FMO DATABASE

FMODB ID: N3RLQ

Calculation Name: 4S03-A-Xray313

Preferred Name:

Target Type:

Ligand Name: (r)-2-amino-3-(4-phenylcyclohexyl)propanoic acid

ligand 3-letter code: BIF

PDB ID: 4S03

Chain ID: A

ChEMBL ID:

UniProt ID: Q9UZ14

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	142
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1341750.925225
FMO2-HF: Nuclear repulsion	1285824.744904
FMO2-HF: Total energy	-55926.180321
FMO2-MP2: Total energy	-56089.675164

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:MET )

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

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.
-255.356	-257.356	66.939	-29.46	-35.477	-0.287

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.684 / q_NPA : 0.823

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	3	VAL	0	0.033	0.012	2.401	1.675	4.015	1.783	-1.036	-3.086	-0.005
4	A	4	LEU	0	0.002	0.014	4.462	1.189	1.240	0.000	-0.025	-0.027	0.000
5	A	5	LEU	0	-0.036	-0.029	7.899	0.570	0.570	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.055	0.020	10.505	0.724	0.724	0.000	0.000	0.000	0.000
7	A	7	HIS	0	0.032	0.036	14.031	0.105	0.105	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.021	-0.002	16.914	0.478	0.478	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.823	-0.885	19.188	-11.502	-11.502	0.000	0.000	0.000	0.000
10	A	10	TYR	0	-0.001	-0.008	21.485	0.223	0.223	0.000	0.000	0.000	0.000
11	A	11	BIF	0	0.046	0.008	14.670	-0.568	-0.568	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.865	-0.941	19.550	-10.845	-10.845	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.081	-0.032	16.887	-0.428	-0.428	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.866	-0.952	19.876	-10.408	-10.408	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.034	-0.020	18.445	-0.343	-0.343	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.846	0.929	20.861	11.927	11.927	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.871	-0.918	22.690	-11.569	-11.569	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.825	0.902	20.166	11.701	11.701	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.021	0.016	16.894	0.262	0.262	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.012	-0.004	14.567	-0.077	-0.077	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.965	0.977	18.757	12.497	12.497	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.035	-0.045	19.968	0.602	0.602	0.000	0.000	0.000	0.000
23	A	23	PRO	0	0.006	0.033	17.000	-0.637	-0.637	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.800	-0.900	13.444	-17.308	-17.308	0.000	0.000	0.000	0.000
25	A	25	PRO	0	-0.032	0.015	16.605	0.483	0.483	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.007	-0.015	18.204	-0.358	-0.358	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.040	-0.076	20.700	0.335	0.335	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.876	-0.976	23.101	-10.445	-10.445	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.837	-0.868	23.236	-11.511	-11.511	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.001	0.031	17.066	-0.281	-0.281	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.910	0.966	19.593	10.512	10.512	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.938	0.971	21.568	10.402	10.402	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.038	0.037	19.464	0.030	0.030	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.813	0.878	20.485	10.879	10.879	0.000	0.000	0.000	0.000
35	A	35	MET	0	-0.061	-0.006	17.046	-0.132	-0.132	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.822	-0.908	20.504	-10.619	-10.619	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.867	-0.921	21.189	-11.883	-11.883	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.030	-0.005	15.702	-0.262	-0.262	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.008	0.003	11.781	-0.132	-0.132	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.025	-0.022	12.229	-0.427	-0.427	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.042	0.003	7.298	-0.822	-0.822	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.022	0.003	8.259	-0.241	-0.241	0.000	0.000	0.000	0.000
