FMO DATABASE

FMODB ID: X1NGZ

Calculation Name: 1YBK-A-Xray26

Preferred Name:

Target Type:

Ligand Name: n-(carboxymethyl)-n,n-dimethyl-3-[(1-oxododecyl)amino]-1-propanaminium inner salt

ligand 3-letter code: BEQ

PDB ID: 1YBK

Chain ID: A

ChEMBL ID:

UniProt ID: Q54436

Base Structure: X-ray

Registration Date: 2018-07-26

Reference:

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water	Apo structure with with a 3 angstrom solvent shell.
Procedure	Auto-FMO protocol ver. 1.20180227

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	121
LigandCharge	SO4=-2
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-296782.695941
FMO2-HF: Nuclear repulsion	270377.552504
FMO2-HF: Total energy	-26405.143437
FMO2-MP2: Total energy	-26479.514097

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:1:GLY)

Summations of interaction energy for fragment #1(A:1:GLY)

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.
-165.737	-157.38	8.776	-9.726	-7.409	-0.113

Interaction energy analysis for fragmet #1(A:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.838 / q_NPA : 0.909

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

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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	3	ILE	0	0.093	0.044	3.798	-3.253	-2.633	0.000	-0.282	-0.338	0.000
4	A	4	ILE	0	0.035	0.014	6.614	1.066	1.066	0.000	0.000	0.000	0.000
5	A	5	ASN	0	-0.005	0.014	2.534	9.792	10.696	0.196	-0.504	-0.596	-0.003
6	A	6	GLU	-1	-0.751	-0.826	1.911	-111.618	-107.670	7.551	-6.646	-4.853	-0.091
7	A	7	THR	0	-0.003	0.001	5.219	6.254	6.301	-0.001	-0.002	-0.045	0.000
8	A	8	ALA	0	-0.017	0.003	8.111	3.360	3.360	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.700	-0.829	5.900	-41.482	-41.482	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.788	-0.881	8.697	-22.073	-22.073	0.000	0.000	0.000	0.000
11	A	11	ILE	0	-0.039	-0.022	10.555	2.684	2.684	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.012	0.004	12.022	1.832	1.832	0.000	0.000	0.000	0.000
13	A	13	TYR	0	0.010	0.010	11.924	1.539	1.539	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.915	0.948	13.821	22.034	22.034	0.000	0.000	0.000	0.000
15	A	15	LEU	0	0.012	-0.004	16.171	1.393	1.393	0.000	0.000	0.000	0.000
16	A	16	THR	0	0.010	0.014	16.381	1.038	1.038	0.000	0.000	0.000	0.000
17	A	17	VAL	0	0.020	0.044	17.262	0.939	0.939	0.000	0.000	0.000	0.000
18	A	18	ILE	0	-0.075	-0.015	19.811	0.992	0.992	0.000	0.000	0.000	0.000
19	A	19	ILE	0	-0.025	-0.017	20.650	0.818	0.818	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.760	-0.854	21.125	-14.205	-14.205	0.000	0.000	0.000	0.000
21	A	21	ASP	-1	-0.711	-0.811	23.699	-12.872	-12.872	0.000	0.000	0.000	0.000
22	A	22	ARG	1	0.841	0.932	25.768	12.489	12.489	0.000	0.000	0.000	0.000
23	A	23	TYR	0	-0.039	-0.028	26.711	0.594	0.594	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.706	-0.850	27.028	-10.734	-10.734	0.000	0.000	0.000	0.000
25	A	25	SER	0	0.023	-0.002	29.573	0.274	0.274	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.080	-0.025	31.483	0.424	0.424	0.000	0.000	0.000	0.000
27	A	27	LYS	1	0.871	0.955	30.776	10.592	10.592	0.000	0.000	0.000	0.000
28	A	28	ASN	0	0.022	0.014	32.169	0.413	0.413	0.000	0.000	0.000	0.000
29	A	29	LEU	0	0.000	0.014	35.464	0.376	0.376	0.000	0.000	0.000	0.000
30	A	30	ILE	0	-0.016	-0.020	35.756	0.318	0.318	0.000	0.000	0.000	0.000
