FMO DATABASE

FMODB ID: 43QVN

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	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	164
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1222003.558725
FMO2-HF: Nuclear repulsion	1157613.063342
FMO2-HF: Total energy	-64390.495382
FMO2-MP2: Total energy	-64575.820675

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.
-2.395	-1.184	-0.011	-0.52	-0.68	0.002

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 : -0.054 / 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	-0.020	-0.011	3.860	-1.612	-0.401	-0.011	-0.520	-0.680	0.002
4	A	37	VAL	0	0.008	0.010	6.375	0.393	0.393	0.000	0.000	0.000	0.000
5	A	38	ASP	-1	-0.792	-0.851	9.581	-0.169	-0.169	0.000	0.000	0.000	0.000
6	A	39	PRO	0	0.068	0.027	10.808	-0.109	-0.109	0.000	0.000	0.000	0.000
7	A	40	ARG	1	0.723	0.825	13.213	0.340	0.340	0.000	0.000	0.000	0.000
8	A	41	ASP	-1	-0.884	-0.942	7.445	-0.784	-0.784	0.000	0.000	0.000	0.000
9	A	42	GLU	-1	-0.897	-0.953	9.040	-0.795	-0.795	0.000	0.000	0.000	0.000
10	A	43	LYS	1	0.898	0.956	10.397	0.373	0.373	0.000	0.000	0.000	0.000
11	A	44	VAL	0	-0.025	-0.011	9.341	0.068	0.068	0.000	0.000	0.000	0.000
12	A	45	ALA	0	0.092	0.058	7.839	0.065	0.065	0.000	0.000	0.000	0.000
13	A	46	ASN	0	-0.056	-0.030	9.809	0.088	0.088	0.000	0.000	0.000	0.000
14	A	47	LEU	0	-0.052	-0.028	13.285	0.068	0.068	0.000	0.000	0.000	0.000
15	A	48	GLU	-1	-0.918	-0.959	9.415	-0.628	-0.628	0.000	0.000	0.000	0.000
16	A	49	ALA	0	-0.001	0.004	12.402	0.053	0.053	0.000	0.000	0.000	0.000
17	A	50	GLN	0	0.016	-0.005	14.021	0.056	0.056	0.000	0.000	0.000	0.000
18	A	51	LEU	0	-0.016	0.002	16.486	0.043	0.043	0.000	0.000	0.000	0.000
19	A	52	ALA	0	0.033	0.017	15.453	0.035	0.035	0.000	0.000	0.000	0.000
20	A	53	GLU	-1	-0.858	-0.903	17.464	-0.222	-0.222	0.000	0.000	0.000	0.000
21	A	54	ALA	0	-0.016	-0.015	19.589	0.029	0.029	0.000	0.000	0.000	0.000
22	A	55	GLN	0	0.030	0.003	19.446	0.012	0.012	0.000	0.000	0.000	0.000
23	A	56	THR	0	-0.068	-0.030	20.264	0.019	0.019	0.000	0.000	0.000	0.000
24	A	57	ARG	1	0.840	0.895	22.675	0.217	0.217	0.000	0.000	0.000	0.000
25	A	58	GLU	-1	-0.973	-0.976	25.305	-0.130	-0.130	0.000	0.000	0.000	0.000
26	A	59	ARG	1	0.932	0.978	21.648	0.179	0.179	0.000	0.000	0.000	0.000
27	A	60	ASP	-1	-0.859	-0.943	25.590	-0.131	-0.131	0.000	0.000	0.000	0.000
28	A	61	GLY	0	-0.019	-0.010	28.703	0.009	0.009	0.000	0.000	0.000	0.000
29	A	62	ILE	0	-0.026	-0.032	30.568	0.011	0.011	0.000	0.000	0.000	0.000
