FMO DATABASE

FMODB ID: GQKM1

Calculation Name: 3D33-A-Xray312

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3D33

Chain ID: A

ChEMBL ID:

UniProt ID: A6KX32

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

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	97
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-675600.19915
FMO2-HF: Nuclear repulsion	638288.158571
FMO2-HF: Total energy	-37312.040579
FMO2-MP2: Total energy	-37420.467496

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:33:ACE )

Summations of interaction energy for fragment #1(A:33: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.
-1.398	-0.861	0.004	-0.336	-0.205	0

Interaction energy analysis for fragmet #1(A:33:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.019

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	35	VAL	0	0.015	0.024	3.845	-0.129	0.408	0.004	-0.336	-0.205
4	A	36	LYS	1	0.884	0.932	6.691	0.477	0.477	0.000	0.000	0.000
5	A	37	ASP	-1	-0.879	-0.947	8.256	-0.290	-0.290	0.000	0.000	0.000
6	A	38	VAL	0	-0.099	-0.047	11.591	0.062	0.062	0.000	0.000	0.000
7	A	39	GLU	-1	-0.888	-0.932	14.677	-0.124	-0.124	0.000	0.000	0.000
8	A	40	LEU	0	-0.081	-0.044	17.096	0.015	0.015	0.000	0.000	0.000
9	A	41	ASP	-1	-0.874	-0.923	20.598	-0.095	-0.095	0.000	0.000	0.000
10	A	42	GLY	0	-0.009	-0.022	23.908	0.001	0.001	0.000	0.000	0.000
11	A	43	ARG	1	0.776	0.880	27.379	0.065	0.065	0.000	0.000	0.000
12	A	44	TRP	0	0.054	0.005	27.549	-0.002	-0.002	0.000	0.000	0.000
13	A	45	ASP	-1	-0.849	-0.914	29.611	-0.070	-0.070	0.000	0.000	0.000
14	A	46	ASP	-1	-0.934	-0.957	32.678	-0.081	-0.081	0.000	0.000	0.000
15	A	47	NME	0	-0.016	0.003	30.766	-0.002	-0.002	0.000	0.000	0.000
16	A	53	ACE	0	-0.005	-0.017	28.158	0.002	0.002	0.000	0.000	0.000
17	A	54	ASN	0	-0.027	-0.027	21.972	-0.005	-0.005	0.000	0.000	0.000
18	A	55	CYS	0	0.011	0.038	22.816	0.005	0.005	0.000	0.000	0.000
19	A	56	PRO	0	0.030	0.023	22.813	-0.016	-0.016	0.000	0.000	0.000
20	A	57	ILE	0	0.003	0.007	21.291	-0.018	-0.018	0.000	0.000	0.000
21	A	58	THR	0	0.000	0.002	16.685	-0.016	-0.016	0.000	0.000	0.000
22	A	59	VAL	0	0.046	0.005	15.514	0.000	0.000	0.000	0.000	0.000
23	A	60	PHE	0	-0.010	0.007	10.670	-0.021	-0.021	0.000	0.000	0.000
24	A	61	THR	0	-0.002	-0.007	9.984	0.106	0.106	0.000	0.000	0.000
25	A	62	ASP	-1	-0.943	-0.970	7.646	-1.568	-1.568	0.000	0.000	0.000
26	A	63	GLY	0	0.025	0.011	8.180	0.172	0.172	0.000	0.000	0.000
