FMO DATABASE

FMODB ID: R9ZJ8

Calculation Name: 3L0X-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3L0X

Chain ID: B

ChEMBL ID:

UniProt ID: P15873

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	91
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-553395.759294
FMO2-HF: Nuclear repulsion	518592.260083
FMO2-HF: Total energy	-34803.499211
FMO2-MP2: Total energy	-34905.844007

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(B:165:GLU)

Summations of interaction energy for fragment #1(B:165:GLU)

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.
12.88	16.976	0.179	-2.04	-2.233	0.009

Interaction energy analysis for fragmet #1(B:165:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.926 / q_NPA : -0.958

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	B	167	ILE	0	0.006	0.016	3.568	-6.532	-3.831	-0.006	-1.416	-1.278	0.006
4	B	168	LYS	1	0.941	0.964	7.113	-25.814	-25.814	0.000	0.000	0.000	0.000
5	B	169	PHE	0	0.007	0.014	9.520	-1.336	-1.336	0.000	0.000	0.000	0.000
6	B	170	VAL	0	0.001	-0.017	12.992	0.142	0.142	0.000	0.000	0.000	0.000
7	B	171	ALA	0	-0.028	0.001	15.611	-0.539	-0.539	0.000	0.000	0.000	0.000
8	B	172	ASP	-1	-0.903	-0.970	19.394	13.902	13.902	0.000	0.000	0.000	0.000
9	B	173	GLY	0	-0.039	-0.019	21.188	-0.295	-0.295	0.000	0.000	0.000	0.000
10	B	174	ASP	-1	-0.925	-0.965	24.859	9.996	9.996	0.000	0.000	0.000	0.000
11	B	175	ILE	0	-0.044	-0.024	27.149	-0.059	-0.059	0.000	0.000	0.000	0.000
12	B	176	GLY	0	0.012	0.006	25.091	-0.090	-0.090	0.000	0.000	0.000	0.000
13	B	177	SER	0	-0.012	0.011	19.792	0.210	0.210	0.000	0.000	0.000	0.000
14	B	178	GLY	0	-0.003	0.004	18.935	-0.201	-0.201	0.000	0.000	0.000	0.000
15	B	179	SER	0	-0.028	-0.032	13.046	0.709	0.709	0.000	0.000	0.000	0.000
16	B	180	VAL	0	-0.005	0.010	12.835	-0.005	-0.005	0.000	0.000	0.000	0.000
17	B	181	ILE	0	-0.014	-0.012	7.045	0.755	0.755	0.000	0.000	0.000	0.000
18	B	182	ILE	0	-0.006	0.004	8.631	-1.009	-1.009	0.000	0.000	0.000	0.000
19	B	183	LYS	1	0.977	0.978	5.223	-36.489	-36.489	0.000	0.000	0.000	0.000
20	B	184	PRO	0	0.038	0.022	4.035	-5.595	-5.179	0.006	-0.140	-0.281	0.001
21	B	185	PHE	0	-0.065	-0.034	6.845	2.493	2.493	0.000	0.000	0.000	0.000
22	B	186	VAL	0	0.009	-0.002	9.625	-1.561	-1.561	0.000	0.000	0.000	0.000
23	B	187	ASP	-1	-0.858	-0.945	13.006	17.218	17.218	0.000	0.000	0.000	0.000
24	B	188	MET	0	-0.028	-0.008	16.279	-0.243	-0.243	0.000	0.000	0.000	0.000
25	B	189	GLU	-1	-0.936	-0.961	19.625	13.799	13.799	0.000	0.000	0.000	0.000