43	A	43	ILE	0	0.000	-0.013	2.555	-4.682	-4.175	2.131	-0.418	-2.220	-0.002
44	A	44	SER	0	-0.039	-0.046	3.730	3.579	3.982	0.004	-0.096	-0.312	0.000
45	A	45	VAL	0	-0.017	-0.005	2.409	-20.491	-17.282	3.077	-2.631	-3.654	-0.027
46	A	46	GLU	-1	-0.819	-0.918	1.658	-103.198	-110.843	21.794	-8.596	-5.553	-0.089
47	A	47	LYS	1	0.963	0.980	4.171	27.986	28.094	0.001	-0.012	-0.097	0.000
48	A	48	VAL	0	-0.047	-0.036	3.451	4.114	4.307	0.006	-0.036	-0.164	0.000
49	A	49	ASP	-1	-0.704	-0.844	1.733	-129.939	-134.686	21.311	-9.391	-7.173	-0.103
50	A	50	GLU	-1	-0.889	-0.961	4.468	-22.341	-22.219	0.000	-0.067	-0.055	0.000
51	A	51	LYS	1	0.879	0.956	7.786	39.072	39.072	0.000	0.000	0.000	0.000
52	A	52	ASN	0	0.002	0.001	7.850	3.366	3.366	0.000	0.000	0.000	0.000
53	A	53	PRO	0	0.086	0.039	6.066	-3.060	-3.060	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.943	-0.954	6.100	-22.098	-22.098	0.000	0.000	0.000	0.000
55	A	55	GLU	-1	-0.797	-0.888	7.570	-32.545	-32.545	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.009	-0.017	2.196	-2.123	-2.236	2.825	-0.582	-2.130	-0.003
57	A	57	SER	0	-0.009	-0.027	3.154	-0.596	0.019	0.033	-0.158	-0.490	-0.001
58	A	58	LEU	0	0.025	0.011	4.157	1.597	1.680	0.000	0.001	-0.084	0.000
59	A	59	LYS	1	0.913	0.972	6.184	29.642	29.642	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.015	-0.003	2.700	0.567	0.150	3.194	-0.918	-1.859	-0.002
61	A	61	ILE	0	-0.012	0.010	4.671	1.978	2.134	0.004	-0.056	-0.104	0.000
62	A	62	GLU	-1	-0.832	-0.897	7.177	-17.331	-17.331	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.931	-0.974	6.814	-24.166	-24.166	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.023	-0.019	5.342	0.936	1.013	0.000	-0.008	-0.069	0.000
65	A	65	SER	0	0.004	-0.011	9.002	1.648	1.648	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.913	0.971	11.937	21.820	21.820	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.023	-0.009	11.876	0.940	0.940	0.000	0.000	0.000	0.000
68	A	68	ALA	0	-0.001	0.011	13.224	1.011	1.011	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.891	-0.953	15.028	-14.906	-14.906	0.000	0.000	0.000	0.000
70	A	70	GLN	0	-0.073	-0.032	16.908	0.163	0.163	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.084	-0.058	16.894	0.694	0.694	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.894	0.949	19.287	12.200	12.200	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.020	0.008	16.557	0.352	0.352	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.888	-0.954	17.804	-11.836	-11.836	0.000	0.000	0.000	0.000
75	A	75	ASN	0	-0.038	-0.013	17.547	-0.157	-0.157	0.000	0.000	0.000	0.000
76	A	76	VAL	0	0.024	0.008	11.035	-0.437	-0.437	0.000	0.000	0.000	0.000
77	A	77	PHE	0	0.027	0.011	12.991	0.402	0.402	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.021	-0.003	6.802	-1.145	-1.145	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.001	-0.011	9.012	1.004	1.004	0.000	0.000	0.000	0.000
80	A	80	PRO	0	-0.006	0.005	7.426	-2.720	-2.720	0.000	0.000	0.000	0.000
81	A	81	TRP	0	0.024	-0.006	7.314	1.966	1.966	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.010	0.028	7.522	-3.591	-3.591	0.000	0.000	0.000	0.000
83	A	83	HIS	0	-0.002	0.002	9.485	-0.066	-0.066	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.010	0.013	5.923	1.587	1.587	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.031	-0.032	5.254	-1.533	-1.533	0.000	0.000	0.000	0.000
86	A	86	SER	0	0.014	0.015	7.365	2.275	2.275	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.949	-0.972	7.588	-26.607	-26.607	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.001	0.016	6.297	-6.262	-6.262	0.000	0.000	0.000	0.000
89	A	89	ALA	0	-0.034	-0.012	6.631	3.052	3.052	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.946	0.980	8.249	24.677	24.677	0.000	0.000	0.000	0.000
