FMO DATABASE

FMODB ID: 6NNQZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-524069.380582
FMO2-HF: Nuclear repulsion	489279.658824
FMO2-HF: Total energy	-34789.721757
FMO2-MP2: Total energy	-34889.870809

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.
-10.301	-0.425	8.497	-6.355	-12.02	-0.002

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 : 0.066 / q_NPA : 0.029

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	4	SER	0	0.009	-0.008	3.813	-0.802	1.137	-0.019	-0.929	-0.992	0.004
4	A	5	PRO	0	0.072	0.020	3.904	-0.338	-0.142	0.002	-0.062	-0.136	0.000
5	A	6	GLU	-1	-0.778	-0.868	5.991	0.049	0.049	0.000	0.000	0.000	0.000
6	A	7	ASP	-1	-0.769	-0.865	2.591	-0.053	0.431	0.365	-0.257	-0.592	0.000
7	A	8	LYS	1	0.824	0.892	2.283	0.749	4.184	1.853	-2.034	-3.254	0.000
8	A	9	LYS	1	0.788	0.879	3.222	0.485	0.256	0.048	0.407	-0.226	0.000
9	A	10	ARG	1	0.847	0.923	5.479	-0.630	-0.630	0.000	0.000	0.000	0.000
10	A	11	ILE	0	0.053	0.033	2.616	-1.059	-0.099	0.349	-0.232	-1.078	0.000
11	A	12	LEU	0	0.001	0.009	5.292	-0.094	-0.094	0.000	0.000	0.000	0.000
12	A	13	THR	0	-0.048	-0.047	6.849	-0.043	-0.043	0.000	0.000	0.000	0.000
13	A	14	ARG	1	0.867	0.921	8.163	-0.558	-0.558	0.000	0.000	0.000	0.000
14	A	15	VAL	0	0.031	0.019	7.467	-0.040	-0.040	0.000	0.000	0.000	0.000
15	A	16	ARG	1	0.941	0.969	10.080	-0.027	-0.027	0.000	0.000	0.000	0.000
16	A	17	ARG	1	0.930	0.974	12.585	-0.166	-0.166	0.000	0.000	0.000	0.000
17	A	18	ILE	0	0.049	0.025	11.318	-0.017	-0.017	0.000	0.000	0.000	0.000
18	A	19	ARG	1	0.845	0.902	14.054	-0.077	-0.077	0.000	0.000	0.000	0.000
19	A	20	GLY	0	0.019	0.011	15.819	-0.014	-0.014	0.000	0.000	0.000	0.000
20	A	21	GLN	0	-0.076	-0.042	16.902	0.005	0.005	0.000	0.000	0.000	0.000
21	A	22	VAL	0	0.039	0.012	17.416	-0.006	-0.006	0.000	0.000	0.000	0.000
22	A	23	GLU	-1	-0.800	-0.875	19.713	0.045	0.045	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.070	-0.035	21.897	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	25	LEU	0	-0.003	0.000	22.335	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	26	GLU	-1	-0.968	-0.986	23.599	0.063	0.063	0.000	0.000	0.000	0.000
26	A	27	ARG	1	0.992	0.994	23.435	-0.065	-0.065	0.000	0.000	0.000	0.000
27	A	28	ALA	0	0.005	0.016	27.803	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.055	-0.033	26.797	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.944	-0.964	29.001	0.042	0.042	0.000	0.000	0.000	0.000
30	A	31	SER	0	-0.069	-0.044	31.713	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	32	GLY	0	-0.038	-0.002	33.748	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	33	GLU	-1	-0.945	-0.975	31.584	0.061	0.061	0.000	0.000	0.000	0.000
33	A	34	PRO	0	-0.014	-0.021	34.168	0.002	0.002	0.000	0.000	0.000	0.000
34	A	35	CYS	0	0.028	0.001	33.153	0.003	0.003	0.000	0.000	0.000	0.000
35	A	36	LEU	0	-0.012	0.006	31.885	0.006	0.006	0.000	0.000	0.000	0.000
36	A	37	ALA	0	0.070	0.036	30.557	0.007	0.007	0.000	0.000	0.000	0.000
37	A	38	ILE	0	0.070	0.035	27.986	0.009	0.009	0.000	0.000	0.000	0.000
38	A	39	LEU	0	-0.007	0.006	26.975	0.010	0.010	0.000	0.000	0.000	0.000
39	A	40	GLN	0	0.010	-0.008	26.518	0.009	0.009	0.000	0.000	0.000	0.000
40	A	41	GLN	0	0.006	0.001	24.072	0.015	0.015	0.000	0.000	0.000	0.000
41	A	42	ILE	0	0.025	0.014	22.423	0.016	0.016	0.000	0.000	0.000	0.000
42	A	43	ALA	0	-0.035	-0.016	21.854	0.021	0.021	0.000	0.000	0.000	0.000
43	A	44	ALA	0	0.005	-0.002	20.945	0.020	0.020	0.000	0.000	0.000	0.000
