FMO DATABASE

FMODB ID: YZMQ2

Calculation Name: 4IDL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4IDL

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	122
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-975682.938555
FMO2-HF: Nuclear repulsion	928262.268631
FMO2-HF: Total energy	-47420.669924
FMO2-MP2: Total energy	-47558.169452

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(A:1:LYS)

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

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.
-36.795	-31.956	25.158	-13.621	-16.377	-0.16

Interaction energy analysis for fragmet #1(A:1:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.860 / q_NPA : 0.936

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	3	GLN	0	0.014	0.028	2.146	-31.082	-26.885	3.933	-3.603	-4.527	-0.034
4	A	4	LEU	0	0.028	0.010	5.276	3.980	4.071	-0.001	-0.005	-0.085	0.000
5	A	5	GLN	0	0.000	0.005	8.356	1.818	1.818	0.000	0.000	0.000	0.000
6	A	6	GLN	0	-0.002	-0.010	11.850	-1.907	-1.907	0.000	0.000	0.000	0.000
7	A	7	SER	0	0.013	0.008	14.692	1.044	1.044	0.000	0.000	0.000	0.000
8	A	8	GLY	0	0.043	0.015	18.518	-0.339	-0.339	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.004	-0.002	21.281	0.223	0.223	0.000	0.000	0.000	0.000
10	A	10	GLY	0	-0.010	-0.002	22.409	0.356	0.356	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.021	-0.020	26.093	-0.223	-0.223	0.000	0.000	0.000	0.000
12	A	12	VAL	0	-0.005	0.010	29.039	0.237	0.237	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.039	0.022	31.585	0.077	0.077	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.011	-0.052	33.376	-0.244	-0.244	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.033	-0.010	33.386	0.289	0.289	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.014	0.005	32.595	0.014	0.014	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.028	-0.061	28.872	-0.085	-0.085	0.000	0.000	0.000	0.000
18	A	18	LEU	0	-0.046	-0.021	24.503	0.055	0.055	0.000	0.000	0.000	0.000
19	A	19	LYS	1	0.885	0.933	20.588	15.228	15.228	0.000	0.000	0.000	0.000
20	A	20	LEU	0	-0.007	0.018	17.992	-0.295	-0.295	0.000	0.000	0.000	0.000
21	A	21	THR	0	0.018	0.006	17.101	0.455	0.455	0.000	0.000	0.000	0.000
22	A	22	CYS	0	-0.036	-0.005	10.875	-0.970	-0.970	0.000	0.000	0.000	0.000
23	A	23	LEU	0	0.015	0.020	12.642	0.778	0.778	0.000	0.000	0.000	0.000
24	A	24	ALA	0	0.020	0.005	8.306	-2.665	-2.665	0.000	0.000	0.000	0.000
25	A	25	SER	0	0.011	0.007	7.436	2.923	2.923	0.000	0.000	0.000	0.000
26	A	26	GLY	0	0.030	0.013	4.392	-6.310	-6.277	-0.001	-0.042	0.010	0.000
27	A	27	ASN	0	0.024	0.003	4.096	4.913	5.459	-0.001	-0.205	-0.341	0.001
28	A	28	THR	0	0.016	-0.003	5.856	-2.898	-2.898	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.044	0.027	8.637	0.325	0.325	0.000	0.000	0.000	0.000
30	A	30	SER	0	-0.075	-0.031	6.146	-1.363	-1.363	0.000	0.000	0.000	0.000
31	A	31	ILE	0	-0.014	0.004	6.824	-1.964	-1.964	0.000	0.000	0.000	0.000
32	A	32	ARG	1	0.775	0.874	8.951	32.088	32.088	0.000	0.000	0.000	0.000
33	A	33	ALA	0	0.009	0.003	9.988	3.073	3.073	0.000	0.000	0.000	0.000
34	A	34	MET	0	-0.037	-0.007	9.395	-3.386	-3.386	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.074	0.040	10.983	2.673	2.673	0.000	0.000	0.000	0.000
