FMO DATABASE

FMODB ID: M382Z

Calculation Name: 2CZJ-A-Xray372

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: 2023-03-13

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	122
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1052260.726426
FMO2-HF: Nuclear repulsion	1004582.505393
FMO2-HF: Total energy	-47678.221033
FMO2-MP2: Total energy	-47822.357632

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:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

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.
-1.913	-9.403	27.06	-12.155	-7.413	-0.052

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : -0.038

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	4	VAL	0	-0.033	-0.009	3.955	-3.233	-1.085	-0.008	-1.307	-0.833	0.002
4	A	5	LEU	0	0.083	0.073	4.873	0.201	0.201	0.000	0.000	0.000	0.000
5	A	6	GLU	-1	-0.839	-0.920	8.218	-0.565	-0.565	0.000	0.000	0.000	0.000
6	A	7	ASN	0	0.006	0.008	11.928	-0.076	-0.076	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.923	0.953	14.490	0.599	0.599	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.911	0.947	16.240	0.517	0.517	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.067	0.034	18.647	0.055	0.055	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.934	0.984	19.865	0.379	0.379	0.000	0.000	0.000	0.000
11	A	12	HIS	0	0.045	0.005	20.046	0.042	0.042	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.873	-0.898	23.462	-0.291	-0.291	0.000	0.000	0.000	0.000
13	A	14	TYR	0	-0.041	-0.030	21.827	0.013	0.013	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.896	-0.950	25.372	-0.263	-0.263	0.000	0.000	0.000	0.000
15	A	16	ILE	0	-0.055	-0.035	22.063	0.007	0.007	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.024	-0.004	25.538	0.017	0.017	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.803	-0.881	26.687	-0.165	-0.165	0.000	0.000	0.000	0.000
18	A	19	THR	0	-0.019	-0.033	21.144	-0.025	-0.025	0.000	0.000	0.000	0.000
19	A	20	TYR	0	-0.044	-0.006	22.206	0.017	0.017	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.851	-0.916	16.122	-0.383	-0.383	0.000	0.000	0.000	0.000
21	A	22	ALA	0	0.000	-0.005	17.641	0.048	0.048	0.000	0.000	0.000	0.000
22	A	23	GLY	0	-0.037	-0.015	15.784	-0.051	-0.051	0.000	0.000	0.000	0.000
23	A	24	ILE	0	0.058	0.027	12.869	0.010	0.010	0.000	0.000	0.000	0.000
24	A	25	ALA	0	-0.007	0.014	16.211	0.035	0.035	0.000	0.000	0.000	0.000
25	A	26	LEU	0	0.007	0.006	11.273	-0.008	-0.008	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.918	0.941	14.938	0.154	0.154	0.000	0.000	0.000	0.000
27	A	28	GLY	0	0.070	0.029	12.953	0.043	0.043	0.000	0.000	0.000	0.000
28	A	29	THR	0	0.049	0.025	11.553	0.028	0.028	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.747	-0.837	10.933	-0.314	-0.314	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.053	0.022	8.086	-0.170	-0.170	0.000	0.000	0.000	0.000
31	A	32	LYS	1	0.915	0.973	6.995	-0.879	-0.879	0.000	0.000	0.000	0.000
32	A	33	SER	0	0.008	-0.018	6.520	0.069	0.069	0.000	0.000	0.000	0.000
33	A	34	LEU	0	-0.003	0.001	6.539	-0.333	-0.333	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.782	0.909	2.838	-3.189	-2.581	0.287	-0.286	-0.609	0.002
35	A	36	ALA	0	0.007	0.056	2.021	9.021	-2.599	26.197	-9.507	-5.070	-0.042
36	A	37	GLY	0	0.048	0.005	2.624	-5.586	-4.247	0.585	-1.053	-0.870	-0.014
