FMO DATABASE

FMODB ID: N9GYQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1577723.406788
FMO2-HF: Nuclear repulsion	1513296.754366
FMO2-HF: Total energy	-64426.652422
FMO2-MP2: Total energy	-64614.691121

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.
-711.209	-1016.878	1472.52	-1115.277	-51.576	-1.082

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 : -0.082 / q_NPA : -0.085

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	0.101	0.082	1.520	-533.834	-843.649	1404.458	-1084.358	-10.285	-0.949
3	B	70	ARG	1	0.791	0.870	2.052	15.448	18.561	6.842	-5.143	-4.812	0.063
4	B	71	ALA	0	0.030	0.024	5.652	-1.508	-1.508	0.000	0.000	0.000	0.000
5	B	72	TYR	0	-0.056	-0.026	7.242	1.011	1.011	0.000	0.000	0.000	0.000
6	B	73	VAL	0	0.002	0.011	6.541	-3.592	-3.592	0.000	0.000	0.000	0.000
7	B	74	LYS	1	0.910	0.962	9.234	22.424	22.424	0.000	0.000	0.000	0.000
8	B	75	HIS	0	0.053	0.022	10.437	-1.892	-1.892	0.000	0.000	0.000	0.000
9	B	76	PRO	0	-0.008	0.005	14.305	0.792	0.792	0.000	0.000	0.000	0.000
10	B	77	ALA	0	0.016	-0.002	17.586	-0.035	-0.035	0.000	0.000	0.000	0.000
11	B	78	ASP	-1	-0.852	-0.902	20.494	-14.100	-14.100	0.000	0.000	0.000	0.000
12	B	79	ILE	0	-0.048	-0.022	15.138	-0.079	-0.079	0.000	0.000	0.000	0.000
13	B	80	PRO	0	-0.009	0.002	16.988	-0.377	-0.377	0.000	0.000	0.000	0.000
14	B	81	ASP	-1	-0.770	-0.895	12.113	-20.708	-20.708	0.000	0.000	0.000	0.000
15	B	82	TYR	0	0.040	0.005	11.002	0.674	0.674	0.000	0.000	0.000	0.000
16	B	83	TRP	0	0.053	0.011	7.359	-0.006	-0.006	0.000	0.000	0.000	0.000
17	B	84	LYS	1	0.850	0.957	10.939	21.273	21.273	0.000	0.000	0.000	0.000
18	B	85	LEU	0	-0.007	0.000	13.553	0.868	0.868	0.000	0.000	0.000	0.000
19	B	86	SER	0	-0.073	-0.056	12.528	0.738	0.738	0.000	0.000	0.000	0.000
20	B	87	PHE	0	-0.019	0.031	10.091	0.405	0.405	0.000	0.000	0.000	0.000
21	B	88	PRO	0	0.022	-0.002	15.690	0.174	0.174	0.000	0.000	0.000	0.000
22	B	89	GLU	-1	-0.823	-0.915	16.344	-11.462	-11.462	0.000	0.000	0.000	0.000
23	B	90	GLY	0	0.020	-0.001	12.815	-0.119	-0.119	0.000	0.000	0.000	0.000
24	B	91	PHE	0	-0.050	-0.044	5.892	-0.191	-0.191	0.000	0.000	0.000	0.000
25	B	92	LYS	1	0.963	0.986	9.421	13.138	13.138	0.000	0.000	0.000	0.000
26	B	93	TRP	0	-0.003	-0.009	2.497	-5.341	-3.539	0.691	-0.514	-1.978	-0.004
27	B	94	GLU	-1	-0.925	-0.953	8.197	-15.796	-15.796	0.000	0.000	0.000	0.000
28	B	95	ARG	1	0.863	0.907	1.818	28.019	26.673	12.247	-4.406	-6.494	0.024
29	B	96	VAL	0	0.001	0.003	7.283	1.262	1.262	0.000	0.000	0.000	0.000
