FMO DATABASE

FMODB ID: 492ZN

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

Total energy (hartree)

FMO2-HF: Electronic energy	-927783.251682
FMO2-HF: Nuclear repulsion	883263.797054
FMO2-HF: Total energy	-44519.454628
FMO2-MP2: Total energy	-44649.774548

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.
-3.756	0.401	0.793	-1.918	-3.03	-0.001

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 : 0.034 / q_NPA : 0.018

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	1	PRO	0	-0.021	0.003	3.211	-4.045	-0.149	0.795	-1.907	-2.784	-0.001
4	A	2	GLU	-1	-0.821	-0.920	4.708	-1.818	-1.651	-0.001	-0.007	-0.158	0.000
5	A	3	GLU	-1	-0.840	-0.895	6.472	-0.649	-0.649	0.000	0.000	0.000	0.000
6	A	4	GLU	-1	-0.772	-0.873	8.151	-1.098	-1.098	0.000	0.000	0.000	0.000
7	A	5	LYS	1	0.880	0.922	4.661	1.577	1.671	-0.001	-0.004	-0.088	0.000
8	A	6	ALA	0	0.011	0.010	7.959	0.250	0.250	0.000	0.000	0.000	0.000
9	A	7	ALA	0	0.024	0.002	10.887	0.158	0.158	0.000	0.000	0.000	0.000
10	A	8	ARG	1	0.948	0.967	9.725	0.142	0.142	0.000	0.000	0.000	0.000
11	A	9	LEU	0	-0.015	-0.006	9.387	0.121	0.121	0.000	0.000	0.000	0.000
12	A	10	PHE	0	0.025	0.007	12.984	0.035	0.035	0.000	0.000	0.000	0.000
13	A	11	ILE	0	-0.014	-0.010	15.457	0.028	0.028	0.000	0.000	0.000	0.000
14	A	12	GLU	-1	-0.873	-0.914	13.652	0.432	0.432	0.000	0.000	0.000	0.000
15	A	13	ALA	0	-0.014	-0.011	16.040	0.032	0.032	0.000	0.000	0.000	0.000
16	A	14	LEU	0	-0.033	-0.009	18.880	-0.001	-0.001	0.000	0.000	0.000	0.000
17	A	15	GLU	-1	-0.853	-0.934	16.140	0.099	0.099	0.000	0.000	0.000	0.000
18	A	16	LYS	1	0.797	0.884	16.143	-0.360	-0.360	0.000	0.000	0.000	0.000
19	A	17	GLY	0	0.047	0.041	20.914	0.006	0.006	0.000	0.000	0.000	0.000
20	A	18	ASP	-1	-0.821	-0.911	20.716	0.150	0.150	0.000	0.000	0.000	0.000
21	A	19	PRO	0	-0.022	-0.025	21.642	-0.020	-0.020	0.000	0.000	0.000	0.000
22	A	20	GLU	-1	-0.815	-0.886	21.839	0.003	0.003	0.000	0.000	0.000	0.000
23	A	21	LEU	0	-0.014	-0.013	14.485	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	22	MET	0	0.006	0.015	17.373	-0.053	-0.053	0.000	0.000	0.000	0.000
25	A	23	ARG	1	0.743	0.830	19.029	-0.027	-0.027	0.000	0.000	0.000	0.000
26	A	24	LYS	1	0.834	0.924	15.630	-0.055	-0.055	0.000	0.000	0.000	0.000
27	A	25	VAL	0	-0.016	0.002	13.626	-0.050	-0.050	0.000	0.000	0.000	0.000
28	A	26	ILE	0	-0.013	0.006	15.772	-0.087	-0.087	0.000	0.000	0.000	0.000
29	A	27	SER	0	-0.034	-0.026	18.470	-0.035	-0.035	0.000	0.000	0.000	0.000
30	A	28	PRO	0	-0.001	-0.014	20.698	0.009	0.009	0.000	0.000	0.000	0.000
31	A	29	ASP	-1	-0.792	-0.861	22.228	-0.368	-0.368	0.000	0.000	0.000	0.000
32	A	30	THR	0	-0.014	-0.007	20.137	-0.016	-0.016	0.000	0.000	0.000	0.000
33	A	31	ARG	1	0.777	0.858	22.750	0.235	0.235	0.000	0.000	0.000	0.000
