FMO DATABASE

FMODB ID: 827YY

Calculation Name: 2GN5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GN5

Chain ID: A

ChEMBL ID:

UniProt ID: P69542

Base Structure: X-ray

Registration Date: 2023-03-13

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	87
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-552628.03453
FMO2-HF: Nuclear repulsion	518766.044859
FMO2-HF: Total energy	-33861.989671
FMO2-MP2: Total energy	-33963.724263

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:1:MET)

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

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.
-5.815	-0.171	0.3	-1.749	-4.195	-0.011

Interaction energy analysis for fragmet #1(A:1:MET)

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 : -0.040

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	3	LYN	0	0.004	-0.002	3.048	-3.121	1.305	0.137	-1.394	-3.169	-0.007
4	A	4	VAL	0	0.051	0.029	5.427	0.346	0.346	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.909	-0.940	6.188	-0.834	-0.834	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.050	0.046	7.375	0.193	0.193	0.000	0.000	0.000	0.000
7	A	7	LYN	0	0.196	0.047	5.287	0.031	0.031	0.000	0.000	0.000	0.000
8	A	8	PRO	0	0.087	0.010	8.133	0.029	0.029	0.000	0.000	0.000	0.000
9	A	9	SER	0	-0.278	0.026	11.708	-0.047	-0.047	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.018	-0.053	13.692	0.029	0.029	0.000	0.000	0.000	0.000
11	A	11	ALA	0	0.167	0.128	16.399	-0.012	-0.012	0.000	0.000	0.000	0.000
12	A	12	GLN	0	-0.056	0.004	19.402	-0.006	-0.006	0.000	0.000	0.000	0.000
13	A	13	PHE	0	-0.093	-0.067	15.594	0.006	0.006	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.049	-0.094	18.707	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	15	THR	0	0.058	0.045	20.712	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	16	ARG	1	1.042	1.009	23.504	0.090	0.090	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.110	-0.083	25.243	0.010	0.010	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.014	-0.012	28.360	0.002	0.002	0.000	0.000	0.000	0.000
19	A	19	VAL	0	0.094	0.054	29.692	0.005	0.005	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.037	-0.011	32.067	0.003	0.003	0.000	0.000	0.000	0.000
21	A	21	ARG	1	0.873	0.961	35.239	0.063	0.063	0.000	0.000	0.000	0.000
22	A	22	GLN	0	-0.043	-0.063	36.731	0.001	0.001	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.024	-0.021	39.044	0.002	0.002	0.000	0.000	0.000	0.000
24	A	24	LYS	1	0.987	0.963	39.804	0.059	0.059	0.000	0.000	0.000	0.000
25	A	25	PRO	0	-0.023	0.001	40.443	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	26	TYR	0	0.103	0.053	39.153	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	27	SER	0	-0.121	-0.029	35.690	0.005	0.005	0.000	0.000	0.000	0.000
28	A	28	LEU	0	-0.030	-0.069	33.408	-0.003	-0.003	0.000	0.000	0.000	0.000
29	A	29	ASN	0	-0.030	0.072	30.712	0.010	0.010	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.804	-0.911	28.014	-0.139	-0.139	0.000	0.000	0.000	0.000
31	A	31	GLN	0	-0.258	-0.106	23.890	0.010	0.010	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.042	-0.002	24.055	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	33	CYS	0	-0.063	0.003	18.697	0.017	0.017	0.000	0.000	0.000	0.000
34	A	34	TYR	0	-0.002	0.010	20.151	-0.012	-0.012	0.000	0.000	0.000	0.000
35	A	35	VAL	0	0.036	0.014	13.758	-0.003	-0.003	0.000	0.000	0.000	0.000
36	A	36	ASP	-1	-0.967	-1.002	14.362	-0.207	-0.207	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.025	-0.050	11.365	-0.047	-0.047	0.000	0.000	0.000	0.000
38	A	38	GLY	0	0.033	0.065	9.615	0.083	0.083	0.000	0.000	0.000	0.000
