FMO DATABASE

FMODB ID: Q1KGY

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:

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. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	164
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1224558.126874
FMO2-HF: Nuclear repulsion	1160171.333862
FMO2-HF: Total energy	-64386.793012
FMO2-MP2: Total energy	-64572.563908

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.
-2.863	-1.704	-0.01	-0.461	-0.687	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 : -0.052 / q_NPA : -0.045

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	-0.003	3.822	-1.438	-0.279	-0.010	-0.461	-0.687	0.001
4	A	37	VAL	0	0.052	0.042	6.409	0.431	0.431	0.000	0.000	0.000	0.000
5	A	38	ASP	-1	-0.842	-0.909	9.386	-0.289	-0.289	0.000	0.000	0.000	0.000
6	A	39	PRO	0	0.089	0.049	10.852	-0.107	-0.107	0.000	0.000	0.000	0.000
7	A	40	ARG	1	0.756	0.845	12.900	0.386	0.386	0.000	0.000	0.000	0.000
8	A	41	ASP	-1	-0.867	-0.943	7.412	-1.223	-1.223	0.000	0.000	0.000	0.000
9	A	42	GLU	-1	-0.897	-0.955	9.037	-0.963	-0.963	0.000	0.000	0.000	0.000
10	A	43	LYS	1	0.882	0.950	10.364	0.519	0.519	0.000	0.000	0.000	0.000
11	A	44	VAL	0	-0.034	-0.019	9.364	0.101	0.101	0.000	0.000	0.000	0.000
12	A	45	ALA	0	0.057	0.036	8.283	0.075	0.075	0.000	0.000	0.000	0.000
13	A	46	ASN	0	-0.017	0.015	10.156	0.064	0.064	0.000	0.000	0.000	0.000
14	A	47	LEU	0	-0.063	-0.026	13.425	0.067	0.067	0.000	0.000	0.000	0.000
15	A	48	GLU	-1	-0.915	-0.967	9.767	-0.758	-0.758	0.000	0.000	0.000	0.000
16	A	49	ALA	0	0.010	0.011	12.747	0.044	0.044	0.000	0.000	0.000	0.000
17	A	50	GLN	0	0.000	-0.015	14.302	0.073	0.073	0.000	0.000	0.000	0.000
18	A	51	LEU	0	-0.004	0.004	17.167	0.040	0.040	0.000	0.000	0.000	0.000
19	A	52	ALA	0	0.075	0.051	15.379	0.036	0.036	0.000	0.000	0.000	0.000
20	A	53	GLU	-1	-0.939	-0.946	17.491	-0.262	-0.262	0.000	0.000	0.000	0.000
21	A	54	ALA	0	-0.137	-0.066	19.859	0.034	0.034	0.000	0.000	0.000	0.000
22	A	55	GLN	0	0.056	0.007	19.104	0.006	0.006	0.000	0.000	0.000	0.000
23	A	56	THR	0	-0.071	-0.046	20.237	0.020	0.020	0.000	0.000	0.000	0.000
24	A	57	ARG	1	0.930	0.955	22.854	0.214	0.214	0.000	0.000	0.000	0.000
25	A	58	GLU	-1	-0.921	-0.951	25.698	-0.142	-0.142	0.000	0.000	0.000	0.000
26	A	59	ARG	1	0.964	0.989	22.039	0.185	0.185	0.000	0.000	0.000	0.000
27	A	60	ASP	-1	-0.869	-0.945	26.096	-0.136	-0.136	0.000	0.000	0.000	0.000
28	A	61	GLY	0	-0.093	-0.054	28.748	0.010	0.010	0.000	0.000	0.000	0.000
29	A	62	ILE	0	-0.014	-0.002	30.486	0.010	0.010	0.000	0.000	0.000	0.000
