FMO DATABASE

FMODB ID: 6YV3Z

Calculation Name: 1WMH-A-Xray372

Preferred Name: Protein kinase C iota

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1WMH

Chain ID: A

ChEMBL ID: CHEMBL2598

UniProt ID: P41743

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:

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	83
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-601221.405823
FMO2-HF: Nuclear repulsion	565830.08229
FMO2-HF: Total energy	-35391.323532
FMO2-MP2: Total energy	-35491.095043

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:16:GLN)

Summations of interaction energy for fragment #1(A:16:GLN)

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.
-42.672	-34.575	13.864	-9.742	-12.219	-0.072

Interaction energy analysis for fragmet #1(A:16:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.072 / q_NPA : -0.047

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	18	ARG	1	0.831	0.926	3.786	-1.257	0.999	-0.013	-1.045	-1.199	0.005
4	A	19	VAL	0	0.031	0.010	5.501	-0.524	-0.524	0.000	0.000	0.000	0.000
5	A	20	LYS	1	0.885	0.948	8.331	0.141	0.141	0.000	0.000	0.000	0.000
6	A	21	ALA	0	0.037	0.007	11.767	-0.171	-0.171	0.000	0.000	0.000	0.000
7	A	22	TYR	0	-0.007	0.001	14.037	0.120	0.120	0.000	0.000	0.000	0.000
8	A	23	TYR	0	0.065	0.008	17.726	-0.086	-0.086	0.000	0.000	0.000	0.000
9	A	24	ARG	1	0.896	0.945	20.124	0.052	0.052	0.000	0.000	0.000	0.000
10	A	25	GLY	0	-0.004	-0.003	22.587	0.012	0.012	0.000	0.000	0.000	0.000
11	A	26	ASP	-1	-0.907	-0.929	19.884	0.243	0.243	0.000	0.000	0.000	0.000
12	A	27	ILE	0	-0.066	-0.043	15.305	-0.049	-0.049	0.000	0.000	0.000	0.000
13	A	28	MET	0	-0.021	-0.008	14.106	0.100	0.100	0.000	0.000	0.000	0.000
14	A	29	ILE	0	-0.049	-0.024	8.771	-0.116	-0.116	0.000	0.000	0.000	0.000
15	A	30	THR	0	0.020	0.015	7.645	0.346	0.346	0.000	0.000	0.000	0.000
16	A	31	HIS	0	-0.017	-0.011	2.595	-1.725	0.157	0.595	-0.816	-1.661	0.007
17	A	32	PHE	0	0.046	0.027	3.311	-1.638	-0.567	0.040	-0.300	-0.811	-0.001
18	A	33	GLU	-1	-0.818	-0.905	1.835	-33.433	-31.264	11.553	-6.420	-7.302	-0.082
19	A	34	PRO	0	0.024	0.001	2.108	1.363	2.076	1.691	-1.152	-1.252	-0.001
20	A	35	SER	0	-0.050	-0.018	5.136	0.517	0.545	-0.001	-0.004	-0.022	0.000
21	A	36	ILE	0	-0.059	-0.010	6.987	0.490	0.490	0.000	0.000	0.000	0.000
22	A	37	SER	0	0.022	0.009	8.811	0.202	0.202	0.000	0.000	0.000	0.000
23	A	38	PHE	0	0.076	0.012	12.135	-0.037	-0.037	0.000	0.000	0.000	0.000
24	A	39	GLU	-1	-0.968	-0.978	14.518	-0.661	-0.661	0.000	0.000	0.000	0.000
25	A	40	GLY	0	0.005	-0.003	11.528	0.085	0.085	0.000	0.000	0.000	0.000
26	A	41	LEU	0	0.028	0.014	9.491	0.073	0.073	0.000	0.000	0.000	0.000
27	A	42	CYS	0	-0.062	-0.037	11.793	0.219	0.219	0.000	0.000	0.000	0.000
28	A	43	ASN	0	-0.004	-0.011	13.915	0.189	0.189	0.000	0.000	0.000	0.000
29	A	44	GLU	-1	-0.870	-0.922	8.998	-0.131	-0.131	0.000	0.000	0.000	0.000
30	A	45	VAL	0	-0.005	-0.015	12.198	0.193	0.193	0.000	0.000	0.000	0.000
31	A	46	ARG	1	0.832	0.919	14.521	0.490	0.490	0.000	0.000	0.000	0.000
32	A	47	ASP	-1	-0.897	-0.929	13.774	0.092	0.092	0.000	0.000	0.000	0.000
33	A	48	MET	0	-0.034	-0.015	11.480	0.046	0.046	0.000	0.000	0.000	0.000
34	A	49	CYS	0	-0.103	-0.046	15.135	0.068	0.068	0.000	0.000	0.000	0.000
35	A	50	SER	0	-0.060	-0.020	18.277	0.014	0.014	0.000	0.000	0.000	0.000
36	A	51	PHE	0	-0.080	-0.044	19.685	0.000	0.000	0.000	0.000	0.000	0.000
37	A	52	ASP	-1	-0.856	-0.926	20.905	-0.103	-0.103	0.000	0.000	0.000	0.000
