FMO DATABASE

FMODB ID: VK221

Calculation Name: 1AUT-L-Xray372

Preferred Name: Vitamin K-dependent protein C

Target Type: SINGLE PROTEIN

Ligand Name: d-phenylalanyl-n-[(2s,3s)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-l-prolinamide

ligand 3-letter code: 0G6

PDB ID: 1AUT

Chain ID: L

ChEMBL ID: CHEMBL4444

UniProt ID: P04070

Base Structure: X-ray

Registration Date: 2023-09-26

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	90
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-601426.341068
FMO2-HF: Nuclear repulsion	560527.384715
FMO2-HF: Total energy	-40898.956354
FMO2-MP2: Total energy	-41005.742204

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(L:49:GLN)

Summations of interaction energy for fragment #1(L:49: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.
-2.62	0.735	0.02	-1.397	-1.979	0.007

Interaction energy analysis for fragmet #1(L:49:GLN)

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 : -0.022

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	L	51	LEU	0	0.058	0.024	3.801	-2.723	-0.792	-0.027	-0.967	-0.937	0.005
4	L	52	VAL	0	-0.017	-0.012	6.705	0.325	0.325	0.000	0.000	0.000	0.000
5	L	53	LEU	0	0.031	0.019	8.974	0.078	0.078	0.000	0.000	0.000	0.000
6	L	54	PRO	0	-0.013	-0.008	11.982	-0.019	-0.019	0.000	0.000	0.000	0.000
7	L	55	LEU	0	-0.028	-0.021	13.801	0.032	0.032	0.000	0.000	0.000	0.000
8	L	56	GLU	-1	-0.914	-0.938	13.297	0.019	0.019	0.000	0.000	0.000	0.000
9	L	57	HIS	1	0.847	0.916	8.572	-0.009	-0.009	0.000	0.000	0.000	0.000
10	L	58	PRO	0	-0.007	0.012	12.312	-0.057	-0.057	0.000	0.000	0.000	0.000
11	L	59	CYS	0	-0.043	-0.023	6.579	-0.232	-0.232	0.000	0.000	0.000	0.000
12	L	60	ALA	0	0.057	0.026	9.274	-0.004	-0.004	0.000	0.000	0.000	0.000
13	L	61	SER	0	0.001	-0.002	3.574	-0.033	0.114	0.001	-0.053	-0.096	0.000
14	L	62	LEU	0	0.051	0.009	5.099	0.203	0.203	0.000	0.000	0.000	0.000
15	L	63	CYS	0	0.009	-0.016	4.954	0.641	0.641	0.000	0.000	0.000	0.000
16	L	65	GLY	0	-0.001	0.012	6.329	-0.298	-0.298	0.000	0.000	0.000	0.000
17	L	66	HIS	1	0.778	0.888	7.325	-1.041	-1.041	0.000	0.000	0.000	0.000
18	L	67	GLY	0	0.086	0.029	6.960	-0.394	-0.394	0.000	0.000	0.000	0.000
19	L	68	THR	0	-0.059	-0.035	3.253	-0.600	0.530	0.047	-0.370	-0.807	0.002
20	L	70	ILE	0	-0.008	0.030	4.749	0.280	0.427	-0.001	-0.007	-0.139	0.000
21	L	71	ASP	-1	-0.926	-0.957	6.612	1.817	1.817	0.000	0.000	0.000	0.000
22	L	72	GLY	0	0.042	0.002	7.970	-0.106	-0.106	0.000	0.000	0.000	0.000