37	A	38	LYS	1	0.887	0.949	5.223	0.952	0.987	-0.001	-0.002	-0.031	0.000
38	A	39	VAL	0	-0.066	-0.012	8.163	0.305	0.305	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.823	-0.913	10.649	-0.750	-0.750	0.000	0.000	0.000	0.000
40	A	41	PHE	0	0.024	0.000	11.580	0.120	0.120	0.000	0.000	0.000	0.000
41	A	42	THR	0	-0.053	-0.042	16.063	0.070	0.070	0.000	0.000	0.000	0.000
42	A	43	GLY	0	0.017	0.010	18.607	0.023	0.023	0.000	0.000	0.000	0.000
43	A	44	SER	0	-0.139	-0.054	17.935	0.011	0.011	0.000	0.000	0.000	0.000
44	A	45	PHE	0	0.024	-0.016	19.995	-0.025	-0.025	0.000	0.000	0.000	0.000
45	A	46	ALA	0	-0.033	-0.023	21.495	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	47	ARG	1	0.946	0.978	23.128	0.212	0.212	0.000	0.000	0.000	0.000
47	A	48	PHE	0	-0.014	-0.020	26.167	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.851	-0.909	27.808	-0.161	-0.161	0.000	0.000	0.000	0.000
49	A	50	ASP	-1	-0.881	-0.930	30.131	-0.095	-0.095	0.000	0.000	0.000	0.000
50	A	51	GLY	0	0.018	0.020	31.652	0.000	0.000	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.866	-0.906	26.656	-0.133	-0.133	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.018	-0.012	23.098	-0.005	-0.005	0.000	0.000	0.000	0.000
53	A	54	TYR	0	-0.042	-0.065	22.514	-0.009	-0.009	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.025	0.012	16.691	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.831	-0.933	20.469	-0.227	-0.227	0.000	0.000	0.000	0.000
56	A	57	ASN	0	0.032	0.015	20.469	-0.044	-0.044	0.000	0.000	0.000	0.000
57	A	58	LEU	0	0.018	0.029	13.193	-0.022	-0.022	0.000	0.000	0.000	0.000
58	A	59	TYR	0	-0.029	-0.020	13.552	0.040	0.040	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.028	-0.040	10.313	-0.142	-0.142	0.000	0.000	0.000	0.000
60	A	61	ALA	0	0.006	0.011	10.334	0.088	0.088	0.000	0.000	0.000	0.000
61	A	62	PRO	0	0.023	0.006	10.803	-0.032	-0.032	0.000	0.000	0.000	0.000
62	A	63	TYR	0	-0.017	-0.021	10.121	0.145	0.145	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.787	-0.877	10.925	-0.323	-0.323	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.919	0.955	6.756	-0.794	-0.794	0.000	0.000	0.000	0.000
65	A	66	GLY	0	0.043	0.018	11.073	0.103	0.103	0.000	0.000	0.000	0.000
66	A	67	SER	0	0.017	0.024	14.714	-0.051	-0.051	0.000	0.000	0.000	0.000
67	A	68	TYR	0	-0.032	-0.028	13.226	0.064	0.064	0.000	0.000	0.000	0.000
68	A	69	ALA	0	0.035	0.028	17.329	-0.027	-0.027	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.087	-0.049	14.787	0.036	0.036	0.000	0.000	0.000	0.000
70	A	71	VAL	0	0.015	-0.008	16.652	0.004	0.004	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.830	-0.919	17.920	-0.244	-0.244	0.000	0.000	0.000	0.000
72	A	73	PRO	0	0.026	0.009	16.204	-0.032	-0.032	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.879	0.960	16.478	0.327	0.327	0.000	0.000	0.000	0.000
74	A	75	ARG	1	0.888	0.954	17.296	0.264	0.264	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.857	0.911	19.508	0.143	0.143	0.000	0.000	0.000	0.000
76	A	77	ARG	1	0.751	0.866	15.489	0.433	0.433	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.836	0.898	19.582	0.119	0.119	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.002	-0.004	18.037	-0.040	-0.040	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.030	-0.015	19.341	0.031	0.031	0.000	0.000	0.000	0.000