30	A	63	LEU	0	-0.006	0.002	30.475	0.008	0.008	0.000	0.000	0.000	0.000
31	A	64	ARG	1	0.864	0.906	32.811	0.093	0.093	0.000	0.000	0.000	0.000
32	A	65	VAL	0	0.035	0.017	34.875	0.006	0.006	0.000	0.000	0.000	0.000
33	A	66	LYS	1	0.921	0.975	34.147	0.083	0.083	0.000	0.000	0.000	0.000
34	A	67	ALA	0	0.058	0.031	37.236	0.005	0.005	0.000	0.000	0.000	0.000
35	A	68	GLU	-1	-0.873	-0.902	38.710	-0.071	-0.071	0.000	0.000	0.000	0.000
36	A	69	MET	0	-0.008	-0.001	40.830	0.004	0.004	0.000	0.000	0.000	0.000
37	A	70	GLU	-1	-0.825	-0.900	41.544	-0.049	-0.049	0.000	0.000	0.000	0.000
38	A	71	ASN	0	-0.029	-0.034	41.765	0.005	0.005	0.000	0.000	0.000	0.000
39	A	72	LEU	0	-0.051	-0.003	44.928	0.002	0.002	0.000	0.000	0.000	0.000
40	A	73	ARG	1	0.894	0.936	43.296	0.052	0.052	0.000	0.000	0.000	0.000
41	A	74	ARG	1	1.030	1.024	47.182	0.044	0.044	0.000	0.000	0.000	0.000
42	A	75	ARG	1	0.836	0.914	45.288	0.052	0.052	0.000	0.000	0.000	0.000
43	A	76	THR	0	0.016	-0.004	51.012	0.002	0.002	0.000	0.000	0.000	0.000
44	A	77	GLU	-1	-0.905	-0.954	50.924	-0.037	-0.037	0.000	0.000	0.000	0.000
45	A	78	LEU	0	-0.009	-0.005	52.489	0.002	0.002	0.000	0.000	0.000	0.000
46	A	79	ASP	-1	-0.908	-0.965	54.091	-0.036	-0.036	0.000	0.000	0.000	0.000
47	A	80	ILE	0	0.000	0.003	55.986	0.001	0.001	0.000	0.000	0.000	0.000
48	A	81	GLU	-1	-0.798	-0.886	58.349	-0.025	-0.025	0.000	0.000	0.000	0.000
49	A	82	LYS	1	0.858	0.930	56.829	0.035	0.035	0.000	0.000	0.000	0.000
50	A	83	ALA	0	-0.006	-0.013	60.994	0.001	0.001	0.000	0.000	0.000	0.000
51	A	84	HIS	0	-0.036	-0.020	62.718	0.001	0.001	0.000	0.000	0.000	0.000
52	A	85	LYS	1	0.829	0.906	62.840	0.026	0.026	0.000	0.000	0.000	0.000
53	A	86	PHE	0	0.022	0.014	62.974	0.000	0.000	0.000	0.000	0.000	0.000
54	A	87	ALA	0	0.014	0.025	66.851	0.000	0.000	0.000	0.000	0.000	0.000
55	A	88	LEU	0	-0.004	-0.009	67.971	0.000	0.000	0.000	0.000	0.000	0.000
56	A	89	GLU	-1	-0.807	-0.890	68.360	-0.024	-0.024	0.000	0.000	0.000	0.000
57	A	90	LYS	1	0.805	0.882	70.783	0.023	0.023	0.000	0.000	0.000	0.000
58	A	91	PHE	0	0.034	0.016	72.451	0.000	0.000	0.000	0.000	0.000	0.000
59	A	92	ILE	0	0.019	-0.003	74.022	0.001	0.001	0.000	0.000	0.000	0.000
60	A	93	ASN	0	0.003	-0.010	72.675	0.001	0.001	0.000	0.000	0.000	0.000
61	A	94	GLU	-1	-0.835	-0.904	76.069	-0.021	-0.021	0.000	0.000	0.000	0.000
62	A	95	LEU	0	-0.003	-0.001	78.572	0.001	0.001	0.000	0.000	0.000	0.000
63	A	96	LEU	0	-0.017	0.016	77.256	0.001	0.001	0.000	0.000	0.000	0.000
64	A	97	PRO	0	0.019	0.014	80.984	0.000	0.000	0.000	0.000	0.000	0.000
