FMO DATABASE

FMODB ID: K9Y53

Calculation Name: 5L33-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5L33

Chain ID: A

ChEMBL ID:

UniProt ID:

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	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	106
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-928097.675541
FMO2-HF: Nuclear repulsion	883578.460129
FMO2-HF: Total energy	-44519.215412
FMO2-MP2: Total energy	-44649.518385

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:-1:HIS)

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

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.
-4.775	-0.199	0.283	-1.954	-2.904	0.003

Interaction energy analysis for fragmet #1(A:-1:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.015

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	1	PRO	0	-0.004	0.005	3.425	-4.289	0.132	0.284	-1.946	-2.759	0.003
4	A	2	GLU	-1	-0.912	-0.972	4.704	-1.148	-0.993	-0.001	-0.008	-0.145	0.000
5	A	3	GLU	-1	-0.838	-0.898	6.454	-0.646	-0.646	0.000	0.000	0.000	0.000
6	A	4	GLU	-1	-0.791	-0.885	8.133	-1.172	-1.172	0.000	0.000	0.000	0.000
7	A	5	LYS	1	0.961	0.973	5.153	0.165	0.165	0.000	0.000	0.000	0.000
8	A	6	ALA	0	0.008	0.008	8.321	0.232	0.232	0.000	0.000	0.000	0.000
9	A	7	ALA	0	0.019	0.002	11.173	0.127	0.127	0.000	0.000	0.000	0.000
10	A	8	ARG	1	0.962	0.971	9.067	0.057	0.057	0.000	0.000	0.000	0.000
11	A	9	LEU	0	-0.022	-0.009	10.063	0.115	0.115	0.000	0.000	0.000	0.000
12	A	10	PHE	0	0.026	0.014	13.525	0.025	0.025	0.000	0.000	0.000	0.000
13	A	11	ILE	0	-0.011	-0.012	15.342	0.020	0.020	0.000	0.000	0.000	0.000
14	A	12	GLU	-1	-0.842	-0.899	13.560	0.538	0.538	0.000	0.000	0.000	0.000
15	A	13	ALA	0	-0.018	-0.010	16.238	0.025	0.025	0.000	0.000	0.000	0.000
16	A	14	LEU	0	-0.040	-0.016	19.130	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	15	GLU	-1	-0.861	-0.926	16.009	0.181	0.181	0.000	0.000	0.000	0.000
18	A	16	LYS	1	0.793	0.882	16.286	-0.454	-0.454	0.000	0.000	0.000	0.000
19	A	17	GLY	0	0.049	0.041	21.005	0.000	0.000	0.000	0.000	0.000	0.000
20	A	18	ASP	-1	-0.859	-0.942	21.038	0.225	0.225	0.000	0.000	0.000	0.000
21	A	19	PRO	0	-0.020	-0.022	21.963	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	20	GLU	-1	-0.819	-0.887	22.351	0.066	0.066	0.000	0.000	0.000	0.000
23	A	21	LEU	0	-0.007	0.006	15.021	-0.010	-0.010	0.000	0.000	0.000	0.000
24	A	22	MET	0	0.012	0.005	18.064	-0.041	-0.041	0.000	0.000	0.000	0.000
25	A	23	ARG	1	0.772	0.867	19.775	-0.080	-0.080	0.000	0.000	0.000	0.000
26	A	24	LYS	1	0.872	0.935	16.373	-0.118	-0.118	0.000	0.000	0.000	0.000
27	A	25	VAL	0	-0.023	0.004	14.386	-0.043	-0.043	0.000	0.000	0.000	0.000
28	A	26	ILE	0	-0.027	0.000	16.342	-0.087	-0.087	0.000	0.000	0.000	0.000
29	A	27	SER	0	-0.025	-0.018	18.621	-0.020	-0.020	0.000	0.000	0.000	0.000
30	A	28	PRO	0	0.004	-0.014	20.877	0.009	0.009	0.000	0.000	0.000	0.000