27	A	64	TYR	0	-0.071	-0.047	9.822	0.026	0.026	0.000	0.000	0.000
28	A	65	LEU	0	-0.022	-0.006	12.708	0.070	0.070	0.000	0.000	0.000
29	A	66	LEU	0	0.021	0.017	13.154	-0.089	-0.089	0.000	0.000	0.000
30	A	67	THR	0	-0.021	-0.021	14.518	0.046	0.046	0.000	0.000	0.000
31	A	68	LEU	0	0.023	0.020	16.209	-0.019	-0.019	0.000	0.000	0.000
32	A	69	LYS	1	0.904	0.941	16.208	0.380	0.380	0.000	0.000	0.000
33	A	70	ASN	0	0.081	0.036	20.153	0.005	0.005	0.000	0.000	0.000
34	A	71	ALA	0	-0.050	-0.033	22.758	0.004	0.004	0.000	0.000	0.000
35	A	72	SER	0	-0.064	-0.049	24.373	0.009	0.009	0.000	0.000	0.000
36	A	73	PRO	0	-0.048	-0.018	27.116	0.005	0.005	0.000	0.000	0.000
37	A	74	ASP	-1	-0.795	-0.873	29.278	-0.099	-0.099	0.000	0.000	0.000
38	A	75	ARG	1	0.763	0.873	31.069	0.102	0.102	0.000	0.000	0.000
39	A	76	ASP	-1	-0.859	-0.918	31.582	-0.092	-0.092	0.000	0.000	0.000
40	A	77	MET	0	-0.048	-0.036	25.142	-0.001	-0.001	0.000	0.000	0.000
41	A	78	THR	0	-0.021	-0.002	29.542	0.004	0.004	0.000	0.000	0.000
42	A	79	ILE	0	-0.052	-0.009	22.955	-0.006	-0.006	0.000	0.000	0.000
43	A	80	ARG	1	0.934	0.965	25.971	0.087	0.087	0.000	0.000	0.000
44	A	81	ILE	0	-0.001	0.004	20.785	-0.007	-0.007	0.000	0.000	0.000
45	A	82	THR	0	-0.026	-0.018	24.445	0.010	0.010	0.000	0.000	0.000
46	A	83	ASP	-1	-0.775	-0.889	24.295	-0.054	-0.054	0.000	0.000	0.000
47	A	84	MET	0	0.003	-0.006	22.987	0.003	0.003	0.000	0.000	0.000
48	A	85	ALA	0	-0.027	0.018	25.796	0.007	0.007	0.000	0.000	0.000
49	A	86	LYS	1	0.820	0.878	27.901	0.032	0.032	0.000	0.000	0.000
50	A	87	GLY	0	0.003	0.019	29.038	0.002	0.002	0.000	0.000	0.000
51	A	88	GLY	0	-0.042	-0.018	29.506	0.000	0.000	0.000	0.000	0.000
52	A	89	VAL	0	-0.010	-0.005	28.119	-0.005	-0.005	0.000	0.000	0.000
53	A	90	VAL	0	-0.037	-0.017	23.727	0.004	0.004	0.000	0.000	0.000
54	A	91	TYR	0	-0.018	-0.013	24.644	-0.006	-0.006	0.000	0.000	0.000
55	A	92	GLU	-1	-0.910	-0.963	26.632	-0.075	-0.075	0.000	0.000	0.000
56	A	93	ASN	0	-0.059	-0.035	26.282	0.009	0.009	0.000	0.000	0.000
57	A	94	ASP	-1	-0.827	-0.891	29.139	-0.087	-0.087	0.000	0.000	0.000
58	A	95	ILE	0	-0.039	-0.029	26.104	-0.002	-0.002	0.000	0.000	0.000
59	A	96	PRO	0	0.003	0.000	30.347	0.002	0.002	0.000	0.000	0.000
60	A	97	GLU	-1	-0.844	-0.921	31.107	-0.099	-0.099	0.000	0.000	0.000
61	A	98	VAL	0	-0.063	-0.029	30.781	-0.008	-0.008	0.000	0.000	0.000
62	A	99	GLN	0	-0.064	-0.045	28.776	-0.008	-0.008	0.000	0.000	0.000
