FMO DATABASE

FMODB ID: VRGJ1

Calculation Name: 4S03-A-Xray372

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: 2023-06-19

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
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	141
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1341085.612073
FMO2-HF: Nuclear repulsion	1285177.976946
FMO2-HF: Total energy	-55907.635127
FMO2-MP2: Total energy	-56071.086434

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.
-32.01	-32.774	52.291	-20.134	-31.39	-0.128

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 : 0 / q_Mulliken : -0.045 / q_NPA : -0.037

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	0.014	-0.007	2.445	-1.120	1.088	2.237	-1.179	-3.266	-0.002
4	A	4	LEU	0	-0.001	0.013	4.442	-0.425	-0.353	-0.001	-0.027	-0.045	0.000
5	A	5	LEU	0	-0.037	-0.026	7.877	0.241	0.241	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.048	0.015	10.497	-0.152	-0.152	0.000	0.000	0.000	0.000
7	A	7	HIS	0	0.015	0.030	14.011	0.045	0.045	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.028	0.000	16.905	-0.062	-0.062	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.804	-0.867	19.163	0.250	0.250	0.000	0.000	0.000	0.000
10	A	10	TYR	0	-0.001	-0.009	21.431	-0.009	-0.009	0.000	0.000	0.000	0.000
11	A	11	BIF	0	0.048	0.007	14.787	-0.015	-0.015	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.828	-0.901	19.599	0.134	0.134	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.074	-0.040	16.960	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.815	-0.903	19.852	0.027	0.027	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.028	-0.020	18.357	-0.017	-0.017	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.841	0.913	20.772	0.016	0.016	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.884	-0.927	22.558	-0.106	-0.106	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.840	0.906	20.000	0.162	0.162	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.029	0.018	16.799	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.019	-0.006	14.091	-0.030	-0.030	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.971	0.977	18.543	0.242	0.242	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.037	-0.041	19.909	0.028	0.028	0.000	0.000	0.000	0.000
23	A	23	PRO	0	0.012	0.036	16.831	-0.031	-0.031	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.761	-0.863	13.408	-0.016	-0.016	0.000	0.000	0.000	0.000
25	A	25	PRO	0	-0.026	0.002	16.493	0.018	0.018	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.013	-0.014	18.165	0.014	0.014	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.004	-0.029	20.647	-0.011	-0.011	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.868	-0.972	23.070	0.003	0.003	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.857	-0.902	23.342	0.081	0.081	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.005	0.019	16.803	0.012	0.012	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.894	0.971	19.569	0.018	0.018	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.884	0.932	21.511	-0.071	-0.071	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.038	0.039	19.497	0.007	0.007	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.772	0.860	20.515	-0.176	-0.176	0.000	0.000	0.000	0.000
35	A	35	MET	0	-0.056	-0.008	17.062	0.021	0.021	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.805	-0.903	20.608	0.185	0.185	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.826	-0.895	21.143	0.328	0.328	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.036	-0.005	15.680	0.036	0.036	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.015	0.007	11.845	-0.023	-0.023	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.020	-0.020	12.156	0.082	0.082	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.036	0.003	7.269	0.074	0.074	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.010	0.003	8.194	0.002	0.002	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.004	-0.014	2.561	-0.808	-0.910	3.183	-0.577	-2.504	-0.001