23	L	73	ILE	0	-0.059	-0.028	11.102	-0.137	-0.137	0.000	0.000	0.000	0.000
24	L	74	GLY	0	0.043	0.012	12.353	-0.107	-0.107	0.000	0.000	0.000	0.000
25	L	75	SER	0	-0.038	-0.017	11.959	-0.083	-0.083	0.000	0.000	0.000	0.000
26	L	76	PHE	0	0.006	0.013	8.204	0.113	0.113	0.000	0.000	0.000	0.000
27	L	77	SER	0	-0.008	-0.011	9.128	-0.204	-0.204	0.000	0.000	0.000	0.000
28	L	79	ASP	-1	-0.896	-0.935	7.695	2.384	2.384	0.000	0.000	0.000	0.000
29	L	80	CYS	0	-0.086	0.000	8.725	0.605	0.605	0.000	0.000	0.000	0.000
30	L	81	ARG	1	0.985	0.984	5.681	-2.860	-2.860	0.000	0.000	0.000	0.000
31	L	82	SER	0	0.014	-0.011	11.744	-0.094	-0.094	0.000	0.000	0.000	0.000
32	L	83	GLY	0	0.039	0.034	15.443	-0.048	-0.048	0.000	0.000	0.000	0.000
33	L	84	TRP	0	0.029	0.014	13.019	-0.070	-0.070	0.000	0.000	0.000	0.000
34	L	85	GLH	0	-0.049	-0.046	15.040	0.077	0.077	0.000	0.000	0.000	0.000
35	L	86	GLY	0	-0.021	-0.011	15.212	-0.075	-0.075	0.000	0.000	0.000	0.000
36	L	87	ARG	1	0.948	0.970	12.837	-0.502	-0.502	0.000	0.000	0.000	0.000
37	L	88	PHE	0	0.039	-0.009	10.092	0.094	0.094	0.000	0.000	0.000	0.000
38	L	90	GLN	0	0.088	0.025	11.601	0.031	0.031	0.000	0.000	0.000	0.000
39	L	91	ARG	1	0.906	0.962	13.801	-0.692	-0.692	0.000	0.000	0.000	0.000
40	L	92	GLU	-1	-0.904	-0.940	16.193	0.549	0.549	0.000	0.000	0.000	0.000
41	L	93	VAL	0	-0.023	-0.016	18.221	-0.042	-0.042	0.000	0.000	0.000	0.000
42	L	94	SER	0	-0.034	0.007	19.915	0.038	0.038	0.000	0.000	0.000	0.000
43	L	95	PHE	0	0.030	-0.012	18.713	0.007	0.007	0.000	0.000	0.000	0.000
44	L	96	LEU	0	-0.016	-0.011	23.032	-0.007	-0.007	0.000	0.000	0.000	0.000
45	L	97	ASN	0	0.054	0.045	25.541	-0.016	-0.016	0.000	0.000	0.000	0.000
46	L	98	CYS	0	-0.032	-0.009	26.316	0.059	0.059	0.000	0.000	0.000	0.000
47	L	99	SER	0	-0.025	-0.021	26.575	-0.007	-0.007	0.000	0.000	0.000	0.000
48	L	100	LEU	0	-0.017	-0.008	21.575	-0.009	-0.009	0.000	0.000	0.000	0.000
49	L	101	ASP	-1	-0.792	-0.893	22.824	0.470	0.470	0.000	0.000	0.000	0.000
50	L	102	ASN	0	0.021	0.017	24.971	0.007	0.007	0.000	0.000	0.000	0.000
51	L	103	GLY	0	0.021	0.013	24.965	-0.004	-0.004	0.000	0.000	0.000	0.000
52	L	104	GLY	0	0.020	0.004	23.008	0.041	0.041	0.000	0.000	0.000	0.000
53	L	105	CYS	0	-0.064	-0.011	23.739	-0.005	-0.005	0.000	0.000	0.000	0.000
54	L	106	THR	0	0.007	0.007	26.752	-0.010	-0.010	0.000	0.000	0.000	0.000
55	L	107	HIS	0	-0.037	-0.023	28.774	-0.022	-0.022	0.000	0.000	0.000	0.000
56	L	108	TYR	0	-0.014	-0.005	32.350	-0.009	-0.009	0.000	0.000	0.000	0.000
