FMO DATABASE

FMODB ID: LNM59

Calculation Name: 2ZKZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2ZKZ

Chain ID: A

ChEMBL ID:

UniProt ID: O31178

Base Structure: X-ray

Registration Date: 2023-09-20

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	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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-623705.008074
FMO2-HF: Nuclear repulsion	588296.80154
FMO2-HF: Total energy	-35408.206534
FMO2-MP2: Total energy	-35509.890101

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:11:TYR)

Summations of interaction energy for fragment #1(A:11: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.
-5.279	0.176	1.753	-2.257	-4.952	0.005

Interaction energy analysis for fragmet #1(A:11:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.027 / q_NPA : 0.009

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	13	SER	0	0.010	-0.018	2.851	-4.223	1.086	1.725	-2.460	-4.575	0.004
4	A	14	LEU	0	0.038	0.018	3.643	-1.070	-0.924	0.028	0.203	-0.377	0.001
5	A	15	GLU	-1	-0.850	-0.938	6.061	-0.337	-0.337	0.000	0.000	0.000	0.000
6	A	16	ASP	-1	-0.838	-0.886	5.679	-1.778	-1.778	0.000	0.000	0.000	0.000
7	A	17	ASP	-1	-0.792	-0.882	6.719	-1.504	-1.504	0.000	0.000	0.000	0.000
8	A	18	ALA	0	0.004	0.007	8.923	0.107	0.107	0.000	0.000	0.000	0.000
9	A	19	GLU	-1	-0.761	-0.859	11.513	-0.380	-0.380	0.000	0.000	0.000	0.000
10	A	20	LEU	0	-0.035	-0.004	9.732	0.088	0.088	0.000	0.000	0.000	0.000
11	A	21	LEU	0	0.035	0.008	12.152	0.099	0.099	0.000	0.000	0.000	0.000
12	A	22	LYS	1	0.853	0.916	14.879	0.461	0.461	0.000	0.000	0.000	0.000
13	A	23	THR	0	-0.108	-0.069	15.696	0.058	0.058	0.000	0.000	0.000	0.000
14	A	24	MET	0	-0.003	-0.009	15.376	0.031	0.031	0.000	0.000	0.000	0.000
15	A	25	ALA	0	0.001	0.037	18.467	0.034	0.034	0.000	0.000	0.000	0.000
16	A	26	HIS	0	0.003	-0.015	20.826	0.019	0.019	0.000	0.000	0.000	0.000
17	A	27	PRO	0	0.076	0.032	24.005	-0.001	-0.001	0.000	0.000	0.000	0.000
18	A	28	MET	0	0.002	0.001	26.105	0.009	0.009	0.000	0.000	0.000	0.000
19	A	29	ARG	1	0.861	0.913	20.486	0.279	0.279	0.000	0.000	0.000	0.000
20	A	30	LEU	0	0.075	0.040	20.376	0.002	0.002	0.000	0.000	0.000	0.000
21	A	31	LYS	1	0.923	0.971	22.678	0.125	0.125	0.000	0.000	0.000	0.000
22	A	32	ILE	0	-0.015	-0.008	21.178	0.009	0.009	0.000	0.000	0.000	0.000
23	A	33	VAL	0	0.018	0.003	17.614	0.010	0.010	0.000	0.000	0.000	0.000
24	A	34	ASN	0	0.036	0.017	20.295	0.014	0.014	0.000	0.000	0.000	0.000
25	A	35	GLU	-1	-0.838	-0.905	22.997	-0.080	-0.080	0.000	0.000	0.000	0.000
26	A	36	LEU	0	-0.024	-0.017	19.160	0.011	0.011	0.000	0.000	0.000	0.000
27	A	37	TYR	0	-0.011	0.004	19.347	0.016	0.016	0.000	0.000	0.000	0.000
28	A	38	LYS	1	0.852	0.916	20.781	0.106	0.106	0.000	0.000	0.000	0.000
29	A	39	HIS	0	0.010	-0.009	24.191	0.017	0.017	0.000	0.000	0.000	0.000
30	A	40	LYS	1	0.823	0.923	19.061	0.046	0.046	0.000	0.000	0.000	0.000
31	A	41	ALA	0	-0.041	-0.030	20.206	-0.009	-0.009	0.000	0.000	0.000	0.000
32	A	42	LEU	0	-0.003	0.009	22.610	0.003	0.003	0.000	0.000	0.000	0.000
33	A	43	ASN	0	0.007	-0.006	24.057	-0.018	-0.018	0.000	0.000	0.000	0.000
34	A	44	VAL	0	0.020	-0.016	25.554	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	45	THR	0	0.023	0.017	27.576	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	46	GLN	0	0.110	0.062	28.128	-0.004	-0.004	0.000	0.000	0.000	0.000
37	A	47	ILE	0	-0.006	0.006	23.791	-0.002	-0.002	0.000	0.000	0.000	0.000
38	A	48	ILE	0	-0.022	-0.007	28.050	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	49	GLN	0	0.020	0.014	31.178	0.001	0.001	0.000	0.000	0.000	0.000