30	B	97	MET	0	-0.065	-0.038	3.015	-3.208	-2.367	0.191	-0.268	-0.765	0.003
31	B	98	ASN	0	0.048	0.025	7.457	2.195	2.195	0.000	0.000	0.000	0.000
32	B	99	PHE	0	0.002	-0.013	6.476	-2.432	-2.432	0.000	0.000	0.000	0.000
33	B	100	GLU	-1	-0.856	-0.937	10.322	-18.053	-18.053	0.000	0.000	0.000	0.000
34	B	101	ASP	-1	-0.831	-0.908	13.110	-17.994	-17.994	0.000	0.000	0.000	0.000
35	B	102	GLY	0	0.011	0.015	14.518	0.962	0.962	0.000	0.000	0.000	0.000
36	B	103	GLY	0	-0.004	0.013	13.046	0.430	0.430	0.000	0.000	0.000	0.000
37	B	104	VAL	0	0.013	0.004	11.387	-1.123	-1.123	0.000	0.000	0.000	0.000
38	B	105	VAL	0	0.006	-0.004	8.324	0.586	0.586	0.000	0.000	0.000	0.000
39	B	106	THR	0	-0.033	-0.007	9.164	-0.488	-0.488	0.000	0.000	0.000	0.000
40	B	107	VAL	0	-0.010	-0.011	6.332	0.386	0.386	0.000	0.000	0.000	0.000
41	B	108	THR	0	-0.013	0.001	8.980	0.584	0.584	0.000	0.000	0.000	0.000
42	B	109	GLN	0	0.030	0.028	5.143	-0.222	-0.222	0.000	0.000	0.000	0.000
43	B	110	ASP	-1	-0.877	-0.930	7.886	-13.042	-13.042	0.000	0.000	0.000	0.000
44	B	111	SER	0	0.019	-0.026	7.118	0.244	0.244	0.000	0.000	0.000	0.000
45	B	112	SER	0	-0.018	-0.024	9.490	-0.001	-0.001	0.000	0.000	0.000	0.000
46	B	113	LEU	0	0.019	0.014	12.556	-0.443	-0.443	0.000	0.000	0.000	0.000
47	B	114	GLN	0	-0.041	-0.032	15.095	0.314	0.314	0.000	0.000	0.000	0.000
48	B	115	ASP	-1	-0.885	-0.932	17.710	-11.002	-11.002	0.000	0.000	0.000	0.000
49	B	116	GLY	0	-0.048	-0.019	18.979	-0.090	-0.090	0.000	0.000	0.000	0.000
50	B	117	GLU	-1	-0.908	-0.936	14.624	-14.346	-14.346	0.000	0.000	0.000	0.000
51	B	118	PHE	0	-0.042	-0.034	10.223	0.371	0.371	0.000	0.000	0.000	0.000
52	B	119	ILE	0	-0.003	0.004	11.711	-0.235	-0.235	0.000	0.000	0.000	0.000
53	B	120	TYR	0	-0.013	-0.029	6.463	1.415	1.415	0.000	0.000	0.000	0.000
54	B	121	LYS	1	0.921	0.963	8.818	13.217	13.217	0.000	0.000	0.000	0.000
55	B	122	VAL	0	0.035	0.012	5.694	0.178	0.178	0.000	0.000	0.000	0.000
56	B	123	LYS	1	0.917	0.965	8.658	14.688	14.688	0.000	0.000	0.000	0.000
57	B	124	LEU	0	0.042	0.021	8.497	-0.925	-0.925	0.000	0.000	0.000	0.000
58	B	125	ARG	1	0.942	0.976	11.308	17.301	17.301	0.000	0.000	0.000	0.000
59	B	126	GLY	0	0.013	0.011	13.148	-1.028	-1.028	0.000	0.000	0.000	0.000
60	B	127	THR	0	-0.048	-0.034	13.878	1.318	1.318	0.000	0.000	0.000	0.000
61	B	128	ASN	0	-0.023	-0.034	15.321	-0.173	-0.173	0.000	0.000	0.000	0.000
62	B	129	PHE	0	0.019	0.024	10.585	-0.228	-0.228	0.000	0.000	0.000	0.000
