FMO DATABASE

FMODB ID: 16JJZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-600225.910173
FMO2-HF: Nuclear repulsion	559326.397083
FMO2-HF: Total energy	-40899.51309
FMO2-MP2: Total energy	-41006.247912

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.
-7.559	-4.028	1.096	-1.693	-2.933	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 : -0.030 / q_NPA : -0.029

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	L	51	LEU	0	0.049	0.026	3.801	-1.641	-0.045	-0.024	-0.751	-0.821	0.003
4	L	52	VAL	0	-0.018	-0.015	6.708	0.608	0.608	0.000	0.000	0.000	0.000
5	L	53	LEU	0	0.012	0.017	8.967	-0.087	-0.087	0.000	0.000	0.000	0.000
6	L	54	PRO	0	-0.008	-0.006	11.971	0.071	0.071	0.000	0.000	0.000	0.000
7	L	55	LEU	0	-0.024	-0.016	14.148	-0.005	-0.005	0.000	0.000	0.000	0.000
8	L	56	GLU	-1	-0.913	-0.946	13.975	0.363	0.363	0.000	0.000	0.000	0.000
9	L	57	HIS	1	0.838	0.895	10.464	-0.921	-0.921	0.000	0.000	0.000	0.000
10	L	58	PRO	0	0.004	0.012	13.359	-0.010	-0.010	0.000	0.000	0.000	0.000
11	L	59	CYS	0	-0.034	-0.014	6.781	-0.459	-0.459	0.000	0.000	0.000	0.000
12	L	60	ALA	0	0.065	0.044	10.122	0.042	0.042	0.000	0.000	0.000	0.000
13	L	61	SER	0	0.003	0.002	4.066	-0.249	-0.100	0.000	-0.062	-0.087	0.000
14	L	62	LEU	0	0.048	0.008	5.994	-0.388	-0.388	0.000	0.000	0.000	0.000
15	L	63	CYS	0	0.000	-0.023	5.015	-0.581	-0.581	0.000	0.000	0.000	0.000
16	L	65	GLY	0	0.005	0.017	6.378	-0.330	-0.330	0.000	0.000	0.000	0.000
17	L	66	HIS	1	0.786	0.891	7.380	-1.550	-1.550	0.000	0.000	0.000	0.000
18	L	67	GLY	0	0.097	0.038	6.690	-0.333	-0.333	0.000	0.000	0.000	0.000
19	L	68	THR	0	-0.053	-0.033	2.250	-0.865	0.784	1.121	-0.869	-1.900	0.004
20	L	70	ILE	0	-0.010	0.025	4.761	-0.250	-0.113	-0.001	-0.011	-0.125	0.000
21	L	71	ASP	-1	-0.926	-0.955	6.876	0.037	0.037	0.000	0.000	0.000	0.000
22	L	72	GLY	0	0.043	0.004	7.984	0.196	0.196	0.000	0.000	0.000	0.000
23	L	73	ILE	0	-0.059	-0.029	11.260	-0.152	-0.152	0.000	0.000	0.000	0.000
24	L	74	GLY	0	0.044	0.015	12.508	-0.108	-0.108	0.000	0.000	0.000	0.000
25	L	75	SER	0	-0.050	-0.017	12.160	0.046	0.046	0.000	0.000	0.000	0.000
26	L	76	PHE	0	0.023	0.013	8.237	-0.051	-0.051	0.000	0.000	0.000	0.000
27	L	77	SER	0	-0.001	-0.004	8.687	0.117	0.117	0.000	0.000	0.000	0.000
28	L	79	ASP	-1	-0.891	-0.933	6.793	1.731	1.731	0.000	0.000	0.000	0.000
29	L	80	CYS	0	-0.103	-0.006	7.875	0.649	0.649	0.000	0.000	0.000	0.000
30	L	81	ARG	1	0.977	0.973	5.536	-3.418	-3.418	0.000	0.000	0.000	0.000
31	L	82	SER	0	0.017	-0.008	11.266	-0.083	-0.083	0.000	0.000	0.000	0.000
32	L	83	GLY	0	0.034	0.027	15.034	0.004	0.004	0.000	0.000	0.000	0.000
33	L	84	TRP	0	-0.006	0.003	12.539	-0.015	-0.015	0.000	0.000	0.000	0.000
34	L	85	GLH	0	-0.040	-0.057	14.353	-0.016	-0.016	0.000	0.000	0.000	0.000
35	L	86	GLY	0	-0.004	-0.002	14.914	-0.010	-0.010	0.000	0.000	0.000	0.000
36	L	87	ARG	1	0.942	0.971	13.011	-0.475	-0.475	0.000	0.000	0.000	0.000
37	L	88	PHE	0	0.034	-0.009	10.183	-0.009	-0.009	0.000	0.000	0.000	0.000
38	L	90	GLN	0	0.089	0.019	11.388	0.081	0.081	0.000	0.000	0.000	0.000
39	L	91	ARG	1	0.833	0.923	13.991	-0.641	-0.641	0.000	0.000	0.000	0.000
40	L	92	GLU	-1	-0.885	-0.933	15.918	0.698	0.698	0.000	0.000	0.000	0.000
41	L	93	VAL	0	-0.028	-0.016	17.686	-0.059	-0.059	0.000	0.000	0.000	0.000
42	L	94	SER	0	-0.039	-0.016	19.470	0.043	0.043	0.000	0.000	0.000	0.000
43	L	95	PHE	0	0.028	-0.012	18.339	-0.008	-0.008	0.000	0.000	0.000	0.000
44	L	96	LEU	0	-0.014	-0.007	22.565	-0.014	-0.014	0.000	0.000	0.000	0.000