31	A	31	THR	0	0.010	0.012	36.907	0.232	0.232	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.012	0.032	39.495	0.256	0.256	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.810	0.868	41.425	7.485	7.485	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.070	0.036	42.738	0.221	0.221	0.000	0.000	0.000	0.000
35	A	35	ASP	-1	-0.718	-0.828	42.443	-7.462	-7.462	0.000	0.000	0.000	0.000
36	A	36	ARG	1	0.881	0.922	45.127	7.173	7.173	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.053	-0.026	46.837	0.181	0.181	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.780	-0.856	46.635	-6.782	-6.782	0.000	0.000	0.000	0.000
39	A	39	MET	0	0.022	0.025	47.978	0.170	0.170	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.014	-0.010	51.222	0.143	0.143	0.000	0.000	0.000	0.000
41	A	41	ILE	0	-0.015	-0.004	51.860	0.150	0.150	0.000	0.000	0.000	0.000
42	A	42	ASN	0	0.071	0.104	51.536	0.201	0.201	0.000	0.000	0.000	0.000
43	A	43	ASP	-1	-0.761	-0.810	55.454	-5.443	-5.443	0.000	0.000	0.000	0.000
44	A	44	ASN	0	0.022	-0.009	57.305	0.141	0.141	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.008	0.002	57.909	0.123	0.123	0.000	0.000	0.000	0.000
46	A	46	SER	0	0.012	-0.011	59.432	0.103	0.103	0.000	0.000	0.000	0.000
47	A	47	THR	0	0.038	0.033	61.702	0.105	0.105	0.000	0.000	0.000	0.000
48	A	48	ILE	0	-0.018	-0.001	62.177	0.095	0.095	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.020	0.022	62.864	0.087	0.087	0.000	0.000	0.000	0.000
50	A	50	ALA	0	-0.033	0.004	66.011	0.088	0.088	0.000	0.000	0.000	0.000
51	A	51	SER	0	-0.076	-0.044	67.540	0.087	0.087	0.000	0.000	0.000	0.000
52	A	52	ILE	-1	-0.992	-0.979	69.144	-4.616	-4.616	0.000	0.000	0.000	0.000
53	A	602	SO4	-2	-1.701	-1.786	31.518	-19.736	-19.736	0.000	0.000	0.000	0.000
54	A	603	HOH	0	-0.023	-0.016	44.584	0.064	0.064	0.000	0.000	0.000	0.000
55	A	604	HOH	0	-0.062	-0.048	34.991	0.121	0.121	0.000	0.000	0.000	0.000
56	A	605	HOH	0	-0.047	-0.034	44.401	0.011	0.011	0.000	0.000	0.000	0.000
57	A	606	HOH	0	-0.044	-0.035	40.825	-0.031	-0.031	0.000	0.000	0.000	0.000
58	A	608	HOH	0	-0.054	-0.039	18.652	-0.194	-0.194	0.000	0.000	0.000	0.000
59	A	609	HOH	0	-0.018	-0.017	37.701	0.003	0.003	0.000	0.000	0.000	0.000
60	A	610	HOH	0	-0.045	-0.032	28.901	-0.163	-0.163	0.000	0.000	0.000	0.000
61	A	611	HOH	0	-0.040	-0.031	47.080	0.043	0.043	0.000	0.000	0.000	0.000
62	A	612	HOH	0	-0.051	-0.044	59.666	0.006	0.006	0.000	0.000	0.000	0.000
63	A	613	HOH	0	0.035	0.035	46.029	0.003	0.003	0.000	0.000	0.000	0.000
64	A	614	HOH	0	-0.036	-0.030	64.395	-0.023	-0.023	0.000	0.000	0.000	0.000
65	A	615	HOH	0	-0.040	-0.036	5.697	2.129	2.129	0.000	0.000	0.000	0.000
66	A	616	HOH	0	0.060	0.040	43.636	0.069	0.069	0.000	0.000	0.000	0.000
67	A	617	HOH	0	0.017	0.017	41.885	0.033	0.033	0.000	0.000	0.000	0.000
68	A	618	HOH	0	-0.028	-0.023	36.549	-0.031	-0.031	0.000	0.000	0.000	0.000
69	A	619	HOH	0	-0.032	-0.021	10.021	0.768	0.768	0.000	0.000	0.000	0.000
70	A	620	HOH	0	0.010	0.001	49.470	0.055	0.055	0.000	0.000	0.000	0.000
71	A	621	HOH	0	-0.031	-0.026	15.494	-0.544	-0.544	0.000	0.000	0.000	0.000
72	A	622	HOH	0	-0.041	-0.045	56.429	-0.046	-0.046	0.000	0.000	0.000	0.000
73	A	623	HOH	0	-0.022	-0.013	60.001	0.042	0.042	0.000	0.000	0.000	0.000
74	A	624	HOH	0	0.007	0.007	2.789	-6.991	-6.100	0.911	-1.061	-0.741	-0.010
75	A	625	HOH	0	-0.017	-0.007	43.384	0.050	0.050	0.000	0.000	0.000	0.000
76	A	626	HOH	0	0.001	-0.004	3.745	5.714	5.850	0.000	-0.056	-0.080	0.000