34	A	32	MET	0	-0.012	0.000	23.873	-0.031	-0.031	0.000	0.000	0.000	0.000
35	A	33	GLU	-1	-0.815	-0.893	25.584	-0.171	-0.171	0.000	0.000	0.000	0.000
36	A	34	ASP	-1	-0.743	-0.843	27.462	-0.104	-0.104	0.000	0.000	0.000	0.000
37	A	35	ASN	0	0.012	-0.001	29.835	0.003	0.003	0.000	0.000	0.000	0.000
38	A	36	GLY	0	-0.021	-0.011	32.319	0.010	0.010	0.000	0.000	0.000	0.000
39	A	37	ARG	1	0.827	0.913	31.853	0.081	0.081	0.000	0.000	0.000	0.000
40	A	38	GLU	-1	-0.804	-0.881	30.318	-0.201	-0.201	0.000	0.000	0.000	0.000
41	A	39	PHE	0	-0.015	0.000	27.705	0.019	0.019	0.000	0.000	0.000	0.000
42	A	40	THR	0	-0.080	-0.072	26.906	-0.027	-0.027	0.000	0.000	0.000	0.000
43	A	41	GLY	0	0.055	0.027	24.362	0.017	0.017	0.000	0.000	0.000	0.000
44	A	42	ASP	-1	-0.832	-0.927	25.034	-0.074	-0.074	0.000	0.000	0.000	0.000
45	A	43	GLU	-1	-0.825	-0.879	26.441	-0.108	-0.108	0.000	0.000	0.000	0.000
46	A	44	VAL	0	-0.013	-0.018	22.345	0.008	0.008	0.000	0.000	0.000	0.000
47	A	45	VAL	0	-0.011	-0.003	23.087	0.015	0.015	0.000	0.000	0.000	0.000
48	A	46	GLU	-1	-0.869	-0.920	25.427	-0.017	-0.017	0.000	0.000	0.000	0.000
49	A	47	TYR	0	-0.064	-0.046	26.411	0.013	0.013	0.000	0.000	0.000	0.000
50	A	48	VAL	0	0.025	0.005	22.671	0.009	0.009	0.000	0.000	0.000	0.000
51	A	49	LYS	1	0.854	0.918	26.085	0.035	0.035	0.000	0.000	0.000	0.000
52	A	50	GLU	-1	-0.805	-0.893	29.013	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	51	ILE	0	-0.058	-0.010	25.319	0.003	0.003	0.000	0.000	0.000	0.000
54	A	52	GLN	0	-0.034	-0.019	26.281	0.004	0.004	0.000	0.000	0.000	0.000
55	A	53	LYS	1	0.759	0.869	29.118	0.012	0.012	0.000	0.000	0.000	0.000
56	A	54	ARG	1	0.731	0.828	30.539	0.014	0.014	0.000	0.000	0.000	0.000
57	A	55	GLY	0	0.021	0.028	30.870	-0.002	-0.002	0.000	0.000	0.000	0.000
58	A	56	GLU	-1	-0.826	-0.868	28.396	-0.019	-0.019	0.000	0.000	0.000	0.000
59	A	57	GLN	0	-0.003	-0.009	23.665	0.007	0.007	0.000	0.000	0.000	0.000
60	A	58	TRP	0	-0.009	-0.023	22.484	-0.033	-0.033	0.000	0.000	0.000	0.000
61	A	59	HIS	0	-0.004	-0.005	20.296	0.045	0.045	0.000	0.000	0.000	0.000
62	A	60	LEU	0	-0.047	-0.017	14.010	-0.045	-0.045	0.000	0.000	0.000	0.000
63	A	61	ARG	1	0.753	0.866	18.058	0.108	0.108	0.000	0.000	0.000	0.000
64	A	62	ARG	1	0.826	0.887	15.966	0.162	0.162	0.000	0.000	0.000	0.000
65	A	63	TYR	0	-0.043	-0.043	9.318	0.115	0.115	0.000	0.000	0.000	0.000
66	A	64	THR	0	-0.019	-0.027	15.178	-0.028	-0.028	0.000	0.000	0.000	0.000
67	A	65	LYS	1	0.843	0.916	13.141	1.106	1.106	0.000	0.000	0.000	0.000
68	A	66	GLU	-1	-0.810	-0.861	16.336	-0.407	-0.407	0.000	0.000	0.000	0.000
69	A	67	GLY	0	0.020	0.003	19.615	0.017	0.017	0.000	0.000	0.000	0.000
70	A	68	ASN	0	-0.040	-0.041	16.195	-0.162	-0.162	0.000	0.000	0.000	0.000
