FMO DATABASE

FMODB ID: GYQQ1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-599663.389637
FMO2-HF: Nuclear repulsion	558763.517935
FMO2-HF: Total energy	-40899.871702
FMO2-MP2: Total energy	-41006.568672

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.
-8.157	-4.626	2.319	-2.341	-3.507	0.012

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 : -0.002 / q_NPA : -0.013

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	0.056	0.036	3.878	-0.923	0.788	-0.021	-0.872	-0.818	0.002
4	L	52	VAL	0	-0.005	-0.003	6.957	0.491	0.491	0.000	0.000	0.000	0.000
5	L	53	LEU	0	-0.010	0.007	9.147	-0.052	-0.052	0.000	0.000	0.000	0.000
6	L	54	PRO	0	0.002	0.005	11.928	0.095	0.095	0.000	0.000	0.000	0.000
7	L	55	LEU	0	-0.017	-0.020	14.043	-0.002	-0.002	0.000	0.000	0.000	0.000
8	L	56	GLU	-1	-0.902	-0.945	13.840	0.367	0.367	0.000	0.000	0.000	0.000
9	L	57	HIS	1	0.844	0.894	9.991	-0.932	-0.932	0.000	0.000	0.000	0.000
10	L	58	PRO	0	-0.011	0.009	12.914	0.019	0.019	0.000	0.000	0.000	0.000
11	L	59	CYS	0	-0.017	-0.001	6.770	-0.159	-0.159	0.000	0.000	0.000	0.000
12	L	60	ALA	0	0.062	0.041	9.721	0.048	0.048	0.000	0.000	0.000	0.000
13	L	61	SER	0	0.004	0.000	3.662	-1.735	-1.264	0.007	-0.263	-0.214	0.002
14	L	62	LEU	0	0.024	-0.005	6.091	-0.593	-0.593	0.000	0.000	0.000	0.000
15	L	63	CYS	0	-0.022	-0.004	4.919	-0.757	-0.757	0.000	0.000	0.000	0.000
16	L	65	GLY	0	0.010	0.018	5.875	-0.257	-0.257	0.000	0.000	0.000	0.000
17	L	66	HIS	1	0.841	0.917	6.836	-1.068	-1.068	0.000	0.000	0.000	0.000
18	L	67	GLY	0	0.095	0.036	6.574	-0.151	-0.151	0.000	0.000	0.000	0.000
19	L	68	THR	0	-0.055	-0.016	2.071	-1.103	0.108	2.334	-1.198	-2.346	0.008
20	L	70	ILE	0	0.019	0.030	4.849	-0.168	-0.030	-0.001	-0.008	-0.129	0.000
21	L	71	ASP	-1	-0.948	-0.965	7.092	-0.749	-0.749	0.000	0.000	0.000	0.000
22	L	72	GLY	0	0.044	0.002	8.306	0.245	0.245	0.000	0.000	0.000	0.000
23	L	73	ILE	0	-0.049	-0.024	11.398	-0.136	-0.136	0.000	0.000	0.000	0.000
24	L	74	GLY	0	0.042	0.016	13.097	-0.064	-0.064	0.000	0.000	0.000	0.000
25	L	75	SER	0	-0.078	-0.033	11.912	0.124	0.124	0.000	0.000	0.000	0.000
26	L	76	PHE	0	0.046	0.023	8.582	-0.136	-0.136	0.000	0.000	0.000	0.000
27	L	77	SER	0	-0.016	-0.029	9.092	0.177	0.177	0.000	0.000	0.000	0.000
28	L	79	ASP	-1	-0.866	-0.922	7.384	1.483	1.483	0.000	0.000	0.000	0.000
29	L	80	CYS	0	-0.116	-0.023	7.987	0.484	0.484	0.000	0.000	0.000	0.000
30	L	81	ARG	1	0.935	0.955	5.063	-2.922	-2.922	0.000	0.000	0.000	0.000
31	L	82	SER	0	0.006	-0.015	11.470	-0.079	-0.079	0.000	0.000	0.000	0.000
32	L	83	GLY	0	0.046	0.036	15.245	0.018	0.018	0.000	0.000	0.000	0.000
33	L	84	TRP	0	-0.032	-0.003	12.326	-0.008	-0.008	0.000	0.000	0.000	0.000
34	L	85	GLH	0	-0.022	-0.039	14.028	-0.019	-0.019	0.000	0.000	0.000	0.000
35	L	86	GLY	0	0.011	0.003	14.536	0.009	0.009	0.000	0.000	0.000	0.000
36	L	87	ARG	1	0.935	0.958	12.809	-0.250	-0.250	0.000	0.000	0.000	0.000
37	L	88	PHE	0	0.039	0.002	10.053	-0.055	-0.055	0.000	0.000	0.000	0.000
38	L	90	GLN	0	0.086	0.028	11.224	0.112	0.112	0.000	0.000	0.000	0.000
39	L	91	ARG	1	0.782	0.876	13.765	-0.472	-0.472	0.000	0.000	0.000	0.000
40	L	92	GLU	-1	-0.878	-0.942	15.751	0.670	0.670	0.000	0.000	0.000	0.000
41	L	93	VAL	0	-0.028	-0.021	17.507	-0.057	-0.057	0.000	0.000	0.000	0.000
42	L	94	SER	0	-0.045	-0.017	19.567	0.035	0.035	0.000	0.000	0.000	0.000
43	L	95	PHE	0	0.019	-0.017	18.285	-0.014	-0.014	0.000	0.000	0.000	0.000
44	L	96	LEU	0	0.023	-0.001	22.570	-0.021	-0.021	0.000	0.000	0.000	0.000
