FMO DATABASE

FMODB ID: 76VJK

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:

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

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	-537198.870983
FMO2-HF: Nuclear repulsion	506121.397657
FMO2-HF: Total energy	-31077.473326
FMO2-MP2: Total energy	-31171.189239

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.
-0.717	2.144	0.103	-1.361	-1.603	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 : 0.021 / 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	0.011	0.015	3.807	0.775	2.545	-0.024	-0.885	-0.861	0.002
4	B	17	GLU	-1	-0.805	-0.887	6.754	0.540	0.540	0.000	0.000	0.000	0.000
5	B	18	VAL	0	0.020	0.013	9.136	0.025	0.025	0.000	0.000	0.000	0.000
6	B	19	LYS	1	0.889	0.950	12.618	-0.553	-0.553	0.000	0.000	0.000	0.000
7	B	20	SER	0	-0.013	-0.021	15.991	0.029	0.029	0.000	0.000	0.000	0.000
8	B	21	LYS	1	0.945	0.981	18.711	-0.303	-0.303	0.000	0.000	0.000	0.000
9	B	22	PHE	0	0.016	0.012	22.348	0.001	0.001	0.000	0.000	0.000	0.000
10	B	23	ASP	-1	-0.823	-0.910	25.138	0.168	0.168	0.000	0.000	0.000	0.000
11	B	24	ALA	0	-0.036	-0.028	27.887	0.011	0.011	0.000	0.000	0.000	0.000
12	B	25	GLU	-1	-0.803	-0.845	24.886	0.211	0.211	0.000	0.000	0.000	0.000
13	B	26	PHE	0	0.000	-0.029	20.990	0.033	0.033	0.000	0.000	0.000	0.000
14	B	27	ARG	1	0.788	0.872	20.006	-0.214	-0.214	0.000	0.000	0.000	0.000
15	B	28	ARG	1	0.830	0.886	13.040	-0.645	-0.645	0.000	0.000	0.000	0.000
16	B	29	PHE	0	0.014	0.015	13.062	-0.070	-0.070	0.000	0.000	0.000	0.000
17	B	30	ALA	0	0.031	0.008	8.773	0.178	0.178	0.000	0.000	0.000	0.000
18	B	31	LEU	0	-0.002	0.009	8.324	-0.251	-0.251	0.000	0.000	0.000	0.000
19	B	32	PRO	0	0.068	0.036	4.904	0.428	0.428	0.000	0.000	0.000	0.000
20	B	33	ARG	1	0.956	0.978	2.936	-1.995	-1.028	0.128	-0.467	-0.628	0.001
21	B	34	ALA	0	-0.027	-0.026	4.479	0.067	0.191	-0.001	-0.009	-0.114	0.000
22	B	35	SER	0	-0.015	-0.011	6.303	-0.068	-0.068	0.000	0.000	0.000	0.000
23	B	36	VAL	0	-0.077	-0.030	8.261	0.066	0.066	0.000	0.000	0.000	0.000
24	B	37	SER	0	-0.045	-0.059	10.363	-0.003	-0.003	0.000	0.000	0.000	0.000
25	B	38	GLY	0	0.094	0.049	13.535	-0.005	-0.005	0.000	0.000	0.000	0.000
26	B	39	PHE	0	-0.044	-0.025	15.513	0.019	0.019	0.000	0.000	0.000	0.000
27	B	40	GLN	0	0.017	0.011	17.665	0.011	0.011	0.000	0.000	0.000	0.000
28	B	41	GLU	-1	-0.825	-0.883	16.034	0.139	0.139	0.000	0.000	0.000	0.000
29	B	42	PHE	0	0.007	0.002	12.168	0.009	0.009	0.000	0.000	0.000	0.000
30	B	43	SER	0	0.032	0.017	15.944	-0.005	-0.005	0.000	0.000	0.000	0.000
31	B	44	ARG	1	0.920	0.957	19.469	-0.105	-0.105	0.000	0.000	0.000	0.000
32	B	45	LEU	0	0.012	0.017	13.848	-0.019	-0.019	0.000	0.000	0.000	0.000
33	B	46	LEU	0	0.020	0.010	16.494	-0.006	-0.006	0.000	0.000	0.000	0.000
34	B	47	ARG	1	0.911	0.953	19.135	-0.204	-0.204	0.000	0.000	0.000	0.000
35	B	48	ALA	0	-0.037	-0.006	20.185	-0.020	-0.020	0.000	0.000	0.000	0.000
36	B	49	VAL	0	-0.006	0.001	17.245	-0.019	-0.019	0.000	0.000	0.000	0.000
37	B	50	HIS	0	-0.055	-0.033	20.697	0.025	0.025	0.000	0.000	0.000	0.000
38	B	51	GLN	0	-0.017	0.008	23.626	-0.005	-0.005	0.000	0.000	0.000	0.000
39	B	52	ILE	0	0.004	0.008	25.094	-0.011	-0.011	0.000	0.000	0.000	0.000