30	A	63	LEU	0	-0.006	-0.011	30.635	0.009	0.009	0.000	0.000	0.000	0.000
31	A	64	ARG	1	0.994	0.985	33.178	0.103	0.103	0.000	0.000	0.000	0.000
32	A	65	VAL	0	0.032	0.027	35.144	0.005	0.005	0.000	0.000	0.000	0.000
33	A	66	LYS	1	0.923	0.971	34.708	0.087	0.087	0.000	0.000	0.000	0.000
34	A	67	ALA	0	-0.002	-0.008	37.072	0.005	0.005	0.000	0.000	0.000	0.000
35	A	68	GLU	-1	-0.973	-0.982	38.616	-0.073	-0.073	0.000	0.000	0.000	0.000
36	A	69	MET	0	-0.004	-0.004	40.567	0.004	0.004	0.000	0.000	0.000	0.000
37	A	70	GLU	-1	-0.895	-0.931	41.507	-0.052	-0.052	0.000	0.000	0.000	0.000
38	A	71	ASN	0	0.003	-0.015	41.889	0.005	0.005	0.000	0.000	0.000	0.000
39	A	72	LEU	0	-0.086	-0.045	45.054	0.002	0.002	0.000	0.000	0.000	0.000
40	A	73	ARG	1	1.009	1.008	44.428	0.054	0.054	0.000	0.000	0.000	0.000
41	A	74	ARG	1	1.014	1.017	47.718	0.044	0.044	0.000	0.000	0.000	0.000
42	A	75	ARG	1	0.874	0.916	45.800	0.054	0.054	0.000	0.000	0.000	0.000
43	A	76	THR	0	0.071	0.031	50.999	0.001	0.001	0.000	0.000	0.000	0.000
44	A	77	GLU	-1	-0.945	-0.954	51.552	-0.038	-0.038	0.000	0.000	0.000	0.000
45	A	78	LEU	0	-0.019	-0.004	52.656	0.002	0.002	0.000	0.000	0.000	0.000
46	A	79	ASP	-1	-0.969	-0.993	54.610	-0.038	-0.038	0.000	0.000	0.000	0.000
47	A	80	ILE	0	-0.020	-0.013	56.780	0.001	0.001	0.000	0.000	0.000	0.000
48	A	81	GLU	-1	-0.907	-0.954	58.426	-0.027	-0.027	0.000	0.000	0.000	0.000
49	A	82	LYS	1	0.882	0.940	58.940	0.034	0.034	0.000	0.000	0.000	0.000
50	A	83	ALA	0	-0.028	-0.023	61.251	0.001	0.001	0.000	0.000	0.000	0.000
51	A	84	HIS	0	0.005	0.020	62.973	0.000	0.000	0.000	0.000	0.000	0.000
52	A	85	LYS	1	0.913	0.961	63.125	0.026	0.026	0.000	0.000	0.000	0.000
53	A	86	PHE	0	-0.027	-0.035	64.006	0.001	0.001	0.000	0.000	0.000	0.000
54	A	87	ALA	0	0.016	0.039	67.378	0.000	0.000	0.000	0.000	0.000	0.000
55	A	88	LEU	0	0.018	-0.015	68.215	0.000	0.000	0.000	0.000	0.000	0.000
56	A	89	GLU	-1	-0.816	-0.897	68.685	-0.024	-0.024	0.000	0.000	0.000	0.000
57	A	90	LYS	1	0.987	0.978	70.796	0.025	0.025	0.000	0.000	0.000	0.000
58	A	91	PHE	0	0.027	0.019	72.487	0.000	0.000	0.000	0.000	0.000	0.000
59	A	92	ILE	0	-0.027	-0.001	74.093	0.001	0.001	0.000	0.000	0.000	0.000
60	A	93	ASN	0	0.015	-0.006	72.624	0.001	0.001	0.000	0.000	0.000	0.000
61	A	94	GLU	-1	-0.995	-1.007	76.340	-0.021	-0.021	0.000	0.000	0.000	0.000
62	A	95	LEU	0	0.003	0.004	78.603	0.000	0.000	0.000	0.000	0.000	0.000
63	A	96	LEU	0	0.021	0.037	77.777	0.001	0.001	0.000	0.000	0.000	0.000
64	A	97	PRO	0	0.008	0.006	80.938	0.001	0.001	0.000	0.000	0.000	0.000
