FMO DATABASE

FMODB ID: NNLRQ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1380244.032347
FMO2-HF: Nuclear repulsion	1321452.758148
FMO2-HF: Total energy	-58791.274199
FMO2-MP2: Total energy	-58964.587807

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.
-190.589	-180.973	76.211	-34.004	-51.824	0.08

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 : 0.023 / q_NPA : 0.018

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	0.012	-0.020	2.544	3.439	6.280	0.925	-1.176	-2.591	-0.004
4	A	4	THR	0	-0.020	-0.013	5.533	0.182	0.182	0.000	0.000	0.000	0.000
5	A	5	CYS	0	-0.022	-0.011	9.214	0.812	0.812	0.000	0.000	0.000	0.000
6	A	6	TRP	0	-0.003	-0.002	11.983	0.108	0.108	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.050	0.016	15.395	0.221	0.221	0.000	0.000	0.000	0.000
8	A	8	GLN	0	0.047	0.027	18.581	-0.055	-0.055	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.866	0.910	21.619	1.438	1.438	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.083	-0.056	22.640	0.117	0.117	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.857	0.934	22.252	0.824	0.824	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.042	0.042	16.573	0.050	0.050	0.000	0.000	0.000	0.000
13	A	13	SER	0	0.017	0.000	20.144	-0.158	-0.158	0.000	0.000	0.000	0.000
14	A	14	ARG	1	1.010	0.976	19.373	1.553	1.553	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.903	-0.942	18.397	-1.343	-1.343	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.062	0.031	18.165	-0.060	-0.060	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.768	0.874	14.850	2.299	2.299	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.090	-0.047	13.434	-0.555	-0.555	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.946	0.967	13.649	0.958	0.958	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.028	0.022	11.381	-0.017	-0.017	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.026	0.013	9.276	-0.166	-0.166	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.854	-0.886	8.812	-2.736	-2.736	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.002	-0.007	10.380	0.140	0.140	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.032	-0.032	5.412	0.426	0.426	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.038	-0.037	5.798	-0.507	-0.507	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.835	-0.913	6.714	-0.493	-0.493	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.048	-0.018	8.281	0.996	0.996	0.000	0.000	0.000	0.000
28	A	28	HIS	0	0.026	0.021	2.621	-18.383	-13.586	3.310	-2.544	-5.564	0.000
29	A	29	HIS	0	-0.047	-0.032	5.292	2.900	2.967	-0.001	0.000	-0.066	0.000
30	A	30	GLU	-1	-0.934	-0.946	7.293	2.473	2.473	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.075	-0.062	5.791	0.151	0.151	0.000	0.000	0.000	0.000
32	A	32	ALA	0	-0.060	-0.050	7.203	2.718	2.718	0.000	0.000	0.000	0.000
33	A	33	HIS	0	-0.012	-0.013	8.546	1.529	1.529	0.000	0.000	0.000	0.000
34	A	34	ALA	0	-0.017	0.019	4.392	-0.409	-0.145	-0.001	-0.030	-0.233	0.000
35	A	35	PRO	0	0.035	0.028	5.118	-2.346	-2.250	-0.001	-0.004	-0.091	0.000
36	A	36	LYS	1	0.865	0.915	4.821	-1.175	-1.103	-0.001	-0.003	-0.067	0.000
37	A	37	TYR	0	0.002	0.001	5.395	-2.952	-2.952	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.042	-0.003	1.669	-3.435	-3.804	8.453	-3.353	-4.731	-0.004
39	A	39	VAL	0	-0.034	0.001	2.193	-29.387	-27.689	11.040	-5.485	-7.254	-0.047
40	A	40	GLN	0	0.000	0.022	2.883	11.104	10.203	0.133	1.785	-1.016	-0.001
41	A	41	VAL	0	0.022	0.004	4.914	-0.450	-0.440	-0.001	-0.016	0.008	0.000
42	A	42	ILE	0	-0.036	-0.013	7.268	1.078	1.078	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.006	-0.004	10.511	0.326	0.326	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.009	0.001	13.580	0.083	0.083	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.811	-0.895	15.973	-2.078	-2.078	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.015	0.001	19.372	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.823	-0.906	21.960	-1.205	-1.205	0.000	0.000	0.000	0.000
