FMO DATABASE

FMODB ID: 6YVKZ

Calculation Name: 2OCT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2OCT

Chain ID: A

ChEMBL ID:

UniProt ID: P04080

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	97
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-586986.000769
FMO2-HF: Nuclear repulsion	548911.012921
FMO2-HF: Total energy	-38074.987849
FMO2-MP2: Total energy	-38188.162848

3D Structure Molmil

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:2:MET)

Summations of interaction energy for fragment #1(A:2: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.
-5.775	-2.077	1.622	-2.174	-3.148	-0.005

Interaction energy analysis for fragmet #1(A:2:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.008

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	4	GLY	0	0.127	0.103	3.698	-4.795	-2.190	0.010	-1.649	-0.966	-0.003
4	A	5	ALA	0	-0.073	-0.039	6.085	0.479	0.479	0.000	0.000	0.000	0.000
5	A	6	PRO	0	-0.003	-0.011	7.218	-0.088	-0.088	0.000	0.000	0.000	0.000
6	A	7	SER	0	0.004	0.010	7.868	0.146	0.146	0.000	0.000	0.000	0.000
7	A	8	ALA	0	0.045	0.032	8.764	-0.051	-0.051	0.000	0.000	0.000	0.000
8	A	9	THR	0	-0.017	-0.022	11.800	-0.028	-0.028	0.000	0.000	0.000	0.000
9	A	10	GLN	0	0.001	0.013	9.504	0.048	0.048	0.000	0.000	0.000	0.000
10	A	11	PRO	0	0.019	0.001	14.698	-0.031	-0.031	0.000	0.000	0.000	0.000
11	A	12	ALA	0	-0.020	-0.015	17.143	0.012	0.012	0.000	0.000	0.000	0.000
12	A	13	THR	0	0.020	0.010	16.055	0.005	0.005	0.000	0.000	0.000	0.000
13	A	14	ALA	0	0.051	0.009	18.812	-0.013	-0.013	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.822	-0.890	15.905	0.110	0.110	0.000	0.000	0.000	0.000
15	A	16	THR	0	-0.012	-0.004	15.963	-0.011	-0.011	0.000	0.000	0.000	0.000
16	A	17	GLN	0	-0.042	-0.030	17.911	-0.015	-0.015	0.000	0.000	0.000	0.000
17	A	18	HIS	0	0.000	-0.010	19.959	-0.019	-0.019	0.000	0.000	0.000	0.000
18	A	19	ILE	0	-0.013	-0.003	15.219	-0.016	-0.016	0.000	0.000	0.000	0.000
19	A	20	ALA	0	-0.021	-0.015	19.757	-0.017	-0.017	0.000	0.000	0.000	0.000
20	A	21	ASP	-1	-0.865	-0.947	22.401	0.025	0.025	0.000	0.000	0.000	0.000
21	A	22	GLN	0	-0.052	-0.011	20.616	0.002	0.002	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.002	-0.003	21.197	-0.011	-0.011	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.840	0.929	24.347	-0.014	-0.014	0.000	0.000	0.000	0.000
24	A	25	SER	0	-0.017	-0.028	27.202	-0.002	-0.002	0.000	0.000	0.000	0.000
25	A	26	GLN	0	0.062	0.045	24.821	0.000	0.000	0.000	0.000	0.000	0.000
26	A	27	LEU	0	0.002	-0.005	25.815	-0.003	-0.003	0.000	0.000	0.000	0.000
