FMO DATABASE

FMODB ID: YYGJ2

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	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	141
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1339859.197706
FMO2-HF: Nuclear repulsion	1283952.225312
FMO2-HF: Total energy	-55906.972394
FMO2-MP2: Total energy	-56070.364163

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.
-18.766	-27.522	63.804	-22.886	-32.164	-0.123

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 : -0.009 / q_NPA : 0.007

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	-0.001	2.401	-2.112	1.832	1.824	-2.097	-3.670	0.007
4	A	4	LEU	0	-0.006	0.010	4.462	-0.597	-0.532	-0.001	-0.024	-0.040	0.000
5	A	5	LEU	0	-0.031	-0.029	7.899	0.303	0.303	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.052	0.020	10.506	-0.163	-0.163	0.000	0.000	0.000	0.000
7	A	7	HIS	0	0.026	0.032	14.032	0.050	0.050	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.025	0.000	16.915	-0.058	-0.058	0.000	0.000	0.000	0.000
9	A	9	ASP	-1	-0.818	-0.884	19.189	0.178	0.178	0.000	0.000	0.000	0.000
10	A	10	TYR	0	-0.005	-0.010	21.485	0.000	0.000	0.000	0.000	0.000	0.000
11	A	11	BIF	0	0.047	0.008	14.670	-0.017	-0.017	0.000	0.000	0.000	0.000
12	A	12	GLU	-1	-0.866	-0.941	19.548	0.154	0.154	0.000	0.000	0.000	0.000
13	A	13	TYR	0	-0.082	-0.033	16.883	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	14	GLU	-1	-0.864	-0.950	19.874	0.083	0.083	0.000	0.000	0.000	0.000
15	A	15	VAL	0	-0.036	-0.021	18.444	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	16	LYS	1	0.847	0.929	20.860	-0.067	-0.067	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.871	-0.918	22.690	0.018	0.018	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.822	0.901	20.167	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.026	0.017	16.893	-0.010	-0.010	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.012	-0.003	14.564	-0.016	-0.016	0.000	0.000	0.000	0.000
21	A	21	LYS	1	0.962	0.976	18.760	0.009	0.009	0.000	0.000	0.000	0.000
22	A	22	ASN	0	-0.033	-0.046	19.968	-0.003	-0.003	0.000	0.000	0.000	0.000
23	A	23	PRO	0	0.009	0.035	17.000	-0.001	-0.001	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.804	-0.900	13.441	0.240	0.240	0.000	0.000	0.000	0.000
25	A	25	PRO	0	-0.028	0.014	16.603	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	26	ILE	0	-0.011	-0.017	18.200	0.017	0.017	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.038	-0.074	20.697	-0.013	-0.013	0.000	0.000	0.000	0.000
28	A	28	GLU	-1	-0.878	-0.977	23.097	0.092	0.092	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.837	-0.869	23.230	0.166	0.166	0.000	0.000	0.000	0.000
