FMO DATABASE

FMODB ID: JQ429

Calculation Name: 1TJC-A-Xray372

Preferred Name: Prolyl 4-hydroxylase subunit alpha-1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1TJC

Chain ID: A

ChEMBL ID: CHEMBL1250350

UniProt ID: P13674

Base Structure: X-ray

Registration Date: 2023-09-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	95
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-726169.21497
FMO2-HF: Nuclear repulsion	687272.759366
FMO2-HF: Total energy	-38896.455604
FMO2-MP2: Total energy	-39010.128117

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:143:MET)

Summations of interaction energy for fragment #1(A:143:MET)

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.
-2.355	0.631	-0.022	-1.665	-1.298	0.003

Interaction energy analysis for fragmet #1(A:143:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.016

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	145	LEU	0	0.015	0.019	3.859	-1.093	1.893	-0.022	-1.665	-1.298	0.003
4	A	146	THR	0	0.099	0.056	6.390	-0.200	-0.200	0.000	0.000	0.000	0.000
5	A	147	ALA	0	0.020	-0.001	9.519	-0.058	-0.058	0.000	0.000	0.000	0.000
6	A	148	GLU	-1	-0.984	-0.989	12.810	0.030	0.030	0.000	0.000	0.000	0.000
7	A	149	ASP	-1	-0.837	-0.916	9.049	0.274	0.274	0.000	0.000	0.000	0.000
8	A	150	SER	0	-0.099	-0.056	9.827	-0.014	-0.014	0.000	0.000	0.000	0.000
9	A	151	PHE	0	0.047	0.009	11.260	0.058	0.058	0.000	0.000	0.000	0.000
10	A	152	GLU	-1	-0.995	-0.994	13.412	0.159	0.159	0.000	0.000	0.000	0.000
11	A	153	LEU	0	0.004	-0.013	9.507	0.019	0.019	0.000	0.000	0.000	0.000
12	A	154	GLY	0	0.006	-0.002	13.690	0.004	0.004	0.000	0.000	0.000	0.000
13	A	155	LYS	1	0.925	0.968	15.982	0.110	0.110	0.000	0.000	0.000	0.000
14	A	156	VAL	0	0.015	0.011	16.673	0.015	0.015	0.000	0.000	0.000	0.000
15	A	157	ALA	0	0.059	0.037	16.438	0.009	0.009	0.000	0.000	0.000	0.000
16	A	158	TYR	0	-0.018	0.000	18.397	0.020	0.020	0.000	0.000	0.000	0.000
17	A	159	THR	0	-0.143	-0.085	21.436	0.019	0.019	0.000	0.000	0.000	0.000
18	A	160	GLU	-1	-1.014	-1.009	19.209	-0.028	-0.028	0.000	0.000	0.000	0.000
19	A	161	ALA	0	-0.007	0.029	22.585	0.006	0.006	0.000	0.000	0.000	0.000
20	A	162	ASP	-1	-0.853	-0.938	18.163	-0.248	-0.248	0.000	0.000	0.000	0.000
21	A	163	TYR	0	0.049	0.002	19.565	-0.029	-0.029	0.000	0.000	0.000	0.000
22	A	164	TYR	0	0.027	0.037	14.740	-0.030	-0.030	0.000	0.000	0.000	0.000
23	A	165	HIS	0	-0.051	-0.047	13.791	-0.125	-0.125	0.000	0.000	0.000	0.000
24	A	166	THR	0	-0.058	-0.034	15.412	-0.037	-0.037	0.000	0.000	0.000	0.000
25	A	167	GLU	-1	-0.856	-0.940	17.353	-0.428	-0.428	0.000	0.000	0.000	0.000
