FMO DATABASE

FMODB ID: LNZQ9

Calculation Name: 2P58-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2P58

Chain ID: C

ChEMBL ID:

UniProt ID: O68690

Base Structure: X-ray

Registration Date: 2023-09-21

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	112
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-876491.360964
FMO2-HF: Nuclear repulsion	831827.011643
FMO2-HF: Total energy	-44664.349322
FMO2-MP2: Total energy	-44794.398578

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(C:3:TYR)

Summations of interaction energy for fragment #1(C:3:TYR)

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.
-56.649	-55.503	27.481	-13.706	-14.919	-0.096

Interaction energy analysis for fragmet #1(C:3:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.042 / q_NPA : -0.062

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	C	5	LEU	0	0.057	0.029	3.608	-2.918	-0.778	0.018	-0.947	-1.212	0.003
4	C	6	ASN	0	0.014	-0.014	4.877	-0.205	-0.054	-0.001	-0.003	-0.147	0.000
5	C	7	VAL	0	-0.007	0.008	2.904	-0.417	0.507	0.094	-0.163	-0.854	0.000
6	C	8	LEU	0	0.031	0.019	2.283	-6.852	-2.766	3.973	-2.016	-6.042	0.009
7	C	9	LEU	0	-0.008	-0.001	3.636	-0.639	-0.467	0.071	0.099	-0.342	0.002
8	C	10	ALA	0	0.043	0.019	6.791	0.090	0.090	0.000	0.000	0.000	0.000
9	C	11	GLU	-1	-0.847	-0.903	1.568	-47.565	-53.892	23.326	-10.676	-6.322	-0.110
10	C	12	ILE	0	-0.012	-0.007	5.738	0.952	0.952	0.000	0.000	0.000	0.000
11	C	13	ALA	0	0.024	0.018	7.838	0.372	0.372	0.000	0.000	0.000	0.000
12	C	14	LEU	0	-0.001	0.001	8.471	0.326	0.326	0.000	0.000	0.000	0.000
13	C	15	ILE	0	0.008	0.012	5.773	0.394	0.394	0.000	0.000	0.000	0.000
14	C	16	GLY	0	0.032	0.022	9.910	0.299	0.299	0.000	0.000	0.000	0.000
15	C	17	THR	0	-0.064	-0.037	12.987	0.155	0.155	0.000	0.000	0.000	0.000
16	C	18	GLY	0	-0.008	0.000	13.288	0.124	0.124	0.000	0.000	0.000	0.000
17	C	19	ASN	0	-0.116	-0.073	12.626	0.189	0.189	0.000	0.000	0.000	0.000
18	C	20	HIS	0	-0.002	-0.013	15.841	0.067	0.067	0.000	0.000	0.000	0.000
19	C	21	TYR	0	-0.007	0.029	15.232	0.070	0.070	0.000	0.000	0.000	0.000
20	C	22	HIS	0	0.028	0.017	16.042	-0.127	-0.127	0.000	0.000	0.000	0.000
21	C	23	GLU	-1	-0.872	-0.918	18.255	-0.469	-0.469	0.000	0.000	0.000	0.000
22	C	24	GLU	-1	-0.840	-0.931	15.706	-0.530	-0.530	0.000	0.000	0.000	0.000
23	C	25	ALA	0	-0.013	-0.011	13.873	-0.060	-0.060	0.000	0.000	0.000	0.000
24	C	26	ASN	0	-0.084	-0.044	14.884	-0.092	-0.092	0.000	0.000	0.000	0.000
25	C	27	CYS	0	0.019	0.008	17.402	0.018	0.018	0.000	0.000	0.000	0.000
26	C	28	ILE	0	-0.044	-0.019	10.723	0.016	0.016	0.000	0.000	0.000	0.000
27	C	29	ALA	0	-0.002	-0.010	13.558	-0.037	-0.037	0.000	0.000	0.000	0.000
28	C	30	GLU	-1	-0.873	-0.931	15.050	-0.375	-0.375	0.000	0.000	0.000	0.000
29	C	31	TRP	0	-0.044	-0.025	10.716	0.130	0.130	0.000	0.000	0.000	0.000
30	C	32	LEU	0	-0.030	-0.031	9.470	0.033	0.033	0.000	0.000	0.000	0.000
31	C	33	HIS	0	-0.075	-0.046	13.616	0.080	0.080	0.000	0.000	0.000	0.000
