FMO DATABASE

FMODB ID: N237Q

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1163486.824765
FMO2-HF: Nuclear repulsion	1100080.2372
FMO2-HF: Total energy	-63406.587565
FMO2-MP2: Total energy	-63579.017611

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.
-77.563	-76.588	44.181	-21.244	-23.909	-0.133

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 : -0.086 / q_NPA : -0.052

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	-0.097	-0.052	2.282	-5.544	-3.001	6.952	-3.960	-5.535	0.036
4	L	4	GLY	0	-0.033	-0.006	4.717	0.471	0.695	-0.001	-0.020	-0.203	0.000
5	L	5	LYS	1	0.453	0.541	6.347	0.709	0.709	0.000	0.000	0.000	0.000
6	L	6	LEU	0	-0.070	-0.029	9.084	0.102	0.102	0.000	0.000	0.000	0.000
7	L	7	CGU	-2	-1.569	-1.773	3.699	-5.848	-5.416	0.006	-0.128	-0.310	-0.001
8	L	8	CGU	-2	-1.468	-1.576	7.145	-3.341	-3.341	0.000	0.000	0.000	0.000
9	L	9	PHE	0	-0.161	-0.081	8.221	0.385	0.385	0.000	0.000	0.000	0.000
10	L	10	VAL	0	-0.113	-0.051	8.735	0.343	0.343	0.000	0.000	0.000	0.000
11	L	11	ARG	1	0.831	0.913	9.445	0.718	0.718	0.000	0.000	0.000	0.000
12	L	12	GLY	0	0.119	0.066	7.739	0.020	0.020	0.000	0.000	0.000	0.000
13	L	13	ASN	0	-0.167	-0.107	7.616	0.160	0.160	0.000	0.000	0.000	0.000
14	L	14	LEU	0	0.088	0.068	7.033	-0.054	-0.054	0.000	0.000	0.000	0.000
15	L	15	CGU	-2	-1.920	-1.965	9.024	-1.151	-1.151	0.000	0.000	0.000	0.000
16	L	16	ARG	1	0.708	0.865	4.472	2.988	3.068	-0.001	-0.008	-0.070	0.000
17	L	17	CGU	-2	-1.513	-1.767	1.942	-15.864	-17.250	9.674	-4.308	-3.979	-0.041
18	L	18	CYS	0	-0.080	0.013	4.052	1.272	1.697	-0.001	0.033	-0.457	0.000
19	L	19	ILE	0	-0.081	-0.051	7.201	0.231	0.231	0.000	0.000	0.000	0.000
20	L	20	CGU	-2	-1.824	-1.887	4.920	-2.981	-2.981	0.000	0.000	0.000	0.000
21	L	21	CGU	-2	-1.807	-1.881	1.605	-43.039	-45.238	27.527	-12.467	-12.860	-0.124
22	L	22	LYS	1	0.732	0.833	4.992	-0.510	-0.510	0.000	0.000	0.000	0.000
23	L	24	SER	0	-0.066	-0.061	5.425	0.420	0.420	0.000	0.000	0.000	0.000
24	L	25	PHE	0	-0.061	-0.041	7.510	-0.024	-0.024	0.000	0.000	0.000	0.000
25	L	26	CGU	-2	-1.743	-1.877	9.029	-0.979	-0.979	0.000	0.000	0.000	0.000
26	L	27	CGU	-2	-1.589	-1.782	3.363	-5.230	-4.374	0.025	-0.386	-0.495	-0.003
27	L	28	ALA	0	0.010	-0.014	6.903	0.160	0.160	0.000	0.000	0.000	0.000
28	L	29	ARG	1	0.690	0.814	9.500	0.690	0.690	0.000	0.000	0.000	0.000
29	L	30	CGU	-2	-1.810	-1.885	10.765	-1.517	-1.517	0.000	0.000	0.000	0.000
30	L	31	VAL	0	-0.079	-0.023	8.593	-0.007	-0.007	0.000	0.000	0.000	0.000
31	L	32	PHE	0	-0.075	-0.045	11.801	0.091	0.091	0.000	0.000	0.000	0.000
32	L	33	CGU	-2	-1.859	-1.914	14.512	-0.693	-0.693	0.000	0.000	0.000	0.000