44	A	45	VAL	0	0.043	0.025	17.263	0.027	0.027	0.000	0.000	0.000	0.000
45	A	46	ARG	1	0.935	0.991	16.979	-0.199	-0.199	0.000	0.000	0.000	0.000
46	A	47	GLY	0	0.014	0.002	17.106	0.034	0.034	0.000	0.000	0.000	0.000
47	A	48	ALA	0	-0.013	-0.012	14.506	0.038	0.038	0.000	0.000	0.000	0.000
48	A	49	SER	0	-0.022	-0.032	12.874	0.063	0.063	0.000	0.000	0.000	0.000
49	A	50	ASN	0	-0.039	-0.026	12.337	0.050	0.050	0.000	0.000	0.000	0.000
50	A	51	GLY	0	0.035	0.022	12.914	0.058	0.058	0.000	0.000	0.000	0.000
51	A	52	LEU	0	-0.019	-0.013	6.322	0.070	0.070	0.000	0.000	0.000	0.000
52	A	53	MET	0	-0.018	0.005	7.931	0.289	0.289	0.000	0.000	0.000	0.000
53	A	54	SER	0	0.047	0.021	9.257	0.180	0.180	0.000	0.000	0.000	0.000
54	A	55	GLU	-1	-0.812	-0.891	7.209	0.699	0.699	0.000	0.000	0.000	0.000
55	A	56	MET	0	0.003	0.001	2.486	-4.448	-3.586	3.089	-1.092	-2.859	0.003
56	A	57	VAL	0	-0.001	-0.002	5.801	0.789	0.789	0.000	0.000	0.000	0.000
57	A	58	GLU	-1	-0.883	-0.917	8.582	0.650	0.650	0.000	0.000	0.000	0.000
58	A	59	ILE	0	-0.032	-0.023	2.293	-1.315	-0.574	2.719	-1.435	-2.025	-0.003
59	A	60	HIS	0	0.036	0.020	4.912	0.107	0.274	-0.001	-0.011	-0.155	0.000
60	A	61	LEU	0	-0.010	-0.016	5.832	-0.763	-0.763	0.000	0.000	0.000	0.000
61	A	62	LYS	1	0.894	0.927	7.356	-0.884	-0.884	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.861	-0.927	3.165	-2.401	-1.155	0.093	-0.705	-0.634	-0.006
63	A	64	HIS	0	-0.055	-0.024	4.190	-0.973	-0.898	-0.001	-0.005	-0.069	0.000
64	A	65	LEU	0	-0.032	-0.017	9.173	-0.082	-0.082	0.000	0.000	0.000	0.000
65	A	66	VAL	0	-0.048	-0.012	10.876	-0.051	-0.051	0.000	0.000	0.000	0.000
66	A	67	SER	0	-0.020	-0.010	9.378	-0.069	-0.069	0.000	0.000	0.000	0.000
67	A	68	GLY	0	-0.023	-0.010	11.590	-0.025	-0.025	0.000	0.000	0.000	0.000
68	A	69	GLU	-1	-0.925	-0.956	13.702	-0.026	-0.026	0.000	0.000	0.000	0.000
69	A	70	THR	0	-0.022	-0.004	13.894	0.006	0.006	0.000	0.000	0.000	0.000
70	A	71	THR	0	-0.008	-0.027	17.222	0.017	0.017	0.000	0.000	0.000	0.000
71	A	72	PRO	0	0.031	-0.011	18.489	0.008	0.008	0.000	0.000	0.000	0.000
72	A	73	ASP	-1	-0.811	-0.882	19.596	0.014	0.014	0.000	0.000	0.000	0.000
73	A	74	GLN	0	0.010	0.006	15.606	0.011	0.011	0.000	0.000	0.000	0.000
74	A	75	ARG	1	0.889	0.934	14.718	-0.027	-0.027	0.000	0.000	0.000	0.000
75	A	76	ALA	0	0.001	0.010	15.614	0.048	0.048	0.000	0.000	0.000	0.000
76	A	77	VAL	0	-0.009	-0.005	14.882	0.028	0.028	0.000	0.000	0.000	0.000
77	A	78	ARG	1	0.908	0.954	11.238	0.130	0.130	0.000	0.000	0.000	0.000
78	A	79	MET	0	-0.018	-0.004	12.374	0.112	0.112	0.000	0.000	0.000	0.000
79	A	80	ALA	0	-0.012	-0.012	14.598	0.046	0.046	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.943	-0.969	11.506	0.113	0.113	0.000	0.000	0.000	0.000
81	A	82	ILE	0	-0.029	-0.011	9.311	0.064	0.064	0.000	0.000	0.000	0.000
82	A	83	GLY	0	0.023	0.013	12.870	0.022	0.022	0.000	0.000	0.000	0.000
83	A	84	HIS	0	-0.003	-0.021	16.251	-0.012	-0.012	0.000	0.000	0.000	0.000
84	A	85	LEU	0	0.027	0.006	10.734	-0.014	-0.014	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.003	0.006	13.148	0.009	0.009	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.915	0.961	16.007	-0.251	-0.251	0.000	0.000	0.000	0.000
87	A	88	ALA	0	-0.040	-0.008	17.326	-0.019	-0.019	0.000	0.000	0.000	0.000
88	A	89	TYR	0	-0.054	-0.015	14.251	-0.025	-0.025	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Manual

Support

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