31	A	29	ASP	-1	-0.820	-0.892	22.560	-0.321	-0.321	0.000	0.000	0.000	0.000
32	A	30	THR	0	-0.031	-0.020	20.413	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	31	ARG	1	0.827	0.904	22.959	0.211	0.211	0.000	0.000	0.000	0.000
34	A	32	MET	0	-0.017	-0.005	24.497	-0.026	-0.026	0.000	0.000	0.000	0.000
35	A	33	GLU	-1	-0.865	-0.928	26.061	-0.143	-0.143	0.000	0.000	0.000	0.000
36	A	34	ASP	-1	-0.728	-0.837	28.007	-0.077	-0.077	0.000	0.000	0.000	0.000
37	A	35	ASN	0	0.007	-0.007	30.106	0.003	0.003	0.000	0.000	0.000	0.000
38	A	36	GLY	0	-0.034	-0.014	33.040	0.010	0.010	0.000	0.000	0.000	0.000
39	A	37	ARG	1	0.841	0.928	32.048	0.051	0.051	0.000	0.000	0.000	0.000
40	A	38	GLU	-1	-0.831	-0.908	30.943	-0.172	-0.172	0.000	0.000	0.000	0.000
41	A	39	PHE	0	-0.028	-0.018	27.913	0.016	0.016	0.000	0.000	0.000	0.000
42	A	40	THR	0	-0.079	-0.057	27.141	-0.026	-0.026	0.000	0.000	0.000	0.000
43	A	41	GLY	0	0.061	0.031	25.005	0.016	0.016	0.000	0.000	0.000	0.000
44	A	42	ASP	-1	-0.874	-0.965	25.656	-0.039	-0.039	0.000	0.000	0.000	0.000
45	A	43	GLU	-1	-0.826	-0.887	27.178	-0.081	-0.081	0.000	0.000	0.000	0.000
46	A	44	VAL	0	-0.013	-0.013	22.843	0.010	0.010	0.000	0.000	0.000	0.000
47	A	45	VAL	0	-0.010	-0.004	23.462	0.016	0.016	0.000	0.000	0.000	0.000
48	A	46	GLU	-1	-0.875	-0.926	25.679	0.012	0.012	0.000	0.000	0.000	0.000
49	A	47	TYR	0	-0.055	-0.049	26.454	0.013	0.013	0.000	0.000	0.000	0.000
50	A	48	VAL	0	0.014	0.002	23.068	0.009	0.009	0.000	0.000	0.000	0.000
51	A	49	LYS	1	0.854	0.915	26.460	0.000	0.000	0.000	0.000	0.000	0.000
52	A	50	GLU	-1	-0.808	-0.896	29.216	0.027	0.027	0.000	0.000	0.000	0.000
53	A	51	ILE	0	-0.060	-0.011	25.430	0.002	0.002	0.000	0.000	0.000	0.000
54	A	52	GLN	0	-0.029	-0.017	26.253	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	53	LYS	1	0.753	0.873	29.031	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	54	ARG	1	0.727	0.824	30.207	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	55	GLY	0	0.038	0.039	30.318	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	56	GLU	-1	-0.834	-0.873	27.992	0.010	0.010	0.000	0.000	0.000	0.000
59	A	57	GLN	0	-0.016	-0.015	24.013	0.011	0.011	0.000	0.000	0.000	0.000
60	A	58	TRP	0	-0.002	-0.008	22.019	-0.031	-0.031	0.000	0.000	0.000	0.000
61	A	59	HIS	0	0.018	0.010	19.823	0.050	0.050	0.000	0.000	0.000	0.000
62	A	60	LEU	0	-0.041	-0.016	13.578	-0.054	-0.054	0.000	0.000	0.000	0.000
63	A	61	ARG	1	0.745	0.867	17.331	0.081	0.081	0.000	0.000	0.000	0.000
64	A	62	ARG	1	0.826	0.883	15.537	0.136	0.136	0.000	0.000	0.000	0.000
65	A	63	TYR	0	-0.032	-0.033	9.119	0.122	0.122	0.000	0.000	0.000	0.000
66	A	64	THR	0	-0.020	-0.018	14.669	-0.035	-0.035	0.000	0.000	0.000	0.000
67	A	65	LYS	1	0.830	0.918	13.515	1.069	1.069	0.000	0.000	0.000	0.000
68	A	66	GLU	-1	-0.824	-0.881	16.219	-0.403	-0.403	0.000	0.000	0.000	0.000