65	A	98	VAL	0	-0.017	0.005	83.851	0.000	0.000	0.000	0.000	0.000	0.000
66	A	99	ILE	0	0.006	0.000	81.930	0.000	0.000	0.000	0.000	0.000	0.000
67	A	100	ASP	-1	-0.784	-0.880	83.389	-0.016	-0.016	0.000	0.000	0.000	0.000
68	A	101	SER	0	-0.117	-0.083	86.750	0.000	0.000	0.000	0.000	0.000	0.000
69	A	102	LEU	0	-0.009	0.006	89.264	0.000	0.000	0.000	0.000	0.000	0.000
70	A	103	ASP	-1	-0.777	-0.884	88.220	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	104	ARG	1	0.944	0.981	88.695	0.015	0.015	0.000	0.000	0.000	0.000
72	A	105	ALA	0	-0.037	-0.021	92.563	0.000	0.000	0.000	0.000	0.000	0.000
73	A	106	LEU	0	-0.023	-0.004	93.251	0.000	0.000	0.000	0.000	0.000	0.000
74	A	107	GLU	-1	-0.938	-0.965	93.081	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	108	VAL	0	-0.075	-0.046	96.009	0.000	0.000	0.000	0.000	0.000	0.000
76	A	109	ALA	0	-0.034	-0.005	98.496	0.000	0.000	0.000	0.000	0.000	0.000
77	A	110	ASP	-1	-0.920	-0.945	99.147	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	111	LYS	1	0.851	0.903	101.156	0.011	0.011	0.000	0.000	0.000	0.000
79	A	112	ALA	0	-0.024	0.006	104.761	0.000	0.000	0.000	0.000	0.000	0.000
80	A	113	ASN	0	-0.046	-0.045	106.618	0.000	0.000	0.000	0.000	0.000	0.000
81	A	114	PRO	0	0.021	0.012	107.623	0.000	0.000	0.000	0.000	0.000	0.000
82	A	115	ASP	-1	-0.863	-0.900	109.152	-0.010	-0.010	0.000	0.000	0.000	0.000
83	A	116	MET	0	-0.026	-0.023	102.345	0.000	0.000	0.000	0.000	0.000	0.000
84	A	117	SER	0	-0.005	-0.020	104.179	0.000	0.000	0.000	0.000	0.000	0.000
85	A	118	ALA	0	0.060	0.031	102.793	0.000	0.000	0.000	0.000	0.000	0.000
86	A	119	MET	0	0.013	0.010	100.299	0.000	0.000	0.000	0.000	0.000	0.000
87	A	120	VAL	0	-0.002	0.001	99.205	0.000	0.000	0.000	0.000	0.000	0.000
88	A	121	GLU	-1	-0.907	-0.957	97.845	-0.011	-0.011	0.000	0.000	0.000	0.000
89	A	122	ASP	-1	-0.902	-0.947	96.890	-0.012	-0.012	0.000	0.000	0.000	0.000
90	A	123	ILE	0	-0.042	-0.014	93.990	0.000	0.000	0.000	0.000	0.000	0.000
91	A	124	GLU	-1	-0.859	-0.931	92.569	-0.013	-0.013	0.000	0.000	0.000	0.000
92	A	125	LEU	0	-0.017	-0.003	92.287	0.000	0.000	0.000	0.000	0.000	0.000
93	A	126	THR	0	-0.057	-0.037	90.292	0.000	0.000	0.000	0.000	0.000	0.000
94	A	127	LEU	0	0.003	0.004	87.521	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	128	LYS	1	0.899	0.929	87.548	0.013	0.013	0.000	0.000	0.000	0.000
96	A	129	SER	0	-0.070	-0.051	86.913	0.000	0.000	0.000	0.000	0.000	0.000
97	A	130	MET	0	-0.014	-0.003	84.150	-0.001	-0.001	0.000	0.000	0.000	0.000
