FMO DATABASE

FMODB ID: 228YR

Calculation Name: 2GMQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GMQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8KUD5

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	102
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-816169.662632
FMO2-HF: Nuclear repulsion	775078.991764
FMO2-HF: Total energy	-41090.670868
FMO2-MP2: Total energy	-41211.793888

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:12:GLY)

Summations of interaction energy for fragment #1(A:12: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.
-0.549	0.82	-0.011	-0.783	-0.575	0.004

Interaction energy analysis for fragmet #1(A:12:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.052 / q_NPA : 0.026

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	14	LYS	1	0.995	1.007	3.831	1.615	2.984	-0.011	-0.783	-0.575	0.004
4	A	15	GLU	-1	-0.900	-0.942	6.772	-0.654	-0.654	0.000	0.000	0.000	0.000
5	A	16	ILE	0	-0.025	-0.019	10.169	0.109	0.109	0.000	0.000	0.000	0.000
6	A	17	ALA	0	0.014	0.023	13.549	0.043	0.043	0.000	0.000	0.000	0.000
7	A	18	ILE	0	-0.052	-0.029	16.884	0.023	0.023	0.000	0.000	0.000	0.000
8	A	19	GLN	0	-0.023	-0.019	19.735	0.030	0.030	0.000	0.000	0.000	0.000
9	A	20	GLU	-1	-0.793	-0.921	23.266	-0.266	-0.266	0.000	0.000	0.000	0.000
10	A	21	LYS	1	0.962	0.987	24.528	0.240	0.240	0.000	0.000	0.000	0.000
11	A	22	ASP	-1	-0.849	-0.913	24.116	-0.304	-0.304	0.000	0.000	0.000	0.000
12	A	23	LEU	0	-0.040	-0.011	20.657	-0.017	-0.017	0.000	0.000	0.000	0.000
13	A	24	THR	0	-0.080	-0.035	24.595	0.038	0.038	0.000	0.000	0.000	0.000
14	A	25	LEU	0	0.040	0.018	23.611	-0.021	-0.021	0.000	0.000	0.000	0.000
15	A	26	GLN	0	0.017	0.015	24.783	0.010	0.010	0.000	0.000	0.000	0.000
16	A	27	TRP	0	0.052	0.035	24.772	-0.013	-0.013	0.000	0.000	0.000	0.000
17	A	28	ARG	1	0.954	0.956	24.359	0.201	0.201	0.000	0.000	0.000	0.000
18	A	29	GLY	0	0.047	0.022	28.602	0.006	0.006	0.000	0.000	0.000	0.000
19	A	30	ASN	0	-0.013	0.007	31.160	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	31	THR	0	0.038	0.019	31.546	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	32	GLY	0	0.010	0.017	29.070	0.003	0.003	0.000	0.000	0.000	0.000
22	A	33	LYS	1	0.982	0.988	19.530	0.269	0.269	0.000	0.000	0.000	0.000
23	A	34	LEU	0	0.015	0.006	20.842	0.008	0.008	0.000	0.000	0.000	0.000
24	A	35	VAL	0	-0.103	-0.039	21.476	-0.015	-0.015	0.000	0.000	0.000	0.000
25	A	36	LYS	1	0.932	0.966	20.273	0.249	0.249	0.000	0.000	0.000	0.000
26	A	37	VAL	0	0.045	0.043	19.059	0.040	0.040	0.000	0.000	0.000	0.000
27	A	38	ARG	1	0.897	0.961	20.553	0.232	0.232	0.000	0.000	0.000	0.000
28	A	39	LEU	0	0.061	0.030	19.422	0.023	0.023	0.000	0.000	0.000	0.000