44	A	44	SER	0	-0.036	-0.038	3.692	-1.062	-0.590	0.004	-0.105	-0.371	0.000
45	A	45	VAL	0	-0.014	0.001	2.387	-4.125	-2.032	4.312	-2.590	-3.814	-0.022
46	A	46	GLU	-1	-0.765	-0.833	1.987	-12.243	-13.052	8.703	-3.878	-4.017	-0.032
47	A	47	LYS	1	0.907	0.948	4.169	1.120	1.230	0.000	-0.010	-0.099	0.000
48	A	48	VAL	0	-0.039	-0.039	3.479	0.366	0.574	0.007	-0.043	-0.170	0.000
49	A	49	ASP	-1	-0.674	-0.842	1.733	-13.991	-21.955	21.601	-7.825	-5.812	-0.067
50	A	50	GLU	-1	-0.831	-0.912	4.450	-0.400	-0.265	-0.001	-0.073	-0.061	0.000
51	A	51	LYS	1	0.878	0.954	7.599	1.215	1.215	0.000	0.000	0.000	0.000
52	A	52	ASN	0	-0.011	-0.008	7.808	0.267	0.267	0.000	0.000	0.000	0.000
53	A	53	PRO	0	0.101	0.054	6.074	0.125	0.125	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.862	-0.901	6.117	0.208	0.208	0.000	0.000	0.000	0.000
55	A	55	GLH	0	0.061	0.059	7.700	0.109	0.109	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.001	-0.005	2.254	-0.144	-0.099	2.587	-0.527	-2.105	0.001
57	A	57	SER	0	0.008	-0.028	3.295	0.921	1.416	0.018	-0.100	-0.413	0.000
58	A	58	LEU	0	0.015	0.008	4.305	0.541	0.627	-0.001	-0.001	-0.084	0.000
59	A	59	LYS	1	0.853	0.927	6.237	-1.712	-1.712	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.028	0.003	2.877	-0.250	-0.582	2.851	-0.828	-1.690	0.001
61	A	61	ILE	0	-0.008	0.016	4.827	-0.753	-0.606	0.002	-0.061	-0.088	0.000
62	A	62	GLU	-1	-0.827	-0.873	7.402	0.870	0.870	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.871	-0.920	6.980	1.302	1.302	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.014	-0.011	5.136	-0.399	-0.301	-0.001	-0.013	-0.085	0.000
65	A	65	SER	0	0.010	-0.019	9.034	-0.387	-0.387	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.871	0.934	11.973	-1.388	-1.388	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.020	-0.006	11.967	-0.156	-0.156	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.010	0.014	13.244	-0.146	-0.146	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.900	-0.955	15.045	0.661	0.661	0.000	0.000	0.000	0.000
70	A	70	GLN	0	-0.078	-0.038	16.946	-0.036	-0.036	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.084	-0.056	16.770	-0.074	-0.074	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.889	0.947	19.306	-0.437	-0.437	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.012	0.014	16.565	-0.036	-0.036	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.881	-0.953	17.805	0.405	0.405	0.000	0.000	0.000	0.000
75	A	75	ASN	0	-0.048	-0.007	17.604	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	76	VAL	0	0.024	0.009	11.148	0.051	0.051	0.000	0.000	0.000	0.000
77	A	77	PHE	0	0.025	0.010	13.107	-0.092	-0.092	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.011	-0.001	6.965	0.166	0.166	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.002	-0.007	9.043	-0.293	-0.293	0.000	0.000	0.000	0.000
80	A	80	PRO	0	-0.002	0.002	7.309	0.107	0.107	0.000	0.000	0.000	0.000
81	A	81	TRP	0	0.019	-0.006	7.274	-0.040	-0.040	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.002	0.019	7.465	-0.231	-0.231	0.000	0.000	0.000	0.000
83	A	83	HIS	0	-0.004	-0.001	9.488	-0.173	-0.173	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.005	0.009	5.996	0.145	0.145	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.039	-0.067	5.269	-0.106	-0.106	0.000	0.000	0.000	0.000
86	A	86	SER	0	0.006	0.012	7.380	0.234	0.234	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.940	-0.966	7.659	-1.192	-1.192	0.000	0.000	0.000	0.000
88	A	88	LEU	0	0.000	0.021	6.113	-0.600	-0.600	0.000	0.000	0.000	0.000
89	A	89	ALA	0	-0.045	-0.014	6.618	0.263	0.263	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.855	0.921	8.243	1.102	1.102	0.000	0.000	0.000	0.000