33	L	34	ASN	0	-0.135	-0.075	16.917	0.040	0.040	0.000	0.000	0.000	0.000
34	L	35	THR	0	0.021	-0.014	17.169	-0.007	-0.007	0.000	0.000	0.000	0.000
35	L	36	CGU	-2	-1.880	-1.922	18.242	-0.375	-0.375	0.000	0.000	0.000	0.000
36	L	37	LYS	1	0.901	0.940	18.150	0.330	0.330	0.000	0.000	0.000	0.000
37	L	38	THR	0	0.025	0.032	12.997	-0.012	-0.012	0.000	0.000	0.000	0.000
38	L	39	ASN	0	-0.053	-0.032	15.450	0.035	0.035	0.000	0.000	0.000	0.000
39	L	40	CGU	-2	-1.757	-1.888	18.005	-0.263	-0.263	0.000	0.000	0.000	0.000
40	L	41	PHE	0	-0.015	-0.002	10.915	0.015	0.015	0.000	0.000	0.000	0.000
41	L	42	TRP	0	0.034	0.016	9.127	0.030	0.030	0.000	0.000	0.000	0.000
42	L	43	LYS	1	0.657	0.824	15.616	0.138	0.138	0.000	0.000	0.000	0.000
43	L	44	GLN	0	-0.075	-0.028	17.549	0.007	0.007	0.000	0.000	0.000	0.000
44	L	45	TYR	0	0.013	0.020	8.677	0.047	0.047	0.000	0.000	0.000	0.000
45	L	46	VAL	0	-0.052	-0.038	12.768	0.052	0.052	0.000	0.000	0.000	0.000
46	L	47	ASP	-1	-0.959	-0.970	15.981	0.162	0.162	0.000	0.000	0.000	0.000
47	L	48	GLY	0	-0.030	-0.015	18.786	-0.020	-0.020	0.000	0.000	0.000	0.000
48	L	49	ASP	-1	-0.838	-0.919	20.134	0.000	0.000	0.000	0.000	0.000	0.000
49	L	50	GLN	0	-0.012	-0.012	22.799	-0.010	-0.010	0.000	0.000	0.000	0.000
50	L	51	CYS	0	-0.068	-0.052	26.000	-0.004	-0.004	0.000	0.000	0.000	0.000
51	L	52	GLU	-1	-0.889	-0.964	26.518	0.052	0.052	0.000	0.000	0.000	0.000
52	L	53	PRO	0	-0.113	-0.074	27.599	-0.004	-0.004	0.000	0.000	0.000	0.000
53	L	54	ASN	0	-0.009	0.011	29.919	-0.002	-0.002	0.000	0.000	0.000	0.000
54	L	55	PRO	0	0.032	0.033	30.991	0.000	0.000	0.000	0.000	0.000	0.000
55	L	56	CYS	0	-0.071	0.000	31.685	0.001	0.001	0.000	0.000	0.000	0.000
56	L	57	LEU	0	0.052	0.031	35.636	-0.003	-0.003	0.000	0.000	0.000	0.000
57	L	58	ASN	0	-0.069	-0.053	38.631	-0.003	-0.003	0.000	0.000	0.000	0.000
58	L	59	GLY	0	-0.004	0.001	37.862	-0.002	-0.002	0.000	0.000	0.000	0.000
59	L	60	GLY	0	-0.038	-0.019	36.719	-0.005	-0.005	0.000	0.000	0.000	0.000
60	L	61	LEU	0	-0.024	-0.017	32.036	0.000	0.000	0.000	0.000	0.000	0.000
61	L	63	LYS	1	0.797	0.900	25.772	0.060	0.060	0.000	0.000	0.000	0.000
62	L	64	BHD	-1	-0.810	-0.921	22.487	-0.044	-0.044	0.000	0.000	0.000	0.000
63	L	65	ASP	-1	-0.777	-0.900	23.751	-0.082	-0.082	0.000	0.000	0.000	0.000
64	L	66	ILE	0	0.036	0.032	20.566	0.018	0.018	0.000	0.000	0.000	0.000
65	L	67	ASN	0	-0.056	-0.026	22.696	0.010	0.010	0.000	0.000	0.000	0.000
66	L	68	SER	0	-0.089	-0.034	25.809	0.006	0.006	0.000	0.000	0.000	0.000
67	L	69	TYR	0	0.032	0.008	27.010	-0.001	-0.001	0.000	0.000	0.000	0.000
68	L	70	GLU	-1	-0.902	-0.925	29.304	-0.053	-0.053	0.000	0.000	0.000	0.000