65	A	98	VAL	0	-0.040	-0.029	83.976	0.000	0.000	0.000	0.000	0.000	0.000
66	A	99	ILE	0	-0.045	-0.024	82.340	0.000	0.000	0.000	0.000	0.000	0.000
67	A	100	ASP	-1	-0.823	-0.911	84.243	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	101	SER	0	-0.106	-0.057	87.127	0.000	0.000	0.000	0.000	0.000	0.000
69	A	102	LEU	0	0.011	0.011	89.256	0.000	0.000	0.000	0.000	0.000	0.000
70	A	103	ASP	-1	-0.751	-0.906	88.248	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	104	ARG	1	0.946	0.995	88.513	0.015	0.015	0.000	0.000	0.000	0.000
72	A	105	ALA	0	-0.070	-0.044	92.541	0.000	0.000	0.000	0.000	0.000	0.000
73	A	106	LEU	0	-0.034	-0.013	93.259	0.000	0.000	0.000	0.000	0.000	0.000
74	A	107	GLU	-1	-0.948	-0.966	92.287	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	108	VAL	0	-0.049	-0.021	96.170	0.000	0.000	0.000	0.000	0.000	0.000
76	A	109	ALA	0	-0.040	0.003	98.705	0.000	0.000	0.000	0.000	0.000	0.000
77	A	110	ASP	-1	-0.953	-0.980	99.284	-0.010	-0.010	0.000	0.000	0.000	0.000
78	A	111	LYS	1	0.856	0.913	101.297	0.011	0.011	0.000	0.000	0.000	0.000
79	A	112	ALA	0	-0.027	0.004	104.860	0.000	0.000	0.000	0.000	0.000	0.000
80	A	113	ASN	0	-0.056	-0.054	106.665	0.000	0.000	0.000	0.000	0.000	0.000
81	A	114	PRO	0	0.030	0.007	107.729	0.000	0.000	0.000	0.000	0.000	0.000
82	A	115	ASP	-1	-0.836	-0.874	109.494	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	116	MET	0	-0.043	-0.032	102.914	0.000	0.000	0.000	0.000	0.000	0.000
84	A	117	SER	0	-0.050	-0.040	104.605	0.000	0.000	0.000	0.000	0.000	0.000
85	A	118	ALA	0	0.084	0.043	103.122	0.000	0.000	0.000	0.000	0.000	0.000
86	A	119	MET	0	0.037	0.014	99.934	0.000	0.000	0.000	0.000	0.000	0.000
87	A	120	VAL	0	0.023	0.008	98.883	0.000	0.000	0.000	0.000	0.000	0.000
88	A	121	GLU	-1	-0.899	-0.958	98.060	-0.011	-0.011	0.000	0.000	0.000	0.000
89	A	122	ASP	-1	-0.956	-0.965	97.463	-0.012	-0.012	0.000	0.000	0.000	0.000
90	A	123	ILE	0	-0.114	-0.077	93.914	0.000	0.000	0.000	0.000	0.000	0.000
91	A	124	GLU	-1	-0.885	-0.934	93.633	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	125	LEU	0	-0.012	-0.003	92.775	0.000	0.000	0.000	0.000	0.000	0.000
93	A	126	THR	0	-0.011	-0.009	90.194	0.000	0.000	0.000	0.000	0.000	0.000
94	A	127	LEU	0	0.007	0.002	87.510	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	128	LYS	1	0.968	0.992	87.809	0.014	0.014	0.000	0.000	0.000	0.000
96	A	129	SER	0	-0.044	-0.033	87.210	0.000	0.000	0.000	0.000	0.000	0.000
