FMO DATABASE

FMODB ID: 7GNZK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1051457.205412
FMO2-HF: Nuclear repulsion	1003777.481997
FMO2-HF: Total energy	-47679.723415
FMO2-MP2: Total energy	-47823.648744

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.
-8.087	-4.961	8.274	-5.698	-5.699	-0.039

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 : 0.024 / q_NPA : 0.010

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	0.007	0.019	3.903	-1.335	0.785	-0.010	-1.067	-1.043	0.001
4	A	5	LEU	0	0.031	0.024	3.829	-0.025	0.153	0.000	-0.040	-0.138	0.000
5	A	6	GLU	-1	-0.810	-0.916	7.491	-0.608	-0.608	0.000	0.000	0.000	0.000
6	A	7	ASN	0	0.009	-0.002	11.223	0.029	0.029	0.000	0.000	0.000	0.000
7	A	8	ARG	1	0.887	0.919	13.478	0.571	0.571	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.886	0.947	15.341	0.447	0.447	0.000	0.000	0.000	0.000
9	A	10	ALA	0	0.059	0.026	17.751	0.050	0.050	0.000	0.000	0.000	0.000
10	A	11	ARG	1	0.958	0.979	19.090	0.389	0.389	0.000	0.000	0.000	0.000
11	A	12	HIS	0	0.045	0.030	19.573	0.028	0.028	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.860	-0.890	22.551	-0.263	-0.263	0.000	0.000	0.000	0.000
13	A	14	TYR	0	-0.052	-0.046	20.666	0.007	0.007	0.000	0.000	0.000	0.000
14	A	15	GLU	-1	-0.896	-0.933	23.783	-0.266	-0.266	0.000	0.000	0.000	0.000
15	A	16	ILE	0	-0.047	-0.039	21.703	0.001	0.001	0.000	0.000	0.000	0.000
16	A	17	LEU	0	-0.015	-0.005	25.210	0.010	0.010	0.000	0.000	0.000	0.000
17	A	18	GLU	-1	-0.789	-0.871	26.341	-0.195	-0.195	0.000	0.000	0.000	0.000
18	A	19	THR	0	-0.018	-0.023	20.992	-0.022	-0.022	0.000	0.000	0.000	0.000
19	A	20	TYR	0	-0.041	-0.034	21.529	0.019	0.019	0.000	0.000	0.000	0.000
20	A	21	GLU	-1	-0.823	-0.887	16.134	-0.533	-0.533	0.000	0.000	0.000	0.000
21	A	22	ALA	0	0.010	0.006	17.700	0.059	0.059	0.000	0.000	0.000	0.000
22	A	23	GLY	0	-0.002	-0.003	16.417	-0.070	-0.070	0.000	0.000	0.000	0.000
23	A	24	ILE	0	0.034	0.006	13.238	0.008	0.008	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.016	0.027	16.568	0.020	0.020	0.000	0.000	0.000	0.000
25	A	26	LEU	0	-0.015	-0.002	11.698	0.021	0.021	0.000	0.000	0.000	0.000
26	A	27	LYS	1	0.891	0.928	15.518	0.163	0.163	0.000	0.000	0.000	0.000
27	A	28	GLY	0	0.068	0.035	13.817	0.030	0.030	0.000	0.000	0.000	0.000
28	A	29	THR	0	0.048	0.025	12.248	0.007	0.007	0.000	0.000	0.000	0.000
29	A	30	GLU	-1	-0.702	-0.818	11.202	-0.213	-0.213	0.000	0.000	0.000	0.000
30	A	31	VAL	0	0.014	0.010	9.029	-0.166	-0.166	0.000	0.000	0.000	0.000
31	A	32	LYS	1	0.902	0.952	7.626	-0.680	-0.680	0.000	0.000	0.000	0.000
32	A	33	SER	0	0.003	-0.014	6.826	0.377	0.377	0.000	0.000	0.000	0.000
33	A	34	LEU	0	0.011	0.004	5.768	-0.147	-0.147	0.000	0.000	0.000	0.000
34	A	35	ARG	1	0.806	0.929	3.065	-2.299	-1.963	0.073	-0.170	-0.238	0.000
35	A	36	ALA	0	0.031	0.021	2.743	2.830	5.080	1.345	-1.477	-2.117	-0.009
36	A	37	GLY	0	0.032	0.007	2.000	-8.471	-10.345	6.866	-2.888	-2.103	-0.031
37	A	38	LYS	1	0.866	0.931	4.291	0.519	0.635	0.000	-0.056	-0.060	0.000
38	A	39	VAL	0	-0.029	-0.008	6.950	0.201	0.201	0.000	0.000	0.000	0.000
