FMO DATABASE

FMODB ID: 2N3KR

Calculation Name: 1WMH-B-Xray372

Preferred Name: Protein kinase C iota

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1WMH

Chain ID: B

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	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	82
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-536660.537715
FMO2-HF: Nuclear repulsion	505582.874889
FMO2-HF: Total energy	-31077.662826
FMO2-MP2: Total energy	-31171.36748

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(B:14:SER)

Summations of interaction energy for fragment #1(B:14:SER)

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.
-2.061	0.76	0.027	-1.365	-1.482	0.003

Interaction energy analysis for fragmet #1(B:14:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

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

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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	B	16	VAL	0	0.013	0.019	3.884	0.366	1.953	-0.014	-0.838	-0.734	0.002
4	B	17	GLU	-1	-0.755	-0.869	6.786	0.203	0.203	0.000	0.000	0.000	0.000
5	B	18	VAL	0	0.013	0.011	9.204	0.064	0.064	0.000	0.000	0.000	0.000
6	B	19	LYS	1	0.880	0.957	12.642	-0.440	-0.440	0.000	0.000	0.000	0.000
7	B	20	SER	0	0.008	0.001	16.193	0.042	0.042	0.000	0.000	0.000	0.000
8	B	21	LYS	1	0.905	0.951	18.838	-0.264	-0.264	0.000	0.000	0.000	0.000
9	B	22	PHE	0	0.031	0.011	22.580	0.009	0.009	0.000	0.000	0.000	0.000
10	B	23	ASP	-1	-0.786	-0.894	25.485	0.148	0.148	0.000	0.000	0.000	0.000
11	B	24	ALA	0	-0.046	-0.023	28.990	0.004	0.004	0.000	0.000	0.000	0.000
12	B	25	GLU	-1	-0.791	-0.834	24.995	0.177	0.177	0.000	0.000	0.000	0.000
13	B	26	PHE	0	0.009	-0.032	21.526	0.027	0.027	0.000	0.000	0.000	0.000
14	B	27	ARG	1	0.784	0.862	20.372	-0.185	-0.185	0.000	0.000	0.000	0.000
15	B	28	ARG	1	0.754	0.836	12.994	-0.464	-0.464	0.000	0.000	0.000	0.000
16	B	29	PHE	0	0.028	0.017	13.161	-0.057	-0.057	0.000	0.000	0.000	0.000
17	B	30	ALA	0	0.028	0.007	8.806	0.137	0.137	0.000	0.000	0.000	0.000
18	B	31	LEU	0	0.004	0.016	8.598	-0.213	-0.213	0.000	0.000	0.000	0.000
19	B	32	PRO	0	0.070	0.029	4.883	0.377	0.413	-0.001	-0.029	-0.006	0.000
20	B	33	ARG	1	0.894	0.940	3.305	-2.845	-1.779	0.043	-0.490	-0.619	0.001
21	B	34	ALA	0	0.004	-0.005	4.766	-0.084	0.048	-0.001	-0.008	-0.123	0.000
22	B	35	SER	0	-0.020	-0.012	6.563	-0.165	-0.165	0.000	0.000	0.000	0.000
23	B	36	VAL	0	-0.061	-0.024	8.890	-0.028	-0.028	0.000	0.000	0.000	0.000
24	B	37	SER	0	-0.057	-0.058	10.875	0.062	0.062	0.000	0.000	0.000	0.000
25	B	38	GLY	0	0.091	0.046	13.665	0.006	0.006	0.000	0.000	0.000	0.000
26	B	39	PHE	0	-0.025	-0.016	16.071	0.010	0.010	0.000	0.000	0.000	0.000
27	B	40	GLN	0	0.016	0.006	18.123	-0.005	-0.005	0.000	0.000	0.000	0.000
28	B	41	GLU	-1	-0.826	-0.882	16.446	0.251	0.251	0.000	0.000	0.000	0.000
29	B	42	PHE	0	0.038	0.015	12.114	-0.006	-0.006	0.000	0.000	0.000	0.000
30	B	43	SER	0	0.016	0.018	16.456	-0.021	-0.021	0.000	0.000	0.000	0.000
31	B	44	ARG	1	0.915	0.955	20.094	-0.167	-0.167	0.000	0.000	0.000	0.000
32	B	45	LEU	0	0.007	0.010	14.123	-0.025	-0.025	0.000	0.000	0.000	0.000
33	B	46	LEU	0	0.017	0.007	17.034	-0.018	-0.018	0.000	0.000	0.000	0.000
34	B	47	ARG	1	0.898	0.944	19.640	-0.243	-0.243	0.000	0.000	0.000	0.000
35	B	48	ALA	0	-0.026	0.001	20.526	-0.022	-0.022	0.000	0.000	0.000	0.000
36	B	49	VAL	0	-0.005	-0.001	17.422	-0.022	-0.022	0.000	0.000	0.000	0.000
