FMO DATABASE

FMODB ID: LNLJ9

Calculation Name: 3DML-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3DML

Chain ID: A

ChEMBL ID:

UniProt ID: Q8KM22

Base Structure: X-ray

Registration Date: 2023-09-20

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	95
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-705194.080355
FMO2-HF: Nuclear repulsion	666895.023505
FMO2-HF: Total energy	-38299.056851
FMO2-MP2: Total energy	-38408.211114

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:2:GLU)

Summations of interaction energy for fragment #1(A:2: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.
108.093	112.47	1.77	-2.045	-4.101	0.011

Interaction energy analysis for fragmet #1(A:2:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.938 / q_NPA : -0.992

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	4	ARG	1	0.892	0.950	3.817	-41.602	-40.157	-0.015	-0.601	-0.829	0.002
4	A	5	LEU	0	0.000	0.013	6.494	-0.465	-0.465	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.012	-0.002	10.256	-1.941	-1.941	0.000	0.000	0.000	0.000
6	A	7	MET	0	-0.029	0.009	12.428	-0.344	-0.344	0.000	0.000	0.000	0.000
7	A	8	PHE	0	-0.001	-0.007	14.602	-0.645	-0.645	0.000	0.000	0.000	0.000
8	A	9	GLU	-1	-0.825	-0.960	18.699	13.487	13.487	0.000	0.000	0.000	0.000
9	A	10	GLN	0	-0.010	-0.005	21.949	-0.406	-0.406	0.000	0.000	0.000	0.000
10	A	11	PRO	0	0.008	-0.004	25.405	-0.090	-0.090	0.000	0.000	0.000	0.000
11	A	12	GLY	0	0.010	0.008	28.484	-0.134	-0.134	0.000	0.000	0.000	0.000
12	A	13	CYS	0	-0.054	0.017	26.187	-0.071	-0.071	0.000	0.000	0.000	0.000
13	A	14	LEU	0	0.040	0.013	27.562	0.208	0.208	0.000	0.000	0.000	0.000
14	A	15	TYR	0	0.007	-0.013	26.016	-0.011	-0.011	0.000	0.000	0.000	0.000
15	A	16	CYS	0	0.010	0.017	23.252	0.474	0.474	0.000	0.000	0.000	0.000
16	A	17	ALA	0	0.052	0.035	23.826	0.258	0.258	0.000	0.000	0.000	0.000
17	A	18	ARG	1	0.917	0.955	26.311	-10.501	-10.501	0.000	0.000	0.000	0.000
18	A	19	TRP	0	0.066	0.040	16.282	-0.038	-0.038	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.813	-0.917	21.256	14.424	14.424	0.000	0.000	0.000	0.000
20	A	21	ALA	0	-0.048	-0.024	22.879	0.014	0.014	0.000	0.000	0.000	0.000
21	A	22	GLU	-1	-0.903	-0.906	24.966	11.620	11.620	0.000	0.000	0.000	0.000
22	A	23	ILE	0	0.008	0.024	18.599	0.175	0.175	0.000	0.000	0.000	0.000
23	A	24	ALA	0	-0.056	-0.028	18.701	0.544	0.544	0.000	0.000	0.000	0.000
24	A	25	PRO	0	-0.029	-0.015	19.051	0.527	0.527	0.000	0.000	0.000	0.000
25	A	26	GLN	0	-0.018	-0.022	20.405	0.165	0.165	0.000	0.000	0.000	0.000
26	A	27	TYR	0	-0.026	-0.007	11.292	-0.110	-0.110	0.000	0.000	0.000	0.000