26	A	168	LEU	0	-0.032	-0.011	10.667	-0.066	-0.066	0.000	0.000	0.000	0.000
27	A	169	TRP	0	-0.012	-0.015	9.265	-0.076	-0.076	0.000	0.000	0.000	0.000
28	A	170	MET	0	0.008	0.010	13.174	-0.040	-0.040	0.000	0.000	0.000	0.000
29	A	171	GLU	-1	-0.891	-0.956	14.644	-0.534	-0.534	0.000	0.000	0.000	0.000
30	A	172	GLN	0	-0.050	-0.028	8.307	-0.064	-0.064	0.000	0.000	0.000	0.000
31	A	173	ALA	0	0.011	0.010	12.129	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	174	LEU	0	-0.041	-0.023	13.934	0.053	0.053	0.000	0.000	0.000	0.000
33	A	175	ARG	1	0.929	0.975	10.621	1.315	1.315	0.000	0.000	0.000	0.000
34	A	176	GLN	0	-0.027	-0.011	9.825	-0.134	-0.134	0.000	0.000	0.000	0.000
35	A	177	LEU	0	-0.017	-0.019	13.251	0.094	0.094	0.000	0.000	0.000	0.000
36	A	178	ASP	-1	-0.948	-0.973	16.918	-0.353	-0.353	0.000	0.000	0.000	0.000
37	A	179	GLU	-1	-1.018	-1.008	12.142	-0.892	-0.892	0.000	0.000	0.000	0.000
38	A	180	GLY	0	-0.056	-0.017	16.136	0.045	0.045	0.000	0.000	0.000	0.000
39	A	181	GLU	-1	-0.854	-0.920	11.401	-0.525	-0.525	0.000	0.000	0.000	0.000
40	A	182	ILE	0	-0.047	-0.025	15.616	0.029	0.029	0.000	0.000	0.000	0.000
41	A	183	SER	0	0.036	0.007	15.371	0.015	0.015	0.000	0.000	0.000	0.000
42	A	184	THR	0	-0.017	-0.005	17.622	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	185	ILE	0	-0.045	0.000	16.371	0.001	0.001	0.000	0.000	0.000	0.000
44	A	186	ASP	-1	-0.738	-0.860	19.201	-0.187	-0.187	0.000	0.000	0.000	0.000
45	A	187	LYS	1	0.984	0.982	20.933	0.271	0.271	0.000	0.000	0.000	0.000
46	A	188	VAL	0	0.000	0.007	21.927	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	189	SER	0	-0.043	-0.044	21.789	0.005	0.005	0.000	0.000	0.000	0.000
48	A	190	VAL	0	0.010	0.005	17.898	0.007	0.007	0.000	0.000	0.000	0.000
49	A	191	LEU	0	-0.020	-0.017	20.539	-0.014	-0.014	0.000	0.000	0.000	0.000
50	A	192	ASP	-1	-0.855	-0.914	23.237	-0.138	-0.138	0.000	0.000	0.000	0.000
51	A	193	TYR	0	-0.024	-0.014	20.882	0.011	0.011	0.000	0.000	0.000	0.000
52	A	194	LEU	0	0.003	0.015	18.789	0.006	0.006	0.000	0.000	0.000	0.000
53	A	195	SER	0	-0.042	-0.020	21.879	0.008	0.008	0.000	0.000	0.000	0.000
54	A	196	TYR	0	-0.028	-0.017	25.335	0.010	0.010	0.000	0.000	0.000	0.000
55	A	197	ALA	0	0.020	-0.005	21.308	0.012	0.012	0.000	0.000	0.000	0.000
56	A	198	VAL	0	0.026	0.023	21.873	0.002	0.002	0.000	0.000	0.000	0.000
57	A	199	TYR	0	0.005	0.018	24.061	0.018	0.018	0.000	0.000	0.000	0.000
58	A	200	GLN	0	-0.088	-0.027	25.715	0.021	0.021	0.000	0.000	0.000	0.000
59	A	201	GLN	0	-0.069	-0.048	20.900	0.007	0.007	0.000	0.000	0.000	0.000
60	A	202	GLY	0	-0.034	-0.013	25.924	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	203	ASP	-1	-0.886	-0.935	25.729	-0.231	-0.231	0.000	0.000	0.000	0.000