40	A	50	ILE	0	0.020	0.026	28.594	0.003	0.003	0.000	0.000	0.000	0.000
41	A	51	LEU	0	-0.080	-0.055	26.774	0.001	0.001	0.000	0.000	0.000	0.000
42	A	52	LYS	1	0.852	0.923	30.842	0.074	0.074	0.000	0.000	0.000	0.000
43	A	53	LEU	0	0.018	0.011	29.411	-0.003	-0.003	0.000	0.000	0.000	0.000
44	A	54	PRO	0	0.077	0.029	33.192	0.002	0.002	0.000	0.000	0.000	0.000
45	A	55	GLN	0	0.079	0.036	31.156	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	56	SER	0	0.038	0.024	30.224	-0.007	-0.007	0.000	0.000	0.000	0.000
47	A	57	THR	0	-0.004	-0.002	29.499	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	58	VAL	0	0.017	0.007	26.610	-0.014	-0.014	0.000	0.000	0.000	0.000
49	A	59	SER	0	0.003	-0.015	25.614	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	60	GLN	0	-0.031	-0.008	24.949	-0.024	-0.024	0.000	0.000	0.000	0.000
51	A	61	HIS	0	0.051	0.033	23.317	-0.035	-0.035	0.000	0.000	0.000	0.000
52	A	62	LEU	0	0.012	0.007	21.116	-0.025	-0.025	0.000	0.000	0.000	0.000
53	A	63	CYS	0	-0.098	-0.037	20.095	-0.028	-0.028	0.000	0.000	0.000	0.000
54	A	64	LYS	1	0.984	0.993	19.791	0.236	0.236	0.000	0.000	0.000	0.000
55	A	65	MET	0	0.028	0.029	16.886	-0.038	-0.038	0.000	0.000	0.000	0.000
56	A	66	ARG	1	0.866	0.923	15.350	0.207	0.207	0.000	0.000	0.000	0.000
57	A	67	GLY	0	-0.014	-0.002	12.761	0.009	0.009	0.000	0.000	0.000	0.000
58	A	68	LYS	1	0.857	0.936	10.901	0.414	0.414	0.000	0.000	0.000	0.000
59	A	69	VAL	0	0.016	-0.004	10.924	-0.046	-0.046	0.000	0.000	0.000	0.000
60	A	70	LEU	0	-0.009	-0.006	13.639	0.054	0.054	0.000	0.000	0.000	0.000
61	A	71	LYS	1	0.909	0.959	13.312	0.058	0.058	0.000	0.000	0.000	0.000
62	A	72	ARG	1	0.941	0.969	15.090	0.193	0.193	0.000	0.000	0.000	0.000
63	A	73	ASN	0	-0.044	-0.020	17.674	0.011	0.011	0.000	0.000	0.000	0.000
64	A	74	ARG	1	0.894	0.932	20.192	0.055	0.055	0.000	0.000	0.000	0.000
65	A	75	GLN	0	-0.010	0.001	23.509	0.017	0.017	0.000	0.000	0.000	0.000
66	A	76	GLY	0	0.086	0.051	26.221	-0.001	-0.001	0.000	0.000	0.000	0.000
67	A	77	LEU	0	0.063	0.020	28.809	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	78	GLU	-1	-0.844	-0.897	26.565	-0.056	-0.056	0.000	0.000	0.000	0.000
69	A	79	ILE	0	-0.051	-0.034	23.255	-0.003	-0.003	0.000	0.000	0.000	0.000
70	A	80	TYR	0	0.026	0.005	20.730	-0.005	-0.005	0.000	0.000	0.000	0.000
71	A	81	TYR	0	-0.012	-0.022	18.761	-0.016	-0.016	0.000	0.000	0.000	0.000
72	A	82	SER	0	0.090	0.044	17.139	0.009	0.009	0.000	0.000	0.000	0.000
73	A	83	ILE	0	0.029	0.015	13.676	-0.043	-0.043	0.000	0.000	0.000	0.000
74	A	84	ASN	0	0.019	-0.003	9.703	-0.003	-0.003	0.000	0.000	0.000	0.000
75	A	85	ASN	0	0.043	0.030	8.183	0.158	0.158	0.000	0.000	0.000	0.000
76	A	86	PRO	0	0.061	0.013	7.338	-0.030	-0.030	0.000	0.000	0.000	0.000
77	A	87	LYS	1	0.858	0.914	4.834	1.353	1.353	0.000	0.000	0.000	0.000
78	A	88	VAL	0	-0.010	0.011	10.350	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	89	GLU	-1	-0.812	-0.898	13.326	-0.017	-0.017	0.000	0.000	0.000	0.000
80	A	90	GLY	0	0.002	0.002	13.601	0.023	0.023	0.000	0.000	0.000	0.000
81	A	91	ILE	0	0.020	-0.002	12.762	0.009	0.009	0.000	0.000	0.000	0.000
82	A	92	ILE	0	-0.037	-0.020	16.066	0.020	0.020	0.000	0.000	0.000	0.000
83	A	93	LYS	1	0.844	0.910	16.332	0.078	0.078	0.000	0.000	0.000	0.000
84	A	94	LEU	0	0.015	0.011	17.193	0.014	0.014	0.000	0.000	0.000	0.000
85	A	95	LEU	0	-0.062	-0.015	19.563	0.000	0.000	0.000	0.000	0.000	0.000
86	A	96	ASN	0	-0.063	-0.015	22.141	0.023	0.023	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:11:TYR)