FMO DATABASE

FMODB ID: 39V1L

Calculation Name: 3LF4-B-Xray372

Preferred Name:

Target Type:

Ligand Name: n-[(2z)-2-amino-3-(4-hydroxyphenyl)prop-2-enoyl]glycine

ligand 3-letter code: 0YG

PDB ID: 3LF4

Chain ID: B

ChEMBL ID:

UniProt ID: D1MPT3

Base Structure: X-ray

Registration Date: 2023-09-19

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	160
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1579585.784653
FMO2-HF: Nuclear repulsion	1515157.721552
FMO2-HF: Total energy	-64428.063101
FMO2-MP2: Total energy	-64616.12281

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:67:0YG)

Summations of interaction energy for fragment #1(B:67:0YG)

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.
-698.482	-959.189	1517.441	-1218.79	-37.949	-1.088

Interaction energy analysis for fragmet #1(B:67:0YG)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : -0.089 / q_NPA : -0.116

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].
2	B	69	SER	-1	0.091	0.073	1.542	-551.745	-839.063	1473.509	-1190.628	4.437	-0.946
3	B	70	ARG	1	0.767	0.861	2.419	18.916	26.821	1.745	-5.009	-4.641	0.044
4	B	71	ALA	0	0.018	0.017	5.180	-1.077	-1.219	0.000	-0.016	0.157	0.000
5	B	72	TYR	0	-0.005	-0.004	6.922	1.134	1.134	0.000	0.000	0.000	0.000
6	B	73	VAL	0	-0.055	-0.003	5.834	-1.631	-1.631	0.000	0.000	0.000	0.000
7	B	74	LYS	1	0.886	0.938	8.088	22.168	22.168	0.000	0.000	0.000	0.000
8	B	75	HIS	0	0.030	0.001	10.815	-2.385	-2.385	0.000	0.000	0.000	0.000
9	B	76	PRO	0	-0.007	0.003	14.125	0.661	0.661	0.000	0.000	0.000	0.000
10	B	77	ALA	0	-0.009	-0.005	17.746	-0.138	-0.138	0.000	0.000	0.000	0.000
11	B	78	ASP	-1	-0.823	-0.894	20.439	-13.813	-13.813	0.000	0.000	0.000	0.000
12	B	79	ILE	0	-0.034	-0.014	15.328	-0.069	-0.069	0.000	0.000	0.000	0.000
13	B	80	PRO	0	-0.014	-0.013	17.084	-0.372	-0.372	0.000	0.000	0.000	0.000
14	B	81	ASP	-1	-0.744	-0.837	12.104	-20.570	-20.570	0.000	0.000	0.000	0.000
15	B	82	TYR	0	0.020	-0.011	11.110	0.564	0.564	0.000	0.000	0.000	0.000
16	B	83	TRP	0	0.042	0.015	7.089	-0.330	-0.330	0.000	0.000	0.000	0.000
17	B	84	LYS	1	0.807	0.894	10.559	21.306	21.306	0.000	0.000	0.000	0.000
18	B	85	LEU	0	-0.012	-0.009	13.269	0.813	0.813	0.000	0.000	0.000	0.000
19	B	86	SER	0	-0.050	-0.039	12.109	0.755	0.755	0.000	0.000	0.000	0.000
20	B	87	PHE	0	-0.029	0.019	9.967	0.404	0.404	0.000	0.000	0.000	0.000
21	B	88	PRO	0	0.021	0.002	15.574	0.210	0.210	0.000	0.000	0.000	0.000
22	B	89	GLU	-1	-0.809	-0.906	16.286	-11.886	-11.886	0.000	0.000	0.000	0.000
23	B	90	GLY	0	0.021	0.005	12.925	-0.170	-0.170	0.000	0.000	0.000	0.000
