FMO DATABASE

FMODB ID: JQV89

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	OptAll
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	-1382556.556328
FMO2-HF: Nuclear repulsion	1323764.641081
FMO2-HF: Total energy	-58791.915247
FMO2-MP2: Total energy	-58965.274483

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.
-210.455	-208.717	92.296	-38.383	-55.649	0.049

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 : 0.011 / q_NPA : 0.013

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	-0.015	2.214	3.187	5.675	2.239	-1.564	-3.163	-0.003
4	A	4	THR	0	-0.035	-0.009	5.352	0.899	0.934	-0.001	-0.002	-0.033	0.000
5	A	5	CYS	0	-0.031	-0.017	8.847	0.851	0.851	0.000	0.000	0.000	0.000
6	A	6	TRP	0	0.013	0.000	11.403	0.225	0.225	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.036	0.016	14.909	0.247	0.247	0.000	0.000	0.000	0.000
8	A	8	GLN	0	0.057	0.025	18.242	-0.025	-0.025	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.835	0.888	21.038	1.661	1.661	0.000	0.000	0.000	0.000
10	A	10	ILE	0	-0.075	-0.042	22.418	0.127	0.127	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.793	0.884	22.529	0.979	0.979	0.000	0.000	0.000	0.000
12	A	12	ILE	0	0.048	0.048	16.707	0.056	0.056	0.000	0.000	0.000	0.000
13	A	13	SER	0	0.033	0.007	20.161	-0.157	-0.157	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.985	0.969	19.142	1.666	1.666	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.895	-0.933	18.218	-1.455	-1.455	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.062	0.032	17.922	-0.088	-0.088	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.783	0.883	14.792	2.362	2.362	0.000	0.000	0.000	0.000
18	A	18	GLN	0	-0.074	-0.041	13.408	-0.594	-0.594	0.000	0.000	0.000	0.000
19	A	19	ARG	1	0.908	0.946	13.442	1.021	1.021	0.000	0.000	0.000	0.000
20	A	20	ILE	0	0.011	0.007	11.186	0.030	0.030	0.000	0.000	0.000	0.000
21	A	21	ALA	0	0.008	-0.003	9.203	-0.261	-0.261	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.860	-0.899	8.803	-2.990	-2.990	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.037	0.019	10.333	0.056	0.056	0.000	0.000	0.000	0.000
24	A	24	ILE	0	-0.025	-0.020	5.328	0.469	0.469	0.000	0.000	0.000	0.000
25	A	25	THR	0	-0.037	-0.030	5.937	-0.693	-0.693	0.000	0.000	0.000	0.000
26	A	26	ASP	-1	-0.839	-0.915	6.982	-0.330	-0.330	0.000	0.000	0.000	0.000
27	A	27	ALA	0	-0.080	-0.035	7.766	1.143	1.143	0.000	0.000	0.000	0.000
28	A	28	HIS	0	0.034	0.012	2.277	-25.452	-20.248	6.991	-3.901	-8.294	0.010
29	A	29	HIS	0	-0.081	-0.031	5.067	3.637	3.709	-0.001	-0.001	-0.071	0.000
30	A	30	GLU	-1	-0.822	-0.932	7.559	2.863	2.863	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.051	-0.011	5.587	-0.044	-0.044	0.000	0.000	0.000	0.000
32	A	32	ALA	0	-0.094	-0.069	7.257	3.341	3.341	0.000	0.000	0.000	0.000