36	A	36	TRP	0	-0.034	-0.012	12.327	-1.550	-1.550	0.000	0.000	0.000	0.000
37	A	37	TYR	0	0.053	0.028	11.524	1.932	1.932	0.000	0.000	0.000	0.000
38	A	38	ARG	1	0.787	0.882	15.595	13.774	13.774	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.930	0.973	17.796	16.077	16.077	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.067	0.035	19.673	0.196	0.196	0.000	0.000	0.000	0.000
41	A	41	PRO	0	0.005	-0.015	23.448	-0.235	-0.235	0.000	0.000	0.000	0.000
42	A	42	GLY	0	0.004	0.010	25.239	0.277	0.277	0.000	0.000	0.000	0.000
43	A	43	LYS	1	0.815	0.917	22.475	13.111	13.111	0.000	0.000	0.000	0.000
44	A	44	GLN	0	0.015	0.005	19.012	-0.450	-0.450	0.000	0.000	0.000	0.000
45	A	45	ARG	1	0.822	0.924	10.068	26.626	26.626	0.000	0.000	0.000	0.000
46	A	46	GLU	-1	-0.746	-0.843	17.169	-13.965	-13.965	0.000	0.000	0.000	0.000
47	A	47	TRP	0	0.020	-0.012	15.095	-0.155	-0.155	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.063	-0.027	17.157	1.124	1.124	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.047	0.013	17.101	1.058	1.058	0.000	0.000	0.000	0.000
50	A	50	SER	0	0.004	0.004	14.789	-1.794	-1.794	0.000	0.000	0.000	0.000
51	A	51	LEU	0	0.031	0.033	14.677	1.271	1.271	0.000	0.000	0.000	0.000
52	A	52	THR	0	0.050	0.027	14.371	-1.797	-1.797	0.000	0.000	0.000	0.000
53	A	53	THR	0	-0.053	-0.060	12.684	0.393	0.393	0.000	0.000	0.000	0.000
54	A	54	THR	0	-0.015	-0.005	15.489	0.331	0.331	0.000	0.000	0.000	0.000
55	A	55	GLY	0	0.006	0.010	18.321	0.915	0.915	0.000	0.000	0.000	0.000
56	A	56	THR	0	-0.031	-0.009	19.253	0.418	0.418	0.000	0.000	0.000	0.000
57	A	57	ALA	0	0.005	0.001	18.681	-1.112	-1.112	0.000	0.000	0.000	0.000
58	A	58	ASP	-1	-0.897	-0.936	19.020	-14.785	-14.785	0.000	0.000	0.000	0.000
59	A	59	TYR	0	0.020	-0.015	19.724	-0.873	-0.873	0.000	0.000	0.000	0.000
60	A	60	GLY	0	0.053	0.037	21.509	0.287	0.287	0.000	0.000	0.000	0.000
61	A	61	ASP	-1	-0.858	-0.932	22.715	-12.039	-12.039	0.000	0.000	0.000	0.000
62	A	62	PHE	0	-0.042	-0.020	21.149	0.705	0.705	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.020	0.006	22.574	0.324	0.324	0.000	0.000	0.000	0.000
64	A	64	LYS	1	0.875	0.914	25.916	11.029	11.029	0.000	0.000	0.000	0.000
65	A	65	GLY	0	0.044	0.020	27.480	0.359	0.359	0.000	0.000	0.000	0.000
66	A	66	ARG	1	0.723	0.848	27.375	11.485	11.485	0.000	0.000	0.000	0.000
67	A	67	PHE	0	-0.019	-0.011	22.461	-0.146	-0.146	0.000	0.000	0.000	0.000
68	A	68	THR	0	-0.003	-0.003	23.420	0.267	0.267	0.000	0.000	0.000	0.000
69	A	69	ILE	0	-0.037	-0.003	15.289	-0.279	-0.279	0.000	0.000	0.000	0.000
70	A	70	SER	0	-0.002	-0.014	18.662	0.525	0.525	0.000	0.000	0.000	0.000
71	A	71	ARG	1	0.847	0.896	12.579	22.204	22.204	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.799	-0.868	16.428	-14.985	-14.985	0.000	0.000	0.000	0.000
73	A	73	ASN	0	0.026	-0.004	16.203	-1.450	-1.450	0.000	0.000	0.000	0.000
74	A	74	ALA	0	-0.016	0.008	16.817	-0.444	-0.444	0.000	0.000	0.000	0.000
75	A	75	ASN	0	-0.062	-0.060	17.427	-0.232	-0.232	0.000	0.000	0.000	0.000
76	A	76	ASN	0	-0.038	0.000	12.087	-2.368	-2.368	0.000	0.000	0.000	0.000
77	A	77	ALA	0	0.016	0.013	12.649	-2.027	-2.027	0.000	0.000	0.000	0.000
78	A	78	ALA	0	0.018	0.000	13.240	0.158	0.158	0.000	0.000	0.000	0.000
79	A	79	THR	0	-0.033	-0.026	14.970	0.566	0.566	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.001	0.006	17.958	-0.188	-0.188	0.000	0.000	0.000	0.000
