FMO DATABASE

FMODB ID: LNQ79

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:

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

Total energy (hartree)

FMO2-HF: Electronic energy	-729906.146895
FMO2-HF: Nuclear repulsion	691008.587455
FMO2-HF: Total energy	-38897.55944
FMO2-MP2: Total energy	-39011.222745

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.
-3.288	-0.447	-0.009	-1.56	-1.271	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 : -0.020 / q_NPA : -0.019

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	-0.011	0.007	3.681	-1.146	1.695	-0.009	-1.560	-1.271	0.003
4	A	146	THR	0	0.033	-0.004	6.323	-0.147	-0.147	0.000	0.000	0.000	0.000
5	A	147	ALA	0	0.027	0.012	9.511	-0.030	-0.030	0.000	0.000	0.000	0.000
6	A	148	GLU	-1	-0.804	-0.871	12.897	-0.071	-0.071	0.000	0.000	0.000	0.000
7	A	149	ASP	-1	-0.823	-0.887	8.476	-0.036	-0.036	0.000	0.000	0.000	0.000
8	A	150	SER	0	-0.066	-0.060	9.857	0.039	0.039	0.000	0.000	0.000	0.000
9	A	151	PHE	0	0.040	0.010	11.402	0.057	0.057	0.000	0.000	0.000	0.000
10	A	152	GLU	-1	-0.893	-0.938	13.335	0.081	0.081	0.000	0.000	0.000	0.000
11	A	153	LEU	0	-0.003	-0.009	9.437	0.035	0.035	0.000	0.000	0.000	0.000
12	A	154	GLY	0	0.009	0.004	13.788	0.013	0.013	0.000	0.000	0.000	0.000
13	A	155	LYS	1	0.857	0.921	16.051	0.078	0.078	0.000	0.000	0.000	0.000
14	A	156	VAL	0	-0.024	-0.005	16.666	0.020	0.020	0.000	0.000	0.000	0.000
15	A	157	ALA	0	0.039	0.032	16.379	0.010	0.010	0.000	0.000	0.000	0.000
16	A	158	TYR	0	-0.001	-0.010	18.414	0.015	0.015	0.000	0.000	0.000	0.000
17	A	159	THR	0	-0.122	-0.079	21.532	0.016	0.016	0.000	0.000	0.000	0.000
18	A	160	GLU	-1	-0.978	-0.969	18.601	0.031	0.031	0.000	0.000	0.000	0.000
19	A	161	ALA	0	-0.041	-0.027	23.000	0.012	0.012	0.000	0.000	0.000	0.000
20	A	162	ASP	-1	-0.810	-0.872	18.544	-0.204	-0.204	0.000	0.000	0.000	0.000
21	A	163	TYR	0	0.061	0.013	19.405	-0.031	-0.031	0.000	0.000	0.000	0.000
22	A	164	TYR	0	0.020	0.036	15.443	-0.048	-0.048	0.000	0.000	0.000	0.000
23	A	165	HIS	0	-0.065	-0.064	13.062	-0.102	-0.102	0.000	0.000	0.000	0.000
24	A	166	THR	0	-0.061	-0.043	15.170	-0.045	-0.045	0.000	0.000	0.000	0.000
25	A	167	GLU	-1	-0.821	-0.896	17.113	-0.433	-0.433	0.000	0.000	0.000	0.000
26	A	168	LEU	0	-0.041	-0.013	11.617	-0.077	-0.077	0.000	0.000	0.000	0.000
27	A	169	TRP	0	-0.031	-0.025	9.659	-0.111	-0.111	0.000	0.000	0.000	0.000
28	A	170	MET	0	0.025	0.025	13.060	-0.046	-0.046	0.000	0.000	0.000	0.000
29	A	171	GLU	-1	-0.809	-0.919	15.150	-0.556	-0.556	0.000	0.000	0.000	0.000
30	A	172	GLN	0	-0.074	-0.031	8.639	-0.191	-0.191	0.000	0.000	0.000	0.000
31	A	173	ALA	0	0.016	0.009	12.265	-0.028	-0.028	0.000	0.000	0.000	0.000
32	A	174	LEU	0	-0.012	-0.009	14.063	0.044	0.044	0.000	0.000	0.000	0.000
33	A	175	ARG	1	0.877	0.953	10.583	1.455	1.455	0.000	0.000	0.000	0.000
34	A	176	GLN	0	-0.025	-0.019	9.631	-0.240	-0.240	0.000	0.000	0.000	0.000