69	L	72	TRP	0	-0.058	-0.030	29.465	-0.001	-0.001	0.000	0.000	0.000	0.000
70	L	73	CYS	0	-0.072	-0.010	35.562	-0.005	-0.005	0.000	0.000	0.000	0.000
71	L	74	GLN	0	-0.045	-0.036	37.269	-0.002	-0.002	0.000	0.000	0.000	0.000
72	L	75	VAL	0	-0.037	-0.030	39.520	-0.001	-0.001	0.000	0.000	0.000	0.000
73	L	76	GLY	0	-0.010	0.000	43.417	0.001	0.001	0.000	0.000	0.000	0.000
74	L	77	PHE	0	0.030	0.026	42.469	0.003	0.003	0.000	0.000	0.000	0.000
75	L	78	GLU	-1	-0.844	-0.898	42.826	-0.031	-0.031	0.000	0.000	0.000	0.000
76	L	79	GLY	0	0.011	0.010	42.111	0.002	0.002	0.000	0.000	0.000	0.000
77	L	80	LYS	1	0.938	0.948	37.057	0.003	0.003	0.000	0.000	0.000	0.000
78	L	81	ASN	0	0.060	0.033	36.057	-0.001	-0.001	0.000	0.000	0.000	0.000
79	L	83	GLU	-1	-0.792	-0.910	40.604	-0.010	-0.010	0.000	0.000	0.000	0.000
80	L	84	LEU	0	-0.056	-0.014	43.258	0.001	0.001	0.000	0.000	0.000	0.000
81	L	85	ASP	-1	-0.866	-0.934	45.607	-0.021	-0.021	0.000	0.000	0.000	0.000
82	L	86	ALA	0	-0.050	-0.018	46.160	0.001	0.001	0.000	0.000	0.000	0.000
83	L	87	THR	0	0.043	-0.010	48.104	0.000	0.000	0.000	0.000	0.000	0.000
84	L	88	CYS	0	0.012	-0.008	51.159	-0.002	-0.002	0.000	0.000	0.000	0.000
85	L	89	ASN	0	-0.018	0.012	52.965	-0.002	-0.002	0.000	0.000	0.000	0.000
86	L	90	ILE	0	0.005	0.014	48.196	0.000	0.000	0.000	0.000	0.000	0.000
87	L	91	LYS	1	0.963	0.966	45.579	0.027	0.027	0.000	0.000	0.000	0.000
88	L	92	ASN	0	-0.009	-0.012	48.040	-0.001	-0.001	0.000	0.000	0.000	0.000
89	L	93	GLY	0	0.069	0.036	48.954	-0.002	-0.002	0.000	0.000	0.000	0.000
90	L	94	ARG	1	0.810	0.870	41.495	0.033	0.033	0.000	0.000	0.000	0.000
91	L	95	CYS	0	-0.053	0.003	45.453	-0.002	-0.002	0.000	0.000	0.000	0.000
92	L	96	LYS	1	0.959	0.977	42.496	0.058	0.058	0.000	0.000	0.000	0.000
93	L	97	GLN	0	-0.002	-0.006	47.826	-0.001	-0.001	0.000	0.000	0.000	0.000
94	L	98	PHE	0	-0.024	-0.004	51.617	0.002	0.002	0.000	0.000	0.000	0.000
95	L	100	LYS	1	0.912	0.947	53.559	0.032	0.032	0.000	0.000	0.000	0.000
96	L	101	THR	0	0.062	0.050	54.888	-0.001	-0.001	0.000	0.000	0.000	0.000
97	L	102	GLY	0	-0.025	-0.025	56.064	0.000	0.000	0.000	0.000	0.000	0.000
98	L	103	ALA	0	-0.031	-0.005	56.367	-0.001	-0.001	0.000	0.000	0.000	0.000
99	L	104	ASP	-1	-0.777	-0.874	53.522	-0.024	-0.024	0.000	0.000	0.000	0.000
100	L	105	SER	0	-0.082	-0.061	54.233	0.002	0.002	0.000	0.000	0.000	0.000
101	L	106	LYS	1	0.947	0.989	49.020	0.028	0.028	0.000	0.000	0.000	0.000
102	L	107	VAL	0	-0.061	-0.037	49.162	0.000	0.000	0.000	0.000	0.000	0.000
103	L	108	LEU	0	0.023	0.022	50.799	-0.001	-0.001	0.000	0.000	0.000	0.000
104	L	110	SER	0	-0.028	-0.021	51.132	0.000	0.000	0.000	0.000	0.000	0.000