81	A	81	GLN	0	-0.004	-0.007	19.821	-0.136	-0.136	0.000	0.000	0.000	0.000
82	A	82	MET	0	-0.043	-0.024	22.453	-0.332	-0.332	0.000	0.000	0.000	0.000
83	A	83	ASP	-1	-0.723	-0.822	25.322	-10.937	-10.937	0.000	0.000	0.000	0.000
84	A	84	SER	0	0.007	0.000	29.136	0.022	0.022	0.000	0.000	0.000	0.000
85	A	85	LEU	0	-0.015	0.010	25.711	-0.064	-0.064	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.867	0.910	29.452	11.238	11.238	0.000	0.000	0.000	0.000
87	A	87	PRO	0	0.041	0.020	29.596	-0.397	-0.397	0.000	0.000	0.000	0.000
88	A	88	GLU	-1	-0.864	-0.919	28.116	-11.226	-11.226	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.755	-0.841	25.599	-12.329	-12.329	0.000	0.000	0.000	0.000
90	A	90	THR	0	0.017	0.026	24.791	-0.564	-0.564	0.000	0.000	0.000	0.000
91	A	91	ALA	0	-0.018	-0.019	21.130	-0.039	-0.039	0.000	0.000	0.000	0.000
92	A	92	VAL	0	-0.038	0.000	17.162	0.042	0.042	0.000	0.000	0.000	0.000
93	A	93	TYR	0	0.052	-0.006	17.380	-0.486	-0.486	0.000	0.000	0.000	0.000
94	A	94	TYR	0	-0.022	-0.025	12.067	0.130	0.130	0.000	0.000	0.000	0.000
95	A	96	ASN	0	-0.043	-0.059	7.805	-0.428	-0.428	0.000	0.000	0.000	0.000
96	A	97	ALA	0	0.022	-0.002	5.509	2.969	2.969	0.000	0.000	0.000	0.000
97	A	98	ASP	-1	-0.817	-0.876	4.966	-45.464	-45.418	-0.001	-0.001	-0.044	0.000
98	A	99	GLY	0	0.077	0.013	6.198	3.818	3.818	0.000	0.000	0.000	0.000
99	A	100	ARG	1	0.884	0.936	7.095	24.209	24.209	0.000	0.000	0.000	0.000
100	A	101	ARG	1	0.960	0.994	2.958	38.392	39.167	0.094	-0.158	-0.712	0.000
101	A	102	PHE	0	0.046	0.034	6.971	0.439	0.439	0.000	0.000	0.000	0.000
102	A	103	ASP	-1	-0.861	-0.949	7.280	-26.622	-26.622	0.000	0.000	0.000	0.000
103	A	104	GLY	0	0.035	0.023	8.343	0.084	0.084	0.000	0.000	0.000	0.000
104	A	105	ALA	0	-0.007	0.002	11.157	1.418	1.418	0.000	0.000	0.000	0.000
105	A	106	ARG	1	0.879	0.931	11.934	23.427	23.427	0.000	0.000	0.000	0.000
106	A	107	TRP	0	0.043	0.026	9.796	-2.314	-2.314	0.000	0.000	0.000	0.000
107	A	108	ARG	1	0.848	0.912	7.634	28.258	28.258	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.818	-0.884	7.362	-30.465	-30.465	0.000	0.000	0.000	0.000
109	A	110	TYR	0	-0.092	-0.061	2.308	-10.573	-8.904	2.954	-1.630	-2.994	-0.021
110	A	111	GLU	-1	-0.695	-0.825	3.706	-33.837	-33.359	0.002	-0.207	-0.273	-0.001
111	A	112	SER	0	-0.095	-0.064	1.791	-68.966	-72.281	18.122	-7.694	-7.112	-0.103
112	A	113	TRP	0	0.011	-0.014	3.258	13.150	13.469	0.057	-0.076	-0.299	-0.002
113	A	114	GLY	0	0.025	0.028	6.871	-1.841	-1.841	0.000	0.000	0.000	0.000
114	A	115	GLN	0	0.000	-0.017	9.850	-0.933	-0.933	0.000	0.000	0.000	0.000
115	A	116	GLY	0	0.014	0.013	12.250	1.235	1.235	0.000	0.000	0.000	0.000
116	A	117	THR	0	-0.072	-0.029	15.143	0.214	0.214	0.000	0.000	0.000	0.000
117	A	118	GLN	0	-0.016	0.006	18.200	0.480	0.480	0.000	0.000	0.000	0.000
118	A	119	VAL	0	0.062	0.042	21.542	0.169	0.169	0.000	0.000	0.000	0.000
119	A	120	THR	0	-0.046	-0.037	23.973	0.051	0.051	0.000	0.000	0.000	0.000
120	A	121	ILE	0	0.014	0.020	26.937	0.124	0.124	0.000	0.000	0.000	0.000
121	A	122	SER	0	0.041	0.028	30.485	-0.025	-0.025	0.000	0.000	0.000	0.000
122	A	123	SER	0	0.021	0.028	34.120	-0.042	-0.042	0.000	0.000	0.000	0.000

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