FMO DATABASE

FMODB ID: ZYMYN

Calculation Name: 1FI8-C-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1FI8

Chain ID: C

ChEMBL ID:

UniProt ID: P23827

Base Structure: X-ray

Registration Date: 2023-06-21

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	79
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-431626.391933
FMO2-HF: Nuclear repulsion	400175.886194
FMO2-HF: Total energy	-31450.505739
FMO2-MP2: Total energy	-31542.300973

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(C:6:PRO)

Summations of interaction energy for fragment #1(C:6:PRO)

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.
-0.423	3.28	0.112	-1.306	-2.509	-0.002

Interaction energy analysis for fragmet #1(C:6:PRO)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.026

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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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	C	8	GLU	-1	-0.783	-0.877	3.336	-3.074	-1.073	0.027	-0.772	-1.256	0.000
4	C	9	LYS	1	0.868	0.947	2.995	1.109	2.532	0.086	-0.494	-1.015	-0.002
5	C	10	ILE	0	-0.037	-0.009	4.505	0.553	0.832	-0.001	-0.040	-0.238	0.000
6	C	11	ALA	0	0.061	0.018	7.130	0.389	0.389	0.000	0.000	0.000	0.000
7	C	12	PRO	0	-0.034	0.007	7.807	-0.236	-0.236	0.000	0.000	0.000	0.000
8	C	13	TYR	0	0.029	0.004	8.587	0.190	0.190	0.000	0.000	0.000	0.000
9	C	14	PRO	0	0.015	0.017	10.248	-0.050	-0.050	0.000	0.000	0.000	0.000
10	C	15	GLN	0	0.019	0.001	7.373	0.053	0.053	0.000	0.000	0.000	0.000
11	C	16	ALA	0	-0.049	-0.021	11.733	0.029	0.029	0.000	0.000	0.000	0.000
12	C	17	GLU	-1	-0.885	-0.939	14.208	-0.089	-0.089	0.000	0.000	0.000	0.000
13	C	18	LYS	1	0.946	0.956	17.711	0.050	0.050	0.000	0.000	0.000	0.000
14	C	19	GLY	0	0.010	0.009	19.183	0.002	0.002	0.000	0.000	0.000	0.000
15	C	20	MET	0	-0.025	0.014	17.293	0.018	0.018	0.000	0.000	0.000	0.000
16	C	21	LYS	1	0.905	0.926	13.524	-0.169	-0.169	0.000	0.000	0.000	0.000
17	C	22	ARG	1	0.824	0.892	6.126	0.568	0.568	0.000	0.000	0.000	0.000
18	C	23	GLN	0	0.018	0.015	9.894	0.065	0.065	0.000	0.000	0.000	0.000
19	C	24	VAL	0	0.022	0.001	6.499	-0.089	-0.089	0.000	0.000	0.000	0.000
20	C	25	ILE	0	0.003	0.000	9.632	0.097	0.097	0.000	0.000	0.000	0.000
21	C	26	GLN	0	-0.018	-0.003	6.699	-0.035	-0.035	0.000	0.000	0.000	0.000
22	C	27	LEU	0	0.023	0.011	10.752	0.048	0.048	0.000	0.000	0.000	0.000
23	C	28	THR	0	-0.030	-0.016	13.342	0.046	0.046	0.000	0.000	0.000	0.000
24	C	29	PRO	0	0.028	0.015	13.848	-0.037	-0.037	0.000	0.000	0.000	0.000
25	C	30	GLN	0	-0.098	-0.055	16.829	-0.010	-0.010	0.000	0.000	0.000	0.000
26	C	31	GLU	-1	-0.950	-0.965	20.693	0.077	0.077	0.000	0.000	0.000	0.000
27	C	32	ASP	-1	-0.790	-0.879	23.769	0.053	0.053	0.000	0.000	0.000	0.000
28	C	33	GLU	-1	-0.849	-0.927	18.477	0.160	0.160	0.000	0.000	0.000	0.000
29	C	34	SER	0	-0.089	-0.050	22.757	-0.003	-0.003	0.000	0.000	0.000	0.000
30	C	35	THR	0	-0.071	-0.052	25.690	-0.001	-0.001	0.000	0.000	0.000	0.000
31	C	36	LEU	0	-0.034	0.003	22.060	0.005	0.005	0.000	0.000	0.000	0.000
32	C	37	LYS	1	0.869	0.920	23.214	-0.087	-0.087	0.000	0.000	0.000	0.000
33	C	38	VAL	0	0.013	0.003	18.277	0.015	0.015	0.000	0.000	0.000	0.000
34	C	39	GLU	-1	-0.914	-0.946	21.664	0.092	0.092	0.000	0.000	0.000	0.000
