FMO DATABASE

FMODB ID: R1JG8

Calculation Name: 2D68-A-Xray310

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2D68

Chain ID: A

ChEMBL ID:

UniProt ID: O95684

Base Structure: X-ray

Registration Date: 2021-09-06

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:

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. 1.20200116
Remarks	Structural optimization was performed under the unconstrained condition of hydrogen and heavy atoms fixed using MOE with Auto-FMO protocol as OptH.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	79
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-471762.910545
FMO2-HF: Nuclear repulsion	441901.38961
FMO2-HF: Total energy	-29861.520936
FMO2-MP2: Total energy	-29951.340335

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:57:ACE )

Summations of interaction energy for fragment #1(A:57:ACE )

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.
0.553	1.324	-0.004	-0.324	-0.442	0

Interaction energy analysis for fragmet #1(A:57:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / q_NPA : -0.008

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].
3	A	59	ASN	0	0.061	0.041	3.870	1.368	2.139	-0.004	-0.324	-0.442
4	A	60	GLU	-1	-0.843	-0.935	6.965	-0.442	-0.442	0.000	0.000	0.000
5	A	61	SER	0	-0.012	-0.006	9.555	0.064	0.064	0.000	0.000	0.000
6	A	62	LEU	0	0.055	0.022	9.599	0.038	0.038	0.000	0.000	0.000
7	A	63	LYS	1	0.960	0.986	9.117	0.741	0.741	0.000	0.000	0.000
8	A	64	LYS	1	0.903	0.941	11.365	0.353	0.353	0.000	0.000	0.000
9	A	65	PHE	0	0.030	0.034	14.625	0.038	0.038	0.000	0.000	0.000
10	A	66	LEU	0	0.024	0.021	11.817	0.050	0.050	0.000	0.000	0.000
11	A	67	ASN	0	-0.082	-0.020	15.621	0.024	0.024	0.000	0.000	0.000
12	A	68	THR	0	-0.050	-0.032	17.257	0.049	0.049	0.000	0.000	0.000
13	A	69	LYS	1	0.980	0.984	20.415	0.140	0.140	0.000	0.000	0.000
14	A	70	ASP	-1	-0.850	-0.938	23.003	-0.145	-0.145	0.000	0.000	0.000
15	A	71	GLY	0	0.018	0.005	19.146	0.000	0.000	0.000	0.000	0.000
16	A	72	ARG	1	0.824	0.909	17.968	0.255	0.255	0.000	0.000	0.000
17	A	73	LEU	0	0.005	0.005	19.679	-0.001	-0.001	0.000	0.000	0.000
18	A	74	VAL	0	0.012	0.010	19.708	0.004	0.004	0.000	0.000	0.000
19	A	75	ALA	0	0.009	-0.003	16.602	0.001	0.001	0.000	0.000	0.000
20	A	76	SER	0	-0.001	-0.009	18.509	-0.003	-0.003	0.000	0.000	0.000
21	A	77	LEU	0	0.009	0.009	20.925	0.014	0.014	0.000	0.000	0.000
22	A	78	VAL	0	-0.034	-0.002	18.079	0.013	0.013	0.000	0.000	0.000
23	A	79	ALA	0	0.024	0.003	18.342	0.011	0.011	0.000	0.000	0.000
24	A	80	GLU	-1	-0.770	-0.881	20.024	-0.102	-0.102	0.000	0.000	0.000
25	A	81	PHE	0	0.011	0.001	22.964	0.016	0.016	0.000	0.000	0.000
26	A	82	LEU	0	-0.031	-0.025	18.091	0.013	0.013	0.000	0.000	0.000
27	A	83	GLN	0	-0.025	-0.013	21.823	-0.006	-0.006	0.000	0.000	0.000
28	A	84	PHE	0	-0.030	0.012	24.164	0.012	0.012	0.000	0.000	0.000
29	A	85	PHE	0	-0.052	-0.030	26.257	0.011	0.011	0.000	0.000	0.000
30	A	86	ASN	0	-0.003	0.008	25.614	0.002	0.002	0.000	0.000	0.000
31	A	87	LEU	0	-0.016	0.005	22.099	0.007	0.007	0.000	0.000	0.000
32	A	88	ASP	-1	-0.859	-0.954	20.902	-0.122	-0.122	0.000	0.000	0.000
33	A	89	PHE	0	-0.033	-0.024	19.346	-0.011	-0.011	0.000	0.000	0.000