80	A	81	LEU	0	0.056	0.003	21.351	-0.020	-0.020	0.000	0.000	0.000	0.000
81	A	82	HIS	0	-0.007	0.013	23.944	0.016	0.016	0.000	0.000	0.000	0.000
82	A	83	LYS	1	1.062	1.021	27.225	0.072	0.072	0.000	0.000	0.000	0.000
83	A	84	HIS	0	-0.011	-0.013	29.737	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.874	-0.943	26.565	-0.154	-0.154	0.000	0.000	0.000	0.000
85	A	86	LEU	0	-0.012	0.007	25.780	-0.015	-0.015	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.978	0.973	28.601	0.090	0.090	0.000	0.000	0.000	0.000
87	A	88	ARG	1	0.908	0.951	30.882	0.119	0.119	0.000	0.000	0.000	0.000
88	A	89	LEU	0	0.060	0.037	25.397	0.003	0.003	0.000	0.000	0.000	0.000
89	A	90	LEU	0	0.049	0.036	29.607	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	91	GLY	0	-0.021	-0.004	31.302	0.003	0.003	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.741	0.858	31.166	0.163	0.163	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.003	-0.026	29.028	-0.009	-0.009	0.000	0.000	0.000	0.000
93	A	94	GLU	-1	-0.853	-0.925	31.848	-0.161	-0.161	0.000	0.000	0.000	0.000
94	A	95	GLN	0	-0.082	-0.017	33.758	0.004	0.004	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.949	0.964	33.824	0.159	0.159	0.000	0.000	0.000	0.000
96	A	97	GLY	0	0.000	0.023	34.426	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	98	LEU	0	-0.046	-0.018	29.853	-0.010	-0.010	0.000	0.000	0.000	0.000
98	A	99	THR	0	-0.013	-0.021	25.758	0.003	0.003	0.000	0.000	0.000	0.000
99	A	100	LEU	0	0.011	0.026	23.329	-0.013	-0.013	0.000	0.000	0.000	0.000
100	A	101	VAL	0	0.057	0.037	21.378	-0.013	-0.013	0.000	0.000	0.000	0.000
101	A	102	PRO	0	-0.031	-0.001	16.206	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	103	LEU	0	-0.001	0.006	17.085	-0.042	-0.042	0.000	0.000	0.000	0.000
103	A	104	LYS	1	0.898	0.936	11.914	0.739	0.739	0.000	0.000	0.000	0.000
104	A	105	ILE	0	0.008	0.007	8.603	0.172	0.172	0.000	0.000	0.000	0.000
105	A	106	TYR	0	-0.013	-0.040	7.556	-0.502	-0.502	0.000	0.000	0.000	0.000
106	A	107	PHE	0	-0.006	-0.005	4.948	0.519	0.519	0.000	0.000	0.000	0.000
107	A	108	ASN	0	0.050	0.022	8.932	0.046	0.046	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.834	-0.912	11.033	0.113	0.113	0.000	0.000	0.000	0.000
109	A	110	ARG	1	0.915	0.952	12.583	0.068	0.068	0.000	0.000	0.000	0.000
110	A	111	GLY	0	0.033	0.026	9.939	0.030	0.030	0.000	0.000	0.000	0.000
111	A	112	TYR	0	-0.043	-0.033	10.616	0.001	0.001	0.000	0.000	0.000	0.000
112	A	113	ALA	0	-0.018	0.005	9.167	-0.067	-0.067	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.832	0.906	10.422	0.412	0.412	0.000	0.000	0.000	0.000
114	A	115	VAL	0	0.023	0.012	12.307	-0.157	-0.157	0.000	0.000	0.000	0.000
115	A	116	LEU	0	0.008	0.029	14.627	0.084	0.084	0.000	0.000	0.000	0.000
116	A	117	LEU	0	0.006	0.008	16.943	-0.036	-0.036	0.000	0.000	0.000	0.000
117	A	118	GLY	0	0.074	0.011	20.147	0.017	0.017	0.000	0.000	0.000	0.000
118	A	119	LEU	0	-0.076	-0.014	23.288	-0.006	-0.006	0.000	0.000	0.000	0.000
119	A	120	ALA	0	0.032	0.020	25.239	-0.012	-0.012	0.000	0.000	0.000	0.000
120	A	121	ARG	1	0.975	0.973	27.270	0.192	0.192	0.000	0.000	0.000	0.000
121	A	122	GLY	0	0.091	0.047	29.100	-0.012	-0.012	0.000	0.000	0.000	0.000
122	A	123	LYS	1	0.804	0.909	27.583	0.268	0.268	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)