91	A	91	PRO	0	0.066	0.011	10.669	-1.223	-1.223	0.000	0.000	0.000	0.000
92	A	92	SER	0	0.024	0.012	10.846	-0.387	-0.387	0.000	0.000	0.000	0.000
93	A	93	VAL	0	0.017	0.010	7.071	0.466	0.466	0.000	0.000	0.000	0.000
94	A	94	ALA	0	0.017	0.011	6.150	-1.855	-1.855	0.000	0.000	0.000	0.000
95	A	95	MET	0	-0.006	-0.013	6.299	-0.193	-0.193	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.883	-0.911	8.694	-23.601	-23.601	0.000	0.000	0.000	0.000
97	A	97	ILE	0	0.015	-0.006	2.417	-0.080	-0.386	2.063	-0.313	-1.444	-0.002
98	A	98	LEU	0	0.002	0.006	4.640	0.407	0.584	0.000	-0.008	-0.168	0.000
99	A	99	ASN	0	0.018	0.010	5.617	2.651	2.651	0.000	0.000	0.000	0.000
100	A	100	ARG	1	0.887	0.935	6.248	24.781	24.781	0.000	0.000	0.000	0.000
101	A	101	VAL	0	0.005	-0.008	2.797	0.307	0.758	0.157	-0.111	-0.497	-0.001
102	A	102	TYR	0	-0.014	-0.005	5.954	1.925	1.925	0.000	0.000	0.000	0.000
103	A	103	GLN	0	-0.036	-0.037	9.325	1.770	1.770	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.043	0.022	9.471	0.958	0.958	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.004	-0.007	8.219	0.755	0.755	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.915	0.961	11.256	15.841	15.841	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-1.001	-0.992	13.683	-14.796	-14.796	0.000	0.000	0.000	0.000
108	A	108	ARG	1	0.847	0.910	11.479	18.810	18.810	0.000	0.000	0.000	0.000
109	A	109	GLY	0	0.001	0.020	15.136	0.480	0.480	0.000	0.000	0.000	0.000
110	A	110	PHE	0	-0.066	-0.011	13.247	0.314	0.314	0.000	0.000	0.000	0.000
111	A	111	ASN	0	0.001	0.009	16.570	0.068	0.068	0.000	0.000	0.000	0.000
112	A	112	VAL	0	0.003	-0.008	11.526	-0.466	-0.466	0.000	0.000	0.000	0.000
113	A	113	GLY	0	0.001	0.002	14.496	0.633	0.633	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.911	0.940	11.478	16.137	16.137	0.000	0.000	0.000	0.000
115	A	115	ALA	0	-0.021	0.010	12.031	1.037	1.037	0.000	0.000	0.000	0.000
116	A	116	PRO	0	-0.013	0.008	12.160	-1.009	-1.009	0.000	0.000	0.000	0.000
117	A	117	PHE	0	0.035	-0.012	8.898	-0.470	-0.470	0.000	0.000	0.000	0.000
118	A	118	GLY	0	0.005	-0.003	12.660	1.074	1.074	0.000	0.000	0.000	0.000
119	A	119	TYR	0	-0.030	-0.053	14.999	1.322	1.322	0.000	0.000	0.000	0.000
120	A	120	TYR	0	0.020	0.019	16.177	-0.887	-0.887	0.000	0.000	0.000	0.000
121	A	121	ILE	0	-0.010	-0.009	15.035	0.647	0.647	0.000	0.000	0.000	0.000
122	A	122	ALA	0	-0.017	0.007	18.681	-0.272	-0.272	0.000	0.000	0.000	0.000
123	A	123	ALA	0	0.028	-0.003	18.275	-0.025	-0.025	0.000	0.000	0.000	0.000
124	A	124	LYS	1	0.841	0.929	20.245	11.730	11.730	0.000	0.000	0.000	0.000
125	A	125	ILE	0	-0.001	-0.011	16.282	-0.289	-0.289	0.000	0.000	0.000	0.000
126	A	126	SER	0	-0.063	-0.024	20.426	0.459	0.459	0.000	0.000	0.000	0.000
127	A	127	CYS	0	-0.002	0.005	18.270	-0.325	-0.325	0.000	0.000	0.000	0.000
128	A	128	LYS	1	0.853	0.921	20.089	12.672	12.672	0.000	0.000	0.000	0.000
129	A	129	GLY	0	0.031	0.006	20.814	-0.421	-0.421	0.000	0.000	0.000	0.000
130	A	130	HIS	0	-0.074	-0.032	19.040	0.397	0.397	0.000	0.000	0.000	0.000
131	A	131	PRO	0	0.029	-0.019	20.829	-0.503	-0.503	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.014	0.005	17.444	-0.528	-0.528	0.000	0.000	0.000	0.000
133	A	133	ALA	0	-0.029	0.000	16.536	-0.733	-0.733	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.884	-0.937	14.389	-16.624	-16.624	0.000	0.000	0.000	0.000
135	A	135	LEU	0	-0.042	-0.013	11.997	-0.091	-0.091	0.000	0.000	0.000	0.000
136	A	136	SER	0	0.017	0.016	8.858	-1.430	-1.430	0.000	0.000	0.000	0.000
137	A	137	ARG	1	0.905	0.948	6.123	25.793	25.793	0.000	0.000	0.000	0.000
138	A	138	THR	0	0.006	0.000	4.358	-5.113	-4.945	0.000	-0.039	-0.128	0.000
139	A	139	ILE	0	-0.023	-0.005	2.180	6.282	8.514	1.794	-1.152	-2.874	0.000
140	A	140	VAL	0	-0.007	-0.017	1.879	-38.355	-38.250	6.761	-3.765	-3.101	-0.052
141	A	141	PRO	0	-0.037	-0.017	3.887	6.321	6.552	0.001	-0.043	-0.188	0.000
142	A	142	NME	0	-0.030	-0.003	6.829	1.689	1.689	0.000	0.000	0.000	0.000

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