FMO DATABASE

FMODB ID: LJ3J9

Calculation Name: 3OL4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3OL4

Chain ID: A

ChEMBL ID:

UniProt ID: A0QRC4

Base Structure: X-ray

Registration Date: 2023-06-19

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	OptAll
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	96
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-634637.96183
FMO2-HF: Nuclear repulsion	598106.110456
FMO2-HF: Total energy	-36531.851374
FMO2-MP2: Total energy	-36640.401734

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:5:THR)

Summations of interaction energy for fragment #1(A:5:THR)

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.
-4.435	-0.79	0.344	-1.466	-2.521	0.007

Interaction energy analysis for fragmet #1(A:5:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.007 / q_NPA : -0.001

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	7	THR	0	0.093	0.057	3.006	-2.082	0.424	0.297	-1.146	-1.656	0.007
4	A	8	PHE	0	0.021	0.026	3.262	-1.886	-0.975	0.048	-0.267	-0.691	0.000
5	A	9	MET	0	-0.002	-0.005	4.518	-0.953	-0.725	-0.001	-0.053	-0.174	0.000
6	A	10	ASP	-1	-0.874	-0.949	6.485	0.903	0.903	0.000	0.000	0.000	0.000
7	A	11	ASN	0	-0.044	-0.028	8.015	-0.506	-0.506	0.000	0.000	0.000	0.000
8	A	12	VAL	0	-0.004	0.003	8.689	-0.242	-0.242	0.000	0.000	0.000	0.000
9	A	13	LEU	0	-0.013	-0.012	10.257	-0.171	-0.171	0.000	0.000	0.000	0.000
10	A	14	GLY	0	0.013	0.009	11.980	-0.121	-0.121	0.000	0.000	0.000	0.000
11	A	15	TRP	0	-0.024	-0.018	13.448	-0.094	-0.094	0.000	0.000	0.000	0.000
12	A	16	LEU	0	-0.010	-0.010	14.538	-0.074	-0.074	0.000	0.000	0.000	0.000
13	A	17	HIS	0	0.022	0.000	15.808	-0.074	-0.074	0.000	0.000	0.000	0.000
14	A	18	LYS	1	0.922	0.969	17.819	-0.366	-0.366	0.000	0.000	0.000	0.000
15	A	19	GLY	0	-0.040	-0.010	19.188	-0.033	-0.033	0.000	0.000	0.000	0.000
16	A	20	TYR	0	-0.064	-0.066	20.073	-0.028	-0.028	0.000	0.000	0.000	0.000
17	A	21	PRO	0	0.009	0.010	21.937	0.002	0.002	0.000	0.000	0.000	0.000
18	A	22	GLU	-1	-0.958	-0.970	23.181	0.164	0.164	0.000	0.000	0.000	0.000
19	A	23	GLY	0	-0.017	0.003	22.583	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	24	VAL	0	-0.018	-0.009	19.822	-0.005	-0.005	0.000	0.000	0.000	0.000
21	A	25	PRO	0	-0.005	0.011	23.205	-0.014	-0.014	0.000	0.000	0.000	0.000
22	A	26	PRO	0	0.051	-0.014	25.838	0.007	0.007	0.000	0.000	0.000	0.000
23	A	27	LYS	1	0.821	0.898	26.905	-0.176	-0.176	0.000	0.000	0.000	0.000
24	A	28	ASP	-1	-0.765	-0.841	23.742	0.197	0.197	0.000	0.000	0.000	0.000
25	A	29	TYR	0	-0.026	-0.010	22.140	0.014	0.014	0.000	0.000	0.000	0.000
