FMO DATABASE

FMODB ID: 9G722

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	OptH
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	-1054173.442356
FMO2-HF: Nuclear repulsion	1006497.42847
FMO2-HF: Total energy	-47676.013886
FMO2-MP2: Total energy	-47820.433031

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.
-1.284	-11.968	32.05	-13.851	-7.52	-0.05

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 : 0.037 / 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	-0.010	-0.001	3.955	-3.289	-1.253	-0.009	-1.231	-0.797	0.000
4	A	5	LEU	0	0.067	0.066	4.192	0.201	0.308	-0.001	-0.013	-0.093	0.000
5	A	6	GLU	-1	-0.866	-0.946	8.036	-0.424	-0.424	0.000	0.000	0.000	0.000
6	A	7	ASN	0	0.004	0.005	11.754	-0.092	-0.092	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.932	0.962	14.283	0.517	0.517	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.961	0.957	16.070	0.502	0.502	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.076	0.037	18.413	0.046	0.046	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.918	0.980	19.695	0.298	0.298	0.000	0.000	0.000	0.000
11	A	12	HIS	0	-0.026	-0.024	19.469	0.044	0.044	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.927	-0.940	23.084	-0.291	-0.291	0.000	0.000	0.000	0.000
13	A	14	TYR	0	-0.051	-0.036	21.487	0.008	0.008	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.895	-0.958	25.187	-0.232	-0.232	0.000	0.000	0.000	0.000
15	A	16	ILE	0	-0.030	-0.024	21.761	0.004	0.004	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.047	-0.016	25.377	0.017	0.017	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.881	-0.946	26.613	-0.139	-0.139	0.000	0.000	0.000	0.000
18	A	19	THR	0	-0.036	-0.055	21.089	-0.025	-0.025	0.000	0.000	0.000	0.000
19	A	20	TYR	0	-0.036	0.020	21.964	0.019	0.019	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.890	-0.957	16.182	-0.281	-0.281	0.000	0.000	0.000	0.000
21	A	22	ALA	0	0.004	-0.009	17.391	0.041	0.041	0.000	0.000	0.000	0.000
22	A	23	GLY	0	-0.027	-0.018	15.560	-0.052	-0.052	0.000	0.000	0.000	0.000
23	A	24	ILE	0	0.055	0.026	12.812	0.008	0.008	0.000	0.000	0.000	0.000
24	A	25	ALA	0	-0.012	0.017	16.011	0.033	0.033	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.013	0.009	10.956	-0.017	-0.017	0.000	0.000	0.000	0.000
26	A	27	LYS	1	1.013	0.984	14.657	0.223	0.223	0.000	0.000	0.000	0.000
27	A	28	GLY	0	0.064	0.028	12.886	0.053	0.053	0.000	0.000	0.000	0.000
28	A	29	THR	0	0.054	0.021	11.501	0.000	0.000	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.828	-0.879	10.839	-0.504	-0.504	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.054	0.018	8.071	-0.197	-0.197	0.000	0.000	0.000	0.000
31	A	32	LYS	1	0.890	0.968	6.879	-0.533	-0.533	0.000	0.000	0.000	0.000
32	A	33	SER	0	0.021	-0.007	6.458	-0.108	-0.108	0.000	0.000	0.000	0.000
33	A	34	LEU	0	0.003	0.007	6.385	-0.386	-0.386	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.816	0.922	2.662	-3.260	-2.698	0.492	-0.308	-0.747	0.002
35	A	36	ALA	0	0.005	0.058	1.990	7.930	-6.485	31.256	-11.698	-5.144	-0.046
36	A	37	GLY	0	0.053	0.011	2.978	-4.455	-3.551	0.313	-0.587	-0.631	-0.006
37	A	38	LYS	1	0.970	1.005	5.424	1.396	1.396	0.000	0.000	0.000	0.000
