FMO DATABASE

FMODB ID: R8GL8

Calculation Name: 2GOM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GOM

Chain ID: A

ChEMBL ID:

UniProt ID: P68799

Base Structure: X-ray

Registration Date: 2023-09-23

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	61
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-365652.065058
FMO2-HF: Nuclear repulsion	340963.46376
FMO2-HF: Total energy	-24688.601298
FMO2-MP2: Total energy	-24762.188231

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:105:ILE)

Summations of interaction energy for fragment #1(A:105:ILE)

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.
-16.795	-9.506	9.572	-6.796	-10.063	-0.017

Interaction energy analysis for fragmet #1(A:105:ILE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.108 / 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	107	LYS	1	0.855	0.932	2.098	-3.329	-0.664	2.312	-1.251	-3.725	0.010
4	A	108	GLU	-1	-0.877	-0.935	1.752	-14.630	-10.757	7.259	-5.375	-5.757	-0.027
5	A	109	GLN	0	0.051	0.012	3.468	0.734	1.371	0.002	-0.164	-0.475	0.000
6	A	110	LYS	1	0.951	0.967	5.311	-0.484	-0.370	-0.001	-0.006	-0.106	0.000
7	A	111	LEU	0	-0.006	0.012	7.111	0.125	0.125	0.000	0.000	0.000	0.000
8	A	112	ILE	0	0.044	0.031	6.987	0.166	0.166	0.000	0.000	0.000	0.000
9	A	113	GLN	0	-0.053	-0.023	9.206	0.145	0.145	0.000	0.000	0.000	0.000
10	A	114	ALA	0	0.017	0.009	11.261	0.053	0.053	0.000	0.000	0.000	0.000
11	A	115	GLN	0	0.008	-0.006	11.136	-0.016	-0.016	0.000	0.000	0.000	0.000
12	A	116	ASN	0	0.022	0.008	12.371	0.018	0.018	0.000	0.000	0.000	0.000
13	A	117	LEU	0	-0.011	-0.010	14.953	0.029	0.029	0.000	0.000	0.000	0.000
14	A	118	VAL	0	0.023	0.013	16.878	0.017	0.017	0.000	0.000	0.000	0.000
15	A	119	ARG	1	0.929	0.972	15.674	0.142	0.142	0.000	0.000	0.000	0.000
16	A	120	GLU	-1	-0.967	-0.987	18.886	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	121	PHE	0	-0.020	-0.013	21.176	0.011	0.011	0.000	0.000	0.000	0.000
18	A	122	GLU	-1	-0.726	-0.842	22.464	-0.091	-0.091	0.000	0.000	0.000	0.000
19	A	123	LYS	1	0.929	0.979	24.136	0.037	0.037	0.000	0.000	0.000	0.000
20	A	124	THR	0	-0.028	-0.022	25.083	0.007	0.007	0.000	0.000	0.000	0.000
21	A	125	HIS	1	0.889	0.964	26.745	0.035	0.035	0.000	0.000	0.000	0.000
22	A	126	THR	0	0.060	0.036	26.619	0.006	0.006	0.000	0.000	0.000	0.000
23	A	127	VAL	0	0.051	0.018	26.975	0.000	0.000	0.000	0.000	0.000	0.000
24	A	128	SER	0	-0.043	-0.018	25.090	0.005	0.005	0.000	0.000	0.000	0.000
25	A	129	ALA	0	0.026	0.005	22.716	0.005	0.005	0.000	0.000	0.000	0.000
26	A	130	HIS	0	0.049	0.035	22.066	0.001	0.001	0.000	0.000	0.000	0.000