39	A	39	ASN	0	0.063	0.083	10.692	-0.001	-0.001	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.983	-0.971	12.695	-0.367	-0.367	0.000	0.000	0.000	0.000
41	A	41	TYR	0	-0.010	-0.066	14.835	0.048	0.048	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.032	-0.026	12.445	-0.033	-0.033	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.090	0.064	13.453	0.035	0.035	0.000	0.000	0.000	0.000
44	A	44	LEU	0	0.016	0.007	15.762	-0.022	-0.022	0.000	0.000	0.000	0.000
45	A	45	VAL	0	-0.095	-0.053	16.734	0.010	0.010	0.000	0.000	0.000	0.000
46	A	46	LYN	0	-0.011	-0.007	18.561	-0.010	-0.010	0.000	0.000	0.000	0.000
47	A	47	ILE	0	-0.059	0.009	15.156	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	48	THR	0	0.009	-0.013	19.744	0.027	0.027	0.000	0.000	0.000	0.000
49	A	49	LEU	0	-0.064	-0.107	19.415	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.694	-0.848	21.549	-0.206	-0.206	0.000	0.000	0.000	0.000
51	A	51	GLU	-1	-0.792	-0.882	24.217	-0.143	-0.143	0.000	0.000	0.000	0.000
52	A	52	GLY	0	-0.042	-0.049	26.518	0.003	0.003	0.000	0.000	0.000	0.000
53	A	53	GLN	0	-0.192	-0.098	22.772	0.006	0.006	0.000	0.000	0.000	0.000
54	A	54	PRO	0	0.086	0.049	22.430	-0.002	-0.002	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.024	0.026	20.759	-0.015	-0.015	0.000	0.000	0.000	0.000
56	A	56	TYR	0	-0.035	-0.001	15.660	-0.017	-0.017	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.013	-0.001	16.344	0.026	0.026	0.000	0.000	0.000	0.000
58	A	58	PRO	0	0.121	-0.074	15.113	-0.045	-0.045	0.000	0.000	0.000	0.000
59	A	59	GLY	0	0.113	0.054	11.974	0.039	0.039	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.190	0.030	4.694	-0.030	0.052	-0.001	-0.004	-0.076	0.000
61	A	61	TYR	0	-0.128	-0.202	8.128	0.040	0.040	0.000	0.000	0.000	0.000
62	A	62	THR	-1	-0.682	-0.849	6.194	-1.853	-1.853	0.000	0.000	0.000	0.000
63	A	63	VAL	0	0.040	0.033	8.282	0.307	0.307	0.000	0.000	0.000	0.000
64	A	64	HIS	0	0.045	0.015	11.178	0.012	0.012	0.000	0.000	0.000	0.000
65	A	65	LEU	0	-0.014	0.008	13.440	0.007	0.007	0.000	0.000	0.000	0.000
66	A	66	SER	0	-0.204	-0.100	16.345	0.035	0.035	0.000	0.000	0.000	0.000
67	A	67	SER	0	0.024	0.005	16.238	-0.053	-0.053	0.000	0.000	0.000	0.000
68	A	68	PHE	0	0.152	-0.011	12.754	0.020	0.020	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.836	0.888	19.147	0.202	0.202	0.000	0.000	0.000	0.000
70	A	70	VAL	0	-0.105	-0.131	22.766	0.000	0.000	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.049	-0.007	25.730	0.004	0.004	0.000	0.000	0.000	0.000
72	A	72	GLN	0	-0.014	-0.007	28.396	0.007	0.007	0.000	0.000	0.000	0.000
73	A	73	PHE	0	0.076	0.011	28.514	-0.006	-0.006	0.000	0.000	0.000	0.000
74	A	74	GLY	0	0.050	0.034	25.643	-0.011	-0.011	0.000	0.000	0.000	0.000
75	A	75	SER	0	-0.124	0.107	19.184	0.001	0.001	0.000	0.000	0.000	0.000
76	A	76	LEU	0	-0.071	-0.085	22.123	0.011	0.011	0.000	0.000	0.000	0.000
77	A	77	MET	0	0.146	0.226	15.734	-0.006	-0.006	0.000	0.000	0.000	0.000
78	A	78	ILE	0	0.068	0.067	20.229	-0.004	-0.004	0.000	0.000	0.000	0.000
79	A	79	ASP	-1	-0.936	-0.858	22.374	-0.207	-0.207	0.000	0.000	0.000	0.000
80	A	80	ARG	0	0.315	0.037	19.939	0.014	0.014	0.000	0.000	0.000	0.000
81	A	81	LEU	0	-0.267	-0.083	13.871	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	82	ARG	1	0.843	0.835	15.814	0.312	0.312	0.000	0.000	0.000	0.000
83	A	83	LEU	0	-0.083	0.013	10.901	-0.089	-0.089	0.000	0.000	0.000	0.000
84	A	84	VAL	0	-0.021	-0.028	10.055	0.122	0.122	0.000	0.000	0.000	0.000
85	A	85	PRO	0	0.089	0.061	8.779	-0.161	-0.161	0.000	0.000	0.000	0.000
86	A	86	ALA	0	0.053	0.069	3.703	-0.347	-0.198	0.003	-0.036	-0.117	0.000
87	A	87	LYS	1	0.766	0.872	2.933	0.012	0.999	0.161	-0.315	-0.833	-0.004

Top

Graph

Manual

About

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