FMO DATABASE

FMODB ID: K9L83

Calculation Name: 2GBJ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2GBJ

Chain ID: A

ChEMBL ID:

UniProt ID: P0CG48

Base Structure: X-ray

Registration Date: 2023-09-19

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	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	81
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-502573.563396
FMO2-HF: Nuclear repulsion	472229.845579
FMO2-HF: Total energy	-30343.717817
FMO2-MP2: Total energy	-30433.478013

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.
-27.188	-25.377	24.973	-6.112	-20.669	-0.059

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 : -0.024 / q_NPA : -0.006

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	3	ILE	0	-0.034	-0.011	2.615	-1.601	1.720	1.127	-1.604	-2.844	-0.006
4	A	4	PHE	0	0.001	-0.002	4.778	0.124	0.168	-0.001	-0.011	-0.032	0.000
5	A	5	VAL	0	-0.008	0.002	8.629	-0.079	-0.079	0.000	0.000	0.000	0.000
6	A	6	LYS	1	0.927	0.975	11.433	0.278	0.278	0.000	0.000	0.000	0.000
7	A	7	THR	0	0.028	0.028	15.133	-0.047	-0.047	0.000	0.000	0.000	0.000
8	A	8	LEU	0	-0.013	-0.017	18.175	0.044	0.044	0.000	0.000	0.000	0.000
9	A	9	THR	0	0.011	-0.006	20.442	-0.011	-0.011	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.029	0.028	23.371	0.002	0.002	0.000	0.000	0.000	0.000
11	A	11	GLY	0	-0.020	-0.022	25.846	0.016	0.016	0.000	0.000	0.000	0.000
12	A	12	GLY	0	0.014	0.005	28.929	0.007	0.007	0.000	0.000	0.000	0.000
13	A	13	GLY	0	-0.026	0.004	28.446	0.010	0.010	0.000	0.000	0.000	0.000
14	A	14	GLY	0	0.038	0.017	29.286	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.033	0.002	27.168	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.002	0.020	24.556	-0.014	-0.014	0.000	0.000	0.000	0.000
17	A	17	GLY	0	-0.007	-0.015	22.139	0.015	0.015	0.000	0.000	0.000	0.000
18	A	18	GLY	0	-0.011	-0.012	18.982	-0.013	-0.013	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.846	0.943	17.602	0.384	0.384	0.000	0.000	0.000	0.000
20	A	20	THR	0	-0.011	-0.011	12.768	-0.027	-0.027	0.000	0.000	0.000	0.000
21	A	21	ILE	0	-0.010	0.008	12.234	0.055	0.055	0.000	0.000	0.000	0.000
22	A	22	THR	0	0.031	0.010	8.657	-0.082	-0.082	0.000	0.000	0.000	0.000
23	A	23	LEU	0	-0.055	-0.031	6.868	0.209	0.209	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.905	-0.935	4.046	-1.767	-1.498	0.000	-0.067	-0.201	0.000
25	A	25	VAL	0	-0.047	-0.038	2.513	0.260	1.992	0.956	-0.695	-1.993	-0.002
26	A	26	GLU	-1	-0.827	-0.913	1.929	-17.495	-17.998	9.116	-4.251	-4.361	-0.051
27	A	27	PRO	0	-0.034	-0.029	2.650	-1.685	0.169	1.529	-0.554	-2.829	-0.001
28	A	28	SER	0	0.028	0.007	3.459	0.983	0.861	0.037	0.253	-0.168	0.000
29	A	29	ASP	-1	-0.803	-0.881	5.437	-4.455	-4.455	0.000	0.000	0.000	0.000
30	A	30	THR	0	0.030	0.005	7.178	0.013	0.013	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.032	-0.017	9.032	-0.217	-0.217	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-0.931	-0.967	11.085	-0.943	-0.943	0.000	0.000	0.000	0.000
33	A	33	ASN	0	0.014	0.007	9.703	-0.058	-0.058	0.000	0.000	0.000	0.000
34	A	34	VAL	0	-0.003	-0.007	7.010	-0.056	-0.056	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.792	0.887	9.839	0.950	0.950	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.022	0.026	13.477	0.140	0.140	0.000	0.000	0.000	0.000
37	A	37	LYS	1	0.851	0.915	6.368	4.164	4.164	0.000	0.000	0.000	0.000