33	A	33	HIS	0	-0.028	-0.014	8.468	1.795	1.795	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.009	0.025	3.893	0.259	0.747	0.006	-0.146	-0.348	0.001
35	A	35	PRO	0	-0.019	-0.002	5.170	-3.009	-2.905	-0.001	-0.005	-0.098	0.000
36	A	36	LYS	1	0.828	0.897	4.987	-2.244	-2.194	-0.001	-0.002	-0.046	0.000
37	A	37	TYR	0	0.019	0.001	6.040	-2.492	-2.492	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.061	-0.001	2.157	-2.950	-0.350	2.254	-1.737	-3.116	0.008
39	A	39	VAL	0	0.023	0.020	1.856	-40.249	-43.882	21.922	-8.762	-9.528	-0.089
40	A	40	GLN	0	0.005	0.024	2.974	11.196	11.207	0.107	0.920	-1.037	-0.001
41	A	41	VAL	0	0.029	0.002	4.487	-1.302	-1.274	-0.001	-0.028	0.002	0.000
42	A	42	ILE	0	-0.036	-0.014	7.132	1.018	1.018	0.000	0.000	0.000	0.000
43	A	43	PHE	0	0.011	0.003	10.308	0.388	0.388	0.000	0.000	0.000	0.000
44	A	44	ASN	0	-0.014	-0.004	13.306	0.096	0.096	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.797	-0.888	15.570	-2.191	-2.191	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.016	0.009	19.016	0.001	0.001	0.000	0.000	0.000	0.000
47	A	47	GLU	-1	-0.779	-0.882	21.860	-1.364	-1.364	0.000	0.000	0.000	0.000
48	A	48	PRO	0	0.001	-0.001	25.313	0.011	0.011	0.000	0.000	0.000	0.000
49	A	49	ASP	-1	-0.918	-0.949	27.126	-0.788	-0.788	0.000	0.000	0.000	0.000
50	A	50	SER	0	-0.080	-0.049	24.500	0.049	0.049	0.000	0.000	0.000	0.000
51	A	51	TYR	0	-0.042	-0.044	18.292	-0.142	-0.142	0.000	0.000	0.000	0.000
52	A	52	PHE	0	-0.044	-0.009	23.323	0.079	0.079	0.000	0.000	0.000	0.000
53	A	53	ILE	0	0.036	0.016	21.910	0.000	0.000	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.015	-0.007	25.115	0.024	0.024	0.000	0.000	0.000	0.000
55	A	55	ALA	0	-0.028	-0.013	27.583	0.019	0.019	0.000	0.000	0.000	0.000
56	A	56	GLN	0	-0.043	-0.018	28.683	0.004	0.004	0.000	0.000	0.000	0.000
57	A	57	SER	0	0.028	0.004	27.766	-0.020	-0.020	0.000	0.000	0.000	0.000
58	A	58	ALA	0	-0.015	0.008	23.517	0.048	0.048	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.022	-0.050	24.401	-0.028	-0.028	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.820	-0.885	24.018	-0.868	-0.868	0.000	0.000	0.000	0.000
61	A	61	ASN	0	-0.067	-0.052	22.667	-0.164	-0.164	0.000	0.000	0.000	0.000
62	A	62	HIS	0	-0.014	0.039	18.557	-0.171	-0.171	0.000	0.000	0.000	0.000
63	A	63	ILE	0	-0.020	-0.015	14.142	-0.194	-0.194	0.000	0.000	0.000	0.000
64	A	64	TRP	0	-0.030	-0.001	13.417	0.064	0.064	0.000	0.000	0.000	0.000
65	A	65	VAL	0	0.008	-0.013	8.409	-0.439	-0.439	0.000	0.000	0.000	0.000
66	A	66	GLN	0	0.008	0.024	8.667	0.334	0.334	0.000	0.000	0.000	0.000
67	A	67	ALA	0	0.027	0.014	4.169	-1.671	-1.617	-0.001	-0.008	-0.046	0.000
68	A	68	THR	0	-0.049	-0.026	3.606	2.628	2.936	0.000	-0.077	-0.231	0.000
69	A	69	ILE	0	-0.013	-0.021	2.176	-13.704	-10.617	7.209	-4.339	-5.957	-0.009
70	A	70	ARG	1	0.756	0.828	1.793	-70.514	-81.772	34.639	-10.487	-12.895	0.126
71	A	71	SER	0	-0.063	-0.037	3.818	-0.357	0.021	0.018	-0.200	-0.195	0.002