32	C	34	LEU	0	-0.007	0.005	17.313	0.058	0.058	0.000	0.000	0.000	0.000
33	C	35	LYS	1	0.776	0.892	13.193	0.316	0.316	0.000	0.000	0.000	0.000
34	C	36	GLY	0	0.059	0.039	15.780	0.053	0.053	0.000	0.000	0.000	0.000
35	C	37	GLU	-1	-0.886	-0.925	10.927	-0.671	-0.671	0.000	0.000	0.000	0.000
36	C	38	GLU	-1	-0.852	-0.934	14.234	-0.604	-0.604	0.000	0.000	0.000	0.000
37	C	39	GLU	-1	-0.882	-0.942	15.201	-0.651	-0.651	0.000	0.000	0.000	0.000
38	C	40	ALA	0	0.015	0.002	10.850	-0.088	-0.088	0.000	0.000	0.000	0.000
39	C	41	VAL	0	0.003	0.012	12.817	-0.092	-0.092	0.000	0.000	0.000	0.000
40	C	42	GLN	0	0.007	-0.002	15.347	-0.001	-0.001	0.000	0.000	0.000	0.000
41	C	43	LEU	0	-0.016	-0.005	11.418	0.027	0.027	0.000	0.000	0.000	0.000
42	C	44	ILE	0	0.017	0.008	10.941	-0.016	-0.016	0.000	0.000	0.000	0.000
43	C	45	ARG	1	0.938	0.983	14.453	0.557	0.557	0.000	0.000	0.000	0.000
44	C	46	LEU	0	-0.018	-0.019	17.910	0.064	0.064	0.000	0.000	0.000	0.000
45	C	47	SER	0	0.004	-0.006	14.110	0.073	0.073	0.000	0.000	0.000	0.000
46	C	48	SER	0	0.012	-0.001	16.473	0.086	0.086	0.000	0.000	0.000	0.000
47	C	49	LEU	0	-0.058	-0.028	18.220	0.061	0.061	0.000	0.000	0.000	0.000
48	C	50	MET	0	-0.031	-0.019	19.186	0.036	0.036	0.000	0.000	0.000	0.000
49	C	51	ASN	0	-0.048	-0.031	15.637	0.073	0.073	0.000	0.000	0.000	0.000
50	C	52	ARG	1	0.862	0.939	19.656	0.546	0.546	0.000	0.000	0.000	0.000
51	C	53	GLY	0	-0.001	0.012	22.766	0.044	0.044	0.000	0.000	0.000	0.000
52	C	54	ASP	-1	-0.814	-0.878	24.445	-0.331	-0.331	0.000	0.000	0.000	0.000
53	C	55	TYR	0	0.059	-0.006	22.377	-0.007	-0.007	0.000	0.000	0.000	0.000
54	C	56	ALA	0	0.016	0.018	25.822	0.003	0.003	0.000	0.000	0.000	0.000
55	C	57	SER	0	-0.055	-0.054	26.293	0.016	0.016	0.000	0.000	0.000	0.000
56	C	58	ALA	0	-0.005	0.005	22.573	-0.005	-0.005	0.000	0.000	0.000	0.000
57	C	59	LEU	0	0.019	0.011	24.243	-0.005	-0.005	0.000	0.000	0.000	0.000
58	C	60	GLN	0	-0.016	0.005	26.612	0.020	0.020	0.000	0.000	0.000	0.000
59	C	61	GLN	0	0.007	-0.014	24.232	-0.007	-0.007	0.000	0.000	0.000	0.000
60	C	62	GLY	0	0.054	0.028	23.368	-0.010	-0.010	0.000	0.000	0.000	0.000
61	C	63	ASN	0	-0.076	-0.041	24.322	0.019	0.019	0.000	0.000	0.000	0.000
62	C	64	LYS	1	0.860	0.924	26.639	0.294	0.294	0.000	0.000	0.000	0.000
63	C	65	LEU	0	-0.031	-0.008	22.287	0.014	0.014	0.000	0.000	0.000	0.000
64	C	66	ALA	0	-0.002	0.009	23.232	-0.032	-0.032	0.000	0.000	0.000	0.000
65	C	67	TYR	0	0.079	0.029	19.224	0.010	0.010	0.000	0.000	0.000	0.000
66	C	68	PRO	0	0.004	-0.006	21.054	-0.024	-0.024	0.000	0.000	0.000	0.000
67	C	69	ASP	-1	-0.765	-0.847	15.994	-0.595	-0.595	0.000	0.000	0.000	0.000
68	C	70	LEU	0	-0.013	-0.009	15.472	-0.064	-0.064	0.000	0.000	0.000	0.000
69	C	71	GLU	-1	-0.756	-0.843	19.011	-0.326	-0.326	0.000	0.000	0.000	0.000
70	C	72	PRO	0	-0.022	-0.011	19.343	0.027	0.027	0.000	0.000	0.000	0.000
71	C	73	TRP	0	0.046	0.021	13.866	0.044	0.044	0.000	0.000	0.000	0.000
72	C	74	LEU	0	-0.011	0.015	20.435	0.033	0.033	0.000	0.000	0.000	0.000
