FMO DATABASE

FMODB ID: 828NY

Calculation Name: 3R84-A-Xray318

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3R84

Chain ID: A

ChEMBL ID:

UniProt ID: Q99278

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	82
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-495571.673691
FMO2-HF: Nuclear repulsion	462446.027297
FMO2-HF: Total energy	-33125.646394
FMO2-MP2: Total energy	-33222.916934

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:4:GLY )

Summations of interaction energy for fragment #1(A:4: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.
-0.605	2.753	5.707	-4.287	-4.776	-0.013

Interaction energy analysis for fragmet #1(A:4:GLY )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.095 / q_NPA : 0.039

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	6	ILE	0	0.069	0.020	3.576	-0.992	0.796	0.006	-0.960	-0.834	0.005
4	A	7	GLN	0	0.035	0.023	2.069	-2.552	-1.995	5.695	-2.952	-3.300	-0.016
5	A	8	GLU	-1	-0.871	-0.927	3.690	-4.419	-3.481	0.006	-0.369	-0.574	-0.002
6	A	9	ARG	1	0.792	0.888	5.831	2.900	2.900	0.000	0.000	0.000	0.000
7	A	10	LEU	0	0.028	0.009	7.282	0.416	0.416	0.000	0.000	0.000	0.000
8	A	11	LYS	1	0.908	0.951	4.192	3.725	3.800	0.000	-0.006	-0.068	0.000
9	A	12	SER	0	-0.057	-0.039	9.477	0.353	0.353	0.000	0.000	0.000	0.000
10	A	13	LEU	0	0.010	-0.009	11.701	0.214	0.214	0.000	0.000	0.000	0.000
11	A	14	ASN	0	-0.037	-0.031	11.688	0.011	0.011	0.000	0.000	0.000	0.000
12	A	15	ASP	-1	-0.899	-0.952	13.587	-0.519	-0.519	0.000	0.000	0.000	0.000
13	A	16	ILE	0	-0.007	-0.012	15.430	0.110	0.110	0.000	0.000	0.000	0.000
14	A	17	GLU	-1	-0.855	-0.923	16.215	-0.478	-0.478	0.000	0.000	0.000	0.000
15	A	18	THR	0	-0.001	0.011	17.539	0.078	0.078	0.000	0.000	0.000	0.000
16	A	19	GLN	0	-0.079	-0.054	17.969	0.101	0.101	0.000	0.000	0.000	0.000
17	A	20	LEU	0	0.022	0.009	21.381	0.044	0.044	0.000	0.000	0.000	0.000
18	A	21	CYS	0	-0.010	-0.002	22.328	0.040	0.040	0.000	0.000	0.000	0.000
19	A	22	SER	0	-0.042	-0.024	23.871	0.032	0.032	0.000	0.000	0.000	0.000
20	A	23	MET	0	-0.026	0.003	25.993	0.015	0.015	0.000	0.000	0.000	0.000
21	A	24	LEU	0	0.019	0.013	26.899	0.021	0.021	0.000	0.000	0.000	0.000
22	A	25	GLN	0	0.032	0.014	28.164	0.021	0.021	0.000	0.000	0.000	0.000
23	A	26	GLU	-1	-0.845	-0.910	29.796	-0.165	-0.165	0.000	0.000	0.000	0.000
24	A	27	ALA	0	0.038	0.030	32.123	0.013	0.013	0.000	0.000	0.000	0.000
25	A	28	SER	0	-0.004	0.015	33.156	0.014	0.014	0.000	0.000	0.000	0.000
26	A	29	GLN	0	-0.039	-0.026	32.371	0.017	0.017	0.000	0.000	0.000	0.000
27	A	30	VAL	0	0.005	0.010	36.110	0.009	0.009	0.000	0.000	0.000	0.000
28	A	31	THR	0	-0.029	-0.032	37.769	0.009	0.009	0.000	0.000	0.000	0.000
29	A	32	PHE	0	-0.004	-0.010	39.474	0.006	0.006	0.000	0.000	0.000	0.000
30	A	33	ILE	0	-0.002	-0.011	38.910	0.005	0.005	0.000	0.000	0.000	0.000
31	A	34	PHE	0	0.003	0.007	42.348	0.006	0.006	0.000	0.000	0.000	0.000
32	A	35	GLY	0	0.005	0.001	44.333	0.005	0.005	0.000	0.000	0.000	0.000
33	A	36	GLU	-1	-0.844	-0.912	44.862	-0.069	-0.069	0.000	0.000	0.000	0.000
34	A	37	LEU	0	-0.009	-0.002	44.752	0.004	0.004	0.000	0.000	0.000	0.000
35	A	38	LYS	1	0.887	0.958	48.319	0.077	0.077	0.000	0.000	0.000	0.000
36	A	39	ARG	1	0.848	0.917	48.908	0.069	0.069	0.000	0.000	0.000	0.000
37	A	40	GLY	0	0.011	0.013	51.767	0.003	0.003	0.000	0.000	0.000	0.000