48	A	48	PRO	0	-0.022	-0.019	25.277	0.011	0.011	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.884	-0.940	27.015	-0.684	-0.684	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.044	-0.028	24.704	0.021	0.021	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.062	-0.045	18.397	-0.096	-0.096	0.000	0.000	0.000	0.000
52	A	52	PHE	0	-0.041	-0.020	23.761	0.066	0.066	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.035	0.020	22.182	0.015	0.015	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.029	-0.013	25.447	0.014	0.014	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.030	-0.019	27.646	0.010	0.010	0.000	0.000	0.000	0.000
56	A	56	GLN	0	-0.028	-0.007	28.706	-0.005	-0.005	0.000	0.000	0.000	0.000
57	A	57	SER	0	0.030	0.003	28.020	-0.024	-0.024	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.012	0.021	23.766	0.046	0.046	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.002	-0.038	24.710	-0.053	-0.053	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.867	-0.924	24.275	-0.733	-0.733	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.056	-0.048	22.951	-0.157	-0.157	0.000	0.000	0.000	0.000
62	A	62	HIS	0	-0.032	0.031	18.764	-0.158	-0.158	0.000	0.000	0.000	0.000
63	A	63	ILE	0	-0.012	-0.009	14.758	-0.183	-0.183	0.000	0.000	0.000	0.000
64	A	64	TRP	0	-0.042	-0.008	13.629	0.069	0.069	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.018	-0.001	8.397	-0.442	-0.442	0.000	0.000	0.000	0.000
66	A	66	GLN	0	0.006	0.017	9.171	0.375	0.375	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.011	-0.004	4.413	-1.524	-1.496	-0.001	-0.005	-0.022	0.000
68	A	68	THR	0	-0.027	-0.014	4.188	2.342	2.509	-0.001	-0.032	-0.133	0.000
69	A	69	ILE	0	-0.021	-0.021	2.189	-11.058	-7.270	4.333	-3.230	-4.891	0.006
70	A	70	ARG	1	0.780	0.858	1.792	-69.217	-77.643	34.488	-11.740	-14.323	0.136
71	A	71	SER	0	-0.011	0.003	3.718	-0.284	0.096	0.022	-0.145	-0.257	0.003
72	A	72	GLY	0	0.003	-0.003	7.030	1.439	1.439	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.880	0.957	1.964	-50.451	-49.966	4.689	-2.394	-2.781	0.041
74	A	74	THR	0	-0.012	-0.028	8.519	-1.744	-1.744	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.813	-0.919	11.749	4.606	4.606	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.865	0.925	14.232	-2.914	-2.914	0.000	0.000	0.000	0.000
77	A	77	GLN	0	0.007	0.010	9.952	0.202	0.202	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.835	0.911	8.751	-5.805	-5.805	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.909	-0.955	10.773	1.804	1.804	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.849	-0.916	13.237	2.281	2.281	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.003	0.014	6.007	-0.482	-0.482	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.025	0.010	10.286	-0.848	-0.848	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.029	0.008	11.776	-0.597	-0.597	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.847	0.925	11.443	-0.784	-0.784	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.003	0.011	7.459	-0.446	-0.446	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.021	-0.034	11.979	-0.291	-0.291	0.000	0.000	0.000	0.000
87	A	87	GLN	0	-0.039	-0.026	15.036	-0.191	-0.191	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.831	-0.907	13.338	-0.355	-0.355	0.000	0.000	0.000	0.000
89	A	89	ILE	0	-0.002	-0.007	11.375	-0.179	-0.179	0.000	0.000	0.000	0.000
90	A	90	ALA	0	0.008	0.017	15.780	-0.062	-0.062	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.014	-0.010	18.912	-0.006	-0.006	0.000	0.000	0.000	0.000
92	A	92	ILE	0	-0.104	-0.045	15.232	-0.038	-0.038	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.023	-0.022	17.691	-0.057	-0.057	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.040	0.006	20.847	0.036	0.036	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.047	-0.020	19.582	0.035	0.035	0.000	0.000	0.000	0.000