27	A	28	PRO	0	-0.013	0.005	14.109	1.182	1.182	0.000	0.000	0.000	0.000
28	A	29	LEU	0	-0.051	-0.029	15.081	0.343	0.343	0.000	0.000	0.000	0.000
29	A	30	THR	0	-0.025	-0.004	15.673	-0.205	-0.205	0.000	0.000	0.000	0.000
30	A	31	ASP	-1	-0.885	-0.965	13.448	20.802	20.802	0.000	0.000	0.000	0.000
31	A	32	GLU	-1	-0.875	-0.957	11.534	22.751	22.751	0.000	0.000	0.000	0.000
32	A	33	GLY	0	0.017	-0.010	10.774	2.250	2.250	0.000	0.000	0.000	0.000
33	A	34	ARG	1	0.818	0.906	10.552	-20.542	-20.542	0.000	0.000	0.000	0.000
34	A	35	ALA	0	-0.015	0.011	7.313	2.391	2.391	0.000	0.000	0.000	0.000
35	A	36	ALA	0	0.016	0.016	5.937	7.121	7.121	0.000	0.000	0.000	0.000
36	A	37	PRO	0	0.018	0.041	6.277	-4.718	-4.718	0.000	0.000	0.000	0.000
37	A	38	VAL	0	0.001	0.007	8.971	0.854	0.854	0.000	0.000	0.000	0.000
38	A	39	GLN	0	-0.056	-0.037	9.382	0.954	0.954	0.000	0.000	0.000	0.000
39	A	40	ARG	1	0.841	0.924	12.664	-15.443	-15.443	0.000	0.000	0.000	0.000
40	A	41	LEU	0	-0.006	-0.001	13.877	-0.068	-0.068	0.000	0.000	0.000	0.000
41	A	42	GLN	0	0.066	0.033	17.702	-0.668	-0.668	0.000	0.000	0.000	0.000
42	A	43	MET	0	-0.031	-0.017	20.864	0.166	0.166	0.000	0.000	0.000	0.000
43	A	44	ARG	1	0.833	0.892	21.998	-11.154	-11.154	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.885	-0.918	21.062	12.521	12.521	0.000	0.000	0.000	0.000
45	A	46	PRO	0	-0.057	-0.036	20.939	0.342	0.342	0.000	0.000	0.000	0.000
46	A	47	LEU	0	0.028	0.012	15.099	0.199	0.199	0.000	0.000	0.000	0.000
47	A	48	PRO	0	-0.009	-0.002	13.237	-0.500	-0.500	0.000	0.000	0.000	0.000
48	A	49	PRO	0	-0.003	-0.022	14.326	0.518	0.518	0.000	0.000	0.000	0.000
49	A	50	GLY	0	0.002	0.006	11.928	0.808	0.808	0.000	0.000	0.000	0.000
50	A	51	LEU	0	-0.018	0.006	9.065	1.742	1.742	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.921	-0.956	10.512	18.449	18.449	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.032	-0.026	11.569	1.581	1.581	0.000	0.000	0.000	0.000
53	A	54	ALA	0	0.002	0.002	14.072	-0.971	-0.971	0.000	0.000	0.000	0.000
54	A	55	ARG	1	0.841	0.918	15.763	-16.960	-16.960	0.000	0.000	0.000	0.000
55	A	56	PRO	0	0.044	0.026	18.134	0.661	0.661	0.000	0.000	0.000	0.000
56	A	57	VAL	0	0.042	0.032	17.840	0.115	0.115	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.031	-0.024	20.440	-0.373	-0.373	0.000	0.000	0.000	0.000
58	A	59	PHE	0	0.003	0.015	22.853	-0.780	-0.780	0.000	0.000	0.000	0.000
59	A	60	THR	0	0.000	0.044	22.416	0.484	0.484	0.000	0.000	0.000	0.000
60	A	61	PRO	0	0.025	-0.009	20.759	-0.706	-0.706	0.000	0.000	0.000	0.000