38	A	38	ILE	0	-0.041	-0.017	11.291	0.096	0.096	0.000	0.000	0.000	0.000
39	A	39	GLN	0	-0.021	-0.008	13.875	0.113	0.113	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.903	-0.956	13.355	-1.018	-1.018	0.000	0.000	0.000	0.000
41	A	41	LYS	1	0.796	0.900	10.682	1.427	1.427	0.000	0.000	0.000	0.000
42	A	42	GLU	-1	-0.859	-0.944	16.849	-0.383	-0.383	0.000	0.000	0.000	0.000
43	A	43	GLY	0	-0.004	0.012	19.226	0.055	0.055	0.000	0.000	0.000	0.000
44	A	44	ILE	0	-0.051	-0.034	18.991	0.020	0.020	0.000	0.000	0.000	0.000
45	A	45	PRO	0	0.067	0.035	19.244	-0.079	-0.079	0.000	0.000	0.000	0.000
46	A	46	PRO	0	0.072	0.029	17.229	0.017	0.017	0.000	0.000	0.000	0.000
47	A	47	ASP	-1	-0.893	-0.942	18.634	-0.527	-0.527	0.000	0.000	0.000	0.000
48	A	48	GLN	0	-0.058	-0.041	21.438	0.034	0.034	0.000	0.000	0.000	0.000
49	A	49	GLN	0	-0.028	-0.026	15.177	-0.039	-0.039	0.000	0.000	0.000	0.000
50	A	50	ARG	1	0.831	0.903	17.162	0.377	0.377	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.055	0.027	10.842	0.010	0.010	0.000	0.000	0.000	0.000
52	A	52	ILE	0	-0.036	-0.014	13.914	0.046	0.046	0.000	0.000	0.000	0.000
53	A	53	PHE	0	0.055	0.019	8.720	-0.130	-0.130	0.000	0.000	0.000	0.000
54	A	54	ALA	0	0.017	0.008	12.282	0.024	0.024	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.005	0.012	14.405	0.020	0.020	0.000	0.000	0.000	0.000
56	A	56	LYS	1	0.831	0.924	14.405	0.434	0.434	0.000	0.000	0.000	0.000
57	A	57	GLN	0	0.044	0.018	15.088	-0.075	-0.075	0.000	0.000	0.000	0.000
58	A	58	LEU	0	-0.064	-0.022	10.287	0.040	0.040	0.000	0.000	0.000	0.000
59	A	59	GLU	-1	-0.762	-0.859	14.079	-0.460	-0.460	0.000	0.000	0.000	0.000
60	A	60	ASP	-1	-0.809	-0.903	13.816	-0.886	-0.886	0.000	0.000	0.000	0.000
61	A	61	GLY	0	0.030	0.018	13.910	-0.129	-0.129	0.000	0.000	0.000	0.000
62	A	62	ARG	1	0.807	0.907	11.519	0.539	0.539	0.000	0.000	0.000	0.000
63	A	63	THR	0	0.000	-0.018	7.361	-0.179	-0.179	0.000	0.000	0.000	0.000
64	A	64	LEU	0	0.006	-0.005	2.757	-0.231	0.335	0.464	-0.180	-0.850	-0.001
65	A	65	SER	0	-0.025	-0.019	5.402	0.770	0.770	0.000	0.000	0.000	0.000
66	A	66	ASP	-1	-0.839	-0.883	6.206	-0.424	-0.424	0.000	0.000	0.000	0.000
67	A	67	TYR	0	-0.050	-0.063	8.077	0.197	0.197	0.000	0.000	0.000	0.000
68	A	68	ASN	0	-0.049	-0.021	6.860	0.215	0.215	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.024	0.010	3.903	0.501	0.696	0.000	-0.031	-0.163	0.000
70	A	70	GLN	0	0.035	0.008	2.722	-4.946	-3.827	2.096	-1.104	-2.111	-0.004
71	A	71	LYS	1	1.035	1.014	2.195	-3.525	-7.419	9.485	-0.965	-4.626	0.003
72	A	72	GLU	-1	-0.937	-0.972	3.180	2.264	-0.506	0.164	3.097	-0.491	0.003
73	A	73	SER	0	-0.022	-0.011	5.285	-0.639	-0.639	0.000	0.000	0.000	0.000
74	A	74	THR	0	-0.019	-0.009	7.019	-0.591	-0.591	0.000	0.000	0.000	0.000
75	A	75	LEU	0	0.008	0.010	7.249	0.166	0.166	0.000	0.000	0.000	0.000
76	A	76	HIS	0	-0.047	-0.032	10.415	0.116	0.116	0.000	0.000	0.000	0.000
77	A	77	LEU	0	0.040	0.020	14.188	-0.020	-0.020	0.000	0.000	0.000	0.000
78	A	78	VAL	0	-0.052	-0.045	15.860	0.094	0.094	0.000	0.000	0.000	0.000
79	A	79	LEU	0	0.044	0.029	19.311	-0.042	-0.042	0.000	0.000	0.000	0.000
80	A	80	ARG	1	0.882	0.950	20.947	0.477	0.477	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.052	0.034	23.532	-0.009	-0.009	0.000	0.000	0.000	0.000

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