FMO DATABASE

FMODB ID: LZJY9

Calculation Name: 3LKL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LKL

Chain ID: A

ChEMBL ID:

UniProt ID: Q3HKG0

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	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	93
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-659600.875206
FMO2-HF: Nuclear repulsion	622482.289652
FMO2-HF: Total energy	-37118.585554
FMO2-MP2: Total energy	-37225.554686

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:-1:ASN)

Summations of interaction energy for fragment #1(A:-1:ASN)

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.
-9.828	-5.353	0.085	-1.99	-2.569	-0.003

Interaction energy analysis for fragmet #1(A:-1:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.014

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	1	PHE	0	0.009	0.021	3.425	-3.253	0.537	0.003	-1.708	-2.084	-0.002
4	A	2	ALA	0	0.022	0.020	3.397	-4.347	-3.708	0.083	-0.282	-0.440	-0.001
5	A	3	VAL	0	0.058	0.038	5.642	1.186	1.186	0.000	0.000	0.000	0.000
6	A	4	SER	0	-0.028	-0.003	8.879	-0.157	-0.157	0.000	0.000	0.000	0.000
7	A	5	SER	0	-0.021	-0.005	11.388	0.282	0.282	0.000	0.000	0.000	0.000
8	A	6	GLU	-1	-0.955	-0.967	15.076	-0.864	-0.864	0.000	0.000	0.000	0.000
9	A	7	LEU	0	-0.066	-0.014	18.422	0.055	0.055	0.000	0.000	0.000	0.000
10	A	8	SER	0	0.011	0.004	21.581	0.032	0.032	0.000	0.000	0.000	0.000
11	A	9	ALA	0	0.026	0.008	25.109	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	10	CYS	0	-0.065	-0.045	27.766	0.017	0.017	0.000	0.000	0.000	0.000
13	A	11	GLY	0	0.058	0.034	25.595	0.015	0.015	0.000	0.000	0.000	0.000
14	A	12	ARG	1	0.887	0.948	26.191	0.338	0.338	0.000	0.000	0.000	0.000
15	A	13	ALA	0	0.010	0.006	24.964	0.018	0.018	0.000	0.000	0.000	0.000
16	A	14	ARG	1	0.899	0.929	17.356	0.914	0.914	0.000	0.000	0.000	0.000
17	A	15	THR	0	-0.048	-0.026	18.084	0.067	0.067	0.000	0.000	0.000	0.000
18	A	16	TYR	0	0.075	0.026	13.530	-0.091	-0.091	0.000	0.000	0.000	0.000
19	A	17	ARG	1	0.905	0.954	12.823	1.461	1.461	0.000	0.000	0.000	0.000
20	A	18	VAL	0	0.001	-0.002	10.223	-0.353	-0.353	0.000	0.000	0.000	0.000
21	A	19	GLU	-1	-0.935	-0.973	8.308	-1.907	-1.907	0.000	0.000	0.000	0.000
22	A	20	GLY	0	-0.030	-0.012	7.453	-0.586	-0.586	0.000	0.000	0.000	0.000
23	A	21	GLN	0	0.030	-0.009	7.324	0.259	0.259	0.000	0.000	0.000	0.000
24	A	22	LEU	0	0.006	0.016	8.305	0.223	0.223	0.000	0.000	0.000	0.000
25	A	23	PHE	0	0.017	0.001	7.024	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	24	TYR	0	0.032	-0.005	11.151	0.061	0.061	0.000	0.000	0.000	0.000