38	A	39	VAL	0	-0.081	-0.029	8.604	0.342	0.342	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.897	-0.957	10.789	-0.814	-0.814	0.000	0.000	0.000	0.000
40	A	41	PHE	0	0.052	0.006	11.146	0.103	0.103	0.000	0.000	0.000	0.000
41	A	42	THR	0	-0.048	-0.025	15.869	0.069	0.069	0.000	0.000	0.000	0.000
42	A	43	GLY	0	0.025	0.023	18.410	0.015	0.015	0.000	0.000	0.000	0.000
43	A	44	SER	0	-0.120	-0.055	17.818	0.009	0.009	0.000	0.000	0.000	0.000
44	A	45	PHE	0	0.024	-0.027	19.917	-0.016	-0.016	0.000	0.000	0.000	0.000
45	A	46	ALA	0	-0.011	-0.028	21.615	-0.014	-0.014	0.000	0.000	0.000	0.000
46	A	47	ARG	1	0.952	1.002	22.828	0.218	0.218	0.000	0.000	0.000	0.000
47	A	48	PHE	0	-0.006	-0.011	25.884	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.924	-0.965	27.808	-0.168	-0.168	0.000	0.000	0.000	0.000
49	A	50	ASP	-1	-0.930	-0.936	29.860	-0.102	-0.102	0.000	0.000	0.000	0.000
50	A	51	GLY	0	0.021	0.012	31.357	0.002	0.002	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.991	-1.004	26.433	-0.144	-0.144	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.017	-0.014	22.609	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	54	TYR	0	-0.030	-0.038	22.252	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	55	LEU	0	0.027	0.018	16.623	-0.005	-0.005	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.869	-0.955	20.190	-0.259	-0.259	0.000	0.000	0.000	0.000
56	A	57	ASN	0	-0.011	0.003	20.656	-0.030	-0.030	0.000	0.000	0.000	0.000
57	A	58	LEU	0	0.026	0.026	13.281	-0.025	-0.025	0.000	0.000	0.000	0.000
58	A	59	TYR	0	-0.024	-0.006	14.354	0.049	0.049	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.015	-0.038	10.415	-0.154	-0.154	0.000	0.000	0.000	0.000
60	A	61	ALA	0	0.014	0.026	10.589	0.069	0.069	0.000	0.000	0.000	0.000
61	A	62	PRO	0	0.017	-0.013	10.917	-0.095	-0.095	0.000	0.000	0.000	0.000
62	A	63	TYR	0	0.001	-0.006	9.743	0.131	0.131	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.861	-0.930	11.019	-0.430	-0.430	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.890	0.938	7.038	-0.069	-0.069	0.000	0.000	0.000	0.000
65	A	66	GLY	0	0.040	0.017	10.912	0.109	0.109	0.000	0.000	0.000	0.000
66	A	67	SER	0	0.009	0.017	14.530	-0.027	-0.027	0.000	0.000	0.000	0.000
67	A	68	TYR	0	-0.040	-0.022	12.976	0.041	0.041	0.000	0.000	0.000	0.000
68	A	69	ALA	0	0.042	0.029	17.182	-0.016	-0.016	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.069	-0.043	14.611	0.047	0.047	0.000	0.000	0.000	0.000
70	A	71	VAL	0	0.010	-0.009	16.668	0.020	0.020	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.865	-0.943	18.025	-0.325	-0.325	0.000	0.000	0.000	0.000
72	A	73	PRO	0	0.018	0.010	16.396	-0.033	-0.033	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.914	0.978	16.734	0.356	0.356	0.000	0.000	0.000	0.000
74	A	75	ARG	1	0.903	0.954	16.705	0.350	0.350	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.986	0.978	19.258	0.157	0.157	0.000	0.000	0.000	0.000
76	A	77	ARG	1	0.748	0.865	15.172	0.527	0.527	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.949	0.978	19.335	0.146	0.146	0.000	0.000	0.000	0.000
78	A	79	LEU	0	0.012	0.001	17.474	-0.041	-0.041	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.032	-0.014	19.094	0.030	0.030	0.000	0.000	0.000	0.000
80	A	81	LEU	0	0.059	0.002	21.114	-0.014	-0.014	0.000	0.000	0.000	0.000