91	A	91	PRO	0	0.072	0.015	10.443	-0.075	-0.075	0.000	0.000	0.000	0.000
92	A	92	SER	0	-0.002	0.005	10.665	-0.024	-0.024	0.000	0.000	0.000	0.000
93	A	93	VAL	0	0.049	0.015	6.988	0.083	0.083	0.000	0.000	0.000	0.000
94	A	94	ALA	0	0.017	0.015	5.945	-0.090	-0.090	0.000	0.000	0.000	0.000
95	A	95	MET	0	-0.004	-0.011	6.170	0.118	0.118	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.878	-0.912	8.654	-0.256	-0.256	0.000	0.000	0.000	0.000
97	A	97	ILE	0	0.005	-0.009	2.431	0.131	-0.538	2.671	-0.376	-1.626	-0.002
98	A	98	LEU	0	0.011	0.009	4.494	0.143	0.346	-0.001	-0.011	-0.190	0.000
99	A	99	ASN	0	0.017	0.014	5.641	0.376	0.376	0.000	0.000	0.000	0.000
100	A	100	ARG	1	0.834	0.900	6.211	0.290	0.290	0.000	0.000	0.000	0.000
101	A	101	VAL	0	-0.006	-0.012	2.760	-0.359	0.120	0.167	-0.125	-0.520	-0.001
102	A	102	TYR	0	-0.007	-0.001	5.995	0.081	0.081	0.000	0.000	0.000	0.000
103	A	103	GLN	0	-0.010	-0.026	9.321	0.024	0.024	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.042	0.022	9.546	-0.028	-0.028	0.000	0.000	0.000	0.000
105	A	105	LEU	0	-0.003	-0.006	8.247	0.010	0.010	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.873	0.933	11.380	-0.417	-0.417	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-1.011	-0.993	13.785	0.443	0.443	0.000	0.000	0.000	0.000
108	A	108	ARG	1	0.853	0.903	12.233	-0.953	-0.953	0.000	0.000	0.000	0.000
109	A	109	GLY	0	0.004	0.022	15.308	-0.026	-0.026	0.000	0.000	0.000	0.000
110	A	110	PHE	0	-0.068	-0.012	13.518	-0.011	-0.011	0.000	0.000	0.000	0.000
111	A	111	ASN	0	-0.001	0.002	16.688	-0.042	-0.042	0.000	0.000	0.000	0.000
112	A	112	VAL	0	-0.005	-0.014	11.557	0.048	0.048	0.000	0.000	0.000	0.000
113	A	113	GLY	0	0.015	0.010	14.635	-0.089	-0.089	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.850	0.893	11.115	0.002	0.002	0.000	0.000	0.000	0.000
115	A	115	ALA	0	-0.005	0.016	12.049	-0.067	-0.067	0.000	0.000	0.000	0.000
116	A	116	PRO	0	-0.019	0.006	12.126	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	117	PHE	0	0.034	-0.009	8.269	-0.028	-0.028	0.000	0.000	0.000	0.000
118	A	118	GLY	0	0.007	-0.005	12.533	0.001	0.001	0.000	0.000	0.000	0.000
119	A	119	TYR	0	-0.031	-0.038	14.822	0.004	0.004	0.000	0.000	0.000	0.000
120	A	120	TYR	0	0.028	0.022	16.103	-0.034	-0.034	0.000	0.000	0.000	0.000
121	A	121	ILE	0	-0.022	-0.013	14.930	0.023	0.023	0.000	0.000	0.000	0.000
122	A	122	ALA	0	-0.014	0.010	18.646	-0.007	-0.007	0.000	0.000	0.000	0.000
123	A	123	ALA	0	0.023	-0.003	18.240	0.020	0.020	0.000	0.000	0.000	0.000
124	A	124	LYS	1	0.826	0.908	20.233	-0.122	-0.122	0.000	0.000	0.000	0.000
125	A	125	ILE	0	0.000	-0.005	16.173	0.028	0.028	0.000	0.000	0.000	0.000
126	A	126	SER	0	-0.064	-0.035	20.370	-0.039	-0.039	0.000	0.000	0.000	0.000
127	A	127	CYS	0	0.001	0.011	18.109	0.038	0.038	0.000	0.000	0.000	0.000
128	A	128	LYS	1	0.793	0.867	20.078	-0.328	-0.328	0.000	0.000	0.000	0.000
129	A	129	GLY	0	0.026	0.001	20.799	0.004	0.004	0.000	0.000	0.000	0.000
130	A	130	HIS	0	-0.071	-0.029	19.136	-0.039	-0.039	0.000	0.000	0.000	0.000
131	A	131	PRO	0	0.036	-0.014	20.835	0.013	0.013	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.025	-0.002	17.499	0.005	0.005	0.000	0.000	0.000	0.000
133	A	133	ALA	0	-0.026	0.006	16.553	0.082	0.082	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.872	-0.936	14.377	0.244	0.244	0.000	0.000	0.000	0.000
135	A	135	LEU	0	-0.043	-0.012	12.076	-0.023	-0.023	0.000	0.000	0.000	0.000
136	A	136	SER	0	0.016	0.013	8.856	0.016	0.016	0.000	0.000	0.000	0.000
137	A	137	ARG	1	0.898	0.947	6.219	-1.029	-1.029	0.000	0.000	0.000	0.000
138	A	138	THR	0	0.011	0.000	4.451	-0.976	-0.820	-0.001	-0.035	-0.120	0.000
139	A	139	ILE	0	-0.067	-0.031	2.216	-2.386	-0.419	1.211	-0.825	-2.353	0.004
140	A	140	VAL	0	0.044	0.023	2.890	5.193	5.140	2.743	-0.898	-1.793	-0.007
141	A	141	PRO	0	-0.078	-0.057	3.917	-0.634	-0.443	0.000	-0.027	-0.164	0.000

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