71	A	69	SER	0	-0.050	0.004	17.798	-0.001	-0.001	0.000	0.000	0.000	0.000
72	A	70	TRP	0	-0.035	-0.046	11.003	-0.007	-0.007	0.000	0.000	0.000	0.000
73	A	71	ARG	1	0.814	0.898	17.503	0.381	0.381	0.000	0.000	0.000	0.000
74	A	72	PHE	0	0.007	-0.017	13.801	-0.030	-0.030	0.000	0.000	0.000	0.000
75	A	73	GLU	-1	-0.759	-0.840	18.849	-0.137	-0.137	0.000	0.000	0.000	0.000
76	A	74	VAL	0	0.000	-0.016	19.566	0.012	0.012	0.000	0.000	0.000	0.000
77	A	75	GLN	0	-0.010	-0.004	21.845	-0.013	-0.013	0.000	0.000	0.000	0.000
78	A	76	VAL	0	0.003	0.005	24.064	0.011	0.011	0.000	0.000	0.000	0.000
79	A	77	ASP	-1	-0.795	-0.865	26.532	0.025	0.025	0.000	0.000	0.000	0.000
80	A	78	ASN	0	0.017	-0.019	29.190	0.014	0.014	0.000	0.000	0.000	0.000
81	A	79	ASN	0	-0.049	-0.019	32.312	-0.001	-0.001	0.000	0.000	0.000	0.000
82	A	80	GLY	0	-0.002	0.006	34.432	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	81	GLN	0	-0.097	-0.041	33.916	0.000	0.000	0.000	0.000	0.000	0.000
84	A	82	THR	0	-0.017	-0.032	28.740	0.006	0.006	0.000	0.000	0.000	0.000
85	A	83	GLU	-1	-0.848	-0.900	29.602	-0.057	-0.057	0.000	0.000	0.000	0.000
86	A	84	GLN	0	-0.019	-0.027	25.303	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	85	TRP	0	-0.012	-0.022	25.341	-0.010	-0.010	0.000	0.000	0.000	0.000
88	A	86	GLU	-1	-0.857	-0.913	23.496	-0.264	-0.264	0.000	0.000	0.000	0.000
89	A	87	VAL	0	0.015	0.003	20.658	0.009	0.009	0.000	0.000	0.000	0.000
90	A	88	GLN	0	0.026	0.014	21.031	-0.039	-0.039	0.000	0.000	0.000	0.000
91	A	89	ILE	0	-0.003	-0.003	16.321	0.014	0.014	0.000	0.000	0.000	0.000
92	A	90	GLU	-1	-0.839	-0.904	18.199	-0.573	-0.573	0.000	0.000	0.000	0.000
93	A	91	VAL	0	-0.001	0.006	12.449	0.027	0.027	0.000	0.000	0.000	0.000
94	A	92	ARG	1	0.807	0.872	15.893	0.596	0.596	0.000	0.000	0.000	0.000
95	A	93	ASN	0	-0.027	-0.018	14.610	-0.016	-0.016	0.000	0.000	0.000	0.000
96	A	94	GLY	0	0.034	0.021	11.689	0.019	0.019	0.000	0.000	0.000	0.000
97	A	95	ARG	1	0.892	0.943	12.594	0.555	0.555	0.000	0.000	0.000	0.000
98	A	96	ILE	0	0.060	0.035	14.409	-0.049	-0.049	0.000	0.000	0.000	0.000
99	A	97	LYS	1	0.774	0.892	17.164	0.425	0.425	0.000	0.000	0.000	0.000
100	A	98	ARG	1	0.973	0.970	20.283	0.341	0.341	0.000	0.000	0.000	0.000
101	A	99	VAL	0	-0.001	0.006	20.033	-0.040	-0.040	0.000	0.000	0.000	0.000
102	A	100	THR	0	-0.046	-0.031	22.616	0.010	0.010	0.000	0.000	0.000	0.000
103	A	101	ILE	0	-0.004	0.006	24.181	-0.012	-0.012	0.000	0.000	0.000	0.000
104	A	102	THR	0	-0.003	-0.003	26.741	0.009	0.009	0.000	0.000	0.000	0.000
105	A	103	HIS	1	0.813	0.900	28.387	0.086	0.086	0.000	0.000	0.000	0.000
106	A	104	VAL	0	0.023	0.034	30.861	0.007	0.007	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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