24	B	91	PHE	0	-0.033	-0.030	5.669	-0.013	-0.013	0.000	0.000	0.000	0.000
25	B	92	LYS	1	0.953	0.984	9.494	13.723	13.723	0.000	0.000	0.000	0.000
26	B	93	TRP	0	0.012	0.007	2.567	-4.807	-2.312	0.722	-0.494	-2.723	-0.022
27	B	94	GLU	-1	-0.926	-0.956	7.889	-16.291	-16.291	0.000	0.000	0.000	0.000
28	B	95	ARG	1	0.822	0.888	1.901	20.875	17.589	15.919	-5.186	-7.447	0.045
29	B	96	VAL	0	0.003	0.011	7.465	1.405	1.405	0.000	0.000	0.000	0.000
30	B	97	MET	0	-0.045	-0.029	2.740	-4.003	-2.955	0.589	-0.348	-1.290	0.004
31	B	98	ASN	0	0.031	0.021	7.035	2.145	2.145	0.000	0.000	0.000	0.000
32	B	99	PHE	0	0.016	-0.011	6.004	-3.061	-3.061	0.000	0.000	0.000	0.000
33	B	100	GLU	-1	-0.834	-0.910	9.878	-18.895	-18.895	0.000	0.000	0.000	0.000
34	B	101	ASP	-1	-0.824	-0.895	12.753	-18.464	-18.464	0.000	0.000	0.000	0.000
35	B	102	GLY	0	0.015	0.015	14.041	1.068	1.068	0.000	0.000	0.000	0.000
36	B	103	GLY	0	0.013	0.017	12.549	0.463	0.463	0.000	0.000	0.000	0.000
37	B	104	VAL	0	-0.007	-0.001	11.103	-1.225	-1.225	0.000	0.000	0.000	0.000
38	B	105	VAL	0	-0.010	-0.010	8.413	0.968	0.968	0.000	0.000	0.000	0.000
39	B	106	THR	0	-0.033	0.000	9.432	-0.359	-0.359	0.000	0.000	0.000	0.000
40	B	107	VAL	0	-0.019	-0.018	6.318	0.620	0.620	0.000	0.000	0.000	0.000
41	B	108	THR	0	0.003	0.004	9.445	0.740	0.740	0.000	0.000	0.000	0.000
42	B	109	GLN	0	0.016	0.014	5.293	0.064	0.064	0.000	0.000	0.000	0.000
43	B	110	ASP	-1	-0.835	-0.916	8.370	-13.451	-13.451	0.000	0.000	0.000	0.000
44	B	111	SER	0	0.036	0.011	7.506	-0.164	-0.164	0.000	0.000	0.000	0.000
45	B	112	SER	0	-0.023	-0.018	9.975	0.099	0.099	0.000	0.000	0.000	0.000
46	B	113	LEU	0	0.011	0.011	12.891	-0.503	-0.503	0.000	0.000	0.000	0.000
47	B	114	GLN	0	-0.047	-0.023	15.470	0.232	0.232	0.000	0.000	0.000	0.000
48	B	115	ASP	-1	-0.904	-0.955	18.089	-10.913	-10.913	0.000	0.000	0.000	0.000
49	B	116	GLY	0	0.009	0.024	19.429	0.052	0.052	0.000	0.000	0.000	0.000
50	B	117	GLU	-1	-0.925	-0.954	14.937	-14.606	-14.606	0.000	0.000	0.000	0.000
51	B	118	PHE	0	-0.046	-0.036	10.392	0.282	0.282	0.000	0.000	0.000	0.000
52	B	119	ILE	0	0.007	0.011	11.920	-0.432	-0.432	0.000	0.000	0.000	0.000
53	B	120	TYR	0	0.016	-0.004	6.473	1.153	1.153	0.000	0.000	0.000	0.000
54	B	121	LYS	1	0.879	0.935	9.480	14.629	14.629	0.000	0.000	0.000	0.000
55	B	122	VAL	0	0.029	0.010	6.411	-0.097	-0.097	0.000	0.000	0.000	0.000
56	B	123	LYS	1	0.947	0.981	9.037	15.579	15.579	0.000	0.000	0.000	0.000
57	B	124	LEU	0	0.012	0.008	8.299	-1.031	-1.031	0.000	0.000	0.000	0.000
58	B	125	ARG	1	0.948	0.968	11.241	17.809	17.809	0.000	0.000	0.000	0.000