61	A	62	THR	0	-0.028	-0.049	17.232	-0.332	-0.332	0.000	0.000	0.000	0.000
62	A	63	PHE	0	0.003	-0.013	14.959	0.081	0.081	0.000	0.000	0.000	0.000
63	A	64	VAL	0	-0.003	-0.013	11.307	-0.245	-0.245	0.000	0.000	0.000	0.000
64	A	65	LEU	0	0.008	0.022	7.574	0.063	0.063	0.000	0.000	0.000	0.000
65	A	66	MET	0	-0.051	-0.010	6.625	-2.226	-2.226	0.000	0.000	0.000	0.000
66	A	67	ALA	0	0.084	0.039	2.891	0.095	2.066	0.271	-1.017	-1.225	0.009
67	A	68	GLY	0	0.017	0.001	2.261	-7.210	-5.785	1.434	-1.192	-1.666	0.000
68	A	69	ASP	-1	-0.976	-0.987	3.038	28.234	27.579	0.081	0.768	-0.194	0.000
69	A	70	VAL	0	0.007	-0.002	6.316	-4.733	-4.733	0.000	0.000	0.000	0.000
70	A	71	GLU	-1	-0.769	-0.862	7.474	25.179	25.179	0.000	0.000	0.000	0.000
71	A	72	SER	0	-0.045	-0.014	6.846	-2.015	-2.015	0.000	0.000	0.000	0.000
72	A	73	GLY	0	-0.013	-0.023	8.956	-2.619	-2.619	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.728	0.830	12.106	-17.784	-17.784	0.000	0.000	0.000	0.000
74	A	75	LEU	0	-0.026	0.001	14.749	-0.920	-0.920	0.000	0.000	0.000	0.000
75	A	76	GLU	-1	-0.872	-0.944	17.692	14.975	14.975	0.000	0.000	0.000	0.000
76	A	77	GLY	0	0.007	-0.002	20.860	-0.570	-0.570	0.000	0.000	0.000	0.000
77	A	78	TYR	0	-0.079	-0.093	21.993	0.885	0.885	0.000	0.000	0.000	0.000
78	A	79	PRO	0	-0.017	-0.015	23.996	-0.516	-0.516	0.000	0.000	0.000	0.000
79	A	80	GLY	0	0.039	0.029	25.076	-0.549	-0.549	0.000	0.000	0.000	0.000
80	A	81	GLU	-1	-0.870	-0.945	23.263	13.086	13.086	0.000	0.000	0.000	0.000
81	A	82	ASP	-1	-0.910	-0.959	22.547	12.849	12.849	0.000	0.000	0.000	0.000
82	A	83	PHE	0	-0.085	-0.047	23.451	0.111	0.111	0.000	0.000	0.000	0.000
83	A	84	PHE	0	0.004	-0.008	15.782	0.596	0.596	0.000	0.000	0.000	0.000
84	A	85	TRP	0	0.079	0.030	15.774	1.116	1.116	0.000	0.000	0.000	0.000
85	A	86	PRO	0	0.035	0.035	17.179	1.078	1.078	0.000	0.000	0.000	0.000
86	A	87	MET	0	-0.069	-0.042	17.674	0.380	0.380	0.000	0.000	0.000	0.000
87	A	88	LEU	0	0.015	0.014	11.748	0.906	0.906	0.000	0.000	0.000	0.000
88	A	89	ALA	0	0.054	0.031	12.991	2.092	2.092	0.000	0.000	0.000	0.000
89	A	90	ARG	1	0.885	0.950	13.158	-18.355	-18.355	0.000	0.000	0.000	0.000
90	A	91	LEU	0	-0.064	-0.027	11.337	0.743	0.743	0.000	0.000	0.000	0.000
91	A	92	ILE	0	0.035	0.005	7.764	2.263	2.263	0.000	0.000	0.000	0.000
92	A	93	GLY	0	0.018	0.015	8.484	2.879	2.879	0.000	0.000	0.000	0.000
93	A	94	GLN	0	-0.067	-0.047	10.609	-1.534	-1.534	0.000	0.000	0.000	0.000
94	A	95	ALA	0	-0.050	-0.018	5.451	-0.463	-0.463	0.000	0.000	0.000	0.000
95	A	96	GLU	-1	-0.998	-0.977	4.871	51.869	52.060	-0.001	-0.003	-0.187	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:GLU)