FMO DATABASE

FMODB ID: 22MLR

Calculation Name: 3D0W-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D0W

Chain ID: A

ChEMBL ID:

UniProt ID: O34306

Base Structure: X-ray

Registration Date: 2023-03-14

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	86
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-566191.982336
FMO2-HF: Nuclear repulsion	532296.533734
FMO2-HF: Total energy	-33895.448602
FMO2-MP2: Total energy	-33996.092515

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:19:GLY)

Summations of interaction energy for fragment #1(A:19: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.
-4.252	-2.137	0.051	-0.959	-1.206	0.003

Interaction energy analysis for fragmet #1(A:19:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / 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

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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	21	ILE	0	-0.020	0.000	3.153	-2.131	-0.128	0.053	-0.906	-1.150	0.003
4	A	22	LYS	1	0.943	0.979	4.198	-0.193	-0.158	-0.001	-0.042	0.009	0.000
5	A	23	GLU	-1	-0.890	-0.960	6.826	-1.410	-1.410	0.000	0.000	0.000	0.000
6	A	24	ASP	-1	-0.854	-0.938	7.623	-0.635	-0.635	0.000	0.000	0.000	0.000
7	A	25	ILE	0	0.015	0.018	8.596	0.119	0.119	0.000	0.000	0.000	0.000
8	A	26	LEU	0	-0.026	-0.010	4.010	0.093	0.170	-0.001	-0.011	-0.065	0.000
9	A	27	LYS	1	0.965	0.980	8.628	0.624	0.624	0.000	0.000	0.000	0.000
10	A	28	ASP	-1	-0.817	-0.901	11.564	-0.265	-0.265	0.000	0.000	0.000	0.000
11	A	29	PHE	0	-0.021	-0.006	11.165	0.113	0.113	0.000	0.000	0.000	0.000
12	A	30	GLU	-1	-1.000	-1.013	10.835	-0.146	-0.146	0.000	0.000	0.000	0.000
13	A	31	GLU	-1	-0.980	-0.986	13.597	-0.220	-0.220	0.000	0.000	0.000	0.000
14	A	32	PHE	0	0.007	0.015	16.231	0.045	0.045	0.000	0.000	0.000	0.000
15	A	33	LYS	1	0.868	0.934	14.420	0.045	0.045	0.000	0.000	0.000	0.000
16	A	34	GLY	0	-0.017	-0.020	17.616	0.022	0.022	0.000	0.000	0.000	0.000
17	A	35	TYR	0	-0.034	-0.015	19.498	0.013	0.013	0.000	0.000	0.000	0.000
18	A	36	LEU	0	0.049	0.027	19.999	0.015	0.015	0.000	0.000	0.000	0.000
19	A	37	LYS	1	0.937	0.972	18.776	0.049	0.049	0.000	0.000	0.000	0.000
20	A	38	LYS	1	0.872	0.940	23.069	0.088	0.088	0.000	0.000	0.000	0.000
21	A	39	GLN	0	0.014	0.014	25.453	0.002	0.002	0.000	0.000	0.000	0.000
22	A	40	VAL	0	0.022	0.013	25.446	0.006	0.006	0.000	0.000	0.000	0.000
23	A	41	ASN	0	-0.009	-0.004	25.644	0.011	0.011	0.000	0.000	0.000	0.000
24	A	42	ARG	1	0.961	0.976	28.876	0.044	0.044	0.000	0.000	0.000	0.000
25	A	43	GLY	0	0.080	0.044	30.849	0.002	0.002	0.000	0.000	0.000	0.000
26	A	44	LYS	1	0.850	0.901	29.477	-0.004	-0.004	0.000	0.000	0.000	0.000
27	A	45	LYS	1	0.808	0.910	30.985	0.022	0.022	0.000	0.000	0.000	0.000
28	A	46	LEU	0	0.066	0.036	34.814	0.000	0.000	0.000	0.000	0.000	0.000
29	A	47	GLY	0	0.029	0.027	36.514	0.001	0.001	0.000	0.000	0.000	0.000
30	A	48	LEU	0	-0.043	-0.017	36.711	0.002	0.002	0.000	0.000	0.000	0.000
31	A	49	ASP	-1	-0.921	-0.961	38.638	-0.017	-0.017	0.000	0.000	0.000	0.000
32	A	50	ASP	-1	-0.958	-0.960	41.007	-0.010	-0.010	0.000	0.000	0.000	0.000
33	A	51	GLY	0	-0.061	-0.036	42.331	0.002	0.002	0.000	0.000	0.000	0.000
34	A	52	LYS	1	0.894	0.941	40.663	0.003	0.003	0.000	0.000	0.000	0.000
35	A	53	LEU	0	-0.006	-0.001	36.597	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	54	VAL	0	0.055	0.036	33.966	0.002	0.002	0.000	0.000	0.000	0.000
37	A	55	LYS	1	0.950	0.963	32.218	-0.027	-0.027	0.000	0.000	0.000	0.000
38	A	56	SER	0	0.055	0.008	27.117	-0.004	-0.004	0.000	0.000	0.000	0.000
39	A	57	ALA	0	0.061	0.031	28.451	-0.004	-0.004	0.000	0.000	0.000	0.000