63	A	100	SER	0	-0.026	-0.022	27.038	-0.013	-0.013	0.000	0.000	0.000
64	A	101	ALA	0	0.030	0.016	24.997	-0.009	-0.009	0.000	0.000	0.000
65	A	102	TYR	0	-0.055	-0.042	17.388	-0.019	-0.019	0.000	0.000	0.000
66	A	103	ILE	0	0.026	0.033	20.939	0.017	0.017	0.000	0.000	0.000
67	A	104	THR	0	-0.043	-0.017	17.696	-0.020	-0.020	0.000	0.000	0.000
68	A	105	ILE	0	0.019	0.013	18.467	0.032	0.032	0.000	0.000	0.000
69	A	106	SER	0	-0.017	-0.002	17.785	-0.031	-0.031	0.000	0.000	0.000
70	A	107	ILE	0	0.035	0.013	14.140	0.024	0.024	0.000	0.000	0.000
71	A	108	ALA	0	-0.007	-0.005	17.158	0.020	0.020	0.000	0.000	0.000
72	A	109	ASN	0	-0.059	-0.041	18.102	0.028	0.028	0.000	0.000	0.000
73	A	110	PHE	0	0.027	0.024	20.139	0.009	0.009	0.000	0.000	0.000
74	A	111	PRO	0	-0.007	-0.010	20.780	0.002	0.002	0.000	0.000	0.000
75	A	112	ALA	0	0.013	0.032	19.247	-0.011	-0.011	0.000	0.000	0.000
76	A	113	GLU	-1	-0.871	-0.927	19.372	-0.022	-0.022	0.000	0.000	0.000
77	A	114	GLU	-1	-0.934	-0.971	19.149	-0.075	-0.075	0.000	0.000	0.000
78	A	115	TYR	0	-0.058	-0.065	19.285	0.007	0.007	0.000	0.000	0.000
79	A	116	LYS	1	0.942	0.974	20.483	0.065	0.065	0.000	0.000	0.000
80	A	117	LEU	0	-0.034	-0.024	18.746	-0.002	-0.002	0.000	0.000	0.000
81	A	118	GLU	-1	-0.912	-0.968	22.290	-0.081	-0.081	0.000	0.000	0.000
82	A	119	ILE	0	0.002	-0.001	21.560	-0.006	-0.006	0.000	0.000	0.000
83	A	120	THR	0	0.004	-0.006	25.941	0.006	0.006	0.000	0.000	0.000
84	A	121	GLY	0	-0.001	-0.005	29.600	-0.005	-0.005	0.000	0.000	0.000
85	A	122	THR	0	-0.043	0.013	31.737	0.008	0.008	0.000	0.000	0.000
86	A	123	PRO	0	-0.011	-0.031	35.392	-0.001	-0.001	0.000	0.000	0.000
87	A	124	SER	0	-0.022	-0.022	34.991	0.002	0.002	0.000	0.000	0.000
88	A	125	GLY	0	0.043	0.029	30.967	-0.005	-0.005	0.000	0.000	0.000
89	A	126	HIS	0	-0.044	-0.031	28.662	-0.003	-0.003	0.000	0.000	0.000
90	A	127	LEU	0	0.017	0.022	23.538	0.003	0.003	0.000	0.000	0.000
91	A	128	THR	0	0.000	-0.014	23.792	0.001	0.001	0.000	0.000	0.000
92	A	129	GLY	0	0.083	0.049	19.722	-0.003	-0.003	0.000	0.000	0.000
93	A	130	TYR	0	-0.031	-0.013	18.730	0.011	0.011	0.000	0.000	0.000
94	A	131	PHE	0	-0.038	-0.024	14.762	-0.028	-0.028	0.000	0.000	0.000
95	A	132	THR	0	0.069	0.035	14.896	0.014	0.014	0.000	0.000	0.000
96	A	133	LYS	1	0.746	0.907	14.317	0.056	0.056	0.000	0.000	0.000
97	A	134	GLU	-2	-1.776	-1.898	12.696	0.013	0.013	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:33:ACE )