63	B	130	PRO	0	0.038	0.038	16.163	0.781	0.781	0.000	0.000	0.000	0.000
64	B	131	SER	0	-0.018	-0.022	18.578	-0.459	-0.459	0.000	0.000	0.000	0.000
65	B	132	ASP	-1	-0.873	-0.923	21.045	-12.377	-12.377	0.000	0.000	0.000	0.000
66	B	133	GLY	0	-0.006	-0.003	17.116	0.038	0.038	0.000	0.000	0.000	0.000
67	B	134	PRO	0	-0.003	-0.026	13.551	0.163	0.163	0.000	0.000	0.000	0.000
68	B	135	VAL	0	0.012	0.023	11.073	-0.616	-0.616	0.000	0.000	0.000	0.000
69	B	136	MET	0	0.008	0.005	13.838	-0.359	-0.359	0.000	0.000	0.000	0.000
70	B	137	GLN	0	-0.053	-0.015	17.237	0.638	0.638	0.000	0.000	0.000	0.000
71	B	138	LYS	1	0.939	0.977	15.735	16.393	16.393	0.000	0.000	0.000	0.000
72	B	139	LYS	1	0.941	0.956	15.785	15.684	15.684	0.000	0.000	0.000	0.000
73	B	140	THR	0	0.011	0.015	10.653	0.491	0.491	0.000	0.000	0.000	0.000
74	B	141	MET	0	-0.022	0.000	11.795	1.241	1.241	0.000	0.000	0.000	0.000
75	B	142	GLY	0	0.019	0.015	8.683	0.025	0.025	0.000	0.000	0.000	0.000
76	B	143	TRP	0	0.006	-0.002	3.743	-5.831	-4.333	0.022	-0.655	-0.866	-0.006
77	B	144	GLU	-1	-0.923	-0.962	6.205	-25.752	-25.752	0.000	0.000	0.000	0.000
78	B	145	ALA	0	-0.032	-0.022	6.102	-5.758	-5.758	0.000	0.000	0.000	0.000
79	B	146	ILE	0	-0.009	-0.002	2.159	-1.161	-5.079	10.118	-1.430	-4.771	-0.010
80	B	147	SER	0	-0.004	0.006	6.094	1.905	1.905	0.000	0.000	0.000	0.000
81	B	148	GLU	-1	-0.830	-0.903	4.630	-44.895	-44.602	-0.001	-0.014	-0.279	0.000
82	B	149	ARG	1	0.919	0.954	7.492	28.788	28.788	0.000	0.000	0.000	0.000
83	B	150	MET	0	-0.030	-0.004	7.842	-1.835	-1.835	0.000	0.000	0.000	0.000
84	B	151	TYR	0	-0.012	-0.016	11.077	1.492	1.492	0.000	0.000	0.000	0.000
85	B	152	PRO	0	-0.021	0.008	13.661	-0.478	-0.478	0.000	0.000	0.000	0.000
86	B	153	GLU	-1	-0.855	-0.953	15.841	-15.378	-15.378	0.000	0.000	0.000	0.000
87	B	154	ASP	-1	-0.910	-0.948	17.064	-12.869	-12.869	0.000	0.000	0.000	0.000
88	B	155	GLY	0	-0.001	0.016	19.056	0.138	0.138	0.000	0.000	0.000	0.000
89	B	156	ALA	0	-0.061	-0.038	13.825	0.049	0.049	0.000	0.000	0.000	0.000
90	B	157	LEU	0	0.004	0.007	10.108	0.195	0.195	0.000	0.000	0.000	0.000
91	B	158	LYS	1	0.874	0.929	10.282	16.100	16.100	0.000	0.000	0.000	0.000
92	B	159	GLY	0	0.043	0.023	7.065	0.022	0.022	0.000	0.000	0.000	0.000
93	B	160	GLU	-1	-0.880	-0.945	7.111	-22.172	-22.172	0.000	0.000	0.000	0.000
94	B	161	ILE	0	-0.023	-0.018	2.445	-1.756	-1.385	3.154	-0.664	-2.860	-0.001
95	B	162	LYS	1	0.879	0.955	6.388	28.320	28.320	0.000	0.000	0.000	0.000