27	A	25	GLY	0	-0.042	-0.027	9.674	-0.185	-0.185	0.000	0.000	0.000	0.000
28	A	26	SER	0	-0.009	-0.005	6.694	0.349	0.349	0.000	0.000	0.000	0.000
29	A	27	VAL	0	0.002	-0.002	7.937	-0.650	-0.650	0.000	0.000	0.000	0.000
30	A	28	GLU	-1	-0.964	-0.973	9.903	-0.164	-0.164	0.000	0.000	0.000	0.000
31	A	29	ASP	-1	-0.858	-0.929	5.064	-2.034	-1.988	-0.001	0.000	-0.045	0.000
32	A	30	PHE	0	-0.060	-0.046	7.913	-0.318	-0.318	0.000	0.000	0.000	0.000
33	A	31	MET	0	-0.086	-0.053	9.632	-0.065	-0.065	0.000	0.000	0.000	0.000
34	A	32	ALA	0	-0.021	-0.007	9.974	0.063	0.063	0.000	0.000	0.000	0.000
35	A	33	ALA	0	-0.011	0.007	9.270	-0.092	-0.092	0.000	0.000	0.000	0.000
36	A	34	PHE	0	-0.072	-0.033	11.218	0.029	0.029	0.000	0.000	0.000	0.000
37	A	35	ASP	-1	-0.869	-0.940	14.972	-0.666	-0.666	0.000	0.000	0.000	0.000
38	A	36	PHE	0	-0.027	-0.044	16.709	0.070	0.070	0.000	0.000	0.000	0.000
39	A	37	ARG	1	0.894	0.945	20.328	0.512	0.512	0.000	0.000	0.000	0.000
40	A	38	GLU	-1	-0.785	-0.854	20.545	-0.709	-0.709	0.000	0.000	0.000	0.000
41	A	39	PRO	0	-0.057	-0.017	23.325	0.017	0.017	0.000	0.000	0.000	0.000
42	A	40	LEU	0	-0.019	-0.019	21.591	-0.018	-0.018	0.000	0.000	0.000	0.000
43	A	41	GLU	-1	-0.842	-0.922	26.287	-0.305	-0.305	0.000	0.000	0.000	0.000
44	A	42	ARG	1	0.903	0.957	25.853	0.376	0.376	0.000	0.000	0.000	0.000
45	A	43	VAL	0	0.039	0.014	20.149	-0.040	-0.040	0.000	0.000	0.000	0.000
46	A	44	THR	0	-0.069	-0.028	20.157	0.071	0.071	0.000	0.000	0.000	0.000
47	A	45	ILE	0	0.009	0.007	15.852	-0.095	-0.095	0.000	0.000	0.000	0.000
48	A	46	ASP	-1	-0.835	-0.897	16.767	-0.679	-0.679	0.000	0.000	0.000	0.000
49	A	47	VAL	0	0.038	0.008	14.628	-0.148	-0.148	0.000	0.000	0.000	0.000
50	A	48	SER	0	-0.022	-0.043	15.692	0.035	0.035	0.000	0.000	0.000	0.000
51	A	49	ARG	1	0.838	0.944	12.313	1.062	1.062	0.000	0.000	0.000	0.000
52	A	50	ALA	0	0.021	0.007	11.836	-0.206	-0.206	0.000	0.000	0.000	0.000
53	A	51	HIS	0	-0.005	0.010	12.130	0.092	0.092	0.000	0.000	0.000	0.000
54	A	52	ILE	0	-0.037	-0.031	13.022	0.053	0.053	0.000	0.000	0.000	0.000
55	A	53	TRP	0	-0.010	-0.027	11.466	0.025	0.025	0.000	0.000	0.000	0.000
56	A	54	ASP	-1	-0.733	-0.872	14.836	0.679	0.679	0.000	0.000	0.000	0.000
57	A	55	ILE	0	0.045	0.009	17.422	-0.075	-0.075	0.000	0.000	0.000	0.000
58	A	56	SER	0	0.006	0.012	16.244	-0.076	-0.076	0.000	0.000	0.000	0.000
59	A	57	SER	0	0.000	0.000	13.800	-0.073	-0.073	0.000	0.000	0.000	0.000