81	A	82	HIS	0	0.001	0.017	23.714	0.010	0.010	0.000	0.000	0.000	0.000
82	A	83	LYS	1	1.057	1.025	27.010	0.070	0.070	0.000	0.000	0.000	0.000
83	A	84	HIS	0	-0.037	-0.025	29.363	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.873	-0.951	26.038	-0.136	-0.136	0.000	0.000	0.000	0.000
85	A	86	LEU	0	0.021	-0.002	25.497	-0.013	-0.013	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.995	0.957	28.346	0.082	0.082	0.000	0.000	0.000	0.000
87	A	88	ARG	1	0.915	0.944	30.464	0.106	0.106	0.000	0.000	0.000	0.000
88	A	89	LEU	0	0.036	0.054	25.505	0.003	0.003	0.000	0.000	0.000	0.000
89	A	90	LEU	0	0.042	0.059	29.325	-0.003	-0.003	0.000	0.000	0.000	0.000
90	A	91	GLY	0	-0.028	-0.007	31.016	0.002	0.002	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.844	0.927	31.342	0.128	0.128	0.000	0.000	0.000	0.000
92	A	93	VAL	0	0.015	-0.008	28.825	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	94	GLU	-1	-0.893	-0.946	31.936	-0.150	-0.150	0.000	0.000	0.000	0.000
94	A	95	GLN	0	-0.038	0.001	33.455	0.002	0.002	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.948	0.963	33.539	0.158	0.158	0.000	0.000	0.000	0.000
96	A	97	GLY	0	-0.006	0.024	34.101	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	98	LEU	0	-0.042	-0.021	29.407	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	99	THR	0	-0.021	-0.024	25.248	0.001	0.001	0.000	0.000	0.000	0.000
99	A	100	LEU	0	0.009	0.022	22.862	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	101	VAL	0	0.057	0.029	20.980	-0.018	-0.018	0.000	0.000	0.000	0.000
101	A	102	PRO	0	-0.029	-0.005	16.202	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	103	LEU	0	-0.008	0.016	16.858	-0.039	-0.039	0.000	0.000	0.000	0.000
103	A	104	LYS	1	0.932	0.979	11.654	0.487	0.487	0.000	0.000	0.000	0.000
104	A	105	ILE	0	-0.013	0.003	8.979	0.141	0.141	0.000	0.000	0.000	0.000
105	A	106	TYR	0	0.003	-0.015	7.303	-0.427	-0.427	0.000	0.000	0.000	0.000
106	A	107	PHE	0	0.000	-0.004	4.473	0.345	0.467	-0.001	-0.014	-0.108	0.000
107	A	108	ASN	0	0.057	0.040	8.776	0.077	0.077	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.836	-0.920	10.818	0.240	0.240	0.000	0.000	0.000	0.000
109	A	110	ARG	1	0.907	0.951	12.394	0.030	0.030	0.000	0.000	0.000	0.000
110	A	111	GLY	0	0.032	0.026	9.612	0.014	0.014	0.000	0.000	0.000	0.000
111	A	112	TYR	0	-0.067	-0.050	10.278	-0.026	-0.026	0.000	0.000	0.000	0.000
112	A	113	ALA	0	-0.014	0.005	9.019	-0.038	-0.038	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.841	0.906	10.226	0.366	0.366	0.000	0.000	0.000	0.000
114	A	115	VAL	0	0.026	0.027	12.047	-0.147	-0.147	0.000	0.000	0.000	0.000
115	A	116	LEU	0	0.022	0.033	14.349	0.083	0.083	0.000	0.000	0.000	0.000
116	A	117	LEU	0	0.007	0.009	16.701	-0.038	-0.038	0.000	0.000	0.000	0.000
117	A	118	GLY	0	0.071	0.008	19.911	0.023	0.023	0.000	0.000	0.000	0.000
118	A	119	LEU	0	-0.076	-0.013	23.154	-0.008	-0.008	0.000	0.000	0.000	0.000
119	A	120	ALA	0	0.052	0.027	25.008	-0.009	-0.009	0.000	0.000	0.000	0.000
120	A	121	ARG	1	0.922	0.948	27.022	0.169	0.169	0.000	0.000	0.000	0.000
121	A	122	GLY	0	0.085	0.052	28.884	-0.009	-0.009	0.000	0.000	0.000	0.000
122	A	123	LYS	1	0.915	0.989	27.606	0.233	0.233	0.000	0.000	0.000	0.000

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