FMO DATABASE

FMODB ID: 14Z1Z

Calculation Name: 4IYL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4IYL

Chain ID: A

ChEMBL ID:

UniProt ID: Q0PA13

Base Structure: X-ray

Registration Date: 2023-06-20

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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-446021.431798
FMO2-HF: Nuclear repulsion	413319.514562
FMO2-HF: Total energy	-32701.917237
FMO2-MP2: Total energy	-32800.49138

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:3:LEU)

Summations of interaction energy for fragment #1(A:3:LEU)

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.
-8.827	-4.508	9.971	-4.283	-10.005	-0.001

Interaction energy analysis for fragmet #1(A:3:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.029 / q_NPA : -0.022

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	5	SER	0	-0.026	-0.036	3.163	-2.711	-0.220	0.099	-1.364	-1.226	0.000
4	A	6	ALA	0	0.029	0.024	5.821	0.237	0.237	0.000	0.000	0.000	0.000
5	A	7	LYS	1	1.052	1.019	3.040	-1.540	-0.978	0.066	-0.151	-0.476	-0.001
6	A	8	LYS	1	0.901	0.952	2.140	-1.113	-0.348	3.231	-0.925	-3.072	0.002
7	A	9	ALA	0	0.009	0.001	4.295	0.020	0.184	0.002	-0.057	-0.108	0.000
8	A	10	GLU	-1	-0.929	-0.955	7.554	0.154	0.154	0.000	0.000	0.000	0.000
9	A	11	ILE	0	-0.059	-0.035	4.814	0.020	0.020	0.000	0.000	0.000	0.000
10	A	12	VAL	0	0.002	0.006	7.516	0.015	0.015	0.000	0.000	0.000	0.000
11	A	13	ALA	0	0.008	0.007	9.782	0.003	0.003	0.000	0.000	0.000	0.000
12	A	14	LYS	1	0.909	0.974	11.669	-0.019	-0.019	0.000	0.000	0.000	0.000
13	A	15	PHE	0	-0.068	-0.055	10.152	-0.003	-0.003	0.000	0.000	0.000	0.000
14	A	16	ALA	0	0.042	0.042	13.247	0.002	0.002	0.000	0.000	0.000	0.000
15	A	17	LYS	1	0.886	0.941	15.167	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	18	LYS	1	0.947	0.971	18.442	0.007	0.007	0.000	0.000	0.000	0.000
17	A	19	PRO	0	0.028	0.004	18.365	0.000	0.000	0.000	0.000	0.000	0.000
18	A	20	GLY	0	0.023	0.013	17.557	0.000	0.000	0.000	0.000	0.000	0.000
19	A	21	ASP	-1	-0.835	-0.893	14.487	0.014	0.014	0.000	0.000	0.000	0.000
20	A	22	THR	0	0.006	-0.015	10.705	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	23	GLY	0	-0.018	-0.021	11.200	0.025	0.025	0.000	0.000	0.000	0.000
22	A	24	SER	0	0.001	0.011	13.479	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	25	THR	0	-0.004	-0.018	13.461	0.012	0.012	0.000	0.000	0.000	0.000
24	A	26	GLU	-1	-0.825	-0.929	13.566	0.007	0.007	0.000	0.000	0.000	0.000
25	A	27	VAL	0	0.023	0.027	9.327	0.001	0.001	0.000	0.000	0.000	0.000
26	A	28	GLN	0	-0.009	0.000	9.051	0.034	0.034	0.000	0.000	0.000	0.000
27	A	29	VAL	0	0.018	0.021	8.711	0.023	0.023	0.000	0.000	0.000	0.000
28	A	30	ALA	0	0.014	0.017	8.681	-0.036	-0.036	0.000	0.000	0.000	0.000
29	A	31	LEU	0	-0.038	-0.040	4.494	-0.209	-0.044	-0.001	-0.008	-0.155	0.000
30	A	32	LEU	0	-0.061	-0.026	4.133	-0.130	0.070	0.000	-0.030	-0.170	0.000
31	A	33	THR	0	-0.022	-0.011	6.165	-0.145	-0.145	0.000	0.000	0.000	0.000
32	A	34	ALA	0	0.033	0.021	3.105	-0.502	-0.033	0.076	-0.128	-0.417	-0.001
33	A	35	ARG	1	0.965	0.984	2.263	-1.319	-2.597	5.303	-0.997	-3.029	0.000
34	A	36	ILE	0	-0.007	-0.007	3.645	-0.209	-0.098	0.018	-0.005	-0.123	0.000
35	A	37	ALA	0	-0.008	-0.004	6.692	0.088	0.088	0.000	0.000	0.000	0.000
36	A	38	GLU	-1	-0.880	-0.944	2.104	-2.489	-1.819	1.177	-0.618	-1.229	-0.001
37	A	39	LEU	0	-0.031	-0.024	5.589	0.366	0.366	0.000	0.000	0.000	0.000
38	A	40	THR	0	-0.052	-0.017	8.201	0.186	0.186	0.000	0.000	0.000	0.000
39	A	41	GLU	-1	-0.950	-0.992	8.959	0.267	0.267	0.000	0.000	0.000	0.000
40	A	42	HIS	0	0.031	0.024	9.383	0.098	0.098	0.000	0.000	0.000	0.000
41	A	43	LEU	0	0.012	0.001	10.853	0.053	0.053	0.000	0.000	0.000	0.000
42	A	44	LYS	1	0.898	0.954	13.405	0.018	0.018	0.000	0.000	0.000	0.000
43	A	45	ILE	0	0.023	-0.002	12.715	0.005	0.005	0.000	0.000	0.000	0.000
44	A	46	TYR	0	0.026	0.036	14.921	0.010	0.010	0.000	0.000	0.000	0.000
45	A	47	LYS	1	0.992	0.992	16.693	0.027	0.027	0.000	0.000	0.000	0.000
46	A	48	LYS	1	0.919	0.956	17.868	-0.060	-0.060	0.000	0.000	0.000	0.000
47	A	49	ASP	-1	-0.858	-0.929	17.658	0.079	0.079	0.000	0.000	0.000	0.000
48	A	50	PHE	0	-0.026	-0.004	20.394	0.000	0.000	0.000	0.000	0.000	0.000
49	A	51	SER	0	-0.039	-0.043	22.388	-0.002	-0.002	0.000	0.000	0.000	0.000
50	A	52	SER	0	-0.068	-0.023	23.213	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	53	ARG	1	0.958	0.981	19.574	-0.043	-0.043	0.000	0.000	0.000	0.000
52	A	54	LEU	0	0.026	0.014	24.955	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	55	GLY	0	-0.008	0.014	27.970	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	56	LEU	0	0.054	0.033	26.858	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	57	LEU	0	0.029	-0.008	25.939	-0.001	-0.001	0.000	0.000	0.000	0.000
56	A	58	LYS	1	0.961	0.993	29.696	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	59	LEU	0	0.043	0.020	32.498	-0.001	-0.001	0.000	0.000	0.000	0.000
58	A	60	VAL	0	0.026	0.016	30.680	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	61	GLY	0	-0.024	-0.031	33.579	0.000	0.000	0.000	0.000	0.000	0.000
60	A	62	GLN	0	0.017	-0.008	35.234	0.001	0.001	0.000	0.000	0.000	0.000
61	A	63	ARG	1	1.018	1.016	34.634	0.003	0.003	0.000	0.000	0.000	0.000
62	A	64	LYS	1	0.913	0.982	35.117	-0.011	-0.011	0.000	0.000	0.000	0.000
63	A	65	ARG	1	0.959	0.964	37.170	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	66	LEU	0	0.011	0.020	41.404	0.000	0.000	0.000	0.000	0.000	0.000
65	A	67	LEU	0	0.073	0.036	39.983	0.000	0.000	0.000	0.000	0.000	0.000
66	A	68	SER	0	-0.084	-0.036	41.901	0.000	0.000	0.000	0.000	0.000	0.000
67	A	69	TYR	0	0.012	-0.005	44.470	0.000	0.000	0.000	0.000	0.000	0.000
68	A	70	LEU	0	-0.006	0.012	46.558	0.000	0.000	0.000	0.000	0.000	0.000
69	A	71	LYS	1	0.935	0.972	42.991	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	72	ARG	1	0.919	0.969	48.642	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	73	LYS	1	0.952	0.980	50.838	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	74	ASP	-1	-0.860	-0.930	51.767	0.000	0.000	0.000	0.000	0.000	0.000
73	A	75	TYR	0	0.075	0.024	48.324	0.000	0.000	0.000	0.000	0.000	0.000
74	A	76	ASN	0	0.048	0.039	51.195	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	77	SER	0	-0.002	0.011	51.375	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	78	TYR	0	0.018	-0.006	44.163	0.000	0.000	0.000	0.000	0.000	0.000
77	A	79	SER	0	-0.045	-0.045	47.205	0.000	0.000	0.000	0.000	0.000	0.000
78	A	80	LYS	1	0.978	0.983	48.181	0.002	0.002	0.000	0.000	0.000	0.000
79	A	81	LEU	0	-0.001	0.004	44.957	0.000	0.000	0.000	0.000	0.000	0.000
80	A	82	ILE	0	-0.065	-0.049	42.780	0.000	0.000	0.000	0.000	0.000	0.000
81	A	83	THR	0	-0.013	0.006	43.129	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	84	GLU	-1	-0.942	-0.966	44.737	-0.007	-0.007	0.000	0.000	0.000	0.000
83	A	85	LEU	0	-0.053	-0.018	40.917	0.000	0.000	0.000	0.000	0.000	0.000
84	A	86	ASN	0	-0.039	-0.006	39.455	0.000	0.000	0.000	0.000	0.000	0.000
85	A	87	LEU	0	-0.064	-0.038	37.655	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:LEU)