26	A	30	PHE	0	0.022	0.015	21.652	0.016	0.016	0.000	0.000	0.000	0.000
27	A	31	ALA	0	0.032	0.013	22.117	0.009	0.009	0.000	0.000	0.000	0.000
28	A	32	LEU	0	0.023	0.014	16.547	0.018	0.018	0.000	0.000	0.000	0.000
29	A	33	LEU	0	-0.004	-0.010	17.389	0.039	0.039	0.000	0.000	0.000	0.000
30	A	34	ALA	0	-0.001	-0.006	17.639	0.015	0.015	0.000	0.000	0.000	0.000
31	A	35	LEU	0	-0.024	-0.007	16.108	0.001	0.001	0.000	0.000	0.000	0.000
32	A	36	LEU	0	-0.014	-0.018	12.198	0.040	0.040	0.000	0.000	0.000	0.000
33	A	37	LYS	1	0.865	0.934	13.246	-0.284	-0.284	0.000	0.000	0.000	0.000
34	A	38	ARG	1	0.735	0.841	15.724	-0.391	-0.391	0.000	0.000	0.000	0.000
35	A	39	SER	0	0.002	-0.005	14.859	0.056	0.056	0.000	0.000	0.000	0.000
36	A	40	LEU	0	-0.021	0.002	16.194	-0.032	-0.032	0.000	0.000	0.000	0.000
37	A	41	THR	0	-0.010	-0.039	18.422	-0.019	-0.019	0.000	0.000	0.000	0.000
38	A	42	GLU	-1	-0.754	-0.849	19.963	0.059	0.059	0.000	0.000	0.000	0.000
39	A	43	ASP	-1	-0.900	-0.950	21.350	0.076	0.076	0.000	0.000	0.000	0.000
40	A	44	GLU	-1	-0.849	-0.902	21.055	0.177	0.177	0.000	0.000	0.000	0.000
41	A	45	VAL	0	0.021	0.010	16.641	0.013	0.013	0.000	0.000	0.000	0.000
42	A	46	VAL	0	-0.029	-0.014	19.017	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	47	ARG	1	0.879	0.954	21.819	-0.137	-0.137	0.000	0.000	0.000	0.000
44	A	48	ALA	0	0.039	0.008	18.600	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	49	ALA	0	0.033	0.014	18.262	0.001	0.001	0.000	0.000	0.000	0.000
46	A	50	GLN	0	0.008	0.013	19.637	-0.004	-0.004	0.000	0.000	0.000	0.000
47	A	51	ALA	0	-0.013	-0.012	22.539	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	52	ILE	0	0.055	0.043	17.206	-0.004	-0.004	0.000	0.000	0.000	0.000
49	A	53	LEU	0	-0.011	0.010	20.155	-0.010	-0.010	0.000	0.000	0.000	0.000
50	A	54	ARG	1	0.826	0.909	22.819	-0.095	-0.095	0.000	0.000	0.000	0.000
51	A	55	SER	0	-0.082	-0.054	23.960	0.000	0.000	0.000	0.000	0.000	0.000
52	A	56	THR	0	-0.008	-0.004	20.484	0.005	0.005	0.000	0.000	0.000	0.000
53	A	57	ASP	-1	-0.810	-0.917	23.354	0.043	0.043	0.000	0.000	0.000	0.000
54	A	58	GLY	0	-0.013	0.002	20.473	-0.014	-0.014	0.000	0.000	0.000	0.000
55	A	59	GLN	0	-0.078	-0.057	20.850	-0.014	-0.014	0.000	0.000	0.000	0.000
56	A	60	SER	0	-0.026	-0.004	20.926	0.003	0.003	0.000	0.000	0.000	0.000
57	A	61	PRO	0	-0.077	-0.037	15.806	0.007	0.007	0.000	0.000	0.000	0.000
58	A	62	VAL	0	0.019	0.019	15.484	0.031	0.031	0.000	0.000	0.000	0.000
59	A	63	THR	0	-0.007	-0.036	13.527	0.046	0.046	0.000	0.000	0.000	0.000
60	A	64	ASP	-1	-0.864	-0.951	9.344	1.079	1.079	0.000	0.000	0.000	0.000
61	A	65	ASP	-1	-0.822	-0.907	12.696	0.450	0.450	0.000	0.000	0.000	0.000
