FMO DATABASE

FMODB ID: LZGR9

Calculation Name: 2SPC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2SPC

Chain ID: A

ChEMBL ID:

UniProt ID: P13395

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	107
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-624533.241466
FMO2-HF: Nuclear repulsion	581378.106695
FMO2-HF: Total energy	-43155.134771
FMO2-MP2: Total energy	-43281.299977

3D Structure Molmil

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:0:GLN)

Summations of interaction energy for fragment #1(A:0:GLN)

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.
-5.481	-3.54	5.027	-3.115	-3.854	-0.006

Interaction energy analysis for fragmet #1(A:0:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.011 / q_NPA : -0.010

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	2	LEU	0	0.024	-0.014	3.808	-2.176	-0.893	0.003	-0.525	-0.762	0.002
4	A	3	ASP	-1	-0.812	-0.909	6.037	0.591	0.591	0.000	0.000	0.000	0.000
5	A	4	LEU	0	0.003	0.003	1.742	0.819	-1.198	4.738	-1.269	-1.452	-0.001
6	A	5	GLN	0	-0.033	-0.033	3.180	-3.774	-1.099	0.286	-1.321	-1.640	-0.007
7	A	6	LEU	0	-0.024	-0.010	5.711	0.130	0.130	0.000	0.000	0.000	0.000
8	A	7	TYR	0	0.083	0.036	7.916	-0.002	-0.002	0.000	0.000	0.000	0.000
9	A	8	MET	0	0.014	0.014	6.110	0.030	0.030	0.000	0.000	0.000	0.000
10	A	9	ARG	1	0.890	0.951	8.845	-0.412	-0.412	0.000	0.000	0.000	0.000
11	A	10	ASP	-1	-0.879	-0.939	11.302	0.225	0.225	0.000	0.000	0.000	0.000
12	A	11	CYS	0	-0.059	-0.022	11.720	0.013	0.013	0.000	0.000	0.000	0.000
13	A	12	GLU	-1	-0.879	-0.939	11.695	-0.553	-0.553	0.000	0.000	0.000	0.000
14	A	13	LEU	0	-0.092	-0.050	14.582	0.032	0.032	0.000	0.000	0.000	0.000
15	A	14	ALA	0	-0.015	-0.015	16.724	0.009	0.009	0.000	0.000	0.000	0.000
16	A	15	GLU	-1	-0.888	-0.947	15.805	-0.325	-0.325	0.000	0.000	0.000	0.000
17	A	16	SER	0	-0.040	-0.005	18.880	0.005	0.005	0.000	0.000	0.000	0.000
18	A	17	TRP	0	-0.038	-0.027	20.738	0.011	0.011	0.000	0.000	0.000	0.000
19	A	18	MET	0	-0.010	-0.015	20.080	0.006	0.006	0.000	0.000	0.000	0.000
20	A	19	SER	0	0.027	0.018	22.457	-0.006	-0.006	0.000	0.000	0.000	0.000
21	A	20	ALA	0	-0.054	-0.017	24.795	0.004	0.004	0.000	0.000	0.000	0.000
22	A	21	ARG	1	0.881	0.930	26.866	0.012	0.012	0.000	0.000	0.000	0.000
23	A	22	GLU	-1	-0.898	-0.955	26.541	-0.098	-0.098	0.000	0.000	0.000	0.000
24	A	23	ALA	0	-0.043	-0.015	29.183	0.001	0.001	0.000	0.000	0.000	0.000
25	A	24	PHE	0	-0.069	-0.038	31.090	0.005	0.005	0.000	0.000	0.000	0.000
26	A	25	LEU	0	0.016	0.004	31.266	0.004	0.004	0.000	0.000	0.000	0.000
27	A	26	ASN	0	-0.004	-0.006	33.794	-0.002	-0.002	0.000	0.000	0.000	0.000
28	A	27	ALA	0	0.003	0.020	35.504	0.002	0.002	0.000	0.000	0.000	0.000
29	A	28	ASP	-1	-0.882	-0.942	37.096	-0.015	-0.015	0.000	0.000	0.000	0.000
30	A	29	ASP	-1	-0.980	-0.987	38.404	-0.051	-0.051	0.000	0.000	0.000	0.000