72	A	72	GLY	0	0.010	0.007	6.850	2.292	2.292	0.000	0.000	0.000	0.000
73	A	73	ARG	1	0.870	0.951	1.805	-53.660	-56.823	9.864	-3.336	-3.364	0.053
74	A	74	THR	0	-0.008	-0.030	8.394	-1.972	-1.972	0.000	0.000	0.000	0.000
75	A	75	GLU	-1	-0.813	-0.915	11.903	4.525	4.525	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.880	0.939	14.085	-3.057	-3.057	0.000	0.000	0.000	0.000
77	A	77	GLN	0	0.008	0.022	10.338	0.126	0.126	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.818	0.899	8.868	-6.026	-6.026	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.918	-0.964	11.048	1.672	1.672	0.000	0.000	0.000	0.000
80	A	80	GLU	-1	-0.847	-0.921	13.399	2.345	2.345	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.006	0.012	5.826	-0.478	-0.478	0.000	0.000	0.000	0.000
82	A	82	LEU	0	0.014	0.006	10.145	-0.894	-0.894	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.006	0.009	12.007	-0.558	-0.558	0.000	0.000	0.000	0.000
84	A	84	ARG	1	0.833	0.918	11.109	-0.560	-0.560	0.000	0.000	0.000	0.000
85	A	85	LEU	0	0.009	0.000	7.199	-0.436	-0.436	0.000	0.000	0.000	0.000
86	A	86	THR	0	-0.023	-0.031	11.704	-0.343	-0.343	0.000	0.000	0.000	0.000
87	A	87	GLN	0	-0.049	-0.034	15.125	-0.172	-0.172	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.822	-0.891	12.742	-0.572	-0.572	0.000	0.000	0.000	0.000
89	A	89	ILE	0	0.002	-0.004	11.342	-0.169	-0.169	0.000	0.000	0.000	0.000
90	A	90	ALA	0	0.013	0.019	15.685	-0.045	-0.045	0.000	0.000	0.000	0.000
91	A	91	LEU	0	-0.016	-0.012	18.876	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	92	ILE	0	-0.096	-0.046	15.067	-0.018	-0.018	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.024	-0.021	17.538	-0.063	-0.063	0.000	0.000	0.000	0.000
94	A	94	GLY	0	-0.040	0.000	20.605	0.040	0.040	0.000	0.000	0.000	0.000
95	A	95	ILE	0	-0.055	-0.025	19.867	0.051	0.051	0.000	0.000	0.000	0.000
96	A	96	PRO	0	0.000	0.002	22.610	0.029	0.029	0.000	0.000	0.000	0.000
97	A	97	ASN	0	0.065	0.002	20.352	-0.133	-0.133	0.000	0.000	0.000	0.000
98	A	98	GLU	-1	-0.907	-0.948	19.803	-0.189	-0.189	0.000	0.000	0.000	0.000
99	A	99	GLU	-1	-0.826	-0.901	20.943	-0.661	-0.661	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.026	-0.008	14.946	-0.178	-0.178	0.000	0.000	0.000	0.000
101	A	101	TRP	0	-0.062	-0.021	15.694	0.187	0.187	0.000	0.000	0.000	0.000
102	A	102	VAL	0	0.024	0.012	9.744	-0.310	-0.310	0.000	0.000	0.000	0.000
103	A	103	TYR	0	-0.012	-0.012	10.442	0.450	0.450	0.000	0.000	0.000	0.000
104	A	104	ILE	0	0.020	0.001	6.993	-0.540	-0.540	0.000	0.000	0.000	0.000
105	A	105	THR	0	-0.016	-0.005	6.984	0.057	0.057	0.000	0.000	0.000	0.000
106	A	106	GLU	-1	-0.836	-0.907	6.636	9.073	9.073	0.000	0.000	0.000	0.000
107	A	107	ILE	0	-0.042	-0.023	5.967	-2.224	-2.224	0.000	0.000	0.000	0.000
108	A	108	PRO	0	0.038	0.032	6.652	2.724	2.724	0.000	0.000	0.000	0.000
