FMO DATABASE

FMODB ID: NNG4Q

Calculation Name: 2Y72-A-Xray372

Preferred Name: Collagenase

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2Y72

Chain ID: A

ChEMBL ID: CHEMBL2268009

UniProt ID: Q9X721

Base Structure: X-ray

Registration Date: 2023-09-23

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	OptH
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	85
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-504604.569111
FMO2-HF: Nuclear repulsion	473642.250034
FMO2-HF: Total energy	-30962.319077
FMO2-MP2: Total energy	-31054.477544

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(A:796:GLY)

Summations of interaction energy for fragment #1(A:796:GLY)

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.
-4.187	-3.092	0.009	-0.528	-0.576	0

Interaction energy analysis for fragmet #1(A:796:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.035

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	A	798	THR	0	-0.078	-0.077	3.683	-2.263	-1.466	0.010	-0.350	-0.457	0.001
4	A	799	ILE	0	-0.070	-0.023	4.386	-0.241	-0.138	-0.001	-0.022	-0.080	0.000
5	A	800	ALA	0	0.044	0.021	6.795	0.290	0.290	0.000	0.000	0.000	0.000
6	A	801	LYS	1	0.950	0.962	10.197	0.715	0.715	0.000	0.000	0.000	0.000
7	A	802	VAL	0	0.034	0.016	12.916	0.050	0.050	0.000	0.000	0.000	0.000
8	A	803	THR	0	-0.058	-0.023	16.370	-0.001	-0.001	0.000	0.000	0.000	0.000
9	A	804	GLY	0	0.063	0.018	19.487	0.015	0.015	0.000	0.000	0.000	0.000
10	A	805	PRO	0	-0.028	0.008	22.798	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	806	SER	0	0.100	0.030	24.444	0.001	0.001	0.000	0.000	0.000	0.000
12	A	807	THR	0	-0.012	0.001	25.576	0.011	0.011	0.000	0.000	0.000	0.000
13	A	808	GLY	0	0.045	0.011	28.964	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	809	ALA	0	-0.077	-0.035	31.111	0.005	0.005	0.000	0.000	0.000	0.000
15	A	810	VAL	0	0.030	0.012	33.813	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	811	GLY	0	-0.028	-0.009	34.703	0.002	0.002	0.000	0.000	0.000	0.000
17	A	812	ARG	1	0.893	0.952	33.581	0.072	0.072	0.000	0.000	0.000	0.000
18	A	813	ASN	0	-0.008	-0.010	31.471	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	814	ILE	0	-0.012	-0.007	26.184	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	815	GLU	-1	-0.933	-0.958	26.218	-0.127	-0.127	0.000	0.000	0.000	0.000
21	A	816	PHE	0	-0.004	0.000	20.961	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	817	SER	0	-0.014	-0.025	20.290	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	818	GLY	0	0.076	0.031	16.269	-0.018	-0.018	0.000	0.000	0.000	0.000
24	A	819	LYS	1	0.799	0.892	15.433	0.248	0.248	0.000	0.000	0.000	0.000
25	A	820	ASP	-1	-0.865	-0.932	14.528	-0.410	-0.410	0.000	0.000	0.000	0.000
26	A	821	SER	0	-0.059	-0.019	11.343	-0.106	-0.106	0.000	0.000	0.000	0.000
27	A	822	LYS	1	0.915	0.950	5.876	2.554	2.554	0.000	0.000	0.000	0.000
28	A	823	ASP	-1	-0.729	-0.858	7.956	-0.836	-0.836	0.000	0.000	0.000	0.000
29	A	824	GLU	-1	-0.999	-1.007	4.362	-4.486	-4.291	0.000	-0.156	-0.039	-0.001
30	A	825	ASP	-1	-0.954	-0.969	8.033	0.014	0.014	0.000	0.000	0.000	0.000
31	A	826	GLY	0	0.046	0.035	10.282	0.197	0.197	0.000	0.000	0.000	0.000
32	A	827	LYS	1	0.895	0.946	12.755	0.094	0.094	0.000	0.000	0.000	0.000
33	A	828	ILE	0	0.014	0.006	10.578	0.048	0.048	0.000	0.000	0.000	0.000
34	A	829	VAL	0	-0.035	-0.016	13.541	0.021	0.021	0.000	0.000	0.000	0.000
35	A	830	SER	0	-0.102	-0.054	15.326	0.032	0.032	0.000	0.000	0.000	0.000
36	A	831	TYR	0	0.061	0.018	15.004	-0.016	-0.016	0.000	0.000	0.000	0.000
37	A	832	ASP	-1	-0.853	-0.931	16.223	-0.051	-0.051	0.000	0.000	0.000	0.000