40	A	58	ALA	0	0.015	0.019	29.426	-0.001	-0.001	0.000	0.000	0.000	0.000
41	A	59	ILE	0	-0.012	0.006	29.355	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	60	LEU	0	-0.013	-0.017	24.061	-0.005	-0.005	0.000	0.000	0.000	0.000
43	A	61	GLY	0	0.048	0.034	28.158	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	62	ASP	-1	-0.903	-0.957	30.664	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	63	TYR	0	-0.124	-0.071	23.890	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	64	LEU	0	0.069	0.036	25.299	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	65	ALA	0	-0.071	-0.026	29.266	-0.001	-0.001	0.000	0.000	0.000	0.000
48	A	66	LYS	1	0.872	0.939	31.536	0.025	0.025	0.000	0.000	0.000	0.000
49	A	67	HIS	0	-0.046	-0.015	30.901	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	68	GLU	-1	-0.871	-0.942	28.505	-0.055	-0.055	0.000	0.000	0.000	0.000
51	A	69	GLU	-1	-0.935	-0.970	28.262	-0.075	-0.075	0.000	0.000	0.000	0.000
52	A	70	PRO	0	-0.021	-0.017	24.144	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	71	GLN	0	-0.057	-0.029	22.962	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	72	ASN	0	0.009	0.008	18.040	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	73	GLY	0	0.030	0.007	17.941	0.021	0.021	0.000	0.000	0.000	0.000
56	A	74	GLU	-1	-0.893	-0.952	14.228	-0.147	-0.147	0.000	0.000	0.000	0.000
57	A	75	GLU	-1	-0.860	-0.939	18.345	-0.072	-0.072	0.000	0.000	0.000	0.000
58	A	76	MET	0	-0.011	0.004	21.689	0.010	0.010	0.000	0.000	0.000	0.000
59	A	77	LEU	0	-0.013	-0.002	18.782	0.014	0.014	0.000	0.000	0.000	0.000
60	A	78	LEU	0	-0.016	-0.023	21.190	0.013	0.013	0.000	0.000	0.000	0.000
61	A	79	GLN	0	0.006	0.004	23.492	0.007	0.007	0.000	0.000	0.000	0.000
62	A	80	GLU	-1	-0.913	-0.951	25.310	-0.011	-0.011	0.000	0.000	0.000	0.000
63	A	81	LEU	0	-0.037	-0.011	22.222	0.008	0.008	0.000	0.000	0.000	0.000
64	A	82	TRP	0	-0.001	-0.014	26.626	0.005	0.005	0.000	0.000	0.000	0.000
65	A	83	SER	0	-0.097	-0.060	29.090	0.001	0.001	0.000	0.000	0.000	0.000
66	A	84	VAL	0	-0.044	-0.021	29.273	0.000	0.000	0.000	0.000	0.000	0.000
67	A	85	ALA	0	-0.047	0.006	29.888	0.004	0.004	0.000	0.000	0.000	0.000
68	A	86	ASP	-1	-0.863	-0.937	31.911	0.033	0.033	0.000	0.000	0.000	0.000
69	A	87	GLU	-1	-0.970	-1.017	33.835	0.020	0.020	0.000	0.000	0.000	0.000
70	A	88	ASP	-1	-0.861	-0.920	34.420	0.039	0.039	0.000	0.000	0.000	0.000
71	A	89	GLU	-1	-0.919	-0.964	30.178	0.051	0.051	0.000	0.000	0.000	0.000
72	A	90	LYS	1	0.873	0.954	29.414	-0.008	-0.008	0.000	0.000	0.000	0.000
73	A	91	GLU	-1	-0.941	-0.960	29.813	0.031	0.031	0.000	0.000	0.000	0.000
74	A	92	HIS	0	-0.034	-0.034	28.413	0.006	0.006	0.000	0.000	0.000	0.000
75	A	93	LEU	0	0.013	0.013	23.246	0.009	0.009	0.000	0.000	0.000	0.000
76	A	94	ALA	0	0.027	0.012	24.828	0.000	0.000	0.000	0.000	0.000	0.000
77	A	95	GLN	0	-0.067	-0.045	25.908	-0.005	-0.005	0.000	0.000	0.000	0.000
78	A	96	LEU	0	-0.040	-0.023	21.019	0.007	0.007	0.000	0.000	0.000	0.000
79	A	97	LEU	0	0.054	0.027	20.335	0.010	0.010	0.000	0.000	0.000	0.000
80	A	98	VAL	0	-0.010	-0.002	21.432	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	99	LYS	1	0.905	0.960	21.085	-0.126	-0.126	0.000	0.000	0.000	0.000
82	A	100	LEU	0	-0.023	0.006	16.198	0.013	0.013	0.000	0.000	0.000	0.000
83	A	101	VAL	0	0.020	-0.005	17.330	-0.009	-0.009	0.000	0.000	0.000	0.000
84	A	102	ASP	-1	-1.010	-1.006	18.969	0.011	0.011	0.000	0.000	0.000	0.000
85	A	103	LYS	1	0.949	0.985	12.444	-0.274	-0.274	0.000	0.000	0.000	0.000
86	A	104	GLN	0	-0.008	-0.005	10.901	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:19:GLY)