45	L	97	ASN	0	0.054	0.045	25.217	-0.013	-0.013	0.000	0.000	0.000	0.000
46	L	98	CYS	0	-0.030	0.004	25.878	0.048	0.048	0.000	0.000	0.000	0.000
47	L	99	SER	0	-0.023	-0.021	26.272	-0.003	-0.003	0.000	0.000	0.000	0.000
48	L	100	LEU	0	-0.006	-0.009	21.528	-0.005	-0.005	0.000	0.000	0.000	0.000
49	L	101	ASP	-1	-0.751	-0.848	22.106	0.467	0.467	0.000	0.000	0.000	0.000
50	L	102	ASN	0	-0.001	-0.004	24.519	-0.003	-0.003	0.000	0.000	0.000	0.000
51	L	103	GLY	0	0.053	0.028	24.386	-0.014	-0.014	0.000	0.000	0.000	0.000
52	L	104	GLY	0	0.020	0.004	22.226	0.031	0.031	0.000	0.000	0.000	0.000
53	L	105	CYS	0	-0.063	-0.005	22.964	-0.013	-0.013	0.000	0.000	0.000	0.000
54	L	106	THR	0	0.018	0.010	26.037	-0.005	-0.005	0.000	0.000	0.000	0.000
55	L	107	HIS	0	-0.041	-0.027	27.978	-0.016	-0.016	0.000	0.000	0.000	0.000
56	L	108	TYR	0	-0.006	0.006	31.557	-0.003	-0.003	0.000	0.000	0.000	0.000
57	L	110	LEU	0	-0.018	-0.004	30.643	-0.015	-0.015	0.000	0.000	0.000	0.000
58	L	111	GLU	-1	-0.800	-0.910	30.221	0.291	0.291	0.000	0.000	0.000	0.000
59	L	112	GLU	-1	-0.859	-0.907	31.100	0.201	0.201	0.000	0.000	0.000	0.000
60	L	113	VAL	0	-0.006	-0.011	32.409	0.003	0.003	0.000	0.000	0.000	0.000
61	L	114	GLY	0	-0.002	0.003	29.327	0.004	0.004	0.000	0.000	0.000	0.000
62	L	115	TRP	0	-0.035	-0.012	26.523	0.029	0.029	0.000	0.000	0.000	0.000
63	L	116	ARG	1	0.890	0.959	22.183	-0.461	-0.461	0.000	0.000	0.000	0.000
64	L	117	ARG	1	0.800	0.877	27.144	-0.203	-0.203	0.000	0.000	0.000	0.000
65	L	119	SER	0	-0.004	-0.007	29.510	-0.016	-0.016	0.000	0.000	0.000	0.000
66	L	120	CYS	0	-0.072	-0.020	26.700	-0.001	-0.001	0.000	0.000	0.000	0.000
67	L	121	ALA	0	0.034	0.037	34.258	-0.010	-0.010	0.000	0.000	0.000	0.000
68	L	122	PRO	0	0.037	-0.013	37.208	0.001	0.001	0.000	0.000	0.000	0.000
69	L	123	GLY	0	0.020	0.015	39.723	-0.004	-0.004	0.000	0.000	0.000	0.000
70	L	124	TYR	0	-0.040	-0.020	33.657	0.001	0.001	0.000	0.000	0.000	0.000
71	L	125	LYS	1	0.942	0.967	33.986	-0.176	-0.176	0.000	0.000	0.000	0.000
72	L	126	LEU	0	0.010	0.004	28.346	0.003	0.003	0.000	0.000	0.000	0.000
73	L	127	GLY	0	-0.017	-0.010	27.355	-0.011	-0.011	0.000	0.000	0.000	0.000
74	L	128	ASP	-1	-0.899	-0.951	24.984	0.270	0.270	0.000	0.000	0.000	0.000
75	L	129	ASP	-1	-0.855	-0.938	21.463	0.456	0.456	0.000	0.000	0.000	0.000
76	L	130	LEU	0	-0.041	-0.017	23.040	0.024	0.024	0.000	0.000	0.000	0.000
77	L	131	LEU	0	-0.008	-0.014	20.797	0.000	0.000	0.000	0.000	0.000	0.000
78	L	132	GLN	0	-0.041	-0.027	22.250	-0.046	-0.046	0.000	0.000	0.000	0.000
79	L	134	HIS	0	0.029	0.009	26.875	-0.014	-0.014	0.000	0.000	0.000	0.000
80	L	135	PRO	0	-0.031	-0.020	31.976	-0.007	-0.007	0.000	0.000	0.000	0.000
81	L	136	ALA	0	-0.017	-0.009	35.670	0.000	0.000	0.000	0.000	0.000	0.000
82	L	137	VAL	0	-0.013	-0.001	37.861	-0.009	-0.009	0.000	0.000	0.000	0.000
83	L	138	LYS	1	0.927	0.971	40.089	-0.106	-0.106	0.000	0.000	0.000	0.000
84	L	139	PHE	0	-0.001	-0.024	41.882	0.000	0.000	0.000	0.000	0.000	0.000
85	L	140	PRO	0	-0.002	0.025	37.804	-0.002	-0.002	0.000	0.000	0.000	0.000
86	L	141	CYS	0	0.070	0.026	39.156	-0.002	-0.002	0.000	0.000	0.000	0.000
87	L	142	GLY	0	-0.001	-0.007	38.703	0.008	0.008	0.000	0.000	0.000	0.000
88	L	143	ARG	1	0.935	0.971	31.817	-0.190	-0.190	0.000	0.000	0.000	0.000
89	L	144	PRO	0	0.023	0.021	38.205	-0.006	-0.006	0.000	0.000	0.000	0.000
90	L	145	TRP	0	0.012	0.015	39.954	0.000	0.000	0.000	0.000	0.000	0.000

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