FMO DATABASE

FMODB ID: JQ919

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

Total energy (hartree)

FMO2-HF: Electronic energy	-505180.583877
FMO2-HF: Nuclear repulsion	474217.878887
FMO2-HF: Total energy	-30962.70499
FMO2-MP2: Total energy	-31054.895462

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.
-2.441	-1.31	0.008	-0.421	-0.717	0.001

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 : 0.001 / q_NPA : -0.017

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	A	798	THR	0	-0.052	-0.074	3.683	-2.483	-1.632	0.010	-0.382	-0.479	0.001
4	A	799	ILE	0	-0.049	-0.025	4.174	-0.323	-0.213	-0.001	-0.024	-0.085	0.000
5	A	800	ALA	0	0.035	0.023	6.801	0.295	0.295	0.000	0.000	0.000	0.000
6	A	801	LYS	1	0.881	0.913	10.200	0.694	0.694	0.000	0.000	0.000	0.000
7	A	802	VAL	0	0.035	0.022	12.918	0.051	0.051	0.000	0.000	0.000	0.000
8	A	803	THR	0	-0.048	-0.016	16.370	-0.003	-0.003	0.000	0.000	0.000	0.000
9	A	804	GLY	0	0.062	0.016	19.488	0.017	0.017	0.000	0.000	0.000	0.000
10	A	805	PRO	0	-0.028	0.005	22.798	-0.007	-0.007	0.000	0.000	0.000	0.000
11	A	806	SER	0	0.099	0.035	24.549	0.001	0.001	0.000	0.000	0.000	0.000
12	A	807	THR	0	-0.031	-0.012	25.571	0.011	0.011	0.000	0.000	0.000	0.000
13	A	808	GLY	0	0.047	0.014	28.959	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	809	ALA	0	-0.078	-0.032	31.107	0.005	0.005	0.000	0.000	0.000	0.000
15	A	810	VAL	0	0.033	0.013	33.810	-0.002	-0.002	0.000	0.000	0.000	0.000
16	A	811	GLY	0	-0.025	-0.008	34.689	0.002	0.002	0.000	0.000	0.000	0.000
17	A	812	ARG	1	0.886	0.948	33.613	0.070	0.070	0.000	0.000	0.000	0.000
18	A	813	ASN	0	0.006	-0.002	31.469	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	814	ILE	0	-0.020	-0.007	26.236	0.000	0.000	0.000	0.000	0.000	0.000
20	A	815	GLU	-1	-0.936	-0.962	26.304	-0.125	-0.125	0.000	0.000	0.000	0.000
21	A	816	PHE	0	-0.005	-0.004	21.004	-0.005	-0.005	0.000	0.000	0.000	0.000
22	A	817	SER	0	-0.017	-0.036	20.295	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	818	GLY	0	0.090	0.042	16.275	-0.019	-0.019	0.000	0.000	0.000	0.000
24	A	819	LYS	1	0.802	0.877	15.440	0.254	0.254	0.000	0.000	0.000	0.000
25	A	820	ASP	-1	-0.842	-0.904	14.597	-0.389	-0.389	0.000	0.000	0.000	0.000
26	A	821	SER	0	-0.028	0.000	11.355	-0.110	-0.110	0.000	0.000	0.000	0.000
27	A	822	LYS	1	0.801	0.878	5.116	3.078	3.078	0.000	0.000	0.000	0.000
28	A	823	ASP	-1	-0.716	-0.853	7.962	-0.771	-0.771	0.000	0.000	0.000	0.000
29	A	824	GLU	-1	-0.940	-0.945	5.133	-3.095	-2.925	-0.001	-0.015	-0.153	0.000
30	A	825	ASP	-1	-0.933	-0.959	8.033	0.070	0.070	0.000	0.000	0.000	0.000
31	A	826	GLY	0	0.036	0.033	10.282	0.193	0.193	0.000	0.000	0.000	0.000
32	A	827	LYS	1	0.897	0.946	12.755	0.065	0.065	0.000	0.000	0.000	0.000
33	A	828	ILE	0	0.000	-0.003	10.229	0.049	0.049	0.000	0.000	0.000	0.000
34	A	829	VAL	0	-0.025	-0.013	13.555	0.017	0.017	0.000	0.000	0.000	0.000
35	A	830	SER	0	-0.092	-0.039	15.331	0.029	0.029	0.000	0.000	0.000	0.000
36	A	831	TYR	0	0.042	0.009	14.916	-0.013	-0.013	0.000	0.000	0.000	0.000
37	A	832	ASP	-1	-0.803	-0.880	16.228	-0.055	-0.055	0.000	0.000	0.000	0.000
38	A	833	TRP	0	0.019	-0.002	17.106	-0.027	-0.027	0.000	0.000	0.000	0.000
39	A	834	ASP	-1	-0.830	-0.912	19.421	-0.054	-0.054	0.000	0.000	0.000	0.000
40	A	835	PHE	0	-0.012	-0.021	20.794	-0.016	-0.016	0.000	0.000	0.000	0.000