38	A	41	ASN	0	-0.045	0.000	47.295	0.003	0.003	0.000	0.000	0.000	0.000
39	A	42	GLU	-1	-0.830	-0.937	48.360	-0.078	-0.078	0.000	0.000	0.000	0.000
40	A	43	SER	0	-0.081	-0.057	47.620	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	44	VAL	0	0.001	0.003	42.970	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	45	LYS	1	0.937	0.983	43.013	0.076	0.076	0.000	0.000	0.000	0.000
43	A	46	PRO	0	0.058	0.014	42.352	-0.005	-0.005	0.000	0.000	0.000	0.000
44	A	47	GLN	0	0.049	0.016	38.957	-0.006	-0.006	0.000	0.000	0.000	0.000
45	A	48	PHE	0	-0.029	-0.005	38.342	-0.009	-0.009	0.000	0.000	0.000	0.000
46	A	49	GLU	-1	-0.891	-0.951	38.918	-0.104	-0.104	0.000	0.000	0.000	0.000
47	A	50	ASN	0	-0.078	-0.047	33.774	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	51	HIS	1	0.856	0.897	33.295	0.134	0.134	0.000	0.000	0.000	0.000
49	A	52	VAL	0	0.024	0.028	34.037	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	53	LYS	1	0.941	0.976	33.494	0.135	0.135	0.000	0.000	0.000	0.000
51	A	54	GLN	0	0.023	0.017	29.327	0.000	0.000	0.000	0.000	0.000	0.000
52	A	55	PHE	0	-0.014	-0.001	29.662	-0.019	-0.019	0.000	0.000	0.000	0.000
53	A	56	TYR	0	0.018	0.013	29.976	-0.013	-0.013	0.000	0.000	0.000	0.000
54	A	57	GLU	-1	-0.900	-0.961	28.194	-0.203	-0.203	0.000	0.000	0.000	0.000
55	A	58	ARG	1	0.865	0.933	24.693	0.223	0.223	0.000	0.000	0.000	0.000
56	A	59	LEU	0	0.013	0.011	25.248	-0.028	-0.028	0.000	0.000	0.000	0.000
57	A	60	ASP	-1	-0.901	-0.934	26.288	-0.277	-0.277	0.000	0.000	0.000	0.000
58	A	61	LYS	1	0.962	0.988	19.515	0.398	0.398	0.000	0.000	0.000	0.000
59	A	62	SER	0	-0.011	-0.015	21.136	-0.039	-0.039	0.000	0.000	0.000	0.000
60	A	63	THR	0	-0.036	-0.035	21.330	-0.037	-0.037	0.000	0.000	0.000	0.000
61	A	64	THR	0	0.011	0.012	21.460	-0.016	-0.016	0.000	0.000	0.000	0.000
62	A	65	GLN	0	-0.066	-0.030	14.840	0.066	0.066	0.000	0.000	0.000	0.000
63	A	66	LEU	0	0.020	-0.006	17.832	-0.068	-0.068	0.000	0.000	0.000	0.000
64	A	67	ARG	1	0.917	0.965	19.322	0.371	0.371	0.000	0.000	0.000	0.000
65	A	68	LYS	1	0.929	0.960	13.311	0.871	0.871	0.000	0.000	0.000	0.000
66	A	69	GLU	-1	-0.753	-0.850	12.964	-1.245	-1.245	0.000	0.000	0.000	0.000
67	A	70	ILE	0	0.005	0.011	15.672	-0.021	-0.021	0.000	0.000	0.000	0.000
68	A	71	GLN	0	0.010	0.025	18.140	0.015	0.015	0.000	0.000	0.000	0.000
69	A	72	LEU	0	-0.021	-0.015	12.022	-0.019	-0.019	0.000	0.000	0.000	0.000
70	A	73	LEU	0	-0.026	0.001	13.796	-0.031	-0.031	0.000	0.000	0.000	0.000
71	A	74	ASP	-1	-0.893	-0.946	15.294	-0.288	-0.288	0.000	0.000	0.000	0.000
72	A	75	GLU	-1	-0.947	-0.973	15.415	-0.468	-0.468	0.000	0.000	0.000	0.000
73	A	76	ASN	0	-0.103	-0.087	10.984	-0.024	-0.024	0.000	0.000	0.000	0.000
74	A	77	VAL	0	0.047	0.037	14.058	0.024	0.024	0.000	0.000	0.000	0.000
75	A	78	GLY	0	-0.028	-0.011	16.428	0.027	0.027	0.000	0.000	0.000	0.000
76	A	79	THR	0	-0.046	-0.016	12.977	0.014	0.014	0.000	0.000	0.000	0.000
77	A	80	ARG	1	0.873	0.937	6.855	0.907	0.907	0.000	0.000	0.000	0.000
78	A	81	LEU	0	-0.034	-0.008	10.903	0.000	0.000	0.000	0.000	0.000	0.000
79	A	82	LEU	0	0.005	0.004	13.547	0.050	0.050	0.000	0.000	0.000	0.000
80	A	83	PRO	0	0.033	0.011	16.693	-0.027	-0.027	0.000	0.000	0.000	0.000
81	A	84	ILE	0	-0.013	-0.011	19.914	0.011	0.011	0.000	0.000	0.000	0.000
82	A	1	NME	0	0.000	0.021	22.849	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:GLY )