FMO DATABASE

FMODB ID: MN1MZ

Calculation Name: 1WMH-B-Xray372

Preferred Name: Protein kinase C iota

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

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
Remarks

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	-536923.501529
FMO2-HF: Nuclear repulsion	505846.279993
FMO2-HF: Total energy	-31077.221536
FMO2-MP2: Total energy	-31170.948661

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(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.
0.896	3.638	0.102	-1.277	-1.567	0.002

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 : 0.032 / 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	B	16	VAL	0	-0.007	0.006	3.807	-1.212	0.492	-0.024	-0.844	-0.836	0.001
4	B	17	GLU	-1	-0.830	-0.925	6.108	0.941	0.941	0.000	0.000	0.000	0.000
5	B	18	VAL	0	0.016	0.013	8.916	-0.128	-0.128	0.000	0.000	0.000	0.000
6	B	19	LYS	1	0.898	0.952	12.108	0.002	0.002	0.000	0.000	0.000	0.000
7	B	20	SER	0	-0.019	-0.035	15.590	-0.046	-0.046	0.000	0.000	0.000	0.000
8	B	21	LYS	1	0.940	0.976	18.068	0.058	0.058	0.000	0.000	0.000	0.000
9	B	22	PHE	0	0.013	0.009	21.706	-0.024	-0.024	0.000	0.000	0.000	0.000
10	B	23	ASP	-1	-0.845	-0.920	24.409	-0.028	-0.028	0.000	0.000	0.000	0.000
11	B	24	ALA	0	-0.052	-0.037	27.248	0.001	0.001	0.000	0.000	0.000	0.000
12	B	25	GLU	-1	-0.822	-0.875	24.059	0.008	0.008	0.000	0.000	0.000	0.000
13	B	26	PHE	0	-0.015	-0.034	20.610	-0.012	-0.012	0.000	0.000	0.000	0.000
14	B	27	ARG	1	0.870	0.940	19.535	0.003	0.003	0.000	0.000	0.000	0.000
15	B	28	ARG	1	0.881	0.935	13.226	-0.325	-0.325	0.000	0.000	0.000	0.000
16	B	29	PHE	0	0.011	0.015	12.887	0.030	0.030	0.000	0.000	0.000	0.000
17	B	30	ALA	0	0.034	0.010	8.739	0.011	0.011	0.000	0.000	0.000	0.000
18	B	31	LEU	0	-0.009	0.003	8.327	0.087	0.087	0.000	0.000	0.000	0.000
19	B	32	PRO	0	0.070	0.037	4.972	-0.389	-0.389	0.000	0.000	0.000	0.000
20	B	33	ARG	1	0.968	0.976	2.973	1.890	2.795	0.127	-0.423	-0.608	0.001
21	B	34	ALA	0	-0.030	-0.019	4.470	0.599	0.732	-0.001	-0.010	-0.123	0.000
22	B	35	SER	0	-0.013	-0.010	6.292	0.332	0.332	0.000	0.000	0.000	0.000
23	B	36	VAL	0	-0.063	-0.021	8.411	0.236	0.236	0.000	0.000	0.000	0.000
24	B	37	SER	0	-0.028	-0.020	10.359	-0.057	-0.057	0.000	0.000	0.000	0.000
25	B	38	GLY	0	0.083	0.045	13.531	0.017	0.017	0.000	0.000	0.000	0.000
26	B	39	PHE	0	-0.029	-0.013	15.515	0.007	0.007	0.000	0.000	0.000	0.000
27	B	40	GLN	0	0.016	0.010	17.600	0.028	0.028	0.000	0.000	0.000	0.000
28	B	41	GLU	-1	-0.851	-0.927	15.972	-0.365	-0.365	0.000	0.000	0.000	0.000
29	B	42	PHE	0	0.009	0.005	11.727	0.022	0.022	0.000	0.000	0.000	0.000
30	B	43	SER	0	0.020	0.009	15.943	0.058	0.058	0.000	0.000	0.000	0.000
31	B	44	ARG	1	0.936	0.960	19.242	0.216	0.216	0.000	0.000	0.000	0.000
32	B	45	LEU	0	0.006	0.013	13.838	0.034	0.034	0.000	0.000	0.000	0.000
33	B	46	LEU	0	0.022	0.008	15.963	0.046	0.046	0.000	0.000	0.000	0.000
34	B	47	ARG	1	0.921	0.961	18.776	0.206	0.206	0.000	0.000	0.000	0.000
35	B	48	ALA	0	-0.036	-0.004	20.139	0.023	0.023	0.000	0.000	0.000	0.000
36	B	49	VAL	0	-0.020	-0.008	17.195	0.029	0.029	0.000	0.000	0.000	0.000
37	B	50	HIS	0	-0.075	-0.040	20.623	0.010	0.010	0.000	0.000	0.000	0.000
38	B	51	GLN	0	-0.037	-0.006	23.338	0.006	0.006	0.000	0.000	0.000	0.000
