FMO DATABASE

FMODB ID: G73Y1

Calculation Name: 1NQJ-B-Xray549

Preferred Name: Collagenase

Target Type: SINGLE PROTEIN

Ligand Name: lithium ion

Ligand 3-letter code: LI

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1NQJ

Chain ID: B

ChEMBL ID: CHEMBL2268009

UniProt ID: Q9X721

Base Structure: X-ray

Registration Date: 2025-10-11

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	114
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-948045.267184
FMO2-HF: Nuclear repulsion	902497.990718
FMO2-HF: Total energy	-45547.276466
FMO2-MP2: Total energy	-45682.2777

3D Structure Molmil

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(B:895:GLU)

Summations of interaction energy for fragment #1(B:895:GLU)

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.
-44.243	-31.462	14.302	-11.615	-15.466	0.013

Interaction energy analysis for fragmet #1(B:895:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.032 / q_NPA : -0.022

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	B	897	LEU	0	0.037	0.018	3.010	4.068	6.498	0.152	-1.204	-1.377	-0.004
5	B	899	GLU	-1	-0.953	-0.964	2.465	-23.606	-17.466	4.221	-5.070	-5.291	-0.046
6	B	900	LYS	1	0.956	0.981	2.250	-26.941	-24.161	8.849	-4.354	-7.275	0.050
7	B	901	GLU	-1	-0.851	-0.929	4.006	0.975	1.299	0.016	-0.175	-0.164	0.001
9	B	903	ASN	0	-0.017	-0.002	2.396	-12.770	-11.663	1.064	-0.812	-1.359	0.012
4	B	898	LYS	1	0.948	0.966	5.509	1.757	1.757	0.000	0.000	0.000	0.000
8	B	902	ASN	0	-0.040	-0.026	7.157	-1.046	-1.046	0.000	0.000	0.000	0.000
10	B	904	ASP	-1	-0.866	-0.932	6.367	10.853	10.853	0.000	0.000	0.000	0.000
11	B	905	SER	0	-0.103	-0.075	8.615	-2.081	-2.081	0.000	0.000	0.000	0.000
12	B	906	SER	0	-0.051	-0.038	9.599	-1.402	-1.402	0.000	0.000	0.000	0.000
13	B	907	ASP	-1	-0.934	-0.955	8.951	9.224	9.224	0.000	0.000	0.000	0.000
14	B	908	LYS	1	0.837	0.925	11.675	-5.364	-5.364	0.000	0.000	0.000	0.000
15	B	909	ALA	0	-0.044	-0.005	14.144	-0.625	-0.625	0.000	0.000	0.000	0.000
16	B	910	THR	0	0.019	0.011	16.132	-0.052	-0.052	0.000	0.000	0.000	0.000
17	B	911	VAL	0	-0.026	-0.021	17.537	-0.108	-0.108	0.000	0.000	0.000	0.000
18	B	912	ILE	0	0.001	-0.007	19.878	-0.136	-0.136	0.000	0.000	0.000	0.000
19	B	913	PRO	0	-0.049	-0.018	23.149	-0.048	-0.048	0.000	0.000	0.000	0.000
20	B	914	ASN	0	-0.024	-0.022	24.573	-0.123	-0.123	0.000	0.000	0.000	0.000
21	B	915	PHE	0	0.038	0.017	24.510	0.038	0.038	0.000	0.000	0.000	0.000
22	B	916	ASN	0	-0.052	-0.056	28.537	-0.010	-0.010	0.000	0.000	0.000	0.000
23	B	917	THR	0	0.006	0.015	28.358	-0.040	-0.040	0.000	0.000	0.000	0.000
24	B	918	THR	0	-0.030	-0.015	29.679	0.015	0.015	0.000	0.000	0.000	0.000
25	B	919	MET	0	-0.011	0.013	24.075	-0.013	-0.013	0.000	0.000	0.000	0.000
26	B	920	GLN	0	-0.028	-0.038	28.646	-0.061	-0.061	0.000	0.000	0.000	0.000
27	B	921	GLY	0	0.045	0.028	27.873	0.110	0.110	0.000	0.000	0.000	0.000
28	B	922	SER	0	-0.033	-0.025	27.953	-0.128	-0.128	0.000	0.000	0.000	0.000
29	B	923	LEU	0	0.000	0.035	25.533	0.071	0.071	0.000	0.000	0.000	0.000
30	B	924	LEU	0	0.012	-0.008	28.909	-0.110	-0.110	0.000	0.000	0.000	0.000