40	B	53	PRO	0	0.012	0.000	26.022	0.007	0.007	0.000	0.000	0.000	0.000
41	B	54	GLY	0	-0.010	-0.018	27.023	-0.007	-0.007	0.000	0.000	0.000	0.000
42	B	55	LEU	0	-0.033	0.002	28.339	-0.004	-0.004	0.000	0.000	0.000	0.000
43	B	56	ASP	-1	-0.809	-0.879	27.840	0.138	0.138	0.000	0.000	0.000	0.000
44	B	57	VAL	0	-0.060	-0.049	24.422	0.000	0.000	0.000	0.000	0.000	0.000
45	B	58	LEU	0	-0.030	-0.006	26.217	0.000	0.000	0.000	0.000	0.000	0.000
46	B	59	LEU	0	-0.005	-0.009	19.890	0.004	0.004	0.000	0.000	0.000	0.000
47	B	60	GLY	0	0.039	0.021	21.246	-0.017	-0.017	0.000	0.000	0.000	0.000
48	B	61	TYR	0	-0.016	-0.013	16.252	0.031	0.031	0.000	0.000	0.000	0.000
49	B	62	THR	0	-0.036	-0.001	17.840	-0.049	-0.049	0.000	0.000	0.000	0.000
50	B	63	ASP	-1	-0.826	-0.929	16.766	0.599	0.599	0.000	0.000	0.000	0.000
51	B	64	ALA	0	-0.005	-0.018	15.686	-0.011	-0.011	0.000	0.000	0.000	0.000
52	B	65	HIS	0	-0.048	-0.014	17.306	-0.029	-0.029	0.000	0.000	0.000	0.000
53	B	66	GLY	0	-0.045	-0.014	20.123	-0.039	-0.039	0.000	0.000	0.000	0.000
54	B	67	ASP	-1	-0.887	-0.931	21.705	0.300	0.300	0.000	0.000	0.000	0.000
55	B	68	LEU	0	-0.093	-0.047	21.353	0.048	0.048	0.000	0.000	0.000	0.000
56	B	69	LEU	0	0.006	0.001	19.747	-0.035	-0.035	0.000	0.000	0.000	0.000
57	B	70	PRO	0	-0.006	0.000	21.408	0.023	0.023	0.000	0.000	0.000	0.000
58	B	71	LEU	0	-0.038	-0.022	16.731	0.031	0.031	0.000	0.000	0.000	0.000
59	B	72	THR	0	-0.025	-0.042	20.368	-0.031	-0.031	0.000	0.000	0.000	0.000
60	B	73	ASN	0	0.038	0.018	20.288	0.000	0.000	0.000	0.000	0.000	0.000
61	B	74	ASP	-1	-0.782	-0.892	16.907	0.316	0.316	0.000	0.000	0.000	0.000
62	B	75	ASP	-1	-0.883	-0.922	16.183	0.358	0.358	0.000	0.000	0.000	0.000
63	B	76	SER	0	-0.033	-0.036	17.111	0.059	0.059	0.000	0.000	0.000	0.000
64	B	77	LEU	0	0.015	0.012	13.031	0.067	0.067	0.000	0.000	0.000	0.000
65	B	78	HIS	0	0.025	-0.004	11.434	0.281	0.281	0.000	0.000	0.000	0.000
66	B	79	ARG	1	0.947	0.975	12.516	-0.284	-0.284	0.000	0.000	0.000	0.000
67	B	80	ALA	0	0.030	0.030	13.819	0.084	0.084	0.000	0.000	0.000	0.000
68	B	81	LEU	0	-0.108	-0.046	8.616	0.185	0.185	0.000	0.000	0.000	0.000
69	B	82	ALA	0	-0.028	-0.014	8.589	0.560	0.560	0.000	0.000	0.000	0.000
70	B	83	SER	0	-0.049	-0.027	10.865	-0.213	-0.213	0.000	0.000	0.000	0.000
71	B	84	GLY	0	0.036	0.025	11.998	-0.112	-0.112	0.000	0.000	0.000	0.000
72	B	85	PRO	0	-0.040	-0.018	9.991	0.299	0.299	0.000	0.000	0.000	0.000
73	B	86	PRO	0	0.019	0.046	7.774	-0.066	-0.066	0.000	0.000	0.000	0.000
74	B	87	PRO	0	-0.088	-0.069	10.246	-0.237	-0.237	0.000	0.000	0.000	0.000
75	B	88	LEU	0	0.050	0.019	10.908	-0.092	-0.092	0.000	0.000	0.000	0.000
76	B	89	ARG	1	0.936	0.952	12.578	-0.785	-0.785	0.000	0.000	0.000	0.000
77	B	90	LEU	0	0.019	0.006	14.680	-0.015	-0.015	0.000	0.000	0.000	0.000
78	B	91	LEU	0	-0.019	-0.003	18.108	-0.035	-0.035	0.000	0.000	0.000	0.000
79	B	92	VAL	0	-0.002	-0.003	21.402	-0.002	-0.002	0.000	0.000	0.000	0.000
80	B	93	GLN	0	0.015	-0.015	23.736	-0.005	-0.005	0.000	0.000	0.000	0.000
81	B	94	LYS	1	0.978	0.995	27.437	-0.146	-0.146	0.000	0.000	0.000	0.000
82	B	95	ARG	1	0.872	0.923	30.378	-0.127	-0.127	0.000	0.000	0.000	0.000

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