98	A	131	LEU	0	-0.007	-0.007	83.029	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	132	ASP	-1	-0.780	-0.867	81.944	-0.015	-0.015	0.000	0.000	0.000	0.000
100	A	133	VAL	0	-0.038	-0.010	80.984	0.000	0.000	0.000	0.000	0.000	0.000
101	A	134	VAL	0	-0.012	-0.014	78.373	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	135	ARG	1	0.864	0.918	77.258	0.015	0.015	0.000	0.000	0.000	0.000
103	A	136	LYS	1	0.797	0.904	75.472	0.017	0.017	0.000	0.000	0.000	0.000
104	A	137	PHE	0	-0.048	-0.024	74.089	0.000	0.000	0.000	0.000	0.000	0.000
105	A	138	GLY	0	0.023	0.020	72.595	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	139	VAL	0	-0.037	-0.026	73.146	0.000	0.000	0.000	0.000	0.000	0.000
107	A	140	GLU	-1	-0.799	-0.873	75.686	-0.016	-0.016	0.000	0.000	0.000	0.000
108	A	141	VAL	0	-0.035	-0.042	77.463	0.000	0.000	0.000	0.000	0.000	0.000
109	A	142	ILE	0	-0.048	-0.017	75.964	0.000	0.000	0.000	0.000	0.000	0.000
110	A	143	ALA	0	0.030	-0.018	79.903	0.000	0.000	0.000	0.000	0.000	0.000
111	A	144	GLU	-1	-0.944	-0.949	80.839	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	145	THR	0	0.007	-0.010	83.406	0.000	0.000	0.000	0.000	0.000	0.000
113	A	146	ASN	0	-0.048	-0.033	85.294	0.000	0.000	0.000	0.000	0.000	0.000
114	A	147	VAL	0	0.038	0.039	79.995	0.000	0.000	0.000	0.000	0.000	0.000
115	A	148	PRO	0	0.001	-0.013	77.372	0.000	0.000	0.000	0.000	0.000	0.000
116	A	149	LEU	0	0.000	0.007	77.204	0.000	0.000	0.000	0.000	0.000	0.000
117	A	150	ASP	-1	-0.790	-0.889	72.396	-0.019	-0.019	0.000	0.000	0.000	0.000
118	A	151	PRO	0	-0.024	-0.019	71.399	0.000	0.000	0.000	0.000	0.000	0.000
119	A	152	ASN	0	-0.096	-0.052	68.248	-0.001	-0.001	0.000	0.000	0.000	0.000
120	A	153	VAL	0	-0.021	0.002	71.158	0.000	0.000	0.000	0.000	0.000	0.000
121	A	154	HIS	0	0.023	0.024	74.329	0.000	0.000	0.000	0.000	0.000	0.000
122	A	155	GLN	0	0.008	-0.009	76.244	0.000	0.000	0.000	0.000	0.000	0.000
123	A	156	ALA	0	0.015	0.004	78.615	0.000	0.000	0.000	0.000	0.000	0.000
124	A	157	ILE	0	-0.044	-0.008	81.105	0.000	0.000	0.000	0.000	0.000	0.000
125	A	158	ALA	0	-0.023	-0.013	83.558	0.000	0.000	0.000	0.000	0.000	0.000
126	A	159	MET	0	-0.023	-0.004	83.799	0.000	0.000	0.000	0.000	0.000	0.000
127	A	160	VAL	0	0.000	-0.005	86.808	0.000	0.000	0.000	0.000	0.000	0.000
128	A	161	GLU	-1	-0.815	-0.901	90.107	-0.012	-0.012	0.000	0.000	0.000	0.000
129	A	162	SER	0	-0.055	-0.053	90.956	0.000	0.000	0.000	0.000	0.000	0.000
130	A	163	ASP	-1	-0.803	-0.913	91.039	-0.011	-0.011	0.000	0.000	0.000	0.000
