FMO DATABASE

FMODB ID: 668MZ

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	OptHSide
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	-815842.263288
FMO2-HF: Nuclear repulsion	774750.688549
FMO2-HF: Total energy	-41091.57474
FMO2-MP2: Total energy	-41212.583055

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.
-0.636	0.72	-0.011	-0.783	-0.563	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 : 0.049 / q_NPA : 0.024

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	0.898	0.940	3.830	1.436	2.792	-0.011	-0.783	-0.563	0.004
4	A	15	GLU	-1	-0.877	-0.918	6.772	-0.648	-0.648	0.000	0.000	0.000	0.000
5	A	16	ILE	0	-0.006	-0.005	10.169	0.118	0.118	0.000	0.000	0.000	0.000
6	A	17	ALA	0	0.010	0.019	13.549	0.043	0.043	0.000	0.000	0.000	0.000
7	A	18	ILE	0	-0.039	-0.022	16.884	0.024	0.024	0.000	0.000	0.000	0.000
8	A	19	GLN	0	0.014	0.011	19.735	0.036	0.036	0.000	0.000	0.000	0.000
9	A	20	GLU	-1	-0.730	-0.884	23.266	-0.258	-0.258	0.000	0.000	0.000	0.000
10	A	21	LYS	1	0.911	0.948	24.528	0.256	0.256	0.000	0.000	0.000	0.000
11	A	22	ASP	-1	-0.819	-0.892	23.889	-0.316	-0.316	0.000	0.000	0.000	0.000
12	A	23	LEU	0	-0.022	-0.006	20.631	-0.014	-0.014	0.000	0.000	0.000	0.000
13	A	24	THR	0	-0.069	-0.032	24.606	0.038	0.038	0.000	0.000	0.000	0.000
14	A	25	LEU	0	0.036	0.020	23.529	-0.022	-0.022	0.000	0.000	0.000	0.000
15	A	26	GLN	0	0.036	0.030	24.789	0.011	0.011	0.000	0.000	0.000	0.000
16	A	27	TRP	0	0.044	0.030	24.697	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	28	ARG	1	0.953	0.960	24.939	0.197	0.197	0.000	0.000	0.000	0.000
18	A	29	GLY	0	0.045	0.019	28.601	0.006	0.006	0.000	0.000	0.000	0.000
19	A	30	ASN	0	-0.040	-0.015	31.156	0.000	0.000	0.000	0.000	0.000	0.000
20	A	31	THR	0	0.057	0.011	31.533	-0.008	-0.008	0.000	0.000	0.000	0.000
21	A	32	GLY	0	0.013	0.023	29.069	0.002	0.002	0.000	0.000	0.000	0.000
22	A	33	LYS	1	0.938	0.957	19.270	0.302	0.302	0.000	0.000	0.000	0.000
23	A	34	LEU	0	0.013	0.018	20.775	0.007	0.007	0.000	0.000	0.000	0.000
24	A	35	VAL	0	-0.100	-0.046	21.475	-0.017	-0.017	0.000	0.000	0.000	0.000
25	A	36	LYS	1	0.915	0.952	20.278	0.248	0.248	0.000	0.000	0.000	0.000
26	A	37	VAL	0	0.037	0.039	19.047	0.040	0.040	0.000	0.000	0.000	0.000
27	A	38	ARG	1	0.889	0.954	20.561	0.231	0.231	0.000	0.000	0.000	0.000
28	A	39	LEU	0	0.045	0.026	19.277	0.024	0.024	0.000	0.000	0.000	0.000
29	A	40	LYS	1	0.848	0.909	23.103	0.283	0.283	0.000	0.000	0.000	0.000
30	A	41	ASN	0	0.003	-0.022	26.066	0.000	0.000	0.000	0.000	0.000	0.000
31	A	42	THR	0	0.025	0.011	27.905	-0.006	-0.006	0.000	0.000	0.000	0.000