77	A	627	HOH	0	-0.036	-0.038	40.699	0.030	0.030	0.000	0.000	0.000	0.000
78	A	628	HOH	0	-0.032	-0.025	51.701	0.027	0.027	0.000	0.000	0.000	0.000
79	A	630	HOH	0	-0.026	-0.019	58.056	-0.019	-0.019	0.000	0.000	0.000	0.000
80	A	632	HOH	0	-0.046	-0.045	29.360	0.044	0.044	0.000	0.000	0.000	0.000
81	A	633	HOH	0	-0.032	-0.023	53.792	-0.035	-0.035	0.000	0.000	0.000	0.000
82	A	634	HOH	0	-0.027	-0.016	45.775	0.040	0.040	0.000	0.000	0.000	0.000
83	A	635	HOH	0	-0.040	-0.035	22.026	-0.143	-0.143	0.000	0.000	0.000	0.000
84	A	636	HOH	0	-0.021	-0.024	58.128	-0.024	-0.024	0.000	0.000	0.000	0.000
85	A	637	HOH	0	-0.019	-0.022	23.904	0.165	0.165	0.000	0.000	0.000	0.000
86	A	638	HOH	0	-0.039	-0.028	24.772	-0.118	-0.118	0.000	0.000	0.000	0.000
87	A	640	HOH	0	-0.017	-0.018	28.320	0.168	0.168	0.000	0.000	0.000	0.000
88	A	641	HOH	0	-0.003	-0.009	34.846	-0.031	-0.031	0.000	0.000	0.000	0.000
89	A	642	HOH	0	-0.031	-0.024	69.910	0.012	0.012	0.000	0.000	0.000	0.000
90	A	643	HOH	0	-0.058	-0.037	62.208	0.034	0.034	0.000	0.000	0.000	0.000
91	A	644	HOH	0	-0.031	-0.031	6.344	1.860	1.860	0.000	0.000	0.000	0.000
92	A	645	HOH	0	-0.008	-0.006	60.388	0.024	0.024	0.000	0.000	0.000	0.000
93	A	646	HOH	0	-0.016	-0.020	49.162	0.064	0.064	0.000	0.000	0.000	0.000
94	A	647	HOH	0	-0.054	-0.046	19.908	-0.288	-0.288	0.000	0.000	0.000	0.000
95	A	648	HOH	0	-0.041	-0.023	70.533	-0.005	-0.005	0.000	0.000	0.000	0.000
96	A	649	HOH	0	-0.066	-0.043	7.053	-0.295	-0.295	0.000	0.000	0.000	0.000
97	A	650	HOH	0	-0.047	-0.030	68.732	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	652	HOH	0	-0.052	-0.039	23.213	-0.085	-0.085	0.000	0.000	0.000	0.000
99	A	662	HOH	0	-0.055	-0.047	35.082	0.109	0.109	0.000	0.000	0.000	0.000
100	A	671	HOH	0	-0.053	-0.035	12.885	0.733	0.733	0.000	0.000	0.000	0.000
101	A	673	HOH	0	-0.023	-0.016	7.253	-0.510	-0.510	0.000	0.000	0.000	0.000
102	A	677	HOH	0	-0.056	-0.045	20.211	-0.312	-0.312	0.000	0.000	0.000	0.000
103	A	682	HOH	0	-0.032	-0.021	30.867	-0.077	-0.077	0.000	0.000	0.000	0.000
104	A	683	HOH	0	-0.042	-0.031	5.691	0.577	0.577	0.000	0.000	0.000	0.000
105	A	684	HOH	0	-0.045	-0.029	5.398	-1.163	-1.163	0.000	0.000	0.000	0.000
106	A	690	HOH	0	-0.027	-0.032	24.040	0.136	0.136	0.000	0.000	0.000	0.000
107	A	694	HOH	0	0.021	0.017	19.009	-0.324	-0.324	0.000	0.000	0.000	0.000
108	A	696	HOH	0	-0.018	-0.019	29.311	-0.055	-0.055	0.000	0.000	0.000	0.000
109	A	700	HOH	0	-0.011	-0.025	54.991	-0.015	-0.015	0.000	0.000	0.000	0.000
110	A	702	HOH	0	-0.032	-0.022	11.069	-0.071	-0.071	0.000	0.000	0.000	0.000
111	A	705	HOH	0	0.002	0.013	57.509	0.041	0.041	0.000	0.000	0.000	0.000
112	A	712	HOH	0	0.008	-0.012	21.102	-0.214	-0.214	0.000	0.000	0.000	0.000
113	A	717	HOH	0	0.030	0.028	17.407	-0.498	-0.498	0.000	0.000	0.000	0.000
114	A	725	HOH	0	-0.050	-0.040	2.845	0.430	0.877	0.018	-0.273	-0.192	-0.002
115	A	733	HOH	0	-0.048	-0.043	2.998	-2.875	-1.511	0.101	-0.902	-0.564	-0.007
116	A	736	HOH	0	0.005	0.030	30.440	-0.122	-0.122	0.000	0.000	0.000	0.000
117	A	737	HOH	0	-0.118	-0.099	54.335	0.035	0.035	0.000	0.000	0.000	0.000
118	A	738	HOH	0	-0.032	-0.021	26.414	0.045	0.045	0.000	0.000	0.000	0.000
119	B	604	HOH	0	-0.011	0.004	46.454	-0.019	-0.019	0.000	0.000	0.000	0.000
120	B	614	HOH	0	0.001	0.006	58.073	-0.035	-0.035	0.000	0.000	0.000	0.000
121	B	669	HOH	0	-0.009	-0.016	46.025	-0.048	-0.048	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:GLY)