29	A	40	LYS	1	0.898	0.935	23.091	0.278	0.278	0.000	0.000	0.000	0.000
30	A	41	ASN	0	-0.008	-0.026	26.053	0.003	0.003	0.000	0.000	0.000	0.000
31	A	42	THR	0	0.022	0.010	27.892	-0.005	-0.005	0.000	0.000	0.000	0.000
32	A	43	ARG	1	0.901	0.956	20.954	0.415	0.415	0.000	0.000	0.000	0.000
33	A	44	ALA	0	0.026	0.009	23.193	-0.021	-0.021	0.000	0.000	0.000	0.000
34	A	45	MET	0	-0.006	-0.008	24.049	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	46	GLU	-1	-0.913	-0.953	24.082	-0.340	-0.340	0.000	0.000	0.000	0.000
36	A	47	MET	0	-0.013	-0.015	19.308	-0.011	-0.011	0.000	0.000	0.000	0.000
37	A	48	TRP	0	0.023	0.025	21.135	-0.016	-0.016	0.000	0.000	0.000	0.000
38	A	49	TYR	0	-0.018	-0.022	23.236	0.009	0.009	0.000	0.000	0.000	0.000
39	A	50	ASN	0	-0.016	-0.012	21.496	0.030	0.030	0.000	0.000	0.000	0.000
40	A	51	LYS	1	0.866	0.944	18.758	0.301	0.301	0.000	0.000	0.000	0.000
41	A	52	GLN	0	0.027	0.031	17.083	-0.010	-0.010	0.000	0.000	0.000	0.000
42	A	53	ILE	0	-0.040	-0.030	14.652	-0.102	-0.102	0.000	0.000	0.000	0.000
43	A	54	THR	0	-0.053	-0.027	15.246	0.112	0.112	0.000	0.000	0.000	0.000
44	A	55	GLU	-1	-0.902	-0.980	15.491	-0.428	-0.428	0.000	0.000	0.000	0.000
45	A	56	GLU	-1	-0.942	-0.968	13.436	-0.543	-0.543	0.000	0.000	0.000	0.000
46	A	57	ASN	0	0.085	0.062	11.310	-0.057	-0.057	0.000	0.000	0.000	0.000
47	A	58	ILE	0	-0.050	-0.024	10.708	-0.263	-0.263	0.000	0.000	0.000	0.000
48	A	59	GLN	0	-0.052	-0.065	9.957	-0.125	-0.125	0.000	0.000	0.000	0.000
49	A	60	GLU	-1	-0.889	-0.931	6.354	-2.041	-2.041	0.000	0.000	0.000	0.000
50	A	61	ILE	0	-0.115	-0.042	6.269	-0.941	-0.941	0.000	0.000	0.000	0.000
51	A	62	THR	0	0.038	0.009	4.894	-0.110	-0.110	0.000	0.000	0.000	0.000
52	A	63	THR	0	-0.015	-0.009	8.166	0.374	0.374	0.000	0.000	0.000	0.000
53	A	64	LEU	0	0.000	0.002	10.859	-0.045	-0.045	0.000	0.000	0.000	0.000
54	A	65	ASN	0	0.025	0.002	14.350	0.129	0.129	0.000	0.000	0.000	0.000
55	A	66	ILE	0	-0.021	-0.009	16.322	0.031	0.031	0.000	0.000	0.000	0.000
56	A	67	ILE	0	0.045	0.026	19.552	0.034	0.034	0.000	0.000	0.000	0.000
57	A	68	LYS	1	0.917	0.938	22.515	0.233	0.233	0.000	0.000	0.000	0.000
58	A	69	ASN	0	-0.064	-0.043	26.267	0.002	0.002	0.000	0.000	0.000	0.000
59	A	70	GLY	0	0.018	0.010	27.239	0.010	0.010	0.000	0.000	0.000	0.000
60	A	71	LYS	1	0.905	0.971	25.149	0.186	0.186	0.000	0.000	0.000	0.000
61	A	72	SER	0	0.013	-0.007	19.752	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	73	LEU	0	-0.017	0.002	19.312	0.029	0.029	0.000	0.000	0.000	0.000
63	A	74	ALA	0	0.037	0.030	13.883	-0.038	-0.038	0.000	0.000	0.000	0.000
64	A	75	LEU	0	-0.053	-0.037	15.084	0.077	0.077	0.000	0.000	0.000	0.000
65	A	76	GLU	-1	-0.847	-0.933	9.654	-0.796	-0.796	0.000	0.000	0.000	0.000
66	A	77	VAL	0	-0.010	-0.005	10.976	0.223	0.223	0.000	0.000	0.000	0.000