39	B	52	ILE	0	-0.004	0.009	24.361	0.002	0.002	0.000	0.000	0.000	0.000
40	B	53	PRO	0	-0.003	-0.009	26.028	-0.015	-0.015	0.000	0.000	0.000	0.000
41	B	54	GLY	0	-0.011	-0.019	27.017	0.008	0.008	0.000	0.000	0.000	0.000
42	B	55	LEU	0	-0.030	0.004	27.891	0.003	0.003	0.000	0.000	0.000	0.000
43	B	56	ASP	-1	-0.855	-0.921	27.475	-0.119	-0.119	0.000	0.000	0.000	0.000
44	B	57	VAL	0	-0.067	-0.050	23.747	0.009	0.009	0.000	0.000	0.000	0.000
45	B	58	LEU	0	-0.028	-0.008	25.318	-0.012	-0.012	0.000	0.000	0.000	0.000
46	B	59	LEU	0	-0.015	-0.014	19.112	0.009	0.009	0.000	0.000	0.000	0.000
47	B	60	GLY	0	0.037	0.022	20.271	-0.005	-0.005	0.000	0.000	0.000	0.000
48	B	61	TYR	0	-0.021	-0.014	15.340	-0.013	-0.013	0.000	0.000	0.000	0.000
49	B	62	THR	0	-0.030	0.001	16.921	0.018	0.018	0.000	0.000	0.000	0.000
50	B	63	ASP	-1	-0.816	-0.918	15.844	-0.245	-0.245	0.000	0.000	0.000	0.000
51	B	64	ALA	0	-0.009	-0.026	14.896	0.032	0.032	0.000	0.000	0.000	0.000
52	B	65	HIS	0	-0.054	-0.017	16.481	0.042	0.042	0.000	0.000	0.000	0.000
53	B	66	GLY	0	-0.042	-0.011	19.291	0.024	0.024	0.000	0.000	0.000	0.000
54	B	67	ASP	-1	-0.897	-0.936	20.858	-0.123	-0.123	0.000	0.000	0.000	0.000
55	B	68	LEU	0	-0.086	-0.045	20.413	-0.019	-0.019	0.000	0.000	0.000	0.000
56	B	69	LEU	0	0.012	0.001	18.848	0.003	0.003	0.000	0.000	0.000	0.000
57	B	70	PRO	0	-0.021	-0.007	20.415	-0.008	-0.008	0.000	0.000	0.000	0.000
58	B	71	LEU	0	-0.023	-0.011	15.760	-0.034	-0.034	0.000	0.000	0.000	0.000
59	B	72	THR	0	-0.022	-0.038	19.382	0.012	0.012	0.000	0.000	0.000	0.000
60	B	73	ASN	0	0.061	0.046	19.622	-0.009	-0.009	0.000	0.000	0.000	0.000
61	B	74	ASP	-1	-0.773	-0.894	16.760	-0.472	-0.472	0.000	0.000	0.000	0.000
62	B	75	ASP	-1	-0.906	-0.945	15.804	-0.478	-0.478	0.000	0.000	0.000	0.000
63	B	76	SER	0	-0.056	-0.045	16.306	-0.036	-0.036	0.000	0.000	0.000	0.000
64	B	77	LEU	0	0.027	0.011	12.513	-0.014	-0.014	0.000	0.000	0.000	0.000
65	B	78	HIS	0	0.008	-0.014	11.235	-0.179	-0.179	0.000	0.000	0.000	0.000
66	B	79	ARG	1	0.947	0.974	11.543	0.304	0.304	0.000	0.000	0.000	0.000
67	B	80	ALA	0	0.023	0.025	12.824	-0.008	-0.008	0.000	0.000	0.000	0.000
68	B	81	LEU	0	-0.116	-0.065	7.631	-0.040	-0.040	0.000	0.000	0.000	0.000
69	B	82	ALA	0	-0.025	-0.012	7.592	-0.329	-0.329	0.000	0.000	0.000	0.000
70	B	83	SER	0	-0.048	-0.011	9.914	0.140	0.140	0.000	0.000	0.000	0.000
71	B	84	GLY	0	0.037	0.024	11.149	0.087	0.087	0.000	0.000	0.000	0.000
72	B	85	PRO	0	-0.049	-0.020	9.766	-0.074	-0.074	0.000	0.000	0.000	0.000
73	B	86	PRO	0	0.022	0.046	7.999	-0.060	-0.060	0.000	0.000	0.000	0.000
74	B	87	PRO	0	-0.094	-0.072	10.064	0.044	0.044	0.000	0.000	0.000	0.000
75	B	88	LEU	0	0.064	0.027	10.039	-0.043	-0.043	0.000	0.000	0.000	0.000
76	B	89	ARG	1	0.928	0.947	11.784	0.037	0.037	0.000	0.000	0.000	0.000
77	B	90	LEU	0	0.022	0.009	13.976	-0.038	-0.038	0.000	0.000	0.000	0.000
78	B	91	LEU	0	-0.017	0.000	17.252	0.041	0.041	0.000	0.000	0.000	0.000
79	B	92	VAL	0	-0.008	-0.005	20.625	-0.024	-0.024	0.000	0.000	0.000	0.000
80	B	93	GLN	0	0.065	0.023	22.901	0.021	0.021	0.000	0.000	0.000	0.000
81	B	94	LYS	1	0.989	0.993	26.581	0.053	0.053	0.000	0.000	0.000	0.000
82	B	95	ARG	1	0.921	0.968	29.537	0.090	0.090	0.000	0.000	0.000	0.000

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