38	A	833	TRP	0	-0.008	-0.021	17.105	-0.026	-0.026	0.000	0.000	0.000	0.000
39	A	834	ASP	-1	-0.846	-0.920	19.419	-0.050	-0.050	0.000	0.000	0.000	0.000
40	A	835	PHE	0	-0.030	-0.029	20.798	-0.015	-0.015	0.000	0.000	0.000	0.000
41	A	836	GLY	0	0.073	0.044	23.242	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	837	ASP	-1	-0.847	-0.914	24.114	-0.063	-0.063	0.000	0.000	0.000	0.000
43	A	838	GLY	0	-0.007	0.004	26.073	0.006	0.006	0.000	0.000	0.000	0.000
44	A	839	ALA	0	-0.059	-0.012	26.979	0.004	0.004	0.000	0.000	0.000	0.000
45	A	840	THR	0	0.034	0.011	22.681	-0.008	-0.008	0.000	0.000	0.000	0.000
46	A	841	SER	0	-0.011	-0.007	22.668	0.007	0.007	0.000	0.000	0.000	0.000
47	A	842	ARG	1	0.917	0.961	19.419	0.064	0.064	0.000	0.000	0.000	0.000
48	A	843	GLY	0	0.019	0.018	20.496	0.006	0.006	0.000	0.000	0.000	0.000
49	A	844	LYS	1	0.918	0.973	18.086	0.271	0.271	0.000	0.000	0.000	0.000
50	A	845	ASN	0	0.030	0.019	19.833	-0.033	-0.033	0.000	0.000	0.000	0.000
51	A	846	SER	0	0.060	0.040	22.542	0.022	0.022	0.000	0.000	0.000	0.000
52	A	847	VAL	0	0.014	0.006	24.187	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	848	HIS	1	0.799	0.886	26.427	0.090	0.090	0.000	0.000	0.000	0.000
54	A	849	ALA	0	0.059	0.045	28.251	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	850	TYR	0	-0.022	-0.023	24.899	0.002	0.002	0.000	0.000	0.000	0.000
56	A	851	LYS	1	1.003	0.983	31.613	0.048	0.048	0.000	0.000	0.000	0.000
57	A	852	LYS	1	0.955	0.983	33.658	0.046	0.046	0.000	0.000	0.000	0.000
58	A	853	ALA	0	-0.025	-0.001	33.073	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	854	GLY	0	-0.001	-0.003	31.107	0.005	0.005	0.000	0.000	0.000	0.000
60	A	855	THR	0	0.051	0.035	25.604	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	856	TYR	0	-0.063	-0.038	25.217	0.009	0.009	0.000	0.000	0.000	0.000
62	A	857	ASN	0	0.043	0.009	17.995	-0.025	-0.025	0.000	0.000	0.000	0.000
63	A	858	VAL	0	-0.025	-0.002	19.164	0.011	0.011	0.000	0.000	0.000	0.000
64	A	859	THR	0	-0.021	-0.017	15.703	-0.020	-0.020	0.000	0.000	0.000	0.000
65	A	860	LEU	0	-0.029	-0.001	13.812	0.021	0.021	0.000	0.000	0.000	0.000
66	A	861	LYS	1	0.925	0.970	12.167	0.010	0.010	0.000	0.000	0.000	0.000
67	A	862	VAL	0	-0.029	-0.021	9.739	0.030	0.030	0.000	0.000	0.000	0.000
68	A	863	THR	0	-0.012	-0.005	10.937	0.041	0.041	0.000	0.000	0.000	0.000
69	A	864	ASP	-1	-0.754	-0.870	8.623	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	865	ASP	-1	-0.868	-0.938	11.836	-0.025	-0.025	0.000	0.000	0.000	0.000
71	A	866	LYS	1	0.791	0.884	9.389	0.070	0.070	0.000	0.000	0.000	0.000
72	A	867	GLY	0	-0.052	-0.016	12.987	0.076	0.076	0.000	0.000	0.000	0.000
73	A	868	ALA	0	-0.015	0.011	7.510	0.076	0.076	0.000	0.000	0.000	0.000
74	A	869	THR	0	-0.057	-0.046	8.793	-0.221	-0.221	0.000	0.000	0.000	0.000
75	A	870	ALA	0	0.023	0.018	6.077	0.098	0.098	0.000	0.000	0.000	0.000
76	A	871	THR	0	-0.040	-0.032	7.910	0.072	0.072	0.000	0.000	0.000	0.000
77	A	872	GLU	-1	-0.890	-0.913	9.681	-0.607	-0.607	0.000	0.000	0.000	0.000
78	A	873	SER	0	-0.087	-0.057	12.001	0.077	0.077	0.000	0.000	0.000	0.000
79	A	874	PHE	0	-0.004	-0.007	15.527	-0.027	-0.027	0.000	0.000	0.000	0.000
80	A	875	THR	0	-0.014	-0.001	18.529	0.022	0.022	0.000	0.000	0.000	0.000
81	A	876	ILE	0	-0.012	0.004	21.856	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	877	GLU	-1	-0.965	-0.971	25.125	-0.084	-0.084	0.000	0.000	0.000	0.000
83	A	878	ILE	0	-0.039	-0.014	28.616	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	879	LYS	1	1.001	0.994	31.233	0.078	0.078	0.000	0.000	0.000	0.000
85	A	880	ASN	0	0.030	-0.001	34.830	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:796:GLY)