FMO DATABASE

FMODB ID: 8NJ6Y

Calculation Name: 1PFX-L-Xray372

Preferred Name:

Target Type:

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: 1PFX

Chain ID: L

ChEMBL ID:

UniProt ID: P16293

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	139
LigandCharge	CGU=-2,BHD=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1163313.90194
FMO2-HF: Nuclear repulsion	1099908.721441
FMO2-HF: Total energy	-63405.180499
FMO2-MP2: Total energy	-63577.840842

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:1:TYR)

Summations of interaction energy for fragment #1(L:1:TYR)

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.
-54.482	-37.994	8.874	-9.446	-15.914	-0.074

Interaction energy analysis for fragmet #1(L:1:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.035 / 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

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	3	SER	0	-0.120	-0.064	2.350	1.104	5.009	1.429	-1.856	-3.477	0.009
4	L	4	GLY	0	-0.038	0.002	4.719	0.547	0.745	-0.001	-0.012	-0.185	0.000
5	L	5	LYS	1	0.388	0.459	6.431	1.177	1.177	0.000	0.000	0.000	0.000
6	L	6	LEU	0	-0.131	-0.058	9.678	0.102	0.102	0.000	0.000	0.000	0.000
7	L	7	CGU	-2	-1.557	-1.804	3.763	-7.847	-7.433	0.005	-0.149	-0.270	-0.001
8	L	8	CGU	-2	-1.321	-1.434	7.371	-3.884	-3.884	0.000	0.000	0.000	0.000
9	L	9	PHE	0	-0.173	-0.089	8.743	0.386	0.386	0.000	0.000	0.000	0.000
10	L	10	VAL	0	-0.081	-0.037	9.341	0.334	0.334	0.000	0.000	0.000	0.000
11	L	11	ARG	1	0.856	0.936	10.182	0.885	0.885	0.000	0.000	0.000	0.000
12	L	12	GLY	0	0.112	0.042	8.475	-0.056	-0.056	0.000	0.000	0.000	0.000
13	L	13	ASN	0	-0.215	-0.141	7.972	0.297	0.297	0.000	0.000	0.000	0.000
14	L	14	LEU	0	0.089	0.065	6.854	-0.071	-0.071	0.000	0.000	0.000	0.000
15	L	15	CGU	-2	-1.919	-1.966	8.423	-1.568	-1.568	0.000	0.000	0.000	0.000
16	L	16	ARG	1	0.774	0.899	4.564	3.690	3.766	-0.001	-0.004	-0.071	0.000
17	L	17	CGU	-2	-1.533	-1.764	2.580	-14.242	-11.711	1.039	-1.713	-1.857	-0.017
18	L	18	CYS	0	-0.103	0.047	4.222	1.589	2.252	0.003	-0.048	-0.618	0.000
19	L	19	ILE	0	-0.103	-0.070	6.526	0.327	0.327	0.000	0.000	0.000	0.000
20	L	20	CGU	-2	-1.872	-1.928	4.611	-4.079	-4.027	-0.001	-0.007	-0.043	0.000
21	L	21	CGU	-2	-1.836	-1.899	2.418	-23.177	-15.512	6.382	-5.244	-8.803	-0.062
22	L	22	LYS	1	0.800	0.845	4.752	-0.943	-0.821	-0.001	-0.011	-0.109	0.000
23	L	24	SER	0	-0.062	-0.073	5.249	1.008	1.008	0.000	0.000	0.000	0.000
24	L	25	PHE	0	-0.056	-0.042	7.369	0.056	0.056	0.000	0.000	0.000	0.000
25	L	26	CGU	-2	-1.743	-1.888	9.417	-1.337	-1.337	0.000	0.000	0.000	0.000
26	L	27	CGU	-2	-1.575	-1.763	3.358	-8.077	-7.215	0.020	-0.402	-0.481	-0.003
27	L	28	ALA	0	0.012	-0.030	7.108	0.222	0.222	0.000	0.000	0.000	0.000
