FMO DATABASE

FMODB ID: 89Q1Y

Calculation Name: 3N4D-A-Xray372

Preferred Name:

Target Type:

Ligand Name: 1-[(2r)-2-carboxy-2-hydroxyethyl]-l-proline

ligand 3-letter code: PR4

PDB ID: 3N4D

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NU77

Base Structure: X-ray

Registration Date: 2023-09-23

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	145
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1379685.644266
FMO2-HF: Nuclear repulsion	1320895.573226
FMO2-HF: Total energy	-58790.071041
FMO2-MP2: Total energy	-58963.443417

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:PR4)

Summations of interaction energy for fragment #1(A:1:PR4)

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.
-163.601	-142.541	56.316	-28.458	-48.914	0.052

Interaction energy analysis for fragmet #1(A:1:PR4)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.015

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	TYR	0	0.006	-0.037	2.538	3.989	6.858	0.923	-1.213	-2.579	-0.005
4	A	4	THR	0	-0.026	-0.011	5.549	-0.009	-0.009	0.000	0.000	0.000	0.000
5	A	5	CYS	0	-0.003	-0.012	9.235	0.711	0.711	0.000	0.000	0.000	0.000
6	A	6	TRP	0	-0.007	0.002	12.048	0.067	0.067	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.050	0.015	15.423	0.181	0.181	0.000	0.000	0.000	0.000
8	A	8	GLN	0	0.062	0.037	18.603	-0.073	-0.073	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.926	0.945	22.067	1.168	1.168	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.097	-0.061	22.743	0.098	0.098	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.869	0.950	22.044	0.713	0.713	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.045	0.044	16.485	0.038	0.038	0.000	0.000	0.000	0.000
13	A	13	SER	0	0.013	-0.002	20.251	-0.152	-0.152	0.000	0.000	0.000	0.000
14	A	14	ARG	1	1.008	0.975	19.467	1.456	1.456	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.935	-0.968	18.483	-1.320	-1.320	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.043	0.023	18.259	-0.067	-0.067	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.823	0.906	14.986	2.091	2.091	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.069	-0.022	13.530	-0.458	-0.458	0.000	0.000	0.000	0.000
19	A	19	ARG	1	1.014	1.005	13.732	0.887	0.887	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.025	0.023	11.476	-0.037	-0.037	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.028	0.012	9.378	-0.144	-0.144	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.891	-0.912	8.898	-2.777	-2.777	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.012	-0.001	10.459	0.080	0.080	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.037	-0.030	5.542	0.393	0.393	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.031	-0.035	5.860	-0.520	-0.520	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.846	-0.919	6.734	-1.121	-1.121	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.052	-0.020	8.293	0.875	0.875	0.000	0.000	0.000	0.000
28	A	28	HIS	0	0.036	0.044	2.391	-16.365	-13.665	6.675	-2.901	-6.475	0.008
29	A	29	HIS	0	-0.036	-0.025	5.347	2.246	2.309	-0.001	0.000	-0.062	0.000
30	A	30	GLU	-1	-0.958	-0.957	7.323	1.605	1.605	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.071	-0.063	5.502	0.277	0.277	0.000	0.000	0.000	0.000
32	A	32	ALA	0	-0.057	-0.053	7.603	2.103	2.103	0.000	0.000	0.000	0.000
33	A	33	HIS	0	-0.007	-0.010	9.164	1.117	1.117	0.000	0.000	0.000	0.000
34	A	34	ALA	0	-0.019	0.018	4.593	-0.407	-0.229	-0.001	-0.009	-0.168	0.000
35	A	35	PRO	0	0.026	0.031	5.272	-1.706	-1.706	0.000	0.000	0.000	0.000
36	A	36	LYS	1	0.896	0.934	4.845	-0.465	-0.401	-0.001	-0.002	-0.060	0.000
37	A	37	TYR	0	-0.010	-0.001	5.439	-2.950	-2.950	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.036	-0.010	1.932	-3.344	-1.748	5.176	-2.374	-4.398	0.001
39	A	39	VAL	0	-0.028	0.005	2.227	-28.877	-27.382	12.136	-5.887	-7.744	-0.055
40	A	40	GLN	0	0.005	0.028	2.932	9.908	9.196	0.118	1.599	-1.005	-0.001
41	A	41	VAL	0	0.021	-0.002	4.977	-0.213	-0.198	-0.001	-0.014	0.000	0.000
42	A	42	ILE	0	-0.037	-0.012	7.346	0.920	0.920	0.000	0.000	0.000	0.000