26	B	190	HIS	0	-0.008	-0.010	20.717	-0.270	-0.270	0.000	0.000	0.000	0.000
27	B	191	PRO	0	0.069	0.038	18.147	0.766	0.766	0.000	0.000	0.000	0.000
28	B	192	GLU	-1	-0.933	-0.966	17.727	15.126	15.126	0.000	0.000	0.000	0.000
29	B	193	THR	0	-0.015	0.001	17.176	-0.207	-0.207	0.000	0.000	0.000	0.000
30	B	194	SER	0	-0.070	-0.041	13.457	1.082	1.082	0.000	0.000	0.000	0.000
31	B	195	ILE	0	-0.031	0.007	8.835	-0.694	-0.694	0.000	0.000	0.000	0.000
32	B	196	LYS	1	0.952	0.967	9.470	-17.402	-17.402	0.000	0.000	0.000	0.000
33	B	197	LEU	0	0.026	-0.002	3.433	-0.872	-0.236	0.154	-0.339	-0.451	0.003
34	B	198	GLU	-1	-0.955	-0.959	6.446	24.672	24.672	0.000	0.000	0.000	0.000
35	B	199	MET	0	-0.049	-0.029	4.153	-0.186	0.157	0.025	-0.145	-0.223	-0.001
36	B	200	ASP	-1	-0.878	-0.924	6.173	21.571	21.571	0.000	0.000	0.000	0.000
37	B	201	GLN	0	-0.067	-0.058	8.674	-1.347	-1.347	0.000	0.000	0.000	0.000
38	B	202	PRO	0	-0.008	0.006	6.981	1.073	1.073	0.000	0.000	0.000	0.000
39	B	203	VAL	0	-0.019	-0.008	7.951	-2.266	-2.266	0.000	0.000	0.000	0.000
40	B	204	ASP	-1	-0.933	-0.968	9.825	20.944	20.944	0.000	0.000	0.000	0.000
41	B	205	LEU	0	0.000	-0.001	12.600	-1.400	-1.400	0.000	0.000	0.000	0.000
42	B	206	THR	0	0.037	0.026	15.367	0.202	0.202	0.000	0.000	0.000	0.000
43	B	207	PHE	0	0.033	0.009	15.503	-0.727	-0.727	0.000	0.000	0.000	0.000
44	B	208	GLY	0	-0.043	-0.024	20.334	-0.093	-0.093	0.000	0.000	0.000	0.000
45	B	209	ALA	0	0.078	0.026	22.964	0.012	0.012	0.000	0.000	0.000	0.000
46	B	210	LYS	1	0.941	0.968	23.924	-9.591	-9.591	0.000	0.000	0.000	0.000
47	B	211	TYR	0	0.063	0.018	24.339	-0.213	-0.213	0.000	0.000	0.000	0.000
48	B	212	LEU	0	0.048	0.032	19.015	-0.058	-0.058	0.000	0.000	0.000	0.000
49	B	213	LEU	0	-0.014	-0.013	22.716	0.108	0.108	0.000	0.000	0.000	0.000
50	B	214	ASP	-1	-0.937	-0.963	25.573	9.846	9.846	0.000	0.000	0.000	0.000
51	B	215	ILE	0	-0.049	-0.017	21.112	-0.125	-0.125	0.000	0.000	0.000	0.000
52	B	216	ILE	0	0.013	0.011	21.234	-0.037	-0.037	0.000	0.000	0.000	0.000
53	B	217	LYS	1	0.949	0.997	23.701	-9.986	-9.986	0.000	0.000	0.000	0.000
54	B	218	GLY	0	-0.007	0.005	25.504	-0.296	-0.296	0.000	0.000	0.000	0.000
55	B	219	SER	0	0.009	-0.033	23.488	0.288	0.288	0.000	0.000	0.000	0.000
56	B	220	SER	0	-0.109	-0.038	24.652	-0.075	-0.075	0.000	0.000	0.000	0.000
57	B	221	LEU	0	-0.052	-0.033	26.677	-0.380	-0.380	0.000	0.000	0.000	0.000
58	B	222	SER	0	-0.078	-0.036	22.136	-0.200	-0.200	0.000	0.000	0.000	0.000