28	L	29	ARG	1	0.668	0.818	9.369	0.907	0.907	0.000	0.000	0.000	0.000
29	L	30	CGU	-2	-1.811	-1.891	11.280	-1.769	-1.769	0.000	0.000	0.000	0.000
30	L	31	VAL	0	-0.095	-0.005	8.755	0.059	0.059	0.000	0.000	0.000	0.000
31	L	32	PHE	0	-0.076	-0.037	11.808	0.130	0.130	0.000	0.000	0.000	0.000
32	L	33	CGU	-2	-1.836	-1.899	14.471	-0.886	-0.886	0.000	0.000	0.000	0.000
33	L	34	ASN	0	-0.168	-0.110	17.031	0.066	0.066	0.000	0.000	0.000	0.000
34	L	35	THR	0	0.059	0.015	16.781	-0.013	-0.013	0.000	0.000	0.000	0.000
35	L	36	CGU	-2	-1.925	-1.961	18.772	-0.449	-0.449	0.000	0.000	0.000	0.000
36	L	37	LYS	1	0.882	0.938	18.864	0.392	0.392	0.000	0.000	0.000	0.000
37	L	38	THR	0	0.032	0.030	13.592	-0.026	-0.026	0.000	0.000	0.000	0.000
38	L	39	ASN	0	-0.062	-0.030	16.101	0.032	0.032	0.000	0.000	0.000	0.000
39	L	40	CGU	-2	-1.781	-1.919	18.504	-0.392	-0.392	0.000	0.000	0.000	0.000
40	L	41	PHE	0	-0.051	-0.024	11.119	0.027	0.027	0.000	0.000	0.000	0.000
41	L	42	TRP	0	0.059	0.027	9.502	0.044	0.044	0.000	0.000	0.000	0.000
42	L	43	LYS	1	0.723	0.885	15.945	0.183	0.183	0.000	0.000	0.000	0.000
43	L	44	GLN	0	-0.061	-0.023	17.284	0.014	0.014	0.000	0.000	0.000	0.000
44	L	45	TYR	0	-0.050	0.010	8.500	0.129	0.129	0.000	0.000	0.000	0.000
45	L	46	VAL	0	-0.052	-0.055	12.822	0.070	0.070	0.000	0.000	0.000	0.000
46	L	47	ASP	-1	-0.991	-0.993	16.117	0.203	0.203	0.000	0.000	0.000	0.000
47	L	48	GLY	0	0.016	0.002	18.728	-0.030	-0.030	0.000	0.000	0.000	0.000
48	L	49	ASP	-1	-0.823	-0.895	20.380	-0.005	-0.005	0.000	0.000	0.000	0.000
49	L	50	GLN	0	0.023	0.023	22.721	-0.009	-0.009	0.000	0.000	0.000	0.000
50	L	51	CYS	0	-0.118	-0.073	25.607	-0.004	-0.004	0.000	0.000	0.000	0.000
51	L	52	GLU	-1	-0.918	-0.972	26.265	0.088	0.088	0.000	0.000	0.000	0.000
52	L	53	PRO	0	-0.115	-0.077	27.254	-0.008	-0.008	0.000	0.000	0.000	0.000
53	L	54	ASN	0	-0.020	-0.006	29.867	0.002	0.002	0.000	0.000	0.000	0.000
54	L	55	PRO	0	0.058	0.051	31.022	0.000	0.000	0.000	0.000	0.000	0.000
55	L	56	CYS	0	-0.076	-0.038	32.007	0.001	0.001	0.000	0.000	0.000	0.000
56	L	57	LEU	0	0.048	0.037	35.661	-0.003	-0.003	0.000	0.000	0.000	0.000
57	L	58	ASN	0	-0.073	-0.054	38.364	-0.005	-0.005	0.000	0.000	0.000	0.000
58	L	59	GLY	0	-0.040	-0.025	37.589	-0.003	-0.003	0.000	0.000	0.000	0.000
59	L	60	GLY	0	-0.035	-0.013	36.443	-0.007	-0.007	0.000	0.000	0.000	0.000
60	L	61	LEU	0	-0.042	-0.032	31.778	0.000	0.000	0.000	0.000	0.000	0.000
61	L	63	LYS	1	0.861	0.927	26.119	0.084	0.084	0.000	0.000	0.000	0.000
62	L	64	BHD	-1	-0.824	-0.937	22.666	-0.059	-0.059	0.000	0.000	0.000	0.000
63	L	65	ASP	-1	-0.837	-0.935	24.034	-0.112	-0.112	0.000	0.000	0.000	0.000
64	L	66	ILE	0	0.046	0.042	20.606	0.020	0.020	0.000	0.000	0.000	0.000
65	L	67	ASN	0	-0.056	-0.017	22.667	0.010	0.010	0.000	0.000	0.000	0.000