27	A	131	ARG	1	0.963	0.977	22.469	-0.041	-0.041	0.000	0.000	0.000	0.000
28	A	132	LYS	1	0.927	0.967	18.949	-0.031	-0.031	0.000	0.000	0.000	0.000
29	A	133	ALA	0	0.038	0.025	17.957	0.003	0.003	0.000	0.000	0.000	0.000
30	A	134	GLN	0	0.036	0.013	17.861	-0.013	-0.013	0.000	0.000	0.000	0.000
31	A	135	LYS	1	0.952	0.973	16.073	-0.165	-0.165	0.000	0.000	0.000	0.000
32	A	136	ALA	0	-0.019	-0.011	13.771	0.028	0.028	0.000	0.000	0.000	0.000
33	A	137	VAL	0	0.058	0.016	13.660	-0.002	-0.002	0.000	0.000	0.000	0.000
34	A	138	ASN	0	-0.012	-0.009	14.629	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	139	LEU	0	-0.072	-0.025	11.021	0.046	0.046	0.000	0.000	0.000	0.000
36	A	140	VAL	0	-0.052	-0.006	10.005	0.088	0.088	0.000	0.000	0.000	0.000
37	A	141	SER	0	-0.011	-0.017	7.990	0.012	0.012	0.000	0.000	0.000	0.000
38	A	142	PHE	0	0.069	0.016	9.878	-0.103	-0.103	0.000	0.000	0.000	0.000
39	A	143	GLU	-1	-0.791	-0.886	6.898	-0.258	-0.258	0.000	0.000	0.000	0.000
40	A	144	TYR	0	-0.014	-0.018	5.814	-0.072	-0.072	0.000	0.000	0.000	0.000
41	A	145	LYS	1	0.981	0.996	11.774	0.084	0.084	0.000	0.000	0.000	0.000
42	A	146	VAL	0	0.110	0.040	15.259	0.015	0.015	0.000	0.000	0.000	0.000
43	A	147	LYS	1	0.960	0.980	11.735	0.481	0.481	0.000	0.000	0.000	0.000
44	A	148	LYS	1	0.854	0.926	13.030	0.001	0.001	0.000	0.000	0.000	0.000
45	A	149	MET	0	-0.008	0.008	16.060	0.019	0.019	0.000	0.000	0.000	0.000
46	A	150	VAL	0	0.056	0.037	18.336	0.011	0.011	0.000	0.000	0.000	0.000
47	A	151	LEU	0	-0.065	-0.044	14.027	0.009	0.009	0.000	0.000	0.000	0.000
48	A	152	GLN	0	-0.028	-0.013	18.649	0.020	0.020	0.000	0.000	0.000	0.000
49	A	153	GLU	-1	-0.878	-0.923	21.091	-0.071	-0.071	0.000	0.000	0.000	0.000
50	A	154	ARG	1	0.778	0.846	17.885	0.141	0.141	0.000	0.000	0.000	0.000
51	A	155	ILE	0	-0.060	-0.028	19.530	0.009	0.009	0.000	0.000	0.000	0.000
52	A	156	ASP	-1	-0.825	-0.916	23.531	-0.024	-0.024	0.000	0.000	0.000	0.000
53	A	157	ASN	0	-0.006	-0.022	26.379	0.011	0.011	0.000	0.000	0.000	0.000
54	A	158	VAL	0	-0.048	-0.011	25.161	0.004	0.004	0.000	0.000	0.000	0.000
55	A	159	LEU	0	-0.015	-0.022	26.599	0.006	0.006	0.000	0.000	0.000	0.000
56	A	160	LYS	1	0.931	0.979	29.305	0.043	0.043	0.000	0.000	0.000	0.000
57	A	161	GLN	0	-0.044	-0.016	29.542	0.002	0.002	0.000	0.000	0.000	0.000
58	A	162	GLY	0	0.024	0.041	32.445	0.002	0.002	0.000	0.000	0.000	0.000
59	A	163	LEU	0	-0.047	-0.029	28.747	-0.001	-0.001	0.000	0.000	0.000	0.000
60	A	164	VAL	0	0.039	0.030	31.509	0.002	0.002	0.000	0.000	0.000	0.000
61	A	165	ARG	1	0.934	0.948	31.487	-0.009	-0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:105:ILE)