FMO DATABASE

FMODB ID: LZKV9

Calculation Name: 2Z0U-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Z0U

Chain ID: A

ChEMBL ID:

UniProt ID: Q8IX03

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	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	126
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1109483.61321
FMO2-HF: Nuclear repulsion	1058166.539557
FMO2-HF: Total energy	-51317.073653
FMO2-MP2: Total energy	-51464.823749

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:21:GLY)

Summations of interaction energy for fragment #1(A:21:GLY)

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.
-1.069	0.299	0.05	-0.561	-0.858	0

Interaction energy analysis for fragmet #1(A:21:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : -0.007

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].
3	A	23	THR	0	0.024	0.024	3.786	1.825	2.795	-0.017	-0.428	-0.525
4	A	24	ARG	1	0.904	0.957	5.963	-2.348	-2.348	0.000	0.000	0.000
5	A	25	ILE	0	0.050	0.021	8.712	-0.146	-0.146	0.000	0.000	0.000
6	A	26	GLN	0	-0.026	0.006	12.476	0.014	0.014	0.000	0.000	0.000
7	A	27	ILE	0	0.035	0.003	14.751	-0.059	-0.059	0.000	0.000	0.000
8	A	28	ALA	0	-0.028	-0.022	18.028	0.014	0.014	0.000	0.000	0.000
9	A	29	LEU	0	-0.021	0.004	20.792	-0.021	-0.021	0.000	0.000	0.000
10	A	30	LYS	1	0.952	0.963	23.711	-0.099	-0.099	0.000	0.000	0.000
11	A	31	TYR	0	-0.021	-0.013	27.392	-0.007	-0.007	0.000	0.000	0.000
12	A	32	ASP	-1	-0.865	-0.924	30.502	0.067	0.067	0.000	0.000	0.000
13	A	33	GLU	-1	-0.858	-0.957	33.990	0.050	0.050	0.000	0.000	0.000
14	A	34	LYS	1	0.914	0.947	36.310	-0.060	-0.060	0.000	0.000	0.000
15	A	35	ASN	0	-0.048	-0.031	37.380	-0.007	-0.007	0.000	0.000	0.000
16	A	36	LYS	1	0.881	0.966	36.550	-0.042	-0.042	0.000	0.000	0.000
17	A	37	GLN	0	0.029	0.018	33.614	-0.003	-0.003	0.000	0.000	0.000
18	A	38	PHE	0	0.000	-0.009	24.654	0.005	0.005	0.000	0.000	0.000
19	A	39	ALA	0	0.009	0.007	28.131	-0.004	-0.004	0.000	0.000	0.000
20	A	40	ILE	0	-0.004	-0.007	22.478	0.011	0.011	0.000	0.000	0.000
21	A	41	LEU	0	-0.012	-0.001	22.151	-0.007	-0.007	0.000	0.000	0.000
22	A	42	ILE	0	0.027	-0.001	18.476	0.029	0.029	0.000	0.000	0.000
23	A	43	ILE	0	-0.010	-0.006	17.790	-0.009	-0.009	0.000	0.000	0.000
24	A	44	GLN	0	0.006	-0.011	14.162	0.000	0.000	0.000	0.000	0.000
25	A	45	LEU	0	0.003	0.004	11.953	0.047	0.047	0.000	0.000	0.000
26	A	46	SER	0	-0.022	-0.009	8.809	0.119	0.119	0.000	0.000	0.000
27	A	47	ASN	0	0.066	0.030	3.072	-0.351	0.012	0.068	-0.125	-0.307
28	A	48	LEU	0	0.007	0.008	6.795	-0.339	-0.339	0.000	0.000	0.000
29	A	49	SER	0	-0.021	-0.017	7.985	-0.198	-0.198	0.000	0.000	0.000
30	A	50	ALA	0	-0.064	-0.031	4.715	-0.183	-0.148	-0.001	-0.008	-0.026
31	A	51	LEU	0	-0.065	-0.026	6.685	-0.119	-0.119	0.000	0.000	0.000
32	A	52	LEU	0	0.012	0.018	9.946	0.052	0.052	0.000	0.000	0.000
33	A	53	GLN	0	0.012	-0.007	10.504	0.093	0.093	0.000	0.000	0.000
34	A	54	GLN	0	-0.038	-0.014	12.663	0.047	0.047	0.000	0.000	0.000
35	A	55	GLN	0	-0.043	-0.040	12.826	0.053	0.053	0.000	0.000	0.000