62	A	66	ASP	-1	-0.861	-0.885	16.260	0.210	0.210	0.000	0.000	0.000	0.000
63	A	67	ILE	0	-0.020	-0.010	12.386	-0.034	-0.034	0.000	0.000	0.000	0.000
64	A	68	ARG	1	0.797	0.877	14.086	-0.588	-0.588	0.000	0.000	0.000	0.000
65	A	69	ASN	0	-0.051	-0.040	17.111	-0.045	-0.045	0.000	0.000	0.000	0.000
66	A	70	ALA	0	0.008	0.010	19.119	-0.022	-0.022	0.000	0.000	0.000	0.000
67	A	71	VAL	0	0.022	0.002	16.320	-0.025	-0.025	0.000	0.000	0.000	0.000
68	A	72	HIS	0	0.002	0.009	19.579	-0.029	-0.029	0.000	0.000	0.000	0.000
69	A	73	GLN	0	-0.039	-0.014	21.782	-0.017	-0.017	0.000	0.000	0.000	0.000
70	A	74	ILE	0	-0.095	-0.043	21.336	-0.024	-0.024	0.000	0.000	0.000	0.000
71	A	75	ILE	0	-0.025	-0.011	19.211	-0.017	-0.017	0.000	0.000	0.000	0.000
72	A	76	GLU	-1	-0.918	-0.943	23.493	0.142	0.142	0.000	0.000	0.000	0.000
73	A	77	LYS	1	0.804	0.886	21.195	-0.224	-0.224	0.000	0.000	0.000	0.000
74	A	78	GLU	-1	-0.799	-0.885	17.436	0.438	0.438	0.000	0.000	0.000	0.000
75	A	79	PRO	0	0.003	0.013	15.675	0.002	0.002	0.000	0.000	0.000	0.000
76	A	80	THR	0	-0.034	-0.008	13.156	0.066	0.066	0.000	0.000	0.000	0.000
77	A	81	ALA	0	0.041	0.009	8.253	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	82	GLU	-1	-0.872	-0.931	9.480	0.612	0.612	0.000	0.000	0.000	0.000
79	A	83	GLU	-1	-0.744	-0.838	10.617	0.299	0.299	0.000	0.000	0.000	0.000
80	A	84	ILE	0	0.004	0.008	10.280	-0.068	-0.068	0.000	0.000	0.000	0.000
81	A	85	ASN	0	-0.039	-0.032	7.233	-0.088	-0.088	0.000	0.000	0.000	0.000
82	A	86	GLN	0	0.011	0.005	9.373	-0.127	-0.127	0.000	0.000	0.000	0.000
83	A	87	VAL	0	0.002	0.004	12.490	-0.087	-0.087	0.000	0.000	0.000	0.000
84	A	88	ALA	0	0.041	0.025	9.432	-0.065	-0.065	0.000	0.000	0.000	0.000
85	A	89	ALA	0	0.008	0.000	9.884	-0.113	-0.113	0.000	0.000	0.000	0.000
86	A	90	ARG	1	0.777	0.860	11.260	-0.102	-0.102	0.000	0.000	0.000	0.000
87	A	91	LEU	0	0.031	0.018	14.080	-0.038	-0.038	0.000	0.000	0.000	0.000
88	A	92	ALA	0	0.031	0.020	11.464	-0.034	-0.034	0.000	0.000	0.000	0.000
89	A	93	SER	0	-0.131	-0.075	13.537	-0.036	-0.036	0.000	0.000	0.000	0.000
90	A	94	VAL	0	-0.054	-0.028	15.924	-0.003	-0.003	0.000	0.000	0.000	0.000
91	A	95	GLY	0	-0.024	-0.010	16.692	0.007	0.007	0.000	0.000	0.000	0.000
92	A	96	TRP	0	-0.046	-0.025	16.896	-0.012	-0.012	0.000	0.000	0.000	0.000
93	A	97	PRO	0	-0.007	-0.003	15.397	0.002	0.002	0.000	0.000	0.000	0.000
94	A	98	LEU	0	0.001	0.010	10.597	0.041	0.041	0.000	0.000	0.000	0.000
95	A	99	ALA	0	-0.032	-0.021	12.970	-0.051	-0.051	0.000	0.000	0.000	0.000
96	A	100	VAL	0	-0.048	-0.012	6.548	-0.013	-0.013	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:5:THR)