31	A	30	ASP	-1	-0.857	-0.923	39.399	-0.044	-0.044	0.000	0.000	0.000	0.000
32	A	31	ALA	0	-0.155	-0.083	42.012	0.003	0.003	0.000	0.000	0.000	0.000
33	A	32	ASN	0	-0.027	0.004	40.895	0.002	0.002	0.000	0.000	0.000	0.000
34	A	33	ALA	0	-0.025	-0.021	42.778	0.003	0.003	0.000	0.000	0.000	0.000
35	A	34	GLY	0	0.060	0.008	44.672	0.000	0.000	0.000	0.000	0.000	0.000
36	A	35	GLY	0	-0.003	0.019	48.395	0.001	0.001	0.000	0.000	0.000	0.000
37	A	36	ASN	0	-0.025	0.001	50.121	0.001	0.001	0.000	0.000	0.000	0.000
38	A	37	VAL	0	0.065	0.007	49.587	0.000	0.000	0.000	0.000	0.000	0.000
39	A	38	GLU	-1	-0.910	-0.961	49.069	0.013	0.013	0.000	0.000	0.000	0.000
40	A	39	ALA	0	-0.035	-0.043	46.249	0.001	0.001	0.000	0.000	0.000	0.000
41	A	40	LEU	0	-0.031	0.012	45.142	-0.001	-0.001	0.000	0.000	0.000	0.000
42	A	41	ILE	0	0.021	0.003	44.193	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	42	LYS	1	0.840	0.926	41.746	-0.022	-0.022	0.000	0.000	0.000	0.000
44	A	43	LYS	1	0.874	0.945	39.701	0.019	0.019	0.000	0.000	0.000	0.000
45	A	44	HIS	0	-0.012	-0.004	39.302	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	45	GLU	-1	-0.818	-0.929	38.786	0.019	0.019	0.000	0.000	0.000	0.000
47	A	46	ASP	-1	-0.881	-0.918	36.678	0.019	0.019	0.000	0.000	0.000	0.000
48	A	47	PHE	0	-0.035	-0.021	34.789	0.001	0.001	0.000	0.000	0.000	0.000
49	A	48	ASP	-1	-0.865	-0.916	33.716	-0.004	-0.004	0.000	0.000	0.000	0.000
50	A	49	LYS	1	0.819	0.890	33.370	-0.022	-0.022	0.000	0.000	0.000	0.000
51	A	50	ALA	0	-0.078	-0.032	30.545	0.003	0.003	0.000	0.000	0.000	0.000
52	A	51	ILE	0	0.008	-0.006	29.164	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	52	ASN	0	0.023	0.017	28.870	-0.005	-0.005	0.000	0.000	0.000	0.000
54	A	53	GLY	0	0.019	0.012	27.515	0.004	0.004	0.000	0.000	0.000	0.000
55	A	54	HIS	0	-0.020	-0.015	24.160	0.004	0.004	0.000	0.000	0.000	0.000
56	A	55	GLU	-1	-0.865	-0.935	23.776	-0.024	-0.024	0.000	0.000	0.000	0.000
57	A	56	GLN	0	-0.020	-0.007	24.161	0.001	0.001	0.000	0.000	0.000	0.000
58	A	57	LYS	1	0.917	0.971	17.211	-0.045	-0.045	0.000	0.000	0.000	0.000
59	A	58	ILE	0	-0.009	-0.011	19.704	0.000	0.000	0.000	0.000	0.000	0.000
60	A	59	ALA	0	0.047	0.020	19.338	-0.003	-0.003	0.000	0.000	0.000	0.000
61	A	60	ALA	0	-0.024	-0.020	19.061	0.011	0.011	0.000	0.000	0.000	0.000
62	A	61	LEU	0	-0.030	-0.024	13.964	0.024	0.024	0.000	0.000	0.000	0.000
63	A	62	GLN	0	0.027	0.018	14.832	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	63	THR	0	0.001	0.000	16.522	0.012	0.012	0.000	0.000	0.000	0.000
65	A	64	VAL	0	-0.018	-0.006	11.232	0.027	0.027	0.000	0.000	0.000	0.000
66	A	65	ALA	0	0.006	-0.002	11.543	0.031	0.031	0.000	0.000	0.000	0.000
67	A	66	ASP	-1	-0.893	-0.942	12.360	0.054	0.054	0.000	0.000	0.000	0.000
68	A	67	GLN	0	-0.067	-0.037	13.409	0.046	0.046	0.000	0.000	0.000	0.000
69	A	68	LEU	0	-0.002	0.014	7.430	0.051	0.051	0.000	0.000	0.000	0.000