45	L	97	ASN	0	0.033	0.048	24.952	-0.011	-0.011	0.000	0.000	0.000	0.000
46	L	98	CYS	0	-0.013	-0.010	25.772	0.029	0.029	0.000	0.000	0.000	0.000
47	L	99	SER	0	-0.049	-0.027	25.830	0.002	0.002	0.000	0.000	0.000	0.000
48	L	100	LEU	0	0.020	0.008	21.269	-0.005	-0.005	0.000	0.000	0.000	0.000
49	L	101	ASP	-1	-0.730	-0.828	21.818	0.374	0.374	0.000	0.000	0.000	0.000
50	L	102	ASN	0	-0.007	-0.006	24.209	-0.005	-0.005	0.000	0.000	0.000	0.000
51	L	103	GLY	0	0.084	0.041	23.885	-0.013	-0.013	0.000	0.000	0.000	0.000
52	L	104	GLY	0	0.009	-0.001	22.381	0.019	0.019	0.000	0.000	0.000	0.000
53	L	105	CYS	0	-0.058	0.013	23.182	-0.011	-0.011	0.000	0.000	0.000	0.000
54	L	106	THR	0	0.014	0.000	26.399	-0.008	-0.008	0.000	0.000	0.000	0.000
55	L	107	HIS	0	-0.050	-0.020	28.281	-0.012	-0.012	0.000	0.000	0.000	0.000
56	L	108	TYR	0	-0.001	0.005	31.753	0.000	0.000	0.000	0.000	0.000	0.000
57	L	110	LEU	0	-0.030	-0.011	30.376	-0.013	-0.013	0.000	0.000	0.000	0.000
58	L	111	GLU	-1	-0.788	-0.907	30.111	0.258	0.258	0.000	0.000	0.000	0.000
59	L	112	GLU	-1	-0.849	-0.898	31.059	0.169	0.169	0.000	0.000	0.000	0.000
60	L	113	VAL	0	-0.026	-0.021	31.845	0.009	0.009	0.000	0.000	0.000	0.000
61	L	114	GLY	0	0.013	0.010	29.270	0.001	0.001	0.000	0.000	0.000	0.000
62	L	115	TRP	0	-0.053	-0.020	26.647	0.027	0.027	0.000	0.000	0.000	0.000
63	L	116	ARG	1	0.876	0.944	21.981	-0.377	-0.377	0.000	0.000	0.000	0.000
64	L	117	ARG	1	0.797	0.882	26.890	-0.166	-0.166	0.000	0.000	0.000	0.000
65	L	119	SER	0	-0.022	-0.010	29.448	-0.015	-0.015	0.000	0.000	0.000	0.000
66	L	120	CYS	0	-0.016	-0.014	26.852	0.001	0.001	0.000	0.000	0.000	0.000
67	L	121	ALA	0	0.034	0.027	34.324	-0.007	-0.007	0.000	0.000	0.000	0.000
68	L	122	PRO	0	0.032	-0.009	37.424	-0.002	-0.002	0.000	0.000	0.000	0.000
69	L	123	GLY	0	0.009	0.004	40.228	-0.002	-0.002	0.000	0.000	0.000	0.000
70	L	124	TYR	0	-0.028	-0.021	34.093	-0.001	-0.001	0.000	0.000	0.000	0.000
71	L	125	LYS	1	0.932	0.962	34.267	-0.114	-0.114	0.000	0.000	0.000	0.000
72	L	126	LEU	0	0.018	0.010	28.370	0.000	0.000	0.000	0.000	0.000	0.000
73	L	127	GLY	0	-0.015	-0.004	27.980	-0.012	-0.012	0.000	0.000	0.000	0.000
74	L	128	ASP	-1	-0.896	-0.955	25.372	0.166	0.166	0.000	0.000	0.000	0.000
75	L	129	ASP	-1	-0.805	-0.885	21.725	0.282	0.282	0.000	0.000	0.000	0.000
76	L	130	LEU	0	-0.050	-0.026	23.157	0.026	0.026	0.000	0.000	0.000	0.000
77	L	131	LEU	0	-0.011	-0.014	20.784	0.008	0.008	0.000	0.000	0.000	0.000
78	L	132	GLN	0	-0.063	-0.055	22.820	-0.033	-0.033	0.000	0.000	0.000	0.000
79	L	134	HIS	0	0.024	0.019	27.014	-0.013	-0.013	0.000	0.000	0.000	0.000
80	L	135	PRO	0	-0.039	-0.032	32.264	-0.003	-0.003	0.000	0.000	0.000	0.000
81	L	136	ALA	0	-0.007	0.000	36.017	-0.001	-0.001	0.000	0.000	0.000	0.000
82	L	137	VAL	0	-0.013	0.001	38.368	-0.006	-0.006	0.000	0.000	0.000	0.000
83	L	138	LYS	1	0.908	0.965	40.604	-0.062	-0.062	0.000	0.000	0.000	0.000
84	L	139	PHE	0	0.018	-0.012	42.237	-0.001	-0.001	0.000	0.000	0.000	0.000
85	L	140	PRO	0	0.009	0.026	38.198	0.000	0.000	0.000	0.000	0.000	0.000
86	L	141	CYS	0	0.041	0.018	38.996	-0.001	-0.001	0.000	0.000	0.000	0.000
87	L	142	GLY	0	0.010	0.004	38.700	0.005	0.005	0.000	0.000	0.000	0.000
88	L	143	ARG	1	0.917	0.952	32.277	-0.125	-0.125	0.000	0.000	0.000	0.000
89	L	144	PRO	0	0.032	0.036	38.662	-0.005	-0.005	0.000	0.000	0.000	0.000
90	L	145	TRP	0	0.002	0.001	40.413	-0.004	-0.004	0.000	0.000	0.000	0.000

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