34	A	90	THR	0	-0.002	-0.002	17.399	-0.005	-0.005	0.000	0.000	0.000
35	A	91	LEU	0	0.028	0.012	16.050	-0.037	-0.037	0.000	0.000	0.000
36	A	92	ALA	0	-0.032	-0.009	15.393	-0.044	-0.044	0.000	0.000	0.000
37	A	93	VAL	0	-0.015	-0.007	11.399	-0.019	-0.019	0.000	0.000	0.000
38	A	94	PHE	0	0.041	0.016	11.227	-0.096	-0.096	0.000	0.000	0.000
39	A	95	GLN	0	0.016	0.022	11.648	-0.087	-0.087	0.000	0.000	0.000
40	A	96	PRO	0	-0.018	-0.013	8.048	-0.155	-0.155	0.000	0.000	0.000
41	A	97	GLU	-1	-0.978	-0.973	7.047	-0.713	-0.713	0.000	0.000	0.000
42	A	98	THR	0	-0.076	-0.047	7.402	-0.257	-0.257	0.000	0.000	0.000
43	A	99	SER	0	-0.062	-0.033	6.455	-0.426	-0.426	0.000	0.000	0.000
44	A	100	THR	0	-0.065	-0.036	8.675	0.153	0.153	0.000	0.000	0.000
45	A	101	LEU	0	0.008	0.006	9.182	0.058	0.058	0.000	0.000	0.000
46	A	102	GLN	0	-0.018	-0.014	13.272	0.076	0.076	0.000	0.000	0.000
47	A	103	GLY	0	0.027	0.019	15.399	-0.030	-0.030	0.000	0.000	0.000
48	A	104	LEU	0	-0.016	-0.015	16.188	-0.008	-0.008	0.000	0.000	0.000
49	A	105	GLU	-1	-0.873	-0.935	19.041	-0.169	-0.169	0.000	0.000	0.000
50	A	106	GLY	0	0.040	0.020	22.809	0.002	0.002	0.000	0.000	0.000
51	A	107	ARG	1	0.755	0.824	25.032	0.097	0.097	0.000	0.000	0.000
52	A	108	GLU	-1	-0.912	-0.945	28.007	-0.089	-0.089	0.000	0.000	0.000
53	A	109	ASN	0	0.029	0.006	26.805	0.015	0.015	0.000	0.000	0.000
54	A	110	LEU	0	0.022	0.028	24.532	0.001	0.001	0.000	0.000	0.000
55	A	111	ALA	0	0.024	0.005	27.708	0.003	0.003	0.000	0.000	0.000
56	A	112	ARG	1	0.892	0.944	29.557	0.115	0.115	0.000	0.000	0.000
57	A	113	ASP	-1	-0.982	-0.994	27.168	-0.133	-0.133	0.000	0.000	0.000
58	A	114	LEU	0	-0.066	-0.035	27.461	0.001	0.001	0.000	0.000	0.000
59	A	115	GLY	0	-0.019	0.006	31.146	0.006	0.006	0.000	0.000	0.000
60	A	116	ILE	0	-0.065	-0.030	31.531	0.006	0.006	0.000	0.000	0.000
61	A	117	ILE	0	-0.028	-0.023	35.193	-0.002	-0.002	0.000	0.000	0.000
62	A	118	GLU	-1	-0.796	-0.867	33.530	-0.082	-0.082	0.000	0.000	0.000
63	A	119	ALA	0	0.022	0.004	37.395	0.003	0.003	0.000	0.000	0.000
64	A	120	GLU	-1	-0.874	-0.943	39.405	-0.051	-0.051	0.000	0.000	0.000
65	A	121	GLY	0	-0.063	-0.024	40.619	0.000	0.000	0.000	0.000	0.000
66	A	122	THR	0	-0.021	-0.025	35.504	0.000	0.000	0.000	0.000	0.000
67	A	123	VAL	0	-0.011	-0.008	35.032	-0.004	-0.004	0.000	0.000	0.000
68	A	124	GLY	0	-0.027	-0.007	34.911	-0.002	-0.002	0.000	0.000	0.000
69	A	125	GLY	0	-0.027	-0.014	32.981	0.002	0.002	0.000	0.000	0.000
70	A	126	PRO	0	0.006	0.029	27.924	-0.003	-0.003	0.000	0.000	0.000
71	A	127	LEU	0	0.059	0.006	28.045	0.005	0.005	0.000	0.000	0.000
72	A	128	LEU	0	-0.003	-0.010	24.780	0.004	0.004	0.000	0.000	0.000
73	A	129	LEU	0	-0.037	-0.014	28.668	0.006	0.006	0.000	0.000	0.000
74	A	130	GLU	-1	-0.853	-0.932	31.906	-0.062	-0.062	0.000	0.000	0.000
75	A	131	VAL	0	-0.028	-0.020	29.574	0.003	0.003	0.000	0.000	0.000
76	A	132	ILE	0	-0.013	-0.010	29.814	0.004	0.004	0.000	0.000	0.000
77	A	133	ARG	1	0.887	0.942	32.976	0.065	0.065	0.000	0.000	0.000
78	A	134	ARG	1	0.834	0.918	35.799	0.070	0.070	0.000	0.000	0.000
79	A	135	TRP	-1	-0.959	-0.941	31.868	-0.060	-0.060	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:57:ACE )