73	C	75	ALA	0	0.033	0.019	23.986	0.031	0.031	0.000	0.000	0.000	0.000
74	C	76	LEU	0	0.001	-0.001	19.878	0.030	0.030	0.000	0.000	0.000	0.000
75	C	77	CYS	0	-0.040	-0.027	22.841	0.013	0.013	0.000	0.000	0.000	0.000
76	C	78	GLU	-1	-0.794	-0.893	25.295	-0.276	-0.276	0.000	0.000	0.000	0.000
77	C	79	TYR	0	-0.010	-0.008	25.909	0.016	0.016	0.000	0.000	0.000	0.000
78	C	80	ARG	1	0.882	0.942	24.128	0.417	0.417	0.000	0.000	0.000	0.000
79	C	81	LEU	0	-0.027	-0.004	27.562	0.012	0.012	0.000	0.000	0.000	0.000
80	C	82	GLY	0	0.025	0.026	30.502	0.019	0.019	0.000	0.000	0.000	0.000
81	C	83	LEU	0	-0.015	-0.001	31.053	0.019	0.019	0.000	0.000	0.000	0.000
82	C	84	GLY	0	0.016	-0.004	33.279	-0.003	-0.003	0.000	0.000	0.000	0.000
83	C	85	SER	0	0.000	-0.010	34.415	0.003	0.003	0.000	0.000	0.000	0.000
84	C	86	ALA	0	-0.036	-0.005	32.482	0.007	0.007	0.000	0.000	0.000	0.000
85	C	87	LEU	0	0.046	0.029	28.022	-0.004	-0.004	0.000	0.000	0.000	0.000
86	C	88	GLU	-1	-0.757	-0.858	30.832	-0.199	-0.199	0.000	0.000	0.000	0.000
87	C	89	SER	0	-0.050	-0.014	33.390	0.007	0.007	0.000	0.000	0.000	0.000
88	C	90	ARG	1	0.742	0.817	26.324	0.330	0.330	0.000	0.000	0.000	0.000
89	C	91	LEU	0	0.010	0.006	27.301	-0.008	-0.008	0.000	0.000	0.000	0.000
90	C	92	ASN	0	-0.010	-0.014	29.905	0.009	0.009	0.000	0.000	0.000	0.000
91	C	93	ARG	1	0.764	0.865	27.440	0.289	0.289	0.000	0.000	0.000	0.000
92	C	94	LEU	0	-0.004	-0.008	24.679	0.005	0.005	0.000	0.000	0.000	0.000
93	C	95	ALA	0	0.013	0.010	27.962	0.002	0.002	0.000	0.000	0.000	0.000
94	C	96	ARG	1	0.917	0.969	30.315	0.165	0.165	0.000	0.000	0.000	0.000
95	C	97	SER	0	-0.003	0.012	24.510	0.020	0.020	0.000	0.000	0.000	0.000
96	C	98	GLN	0	0.018	0.003	27.199	0.012	0.012	0.000	0.000	0.000	0.000
97	C	99	ASP	-1	-0.793	-0.868	20.487	-0.341	-0.341	0.000	0.000	0.000	0.000
98	C	100	PRO	0	0.045	0.013	21.658	-0.017	-0.017	0.000	0.000	0.000	0.000
99	C	101	ARG	1	0.758	0.838	15.394	0.517	0.517	0.000	0.000	0.000	0.000
100	C	102	ILE	0	0.019	0.013	20.435	-0.017	-0.017	0.000	0.000	0.000	0.000
101	C	103	GLN	0	-0.018	-0.025	22.695	-0.002	-0.002	0.000	0.000	0.000	0.000
102	C	104	THR	0	-0.032	-0.016	21.171	0.019	0.019	0.000	0.000	0.000	0.000
103	C	105	PHE	0	0.007	0.006	20.886	0.000	0.000	0.000	0.000	0.000	0.000
104	C	106	VAL	0	-0.005	-0.008	22.788	0.010	0.010	0.000	0.000	0.000	0.000
105	C	107	ASN	0	-0.033	-0.032	26.525	0.025	0.025	0.000	0.000	0.000	0.000
106	C	108	GLY	0	0.031	0.020	24.370	0.013	0.013	0.000	0.000	0.000	0.000
107	C	109	MET	0	-0.011	-0.003	24.389	0.009	0.009	0.000	0.000	0.000	0.000
108	C	110	ARG	1	0.806	0.862	26.718	0.215	0.215	0.000	0.000	0.000	0.000
109	C	111	GLU	-1	-0.819	-0.879	27.963	-0.167	-0.167	0.000	0.000	0.000	0.000
110	C	112	GLN	0	-0.046	-0.024	26.729	-0.005	-0.005	0.000	0.000	0.000	0.000
111	C	113	LEU	0	-0.045	-0.032	28.940	0.008	0.008	0.000	0.000	0.000	0.000
112	C	114	LYS	1	0.732	0.877	31.905	0.194	0.194	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(C:3:TYR)