59	B	126	GLY	0	0.016	0.015	12.829	-1.131	-1.131	0.000	0.000	0.000	0.000
60	B	127	THR	0	-0.058	-0.047	13.620	1.608	1.608	0.000	0.000	0.000	0.000
61	B	128	ASN	0	-0.019	-0.035	14.720	-0.250	-0.250	0.000	0.000	0.000	0.000
62	B	129	PHE	0	0.029	0.030	10.143	-0.118	-0.118	0.000	0.000	0.000	0.000
63	B	130	PRO	0	0.018	0.023	15.890	0.760	0.760	0.000	0.000	0.000	0.000
64	B	131	SER	0	-0.010	-0.024	18.422	-0.615	-0.615	0.000	0.000	0.000	0.000
65	B	132	ASP	-1	-0.872	-0.908	20.958	-12.796	-12.796	0.000	0.000	0.000	0.000
66	B	133	GLY	0	0.015	0.012	16.770	-0.082	-0.082	0.000	0.000	0.000	0.000
67	B	134	PRO	0	-0.026	-0.023	13.065	0.132	0.132	0.000	0.000	0.000	0.000
68	B	135	VAL	0	-0.017	-0.003	11.052	-0.403	-0.403	0.000	0.000	0.000	0.000
69	B	136	MET	0	-0.004	0.003	13.781	-0.198	-0.198	0.000	0.000	0.000	0.000
70	B	137	GLN	0	-0.037	-0.017	17.303	0.680	0.680	0.000	0.000	0.000	0.000
71	B	138	LYS	1	0.940	0.984	15.692	17.449	17.449	0.000	0.000	0.000	0.000
72	B	139	LYS	1	0.910	0.944	16.314	15.939	15.939	0.000	0.000	0.000	0.000
73	B	140	THR	0	-0.008	0.005	10.867	0.389	0.389	0.000	0.000	0.000	0.000
74	B	141	MET	0	-0.003	0.004	11.714	1.302	1.302	0.000	0.000	0.000	0.000
75	B	142	GLY	0	0.038	0.020	8.284	-0.360	-0.360	0.000	0.000	0.000	0.000
76	B	143	TRP	0	-0.008	-0.010	3.565	-6.821	-4.603	0.096	-0.842	-1.472	-0.008
77	B	144	GLU	-1	-0.846	-0.929	6.059	-23.147	-23.147	0.000	0.000	0.000	0.000
78	B	145	ALA	0	-0.029	-0.014	6.636	-4.441	-4.441	0.000	0.000	0.000	0.000
79	B	146	ILE	0	-0.038	-0.016	3.025	-3.196	-1.551	0.298	-0.397	-1.546	0.002
80	B	147	SER	0	0.008	-0.016	6.339	2.736	2.736	0.000	0.000	0.000	0.000
81	B	148	GLU	-1	-0.786	-0.854	4.247	-44.517	-44.146	0.000	-0.042	-0.329	0.000
82	B	149	ARG	1	0.936	0.959	7.324	27.999	27.999	0.000	0.000	0.000	0.000
83	B	150	MET	0	-0.041	0.000	8.335	-1.821	-1.821	0.000	0.000	0.000	0.000
84	B	151	TYR	0	-0.017	-0.023	11.134	1.618	1.618	0.000	0.000	0.000	0.000
85	B	152	PRO	0	0.001	0.020	13.830	-0.465	-0.465	0.000	0.000	0.000	0.000
86	B	153	GLU	-1	-0.823	-0.917	15.129	-16.369	-16.369	0.000	0.000	0.000	0.000
87	B	154	ASP	-1	-0.923	-0.963	16.888	-13.364	-13.364	0.000	0.000	0.000	0.000
88	B	155	GLY	0	0.015	0.017	18.541	-0.035	-0.035	0.000	0.000	0.000	0.000
89	B	156	ALA	0	-0.069	-0.040	13.757	0.075	0.075	0.000	0.000	0.000	0.000
90	B	157	LEU	0	0.013	0.008	10.849	0.239	0.239	0.000	0.000	0.000	0.000
91	B	158	LYS	1	0.811	0.900	10.442	16.070	16.070	0.000	0.000	0.000	0.000
92	B	159	GLY	0	0.059	0.017	7.360	0.078	0.078	0.000	0.000	0.000	0.000