97	A	130	MET	0	-0.027	-0.007	84.017	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	131	LEU	0	0.009	-0.002	82.913	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	132	ASP	-1	-0.863	-0.942	82.170	-0.015	-0.015	0.000	0.000	0.000	0.000
100	A	133	VAL	0	-0.059	-0.011	80.967	0.000	0.000	0.000	0.000	0.000	0.000
101	A	134	VAL	0	-0.031	-0.019	78.573	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	135	ARG	1	0.944	0.958	77.478	0.015	0.015	0.000	0.000	0.000	0.000
103	A	136	LYS	1	0.796	0.911	76.075	0.018	0.018	0.000	0.000	0.000	0.000
104	A	137	PHE	0	-0.080	-0.046	74.259	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	138	GLY	0	0.024	0.008	72.676	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	139	VAL	0	-0.018	-0.005	73.525	0.000	0.000	0.000	0.000	0.000	0.000
107	A	140	GLU	-1	-0.789	-0.872	75.923	-0.016	-0.016	0.000	0.000	0.000	0.000
108	A	141	VAL	0	-0.057	-0.051	77.645	0.000	0.000	0.000	0.000	0.000	0.000
109	A	142	ILE	0	-0.047	-0.007	76.218	0.000	0.000	0.000	0.000	0.000	0.000
110	A	143	ALA	0	0.009	-0.066	79.952	0.000	0.000	0.000	0.000	0.000	0.000
111	A	144	GLU	-1	-0.932	-0.947	81.286	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	145	THR	0	-0.006	-0.043	83.121	0.000	0.000	0.000	0.000	0.000	0.000
113	A	146	ASN	0	-0.005	-0.014	84.813	0.000	0.000	0.000	0.000	0.000	0.000
114	A	147	VAL	0	0.052	0.049	80.148	0.000	0.000	0.000	0.000	0.000	0.000
115	A	148	PRO	0	-0.029	-0.017	77.936	0.000	0.000	0.000	0.000	0.000	0.000
116	A	149	LEU	0	-0.019	-0.007	77.126	0.000	0.000	0.000	0.000	0.000	0.000
117	A	150	ASP	-1	-0.795	-0.919	72.869	-0.018	-0.018	0.000	0.000	0.000	0.000
118	A	151	PRO	0	-0.050	-0.041	72.090	0.000	0.000	0.000	0.000	0.000	0.000
119	A	152	ASN	0	-0.063	-0.024	68.214	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	153	VAL	0	-0.036	-0.022	71.732	-0.001	-0.001	0.000	0.000	0.000	0.000
121	A	154	HIS	0	0.068	0.057	74.774	0.000	0.000	0.000	0.000	0.000	0.000
122	A	155	GLN	0	-0.005	-0.013	76.707	0.000	0.000	0.000	0.000	0.000	0.000
123	A	156	ALA	0	-0.001	-0.008	78.930	0.000	0.000	0.000	0.000	0.000	0.000
124	A	157	ILE	0	0.012	0.012	81.317	0.000	0.000	0.000	0.000	0.000	0.000
125	A	158	ALA	0	-0.048	-0.038	83.737	0.000	0.000	0.000	0.000	0.000	0.000
126	A	159	MET	0	-0.056	-0.005	83.885	0.000	0.000	0.000	0.000	0.000	0.000
127	A	160	VAL	0	0.034	0.013	87.073	0.000	0.000	0.000	0.000	0.000	0.000
128	A	161	GLU	-1	-0.887	-0.935	90.206	-0.010	-0.010	0.000	0.000	0.000	0.000
129	A	162	SER	0	0.002	-0.005	91.516	0.000	0.000	0.000	0.000	0.000	0.000
130	A	163	ASP	-1	-0.840	-0.926	91.535	-0.009	-0.009	0.000	0.000	0.000	0.000
