FMO DATABASE

FMODB ID: 1JGMZ

Calculation Name: 2CZJ-A-Xray310

Preferred Name:

Target Type:

Ligand Name: pseudouridine-5'-monophosphate

ligand 3-letter code: PSU

PDB ID: 2CZJ

Chain ID: A

ChEMBL ID:

UniProt ID: Q8RR57

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	123
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1058956.279115
FMO2-HF: Nuclear repulsion	1011128.946809
FMO2-HF: Total energy	-47827.332307
FMO2-MP2: Total energy	-47972.180339

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:ACE )

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

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.
-0.776	0.83	0.713	-1.477	-0.841	-0.01

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

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 : -0.009

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	PRO	0	-0.115	-0.083	3.863	1.015	1.844	-0.005	-0.389	-0.435	0.000
4	A	4	VAL	0	-0.008	0.001	6.691	0.055	0.055	0.000	0.000	0.000	0.000
5	A	5	LEU	0	0.063	0.063	5.174	0.099	0.099	0.000	0.000	0.000	0.000
6	A	6	GLU	-1	-0.864	-0.946	9.553	-0.066	-0.066	0.000	0.000	0.000	0.000
7	A	7	ASN	0	0.003	0.005	12.696	0.076	0.076	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.928	0.960	14.927	-0.116	-0.116	0.000	0.000	0.000	0.000
9	A	9	ARG	1	0.958	0.955	16.743	-0.107	-0.107	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.080	0.038	18.908	-0.005	-0.005	0.000	0.000	0.000	0.000
11	A	11	ARG	1	0.914	0.977	20.608	-0.036	-0.036	0.000	0.000	0.000	0.000
12	A	12	HIS	0	-0.031	-0.027	19.977	-0.008	-0.008	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.924	-0.939	23.684	0.062	0.062	0.000	0.000	0.000	0.000
14	A	14	TYR	0	-0.044	-0.033	22.307	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	15	GLU	-1	-0.896	-0.957	26.225	0.026	0.026	0.000	0.000	0.000	0.000
16	A	16	ILE	0	-0.035	-0.028	23.125	-0.004	-0.004	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.045	-0.014	26.885	0.000	0.000	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.890	-0.951	28.562	-0.035	-0.035	0.000	0.000	0.000	0.000
19	A	19	THR	0	-0.035	-0.054	23.183	0.002	0.002	0.000	0.000	0.000	0.000
20	A	20	TYR	0	-0.036	0.019	24.323	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.894	-0.957	19.426	-0.162	-0.162	0.000	0.000	0.000	0.000
22	A	22	ALA	0	0.002	-0.011	20.414	0.004	0.004	0.000	0.000	0.000	0.000
23	A	23	GLY	0	-0.027	-0.019	19.099	-0.016	-0.016	0.000	0.000	0.000	0.000
24	A	24	ILE	0	0.059	0.028	15.935	0.016	0.016	0.000	0.000	0.000	0.000
25	A	25	ALA	0	-0.015	0.016	19.292	-0.016	-0.016	0.000	0.000	0.000	0.000
26	A	26	LEU	0	-0.010	0.010	13.883	0.012	0.012	0.000	0.000	0.000	0.000
27	A	27	LYS	1	1.009	0.983	16.954	0.105	0.105	0.000	0.000	0.000	0.000
28	A	28	GLY	0	0.064	0.027	15.675	0.000	0.000	0.000	0.000	0.000	0.000
29	A	29	THR	0	0.051	0.018	13.752	-0.061	-0.061	0.000	0.000	0.000	0.000
30	A	30	GLU	-1	-0.821	-0.876	12.068	-0.138	-0.138	0.000	0.000	0.000	0.000
31	A	31	VAL	0	0.046	0.015	11.150	-0.027	-0.027	0.000	0.000	0.000	0.000
32	A	32	LYS	1	0.893	0.969	9.351	0.414	0.414	0.000	0.000	0.000	0.000
33	A	33	SER	0	0.019	-0.008	7.507	-0.132	-0.132	0.000	0.000	0.000	0.000
34	A	34	LEU	0	-0.002	0.004	6.933	0.052	0.052	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.817	0.921	5.837	0.972	0.972	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.023	0.067	2.723	-2.146	-2.247	0.411	-0.334	0.025	-0.001