66	L	68	SER	0	-0.021	-0.018	25.633	0.010	0.010	0.000	0.000	0.000	0.000
67	L	69	TYR	0	0.026	0.020	26.944	-0.001	-0.001	0.000	0.000	0.000	0.000
68	L	70	GLU	-1	-0.965	-0.967	29.148	-0.058	-0.058	0.000	0.000	0.000	0.000
69	L	72	TRP	0	-0.067	-0.022	29.744	-0.001	-0.001	0.000	0.000	0.000	0.000
70	L	73	CYS	0	-0.026	-0.003	35.442	-0.002	-0.002	0.000	0.000	0.000	0.000
71	L	74	GLN	0	-0.057	-0.023	37.072	-0.001	-0.001	0.000	0.000	0.000	0.000
72	L	75	VAL	0	-0.018	-0.026	39.884	0.000	0.000	0.000	0.000	0.000	0.000
73	L	76	GLY	0	0.012	0.000	43.661	0.001	0.001	0.000	0.000	0.000	0.000
74	L	77	PHE	0	0.027	0.027	42.444	0.003	0.003	0.000	0.000	0.000	0.000
75	L	78	GLU	-1	-0.879	-0.913	43.024	-0.037	-0.037	0.000	0.000	0.000	0.000
76	L	79	GLY	0	0.037	0.015	42.416	0.003	0.003	0.000	0.000	0.000	0.000
77	L	80	LYS	1	0.936	0.951	37.007	0.003	0.003	0.000	0.000	0.000	0.000
78	L	81	ASN	0	0.086	0.054	36.137	-0.001	-0.001	0.000	0.000	0.000	0.000
79	L	83	GLU	-1	-0.792	-0.910	40.828	-0.007	-0.007	0.000	0.000	0.000	0.000
80	L	84	LEU	0	-0.050	-0.012	43.343	0.000	0.000	0.000	0.000	0.000	0.000
81	L	85	ASP	-1	-0.832	-0.899	45.409	-0.022	-0.022	0.000	0.000	0.000	0.000
82	L	86	ALA	0	-0.086	-0.033	46.490	0.001	0.001	0.000	0.000	0.000	0.000
83	L	87	THR	0	0.057	0.003	48.356	0.000	0.000	0.000	0.000	0.000	0.000
84	L	88	CYS	0	-0.033	-0.018	51.537	-0.003	-0.003	0.000	0.000	0.000	0.000
85	L	89	ASN	0	-0.010	0.020	53.374	-0.002	-0.002	0.000	0.000	0.000	0.000
86	L	90	ILE	0	0.007	0.015	48.492	0.000	0.000	0.000	0.000	0.000	0.000
87	L	91	LYS	1	0.983	0.973	45.529	0.033	0.033	0.000	0.000	0.000	0.000
88	L	92	ASN	0	-0.008	-0.018	48.022	-0.001	-0.001	0.000	0.000	0.000	0.000
89	L	93	GLY	0	0.078	0.047	49.272	-0.001	-0.001	0.000	0.000	0.000	0.000
90	L	94	ARG	1	0.780	0.851	42.456	0.039	0.039	0.000	0.000	0.000	0.000
91	L	95	CYS	0	-0.067	-0.003	45.574	-0.003	-0.003	0.000	0.000	0.000	0.000
92	L	96	LYS	1	0.968	0.967	42.656	0.071	0.071	0.000	0.000	0.000	0.000
93	L	97	GLN	0	-0.003	-0.010	48.081	0.001	0.001	0.000	0.000	0.000	0.000
94	L	98	PHE	0	-0.046	-0.014	51.783	0.003	0.003	0.000	0.000	0.000	0.000
95	L	100	LYS	1	0.902	0.950	53.806	0.038	0.038	0.000	0.000	0.000	0.000
96	L	101	THR	0	0.061	0.032	55.322	-0.002	-0.002	0.000	0.000	0.000	0.000
97	L	102	GLY	0	0.001	-0.013	56.390	0.000	0.000	0.000	0.000	0.000	0.000
98	L	103	ALA	0	-0.048	-0.015	56.663	-0.001	-0.001	0.000	0.000	0.000	0.000
99	L	104	ASP	-1	-0.752	-0.874	53.606	-0.027	-0.027	0.000	0.000	0.000	0.000
100	L	105	SER	0	-0.086	-0.051	54.337	0.002	0.002	0.000	0.000	0.000	0.000
101	L	106	LYS	1	0.926	0.989	49.089	0.032	0.032	0.000	0.000	0.000	0.000
102	L	107	VAL	0	-0.051	-0.032	48.918	0.000	0.000	0.000	0.000	0.000	0.000
103	L	108	LEU	0	0.061	0.028	51.334	-0.001	-0.001	0.000	0.000	0.000	0.000