93	B	160	GLU	-1	-0.840	-0.911	6.796	-23.054	-23.054	0.000	0.000	0.000	0.000
94	B	161	ILE	0	-0.056	-0.012	2.387	-2.480	-1.981	4.319	-1.014	-3.805	-0.001
95	B	162	LYS	1	0.853	0.922	5.814	26.851	26.851	0.000	0.000	0.000	0.000
96	B	163	GLN	0	-0.043	-0.025	3.286	-1.629	-1.182	0.020	-0.106	-0.361	0.000
97	B	164	ARG	1	0.857	0.920	5.730	24.965	24.965	0.000	0.000	0.000	0.000
98	B	165	LEU	0	-0.053	-0.015	6.685	-3.418	-3.418	0.000	0.000	0.000	0.000
99	B	166	LYS	1	0.888	0.938	8.168	32.490	32.490	0.000	0.000	0.000	0.000
100	B	167	LEU	0	-0.005	-0.005	11.463	-0.641	-0.641	0.000	0.000	0.000	0.000
101	B	168	LYS	1	0.891	0.915	14.610	19.252	19.252	0.000	0.000	0.000	0.000
102	B	169	ASP	-1	-0.877	-0.920	17.807	-15.935	-15.935	0.000	0.000	0.000	0.000
103	B	170	GLY	0	-0.019	0.005	18.386	0.644	0.644	0.000	0.000	0.000	0.000
104	B	171	GLY	0	0.019	0.012	16.641	0.464	0.464	0.000	0.000	0.000	0.000
105	B	172	HIS	0	-0.081	-0.047	11.724	-0.155	-0.155	0.000	0.000	0.000	0.000
106	B	173	TYR	0	-0.022	-0.041	9.451	0.493	0.493	0.000	0.000	0.000	0.000
107	B	174	ASP	-1	-0.796	-0.882	8.388	-28.392	-28.392	0.000	0.000	0.000	0.000
108	B	175	ALA	0	0.006	-0.009	4.737	0.864	0.947	-0.001	-0.002	-0.080	0.000
109	B	176	GLU	-1	-0.879	-0.920	6.121	-24.471	-24.471	0.000	0.000	0.000	0.000
110	B	177	VAL	0	-0.038	-0.036	2.622	-1.898	-0.704	1.120	-0.521	-1.793	0.002
111	B	178	LYS	1	0.899	0.960	5.648	20.276	20.280	-0.001	-0.001	-0.002	0.000
112	B	179	THR	0	-0.008	0.007	4.561	-1.436	-1.101	-0.001	-0.007	-0.327	0.000
113	B	180	THR	0	0.015	0.013	6.990	1.350	1.350	0.000	0.000	0.000	0.000
114	B	181	TYR	0	-0.012	-0.054	4.158	-0.136	0.448	0.000	-0.028	-0.557	0.000
115	B	182	LYS	1	0.882	0.936	9.318	14.109	14.109	0.000	0.000	0.000	0.000
116	B	183	ALA	0	0.055	0.028	12.203	0.143	0.143	0.000	0.000	0.000	0.000
117	B	184	LYS	1	0.726	0.846	12.941	13.945	13.945	0.000	0.000	0.000	0.000
118	B	185	LYS	1	0.840	0.937	16.083	12.658	12.658	0.000	0.000	0.000	0.000
119	B	186	PRO	0	-0.012	-0.022	17.907	-0.484	-0.484	0.000	0.000	0.000	0.000
120	B	187	VAL	0	-0.006	0.004	15.567	0.087	0.087	0.000	0.000	0.000	0.000
121	B	188	GLN	0	0.007	0.005	18.537	0.034	0.034	0.000	0.000	0.000	0.000
122	B	189	LEU	0	-0.005	0.001	15.315	-0.629	-0.629	0.000	0.000	0.000	0.000
123	B	190	PRO	0	0.004	0.015	14.285	0.686	0.686	0.000	0.000	0.000	0.000
124	B	191	GLY	0	0.055	0.018	17.544	0.240	0.240	0.000	0.000	0.000	0.000
125	B	192	ALA	0	-0.017	-0.023	15.852	-0.896	-0.896	0.000	0.000	0.000	0.000
126	B	193	TYR	0	-0.088	-0.057	11.926	0.392	0.392	0.000	0.000	0.000	0.000
127	B	194	ASN	0	0.027	0.012	11.497	-1.187	-1.187	0.000	0.000	0.000	0.000