62	A	204	LEU	0	0.007	-0.025	27.863	-0.005	-0.005	0.000	0.000	0.000	0.000
63	A	205	ASP	-1	-0.902	-0.940	30.042	-0.161	-0.161	0.000	0.000	0.000	0.000
64	A	206	LYS	1	0.871	0.950	20.216	0.400	0.400	0.000	0.000	0.000	0.000
65	A	207	ALA	0	0.026	0.018	26.978	-0.005	-0.005	0.000	0.000	0.000	0.000
66	A	208	LEU	0	0.009	0.016	27.890	0.006	0.006	0.000	0.000	0.000	0.000
67	A	209	LEU	0	-0.021	-0.006	25.794	0.005	0.005	0.000	0.000	0.000	0.000
68	A	210	LEU	0	0.015	-0.010	22.659	0.003	0.003	0.000	0.000	0.000	0.000
69	A	211	THR	0	-0.029	-0.022	26.743	0.007	0.007	0.000	0.000	0.000	0.000
70	A	212	LYS	1	0.937	0.963	29.730	0.148	0.148	0.000	0.000	0.000	0.000
71	A	213	LYS	1	0.977	0.991	23.944	0.285	0.285	0.000	0.000	0.000	0.000
72	A	214	LEU	0	-0.017	-0.008	26.874	0.004	0.004	0.000	0.000	0.000	0.000
73	A	215	LEU	0	-0.037	-0.030	28.476	0.008	0.008	0.000	0.000	0.000	0.000
74	A	216	GLU	-1	-0.976	-0.977	30.236	-0.163	-0.163	0.000	0.000	0.000	0.000
75	A	217	LEU	0	-0.105	-0.046	26.586	0.003	0.003	0.000	0.000	0.000	0.000
76	A	218	ASP	-1	-0.903	-0.964	30.053	-0.101	-0.101	0.000	0.000	0.000	0.000
77	A	219	PRO	0	-0.001	0.007	31.850	0.000	0.000	0.000	0.000	0.000	0.000
78	A	220	GLU	-1	-0.873	-0.952	35.127	-0.080	-0.080	0.000	0.000	0.000	0.000
79	A	221	HIS	0	0.004	0.032	28.590	0.007	0.007	0.000	0.000	0.000	0.000
80	A	222	GLN	0	-0.008	-0.008	33.360	0.001	0.001	0.000	0.000	0.000	0.000
81	A	223	ARG	1	0.833	0.897	28.356	0.117	0.117	0.000	0.000	0.000	0.000
82	A	224	ALA	0	0.051	0.035	30.472	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	225	ASN	0	-0.031	-0.028	32.266	-0.002	-0.002	0.000	0.000	0.000	0.000
84	A	226	GLY	0	-0.035	-0.015	35.919	0.002	0.002	0.000	0.000	0.000	0.000
85	A	227	ASN	0	0.039	0.003	30.232	0.012	0.012	0.000	0.000	0.000	0.000
86	A	228	LEU	0	-0.003	0.023	34.072	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	229	LYS	1	0.937	0.959	35.587	0.080	0.080	0.000	0.000	0.000	0.000
88	A	230	TYR	0	-0.078	-0.043	33.440	0.007	0.007	0.000	0.000	0.000	0.000
89	A	231	PHE	0	0.055	0.004	30.084	0.002	0.002	0.000	0.000	0.000	0.000
90	A	232	GLU	-1	-0.904	-0.953	35.177	-0.109	-0.109	0.000	0.000	0.000	0.000
91	A	233	TYR	0	-0.076	-0.033	38.043	0.006	0.006	0.000	0.000	0.000	0.000
92	A	234	ILE	0	-0.044	-0.021	34.816	0.004	0.004	0.000	0.000	0.000	0.000
93	A	235	MET	0	-0.007	-0.008	34.818	0.000	0.000	0.000	0.000	0.000	0.000
94	A	236	ALA	0	-0.022	0.009	37.960	0.003	0.003	0.000	0.000	0.000	0.000
95	A	237	LYS	1	0.882	0.960	40.961	0.078	0.078	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:143:MET)