104	L	110	SER	0	-0.010	-0.014	51.433	0.001	0.001	0.000	0.000	0.000	0.000
105	L	111	CYS	0	-0.043	-0.017	45.596	0.000	0.000	0.000	0.000	0.000	0.000
106	L	112	THR	0	0.018	0.015	53.675	0.001	0.001	0.000	0.000	0.000	0.000
107	L	113	THR	0	0.038	0.008	55.881	-0.002	-0.002	0.000	0.000	0.000	0.000
108	L	114	GLY	0	0.035	0.013	56.216	0.000	0.000	0.000	0.000	0.000	0.000
109	L	115	TYR	0	-0.058	-0.045	50.582	-0.005	-0.005	0.000	0.000	0.000	0.000
110	L	116	ARG	1	0.915	0.959	48.467	0.081	0.081	0.000	0.000	0.000	0.000
111	L	117	LEU	0	0.033	0.011	47.699	-0.002	-0.002	0.000	0.000	0.000	0.000
112	L	118	ALA	0	-0.089	-0.049	43.348	-0.002	-0.002	0.000	0.000	0.000	0.000
113	L	119	PRO	0	0.052	0.008	41.216	0.003	0.003	0.000	0.000	0.000	0.000
114	L	120	ASP	-1	-0.694	-0.827	40.583	-0.074	-0.074	0.000	0.000	0.000	0.000
115	L	121	GLN	0	-0.013	-0.006	42.105	0.006	0.006	0.000	0.000	0.000	0.000
116	L	122	LYS	1	0.885	0.935	40.263	0.070	0.070	0.000	0.000	0.000	0.000
117	L	123	SER	0	-0.062	-0.035	42.916	0.002	0.002	0.000	0.000	0.000	0.000
118	L	125	LYS	1	0.954	0.978	43.886	0.085	0.085	0.000	0.000	0.000	0.000
119	L	126	PRO	0	0.016	0.009	47.675	0.003	0.003	0.000	0.000	0.000	0.000
120	L	127	ALA	0	-0.031	-0.018	50.107	-0.003	-0.003	0.000	0.000	0.000	0.000
121	L	128	VAL	0	0.032	0.016	52.696	0.002	0.002	0.000	0.000	0.000	0.000
122	L	129	PRO	0	0.004	0.008	52.945	-0.001	-0.001	0.000	0.000	0.000	0.000
123	L	130	PHE	0	0.016	0.011	53.609	-0.001	-0.001	0.000	0.000	0.000	0.000
124	L	131	PRO	0	-0.021	-0.001	51.950	0.003	0.003	0.000	0.000	0.000	0.000
125	L	132	CYS	0	-0.032	-0.016	55.230	0.000	0.000	0.000	0.000	0.000	0.000
126	L	133	GLY	0	0.040	0.010	55.687	-0.001	-0.001	0.000	0.000	0.000	0.000
127	L	134	ARG	1	0.965	1.002	47.558	0.076	0.076	0.000	0.000	0.000	0.000
128	L	135	VAL	0	0.050	0.025	52.174	0.000	0.000	0.000	0.000	0.000	0.000
129	L	136	SER	0	0.031	0.003	52.369	-0.003	-0.003	0.000	0.000	0.000	0.000
130	L	137	VAL	0	-0.005	0.000	52.156	-0.003	-0.003	0.000	0.000	0.000	0.000
131	L	138	SER	0	0.006	0.004	49.919	-0.001	-0.001	0.000	0.000	0.000	0.000
132	L	139	HIS	0	-0.047	-0.022	46.702	-0.004	-0.004	0.000	0.000	0.000	0.000
133	L	140	SER	0	-0.040	0.017	47.115	-0.005	-0.005	0.000	0.000	0.000	0.000
134	L	141	PRO	0	-0.011	-0.004	45.248	0.002	0.002	0.000	0.000	0.000	0.000
135	L	142	THR	0	0.024	-0.035	41.026	-0.002	-0.002	0.000	0.000	0.000	0.000
136	L	143	THR	0	-0.033	0.004	42.781	-0.006	-0.006	0.000	0.000	0.000	0.000
137	L	144	LEU	0	0.042	0.006	44.188	0.003	0.003	0.000	0.000	0.000	0.000
138	L	145	THR	0	-0.043	-0.015	46.443	-0.002	-0.002	0.000	0.000	0.000	0.000
139	L	146	ARG	1	1.025	1.026	43.699	0.104	0.104	0.000	0.000	0.000	0.000

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