69	A	67	GLY	0	0.020	0.011	19.965	0.023	0.023	0.000	0.000	0.000	0.000
70	A	68	ASN	0	-0.028	-0.043	16.587	-0.152	-0.152	0.000	0.000	0.000	0.000
71	A	69	SER	0	-0.060	-0.016	18.080	0.011	0.011	0.000	0.000	0.000	0.000
72	A	70	TRP	0	-0.014	-0.027	10.873	0.011	0.011	0.000	0.000	0.000	0.000
73	A	71	ARG	1	0.851	0.927	17.215	0.377	0.377	0.000	0.000	0.000	0.000
74	A	72	PHE	0	-0.009	-0.021	13.383	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	73	GLU	-1	-0.738	-0.833	18.465	-0.124	-0.124	0.000	0.000	0.000	0.000
76	A	74	VAL	0	0.004	-0.018	19.225	0.017	0.017	0.000	0.000	0.000	0.000
77	A	75	GLN	0	-0.037	-0.021	21.444	-0.018	-0.018	0.000	0.000	0.000	0.000
78	A	76	VAL	0	0.008	-0.004	23.847	0.018	0.018	0.000	0.000	0.000	0.000
79	A	77	ASP	-1	-0.805	-0.881	26.429	0.057	0.057	0.000	0.000	0.000	0.000
80	A	78	ASN	0	0.018	-0.020	29.027	0.012	0.012	0.000	0.000	0.000	0.000
81	A	79	ASN	0	-0.044	-0.007	32.095	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	80	GLY	0	-0.008	-0.001	33.989	-0.004	-0.004	0.000	0.000	0.000	0.000
83	A	81	GLN	0	-0.081	-0.030	33.626	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	82	THR	0	-0.033	-0.039	28.204	0.005	0.005	0.000	0.000	0.000	0.000
85	A	83	GLU	-1	-0.851	-0.912	29.132	-0.035	-0.035	0.000	0.000	0.000	0.000
86	A	84	GLN	0	-0.037	-0.024	24.870	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	85	TRP	0	-0.013	-0.022	25.108	-0.012	-0.012	0.000	0.000	0.000	0.000
88	A	86	GLU	-1	-0.885	-0.941	23.035	-0.234	-0.234	0.000	0.000	0.000	0.000
89	A	87	VAL	0	0.001	-0.008	20.557	0.006	0.006	0.000	0.000	0.000	0.000
90	A	88	GLN	0	0.035	0.023	20.472	-0.038	-0.038	0.000	0.000	0.000	0.000
91	A	89	ILE	0	0.004	0.000	16.708	0.013	0.013	0.000	0.000	0.000	0.000
92	A	90	GLU	-1	-0.842	-0.902	18.214	-0.541	-0.541	0.000	0.000	0.000	0.000
93	A	91	VAL	0	0.004	0.003	12.564	0.042	0.042	0.000	0.000	0.000	0.000
94	A	92	ARG	1	0.801	0.883	15.658	0.501	0.501	0.000	0.000	0.000	0.000
95	A	93	ASN	0	-0.021	-0.022	14.848	-0.007	-0.007	0.000	0.000	0.000	0.000
96	A	94	GLY	0	0.046	0.023	11.895	0.025	0.025	0.000	0.000	0.000	0.000
97	A	95	ARG	1	0.907	0.963	12.735	0.505	0.505	0.000	0.000	0.000	0.000
98	A	96	ILE	0	0.025	0.014	14.632	-0.043	-0.043	0.000	0.000	0.000	0.000
99	A	97	LYS	1	0.832	0.925	17.458	0.386	0.386	0.000	0.000	0.000	0.000
100	A	98	ARG	1	0.967	0.971	20.466	0.318	0.318	0.000	0.000	0.000	0.000
101	A	99	VAL	0	-0.003	0.002	20.279	-0.037	-0.037	0.000	0.000	0.000	0.000
102	A	100	THR	0	-0.016	-0.002	22.827	0.010	0.010	0.000	0.000	0.000	0.000
103	A	101	ILE	0	-0.007	0.001	24.635	-0.010	-0.010	0.000	0.000	0.000	0.000
104	A	102	THR	0	0.004	-0.004	26.566	0.004	0.004	0.000	0.000	0.000	0.000
105	A	103	HIS	1	0.844	0.919	27.915	0.066	0.066	0.000	0.000	0.000	0.000
106	A	104	VAL	0	0.032	0.040	30.455	0.007	0.007	0.000	0.000	0.000	0.000

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