39	A	40	ASP	-1	-0.772	-0.861	9.261	-0.528	-0.528	0.000	0.000	0.000	0.000
40	A	41	PHE	0	0.017	0.006	10.542	0.088	0.088	0.000	0.000	0.000	0.000
41	A	42	THR	0	-0.037	-0.040	14.676	0.064	0.064	0.000	0.000	0.000	0.000
42	A	43	GLY	0	0.023	0.017	17.757	0.026	0.026	0.000	0.000	0.000	0.000
43	A	44	SER	0	-0.101	-0.036	16.988	0.005	0.005	0.000	0.000	0.000	0.000
44	A	45	PHE	0	0.032	0.005	18.969	-0.014	-0.014	0.000	0.000	0.000	0.000
45	A	46	ALA	0	-0.028	-0.020	20.598	-0.005	-0.005	0.000	0.000	0.000	0.000
46	A	47	ARG	1	0.860	0.930	22.352	0.204	0.204	0.000	0.000	0.000	0.000
47	A	48	PHE	0	-0.002	-0.016	25.869	-0.009	-0.009	0.000	0.000	0.000	0.000
48	A	49	GLU	-1	-0.830	-0.899	26.789	-0.154	-0.154	0.000	0.000	0.000	0.000
49	A	50	ASP	-1	-0.829	-0.893	29.499	-0.103	-0.103	0.000	0.000	0.000	0.000
50	A	51	GLY	0	-0.062	-0.037	31.538	-0.006	-0.006	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.849	-0.894	26.805	-0.157	-0.157	0.000	0.000	0.000	0.000
52	A	53	LEU	0	-0.018	0.000	22.900	-0.002	-0.002	0.000	0.000	0.000	0.000
53	A	54	TYR	0	-0.006	-0.036	22.182	-0.010	-0.010	0.000	0.000	0.000	0.000
54	A	55	LEU	0	-0.003	0.008	15.407	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	56	GLU	-1	-0.787	-0.895	19.658	-0.198	-0.198	0.000	0.000	0.000	0.000
56	A	57	ASN	0	0.030	0.003	19.460	-0.028	-0.028	0.000	0.000	0.000	0.000
57	A	58	LEU	0	-0.002	0.012	12.247	-0.013	-0.013	0.000	0.000	0.000	0.000
58	A	59	TYR	0	-0.066	-0.068	12.223	0.040	0.040	0.000	0.000	0.000	0.000
59	A	60	ILE	0	-0.033	-0.039	9.622	-0.140	-0.140	0.000	0.000	0.000	0.000
60	A	61	ALA	0	0.031	0.008	9.270	0.091	0.091	0.000	0.000	0.000	0.000
61	A	62	PRO	0	0.015	0.012	10.440	0.075	0.075	0.000	0.000	0.000	0.000
62	A	63	TYR	0	-0.017	-0.028	10.222	0.138	0.138	0.000	0.000	0.000	0.000
63	A	64	GLU	-1	-0.765	-0.824	10.492	0.058	0.058	0.000	0.000	0.000	0.000
64	A	65	LYS	1	0.901	0.934	7.199	-1.256	-1.256	0.000	0.000	0.000	0.000
65	A	66	GLY	0	0.055	0.028	11.406	0.054	0.054	0.000	0.000	0.000	0.000
66	A	67	SER	0	-0.009	0.005	15.207	-0.059	-0.059	0.000	0.000	0.000	0.000
67	A	68	TYR	0	-0.021	-0.012	13.351	0.056	0.056	0.000	0.000	0.000	0.000
68	A	69	ALA	0	0.041	0.027	17.621	-0.031	-0.031	0.000	0.000	0.000	0.000
69	A	70	ASN	0	-0.045	-0.025	14.754	0.010	0.010	0.000	0.000	0.000	0.000
70	A	71	VAL	0	0.005	-0.003	16.316	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	72	ASP	-1	-0.800	-0.907	17.336	-0.161	-0.161	0.000	0.000	0.000	0.000
72	A	73	PRO	0	0.033	0.008	15.298	-0.035	-0.035	0.000	0.000	0.000	0.000
73	A	74	ARG	1	0.806	0.909	15.483	0.251	0.251	0.000	0.000	0.000	0.000
74	A	75	ARG	1	0.842	0.930	17.250	0.212	0.212	0.000	0.000	0.000	0.000
75	A	76	LYS	1	0.816	0.887	18.735	0.134	0.134	0.000	0.000	0.000	0.000
76	A	77	ARG	1	0.724	0.841	15.096	0.348	0.348	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.858	0.914	19.269	0.126	0.126	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.022	-0.014	17.667	-0.031	-0.031	0.000	0.000	0.000	0.000
79	A	80	LEU	0	-0.049	-0.015	19.664	0.034	0.034	0.000	0.000	0.000	0.000
80	A	81	LEU	0	0.062	0.010	21.330	-0.024	-0.024	0.000	0.000	0.000	0.000