43	A	43	PHE	0	-0.008	-0.013	10.584	0.327	0.327	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.012	0.002	13.675	-0.005	-0.005	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.850	-0.927	15.984	-1.852	-1.852	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.038	-0.008	19.387	0.008	0.008	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.850	-0.928	21.986	-0.977	-0.977	0.000	0.000	0.000	0.000
48	A	48	PRO	0	-0.034	-0.013	25.308	0.014	0.014	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.853	-0.952	27.044	-0.544	-0.544	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.046	-0.012	24.521	0.029	0.029	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.033	-0.019	18.210	-0.071	-0.071	0.000	0.000	0.000	0.000
52	A	52	PHE	0	-0.047	-0.021	23.813	0.048	0.048	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.041	0.020	22.305	0.029	0.029	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.035	-0.015	25.508	0.002	0.002	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.029	-0.016	27.712	0.000	0.000	0.000	0.000	0.000	0.000
56	A	56	GLN	0	-0.025	-0.010	28.776	-0.025	-0.025	0.000	0.000	0.000	0.000
57	A	57	SER	0	0.036	0.006	28.074	-0.018	-0.018	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.013	0.019	23.836	0.039	0.039	0.000	0.000	0.000	0.000
59	A	59	SER	0	0.016	0.005	24.909	-0.065	-0.065	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.887	-0.951	24.308	-0.587	-0.587	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.035	-0.037	22.980	-0.155	-0.155	0.000	0.000	0.000	0.000
62	A	62	HIS	0	-0.069	-0.003	19.007	-0.131	-0.131	0.000	0.000	0.000	0.000
63	A	63	ILE	0	-0.002	0.000	14.434	-0.164	-0.164	0.000	0.000	0.000	0.000
64	A	64	TRP	0	-0.049	-0.008	13.714	0.078	0.078	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.013	0.000	8.463	-0.416	-0.416	0.000	0.000	0.000	0.000
66	A	66	GLN	0	0.007	0.020	9.343	0.415	0.415	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.012	-0.008	4.448	-1.442	-1.414	-0.001	-0.004	-0.022	0.000
68	A	68	THR	0	-0.017	-0.010	4.259	1.857	2.034	-0.001	-0.031	-0.145	0.000
69	A	69	ILE	0	-0.021	-0.022	2.246	-10.143	-5.976	5.074	-3.961	-5.279	0.011
70	A	70	ARG	1	0.869	0.931	1.876	-58.417	-58.606	20.940	-8.080	-12.670	0.110
71	A	71	SER	0	-0.002	0.001	3.724	-2.230	-1.775	0.033	-0.212	-0.275	0.003
72	A	72	GLY	0	0.015	0.007	7.230	0.905	0.905	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.918	0.979	3.422	-26.043	-25.126	0.005	-0.452	-0.470	0.003
74	A	74	THR	0	-0.005	-0.019	8.710	-1.372	-1.372	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.858	-0.948	11.755	3.972	3.972	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.933	0.970	14.205	-2.508	-2.508	0.000	0.000	0.000	0.000
77	A	77	GLN	0	0.007	0.006	10.044	0.311	0.311	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.894	0.947	8.785	-6.182	-6.182	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.921	-0.956	10.831	1.765	1.765	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.923	-0.970	13.064	2.048	2.048	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.012	0.010	5.931	-0.455	-0.455	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.021	0.005	10.356	-0.789	-0.789	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.021	0.007	11.818	-0.561	-0.561	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.942	0.983	11.376	-0.783	-0.783	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.009	0.004	7.548	-0.435	-0.435	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.017	-0.026	12.031	-0.285	-0.285	0.000	0.000	0.000	0.000
87	A	87	GLN	0	-0.025	-0.020	15.063	-0.169	-0.169	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.941	-0.972	13.763	-0.524	-0.524	0.000	0.000	0.000	0.000
89	A	89	ILE	0	-0.012	-0.004	11.451	-0.181	-0.181	0.000	0.000	0.000	0.000
90	A	90	ALA	0	0.008	0.014	15.915	-0.058	-0.058	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.006	-0.009	18.956	-0.011	-0.011	0.000	0.000	0.000	0.000