96	B	163	GLN	0	-0.015	-0.017	3.688	-0.489	-0.196	0.002	-0.047	-0.248	0.000
97	B	164	ARG	1	0.890	0.951	5.839	23.936	23.936	0.000	0.000	0.000	0.000
98	B	165	LEU	0	-0.048	-0.024	6.849	-3.604	-3.604	0.000	0.000	0.000	0.000
99	B	166	LYS	1	0.918	0.950	8.249	31.521	31.521	0.000	0.000	0.000	0.000
100	B	167	LEU	0	0.044	0.016	11.702	-0.652	-0.652	0.000	0.000	0.000	0.000
101	B	168	LYS	1	0.920	0.925	14.560	18.108	18.108	0.000	0.000	0.000	0.000
102	B	169	ASP	-1	-0.986	-0.979	17.863	-15.418	-15.418	0.000	0.000	0.000	0.000
103	B	170	GLY	0	-0.014	0.020	18.457	0.558	0.558	0.000	0.000	0.000	0.000
104	B	171	GLY	0	0.088	0.033	16.481	0.671	0.671	0.000	0.000	0.000	0.000
105	B	172	HIS	0	-0.085	-0.045	11.959	-0.599	-0.599	0.000	0.000	0.000	0.000
106	B	173	TYR	0	-0.028	-0.029	9.784	0.392	0.392	0.000	0.000	0.000	0.000
107	B	174	ASP	-1	-0.785	-0.868	8.615	-27.729	-27.729	0.000	0.000	0.000	0.000
108	B	175	ALA	0	0.006	-0.003	5.119	0.939	0.939	0.000	0.000	0.000	0.000
109	B	176	GLU	-1	-0.966	-0.983	7.022	-22.400	-22.400	0.000	0.000	0.000	0.000
110	B	177	VAL	0	-0.045	-0.034	2.538	-1.662	-0.269	0.613	-0.411	-1.594	0.002
111	B	178	LYS	1	0.965	0.993	5.769	19.350	19.350	0.000	0.000	0.000	0.000
112	B	179	THR	0	-0.029	-0.003	4.439	-1.358	-1.090	-0.001	-0.006	-0.261	0.000
113	B	180	THR	0	0.015	0.012	7.011	0.768	0.768	0.000	0.000	0.000	0.000
114	B	181	TYR	0	-0.017	-0.029	4.259	0.207	1.040	0.000	-0.053	-0.781	0.000
115	B	182	LYS	1	0.890	0.934	9.723	13.567	13.567	0.000	0.000	0.000	0.000
116	B	183	ALA	0	0.025	0.013	12.244	0.152	0.152	0.000	0.000	0.000	0.000
117	B	184	LYS	1	0.813	0.913	13.001	13.407	13.407	0.000	0.000	0.000	0.000
118	B	185	LYS	1	0.857	0.952	16.336	12.327	12.327	0.000	0.000	0.000	0.000
119	B	186	PRO	0	-0.027	-0.030	17.947	-0.531	-0.531	0.000	0.000	0.000	0.000
120	B	187	VAL	0	-0.009	0.007	15.836	0.135	0.135	0.000	0.000	0.000	0.000
121	B	188	GLN	0	0.018	0.013	18.770	-0.078	-0.078	0.000	0.000	0.000	0.000
122	B	189	LEU	0	-0.022	-0.013	15.228	-0.621	-0.621	0.000	0.000	0.000	0.000
123	B	190	PRO	0	0.007	0.020	13.721	0.644	0.644	0.000	0.000	0.000	0.000
124	B	191	GLY	0	0.063	0.022	17.064	0.286	0.286	0.000	0.000	0.000	0.000
125	B	192	ALA	0	-0.009	-0.023	15.368	-0.842	-0.842	0.000	0.000	0.000	0.000
126	B	193	TYR	0	-0.090	-0.043	11.276	0.431	0.431	0.000	0.000	0.000	0.000
127	B	194	ASN	0	0.032	0.014	11.167	-1.075	-1.075	0.000	0.000	0.000	0.000
128	B	195	VAL	0	0.013	0.005	5.784	0.969	0.969	0.000	0.000	0.000	0.000
129	B	196	ASN	0	-0.039	-0.015	7.211	-4.026	-4.026	0.000	0.000	0.000	0.000