81	A	82	HIS	0	0.032	0.028	24.172	0.026	0.026	0.000	0.000	0.000	0.000
82	A	83	LYS	1	1.022	1.000	27.400	0.107	0.107	0.000	0.000	0.000	0.000
83	A	84	HIS	0	-0.018	-0.012	29.895	0.009	0.009	0.000	0.000	0.000	0.000
84	A	85	GLU	-1	-0.826	-0.897	26.877	-0.197	-0.197	0.000	0.000	0.000	0.000
85	A	86	LEU	0	0.005	0.000	25.943	-0.007	-0.007	0.000	0.000	0.000	0.000
86	A	87	ARG	1	0.961	0.981	28.557	0.116	0.116	0.000	0.000	0.000	0.000
87	A	88	ARG	1	0.880	0.934	30.688	0.149	0.149	0.000	0.000	0.000	0.000
88	A	89	LEU	0	0.039	0.023	24.805	0.004	0.004	0.000	0.000	0.000	0.000
89	A	90	LEU	0	0.032	0.022	29.132	0.002	0.002	0.000	0.000	0.000	0.000
90	A	91	GLY	0	-0.014	-0.003	30.757	0.005	0.005	0.000	0.000	0.000	0.000
91	A	92	LYS	1	0.767	0.860	30.545	0.193	0.193	0.000	0.000	0.000	0.000
92	A	93	VAL	0	0.022	0.008	27.909	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	94	GLU	-1	-0.834	-0.918	30.388	-0.168	-0.168	0.000	0.000	0.000	0.000
94	A	95	GLN	0	-0.053	-0.013	32.688	0.009	0.009	0.000	0.000	0.000	0.000
95	A	96	LYS	1	0.933	0.957	32.527	0.151	0.151	0.000	0.000	0.000	0.000
96	A	97	GLY	0	0.018	0.029	33.180	-0.002	-0.002	0.000	0.000	0.000	0.000
97	A	98	LEU	0	-0.052	-0.024	28.938	-0.007	-0.007	0.000	0.000	0.000	0.000
98	A	99	THR	0	-0.013	-0.008	24.550	0.007	0.007	0.000	0.000	0.000	0.000
99	A	100	LEU	0	0.002	0.016	22.359	-0.011	-0.011	0.000	0.000	0.000	0.000
100	A	101	VAL	0	0.046	0.027	19.994	-0.005	-0.005	0.000	0.000	0.000	0.000
101	A	102	PRO	0	-0.011	0.002	14.899	-0.015	-0.015	0.000	0.000	0.000	0.000
102	A	103	LEU	0	-0.008	-0.007	16.206	-0.012	-0.012	0.000	0.000	0.000	0.000
103	A	104	LYS	1	0.857	0.924	11.678	0.896	0.896	0.000	0.000	0.000	0.000
104	A	105	ILE	0	-0.014	0.005	8.230	0.196	0.196	0.000	0.000	0.000	0.000
105	A	106	TYR	0	-0.026	-0.044	7.630	-0.457	-0.457	0.000	0.000	0.000	0.000
106	A	107	PHE	0	-0.043	-0.029	5.269	0.501	0.501	0.000	0.000	0.000	0.000
107	A	108	ASN	0	0.021	0.016	9.167	0.038	0.038	0.000	0.000	0.000	0.000
108	A	109	GLU	-1	-0.843	-0.926	12.118	-0.205	-0.205	0.000	0.000	0.000	0.000
109	A	110	ARG	1	0.918	0.964	14.067	0.195	0.195	0.000	0.000	0.000	0.000
110	A	111	GLY	0	0.035	0.026	10.905	0.049	0.049	0.000	0.000	0.000	0.000
111	A	112	TYR	0	-0.019	-0.020	10.534	-0.032	-0.032	0.000	0.000	0.000	0.000
112	A	113	ALA	0	-0.006	-0.001	10.096	-0.070	-0.070	0.000	0.000	0.000	0.000
113	A	114	LYS	1	0.826	0.917	11.008	0.625	0.625	0.000	0.000	0.000	0.000
114	A	115	VAL	0	0.024	0.008	11.993	-0.203	-0.203	0.000	0.000	0.000	0.000
115	A	116	LEU	0	0.019	0.026	14.292	0.101	0.101	0.000	0.000	0.000	0.000
116	A	117	LEU	0	0.013	-0.004	16.431	-0.046	-0.046	0.000	0.000	0.000	0.000
117	A	118	GLY	0	0.060	0.007	19.201	0.016	0.016	0.000	0.000	0.000	0.000
118	A	119	LEU	0	-0.065	-0.011	22.516	-0.001	-0.001	0.000	0.000	0.000	0.000
119	A	120	ALA	0	0.028	0.014	23.863	0.002	0.002	0.000	0.000	0.000	0.000
120	A	121	ARG	1	0.970	0.980	25.903	0.197	0.197	0.000	0.000	0.000	0.000
121	A	122	GLY	0	0.091	0.049	27.909	-0.017	-0.017	0.000	0.000	0.000	0.000
122	A	123	LYS	1	0.784	0.883	26.654	0.250	0.250	0.000	0.000	0.000	0.000

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