30	A	30	MET	0	-0.002	0.031	17.059	0.010	0.010	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.914	0.968	19.590	-0.078	-0.078	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.937	0.970	21.565	-0.122	-0.122	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.037	0.036	19.459	0.008	0.008	0.000	0.000	0.000	0.000
34	A	34	ARG	1	0.810	0.877	20.481	-0.173	-0.173	0.000	0.000	0.000	0.000
35	A	35	MET	0	-0.060	-0.005	17.040	0.022	0.022	0.000	0.000	0.000	0.000
36	A	36	GLU	-1	-0.822	-0.907	20.499	0.162	0.162	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.868	-0.922	21.189	0.247	0.247	0.000	0.000	0.000	0.000
38	A	38	VAL	0	-0.035	-0.007	15.702	0.032	0.032	0.000	0.000	0.000	0.000
39	A	39	LEU	0	0.011	0.005	11.781	-0.033	-0.033	0.000	0.000	0.000	0.000
40	A	40	VAL	0	-0.021	-0.021	12.230	0.099	0.099	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.036	0.001	7.299	0.026	0.026	0.000	0.000	0.000	0.000
42	A	42	PHE	0	-0.017	0.003	8.260	0.059	0.059	0.000	0.000	0.000	0.000
43	A	43	ILE	0	-0.004	-0.015	2.553	-1.163	-0.648	2.167	-0.455	-2.227	-0.001
44	A	44	SER	0	-0.047	-0.050	3.712	-0.892	-0.454	0.003	-0.098	-0.343	0.000
45	A	45	VAL	0	-0.020	-0.003	2.405	-4.512	-2.122	3.568	-2.425	-3.534	-0.021
46	A	46	GLU	-1	-0.822	-0.915	1.648	-12.860	-26.644	26.729	-8.368	-4.577	-0.052
47	A	47	LYS	1	0.953	0.974	4.182	0.659	0.767	0.000	-0.009	-0.099	0.000
48	A	48	VAL	0	-0.066	-0.046	3.753	-0.194	0.041	0.006	-0.074	-0.167	0.000
49	A	49	ASP	-1	-0.706	-0.873	2.430	13.433	10.737	10.428	-2.802	-4.931	-0.030
50	A	50	GLU	-1	-0.901	-0.968	5.419	-0.553	-0.553	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.867	0.952	8.188	0.174	0.174	0.000	0.000	0.000	0.000
52	A	52	ASN	0	-0.016	-0.011	8.434	-0.044	-0.044	0.000	0.000	0.000	0.000
53	A	53	PRO	0	0.106	0.050	6.073	0.104	0.104	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.941	-0.950	6.090	0.308	0.308	0.000	0.000	0.000	0.000
55	A	55	GLH	0	0.020	-0.013	7.560	0.089	0.089	0.000	0.000	0.000	0.000
56	A	56	VAL	0	-0.005	-0.011	2.201	-0.453	-0.516	2.739	-0.545	-2.132	0.000
57	A	57	SER	0	0.010	-0.016	3.148	0.408	1.009	0.034	-0.155	-0.480	-0.001
58	A	58	LEU	0	0.016	0.007	4.150	0.391	0.481	-0.001	0.003	-0.092	0.000
59	A	59	LYS	1	0.904	0.966	6.185	-0.542	-0.542	0.000	0.000	0.000	0.000
60	A	60	ALA	0	0.030	0.007	2.697	-0.286	-0.801	3.369	-0.984	-1.870	0.001
61	A	61	ILE	0	-0.017	0.008	4.671	-0.731	-0.567	0.003	-0.058	-0.110	0.000
62	A	62	GLU	-1	-0.834	-0.899	7.181	0.552	0.552	0.000	0.000	0.000	0.000
63	A	63	GLU	-1	-0.930	-0.973	6.815	0.541	0.541	0.000	0.000	0.000	0.000
64	A	64	ILE	0	-0.015	-0.015	5.344	-0.328	-0.246	-0.001	-0.008	-0.072	0.000
65	A	65	SER	0	0.002	-0.011	9.002	-0.331	-0.331	0.000	0.000	0.000	0.000
66	A	66	LYS	1	0.910	0.969	11.937	-0.712	-0.712	0.000	0.000	0.000	0.000
67	A	67	VAL	0	-0.020	-0.007	11.875	-0.135	-0.135	0.000	0.000	0.000	0.000
68	A	68	ALA	0	0.002	0.012	13.224	-0.111	-0.111	0.000	0.000	0.000	0.000