38	A	53	ASN	0	-0.010	-0.031	20.575	-0.054	-0.054	0.000	0.000	0.000	0.000
39	A	54	GLU	-1	-0.938	-0.966	22.224	-0.232	-0.232	0.000	0.000	0.000	0.000
40	A	55	GLN	0	-0.053	0.000	22.573	0.005	0.005	0.000	0.000	0.000	0.000
41	A	56	LEU	0	-0.010	-0.011	22.946	-0.040	-0.040	0.000	0.000	0.000	0.000
42	A	57	PHE	0	-0.043	-0.043	17.517	0.039	0.039	0.000	0.000	0.000	0.000
43	A	58	THR	0	-0.018	-0.003	21.780	-0.034	-0.034	0.000	0.000	0.000	0.000
44	A	59	MET	0	0.006	0.022	15.584	0.041	0.041	0.000	0.000	0.000	0.000
45	A	60	LYS	1	0.928	0.964	18.488	0.246	0.246	0.000	0.000	0.000	0.000
46	A	61	TRP	0	0.045	0.030	14.560	0.023	0.023	0.000	0.000	0.000	0.000
47	A	62	ILE	0	-0.066	-0.026	16.348	0.039	0.039	0.000	0.000	0.000	0.000
48	A	63	ASP	-1	-0.798	-0.901	16.628	-0.485	-0.485	0.000	0.000	0.000	0.000
49	A	64	GLU	-1	-0.947	-0.986	17.654	-0.412	-0.412	0.000	0.000	0.000	0.000
50	A	65	GLU	-1	-1.009	-0.995	18.997	-0.281	-0.281	0.000	0.000	0.000	0.000
51	A	66	GLY	0	-0.090	-0.037	21.150	0.044	0.044	0.000	0.000	0.000	0.000
52	A	67	ASP	-1	-0.902	-0.945	22.215	-0.234	-0.234	0.000	0.000	0.000	0.000
53	A	68	PRO	0	-0.133	-0.069	20.677	-0.042	-0.042	0.000	0.000	0.000	0.000
54	A	69	CYS	0	0.032	0.010	18.570	0.016	0.016	0.000	0.000	0.000	0.000
55	A	70	THR	0	-0.065	-0.054	18.987	-0.024	-0.024	0.000	0.000	0.000	0.000
56	A	71	VAL	0	0.001	0.024	14.824	-0.024	-0.024	0.000	0.000	0.000	0.000
57	A	72	SER	0	-0.039	-0.040	18.223	0.035	0.035	0.000	0.000	0.000	0.000
58	A	73	SER	0	-0.044	-0.043	18.385	0.012	0.012	0.000	0.000	0.000	0.000
59	A	74	GLN	0	0.052	0.017	13.021	0.023	0.023	0.000	0.000	0.000	0.000
60	A	75	LEU	0	-0.005	0.001	15.302	-0.088	-0.088	0.000	0.000	0.000	0.000
61	A	76	GLU	-1	-0.814	-0.898	16.461	-0.642	-0.642	0.000	0.000	0.000	0.000
62	A	77	LEU	0	-0.010	0.008	10.671	0.006	0.006	0.000	0.000	0.000	0.000
63	A	78	GLU	-1	-0.892	-0.950	11.628	-1.376	-1.376	0.000	0.000	0.000	0.000
64	A	79	GLU	-1	-0.758	-0.844	12.109	-1.020	-1.020	0.000	0.000	0.000	0.000
65	A	80	ALA	0	-0.021	0.001	11.974	-0.017	-0.017	0.000	0.000	0.000	0.000
66	A	81	PHE	0	0.019	-0.013	7.788	-0.226	-0.226	0.000	0.000	0.000	0.000
67	A	82	ARG	1	0.780	0.862	9.025	0.708	0.708	0.000	0.000	0.000	0.000
68	A	83	LEU	0	-0.012	-0.019	11.302	0.018	0.018	0.000	0.000	0.000	0.000
69	A	84	TYR	0	0.014	0.046	4.922	-0.141	-0.141	0.000	0.000	0.000	0.000
70	A	85	GLU	-1	-0.913	-0.968	4.786	-5.086	-5.108	-0.001	-0.005	0.028	0.000
71	A	86	LEU	0	-0.102	-0.041	8.454	0.320	0.320	0.000	0.000	0.000	0.000
72	A	87	ASN	0	-0.012	-0.015	12.107	0.215	0.215	0.000	0.000	0.000	0.000
73	A	88	LYS	1	0.818	0.921	9.582	0.843	0.843	0.000	0.000	0.000	0.000
74	A	89	ASP	-1	-0.836	-0.904	10.207	-0.637	-0.637	0.000	0.000	0.000	0.000
75	A	90	SER	0	-0.077	-0.052	8.440	-0.163	-0.163	0.000	0.000	0.000	0.000
76	A	91	GLU	-1	-0.896	-0.974	8.402	0.693	0.693	0.000	0.000	0.000	0.000
77	A	92	LEU	0	0.064	0.056	9.024	-0.052	-0.052	0.000	0.000	0.000	0.000
78	A	93	LEU	0	-0.037	-0.019	10.661	0.177	0.177	0.000	0.000	0.000	0.000
79	A	94	ILE	0	0.039	0.011	11.310	-0.077	-0.077	0.000	0.000	0.000	0.000
80	A	95	HIS	0	-0.014	0.004	14.890	0.113	0.113	0.000	0.000	0.000	0.000
81	A	96	VAL	0	0.019	0.002	16.581	-0.062	-0.062	0.000	0.000	0.000	0.000
82	A	97	PHE	0	-0.048	-0.038	19.243	0.059	0.059	0.000	0.000	0.000	0.000
83	A	98	PRO	0	0.011	0.011	22.955	-0.022	-0.022	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:16:GLN)