36	A	56	ASP	-1	-0.912	-0.961	16.503	-0.048	-0.048	0.000	0.000	0.000
37	A	57	GLN	0	0.059	0.046	19.607	0.015	0.015	0.000	0.000	0.000
38	A	58	LYS	1	0.825	0.900	19.895	-0.009	-0.009	0.000	0.000	0.000
39	A	59	VAL	0	-0.001	0.017	15.935	-0.018	-0.018	0.000	0.000	0.000
40	A	60	ASN	0	-0.034	-0.013	19.285	0.018	0.018	0.000	0.000	0.000
41	A	61	ILE	0	0.031	0.016	16.114	-0.013	-0.013	0.000	0.000	0.000
42	A	62	ARG	1	0.947	0.976	19.458	0.050	0.050	0.000	0.000	0.000
43	A	63	VAL	0	0.002	-0.011	20.459	0.006	0.006	0.000	0.000	0.000
44	A	64	ALA	0	0.008	0.012	22.479	-0.008	-0.008	0.000	0.000	0.000
45	A	65	VAL	0	0.019	0.013	23.604	0.006	0.006	0.000	0.000	0.000
46	A	66	LEU	0	-0.025	0.005	23.492	-0.007	-0.007	0.000	0.000	0.000
47	A	67	PRO	0	0.060	-0.004	26.818	0.005	0.005	0.000	0.000	0.000
48	A	68	CYS	0	-0.022	0.009	29.178	0.009	0.009	0.000	0.000	0.000
49	A	69	SER	0	-0.024	-0.011	30.897	-0.003	-0.003	0.000	0.000	0.000
50	A	70	GLU	-1	-0.900	-0.967	33.630	0.010	0.010	0.000	0.000	0.000
51	A	71	SER	0	0.025	-0.019	31.790	0.003	0.003	0.000	0.000	0.000
52	A	72	THR	0	-0.009	0.000	32.122	0.003	0.003	0.000	0.000	0.000
53	A	73	THR	0	0.029	0.022	33.484	0.004	0.004	0.000	0.000	0.000
54	A	75	LEU	0	-0.022	-0.003	27.258	-0.002	-0.002	0.000	0.000	0.000
55	A	76	PHE	0	0.000	-0.004	25.777	0.002	0.002	0.000	0.000	0.000
56	A	77	ARG	1	0.792	0.865	23.692	0.005	0.005	0.000	0.000	0.000
57	A	78	THR	0	-0.051	0.012	21.080	0.001	0.001	0.000	0.000	0.000
58	A	79	ARG	1	0.920	0.937	23.998	-0.067	-0.067	0.000	0.000	0.000
59	A	80	PRO	0	-0.014	-0.020	22.947	0.006	0.006	0.000	0.000	0.000
60	A	81	LEU	0	-0.022	-0.006	20.036	0.006	0.006	0.000	0.000	0.000
61	A	82	ASP	-1	-0.841	-0.912	20.352	0.017	0.017	0.000	0.000	0.000
62	A	83	ALA	0	0.007	0.006	15.916	0.019	0.019	0.000	0.000	0.000
63	A	84	SER	0	0.024	0.008	15.232	0.004	0.004	0.000	0.000	0.000
64	A	85	ASP	-1	-0.821	-0.891	9.142	0.308	0.308	0.000	0.000	0.000
65	A	86	THR	0	-0.039	-0.027	10.916	0.128	0.128	0.000	0.000	0.000
66	A	87	LEU	0	-0.011	-0.003	13.156	-0.049	-0.049	0.000	0.000	0.000
67	A	88	VAL	0	0.006	0.002	15.970	0.038	0.038	0.000	0.000	0.000
68	A	89	PHE	0	-0.001	-0.008	16.605	-0.024	-0.024	0.000	0.000	0.000
69	A	90	ASN	0	-0.034	-0.026	20.863	0.002	0.002	0.000	0.000	0.000
70	A	91	GLU	-1	-0.783	-0.873	22.704	0.064	0.064	0.000	0.000	0.000
71	A	92	VAL	0	-0.032	-0.018	23.924	0.012	0.012	0.000	0.000	0.000
72	A	93	PHE	0	-0.006	0.001	23.461	-0.010	-0.010	0.000	0.000	0.000
73	A	94	TRP	0	0.025	0.001	27.922	0.008	0.008	0.000	0.000	0.000
74	A	95	VAL	0	0.024	0.018	29.065	-0.006	-0.006	0.000	0.000	0.000
75	A	96	SER	0	0.013	0.017	32.057	0.003	0.003	0.000	0.000	0.000
76	A	97	MET	0	-0.021	-0.002	29.958	-0.002	-0.002	0.000	0.000	0.000
77	A	98	SER	0	0.028	0.027	34.933	0.004	0.004	0.000	0.000	0.000
78	A	99	TYR	0	0.080	0.037	30.138	-0.002	-0.002	0.000	0.000	0.000
79	A	100	PRO	0	0.026	-0.005	32.570	0.001	0.001	0.000	0.000	0.000
80	A	101	ALA	0	-0.001	0.013	33.153	-0.002	-0.002	0.000	0.000	0.000
81	A	102	LEU	0	0.019	-0.008	27.030	-0.002	-0.002	0.000	0.000	0.000
82	A	103	HIS	0	-0.011	-0.005	28.364	0.004	0.004	0.000	0.000	0.000