96	A	96	PRO	0	0.023	0.009	22.477	0.033	0.033	0.000	0.000	0.000	0.000
97	A	97	ASN	0	0.081	0.007	20.128	-0.121	-0.121	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.977	-0.972	19.725	-0.046	-0.046	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.823	-0.905	21.016	-0.448	-0.448	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.009	0.004	14.764	-0.159	-0.159	0.000	0.000	0.000	0.000
101	A	101	TRP	0	-0.078	-0.030	15.697	0.202	0.202	0.000	0.000	0.000	0.000
102	A	102	VAL	0	0.041	0.015	9.721	-0.301	-0.301	0.000	0.000	0.000	0.000
103	A	103	TYR	0	-0.031	-0.017	10.564	0.372	0.372	0.000	0.000	0.000	0.000
104	A	104	ILE	0	0.041	0.020	6.861	-0.485	-0.485	0.000	0.000	0.000	0.000
105	A	105	THR	0	-0.048	-0.014	7.286	-0.104	-0.104	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.849	-0.928	6.734	9.557	9.557	0.000	0.000	0.000	0.000
107	A	107	ILE	0	-0.028	-0.013	6.145	-2.312	-2.312	0.000	0.000	0.000	0.000
108	A	108	PRO	0	0.039	0.021	6.594	2.648	2.648	0.000	0.000	0.000	0.000
109	A	109	GLY	0	0.090	0.030	5.527	-0.888	-0.888	0.000	0.000	0.000	0.000
110	A	110	SER	0	-0.070	-0.021	6.299	-2.084	-2.084	0.000	0.000	0.000	0.000
111	A	111	ASN	0	-0.074	-0.050	8.360	-0.387	-0.387	0.000	0.000	0.000	0.000
112	A	112	MET	0	-0.006	0.021	2.897	-6.856	-4.750	1.068	-1.048	-2.127	0.004
113	A	113	THR	0	-0.046	-0.041	6.799	1.587	1.587	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.808	-0.907	2.124	-50.944	-49.469	7.218	-4.247	-4.446	-0.052
115	A	115	TYR	0	-0.047	-0.058	6.358	3.598	3.598	0.000	0.000	0.000	0.000
116	A	116	GLY	0	-0.048	-0.019	9.683	1.060	1.060	0.000	0.000	0.000	0.000
117	A	117	ARG	1	0.843	0.919	9.953	2.361	2.361	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.019	0.015	8.878	-1.073	-1.073	0.000	0.000	0.000	0.000
119	A	119	LEU	0	-0.006	0.010	2.490	-0.176	0.592	0.541	-0.325	-0.984	-0.002
120	A	120	MET	0	-0.046	-0.017	5.843	-0.018	-0.018	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.806	-0.902	5.686	11.546	11.546	0.000	0.000	0.000	0.000
122	A	122	PRO	0	0.003	-0.004	4.632	-0.610	-0.426	-0.001	-0.010	-0.172	0.000
123	A	123	GLY	0	-0.012	-0.007	6.535	-2.258	-2.258	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.838	-0.915	9.567	2.998	2.998	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.835	-0.918	5.273	16.093	16.179	-0.001	-0.002	-0.083	0.000
126	A	126	GLU	-1	-0.801	-0.903	9.019	2.493	2.493	0.000	0.000	0.000	0.000
127	A	127	LYS	1	0.851	0.912	12.500	-3.037	-3.037	0.000	0.000	0.000	0.000
128	A	128	TRP	0	-0.014	-0.014	7.245	-0.648	-0.648	0.000	0.000	0.000	0.000
129	A	129	PHE	0	0.046	0.031	9.798	-0.698	-0.698	0.000	0.000	0.000	0.000
130	A	130	ASN	0	-0.040	-0.026	11.154	-0.603	-0.603	0.000	0.000	0.000	0.000
131	A	131	SER	0	-0.057	-0.035	12.878	0.032	0.032	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.039	-0.005	10.262	-0.176	-0.176	0.000	0.000	0.000	0.000
133	A	133	PRO	0	-0.033	-0.016	14.377	0.183	0.183	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.832	-0.909	16.769	-0.678	-0.678	0.000	0.000	0.000	0.000
135	A	135	GLY	0	0.085	0.039	18.714	-0.039	-0.039	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.086	-0.054	12.046	-0.073	-0.073	0.000	0.000	0.000	0.000
137	A	137	ARG	1	0.892	0.938	13.679	0.408	0.408	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.931	-0.944	14.762	-0.913	-0.913	0.000	0.000	0.000	0.000
139	A	139	ARG	1	0.929	0.950	15.618	2.340	2.340	0.000	0.000	0.000	0.000
140	A	140	LEU	0	-0.042	0.002	8.790	-0.007	-0.007	0.000	0.000	0.000	0.000
141	A	141	THR	0	-0.029	-0.026	12.367	-0.008	-0.008	0.000	0.000	0.000	0.000
142	A	142	GLU	-1	-0.978	-0.980	14.274	-1.466	-1.466	0.000	0.000	0.000	0.000
143	A	143	LEU	0	-0.028	-0.013	10.672	-0.067	-0.067	0.000	0.000	0.000	0.000
144	A	144	GLU	-1	-0.834	-0.922	8.958	-2.440	-2.440	0.000	0.000	0.000	0.000
145	A	145	GLY	0	-0.037	0.000	12.509	0.508	0.508	0.000	0.000	0.000	0.000

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