FMO DATABASE

FMODB ID: Z66QN

Calculation Name: 5LCY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LCY

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2023-06-21

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	88
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-527177.77726
FMO2-HF: Nuclear repulsion	492387.860006
FMO2-HF: Total energy	-34789.917255
FMO2-MP2: Total energy	-34890.08162

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:2:PRO)

Summations of interaction energy for fragment #1(A:2:PRO)

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.
-11.137	-1.665	12.2	-7.762	-13.909	-0.019

Interaction energy analysis for fragmet #1(A:2:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.058 / q_NPA : 0.032

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

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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	4	SER	0	-0.018	-0.030	3.882	-0.394	1.395	-0.011	-0.873	-0.906	0.003
4	A	5	PRO	0	0.035	0.005	3.602	-1.007	-0.671	0.010	-0.187	-0.159	-0.001
5	A	6	GLU	-1	-0.764	-0.867	5.755	-0.086	-0.086	0.000	0.000	0.000	0.000
6	A	7	ASP	-1	-0.771	-0.849	2.294	-0.074	0.115	1.323	-0.538	-0.973	0.000
7	A	8	LYS	1	0.838	0.896	2.344	1.924	4.595	2.992	-2.007	-3.656	-0.002
8	A	9	LYS	1	0.806	0.897	3.285	0.989	0.601	0.053	0.581	-0.245	0.000
9	A	10	ARG	1	0.759	0.856	5.508	-0.632	-0.632	0.000	0.000	0.000	0.000
10	A	11	ILE	0	0.048	0.029	2.509	-1.100	-0.157	0.453	-0.255	-1.141	0.000
11	A	12	LEU	0	-0.005	-0.002	5.257	-0.110	-0.110	0.000	0.000	0.000	0.000
12	A	13	THR	0	-0.045	-0.041	6.885	-0.068	-0.068	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.853	0.916	8.337	-0.596	-0.596	0.000	0.000	0.000	0.000
14	A	15	VAL	0	0.013	0.011	7.547	-0.051	-0.051	0.000	0.000	0.000	0.000
15	A	16	ARG	1	0.949	0.974	10.208	-0.045	-0.045	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.910	0.966	12.693	-0.190	-0.190	0.000	0.000	0.000	0.000
17	A	18	ILE	0	0.047	0.021	11.367	-0.027	-0.027	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.861	0.917	14.304	-0.114	-0.114	0.000	0.000	0.000	0.000
19	A	20	GLY	0	0.023	0.007	16.110	-0.019	-0.019	0.000	0.000	0.000	0.000
20	A	21	GLN	0	-0.096	-0.054	16.954	0.003	0.003	0.000	0.000	0.000	0.000
21	A	22	VAL	0	0.017	0.006	17.491	-0.008	-0.008	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.735	-0.841	20.158	0.065	0.065	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.082	-0.022	22.328	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	25	LEU	0	0.014	0.005	22.527	-0.005	-0.005	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.957	-0.974	23.664	0.090	0.090	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.954	0.961	23.219	-0.081	-0.081	0.000	0.000	0.000	0.000
27	A	28	ALA	0	0.001	0.021	27.874	-0.006	-0.006	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.071	-0.040	26.850	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.947	-0.975	29.180	0.056	0.056	0.000	0.000	0.000	0.000
30	A	31	SER	0	-0.069	-0.046	31.941	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	32	GLY	0	-0.043	-0.006	33.777	-0.003	-0.003	0.000	0.000	0.000	0.000
32	A	33	GLU	-1	-0.924	-0.968	31.338	0.074	0.074	0.000	0.000	0.000	0.000
33	A	34	PRO	0	-0.005	-0.016	34.316	0.003	0.003	0.000	0.000	0.000	0.000
34	A	35	CYS	0	0.025	-0.004	33.160	0.004	0.004	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.008	0.011	31.808	0.007	0.007	0.000	0.000	0.000	0.000
36	A	37	ALA	0	0.083	0.042	30.378	0.008	0.008	0.000	0.000	0.000	0.000
37	A	38	ILE	0	0.037	0.026	28.248	0.010	0.010	0.000	0.000	0.000	0.000
38	A	39	LEU	0	0.001	0.001	26.985	0.012	0.012	0.000	0.000	0.000	0.000
39	A	40	GLN	0	-0.003	-0.015	26.503	0.010	0.010	0.000	0.000	0.000	0.000