92	A	92	ILE	0	-0.106	-0.043	15.231	-0.047	-0.047	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.035	-0.031	17.520	-0.056	-0.056	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.042	0.008	20.978	0.035	0.035	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.052	-0.023	19.467	0.037	0.037	0.000	0.000	0.000	0.000
96	A	96	PRO	0	0.022	0.010	22.493	0.031	0.031	0.000	0.000	0.000	0.000
97	A	97	ASN	0	0.091	0.010	20.152	-0.102	-0.102	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.992	-0.979	19.762	0.049	0.049	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.880	-0.958	21.054	-0.280	-0.280	0.000	0.000	0.000	0.000
100	A	100	VAL	0	0.010	0.004	14.758	-0.137	-0.137	0.000	0.000	0.000	0.000
101	A	101	TRP	0	-0.074	-0.021	15.750	0.210	0.210	0.000	0.000	0.000	0.000
102	A	102	VAL	0	0.043	0.013	9.757	-0.256	-0.256	0.000	0.000	0.000	0.000
103	A	103	TYR	0	-0.041	-0.022	10.628	0.343	0.343	0.000	0.000	0.000	0.000
104	A	104	ILE	0	0.051	0.024	6.911	-0.334	-0.334	0.000	0.000	0.000	0.000
105	A	105	THR	0	-0.073	-0.026	7.384	-0.484	-0.484	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.863	-0.931	6.629	9.999	9.999	0.000	0.000	0.000	0.000
107	A	107	ILE	0	-0.022	-0.009	5.713	-2.840	-2.840	0.000	0.000	0.000	0.000
108	A	108	PRO	0	0.037	0.023	6.335	3.113	3.113	0.000	0.000	0.000	0.000
109	A	109	GLY	0	0.126	0.039	5.248	-0.223	-0.223	0.000	0.000	0.000	0.000
110	A	110	SER	0	-0.051	-0.015	6.084	-2.015	-2.015	0.000	0.000	0.000	0.000
111	A	111	ASN	0	-0.054	-0.031	8.016	-1.090	-1.090	0.000	0.000	0.000	0.000
112	A	112	MET	0	-0.033	0.003	2.425	-7.928	-5.786	2.686	-1.581	-3.247	0.014
113	A	113	THR	0	-0.038	-0.034	6.695	1.035	1.035	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.831	-0.921	2.609	-46.625	-42.419	1.893	-3.006	-3.093	-0.036
115	A	115	TYR	0	-0.050	-0.051	6.264	3.407	3.407	0.000	0.000	0.000	0.000
116	A	116	GLY	0	-0.048	-0.019	9.553	0.970	0.970	0.000	0.000	0.000	0.000
117	A	117	ARG	1	0.845	0.920	9.945	2.306	2.306	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.023	0.018	8.977	-0.934	-0.934	0.000	0.000	0.000	0.000
119	A	119	LEU	0	-0.031	-0.004	2.470	-0.527	0.222	0.664	-0.327	-1.086	-0.001
120	A	120	MET	0	-0.044	-0.024	6.001	-0.137	-0.137	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.905	-0.946	5.856	10.089	10.089	0.000	0.000	0.000	0.000
122	A	122	PRO	0	-0.038	-0.020	4.976	-0.532	-0.392	-0.001	-0.003	-0.136	0.000
123	A	123	GLY	0	-0.013	-0.001	7.243	-1.528	-1.528	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.877	-0.957	9.459	3.573	3.573	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.862	-0.955	6.013	8.289	8.289	0.000	0.000	0.000	0.000
126	A	126	GLU	-1	-0.809	-0.911	8.828	1.753	1.753	0.000	0.000	0.000	0.000
127	A	127	LYS	1	0.962	0.990	12.368	-1.901	-1.901	0.000	0.000	0.000	0.000
128	A	128	TRP	0	-0.021	-0.009	7.179	-0.623	-0.623	0.000	0.000	0.000	0.000
129	A	129	PHE	0	0.056	0.021	9.800	-0.544	-0.544	0.000	0.000	0.000	0.000
130	A	130	ASN	0	-0.055	-0.039	11.048	-0.459	-0.459	0.000	0.000	0.000	0.000
131	A	131	SER	0	-0.044	-0.021	12.767	0.115	0.115	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.034	-0.004	10.217	-0.091	-0.091	0.000	0.000	0.000	0.000
133	A	133	PRO	0	-0.037	-0.011	14.254	0.181	0.181	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.888	-0.961	16.752	-0.893	-0.893	0.000	0.000	0.000	0.000
135	A	135	GLY	0	0.089	0.047	18.774	-0.054	-0.054	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.098	-0.065	11.802	-0.069	-0.069	0.000	0.000	0.000	0.000
137	A	137	ARG	1	0.954	0.986	13.749	0.682	0.682	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.914	-0.940	14.823	-1.082	-1.082	0.000	0.000	0.000	0.000
139	A	139	ARG	1	0.931	0.948	15.697	2.476	2.476	0.000	0.000	0.000	0.000
140	A	140	LEU	0	-0.053	0.007	9.132	-0.001	-0.001	0.000	0.000	0.000	0.000
141	A	141	THR	0	-0.041	-0.027	12.578	-0.064	-0.064	0.000	0.000	0.000	0.000
142	A	142	GLU	-1	-0.983	-0.991	14.535	-1.614	-1.614	0.000	0.000	0.000	0.000
143	A	143	LEU	0	-0.041	-0.009	10.302	-0.091	-0.091	0.000	0.000	0.000	0.000
144	A	144	GLU	-1	-0.848	-0.937	9.218	-3.376	-3.376	0.000	0.000	0.000	0.000
145	A	145	GLY	0	-0.013	0.010	12.536	0.476	0.476	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:PR4)