31	B	925	GLY	0	0.019	0.011	29.902	0.068	0.068	0.000	0.000	0.000	0.000
32	B	926	ASP	-1	-0.923	-0.960	27.231	1.543	1.543	0.000	0.000	0.000	0.000
33	B	927	ASP	-1	-0.862	-0.919	24.764	1.967	1.967	0.000	0.000	0.000	0.000
34	B	928	SER	0	-0.027	-0.027	24.595	-0.082	-0.082	0.000	0.000	0.000	0.000
35	B	929	ARG	1	0.864	0.919	19.236	-2.460	-2.460	0.000	0.000	0.000	0.000
36	B	930	ASP	-1	-0.690	-0.777	21.712	1.911	1.911	0.000	0.000	0.000	0.000
37	B	931	TYR	0	-0.006	-0.031	16.836	0.118	0.118	0.000	0.000	0.000	0.000
38	B	932	TYR	0	0.007	0.002	19.042	0.033	0.033	0.000	0.000	0.000	0.000
39	B	933	SER	0	-0.011	-0.010	16.026	0.178	0.178	0.000	0.000	0.000	0.000
40	B	934	PHE	0	0.022	0.011	18.139	-0.139	-0.139	0.000	0.000	0.000	0.000
41	B	935	GLU	-1	-0.883	-0.950	17.099	1.513	1.513	0.000	0.000	0.000	0.000
42	B	936	VAL	0	-0.050	-0.013	20.591	-0.088	-0.088	0.000	0.000	0.000	0.000
43	B	937	LYS	1	0.983	0.984	22.281	-0.663	-0.663	0.000	0.000	0.000	0.000
44	B	938	GLU	-1	-0.910	-0.953	24.626	0.129	0.129	0.000	0.000	0.000	0.000
45	B	939	GLU	-1	-0.836	-0.904	27.060	-0.019	-0.019	0.000	0.000	0.000	0.000
46	B	940	GLY	0	-0.009	-0.008	27.905	-0.019	-0.019	0.000	0.000	0.000	0.000
47	B	941	GLU	-1	-0.938	-0.976	28.982	0.358	0.358	0.000	0.000	0.000	0.000
48	B	942	VAL	0	0.020	0.018	26.359	0.022	0.022	0.000	0.000	0.000	0.000
49	B	943	ASN	0	-0.013	-0.018	29.730	-0.038	-0.038	0.000	0.000	0.000	0.000
50	B	944	ILE	0	0.005	0.016	24.989	0.033	0.033	0.000	0.000	0.000	0.000
51	B	945	GLU	-1	-0.846	-0.930	28.971	0.555	0.555	0.000	0.000	0.000	0.000
52	B	946	LEU	0	-0.005	0.014	28.596	0.050	0.050	0.000	0.000	0.000	0.000
53	B	947	ASP	-1	-0.858	-0.936	31.406	0.607	0.607	0.000	0.000	0.000	0.000
54	B	948	LYS	1	0.807	0.899	34.264	-0.674	-0.674	0.000	0.000	0.000	0.000
55	B	949	LYS	1	0.734	0.847	35.374	-0.786	-0.786	0.000	0.000	0.000	0.000
56	B	950	ASP	-1	-0.788	-0.879	36.787	0.782	0.782	0.000	0.000	0.000	0.000
57	B	951	GLU	-1	-0.864	-0.927	37.014	0.700	0.700	0.000	0.000	0.000	0.000
58	B	952	PHE	0	-0.032	-0.009	30.697	0.016	0.016	0.000	0.000	0.000	0.000
59	B	953	GLY	0	0.033	0.019	33.978	-0.016	-0.016	0.000	0.000	0.000	0.000
60	B	954	VAL	0	0.019	0.016	28.856	0.070	0.070	0.000	0.000	0.000	0.000
61	B	955	THR	0	-0.004	-0.015	27.503	-0.083	-0.083	0.000	0.000	0.000	0.000
62	B	956	TRP	0	0.006	0.013	24.812	0.131	0.131	0.000	0.000	0.000	0.000
63	B	957	THR	0	-0.063	-0.053	21.402	-0.132	-0.132	0.000	0.000	0.000	0.000
64	B	958	LEU	0	-0.014	0.015	20.902	0.188	0.188	0.000	0.000	0.000	0.000
65	B	959	HIS	0	0.013	-0.009	13.319	-0.037	-0.037	0.000	0.000	0.000	0.000
66	B	960	PRO	0	-0.007	-0.007	16.428	0.183	0.183	0.000	0.000	0.000	0.000
67	B	961	GLU	-1	-0.837	-0.916	11.349	2.718	2.718	0.000	0.000	0.000	0.000
68	B	962	SER	0	-0.061	-0.023	11.877	-0.272	-0.272	0.000	0.000	0.000	0.000
69	B	963	ASN	0	0.020	0.011	8.921	0.504	0.504	0.000	0.000	0.000	0.000
70	B	964	ILE	0	0.017	0.011	12.626	-0.464	-0.464	0.000	0.000	0.000	0.000
71	B	965	ASN	0	-0.032	-0.027	16.288	0.055	0.055	0.000	0.000	0.000	0.000
72	B	966	ASP	-1	-0.807	-0.904	14.231	0.046	0.046	0.000	0.000	0.000	0.000