37	B	50	HIS	0	-0.040	-0.025	20.863	0.019	0.019	0.000	0.000	0.000	0.000
38	B	51	GLN	0	-0.015	0.010	23.913	-0.007	-0.007	0.000	0.000	0.000	0.000
39	B	52	ILE	0	0.001	0.013	25.608	-0.012	-0.012	0.000	0.000	0.000	0.000
40	B	53	PRO	0	0.006	-0.004	26.612	0.011	0.011	0.000	0.000	0.000	0.000
41	B	54	GLY	0	-0.004	-0.012	27.516	-0.009	-0.009	0.000	0.000	0.000	0.000
42	B	55	LEU	0	-0.030	0.000	28.927	-0.004	-0.004	0.000	0.000	0.000	0.000
43	B	56	ASP	-1	-0.804	-0.886	28.396	0.155	0.155	0.000	0.000	0.000	0.000
44	B	57	VAL	0	-0.068	-0.041	24.959	-0.004	-0.004	0.000	0.000	0.000	0.000
45	B	58	LEU	0	-0.018	0.002	26.594	0.007	0.007	0.000	0.000	0.000	0.000
46	B	59	LEU	0	-0.003	-0.014	20.612	0.002	0.002	0.000	0.000	0.000	0.000
47	B	60	GLY	0	0.034	0.009	21.058	-0.012	-0.012	0.000	0.000	0.000	0.000
48	B	61	TYR	0	-0.022	-0.019	16.267	0.031	0.031	0.000	0.000	0.000	0.000
49	B	62	THR	0	-0.036	-0.004	17.778	-0.042	-0.042	0.000	0.000	0.000	0.000
50	B	63	ASP	-1	-0.856	-0.941	16.516	0.579	0.579	0.000	0.000	0.000	0.000
51	B	64	ALA	0	-0.014	-0.013	15.757	-0.036	-0.036	0.000	0.000	0.000	0.000
52	B	65	HIS	0	-0.042	-0.009	17.356	-0.049	-0.049	0.000	0.000	0.000	0.000
53	B	66	GLY	0	-0.036	-0.010	20.208	-0.038	-0.038	0.000	0.000	0.000	0.000
54	B	67	ASP	-1	-0.901	-0.941	21.683	0.285	0.285	0.000	0.000	0.000	0.000
55	B	68	LEU	0	-0.078	-0.041	21.197	0.045	0.045	0.000	0.000	0.000	0.000
56	B	69	LEU	0	0.010	0.008	19.544	-0.030	-0.030	0.000	0.000	0.000	0.000
57	B	70	PRO	0	0.004	0.003	21.334	0.020	0.020	0.000	0.000	0.000	0.000
58	B	71	LEU	0	-0.031	-0.021	16.795	0.045	0.045	0.000	0.000	0.000	0.000
59	B	72	THR	0	0.003	-0.016	20.439	-0.019	-0.019	0.000	0.000	0.000	0.000
60	B	73	ASN	0	-0.004	-0.016	20.642	-0.009	-0.009	0.000	0.000	0.000	0.000
61	B	74	ASP	-1	-0.784	-0.888	17.147	0.435	0.435	0.000	0.000	0.000	0.000
62	B	75	ASP	-1	-0.890	-0.918	16.398	0.483	0.483	0.000	0.000	0.000	0.000
63	B	76	SER	0	-0.041	-0.033	17.086	0.060	0.060	0.000	0.000	0.000	0.000
64	B	77	LEU	0	0.010	0.008	13.479	0.051	0.051	0.000	0.000	0.000	0.000
65	B	78	HIS	0	0.047	0.010	11.856	0.330	0.330	0.000	0.000	0.000	0.000
66	B	79	ARG	1	0.956	0.983	12.237	-0.349	-0.349	0.000	0.000	0.000	0.000
67	B	80	ALA	0	0.040	0.028	13.715	0.073	0.073	0.000	0.000	0.000	0.000
68	B	81	LEU	0	-0.099	-0.050	8.871	0.133	0.133	0.000	0.000	0.000	0.000
69	B	82	ALA	0	-0.029	-0.018	8.570	0.594	0.594	0.000	0.000	0.000	0.000
70	B	83	SER	0	-0.034	-0.014	10.723	-0.168	-0.168	0.000	0.000	0.000	0.000
71	B	84	GLY	0	0.054	0.020	11.358	-0.186	-0.186	0.000	0.000	0.000	0.000
72	B	85	PRO	0	-0.031	-0.004	10.308	0.254	0.254	0.000	0.000	0.000	0.000
73	B	86	PRO	0	0.028	0.037	8.426	-0.025	-0.025	0.000	0.000	0.000	0.000
74	B	87	PRO	0	-0.055	-0.035	10.570	-0.178	-0.178	0.000	0.000	0.000	0.000
75	B	88	LEU	0	0.043	0.016	10.825	-0.076	-0.076	0.000	0.000	0.000	0.000
76	B	89	ARG	1	0.881	0.932	12.405	-0.718	-0.718	0.000	0.000	0.000	0.000
77	B	90	LEU	0	0.018	0.001	14.813	0.011	0.011	0.000	0.000	0.000	0.000
78	B	91	LEU	0	-0.038	-0.015	18.121	-0.044	-0.044	0.000	0.000	0.000	0.000
79	B	92	VAL	0	0.016	0.013	21.603	0.008	0.008	0.000	0.000	0.000	0.000
80	B	93	GLN	0	-0.005	-0.031	23.971	-0.010	-0.010	0.000	0.000	0.000	0.000
81	B	94	LYS	1	0.952	0.988	27.722	-0.137	-0.137	0.000	0.000	0.000	0.000
82	B	95	ARG	1	0.873	0.925	30.761	-0.139	-0.139	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:14:SER)