69	A	69	GLU	-1	-0.898	-0.956	15.028	0.459	0.459	0.000	0.000	0.000	0.000
70	A	70	GLN	0	-0.069	-0.032	16.908	-0.042	-0.042	0.000	0.000	0.000	0.000
71	A	71	VAL	0	-0.083	-0.056	16.893	-0.057	-0.057	0.000	0.000	0.000	0.000
72	A	72	LYS	1	0.895	0.949	19.287	-0.264	-0.264	0.000	0.000	0.000	0.000
73	A	73	ALA	0	-0.019	0.009	16.557	-0.022	-0.022	0.000	0.000	0.000	0.000
74	A	74	GLU	-1	-0.888	-0.954	17.804	0.323	0.323	0.000	0.000	0.000	0.000
75	A	75	ASN	0	-0.038	-0.013	17.560	0.023	0.023	0.000	0.000	0.000	0.000
76	A	76	VAL	0	0.023	0.008	11.048	0.032	0.032	0.000	0.000	0.000	0.000
77	A	77	PHE	0	0.021	0.009	12.986	-0.063	-0.063	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.016	-0.002	6.796	0.139	0.139	0.000	0.000	0.000	0.000
79	A	79	ILE	0	-0.003	-0.012	9.009	-0.235	-0.235	0.000	0.000	0.000	0.000
80	A	80	PRO	0	-0.004	0.005	7.427	0.129	0.129	0.000	0.000	0.000	0.000
81	A	81	TRP	0	0.021	-0.008	7.315	-0.089	-0.089	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.008	0.027	7.520	-0.171	-0.171	0.000	0.000	0.000	0.000
83	A	83	HIS	0	-0.005	0.000	9.489	-0.127	-0.127	0.000	0.000	0.000	0.000
84	A	84	LEU	0	0.008	0.012	5.923	0.052	0.052	0.000	0.000	0.000	0.000
85	A	85	SER	0	-0.026	-0.029	5.266	-0.227	-0.227	0.000	0.000	0.000	0.000
86	A	86	SER	0	0.008	0.011	7.377	0.228	0.228	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.956	-0.976	7.562	-0.378	-0.378	0.000	0.000	0.000	0.000
88	A	88	LEU	0	0.004	0.020	6.306	0.007	0.007	0.000	0.000	0.000	0.000
89	A	89	ALA	0	-0.035	-0.011	6.626	0.093	0.093	0.000	0.000	0.000	0.000
90	A	90	LYS	1	0.941	0.977	8.254	-0.090	-0.090	0.000	0.000	0.000	0.000
91	A	91	PRO	0	0.067	0.012	10.673	0.028	0.028	0.000	0.000	0.000	0.000
92	A	92	SER	0	0.020	0.009	10.847	0.013	0.013	0.000	0.000	0.000	0.000
93	A	93	VAL	0	0.015	0.010	7.078	0.015	0.015	0.000	0.000	0.000	0.000
94	A	94	ALA	0	0.026	0.016	6.154	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	95	MET	0	-0.008	-0.014	6.298	0.004	0.004	0.000	0.000	0.000	0.000
96	A	96	ASP	-1	-0.884	-0.912	8.690	0.284	0.284	0.000	0.000	0.000	0.000
97	A	97	ILE	0	0.012	-0.007	2.421	-0.128	-0.434	2.067	-0.298	-1.463	-0.001
98	A	98	LEU	0	0.011	0.011	4.636	-0.054	0.119	-0.001	-0.008	-0.164	0.000
99	A	99	ASN	0	0.016	0.009	5.611	0.185	0.185	0.000	0.000	0.000	0.000
100	A	100	ARG	1	0.882	0.932	6.250	-0.245	-0.245	0.000	0.000	0.000	0.000
101	A	101	VAL	0	-0.001	-0.009	2.810	-0.428	0.017	0.155	-0.109	-0.491	-0.001
102	A	102	TYR	0	-0.006	-0.002	5.963	0.031	0.031	0.000	0.000	0.000	0.000
103	A	103	GLN	0	-0.037	-0.037	9.338	-0.034	-0.034	0.000	0.000	0.000	0.000
104	A	104	GLY	0	0.040	0.020	9.476	-0.046	-0.046	0.000	0.000	0.000	0.000
105	A	105	LEU	0	0.000	-0.005	8.231	-0.016	-0.016	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.918	0.962	11.265	-0.470	-0.470	0.000	0.000	0.000	0.000
