	193	ALA	0	0.054	0.041	98.730	-0.031	-0.031	0.000	0.000	0.000	0.000
150	B	194	LYS	1	0.787	0.867	101.139	-3.057	-3.057	0.000	0.000	0.000	0.000
151	B	195	ALA	0	0.007	-0.023	103.619	-0.033	-0.033	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)