FMO DATABASE

FMODB ID: 229MR

Calculation Name: 3G1J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3G1J

Chain ID: A

ChEMBL ID:

UniProt ID: D0VX16

Base Structure: X-ray

Registration Date: 2023-06-19

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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-693713.798232
FMO2-HF: Nuclear repulsion	655547.31555
FMO2-HF: Total energy	-38166.482681
FMO2-MP2: Total energy	-38274.892169

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:0:GLY)

Summations of interaction energy for fragment #1(A:0: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.
-6.444	-3.091	1.321	-2.656	-2.018	-0.017

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : 0.000

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	2	ASP	-1	-0.845	-0.933	3.788	-4.066	-2.726	-0.005	-0.752	-0.583	0.004
4	A	3	ARG	1	0.941	0.939	5.323	2.774	2.774	0.000	0.000	0.000	0.000
5	A	4	ASP	-1	-0.876	-0.915	8.009	-0.873	-0.873	0.000	0.000	0.000	0.000
6	A	5	TYR	0	-0.088	-0.033	9.939	0.361	0.361	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.125	-0.046	7.648	0.212	0.212	0.000	0.000	0.000	0.000
8	A	7	GLN	0	-0.034	-0.020	11.860	0.095	0.095	0.000	0.000	0.000	0.000
9	A	8	SER	0	0.029	-0.003	14.247	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	9	GLU	-1	-0.846	-0.914	15.630	-0.240	-0.240	0.000	0.000	0.000	0.000
11	A	10	TYR	0	0.011	0.007	17.237	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	11	GLY	0	0.024	0.018	19.029	0.027	0.027	0.000	0.000	0.000	0.000
13	A	12	VAL	0	0.011	0.003	21.375	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	13	LEU	0	-0.062	-0.008	16.048	0.016	0.016	0.000	0.000	0.000	0.000
15	A	14	LYS	1	0.932	0.941	17.974	0.219	0.219	0.000	0.000	0.000	0.000
16	A	15	ALA	0	0.021	0.001	13.295	0.037	0.037	0.000	0.000	0.000	0.000
17	A	16	GLY	0	-0.046	-0.027	13.828	0.028	0.028	0.000	0.000	0.000	0.000
18	A	17	GLN	0	-0.022	-0.006	15.127	0.091	0.091	0.000	0.000	0.000	0.000
19	A	18	CYS	0	0.000	-0.009	16.169	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	19	TYR	0	0.009	0.006	16.883	-0.018	-0.018	0.000	0.000	0.000	0.000
21	A	20	LYS	1	0.984	1.000	18.728	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	21	VAL	0	0.023	0.012	18.925	-0.024	-0.024	0.000	0.000	0.000	0.000
23	A	22	VAL	0	-0.047	-0.043	21.522	0.017	0.017	0.000	0.000	0.000	0.000
24	A	23	ARG	1	0.931	0.969	24.160	0.023	0.023	0.000	0.000	0.000	0.000
25	A	24	SER	0	0.013	0.013	23.202	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	25	PHE	0	-0.012	0.004	17.522	-0.014	-0.014	0.000	0.000	0.000	0.000
27	A	26	ARG	1	0.961	0.984	20.669	-0.073	-0.073	0.000	0.000	0.000	0.000
28	A	27	ASP	-1	-0.778	-0.884	15.380	0.010	0.010	0.000	0.000	0.000	0.000
29	A	28	TYR	0	-0.028	-0.017	17.921	0.015	0.015	0.000	0.000	0.000	0.000
30	A	29	ARG	1	0.887	0.948	11.559	0.135	0.135	0.000	0.000	0.000	0.000
31	A	30	ASN	0	-0.034	-0.024	17.973	0.045	0.045	0.000	0.000	0.000	0.000
32	A	31	ILE	0	0.022	0.021	15.219	0.031	0.031	0.000	0.000	0.000	0.000
33	A	32	ASN	0	-0.023	-0.025	18.311	-0.053	-0.053	0.000	0.000	0.000	0.000
34	A	33	TYR	0	-0.038	-0.034	13.819	0.049	0.049	0.000	0.000	0.000	0.000
35	A	34	GLU	-1	-0.924	-0.961	19.158	0.120	0.120	0.000	0.000	0.000	0.000
36	A	35	ARG	1	0.943	0.953	21.636	-0.044	-0.044	0.000	0.000	0.000	0.000
37	A	36	GLY	0	-0.053	-0.032	23.508	0.009	0.009	0.000	0.000	0.000	0.000
38	A	37	ASP	-1	-0.852	-0.920	18.002	0.205	0.205	0.000	0.000	0.000	0.000
39	A	38	VAL	0	-0.043	-0.024	17.881	-0.034	-0.034	0.000	0.000	0.000	0.000
40	A	39	MET	0	-0.059	-0.018	13.256	0.072	0.072	0.000	0.000	0.000	0.000
41	A	40	ARG	1	0.964	0.991	10.184	0.029	0.029	0.000	0.000	0.000	0.000