70	A	69	ILE	0	0.015	0.001	10.313	0.116	0.116	0.000	0.000	0.000	0.000
71	A	70	ALA	0	0.022	0.022	11.902	0.021	0.021	0.000	0.000	0.000	0.000
72	A	71	GLN	0	-0.046	-0.025	9.786	-0.058	-0.058	0.000	0.000	0.000	0.000
73	A	72	ASN	0	-0.004	-0.009	7.397	0.221	0.221	0.000	0.000	0.000	0.000
74	A	73	HIS	0	-0.009	-0.007	11.219	-0.049	-0.049	0.000	0.000	0.000	0.000
75	A	74	TYR	0	-0.019	0.001	14.822	-0.046	-0.046	0.000	0.000	0.000	0.000
76	A	75	ALA	0	0.017	0.005	12.299	-0.032	-0.032	0.000	0.000	0.000	0.000
77	A	76	SER	0	0.008	-0.008	13.034	-0.064	-0.064	0.000	0.000	0.000	0.000
78	A	77	ASN	0	0.011	0.007	15.239	-0.064	-0.064	0.000	0.000	0.000	0.000
79	A	78	LEU	0	-0.027	0.002	16.952	-0.030	-0.030	0.000	0.000	0.000	0.000
80	A	79	VAL	0	-0.011	-0.011	14.434	-0.028	-0.028	0.000	0.000	0.000	0.000
81	A	80	ASP	-1	-0.828	-0.894	17.693	-0.040	-0.040	0.000	0.000	0.000	0.000
82	A	81	GLU	-1	-0.851	-0.938	20.220	0.017	0.017	0.000	0.000	0.000	0.000
83	A	82	LYS	1	0.924	0.973	20.800	-0.086	-0.086	0.000	0.000	0.000	0.000
84	A	83	ARG	1	0.842	0.894	21.044	0.017	0.017	0.000	0.000	0.000	0.000
85	A	84	LYS	1	0.928	0.965	22.933	-0.017	-0.017	0.000	0.000	0.000	0.000
86	A	85	GLN	0	-0.005	0.002	25.860	0.001	0.001	0.000	0.000	0.000	0.000
87	A	86	VAL	0	-0.035	-0.017	24.240	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	87	LEU	0	-0.021	-0.023	25.915	-0.006	-0.006	0.000	0.000	0.000	0.000
89	A	88	GLU	-1	-0.812	-0.892	28.554	-0.014	-0.014	0.000	0.000	0.000	0.000
90	A	89	ARG	1	0.918	0.965	27.820	-0.038	-0.038	0.000	0.000	0.000	0.000
91	A	90	TRP	0	-0.023	-0.016	30.612	0.000	0.000	0.000	0.000	0.000	0.000
92	A	91	ARG	1	0.923	0.938	32.397	0.013	0.013	0.000	0.000	0.000	0.000
93	A	92	HIS	0	0.020	0.017	34.692	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	93	LEU	0	-0.003	0.014	34.142	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	94	LYS	1	0.906	0.945	35.670	0.044	0.044	0.000	0.000	0.000	0.000
96	A	95	GLU	-1	-0.902	-0.948	37.528	-0.018	-0.018	0.000	0.000	0.000	0.000
97	A	96	GLY	0	0.014	0.024	40.216	0.000	0.000	0.000	0.000	0.000	0.000
98	A	97	LEU	0	-0.077	-0.047	37.333	-0.001	-0.001	0.000	0.000	0.000	0.000
99	A	98	ILE	0	0.011	-0.016	40.111	-0.001	-0.001	0.000	0.000	0.000	0.000
100	A	99	GLU	-1	-0.823	-0.897	43.178	-0.015	-0.015	0.000	0.000	0.000	0.000
101	A	100	LYS	1	0.888	0.934	44.986	0.008	0.008	0.000	0.000	0.000	0.000
102	A	101	ARG	1	0.915	0.958	43.421	0.031	0.031	0.000	0.000	0.000	0.000
103	A	102	SER	0	0.012	0.005	46.865	-0.002	-0.002	0.000	0.000	0.000	0.000
104	A	103	ARG	1	0.951	0.963	48.980	0.007	0.007	0.000	0.000	0.000	0.000
105	A	104	LEU	0	-0.127	-0.044	48.957	0.001	0.001	0.000	0.000	0.000	0.000
106	A	105	GLY	0	-0.005	0.003	52.036	0.001	0.001	0.000	0.000	0.000	0.000
107	A	106	ASP	-1	-0.978	-0.966	53.988	-0.015	-0.015	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLN)