FMO DATABASE

FMODB ID: 66ZVZ

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1093588.465577
FMO2-HF: Nuclear repulsion	1033796.339494
FMO2-HF: Total energy	-59792.126083
FMO2-MP2: Total energy	-59964.312011

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.
16.087	14.762	18.53	-9.32	-7.885	-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 : -0.911 / q_NPA : -0.977

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	0.887	0.923	3.149	-39.127	-37.331	0.010	-0.824	-0.982	0.004
4	B	41	ASP	-1	-0.797	-0.864	1.768	35.208	29.188	17.866	-7.211	-4.635	-0.054
5	B	42	GLU	-1	-0.885	-0.939	2.663	47.679	50.398	0.654	-1.243	-2.130	0.012
6	B	43	LYS	1	0.885	0.943	4.442	-35.246	-35.066	0.000	-0.042	-0.138	0.000
7	B	44	VAL	0	-0.025	-0.033	6.618	-4.173	-4.173	0.000	0.000	0.000	0.000
8	B	45	ALA	0	0.056	0.041	7.458	-3.133	-3.133	0.000	0.000	0.000	0.000
9	B	46	ASN	0	-0.021	-0.023	8.904	-3.908	-3.908	0.000	0.000	0.000	0.000
10	B	47	LEU	0	-0.046	-0.014	10.897	-2.410	-2.410	0.000	0.000	0.000	0.000
11	B	48	GLU	-1	-0.886	-0.943	11.840	21.293	21.293	0.000	0.000	0.000	0.000
12	B	49	ALA	0	-0.001	0.000	13.436	-1.535	-1.535	0.000	0.000	0.000	0.000
13	B	50	GLN	0	-0.056	-0.032	14.218	-2.769	-2.769	0.000	0.000	0.000	0.000
14	B	51	LEU	0	-0.024	0.000	16.775	-1.172	-1.172	0.000	0.000	0.000	0.000
15	B	52	ALA	0	0.031	0.011	18.149	-1.008	-1.008	0.000	0.000	0.000	0.000
16	B	53	GLU	-1	-0.931	-0.952	19.288	13.992	13.992	0.000	0.000	0.000	0.000
17	B	54	ALA	0	-0.015	-0.022	21.071	-0.816	-0.816	0.000	0.000	0.000	0.000
18	B	55	GLN	0	0.014	0.028	22.541	-0.343	-0.343	0.000	0.000	0.000	0.000
19	B	56	THR	0	-0.045	-0.049	23.308	-0.706	-0.706	0.000	0.000	0.000	0.000
20	B	57	ARG	1	0.945	0.983	22.285	-13.735	-13.735	0.000	0.000	0.000	0.000
21	B	58	GLU	-1	-0.950	-0.961	26.683	10.134	10.134	0.000	0.000	0.000	0.000
22	B	59	ARG	1	0.900	0.938	27.435	-11.520	-11.520	0.000	0.000	0.000	0.000
23	B	60	ASP	-1	-0.871	-0.943	29.239	10.431	10.431	0.000	0.000	0.000	0.000
24	B	61	GLY	0	0.015	0.006	30.562	-0.382	-0.382	0.000	0.000	0.000	0.000
25	B	62	ILE	0	-0.028	-0.009	32.404	-0.459	-0.459	0.000	0.000	0.000	0.000
26	B	63	LEU	0	-0.004	-0.009	34.209	-0.361	-0.361	0.000	0.000	0.000	0.000
27	B	64	ARG	1	0.894	0.955	35.095	-8.506	-8.506	0.000	0.000	0.000	0.000
28	B	65	VAL	0	0.109	0.025	36.801	-0.278	-0.278	0.000	0.000	0.000	0.000
29	B	66	LYS	1	0.919	0.961	37.764	-8.542	-8.542	0.000	0.000	0.000	0.000
30	B	67	ALA	0	-0.020	-0.007	39.880	-0.211	-0.211	0.000	0.000	0.000	0.000
31	B	68	GLU	-1	-0.971	-0.961	39.456	7.842	7.842	0.000	0.000	0.000	0.000
32	B	69	MET	0	-0.010	-0.021	42.347	-0.199	-0.199	0.000	0.000	0.000	0.000
33	B	70	GLU	-1	-0.893	-0.952	44.421	6.500	6.500	0.000	0.000	0.000	0.000
34	B	71	ASN	0	0.007	0.013	44.480	-0.209	-0.209	0.000	0.000	0.000	0.000
35	B	72	LEU	0	-0.029	-0.005	46.840	-0.142	-0.142	0.000	0.000	0.000	0.000
36	B	73	ARG	1	0.983	0.989	47.591	-6.704	-6.704	0.000	0.000	0.000	0.000
37	B	74	ARG	1	0.942	0.973	46.627	-6.793	-6.793	0.000	0.000	0.000	0.000
38	B	75	ARG	1	0.927	0.956	47.254	-6.636	-6.636	0.000	0.000	0.000	0.000
39	B	76	THR	0	-0.028	-0.011	52.687	-0.105	-0.105	0.000	0.000	0.000	0.000
40	B	77	GLU	-1	-0.893	-0.937	54.900	5.387	5.387	0.000	0.000	0.000	0.000
41	B	78	LEU	0	0.009	0.006	55.865	-0.114	-0.114	0.000	0.000	0.000	0.000
42	B	79	ASP	-1	-0.888	-0.976	55.592	5.677	5.677	0.000	0.000	0.000	0.000
43	B	80	ILE	0	-0.008	0.009	58.421	-0.078	-0.078	0.000	0.000	0.000	0.000
44	B	81	GLU	-1	-0.921	-0.966	60.634	4.918	4.918	0.000	0.000	0.000	0.000
45	B	82	LYS	1	0.780	0.907	57.906	-5.616	-5.616	0.000	0.000	0.000	0.000
46	B	83	ALA	0	-0.001	-0.010	63.086	-0.093	-0.093	0.000	0.000	0.000	0.000
47	B	84	HIS	0	0.039	0.033	64.988	-0.068	-0.068	0.000	0.000	0.000	0.000
48	B	85	LYS	1	0.977	1.000	65.934	-4.912	-4.912	0.000	0.000	0.000	0.000
49	B	86	PHE	0	-0.006	-0.012	67.484	-0.080	-0.080	0.000	0.000	0.000	0.000
50	B	87	ALA	0	0.002	-0.001	69.057	-0.075	-0.075	0.000	0.000	0.000	0.000
51	B	88	LEU	0	-0.020	-0.015	70.707	-0.079	-0.079	0.000	0.000	0.000	0.000
52	B	89	GLU	-1	-0.912	-0.972	71.139	4.509	4.509	0.000	0.000	0.000	0.000
53	B	90	LYS	1	0.970	0.991	73.572	-4.426	-4.426	0.000	0.000	0.000	0.000
54	B	91	PHE	0	-0.023	-0.010	75.105	-0.071	-0.071	0.000	0.000	0.000	0.000
55	B	92	ILE	0	0.011	-0.002	75.974	-0.066	-0.066	0.000	0.000	0.000	0.000
56	B	93	ASN	0	0.000	-0.003	77.776	-0.071	-0.071	0.000	0.000	0.000	0.000
57	B	94	GLU	-1	-0.965	-0.982	79.103	4.040	4.040	0.000	0.000	0.000	0.000
58	B	95	LEU	0	-0.018	-0.002	80.721	-0.054	-0.054	0.000	0.000	0.000	0.000
59	B	96	LEU	0	0.013	0.002	82.445	-0.055	-0.055	0.000	0.000	0.000	0.000
60	B	97	PRO	0	-0.005	0.012	84.447	-0.051	-0.051	0.000	0.000	0.000	0.000
61	B	98	VAL	0	-0.006	-0.006	86.174	-0.056	-0.056	0.000	0.000	0.000	0.000
62	B	99	ILE	0	-0.004	-0.005	84.742	-0.038	-0.038	0.000	0.000	0.000	0.000
63	B	100	ASP	-1	-0.755	-0.878	88.844	3.626	3.626	0.000	0.000	0.000	0.000
64	B	101	SER	0	-0.145	-0.097	91.040	-0.070	-0.070	0.000	0.000	0.000	0.000
65	B	102	LEU	0	0.016	-0.003	90.544	-0.043	-0.043	0.000	0.000	0.000	0.000
66	B	103	ASP	-1	-0.814	-0.905	92.062	3.501	3.501	0.000	0.000	0.000	0.000
67	B	104	ARG	1	0.909	0.986	94.898	-3.437	-3.437	0.000	0.000	0.000	0.000
68	B	105	ALA	0	-0.063	-0.036	96.789	-0.039	-0.039	0.000	0.000	0.000	0.000
69	B	106	LEU	0	-0.022	-0.016	96.572	-0.032	-0.032	0.000	0.000	0.000	0.000
70	B	107	GLU	-1	-0.960	-0.963	98.289	3.247	3.247	0.000	0.000	0.000	0.000
71	B	108	VAL	0	-0.122	-0.047	100.848	-0.042	-0.042	0.000	0.000	0.000	0.000
72	B	116	MET	0	0.023	-0.017	106.130	-0.010	-0.010	0.000	0.000	0.000	0.000
73	B	117	SER	0	0.002	-0.004	105.202	0.030	0.030	0.000	0.000	0.000	0.000
74	B	118	ALA	0	0.066	0.034	104.112	0.014	0.014	0.000	0.000	0.000	0.000
75	B	119	MET	0	-0.034	0.011	99.998	0.028	0.028	0.000	0.000	0.000	0.000
76	B	120	VAL	0	0.050	0.010	100.523	0.038	0.038	0.000	0.000	0.000	0.000
77	B	121	GLU	-1	-0.924	-0.948	99.538	3.238	3.238	0.000	0.000	0.000	0.000
78	B	122	ASP	-1	-0.881	-0.944	97.642	3.323	3.323	0.000	0.000	0.000	0.000
79	B	123	ILE	0	-0.067	-0.031	95.940	0.055	0.055	0.000	0.000	0.000	0.000
80	B	124	GLU	-1	-0.859	-0.937	95.136	3.326	3.326	0.000	0.000	0.000	0.000
81	B	125	LEU	0	-0.031	-0.012	93.011	0.051	0.051	0.000	0.000	0.000	0.000
82	B	126	THR	0	-0.085	-0.046	91.090	0.056	0.056	0.000	0.000	0.000	0.000
83	B	127	LEU	0	0.017	0.009	90.216	0.060	0.060	0.000	0.000	0.000	0.000
84	B	128	LYS	1	0.921	0.977	89.292	-3.559	-3.559	0.000	0.000	0.000	0.000
85	B	129	SER	0	-0.013	-0.027	87.439	0.048	0.048	0.000	0.000	0.000	0.000
86	B	130	MET	0	-0.016	0.008	85.623	0.078	0.078	0.000	0.000	0.000	0.000
87	B	131	LEU	0	0.009	-0.003	84.724	0.061	0.061	0.000	0.000	0.000	0.000
88	B	132	ASP	-1	-0.938	-0.971	83.995	3.822	3.822	0.000	0.000	0.000	0.000
89	B	133	VAL	0	-0.088	-0.052	80.530	0.065	0.065	0.000	0.000	0.000	0.000
90	B	134	VAL	0	0.052	0.015	80.063	0.073	0.073	0.000	0.000	0.000	0.000
91	B	135	ARG	1	1.004	1.028	79.263	-3.802	-3.802	0.000	0.000	0.000	0.000
92	B	136	LYS	1	0.877	0.948	77.077	-4.036	-4.036	0.000	0.000	0.000	0.000
93	B	137	PHE	0	-0.083	-0.044	73.734	0.075	0.075	0.000	0.000	0.000	0.000
94	B	138	GLY	0	0.012	0.003	75.142	0.049	0.049	0.000	0.000	0.000	0.000
95	B	139	VAL	0	-0.081	0.011	76.666	-0.006	-0.006	0.000	0.000	0.000	0.000
96	B	140	GLU	-1	-0.874	-0.961	79.792	3.901	3.901	0.000	0.000	0.000	0.000
97	B	141	VAL	0	-0.031	-0.028	82.557	-0.003	-0.003	0.000	0.000	0.000	0.000
98	B	142	ILE	0	-0.037	0.011	83.942	-0.006	-0.006	0.000	0.000	0.000	0.000
99	B	143	ALA	0	0.001	-0.031	87.530	-0.021	-0.021	0.000	0.000	0.000	0.000
100	B	144	GLU	-1	-0.939	-0.938	90.222	3.564	3.564	0.000	0.000	0.000	0.000
101	B	145	THR	0	0.028	-0.018	92.158	-0.001	-0.001	0.000	0.000	0.000	0.000
102	B	146	ASN	0	-0.053	-0.037	94.940	-0.003	-0.003	0.000	0.000	0.000	0.000
103	B	147	VAL	0	0.003	0.042	90.829	0.007	0.007	0.000	0.000	0.000	0.000
104	B	148	PRO	0	0.000	-0.002	91.359	-0.010	-0.010	0.000	0.000	0.000	0.000
105	B	149	LEU	0	-0.026	-0.011	90.762	0.033	0.033	0.000	0.000	0.000	0.000
106	B	150	ASP	-1	-0.792	-0.896	85.189	3.877	3.877	0.000	0.000	0.000	0.000
107	B	151	PRO	0	-0.033	-0.027	85.480	0.010	0.010	0.000	0.000	0.000	0.000
108	B	152	ASN	0	-0.067	-0.017	80.835	0.064	0.064	0.000	0.000	0.000	0.000
109	B	153	VAL	0	-0.023	-0.006	82.930	0.038	0.038	0.000	0.000	0.000	0.000
110	B	154	HIS	0	0.033	-0.004	85.408	-0.021	-0.021	0.000	0.000	0.000	0.000
111	B	155	GLN	0	0.001	0.005	88.031	-0.002	-0.002	0.000	0.000	0.000	0.000
112	B	156	ALA	0	-0.009	0.008	90.092	-0.029	-0.029	0.000	0.000	0.000	0.000
113	B	157	ILE	0	-0.014	-0.007	93.597	0.011	0.011	0.000	0.000	0.000	0.000