35	C	40	LEU	0	-0.027	-0.021	17.873	0.023	0.023	0.000	0.000	0.000	0.000
36	C	41	LEU	0	0.008	0.010	21.009	-0.016	-0.016	0.000	0.000	0.000	0.000
37	C	42	ILE	0	-0.048	-0.019	19.532	0.015	0.015	0.000	0.000	0.000	0.000
38	C	43	GLY	0	0.017	-0.004	21.822	-0.014	-0.014	0.000	0.000	0.000	0.000
39	C	44	GLN	0	-0.062	-0.037	22.297	0.004	0.004	0.000	0.000	0.000	0.000
40	C	45	THR	0	-0.001	-0.002	24.242	-0.005	-0.005	0.000	0.000	0.000	0.000
41	C	46	LEU	0	-0.008	0.001	26.174	-0.002	-0.002	0.000	0.000	0.000	0.000
42	C	47	GLU	-1	-0.910	-0.948	29.667	0.079	0.079	0.000	0.000	0.000	0.000
43	C	48	VAL	0	-0.045	-0.032	32.873	-0.005	-0.005	0.000	0.000	0.000	0.000
44	C	49	ASP	-1	-0.854	-0.908	35.513	0.051	0.051	0.000	0.000	0.000	0.000
45	C	50	CYS	0	-0.077	-0.033	37.531	0.000	0.000	0.000	0.000	0.000	0.000
46	C	51	ASN	0	0.039	-0.005	35.925	-0.006	-0.006	0.000	0.000	0.000	0.000
47	C	52	LEU	0	-0.011	0.008	35.440	0.003	0.003	0.000	0.000	0.000	0.000
48	C	53	HIS	1	0.823	0.901	33.878	-0.055	-0.055	0.000	0.000	0.000	0.000
49	C	54	ARG	1	0.948	0.971	28.830	-0.065	-0.065	0.000	0.000	0.000	0.000
50	C	55	LEU	0	-0.006	0.011	25.314	-0.004	-0.004	0.000	0.000	0.000	0.000
51	C	56	GLY	0	0.071	0.036	29.537	-0.002	-0.002	0.000	0.000	0.000	0.000
52	C	57	GLY	0	0.007	-0.002	27.087	0.004	0.004	0.000	0.000	0.000	0.000
53	C	58	LYS	1	0.780	0.872	26.468	0.006	0.006	0.000	0.000	0.000	0.000
54	C	59	LEU	0	-0.004	-0.003	19.836	0.000	0.000	0.000	0.000	0.000	0.000
55	C	60	GLU	-1	-0.755	-0.837	22.282	-0.015	-0.015	0.000	0.000	0.000	0.000
56	C	61	ASN	0	-0.026	-0.044	20.148	0.001	0.001	0.000	0.000	0.000	0.000
57	C	62	LYS	1	0.911	0.958	18.493	0.075	0.075	0.000	0.000	0.000	0.000
58	C	63	THR	0	0.035	0.010	18.204	-0.004	-0.004	0.000	0.000	0.000	0.000
59	C	64	LEU	0	-0.090	-0.039	12.520	0.003	0.003	0.000	0.000	0.000	0.000
60	C	65	GLU	-1	-0.839	-0.928	16.765	-0.179	-0.179	0.000	0.000	0.000	0.000
61	C	66	GLY	0	-0.045	-0.024	17.436	-0.039	-0.039	0.000	0.000	0.000	0.000
62	C	67	TRP	0	-0.063	-0.041	11.164	-0.064	-0.064	0.000	0.000	0.000	0.000
63	C	68	GLY	0	0.002	0.009	16.646	0.012	0.012	0.000	0.000	0.000	0.000
64	C	69	TYR	0	-0.043	-0.015	11.122	0.050	0.050	0.000	0.000	0.000	0.000
65	C	70	ASP	-1	-0.764	-0.856	15.791	-0.095	-0.095	0.000	0.000	0.000	0.000
66	C	71	TYR	0	-0.052	-0.035	13.756	-0.005	-0.005	0.000	0.000	0.000	0.000
67	C	72	TYR	0	0.037	0.017	15.615	0.008	0.008	0.000	0.000	0.000	0.000
68	C	73	VAL	0	-0.036	-0.021	16.536	0.001	0.001	0.000	0.000	0.000	0.000
69	C	74	PHE	0	0.006	0.009	19.029	0.002	0.002	0.000	0.000	0.000	0.000
70	C	75	ASP	-1	-0.802	-0.901	21.487	-0.008	-0.008	0.000	0.000	0.000	0.000
71	C	76	LYS	1	0.768	0.840	24.176	0.016	0.016	0.000	0.000	0.000	0.000
72	C	77	VAL	0	-0.011	0.012	24.674	0.002	0.002	0.000	0.000	0.000	0.000
73	C	78	SER	0	-0.021	-0.009	27.859	-0.005	-0.005	0.000	0.000	0.000	0.000
74	C	79	SER	0	0.007	0.001	30.936	0.005	0.005	0.000	0.000	0.000	0.000
75	C	80	PRO	0	-0.034	-0.010	32.214	-0.001	-0.001	0.000	0.000	0.000	0.000
76	C	81	ILE	0	0.000	0.000	32.958	-0.003	-0.003	0.000	0.000	0.000	0.000
77	C	82	GLU	-1	-0.841	-0.924	35.639	0.047	0.047	0.000	0.000	0.000	0.000
78	C	83	PRO	0	-0.041	0.006	38.464	-0.003	-0.003	0.000	0.000	0.000	0.000
79	C	84	ASP	-1	-0.975	-0.994	41.820	0.026	0.026	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:6:PRO)