27	A	28	GLU	-1	-0.752	-0.871	28.734	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	29	GLU	-1	-0.853	-0.907	31.800	-0.049	-0.049	0.000	0.000	0.000	0.000
29	A	30	LYS	1	0.765	0.884	28.515	0.053	0.053	0.000	0.000	0.000	0.000
30	A	31	TYR	0	-0.022	-0.015	29.252	0.003	0.003	0.000	0.000	0.000	0.000
31	A	32	ASN	0	0.000	0.010	34.706	0.002	0.002	0.000	0.000	0.000	0.000
32	A	33	LYS	1	0.893	0.961	33.681	0.011	0.011	0.000	0.000	0.000	0.000
33	A	34	LYS	1	0.896	0.939	33.693	0.005	0.005	0.000	0.000	0.000	0.000
34	A	35	PHE	0	-0.015	-0.017	30.118	0.001	0.001	0.000	0.000	0.000	0.000
35	A	36	PRO	0	-0.011	-0.006	33.656	0.001	0.001	0.000	0.000	0.000	0.000
36	A	37	VAL	0	-0.014	-0.019	30.101	0.003	0.003	0.000	0.000	0.000	0.000
37	A	38	PHE	0	0.002	-0.009	24.743	-0.004	-0.004	0.000	0.000	0.000	0.000
38	A	39	LYS	1	0.983	1.009	25.948	-0.060	-0.060	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.029	0.023	20.544	-0.002	-0.002	0.000	0.000	0.000	0.000
40	A	41	VAL	0	-0.005	-0.014	22.004	0.008	0.008	0.000	0.000	0.000	0.000
41	A	42	SER	0	-0.022	-0.025	18.307	0.011	0.011	0.000	0.000	0.000	0.000
42	A	43	PHE	0	-0.003	0.010	11.302	-0.025	-0.025	0.000	0.000	0.000	0.000
43	A	44	LYS	1	0.875	0.934	12.227	-0.071	-0.071	0.000	0.000	0.000	0.000
44	A	45	SER	0	0.025	0.012	8.179	-0.015	-0.015	0.000	0.000	0.000	0.000
45	A	46	GLN	0	-0.008	-0.014	7.717	0.109	0.109	0.000	0.000	0.000	0.000
46	A	47	VAL	0	0.017	0.024	2.392	-1.165	-0.210	1.613	-0.514	-2.055	-0.002
47	A	48	VAL	0	-0.008	-0.011	5.586	-0.393	-0.393	0.000	0.000	0.000	0.000
48	A	49	ALA	0	0.025	0.008	4.286	-0.055	0.083	-0.001	-0.011	-0.127	0.000
49	A	50	GLY	0	0.014	0.007	6.279	-0.157	-0.157	0.000	0.000	0.000	0.000
50	A	51	THR	0	-0.024	-0.001	9.434	0.056	0.056	0.000	0.000	0.000	0.000
51	A	52	ASN	0	-0.028	-0.013	13.004	0.036	0.036	0.000	0.000	0.000	0.000
52	A	53	TYR	0	-0.011	-0.016	15.797	0.026	0.026	0.000	0.000	0.000	0.000
53	A	54	PHE	0	0.002	-0.004	18.699	0.003	0.003	0.000	0.000	0.000	0.000
54	A	55	ILE	0	-0.002	-0.006	21.985	0.004	0.004	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.806	0.896	25.186	0.132	0.132	0.000	0.000	0.000	0.000
56	A	57	VAL	0	-0.015	-0.013	28.322	-0.003	-0.003	0.000	0.000	0.000	0.000
57	A	58	HIS	0	-0.047	-0.040	31.000	0.001	0.001	0.000	0.000	0.000	0.000
58	A	59	VAL	0	-0.058	-0.041	33.682	-0.003	-0.003	0.000	0.000	0.000	0.000
59	A	60	GLY	0	0.038	0.033	36.349	0.004	0.004	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.856	-0.931	39.967	-0.067	-0.067	0.000	0.000	0.000	0.000
61	A	62	GLU	-1	-0.996	-0.988	40.802	-0.071	-0.071	0.000	0.000	0.000	0.000
62	A	63	ASP	-1	-0.905	-0.934	37.819	-0.081	-0.081	0.000	0.000	0.000	0.000