41	A	836	GLY	0	0.061	0.041	23.280	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	837	ASP	-1	-0.865	-0.940	24.108	-0.065	-0.065	0.000	0.000	0.000	0.000
43	A	838	GLY	0	0.000	0.010	26.069	0.006	0.006	0.000	0.000	0.000	0.000
44	A	839	ALA	0	-0.062	-0.011	26.976	0.004	0.004	0.000	0.000	0.000	0.000
45	A	840	THR	0	0.052	0.019	22.539	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	841	SER	0	-0.023	-0.012	22.669	0.003	0.003	0.000	0.000	0.000	0.000
47	A	842	ARG	1	0.889	0.932	19.240	0.057	0.057	0.000	0.000	0.000	0.000
48	A	843	GLY	0	0.023	0.022	20.504	0.006	0.006	0.000	0.000	0.000	0.000
49	A	844	LYS	1	0.921	0.976	17.585	0.276	0.276	0.000	0.000	0.000	0.000
50	A	845	ASN	0	0.029	0.024	19.841	-0.039	-0.039	0.000	0.000	0.000	0.000
51	A	846	SER	0	0.015	0.017	22.677	0.020	0.020	0.000	0.000	0.000	0.000
52	A	847	VAL	0	0.039	0.015	24.191	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	848	HIS	1	0.804	0.907	26.420	0.092	0.092	0.000	0.000	0.000	0.000
54	A	849	ALA	0	0.047	0.035	28.251	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	850	TYR	0	-0.028	-0.028	24.924	0.002	0.002	0.000	0.000	0.000	0.000
56	A	851	LYS	1	1.004	0.985	31.609	0.051	0.051	0.000	0.000	0.000	0.000
57	A	852	LYS	1	0.924	0.965	33.654	0.051	0.051	0.000	0.000	0.000	0.000
58	A	853	ALA	0	-0.001	0.016	33.067	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	854	GLY	0	-0.011	-0.009	31.096	0.006	0.006	0.000	0.000	0.000	0.000
60	A	855	THR	0	0.023	0.026	25.679	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	856	TYR	0	-0.054	-0.037	25.268	0.009	0.009	0.000	0.000	0.000	0.000
62	A	857	ASN	0	0.033	0.009	17.840	-0.021	-0.021	0.000	0.000	0.000	0.000
63	A	858	VAL	0	-0.020	-0.001	19.263	0.011	0.011	0.000	0.000	0.000	0.000
64	A	859	THR	0	-0.024	-0.017	15.700	-0.020	-0.020	0.000	0.000	0.000	0.000
65	A	860	LEU	0	-0.037	-0.006	13.835	0.024	0.024	0.000	0.000	0.000	0.000
66	A	861	LYS	1	0.876	0.932	12.386	0.030	0.030	0.000	0.000	0.000	0.000
67	A	862	VAL	0	-0.036	-0.025	9.734	0.033	0.033	0.000	0.000	0.000	0.000
68	A	863	THR	0	0.013	-0.008	10.944	0.030	0.030	0.000	0.000	0.000	0.000
69	A	864	ASP	-1	-0.760	-0.856	8.525	0.038	0.038	0.000	0.000	0.000	0.000
70	A	865	ASP	-1	-0.871	-0.932	11.850	-0.006	-0.006	0.000	0.000	0.000	0.000
71	A	866	LYS	1	0.770	0.859	9.589	0.028	0.028	0.000	0.000	0.000	0.000
72	A	867	GLY	0	-0.049	-0.012	13.000	0.072	0.072	0.000	0.000	0.000	0.000
73	A	868	ALA	0	-0.006	0.012	7.462	0.064	0.064	0.000	0.000	0.000	0.000
74	A	869	THR	0	-0.031	-0.029	8.921	-0.196	-0.196	0.000	0.000	0.000	0.000
75	A	870	ALA	0	-0.017	-0.001	6.101	0.098	0.098	0.000	0.000	0.000	0.000
76	A	871	THR	0	-0.027	-0.028	7.911	0.075	0.075	0.000	0.000	0.000	0.000
77	A	872	GLU	-1	-0.873	-0.900	9.675	-0.614	-0.614	0.000	0.000	0.000	0.000
78	A	873	SER	0	-0.082	-0.061	11.996	0.081	0.081	0.000	0.000	0.000	0.000
79	A	874	PHE	0	-0.012	-0.007	15.520	-0.026	-0.026	0.000	0.000	0.000	0.000
80	A	875	THR	0	-0.005	0.002	18.523	0.020	0.020	0.000	0.000	0.000	0.000
81	A	876	ILE	0	-0.021	0.002	21.849	-0.003	-0.003	0.000	0.000	0.000	0.000
82	A	877	GLU	-1	-0.916	-0.957	25.118	-0.084	-0.084	0.000	0.000	0.000	0.000
83	A	878	ILE	0	-0.049	-0.017	28.509	0.000	0.000	0.000	0.000	0.000	0.000
84	A	879	LYS	1	0.997	0.990	31.227	0.083	0.083	0.000	0.000	0.000	0.000
85	A	880	ASN	0	0.048	0.006	34.823	-0.002	-0.002	0.000	0.000	0.000	0.000

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