131	A	164	ASP	-1	-0.911	-0.921	92.296	-0.011	-0.011	0.000	0.000	0.000	0.000
132	A	165	VAL	0	-0.012	-0.003	87.157	0.000	0.000	0.000	0.000	0.000	0.000
133	A	166	ALA	0	-0.002	0.013	85.078	0.000	0.000	0.000	0.000	0.000	0.000
134	A	167	PRO	0	0.022	-0.014	85.042	0.000	0.000	0.000	0.000	0.000	0.000
135	A	168	GLY	0	-0.032	-0.010	81.689	0.000	0.000	0.000	0.000	0.000	0.000
136	A	169	ASN	0	-0.066	-0.036	81.068	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	170	VAL	0	-0.008	-0.007	81.238	0.000	0.000	0.000	0.000	0.000	0.000
138	A	171	LEU	0	0.006	-0.002	84.076	0.000	0.000	0.000	0.000	0.000	0.000
139	A	172	GLY	0	0.018	0.005	86.906	0.000	0.000	0.000	0.000	0.000	0.000
140	A	173	ILE	0	-0.040	-0.018	84.283	0.000	0.000	0.000	0.000	0.000	0.000
141	A	174	MET	0	-0.013	-0.005	85.985	0.000	0.000	0.000	0.000	0.000	0.000
142	A	175	GLN	0	-0.028	-0.027	82.922	0.000	0.000	0.000	0.000	0.000	0.000
143	A	176	LYS	1	0.876	0.935	83.288	0.014	0.014	0.000	0.000	0.000	0.000
144	A	177	GLY	0	0.048	0.030	79.203	0.000	0.000	0.000	0.000	0.000	0.000
145	A	178	TYR	0	-0.016	-0.009	77.288	0.000	0.000	0.000	0.000	0.000	0.000
146	A	179	THR	0	0.019	0.005	72.506	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	180	LEU	0	0.015	0.002	69.989	0.000	0.000	0.000	0.000	0.000	0.000
148	A	181	ASN	0	-0.067	-0.049	67.672	0.000	0.000	0.000	0.000	0.000	0.000
149	A	182	GLY	0	0.006	0.008	66.983	-0.001	-0.001	0.000	0.000	0.000	0.000
150	A	183	ARG	1	0.765	0.894	64.210	0.025	0.025	0.000	0.000	0.000	0.000
151	A	184	THR	0	0.022	-0.019	68.506	0.001	0.001	0.000	0.000	0.000	0.000
152	A	185	ILE	0	-0.095	-0.037	70.762	-0.001	-0.001	0.000	0.000	0.000	0.000
153	A	186	ARG	1	0.838	0.901	73.000	0.017	0.017	0.000	0.000	0.000	0.000
154	A	187	ALA	0	0.016	0.018	75.068	0.000	0.000	0.000	0.000	0.000	0.000
155	A	188	ALA	0	0.027	0.017	76.630	0.000	0.000	0.000	0.000	0.000	0.000
156	A	189	MET	0	-0.035	0.000	80.123	0.000	0.000	0.000	0.000	0.000	0.000
157	A	190	VAL	0	0.010	0.005	81.040	0.000	0.000	0.000	0.000	0.000	0.000
158	A	191	THR	0	0.000	0.002	83.726	0.000	0.000	0.000	0.000	0.000	0.000
159	A	192	VAL	0	0.020	0.005	81.795	0.000	0.000	0.000	0.000	0.000	0.000
160	A	193	ALA	0	0.050	0.044	85.173	0.000	0.000	0.000	0.000	0.000	0.000
161	A	194	LYS	1	0.783	0.861	85.995	0.011	0.011	0.000	0.000	0.000	0.000
162	A	195	ALA	0	0.048	0.019	88.110	0.000	0.000	0.000	0.000	0.000	0.000
163	A	196	LYS	1	0.874	0.938	90.251	0.010	0.010	0.000	0.000	0.000	0.000
164	A	197	ALA	0	-0.066	-0.008	93.110	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)