37	A	37	GLY	0	0.040	0.004	2.999	-1.073	-0.278	0.307	-0.749	-0.353	-0.009
38	A	38	LYS	1	0.969	1.002	4.733	-0.154	-0.071	0.000	-0.005	-0.078	0.000
39	A	39	VAL	0	-0.085	-0.030	7.917	-0.110	-0.110	0.000	0.000	0.000	0.000
40	A	40	ASP	-1	-0.894	-0.956	10.369	0.207	0.207	0.000	0.000	0.000	0.000
41	A	41	PHE	0	0.052	0.005	11.805	-0.033	-0.033	0.000	0.000	0.000	0.000
42	A	42	THR	0	-0.047	-0.022	16.158	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	43	GLY	0	0.020	0.021	18.334	0.000	0.000	0.000	0.000	0.000	0.000
44	A	44	SER	0	-0.118	-0.055	18.277	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	45	PHE	0	0.031	-0.025	20.298	0.000	0.000	0.000	0.000	0.000	0.000
46	A	46	ALA	0	-0.013	-0.029	22.524	-0.006	-0.006	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.956	1.004	24.154	0.007	0.007	0.000	0.000	0.000	0.000
48	A	48	PHE	0	-0.006	-0.012	27.564	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	49	GLU	-1	-0.925	-0.965	29.208	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.932	-0.937	31.514	-0.026	-0.026	0.000	0.000	0.000	0.000
51	A	51	GLY	0	0.022	0.012	33.706	0.001	0.001	0.000	0.000	0.000	0.000
52	A	52	GLU	-1	-0.993	-1.005	29.012	-0.059	-0.059	0.000	0.000	0.000	0.000
53	A	53	LEU	0	-0.016	-0.013	24.915	0.004	0.004	0.000	0.000	0.000	0.000
54	A	54	TYR	0	-0.033	-0.040	24.274	-0.012	-0.012	0.000	0.000	0.000	0.000
55	A	55	LEU	0	0.027	0.019	18.139	0.006	0.006	0.000	0.000	0.000	0.000
56	A	56	GLU	-1	-0.866	-0.955	21.513	-0.016	-0.016	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.014	0.002	20.732	0.012	0.012	0.000	0.000	0.000	0.000
58	A	58	LEU	0	0.027	0.027	14.218	0.011	0.011	0.000	0.000	0.000	0.000
59	A	59	TYR	0	-0.024	-0.005	13.316	-0.033	-0.033	0.000	0.000	0.000	0.000
60	A	60	ILE	0	-0.014	-0.038	10.816	0.009	0.009	0.000	0.000	0.000	0.000
61	A	61	ALA	0	0.014	0.025	9.789	-0.025	-0.025	0.000	0.000	0.000	0.000
62	A	62	PRO	0	0.017	-0.013	10.534	-0.014	-0.014	0.000	0.000	0.000	0.000
63	A	63	TYR	0	0.002	-0.006	9.822	-0.045	-0.045	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.861	-0.929	9.951	0.197	0.197	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.889	0.937	5.948	0.169	0.169	0.000	0.000	0.000	0.000
66	A	66	GLY	0	0.037	0.016	9.526	-0.034	-0.034	0.000	0.000	0.000	0.000
67	A	67	SER	0	0.008	0.016	13.159	0.017	0.017	0.000	0.000	0.000	0.000
68	A	68	TYR	0	-0.039	-0.021	12.201	-0.032	-0.032	0.000	0.000	0.000	0.000
69	A	69	ALA	0	0.041	0.029	16.850	0.011	0.011	0.000	0.000	0.000	0.000
70	A	70	ASN	0	-0.072	-0.044	14.578	-0.040	-0.040	0.000	0.000	0.000	0.000
71	A	71	VAL	0	0.007	-0.011	17.218	0.006	0.006	0.000	0.000	0.000	0.000
72	A	72	ASP	-1	-0.859	-0.942	18.039	0.014	0.014	0.000	0.000	0.000	0.000
73	A	73	PRO	0	0.014	0.007	16.161	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	74	ARG	1	0.920	0.982	16.686	-0.086	-0.086	0.000	0.000	0.000	0.000
75	A	75	ARG	1	0.902	0.953	18.700	0.086	0.086	0.000	0.000	0.000	0.000
76	A	76	LYS	1	0.988	0.978	20.224	0.010	0.010	0.000	0.000	0.000	0.000
77	A	77	ARG	1	0.744	0.864	16.089	0.047	0.047	0.000	0.000	0.000	0.000
78	A	78	LYS	1	0.951	0.978	21.148	0.067	0.067	0.000	0.000	0.000	0.000
79	A	79	LEU	0	0.016	0.004	19.821	-0.014	-0.014	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.037	-0.016	22.415	0.005	0.005	0.000	0.000	0.000	0.000