109	A	109	GLY	0	0.055	0.008	5.643	-1.461	-1.461	0.000	0.000	0.000	0.000
110	A	110	SER	0	-0.035	-0.027	6.499	-1.993	-1.993	0.000	0.000	0.000	0.000
111	A	111	ASN	0	-0.084	-0.036	8.998	-0.305	-0.305	0.000	0.000	0.000	0.000
112	A	112	MET	0	0.006	0.031	2.504	-5.339	-3.944	1.851	-0.911	-2.335	0.000
113	A	113	THR	0	-0.056	-0.049	6.393	1.888	1.888	0.000	0.000	0.000	0.000
114	A	114	GLU	-1	-0.840	-0.917	2.114	-49.631	-47.318	4.670	-3.407	-3.577	-0.047
115	A	115	TYR	0	-0.047	-0.057	6.442	3.594	3.594	0.000	0.000	0.000	0.000
116	A	116	GLY	0	-0.022	-0.001	10.233	1.010	1.010	0.000	0.000	0.000	0.000
117	A	117	ARG	1	0.810	0.894	10.149	2.060	2.060	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.037	0.024	8.802	-1.084	-1.084	0.000	0.000	0.000	0.000
119	A	119	LEU	0	0.015	0.019	2.587	-0.220	0.503	0.532	-0.310	-0.945	-0.002
120	A	120	MET	0	-0.041	-0.011	6.066	-0.090	-0.090	0.000	0.000	0.000	0.000
121	A	121	GLU	-1	-0.747	-0.862	5.838	12.622	12.622	0.000	0.000	0.000	0.000
122	A	122	PRO	0	-0.049	-0.034	4.027	-0.244	0.076	0.001	-0.078	-0.242	0.000
123	A	123	GLY	0	-0.023	0.002	6.104	-2.926	-2.926	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.821	-0.901	8.483	2.724	2.724	0.000	0.000	0.000	0.000
125	A	125	GLU	-1	-0.716	-0.854	5.235	18.626	18.760	-0.001	-0.002	-0.130	0.000
126	A	126	GLU	-1	-0.842	-0.917	8.906	2.734	2.734	0.000	0.000	0.000	0.000
127	A	127	LYS	1	0.840	0.896	12.517	-3.909	-3.909	0.000	0.000	0.000	0.000
128	A	128	TRP	0	-0.021	-0.022	7.846	-0.618	-0.618	0.000	0.000	0.000	0.000
129	A	129	PHE	0	0.052	0.042	10.410	-0.775	-0.775	0.000	0.000	0.000	0.000
130	A	130	ASN	0	-0.083	-0.051	11.728	-0.714	-0.714	0.000	0.000	0.000	0.000
131	A	131	SER	0	-0.031	-0.019	13.135	-0.133	-0.133	0.000	0.000	0.000	0.000
132	A	132	LEU	0	-0.031	-0.003	10.567	-0.279	-0.279	0.000	0.000	0.000	0.000
133	A	133	PRO	0	-0.029	-0.015	14.852	0.213	0.213	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.790	-0.876	17.456	-0.538	-0.538	0.000	0.000	0.000	0.000
135	A	135	GLY	0	0.099	0.049	18.637	-0.047	-0.047	0.000	0.000	0.000	0.000
136	A	136	LEU	0	-0.129	-0.054	12.539	-0.178	-0.178	0.000	0.000	0.000	0.000
137	A	137	ARG	1	0.875	0.908	13.989	0.058	0.058	0.000	0.000	0.000	0.000
138	A	138	GLU	-1	-0.915	-0.941	15.023	-0.902	-0.902	0.000	0.000	0.000	0.000
139	A	139	ARG	1	0.899	0.926	15.817	2.115	2.115	0.000	0.000	0.000	0.000
140	A	140	LEU	0	-0.033	-0.006	8.921	-0.084	-0.084	0.000	0.000	0.000	0.000
141	A	141	THR	0	-0.013	-0.024	11.899	-0.037	-0.037	0.000	0.000	0.000	0.000
142	A	142	GLU	-1	-0.994	-0.985	14.025	-1.481	-1.481	0.000	0.000	0.000	0.000
143	A	143	LEU	0	0.008	0.014	10.789	-0.028	-0.028	0.000	0.000	0.000	0.000
144	A	144	GLU	-1	-0.830	-0.891	8.917	-1.884	-1.884	0.000	0.000	0.000	0.000
145	A	145	GLY	0	-0.063	-0.041	12.579	0.607	0.607	0.000	0.000	0.000	0.000

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