57	L	110	LEU	0	-0.027	-0.010	31.340	-0.019	-0.019	0.000	0.000	0.000	0.000
58	L	111	GLU	-1	-0.801	-0.922	30.738	0.259	0.259	0.000	0.000	0.000	0.000
59	L	112	GLU	-1	-0.905	-0.942	31.547	0.213	0.213	0.000	0.000	0.000	0.000
60	L	113	VAL	0	-0.012	-0.015	32.750	-0.002	-0.002	0.000	0.000	0.000	0.000
61	L	114	GLY	0	-0.002	0.003	29.792	-0.003	-0.003	0.000	0.000	0.000	0.000
62	L	115	TRP	0	-0.042	-0.019	26.870	0.026	0.026	0.000	0.000	0.000	0.000
63	L	116	ARG	1	0.934	0.984	22.976	-0.497	-0.497	0.000	0.000	0.000	0.000
64	L	117	ARG	1	0.845	0.925	27.741	-0.223	-0.223	0.000	0.000	0.000	0.000
65	L	119	SER	0	-0.016	-0.012	30.309	-0.014	-0.014	0.000	0.000	0.000	0.000
66	L	120	CYS	0	-0.076	-0.019	27.585	0.002	0.002	0.000	0.000	0.000	0.000
67	L	121	ALA	0	0.033	0.037	35.132	-0.013	-0.013	0.000	0.000	0.000	0.000
68	L	122	PRO	0	0.031	-0.014	38.052	0.005	0.005	0.000	0.000	0.000	0.000
69	L	123	GLY	0	0.030	0.019	40.609	-0.005	-0.005	0.000	0.000	0.000	0.000
70	L	124	TYR	0	-0.045	-0.025	34.401	0.006	0.006	0.000	0.000	0.000	0.000
71	L	125	LYS	1	0.948	0.959	34.738	-0.252	-0.252	0.000	0.000	0.000	0.000
72	L	126	LEU	0	0.020	0.006	28.920	0.002	0.002	0.000	0.000	0.000	0.000
73	L	127	GLY	0	-0.026	-0.017	28.016	-0.009	-0.009	0.000	0.000	0.000	0.000
74	L	128	ASP	-1	-0.903	-0.954	25.224	0.414	0.414	0.000	0.000	0.000	0.000
75	L	129	ASP	-1	-0.867	-0.941	22.166	0.624	0.624	0.000	0.000	0.000	0.000
76	L	130	LEU	0	-0.055	-0.024	23.737	0.016	0.016	0.000	0.000	0.000	0.000
77	L	131	LEU	0	0.004	-0.009	21.606	-0.023	-0.023	0.000	0.000	0.000	0.000
78	L	132	GLN	0	-0.020	-0.020	23.097	-0.048	-0.048	0.000	0.000	0.000	0.000
79	L	134	HIS	0	0.027	0.005	27.878	-0.019	-0.019	0.000	0.000	0.000	0.000
80	L	135	PRO	0	-0.051	-0.026	32.856	-0.011	-0.011	0.000	0.000	0.000	0.000
81	L	136	ALA	0	0.010	0.002	36.452	0.006	0.006	0.000	0.000	0.000	0.000
82	L	137	VAL	0	-0.030	0.003	38.610	-0.010	-0.010	0.000	0.000	0.000	0.000
83	L	138	LYS	1	0.938	0.970	40.947	-0.153	-0.153	0.000	0.000	0.000	0.000
84	L	139	PHE	0	0.004	-0.024	42.703	0.001	0.001	0.000	0.000	0.000	0.000
85	L	140	PRO	0	-0.008	0.021	38.656	-0.004	-0.004	0.000	0.000	0.000	0.000
86	L	141	CYS	0	0.049	0.018	40.975	-0.002	-0.002	0.000	0.000	0.000	0.000
87	L	142	GLY	0	0.021	0.004	39.477	0.010	0.010	0.000	0.000	0.000	0.000
88	L	143	ARG	1	0.957	0.987	32.173	-0.244	-0.244	0.000	0.000	0.000	0.000
89	L	144	PRO	0	0.012	0.015	38.794	-0.006	-0.006	0.000	0.000	0.000	0.000
90	L	145	TRP	0	0.000	0.013	40.575	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(L:49:GLN)