32	A	43	ARG	1	0.815	0.889	21.121	0.407	0.407	0.000	0.000	0.000	0.000
33	A	44	ALA	0	0.032	0.020	23.204	-0.021	-0.021	0.000	0.000	0.000	0.000
34	A	45	MET	0	0.009	0.000	24.043	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	46	GLU	-1	-0.842	-0.894	23.622	-0.353	-0.353	0.000	0.000	0.000	0.000
36	A	47	MET	0	-0.001	-0.009	19.518	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	48	TRP	0	0.031	0.027	21.158	-0.015	-0.015	0.000	0.000	0.000	0.000
38	A	49	TYR	0	-0.008	-0.009	23.227	0.009	0.009	0.000	0.000	0.000	0.000
39	A	50	ASN	0	-0.032	-0.019	21.435	0.030	0.030	0.000	0.000	0.000	0.000
40	A	51	LYS	1	0.846	0.928	18.700	0.300	0.300	0.000	0.000	0.000	0.000
41	A	52	GLN	0	0.017	0.024	17.056	-0.024	-0.024	0.000	0.000	0.000	0.000
42	A	53	ILE	0	-0.027	-0.025	14.613	-0.100	-0.100	0.000	0.000	0.000	0.000
43	A	54	THR	0	-0.038	-0.030	15.445	0.109	0.109	0.000	0.000	0.000	0.000
44	A	55	GLU	-1	-0.888	-0.970	15.503	-0.453	-0.453	0.000	0.000	0.000	0.000
45	A	56	GLU	-1	-0.921	-0.951	13.705	-0.474	-0.474	0.000	0.000	0.000	0.000
46	A	57	ASN	0	0.021	0.030	11.350	-0.079	-0.079	0.000	0.000	0.000	0.000
47	A	58	ILE	0	-0.054	-0.019	10.721	-0.268	-0.268	0.000	0.000	0.000	0.000
48	A	59	GLN	0	-0.050	-0.054	10.043	-0.119	-0.119	0.000	0.000	0.000	0.000
49	A	60	GLU	-1	-0.791	-0.872	6.359	-1.952	-1.952	0.000	0.000	0.000	0.000
50	A	61	ILE	0	-0.100	-0.034	6.282	-0.939	-0.939	0.000	0.000	0.000	0.000
51	A	62	THR	0	0.054	0.019	4.818	-0.125	-0.125	0.000	0.000	0.000	0.000
52	A	63	THR	0	-0.038	-0.027	8.166	0.359	0.359	0.000	0.000	0.000	0.000
53	A	64	LEU	0	0.011	0.014	10.859	-0.039	-0.039	0.000	0.000	0.000	0.000
54	A	65	ASN	0	-0.016	-0.033	14.350	0.146	0.146	0.000	0.000	0.000	0.000
55	A	66	ILE	0	-0.014	-0.008	16.322	0.033	0.033	0.000	0.000	0.000	0.000
56	A	67	ILE	0	0.044	0.019	19.285	0.035	0.035	0.000	0.000	0.000	0.000
57	A	68	LYS	1	0.846	0.913	22.515	0.239	0.239	0.000	0.000	0.000	0.000
58	A	69	ASN	0	-0.049	-0.032	26.267	0.000	0.000	0.000	0.000	0.000	0.000
59	A	70	GLY	0	0.019	0.011	27.239	0.011	0.011	0.000	0.000	0.000	0.000
60	A	71	LYS	1	0.914	0.978	25.118	0.184	0.184	0.000	0.000	0.000	0.000
61	A	72	SER	0	0.021	0.004	19.705	-0.011	-0.011	0.000	0.000	0.000	0.000
62	A	73	LEU	0	-0.020	-0.010	19.570	0.028	0.028	0.000	0.000	0.000	0.000
63	A	74	ALA	0	0.038	0.030	13.943	-0.038	-0.038	0.000	0.000	0.000	0.000
64	A	75	LEU	0	-0.053	-0.035	15.069	0.078	0.078	0.000	0.000	0.000	0.000
65	A	76	GLU	-1	-0.763	-0.872	9.447	-0.840	-0.840	0.000	0.000	0.000	0.000
66	A	77	VAL	0	-0.019	-0.012	11.010	0.226	0.226	0.000	0.000	0.000	0.000
67	A	78	TYR	0	-0.010	-0.026	11.138	-0.046	-0.046	0.000	0.000	0.000	0.000