105	L	111	CYS	0	-0.045	-0.026	45.523	-0.001	-0.001	0.000	0.000	0.000	0.000
106	L	112	THR	0	0.025	0.004	53.491	0.001	0.001	0.000	0.000	0.000	0.000
107	L	113	THR	0	0.021	-0.001	55.632	-0.001	-0.001	0.000	0.000	0.000	0.000
108	L	114	GLY	0	0.044	0.023	56.033	0.000	0.000	0.000	0.000	0.000	0.000
109	L	115	TYR	0	-0.050	-0.020	50.659	-0.004	-0.004	0.000	0.000	0.000	0.000
110	L	116	ARG	1	0.912	0.950	48.496	0.065	0.065	0.000	0.000	0.000	0.000
111	L	117	LEU	0	0.063	0.040	47.400	-0.002	-0.002	0.000	0.000	0.000	0.000
112	L	118	ALA	0	-0.067	-0.045	42.899	-0.003	-0.003	0.000	0.000	0.000	0.000
113	L	119	PRO	0	0.049	0.011	40.645	0.003	0.003	0.000	0.000	0.000	0.000
114	L	120	ASP	-1	-0.688	-0.813	40.496	-0.059	-0.059	0.000	0.000	0.000	0.000
115	L	121	GLN	0	-0.011	-0.010	41.854	0.005	0.005	0.000	0.000	0.000	0.000
116	L	122	LYS	1	0.897	0.934	40.420	0.058	0.058	0.000	0.000	0.000	0.000
117	L	123	SER	0	-0.074	-0.057	42.922	0.002	0.002	0.000	0.000	0.000	0.000
118	L	125	LYS	1	0.951	0.989	43.935	0.067	0.067	0.000	0.000	0.000	0.000
119	L	126	PRO	0	0.023	-0.001	47.166	0.003	0.003	0.000	0.000	0.000	0.000
120	L	127	ALA	0	-0.046	-0.024	49.734	-0.002	-0.002	0.000	0.000	0.000	0.000
121	L	128	VAL	0	0.018	0.019	52.572	0.001	0.001	0.000	0.000	0.000	0.000
122	L	129	PRO	0	0.016	0.002	52.779	-0.001	-0.001	0.000	0.000	0.000	0.000
123	L	130	PHE	0	0.022	0.015	53.447	-0.001	-0.001	0.000	0.000	0.000	0.000
124	L	131	PRO	0	-0.023	-0.007	51.534	0.002	0.002	0.000	0.000	0.000	0.000
125	L	132	CYS	0	-0.017	-0.002	54.829	0.000	0.000	0.000	0.000	0.000	0.000
126	L	133	GLY	0	0.030	0.013	55.160	-0.001	-0.001	0.000	0.000	0.000	0.000
127	L	134	ARG	1	0.932	0.971	47.128	0.061	0.061	0.000	0.000	0.000	0.000
128	L	135	VAL	0	0.081	0.036	51.882	0.000	0.000	0.000	0.000	0.000	0.000
129	L	136	SER	0	0.015	0.002	52.082	-0.003	-0.003	0.000	0.000	0.000	0.000
130	L	137	VAL	0	0.005	0.009	51.639	-0.003	-0.003	0.000	0.000	0.000	0.000
131	L	138	SER	0	-0.007	-0.003	49.675	-0.001	-0.001	0.000	0.000	0.000	0.000
132	L	139	HIS	0	-0.053	-0.029	46.545	-0.003	-0.003	0.000	0.000	0.000	0.000
133	L	140	SER	0	-0.049	0.006	46.803	-0.003	-0.003	0.000	0.000	0.000	0.000
134	L	141	PRO	0	-0.004	0.000	45.005	0.001	0.001	0.000	0.000	0.000	0.000
135	L	142	THR	0	0.001	-0.036	40.707	-0.002	-0.002	0.000	0.000	0.000	0.000
136	L	143	THR	0	-0.033	-0.002	42.522	-0.004	-0.004	0.000	0.000	0.000	0.000
137	L	144	LEU	0	0.062	0.015	44.206	0.003	0.003	0.000	0.000	0.000	0.000
138	L	145	THR	0	-0.031	-0.004	46.323	-0.002	-0.002	0.000	0.000	0.000	0.000
139	L	146	ARG	1	0.998	1.011	43.316	0.086	0.086	0.000	0.000	0.000	0.000

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