73	B	967	ARG	1	0.876	0.935	17.148	0.304	0.304	0.000	0.000	0.000	0.000
74	B	968	ILE	0	0.053	0.031	19.152	0.073	0.073	0.000	0.000	0.000	0.000
75	B	969	THR	0	-0.070	-0.042	21.576	-0.156	-0.156	0.000	0.000	0.000	0.000
76	B	970	TYR	0	0.018	0.015	24.444	0.085	0.085	0.000	0.000	0.000	0.000
77	B	971	GLY	0	0.036	0.025	27.043	-0.071	-0.071	0.000	0.000	0.000	0.000
78	B	972	GLN	0	-0.064	-0.043	29.394	-0.035	-0.035	0.000	0.000	0.000	0.000
79	B	973	VAL	0	-0.012	-0.015	33.077	0.011	0.011	0.000	0.000	0.000	0.000
80	B	974	ASP	-1	-0.922	-0.949	35.292	0.409	0.409	0.000	0.000	0.000	0.000
81	B	975	GLY	0	0.022	0.008	38.696	0.005	0.005	0.000	0.000	0.000	0.000
82	B	976	ASN	0	0.021	-0.002	37.935	0.035	0.035	0.000	0.000	0.000	0.000
83	B	977	LYS	1	0.847	0.938	35.796	-0.574	-0.574	0.000	0.000	0.000	0.000
84	B	978	VAL	0	0.022	0.009	30.816	-0.010	-0.010	0.000	0.000	0.000	0.000
85	B	979	SER	0	-0.002	0.014	31.420	0.056	0.056	0.000	0.000	0.000	0.000
86	B	980	ASN	0	-0.005	-0.016	29.608	-0.072	-0.072	0.000	0.000	0.000	0.000
87	B	981	LYS	1	0.886	0.969	30.835	-0.391	-0.391	0.000	0.000	0.000	0.000
88	B	982	VAL	0	0.026	0.013	26.141	-0.039	-0.039	0.000	0.000	0.000	0.000
89	B	983	LYS	1	0.834	0.913	28.087	-0.035	-0.035	0.000	0.000	0.000	0.000
90	B	984	LEU	0	-0.002	0.014	23.158	-0.050	-0.050	0.000	0.000	0.000	0.000
91	B	985	ARG	1	0.889	0.921	22.668	0.093	0.093	0.000	0.000	0.000	0.000
92	B	986	PRO	0	0.018	0.002	22.222	0.104	0.104	0.000	0.000	0.000	0.000
93	B	987	GLY	0	0.007	0.017	18.244	-0.143	-0.143	0.000	0.000	0.000	0.000
94	B	988	LYS	1	0.925	0.989	12.206	-3.547	-3.547	0.000	0.000	0.000	0.000
95	B	989	TYR	0	-0.065	-0.056	16.753	-0.156	-0.156	0.000	0.000	0.000	0.000
96	B	990	TYR	0	0.046	0.017	11.176	0.338	0.338	0.000	0.000	0.000	0.000
97	B	991	LEU	0	-0.036	-0.022	16.975	-0.282	-0.282	0.000	0.000	0.000	0.000
98	B	992	LEU	0	0.004	0.019	18.730	0.151	0.151	0.000	0.000	0.000	0.000
99	B	993	VAL	0	0.021	-0.001	20.733	-0.231	-0.231	0.000	0.000	0.000	0.000
100	B	994	TYR	0	-0.027	-0.018	23.449	0.118	0.118	0.000	0.000	0.000	0.000
101	B	995	LYS	1	0.794	0.891	25.445	-1.384	-1.384	0.000	0.000	0.000	0.000
102	B	996	TYR	0	-0.036	-0.007	28.069	0.036	0.036	0.000	0.000	0.000	0.000
103	B	997	SER	0	-0.030	-0.020	30.522	-0.060	-0.060	0.000	0.000	0.000	0.000
104	B	998	GLY	0	0.049	0.025	33.373	0.013	0.013	0.000	0.000	0.000	0.000
105	B	999	SER	0	-0.035	-0.043	32.694	0.097	0.097	0.000	0.000	0.000	0.000
106	B	1000	GLY	0	0.019	0.024	32.668	-0.073	-0.073	0.000	0.000	0.000	0.000
107	B	1001	ASN	0	-0.034	-0.035	32.168	0.137	0.137	0.000	0.000	0.000	0.000
108	B	1002	TYR	0	-0.082	-0.091	25.929	-0.075	-0.075	0.000	0.000	0.000	0.000
109	B	1003	GLU	-1	-0.795	-0.856	31.552	0.832	0.832	0.000	0.000	0.000	0.000
110	B	1004	LEU	0	-0.016	-0.014	24.989	-0.031	-0.031	0.000	0.000	0.000	0.000
111	B	1005	ARG	1	0.822	0.913	29.435	-0.697	-0.697	0.000	0.000	0.000	0.000
112	B	1006	VAL	0	0.038	0.026	24.709	-0.025	-0.025	0.000	0.000	0.000	0.000
113	B	1007	ASN	0	-0.014	-0.021	28.152	-0.018	-0.018	0.000	0.000	0.000	0.000
114	B	1008	LYS	0	0.053	0.063	27.449	0.062	0.062	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:895:GLU)