59	B	223	ASP	-1	-0.866	-0.909	22.069	12.353	12.353	0.000	0.000	0.000	0.000
60	B	224	ARG	1	0.811	0.907	13.808	-17.144	-17.144	0.000	0.000	0.000	0.000
61	B	225	VAL	0	-0.002	0.001	16.225	-0.649	-0.649	0.000	0.000	0.000	0.000
62	B	226	GLY	0	-0.013	-0.007	15.531	1.085	1.085	0.000	0.000	0.000	0.000
63	B	227	ILE	0	-0.025	-0.025	13.084	-0.800	-0.800	0.000	0.000	0.000	0.000
64	B	228	ARG	1	0.943	0.981	12.957	-14.420	-14.420	0.000	0.000	0.000	0.000
65	B	229	LEU	0	0.008	-0.008	10.798	-0.925	-0.925	0.000	0.000	0.000	0.000
66	B	230	SER	0	0.027	-0.001	12.925	0.563	0.563	0.000	0.000	0.000	0.000
67	B	231	SER	0	0.010	0.011	14.883	-0.004	-0.004	0.000	0.000	0.000	0.000
68	B	232	GLU	-1	-0.908	-0.946	16.613	12.931	12.931	0.000	0.000	0.000	0.000
69	B	233	ALA	0	-0.054	-0.027	18.734	-0.772	-0.772	0.000	0.000	0.000	0.000
70	B	234	PRO	0	-0.040	-0.029	19.257	0.420	0.420	0.000	0.000	0.000	0.000
71	B	235	ALA	0	0.012	0.032	16.670	0.188	0.188	0.000	0.000	0.000	0.000
72	B	236	LEU	0	-0.039	-0.015	17.196	-0.732	-0.732	0.000	0.000	0.000	0.000
73	B	237	PHE	0	0.005	-0.004	16.912	0.936	0.936	0.000	0.000	0.000	0.000
74	B	238	GLN	0	-0.010	-0.008	18.965	-0.783	-0.783	0.000	0.000	0.000	0.000
75	B	239	PHE	0	0.071	0.039	20.166	0.595	0.595	0.000	0.000	0.000	0.000
76	B	240	ASP	-1	-0.871	-0.943	21.355	12.570	12.570	0.000	0.000	0.000	0.000
77	B	241	LEU	0	0.015	0.008	24.323	-0.153	-0.153	0.000	0.000	0.000	0.000
78	B	242	LYS	1	0.954	0.969	27.547	-8.993	-8.993	0.000	0.000	0.000	0.000
79	B	243	SER	0	-0.061	-0.047	29.067	-0.345	-0.345	0.000	0.000	0.000	0.000
80	B	244	GLY	0	0.038	0.023	28.555	-0.379	-0.379	0.000	0.000	0.000	0.000
81	B	245	PHE	0	-0.019	0.001	24.882	0.369	0.369	0.000	0.000	0.000	0.000
82	B	246	LEU	0	0.011	0.021	25.646	-0.424	-0.424	0.000	0.000	0.000	0.000
83	B	247	GLN	0	-0.037	-0.025	22.859	0.105	0.105	0.000	0.000	0.000	0.000
84	B	248	PHE	0	0.022	0.005	22.540	-0.462	-0.462	0.000	0.000	0.000	0.000
85	B	249	PHE	0	0.021	0.010	21.699	0.589	0.589	0.000	0.000	0.000	0.000
86	B	250	LEU	0	-0.040	-0.017	20.679	-0.520	-0.520	0.000	0.000	0.000	0.000
87	B	251	ALA	0	-0.001	-0.010	20.875	0.516	0.516	0.000	0.000	0.000	0.000
88	B	252	PRO	0	0.028	0.028	18.562	-0.200	-0.200	0.000	0.000	0.000	0.000
89	B	253	LYS	1	0.897	0.932	20.700	-12.208	-12.208	0.000	0.000	0.000	0.000
90	B	254	PHE	0	0.015	0.006	21.537	0.336	0.336	0.000	0.000	0.000	0.000
91	B	255	ASN	0	0.014	0.022	22.935	0.516	0.516	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:165:GLU)