107	A	107	GLU	-1	-1.006	-0.994	13.690	0.377	0.377	0.000	0.000	0.000	0.000
108	A	108	ARG	1	0.846	0.909	11.478	-0.760	-0.760	0.000	0.000	0.000	0.000
109	A	109	GLY	0	0.000	0.019	15.143	-0.033	-0.033	0.000	0.000	0.000	0.000
110	A	110	PHE	0	-0.065	-0.009	13.254	-0.011	-0.011	0.000	0.000	0.000	0.000
111	A	111	ASN	0	0.000	0.009	16.581	-0.019	-0.019	0.000	0.000	0.000	0.000
112	A	112	VAL	0	0.003	-0.008	11.540	0.039	0.039	0.000	0.000	0.000	0.000
113	A	113	GLY	0	0.002	0.003	14.490	-0.072	-0.072	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.908	0.939	11.472	-0.226	-0.226	0.000	0.000	0.000	0.000
115	A	115	ALA	0	-0.014	0.012	12.027	-0.070	-0.070	0.000	0.000	0.000	0.000
116	A	116	PRO	0	-0.018	0.006	12.157	0.026	0.026	0.000	0.000	0.000	0.000
117	A	117	PHE	0	0.039	-0.010	8.901	-0.019	-0.019	0.000	0.000	0.000	0.000
118	A	118	GLY	0	0.004	-0.003	12.659	-0.016	-0.016	0.000	0.000	0.000	0.000
119	A	119	TYR	0	-0.033	-0.055	15.000	-0.025	-0.025	0.000	0.000	0.000	0.000
120	A	120	TYR	0	0.024	0.021	16.177	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	121	ILE	0	-0.012	-0.010	15.034	0.013	0.013	0.000	0.000	0.000	0.000
122	A	122	ALA	0	-0.017	0.007	18.681	-0.013	-0.013	0.000	0.000	0.000	0.000
123	A	123	ALA	0	0.024	-0.004	18.276	0.022	0.022	0.000	0.000	0.000	0.000
124	A	124	LYS	1	0.844	0.930	20.246	-0.145	-0.145	0.000	0.000	0.000	0.000
125	A	125	ILE	0	-0.003	-0.011	16.284	0.030	0.030	0.000	0.000	0.000	0.000
126	A	126	SER	0	-0.063	-0.024	20.427	-0.036	-0.036	0.000	0.000	0.000	0.000
127	A	127	CYS	0	-0.001	0.006	18.270	0.038	0.038	0.000	0.000	0.000	0.000
128	A	128	LYS	1	0.855	0.922	20.090	-0.239	-0.239	0.000	0.000	0.000	0.000
129	A	129	GLY	0	0.029	0.005	20.815	-0.004	-0.004	0.000	0.000	0.000	0.000
130	A	130	HIS	0	-0.074	-0.031	19.041	-0.045	-0.045	0.000	0.000	0.000	0.000
131	A	131	PRO	0	0.028	-0.021	20.830	0.006	0.006	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.013	0.005	17.444	-0.017	-0.017	0.000	0.000	0.000	0.000
133	A	133	ALA	0	-0.029	0.000	16.537	0.064	0.064	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.884	-0.937	14.390	0.081	0.081	0.000	0.000	0.000	0.000
135	A	135	LEU	0	-0.043	-0.014	11.998	-0.069	-0.069	0.000	0.000	0.000	0.000
136	A	136	SER	0	0.016	0.017	8.858	0.052	0.052	0.000	0.000	0.000	0.000
137	A	137	ARG	1	0.898	0.944	6.122	-0.287	-0.287	0.000	0.000	0.000	0.000
138	A	138	THR	0	0.008	0.002	4.391	-0.719	-0.550	-0.001	-0.040	-0.128	0.000
139	A	139	ILE	0	-0.036	-0.011	2.187	-1.228	1.097	1.769	-1.173	-2.921	0.004
140	A	140	VAL	0	0.033	0.017	1.877	-6.016	-9.403	8.947	-3.116	-2.444	-0.028
141	A	141	PRO	0	-0.017	0.029	3.838	0.410	0.661	0.001	-0.043	-0.209	0.000

Top

Graph

Manual

About

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