FMO DATABASE

FMODB ID: KGLV3

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	OptAll
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	-366363.245827
FMO2-HF: Nuclear repulsion	341674.167943
FMO2-HF: Total energy	-24689.077884
FMO2-MP2: Total energy	-24762.628997

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.
-16.503	-12.063	11.073	-6.351	-9.163	-0.049

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 : 0.046 / q_NPA : 0.017

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	107	LYS	1	0.793	0.882	2.203	0.205	3.081	1.623	-1.159	-3.340	0.007
4	A	108	GLU	-1	-0.701	-0.854	1.981	-15.295	-14.487	9.446	-4.944	-5.311	-0.056
5	A	109	GLN	0	0.000	0.000	3.898	0.065	0.821	0.004	-0.248	-0.512	0.000
6	A	110	LYS	1	0.908	0.945	5.879	-0.498	-0.498	0.000	0.000	0.000	0.000
7	A	111	LEU	0	-0.022	0.008	7.335	0.055	0.055	0.000	0.000	0.000	0.000
8	A	112	ILE	0	0.038	0.013	7.458	0.012	0.012	0.000	0.000	0.000	0.000
9	A	113	GLN	0	-0.020	0.000	9.599	0.046	0.046	0.000	0.000	0.000	0.000
10	A	114	ALA	0	0.024	0.004	11.689	-0.038	-0.038	0.000	0.000	0.000	0.000
11	A	115	GLN	0	-0.004	-0.007	11.119	0.027	0.027	0.000	0.000	0.000	0.000
12	A	116	ASN	0	-0.021	-0.016	12.688	-0.030	-0.030	0.000	0.000	0.000	0.000
13	A	117	LEU	0	-0.009	-0.005	15.352	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	118	VAL	0	0.020	0.010	17.335	-0.012	-0.012	0.000	0.000	0.000	0.000
15	A	119	ARG	1	0.938	0.976	16.719	-0.200	-0.200	0.000	0.000	0.000	0.000
16	A	120	GLU	-1	-0.858	-0.916	19.599	0.223	0.223	0.000	0.000	0.000	0.000
17	A	121	PHE	0	-0.013	0.002	21.708	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	122	GLU	-1	-0.720	-0.833	21.956	0.023	0.023	0.000	0.000	0.000	0.000
19	A	123	LYS	1	0.932	0.968	24.392	-0.119	-0.119	0.000	0.000	0.000	0.000
20	A	124	THR	0	-0.025	-0.027	25.464	-0.003	-0.003	0.000	0.000	0.000	0.000
21	A	125	HIS	1	0.877	0.937	27.290	-0.053	-0.053	0.000	0.000	0.000	0.000
22	A	126	THR	0	0.038	0.025	26.980	0.000	0.000	0.000	0.000	0.000	0.000
23	A	127	VAL	0	0.038	0.011	27.258	0.003	0.003	0.000	0.000	0.000	0.000
24	A	128	SER	0	-0.026	-0.007	25.870	0.008	0.008	0.000	0.000	0.000	0.000
25	A	129	ALA	0	0.037	0.011	23.003	0.011	0.011	0.000	0.000	0.000	0.000
26	A	130	HIS	0	0.026	0.034	22.335	0.011	0.011	0.000	0.000	0.000	0.000
27	A	131	ARG	1	0.973	0.981	22.676	-0.097	-0.097	0.000	0.000	0.000	0.000
28	A	132	LYS	1	0.801	0.890	19.395	-0.227	-0.227	0.000	0.000	0.000	0.000
29	A	133	ALA	0	0.017	0.012	18.295	0.016	0.016	0.000	0.000	0.000	0.000
30	A	134	GLN	0	0.030	-0.009	18.087	-0.007	-0.007	0.000	0.000	0.000	0.000
31	A	135	LYS	1	0.955	0.981	16.562	-0.248	-0.248	0.000	0.000	0.000	0.000
32	A	136	ALA	0	-0.004	-0.003	14.097	0.008	0.008	0.000	0.000	0.000	0.000
33	A	137	VAL	0	0.048	0.011	13.735	-0.022	-0.022	0.000	0.000	0.000	0.000
34	A	138	ASN	0	0.009	0.004	15.037	-0.051	-0.051	0.000	0.000	0.000	0.000
35	A	139	LEU	0	-0.021	-0.006	11.497	-0.013	-0.013	0.000	0.000	0.000	0.000
36	A	140	VAL	0	-0.010	0.016	10.081	0.014	0.014	0.000	0.000	0.000	0.000
37	A	141	SER	0	0.000	-0.023	7.688	0.107	0.107	0.000	0.000	0.000	0.000
38	A	142	PHE	0	0.088	0.024	9.829	-0.026	-0.026	0.000	0.000	0.000	0.000
39	A	143	GLU	-1	-0.775	-0.836	6.706	-1.357	-1.357	0.000	0.000	0.000	0.000
40	A	144	TYR	0	-0.007	-0.010	5.683	0.077	0.077	0.000	0.000	0.000	0.000
41	A	145	LYS	1	0.948	0.984	12.013	0.232	0.232	0.000	0.000	0.000	0.000
42	A	146	VAL	0	0.075	0.026	15.547	0.040	0.040	0.000	0.000	0.000	0.000
43	A	147	LYS	1	0.972	0.982	11.501	0.441	0.441	0.000	0.000	0.000	0.000
44	A	148	LYS	1	0.797	0.895	13.271	0.132	0.132	0.000	0.000	0.000	0.000
45	A	149	MET	0	0.005	0.011	16.354	0.026	0.026	0.000	0.000	0.000	0.000
46	A	150	VAL	0	0.063	0.039	18.493	0.021	0.021	0.000	0.000	0.000	0.000
47	A	151	LEU	0	-0.066	-0.037	14.117	0.023	0.023	0.000	0.000	0.000	0.000
48	A	152	GLN	0	-0.024	-0.010	18.713	0.024	0.024	0.000	0.000	0.000	0.000
49	A	153	GLU	-1	-0.820	-0.891	21.315	-0.037	-0.037	0.000	0.000	0.000	0.000
50	A	154	ARG	1	0.777	0.850	17.899	0.008	0.008	0.000	0.000	0.000	0.000
51	A	155	ILE	0	-0.042	-0.017	19.930	0.015	0.015	0.000	0.000	0.000	0.000
52	A	156	ASP	-1	-0.794	-0.900	23.845	0.000	0.000	0.000	0.000	0.000	0.000
53	A	157	ASN	0	-0.049	-0.053	26.266	0.005	0.005	0.000	0.000	0.000	0.000
54	A	158	VAL	0	-0.035	0.002	25.546	0.002	0.002	0.000	0.000	0.000	0.000
55	A	159	LEU	0	-0.017	-0.021	26.782	0.004	0.004	0.000	0.000	0.000	0.000
56	A	160	LYS	1	0.893	0.956	29.642	0.011	0.011	0.000	0.000	0.000	0.000
57	A	161	GLN	0	-0.021	0.006	29.776	0.003	0.003	0.000	0.000	0.000	0.000
58	A	162	GLY	0	0.012	0.028	32.986	0.002	0.002	0.000	0.000	0.000	0.000
59	A	163	LEU	0	-0.024	-0.021	29.028	0.004	0.004	0.000	0.000	0.000	0.000
60	A	164	VAL	0	0.033	0.032	31.736	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	165	ARG	1	0.927	0.944	31.953	-0.052	-0.052	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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