81	A	81	LEU	0	0.062	0.002	24.377	-0.004	-0.004	0.000	0.000	0.000	0.000
82	A	82	HIS	0	-0.003	0.015	27.063	0.008	0.008	0.000	0.000	0.000	0.000
83	A	83	LYS	1	1.056	1.025	30.545	0.045	0.045	0.000	0.000	0.000	0.000
84	A	84	HIS	0	-0.037	-0.026	33.144	0.007	0.007	0.000	0.000	0.000	0.000
85	A	85	GLU	-1	-0.874	-0.951	29.300	-0.055	-0.055	0.000	0.000	0.000	0.000
86	A	86	LEU	0	0.020	-0.003	28.369	0.001	0.001	0.000	0.000	0.000	0.000
87	A	87	ARG	1	0.996	0.956	31.263	0.036	0.036	0.000	0.000	0.000	0.000
88	A	88	ARG	1	0.914	0.945	33.257	0.034	0.034	0.000	0.000	0.000	0.000
89	A	89	LEU	0	0.036	0.053	28.018	0.004	0.004	0.000	0.000	0.000	0.000
90	A	90	LEU	0	0.039	0.058	31.608	0.003	0.003	0.000	0.000	0.000	0.000
91	A	91	GLY	0	-0.026	-0.006	33.141	0.003	0.003	0.000	0.000	0.000	0.000
92	A	92	LYS	1	0.841	0.926	33.461	0.026	0.026	0.000	0.000	0.000	0.000
93	A	93	VAL	0	0.017	-0.007	30.519	0.002	0.002	0.000	0.000	0.000	0.000
94	A	94	GLU	-1	-0.893	-0.947	33.220	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	95	GLN	0	-0.041	-0.001	34.781	0.003	0.003	0.000	0.000	0.000	0.000
96	A	96	LYS	1	0.947	0.961	34.332	-0.006	-0.006	0.000	0.000	0.000	0.000
97	A	97	GLY	0	0.000	0.029	35.003	0.003	0.003	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.039	-0.017	30.730	0.001	0.001	0.000	0.000	0.000	0.000
99	A	99	THR	0	-0.021	-0.025	26.186	0.002	0.002	0.000	0.000	0.000	0.000
100	A	100	LEU	0	0.009	0.021	24.765	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	101	VAL	0	0.061	0.032	22.117	0.002	0.002	0.000	0.000	0.000	0.000
102	A	102	PRO	0	-0.037	-0.009	17.284	-0.010	-0.010	0.000	0.000	0.000	0.000
103	A	103	LEU	0	-0.003	0.020	18.074	0.017	0.017	0.000	0.000	0.000	0.000
104	A	104	LYS	1	0.932	0.978	13.609	0.163	0.163	0.000	0.000	0.000	0.000
105	A	105	ILE	0	-0.017	0.002	11.216	-0.012	-0.012	0.000	0.000	0.000	0.000
106	A	106	TYR	0	0.007	-0.014	10.552	-0.038	-0.038	0.000	0.000	0.000	0.000
107	A	107	PHE	0	-0.007	-0.007	8.221	0.041	0.041	0.000	0.000	0.000	0.000
108	A	108	ASN	0	0.060	0.041	12.997	-0.024	-0.024	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.835	-0.920	15.811	-0.249	-0.249	0.000	0.000	0.000	0.000
110	A	110	ARG	1	0.906	0.951	17.666	0.140	0.140	0.000	0.000	0.000	0.000
111	A	111	GLY	0	0.031	0.026	14.747	0.002	0.002	0.000	0.000	0.000	0.000
112	A	112	TYR	0	-0.063	-0.049	15.029	-0.026	-0.026	0.000	0.000	0.000	0.000
113	A	113	ALA	0	-0.020	0.003	12.749	0.002	0.002	0.000	0.000	0.000	0.000
114	A	114	LYS	1	0.838	0.906	14.093	0.268	0.268	0.000	0.000	0.000	0.000
115	A	115	VAL	0	0.028	0.028	15.131	-0.017	-0.017	0.000	0.000	0.000	0.000
116	A	116	LEU	0	0.021	0.032	17.022	0.004	0.004	0.000	0.000	0.000	0.000
117	A	117	LEU	0	0.006	0.009	19.052	0.014	0.014	0.000	0.000	0.000	0.000
118	A	118	GLY	0	0.070	0.007	21.830	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	119	LEU	0	-0.080	-0.015	24.797	0.005	0.005	0.000	0.000	0.000	0.000
120	A	120	ALA	0	0.046	0.024	26.156	0.002	0.002	0.000	0.000	0.000	0.000
121	A	121	ARG	1	0.913	0.934	28.228	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	122	GLY	0	0.040	0.024	29.923	0.000	0.000	0.000	0.000	0.000	0.000
123	A	123	LYS	0	0.014	0.053	28.061	-0.016	-0.016	0.000	0.000	0.000	0.000

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