67	A	78	TYR	0	-0.042	-0.042	11.139	-0.047	-0.047	0.000	0.000	0.000	0.000
68	A	79	PRO	0	0.076	0.031	7.672	0.191	0.191	0.000	0.000	0.000	0.000
69	A	80	GLU	-1	-0.877	-0.933	8.680	-0.778	-0.778	0.000	0.000	0.000	0.000
70	A	81	LYS	1	0.843	0.930	12.131	0.466	0.466	0.000	0.000	0.000	0.000
71	A	82	SER	0	-0.039	-0.005	12.249	0.105	0.105	0.000	0.000	0.000	0.000
72	A	83	ILE	0	0.029	0.033	14.926	0.019	0.019	0.000	0.000	0.000	0.000
73	A	84	TYR	0	0.066	0.028	16.957	-0.025	-0.025	0.000	0.000	0.000	0.000
74	A	85	VAL	0	-0.044	-0.017	20.730	0.034	0.034	0.000	0.000	0.000	0.000
75	A	86	LYS	1	1.037	1.006	24.212	0.162	0.162	0.000	0.000	0.000	0.000
76	A	87	PRO	0	-0.055	-0.020	27.776	0.000	0.000	0.000	0.000	0.000	0.000
77	A	88	ASN	0	-0.015	-0.004	29.163	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	89	LEU	0	0.012	-0.007	32.381	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	90	GLY	0	0.060	0.023	33.583	0.002	0.002	0.000	0.000	0.000	0.000
80	A	91	ARG	1	0.912	0.976	31.073	0.176	0.176	0.000	0.000	0.000	0.000
81	A	92	ILE	0	0.040	0.025	24.581	0.006	0.006	0.000	0.000	0.000	0.000
82	A	93	ASN	0	0.017	0.003	23.969	0.018	0.018	0.000	0.000	0.000	0.000
83	A	94	VAL	0	-0.022	-0.015	23.113	-0.012	-0.012	0.000	0.000	0.000	0.000
84	A	95	PRO	0	0.058	0.040	17.886	0.015	0.015	0.000	0.000	0.000	0.000
85	A	96	VAL	0	-0.080	-0.034	18.791	0.033	0.033	0.000	0.000	0.000	0.000
86	A	97	PHE	0	0.077	0.036	12.962	-0.010	-0.010	0.000	0.000	0.000	0.000
87	A	98	PHE	0	-0.012	-0.023	15.926	0.100	0.100	0.000	0.000	0.000	0.000
88	A	99	ILE	0	-0.011	-0.012	15.642	-0.076	-0.076	0.000	0.000	0.000	0.000
89	A	100	LYS	1	0.871	0.946	9.244	0.792	0.792	0.000	0.000	0.000	0.000
90	A	101	THR	0	0.033	0.018	14.517	0.044	0.044	0.000	0.000	0.000	0.000
91	A	102	PRO	0	-0.059	-0.027	16.380	0.003	0.003	0.000	0.000	0.000	0.000
92	A	103	ILE	0	0.087	0.046	20.109	0.008	0.008	0.000	0.000	0.000	0.000
93	A	104	ASN	0	0.024	-0.002	22.418	-0.017	-0.017	0.000	0.000	0.000	0.000
94	A	105	ARG	1	0.842	0.912	26.092	0.174	0.174	0.000	0.000	0.000	0.000
95	A	106	GLY	0	0.046	0.024	28.422	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	107	VAL	0	0.067	0.032	25.277	-0.001	-0.001	0.000	0.000	0.000	0.000
97	A	108	PHE	0	-0.018	-0.017	22.485	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	109	GLU	-1	-0.829	-0.923	26.340	-0.201	-0.201	0.000	0.000	0.000	0.000
99	A	110	GLU	-1	-0.963	-0.968	29.544	-0.124	-0.124	0.000	0.000	0.000	0.000
100	A	111	ILE	0	-0.065	-0.024	23.452	0.003	0.003	0.000	0.000	0.000	0.000
101	A	112	PHE	0	-0.038	-0.025	22.410	0.004	0.004	0.000	0.000	0.000	0.000
102	A	113	GLY	0	0.001	0.026	28.435	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:12:GLY)