83	A	104	GLN	0	-0.031	-0.010	28.357	-0.002	-0.002	0.000	0.000	0.000
84	A	105	LYS	1	0.809	0.921	26.819	-0.029	-0.029	0.000	0.000	0.000
85	A	106	THR	0	0.001	0.000	21.194	0.004	0.004	0.000	0.000	0.000
86	A	107	LEU	0	-0.040	-0.021	19.785	-0.006	-0.006	0.000	0.000	0.000
87	A	108	ARG	1	0.816	0.892	16.415	0.083	0.083	0.000	0.000	0.000
88	A	109	VAL	0	-0.011	-0.006	15.391	0.008	0.008	0.000	0.000	0.000
89	A	110	ASP	-1	-0.765	-0.882	16.199	-0.089	-0.089	0.000	0.000	0.000
90	A	111	VAL	0	0.009	0.024	12.700	0.035	0.035	0.000	0.000	0.000
91	A	112	CYS	0	-0.149	-0.083	16.048	-0.030	-0.030	0.000	0.000	0.000
92	A	113	THR	0	0.014	-0.013	17.886	0.022	0.022	0.000	0.000	0.000
93	A	114	THR	0	-0.002	0.003	19.780	-0.005	-0.005	0.000	0.000	0.000
94	A	115	ASP	-1	-0.753	-0.857	23.281	-0.067	-0.067	0.000	0.000	0.000
95	A	116	ARG	1	0.957	0.941	24.417	0.049	0.049	0.000	0.000	0.000
96	A	117	SER	0	-0.074	-0.028	27.690	0.008	0.008	0.000	0.000	0.000
97	A	118	HIS	0	-0.069	-0.040	28.028	0.003	0.003	0.000	0.000	0.000
98	A	119	LEU	0	-0.011	0.011	25.065	0.004	0.004	0.000	0.000	0.000
99	A	120	GLU	-1	-0.868	-0.919	22.473	-0.040	-0.040	0.000	0.000	0.000
100	A	121	GLU	-1	-0.923	-0.957	18.562	-0.206	-0.206	0.000	0.000	0.000
101	A	123	LEU	0	0.067	0.028	13.485	-0.015	-0.015	0.000	0.000	0.000
102	A	124	GLY	0	0.045	0.024	12.329	-0.093	-0.093	0.000	0.000	0.000
103	A	125	GLY	0	0.005	-0.012	13.342	0.077	0.077	0.000	0.000	0.000
104	A	126	ALA	0	-0.058	-0.017	12.576	-0.037	-0.037	0.000	0.000	0.000
105	A	127	GLN	0	-0.033	-0.014	14.510	0.017	0.017	0.000	0.000	0.000
106	A	128	ILE	0	0.003	0.000	15.800	0.009	0.009	0.000	0.000	0.000
107	A	129	SER	0	0.034	0.025	18.325	-0.014	-0.014	0.000	0.000	0.000
108	A	130	LEU	0	0.022	-0.006	21.237	0.020	0.020	0.000	0.000	0.000
109	A	131	ALA	0	0.016	0.019	23.861	0.001	0.001	0.000	0.000	0.000
110	A	132	GLU	-1	-0.951	-0.980	21.215	0.131	0.131	0.000	0.000	0.000
111	A	133	VAL	0	-0.066	-0.017	24.215	0.009	0.009	0.000	0.000	0.000
112	A	134	CYS	0	0.011	0.006	26.021	-0.008	-0.008	0.000	0.000	0.000
113	A	135	ARG	1	0.922	0.969	29.004	-0.055	-0.055	0.000	0.000	0.000
114	A	136	SER	0	-0.061	-0.076	31.899	-0.004	-0.004	0.000	0.000	0.000
115	A	137	GLY	0	0.009	0.015	31.360	-0.001	-0.001	0.000	0.000	0.000
116	A	138	GLU	-1	-0.846	-0.892	27.871	0.103	0.103	0.000	0.000	0.000
117	A	139	ARG	1	0.904	0.957	23.390	-0.178	-0.178	0.000	0.000	0.000
118	A	140	SER	0	0.011	0.000	21.497	0.007	0.007	0.000	0.000	0.000
119	A	141	THR	0	-0.021	-0.007	18.055	-0.012	-0.012	0.000	0.000	0.000
120	A	142	ARG	1	0.917	0.970	15.327	-0.244	-0.244	0.000	0.000	0.000
121	A	143	TRP	0	0.029	0.015	10.583	0.073	0.073	0.000	0.000	0.000
122	A	144	TYR	0	0.000	-0.003	11.125	-0.025	-0.025	0.000	0.000	0.000
123	A	145	ASN	0	0.021	0.003	6.187	0.754	0.754	0.000	0.000	0.000
124	A	146	LEU	0	-0.046	-0.008	8.440	-0.140	-0.140	0.000	0.000	0.000
125	A	147	LEU	0	-0.019	-0.014	7.634	-0.209	-0.209	0.000	0.000	0.000
126	A	148	SER	0	0.052	0.032	10.232	0.110	0.110	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:21:GLY)