130	B	197	ILE	0	0.018	-0.011	2.085	-7.980	-7.168	4.703	-1.642	-3.874	-0.022
131	B	198	LYS	1	0.910	0.965	5.305	36.469	36.877	-0.001	-0.006	-0.401	0.000
132	B	199	LEU	0	-0.011	-0.009	2.566	-6.357	-4.773	0.590	-0.509	-1.665	-0.004
133	B	200	ASP	-1	-0.887	-0.936	5.519	-30.884	-30.884	0.000	0.000	0.000	0.000
134	B	201	ILE	0	-0.017	-0.020	8.689	-1.005	-1.005	0.000	0.000	0.000	0.000
135	B	202	THR	0	-0.031	-0.032	10.534	1.325	1.325	0.000	0.000	0.000	0.000
136	B	203	SER	0	0.002	0.006	13.192	2.074	2.074	0.000	0.000	0.000	0.000
137	B	204	HIS	0	-0.002	-0.010	14.603	-1.814	-1.814	0.000	0.000	0.000	0.000
138	B	205	ASN	0	0.031	0.026	16.749	0.199	0.199	0.000	0.000	0.000	0.000
139	B	206	GLU	-1	-0.929	-0.973	19.252	-13.561	-13.561	0.000	0.000	0.000	0.000
140	B	207	ASP	-1	-0.880	-0.937	20.816	-15.101	-15.101	0.000	0.000	0.000	0.000
141	B	208	TYR	0	-0.096	-0.045	13.849	-0.438	-0.438	0.000	0.000	0.000	0.000
142	B	209	THR	0	-0.032	-0.013	16.428	-0.663	-0.663	0.000	0.000	0.000	0.000
143	B	210	ILE	0	-0.033	-0.017	16.350	0.088	0.088	0.000	0.000	0.000	0.000
144	B	211	VAL	0	-0.038	-0.020	11.348	-0.237	-0.237	0.000	0.000	0.000	0.000
145	B	212	GLU	-1	-0.941	-0.951	12.020	-19.747	-19.747	0.000	0.000	0.000	0.000
146	B	213	GLN	0	0.000	-0.012	5.937	-7.648	-7.648	0.000	0.000	0.000	0.000
147	B	214	TYR	0	0.001	0.013	8.299	2.141	2.141	0.000	0.000	0.000	0.000
148	B	215	GLU	-1	-0.771	-0.843	1.692	-151.327	-155.426	28.892	-15.151	-9.642	-0.178
149	B	216	ARG	1	0.923	0.980	6.038	31.794	31.794	0.000	0.000	0.000	0.000
150	B	217	ALA	0	0.031	0.003	5.016	-4.451	-4.451	0.000	0.000	0.000	0.000
151	B	218	GLU	-1	-0.928	-0.978	6.959	-17.521	-17.521	0.000	0.000	0.000	0.000
152	B	219	GLY	0	0.010	0.017	9.893	-1.441	-1.441	0.000	0.000	0.000	0.000
153	B	220	ARG	1	0.845	0.911	11.363	22.382	22.382	0.000	0.000	0.000	0.000
154	B	221	HIS	0	0.051	0.013	14.224	-0.981	-0.981	0.000	0.000	0.000	0.000
155	B	222	SER	0	-0.026	-0.017	15.744	-0.162	-0.162	0.000	0.000	0.000	0.000
156	B	223	THR	0	-0.036	-0.017	17.611	0.717	0.717	0.000	0.000	0.000	0.000
157	B	224	GLY	0	0.070	0.022	21.235	-0.268	-0.268	0.000	0.000	0.000	0.000
158	B	225	GLY	0	-0.026	-0.007	23.731	0.425	0.425	0.000	0.000	0.000	0.000
159	B	226	MET	0	-0.028	-0.024	23.652	-0.573	-0.573	0.000	0.000	0.000	0.000
160	B	227	ASP	-1	-0.964	-0.954	23.424	-11.057	-11.057	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

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