60	A	58	VAL	0	-0.030	-0.004	15.517	-0.112	-0.112	0.000	0.000	0.000	0.000
61	A	59	GLN	0	-0.002	-0.005	18.624	-0.037	-0.037	0.000	0.000	0.000	0.000
62	A	60	ALA	0	0.020	0.016	15.106	-0.040	-0.040	0.000	0.000	0.000	0.000
63	A	61	LEU	0	0.010	-0.003	16.301	-0.097	-0.097	0.000	0.000	0.000	0.000
64	A	62	ASP	-1	-0.887	-0.940	17.547	-0.187	-0.187	0.000	0.000	0.000	0.000
65	A	63	MET	0	-0.075	-0.046	19.166	0.000	0.000	0.000	0.000	0.000	0.000
66	A	64	ALA	0	0.007	0.011	16.677	-0.014	-0.014	0.000	0.000	0.000	0.000
67	A	65	VAL	0	0.021	0.001	18.889	-0.011	-0.011	0.000	0.000	0.000	0.000
68	A	66	LEU	0	-0.040	-0.031	21.847	0.006	0.006	0.000	0.000	0.000	0.000
69	A	67	LYS	1	0.858	0.943	20.898	0.375	0.375	0.000	0.000	0.000	0.000
70	A	68	PHE	0	0.050	0.013	18.144	0.010	0.010	0.000	0.000	0.000	0.000
71	A	69	ARG	1	0.923	0.959	23.296	0.272	0.272	0.000	0.000	0.000	0.000
72	A	70	ARG	1	0.891	0.967	24.252	0.248	0.248	0.000	0.000	0.000	0.000
73	A	71	GLU	-1	-0.910	-0.958	24.215	-0.316	-0.316	0.000	0.000	0.000	0.000
74	A	72	GLY	0	-0.019	0.001	27.270	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	73	ALA	0	-0.034	0.004	25.106	0.002	0.002	0.000	0.000	0.000	0.000
76	A	74	GLU	-1	-0.934	-0.969	27.178	-0.281	-0.281	0.000	0.000	0.000	0.000
77	A	75	VAL	0	-0.059	-0.040	22.243	-0.037	-0.037	0.000	0.000	0.000	0.000
78	A	76	ARG	1	0.946	0.975	23.662	0.430	0.430	0.000	0.000	0.000	0.000
79	A	77	ILE	0	0.013	0.011	19.597	-0.052	-0.052	0.000	0.000	0.000	0.000
80	A	78	VAL	0	-0.062	-0.037	20.295	0.056	0.056	0.000	0.000	0.000	0.000
81	A	79	GLY	0	0.115	0.050	19.536	-0.059	-0.059	0.000	0.000	0.000	0.000
82	A	80	MET	0	-0.023	0.000	19.795	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	81	ASN	0	-0.006	-0.002	21.140	0.013	0.013	0.000	0.000	0.000	0.000
84	A	82	GLU	-1	-0.847	-0.934	19.346	-0.319	-0.319	0.000	0.000	0.000	0.000
85	A	83	ALA	0	-0.012	0.003	16.321	0.048	0.048	0.000	0.000	0.000	0.000
86	A	84	SER	0	-0.044	-0.038	17.625	0.096	0.096	0.000	0.000	0.000	0.000
87	A	85	GLU	-1	-0.866	-0.916	20.200	0.025	0.025	0.000	0.000	0.000	0.000
88	A	86	THR	0	-0.020	-0.013	16.457	0.018	0.018	0.000	0.000	0.000	0.000
89	A	87	LEU	0	-0.026	-0.009	18.486	0.047	0.047	0.000	0.000	0.000	0.000
90	A	88	VAL	0	-0.040	-0.010	20.577	0.013	0.013	0.000	0.000	0.000	0.000
91	A	89	ASP	-1	-0.901	-0.933	24.107	0.093	0.093	0.000	0.000	0.000	0.000
92	A	90	ARG	1	0.778	0.885	21.001	-0.231	-0.231	0.000	0.000	0.000	0.000
93	A	91	LEU	0	-0.046	-0.021	22.559	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:-1:ASN)