131	A	164	ASP	-1	-0.942	-0.959	92.591	-0.010	-0.010	0.000	0.000	0.000	0.000
132	A	165	VAL	0	-0.034	-0.027	87.578	0.000	0.000	0.000	0.000	0.000	0.000
133	A	166	ALA	0	-0.027	-0.002	85.372	0.000	0.000	0.000	0.000	0.000	0.000
134	A	167	PRO	0	0.010	-0.018	85.195	0.000	0.000	0.000	0.000	0.000	0.000
135	A	168	GLY	0	-0.037	-0.022	82.051	0.000	0.000	0.000	0.000	0.000	0.000
136	A	169	ASN	0	-0.002	0.000	81.514	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	170	VAL	0	-0.077	0.011	81.552	0.000	0.000	0.000	0.000	0.000	0.000
138	A	171	LEU	0	0.024	-0.012	84.161	0.000	0.000	0.000	0.000	0.000	0.000
139	A	172	GLY	0	0.025	-0.016	87.182	0.000	0.000	0.000	0.000	0.000	0.000
140	A	173	ILE	0	-0.082	-0.017	84.414	0.000	0.000	0.000	0.000	0.000	0.000
141	A	174	MET	0	0.018	0.017	86.281	0.000	0.000	0.000	0.000	0.000	0.000
142	A	175	GLN	0	0.011	-0.009	83.095	0.000	0.000	0.000	0.000	0.000	0.000
143	A	176	LYS	1	0.924	0.985	83.032	0.014	0.014	0.000	0.000	0.000	0.000
144	A	177	GLY	0	0.040	0.027	79.278	0.000	0.000	0.000	0.000	0.000	0.000
145	A	178	TYR	0	0.035	0.026	77.502	0.000	0.000	0.000	0.000	0.000	0.000
146	A	179	THR	0	0.015	0.003	72.498	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	180	LEU	0	0.030	0.039	70.503	0.000	0.000	0.000	0.000	0.000	0.000
148	A	181	ASN	0	-0.069	-0.052	67.728	0.000	0.000	0.000	0.000	0.000	0.000
149	A	182	GLY	0	0.010	-0.002	67.520	-0.001	-0.001	0.000	0.000	0.000	0.000
150	A	183	ARG	1	0.846	0.938	64.028	0.026	0.026	0.000	0.000	0.000	0.000
151	A	184	THR	0	0.000	-0.015	68.420	0.000	0.000	0.000	0.000	0.000	0.000
152	A	185	ILE	0	-0.074	-0.030	71.189	-0.001	-0.001	0.000	0.000	0.000	0.000
153	A	186	ARG	1	0.817	0.892	73.342	0.017	0.017	0.000	0.000	0.000	0.000
154	A	187	ALA	0	0.026	0.027	75.171	0.000	0.000	0.000	0.000	0.000	0.000
155	A	188	ALA	0	0.043	0.030	76.754	0.000	0.000	0.000	0.000	0.000	0.000
156	A	189	MET	0	-0.038	-0.003	80.047	0.000	0.000	0.000	0.000	0.000	0.000
157	A	190	VAL	0	-0.006	-0.006	81.297	0.000	0.000	0.000	0.000	0.000	0.000
158	A	191	THR	0	0.016	0.032	83.862	0.000	0.000	0.000	0.000	0.000	0.000
159	A	192	VAL	0	0.027	0.026	81.790	0.000	0.000	0.000	0.000	0.000	0.000
160	A	193	ALA	0	0.060	0.041	84.966	0.000	0.000	0.000	0.000	0.000	0.000
161	A	194	LYS	1	0.813	0.896	86.253	0.010	0.010	0.000	0.000	0.000	0.000
162	A	195	ALA	0	0.016	-0.012	88.220	0.000	0.000	0.000	0.000	0.000	0.000
163	A	196	LYS	1	0.949	0.997	90.282	0.009	0.009	0.000	0.000	0.000	0.000
164	A	197	ALA	0	-0.059	-0.014	93.391	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)