63	A	64	PHE	0	-0.060	-0.041	33.241	-0.006	-0.006	0.000	0.000	0.000	0.000
64	A	65	VAL	0	-0.007	-0.002	29.046	0.002	0.002	0.000	0.000	0.000	0.000
65	A	66	HIS	0	-0.024	0.001	26.921	-0.001	-0.001	0.000	0.000	0.000	0.000
66	A	67	LEU	0	0.015	0.003	23.950	0.003	0.003	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.916	0.967	17.167	0.293	0.293	0.000	0.000	0.000	0.000
68	A	69	VAL	0	0.014	0.009	18.756	0.008	0.008	0.000	0.000	0.000	0.000
69	A	70	PHE	0	0.003	-0.003	9.043	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	71	GLN	0	0.051	0.031	13.120	0.061	0.061	0.000	0.000	0.000	0.000
71	A	72	SER	0	-0.046	-0.021	7.839	-0.108	-0.108	0.000	0.000	0.000	0.000
72	A	73	LEU	0	0.028	0.030	5.318	0.138	0.138	0.000	0.000	0.000	0.000
73	A	74	PRO	0	0.013	0.001	8.051	-0.147	-0.147	0.000	0.000	0.000	0.000
74	A	75	HIS	0	0.054	0.009	8.927	0.167	0.167	0.000	0.000	0.000	0.000
75	A	76	GLU	-1	-0.909	-0.958	11.925	-0.643	-0.643	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.047	-0.018	11.835	0.193	0.193	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.925	0.963	13.758	0.378	0.378	0.000	0.000	0.000	0.000
78	A	79	SER	0	-0.026	0.000	15.052	0.060	0.060	0.000	0.000	0.000	0.000
79	A	80	LEU	0	0.015	0.000	15.065	-0.073	-0.073	0.000	0.000	0.000	0.000
80	A	81	THR	0	-0.010	0.000	15.601	0.028	0.028	0.000	0.000	0.000	0.000
81	A	82	LEU	0	0.003	-0.007	17.668	-0.018	-0.018	0.000	0.000	0.000	0.000
82	A	83	SER	0	-0.081	-0.036	17.349	-0.013	-0.013	0.000	0.000	0.000	0.000
83	A	84	ASN	0	-0.006	-0.014	19.540	0.026	0.026	0.000	0.000	0.000	0.000
84	A	85	TYR	0	-0.007	-0.003	23.011	-0.012	-0.012	0.000	0.000	0.000	0.000
85	A	86	GLN	0	0.011	0.007	26.294	0.007	0.007	0.000	0.000	0.000	0.000
86	A	87	THR	0	0.036	0.002	29.395	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	88	ASN	0	0.023	0.020	32.877	0.000	0.000	0.000	0.000	0.000	0.000
88	A	89	LYS	1	0.836	0.933	30.310	0.118	0.118	0.000	0.000	0.000	0.000
89	A	90	ALA	0	0.112	0.053	34.580	0.003	0.003	0.000	0.000	0.000	0.000
90	A	91	LYS	1	0.983	0.998	34.795	0.081	0.081	0.000	0.000	0.000	0.000
91	A	92	HIS	0	-0.039	-0.048	34.741	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	93	ASP	-1	-0.798	-0.871	32.334	-0.100	-0.100	0.000	0.000	0.000	0.000
93	A	94	GLU	-1	-0.870	-0.941	29.026	-0.129	-0.129	0.000	0.000	0.000	0.000
94	A	95	LEU	0	-0.079	-0.032	25.231	-0.001	-0.001	0.000	0.000	0.000	0.000
95	A	96	THR	0	0.012	0.010	25.182	-0.009	-0.009	0.000	0.000	0.000	0.000
96	A	97	TYR	0	-0.003	-0.012	17.885	-0.019	-0.019	0.000	0.000	0.000	0.000
97	A	98	PHE	0	0.025	0.024	21.765	0.003	0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:MET)