114	B	158	ALA	0	-0.037	-0.032	95.699	-0.032	-0.032	0.000	0.000	0.000	0.000
115	B	159	MET	0	-0.027	-0.011	98.688	0.032	0.032	0.000	0.000	0.000	0.000
116	B	160	VAL	0	-0.018	-0.016	100.829	-0.027	-0.027	0.000	0.000	0.000	0.000
117	B	161	GLU	-1	-0.776	-0.869	104.056	3.066	3.066	0.000	0.000	0.000	0.000
118	B	162	SER	0	0.000	-0.013	104.750	-0.018	-0.018	0.000	0.000	0.000	0.000
119	B	163	ASP	-1	-0.895	-0.935	106.141	3.005	3.005	0.000	0.000	0.000	0.000
120	B	164	ASP	-1	-0.996	-0.992	104.077	3.089	3.089	0.000	0.000	0.000	0.000
121	B	165	VAL	0	-0.054	-0.029	99.810	0.029	0.029	0.000	0.000	0.000	0.000
122	B	166	ALA	0	-0.027	0.001	99.948	-0.013	-0.013	0.000	0.000	0.000	0.000
123	B	167	PRO	0	0.037	-0.002	100.431	0.021	0.021	0.000	0.000	0.000	0.000
124	B	168	GLY	0	-0.051	-0.017	97.243	0.021	0.021	0.000	0.000	0.000	0.000
125	B	169	ASN	0	0.010	-0.002	95.511	0.078	0.078	0.000	0.000	0.000	0.000
126	B	170	VAL	0	-0.028	-0.015	92.422	-0.037	-0.037	0.000	0.000	0.000	0.000
127	B	171	LEU	0	0.076	0.023	95.769	-0.009	-0.009	0.000	0.000	0.000	0.000
128	B	172	GLY	0	0.057	0.065	98.691	-0.011	-0.011	0.000	0.000	0.000	0.000
129	B	173	ILE	0	-0.018	-0.015	92.890	0.031	0.031	0.000	0.000	0.000	0.000
130	B	174	MET	0	-0.013	0.001	95.387	-0.016	-0.016	0.000	0.000	0.000	0.000
131	B	175	GLN	0	0.006	-0.011	90.037	0.037	0.037	0.000	0.000	0.000	0.000
132	B	176	LYS	1	0.946	0.982	89.481	-3.549	-3.549	0.000	0.000	0.000	0.000
133	B	177	GLY	0	0.027	-0.001	86.939	0.019	0.019	0.000	0.000	0.000	0.000
134	B	178	TYR	0	0.007	-0.003	82.746	-0.007	-0.007	0.000	0.000	0.000	0.000
135	B	179	THR	0	0.008	-0.003	79.626	0.027	0.027	0.000	0.000	0.000	0.000
136	B	180	LEU	0	0.013	0.010	74.095	-0.009	-0.009	0.000	0.000	0.000	0.000
137	B	181	ASN	0	-0.055	-0.047	72.964	0.053	0.053	0.000	0.000	0.000	0.000
138	B	182	GLY	0	0.032	0.028	75.618	0.035	0.035	0.000	0.000	0.000	0.000
139	B	183	ARG	1	0.929	0.960	71.654	-4.472	-4.472	0.000	0.000	0.000	0.000
140	B	184	THR	0	-0.005	-0.021	76.645	-0.001	-0.001	0.000	0.000	0.000	0.000
141	B	185	ILE	0	-0.092	-0.024	77.483	0.037	0.037	0.000	0.000	0.000	0.000
142	B	186	ARG	1	0.813	0.889	79.843	-3.743	-3.743	0.000	0.000	0.000	0.000
143	B	187	ALA	0	0.020	0.016	83.485	-0.019	-0.019	0.000	0.000	0.000	0.000
144	B	188	ALA	0	0.012	0.013	86.030	-0.022	-0.022	0.000	0.000	0.000	0.000
145	B	189	MET	0	-0.026	-0.001	89.363	-0.012	-0.012	0.000	0.000	0.000	0.000
146	B	190	VAL	0	-0.026	-0.012	91.993	-0.025	-0.025	0.000	0.000	0.000	0.000
147	B	191	THR	0	-0.078	-0.062	94.592	-0.013	-0.013	0.000	0.000	0.000	0.000
148	B	192	VAL	0	0.051	0.019	95.263	-0.005	-0.005	0.000	0.000	0.000	0.000
149	B	193	ALA	0	0.047	0.040	97.917	-0.032	-0.032	0.000	0.000	0.000	0.000
150	B	194	LYS	1	0.771	0.863	101.002	-3.058	-3.058	0.000	0.000	0.000	0.000
151	B	195	ALA	0	0.005	0.012	103.037	-0.039	-0.039	0.000	0.000	0.000	0.000

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