42	A	41	PHE	0	0.011	0.014	11.733	-0.031	-0.031	0.000	0.000	0.000	0.000
43	A	42	LEU	0	-0.060	-0.038	6.391	0.006	0.006	0.000	0.000	0.000	0.000
44	A	43	GLY	0	0.077	0.038	10.295	-0.118	-0.118	0.000	0.000	0.000	0.000
45	A	44	SER	0	-0.056	-0.028	11.187	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	45	ASN	0	0.084	0.041	12.119	-0.052	-0.052	0.000	0.000	0.000	0.000
47	A	46	PHE	0	-0.006	-0.002	13.827	0.080	0.080	0.000	0.000	0.000	0.000
48	A	47	VAL	0	0.048	0.041	15.768	-0.015	-0.015	0.000	0.000	0.000	0.000
49	A	48	PRO	0	0.000	-0.032	18.464	0.047	0.047	0.000	0.000	0.000	0.000
50	A	49	TYR	0	-0.026	0.005	21.974	0.029	0.029	0.000	0.000	0.000	0.000
51	A	50	GLU	-1	-0.885	-0.957	17.899	-0.308	-0.308	0.000	0.000	0.000	0.000
52	A	51	SER	0	-0.052	-0.018	21.833	0.023	0.023	0.000	0.000	0.000	0.000
53	A	52	GLY	0	0.021	0.012	17.907	0.028	0.028	0.000	0.000	0.000	0.000
54	A	53	LEU	0	-0.039	-0.008	16.256	-0.058	-0.058	0.000	0.000	0.000	0.000
55	A	54	SER	0	-0.015	-0.006	10.992	0.047	0.047	0.000	0.000	0.000	0.000
56	A	55	LEU	0	-0.023	-0.017	12.644	-0.081	-0.081	0.000	0.000	0.000	0.000
57	A	56	PHE	0	0.072	0.031	6.333	0.069	0.069	0.000	0.000	0.000	0.000
58	A	57	PHE	0	0.007	-0.007	8.952	-0.026	-0.026	0.000	0.000	0.000	0.000
59	A	58	ASP	-1	-0.884	-0.936	8.369	0.646	0.646	0.000	0.000	0.000	0.000
60	A	59	LYS	1	0.929	0.948	9.563	-0.411	-0.411	0.000	0.000	0.000	0.000
61	A	60	ASN	0	-0.045	-0.030	11.616	0.084	0.084	0.000	0.000	0.000	0.000
62	A	61	GLY	0	0.032	0.024	10.267	0.055	0.055	0.000	0.000	0.000	0.000
63	A	62	SER	0	-0.028	0.000	7.629	0.474	0.474	0.000	0.000	0.000	0.000
64	A	63	GLU	-1	-0.822	-0.914	2.585	-5.953	-3.940	1.326	-1.904	-1.435	-0.021
65	A	64	ARG	1	0.900	0.947	5.955	-0.319	-0.319	0.000	0.000	0.000	0.000
66	A	65	GLN	0	0.019	0.005	7.744	-0.165	-0.165	0.000	0.000	0.000	0.000
67	A	66	ILE	0	-0.022	-0.004	9.260	0.085	0.085	0.000	0.000	0.000	0.000
68	A	67	MET	0	-0.029	0.012	13.005	-0.101	-0.101	0.000	0.000	0.000	0.000
69	A	68	LEU	0	0.002	-0.009	14.819	0.063	0.063	0.000	0.000	0.000	0.000
70	A	69	CYS	0	0.067	0.045	18.305	-0.034	-0.034	0.000	0.000	0.000	0.000
71	A	70	VAL	0	-0.022	-0.016	20.599	0.027	0.027	0.000	0.000	0.000	0.000
72	A	71	ARG	1	0.939	0.940	23.100	0.118	0.118	0.000	0.000	0.000	0.000
73	A	72	PRO	0	-0.009	-0.013	26.485	0.005	0.005	0.000	0.000	0.000	0.000
74	A	73	GLH	0	0.053	0.037	28.275	0.003	0.003	0.000	0.000	0.000	0.000
75	A	74	PHE	0	-0.013	-0.004	23.805	0.007	0.007	0.000	0.000	0.000	0.000
76	A	75	GLN	0	0.099	0.043	21.165	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	76	MET	0	-0.024	0.005	23.148	-0.009	-0.009	0.000	0.000	0.000	0.000
78	A	77	GLU	-1	-0.850	-0.898	25.273	-0.067	-0.067	0.000	0.000	0.000	0.000
79	A	78	ILE	0	0.045	0.024	20.496	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	79	ALA	0	0.016	0.002	20.985	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	80	HIS	1	0.881	0.924	22.040	0.132	0.132	0.000	0.000	0.000	0.000
82	A	81	HIS	1	0.891	0.955	24.864	0.089	0.089	0.000	0.000	0.000	0.000
83	A	82	LEU	0	0.074	0.043	19.733	0.012	0.012	0.000	0.000	0.000	0.000
84	A	83	ASP	-1	-0.875	-0.926	23.103	-0.083	-0.083	0.000	0.000	0.000	0.000
85	A	84	SER	0	-0.054	-0.025	25.460	0.015	0.015	0.000	0.000	0.000	0.000
86	A	85	TYR	0	-0.138	-0.100	21.817	0.018	0.018	0.000	0.000	0.000	0.000
87	A	86	PHE	0	-0.003	0.003	17.055	0.016	0.016	0.000	0.000	0.000	0.000
88	A	87	CYS	0	0.022	0.008	21.824	-0.012	-0.012	0.000	0.000	0.000	0.000
89	A	88	LYS	1	0.917	0.976	21.449	0.100	0.100	0.000	0.000	0.000	0.000
90	A	89	LEU	0	-0.001	-0.001	21.631	0.016	0.016	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)