40	A	41	GLN	0	0.013	0.005	23.993	0.016	0.016	0.000	0.000	0.000	0.000
41	A	42	ILE	0	0.020	0.014	22.420	0.020	0.020	0.000	0.000	0.000	0.000
42	A	43	ALA	0	-0.026	-0.012	21.821	0.024	0.024	0.000	0.000	0.000	0.000
43	A	44	ALA	0	0.028	0.013	20.959	0.023	0.023	0.000	0.000	0.000	0.000
44	A	45	VAL	0	0.014	0.005	17.460	0.030	0.030	0.000	0.000	0.000	0.000
45	A	46	ARG	1	0.929	0.981	16.923	-0.228	-0.228	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.008	0.001	17.202	0.037	0.037	0.000	0.000	0.000	0.000
47	A	48	ALA	0	-0.007	-0.009	14.733	0.042	0.042	0.000	0.000	0.000	0.000
48	A	49	SER	0	-0.009	-0.022	12.784	0.075	0.075	0.000	0.000	0.000	0.000
49	A	50	ASN	0	-0.029	-0.014	12.411	0.052	0.052	0.000	0.000	0.000	0.000
50	A	51	GLY	0	0.031	0.022	12.809	0.059	0.059	0.000	0.000	0.000	0.000
51	A	52	LEU	0	-0.028	-0.022	6.448	0.073	0.073	0.000	0.000	0.000	0.000
52	A	53	MET	0	-0.008	0.006	8.011	0.315	0.315	0.000	0.000	0.000	0.000
53	A	54	SER	0	0.036	0.019	9.499	0.154	0.154	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.785	-0.863	7.067	0.720	0.720	0.000	0.000	0.000	0.000
55	A	56	MET	0	0.002	-0.001	2.558	-3.977	-2.807	2.240	-0.882	-2.528	0.003
56	A	57	VAL	0	0.001	0.003	5.791	0.812	0.812	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.778	-0.861	8.268	0.828	0.828	0.000	0.000	0.000	0.000
58	A	59	ILE	0	-0.039	-0.004	2.217	-1.541	-0.810	3.607	-1.752	-2.586	-0.002
59	A	60	HIS	0	0.037	0.031	5.127	-0.072	-0.072	0.000	0.000	0.000	0.000
60	A	61	LEU	0	0.011	-0.006	5.870	-0.738	-0.738	0.000	0.000	0.000	0.000
61	A	62	LYS	1	0.857	0.901	7.286	-0.959	-0.959	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.792	-0.898	2.490	-4.602	-2.621	1.534	-1.845	-1.671	-0.020
63	A	64	HIS	0	-0.049	-0.017	4.426	-0.999	-0.949	-0.001	-0.004	-0.044	0.000
64	A	65	LEU	0	-0.038	-0.018	8.922	-0.091	-0.091	0.000	0.000	0.000	0.000
65	A	66	VAL	0	-0.040	-0.009	10.738	-0.030	-0.030	0.000	0.000	0.000	0.000
66	A	67	SER	0	-0.032	-0.019	8.844	-0.084	-0.084	0.000	0.000	0.000	0.000
67	A	68	GLY	0	-0.019	-0.007	10.923	-0.028	-0.028	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.903	-0.943	13.222	-0.042	-0.042	0.000	0.000	0.000	0.000
69	A	70	THR	0	-0.040	-0.033	14.012	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.027	-0.041	17.326	0.022	0.022	0.000	0.000	0.000	0.000
71	A	72	PRO	0	0.016	-0.011	18.405	0.012	0.012	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.794	-0.868	19.326	0.023	0.023	0.000	0.000	0.000	0.000
73	A	74	GLN	0	0.018	0.012	15.439	0.015	0.015	0.000	0.000	0.000	0.000
74	A	75	ARG	1	0.898	0.954	14.417	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	76	ALA	0	0.004	0.003	15.413	0.054	0.054	0.000	0.000	0.000	0.000
76	A	77	VAL	0	-0.014	-0.005	14.575	0.032	0.032	0.000	0.000	0.000	0.000
77	A	78	ARG	1	0.921	0.954	10.815	0.147	0.147	0.000	0.000	0.000	0.000
78	A	79	MET	0	-0.023	0.002	11.905	0.149	0.149	0.000	0.000	0.000	0.000
79	A	80	ALA	0	-0.013	-0.012	14.466	0.049	0.049	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.936	-0.971	11.179	0.184	0.184	0.000	0.000	0.000	0.000
81	A	82	ILE	0	-0.019	-0.003	9.145	0.078	0.078	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.035	0.015	12.695	0.012	0.012	0.000	0.000	0.000	0.000
83	A	84	HIS	0	0.018	0.003	16.358	-0.032	-0.032	0.000	0.000	0.000	0.000
84	A	85	LEU	0	0.024	0.008	10.853	-0.019	-0.019	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.008	-0.002	13.055	0.004	0.004	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.877	0.935	16.078	-0.297	-0.297	0.000	0.000	0.000	0.000
87	A	88	ALA	0	-0.032	-0.001	16.980	-0.028	-0.028	0.000	0.000	0.000	0.000
88	A	89	TYR	0	-0.070	-0.042	14.150	-0.042	-0.042	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:PRO)