128	B	195	VAL	0	0.025	0.007	7.095	1.069	1.069	0.000	0.000	0.000	0.000
129	B	196	ASN	0	0.010	0.028	8.148	-4.475	-4.475	0.000	0.000	0.000	0.000
130	B	197	ILE	0	-0.019	-0.023	2.609	-4.193	-1.974	0.536	-0.503	-2.253	-0.002
131	B	198	LYS	1	0.807	0.896	5.851	38.776	38.776	0.000	0.000	0.000	0.000
132	B	199	LEU	0	-0.016	-0.012	2.452	-9.766	-7.510	1.402	-0.810	-2.849	-0.005
133	B	200	ASP	-1	-0.847	-0.905	5.307	-30.864	-30.857	-0.001	-0.004	-0.002	0.000
134	B	201	ILE	0	0.024	0.008	8.099	-1.603	-1.603	0.000	0.000	0.000	0.000
135	B	202	THR	0	-0.035	-0.017	10.632	0.745	0.745	0.000	0.000	0.000	0.000
136	B	203	SER	0	-0.041	-0.043	13.160	1.731	1.731	0.000	0.000	0.000	0.000
137	B	204	HIS	0	0.003	-0.015	14.263	-1.949	-1.949	0.000	0.000	0.000	0.000
138	B	205	ASN	0	0.025	0.022	16.533	0.123	0.123	0.000	0.000	0.000	0.000
139	B	206	GLU	-1	-0.933	-0.961	19.168	-13.395	-13.395	0.000	0.000	0.000	0.000
140	B	207	ASP	-1	-0.809	-0.888	20.871	-15.261	-15.261	0.000	0.000	0.000	0.000
141	B	208	TYR	0	-0.119	-0.066	14.297	-0.837	-0.837	0.000	0.000	0.000	0.000
142	B	209	THR	0	-0.042	-0.035	16.216	-0.839	-0.839	0.000	0.000	0.000	0.000
143	B	210	ILE	0	-0.053	-0.025	16.489	-0.019	-0.019	0.000	0.000	0.000	0.000
144	B	211	VAL	0	-0.024	-0.015	11.221	-0.136	-0.136	0.000	0.000	0.000	0.000
145	B	212	GLU	-1	-0.847	-0.873	11.970	-19.482	-19.482	0.000	0.000	0.000	0.000
146	B	213	GLN	0	-0.034	-0.044	6.117	-6.800	-6.800	0.000	0.000	0.000	0.000
147	B	214	TYR	0	0.018	0.017	7.775	1.977	1.977	0.000	0.000	0.000	0.000
148	B	215	GLU	-1	-0.727	-0.825	1.742	-118.001	-111.136	17.171	-12.824	-11.212	-0.201
149	B	216	ARG	1	0.935	0.977	5.535	31.271	31.271	0.000	0.000	0.000	0.000
150	B	217	ALA	0	0.041	0.015	4.398	-3.449	-3.585	-0.001	-0.008	0.146	0.000
151	B	218	GLU	-1	-0.810	-0.878	6.532	-17.281	-17.281	0.000	0.000	0.000	0.000
152	B	219	GLY	0	0.003	0.009	10.036	-1.067	-1.067	0.000	0.000	0.000	0.000
153	B	220	ARG	1	0.789	0.862	12.045	21.359	21.359	0.000	0.000	0.000	0.000
154	B	221	HIS	0	0.059	0.014	15.189	-1.371	-1.371	0.000	0.000	0.000	0.000
155	B	222	SER	0	-0.037	-0.016	16.064	-0.180	-0.180	0.000	0.000	0.000	0.000
156	B	223	THR	0	-0.025	-0.016	17.992	0.690	0.690	0.000	0.000	0.000	0.000
157	B	224	GLY	0	0.033	0.012	21.731	-0.278	-0.278	0.000	0.000	0.000	0.000
158	B	225	GLY	0	0.022	0.021	24.304	0.469	0.469	0.000	0.000	0.000	0.000
159	B	226	MET	0	-0.033	-0.029	25.031	-0.540	-0.540	0.000	0.000	0.000	0.000
160	B	227	ASP	-1	-0.981	-0.969	24.897	-11.289	-11.289	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:67:0YG)