68	A	79	PRO	0	0.068	0.036	7.352	0.189	0.189	0.000	0.000	0.000	0.000
69	A	80	GLU	-1	-0.872	-0.936	8.834	-0.782	-0.782	0.000	0.000	0.000	0.000
70	A	81	LYS	1	0.814	0.915	12.132	0.479	0.479	0.000	0.000	0.000	0.000
71	A	82	SER	0	-0.034	-0.004	12.127	0.106	0.106	0.000	0.000	0.000	0.000
72	A	83	ILE	0	0.022	0.022	14.933	0.021	0.021	0.000	0.000	0.000	0.000
73	A	84	TYR	0	0.066	0.029	16.982	-0.027	-0.027	0.000	0.000	0.000	0.000
74	A	85	VAL	0	-0.042	-0.019	20.739	0.035	0.035	0.000	0.000	0.000	0.000
75	A	86	LYS	1	1.036	1.007	24.220	0.159	0.159	0.000	0.000	0.000	0.000
76	A	87	PRO	0	-0.033	-0.004	27.785	0.000	0.000	0.000	0.000	0.000	0.000
77	A	88	ASN	0	-0.026	-0.011	29.173	-0.002	-0.002	0.000	0.000	0.000	0.000
78	A	89	LEU	0	0.023	-0.002	32.416	-0.003	-0.003	0.000	0.000	0.000	0.000
79	A	90	GLY	0	0.048	0.018	33.379	0.001	0.001	0.000	0.000	0.000	0.000
80	A	91	ARG	1	0.911	0.970	31.189	0.174	0.174	0.000	0.000	0.000	0.000
81	A	92	ILE	0	0.039	0.024	24.336	0.005	0.005	0.000	0.000	0.000	0.000
82	A	93	ASN	0	0.021	0.007	24.071	0.018	0.018	0.000	0.000	0.000	0.000
83	A	94	VAL	0	-0.017	-0.012	23.101	-0.013	-0.013	0.000	0.000	0.000	0.000
84	A	95	PRO	0	0.047	0.039	17.954	0.016	0.016	0.000	0.000	0.000	0.000
85	A	96	VAL	0	-0.065	-0.036	18.791	0.033	0.033	0.000	0.000	0.000	0.000
86	A	97	PHE	0	0.085	0.039	12.962	-0.009	-0.009	0.000	0.000	0.000	0.000
87	A	98	PHE	0	-0.008	-0.019	15.940	0.100	0.100	0.000	0.000	0.000	0.000
88	A	99	ILE	0	0.012	-0.005	15.646	-0.074	-0.074	0.000	0.000	0.000	0.000
89	A	100	LYS	1	0.801	0.889	9.682	0.773	0.773	0.000	0.000	0.000	0.000
90	A	101	THR	0	0.034	0.024	14.623	0.043	0.043	0.000	0.000	0.000	0.000
91	A	102	PRO	0	-0.037	-0.028	16.379	0.005	0.005	0.000	0.000	0.000	0.000
92	A	103	ILE	0	0.062	0.041	20.108	0.009	0.009	0.000	0.000	0.000	0.000
93	A	104	ASN	0	0.020	-0.004	22.417	-0.015	-0.015	0.000	0.000	0.000	0.000
94	A	105	ARG	1	0.811	0.908	26.091	0.176	0.176	0.000	0.000	0.000	0.000
95	A	106	GLY	0	0.043	0.024	28.421	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	107	VAL	0	0.061	0.029	25.441	0.000	0.000	0.000	0.000	0.000	0.000
97	A	108	PHE	0	-0.011	-0.011	22.538	-0.011	-0.011	0.000	0.000	0.000	0.000
98	A	109	GLU	-1	-0.812	-0.906	26.339	-0.197	-0.197	0.000	0.000	0.000	0.000
99	A	110	GLU	-1	-0.945	-0.952	29.581	-0.126	-0.126	0.000	0.000	0.000	0.000
100	A	111	ILE	0	-0.061	-0.029	23.550	0.002	0.002	0.000	0.000	0.000	0.000
101	A	112	PHE	0	-0.051	-0.032	22.392	0.003	0.003	0.000	0.000	0.000	0.000
102	A	113	GLY	0	-0.001	0.015	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)