35	A	177	LEU	0	-0.009	-0.001	13.226	0.083	0.083	0.000	0.000	0.000	0.000
36	A	178	ASP	-1	-0.840	-0.899	16.935	-0.361	-0.361	0.000	0.000	0.000	0.000
37	A	179	GLU	-1	-1.002	-1.001	12.066	-1.123	-1.123	0.000	0.000	0.000	0.000
38	A	180	GLY	0	-0.049	-0.018	15.892	0.035	0.035	0.000	0.000	0.000	0.000
39	A	181	GLU	-1	-0.829	-0.909	11.379	-0.651	-0.651	0.000	0.000	0.000	0.000
40	A	182	ILE	0	-0.053	-0.030	15.374	0.037	0.037	0.000	0.000	0.000	0.000
41	A	183	SER	0	-0.026	-0.016	15.296	0.002	0.002	0.000	0.000	0.000	0.000
42	A	184	THR	0	-0.091	-0.069	17.278	0.015	0.015	0.000	0.000	0.000	0.000
43	A	185	ILE	0	-0.054	-0.005	16.092	0.013	0.013	0.000	0.000	0.000	0.000
44	A	186	ASP	-1	-0.733	-0.857	19.317	-0.223	-0.223	0.000	0.000	0.000	0.000
45	A	187	LYS	1	0.845	0.894	21.189	0.339	0.339	0.000	0.000	0.000	0.000
46	A	188	VAL	0	-0.004	-0.017	22.175	-0.013	-0.013	0.000	0.000	0.000	0.000
47	A	189	SER	0	-0.033	-0.043	22.154	0.009	0.009	0.000	0.000	0.000	0.000
48	A	190	VAL	0	-0.015	-0.013	17.557	0.008	0.008	0.000	0.000	0.000	0.000
49	A	191	LEU	0	0.005	-0.006	20.449	-0.011	-0.011	0.000	0.000	0.000	0.000
50	A	192	ASP	-1	-0.799	-0.854	23.208	-0.139	-0.139	0.000	0.000	0.000	0.000
51	A	193	TYR	0	-0.011	-0.006	21.096	0.012	0.012	0.000	0.000	0.000	0.000
52	A	194	LEU	0	-0.007	0.011	18.838	0.011	0.011	0.000	0.000	0.000	0.000
53	A	195	SER	0	-0.052	-0.027	21.853	0.009	0.009	0.000	0.000	0.000	0.000
54	A	196	TYR	0	-0.036	-0.031	25.551	0.011	0.011	0.000	0.000	0.000	0.000
55	A	197	ALA	0	0.015	0.000	21.165	0.013	0.013	0.000	0.000	0.000	0.000
56	A	198	VAL	0	0.014	0.020	22.143	0.002	0.002	0.000	0.000	0.000	0.000
57	A	199	TYR	0	0.006	0.004	24.202	0.018	0.018	0.000	0.000	0.000	0.000
58	A	200	GLN	0	-0.090	-0.027	25.469	0.023	0.023	0.000	0.000	0.000	0.000
59	A	201	GLN	0	-0.058	-0.050	21.204	0.006	0.006	0.000	0.000	0.000	0.000
60	A	202	GLY	0	-0.018	-0.004	26.014	0.003	0.003	0.000	0.000	0.000	0.000
61	A	203	ASP	-1	-0.879	-0.929	25.765	-0.244	-0.244	0.000	0.000	0.000	0.000
62	A	204	LEU	0	0.005	-0.022	28.094	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	205	ASP	-1	-0.878	-0.933	30.320	-0.170	-0.170	0.000	0.000	0.000	0.000
64	A	206	LYS	1	0.812	0.890	20.548	0.407	0.407	0.000	0.000	0.000	0.000
65	A	207	ALA	0	0.029	0.021	26.942	-0.009	-0.009	0.000	0.000	0.000	0.000
66	A	208	LEU	0	-0.037	-0.007	27.957	0.005	0.005	0.000	0.000	0.000	0.000
67	A	209	LEU	0	-0.042	-0.014	26.373	0.005	0.005	0.000	0.000	0.000	0.000
68	A	210	LEU	0	0.022	-0.002	22.845	0.002	0.002	0.000	0.000	0.000	0.000
69	A	211	THR	0	-0.011	-0.021	26.704	0.007	0.007	0.000	0.000	0.000	0.000
70	A	212	LYS	1	0.811	0.895	29.621	0.156	0.156	0.000	0.000	0.000	0.000
71	A	213	LYS	1	0.850	0.889	25.964	0.252	0.252	0.000	0.000	0.000	0.000
72	A	214	LEU	0	-0.017	0.019	26.764	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	215	LEU	0	-0.025	-0.019	28.432	0.008	0.008	0.000	0.000	0.000	0.000
74	A	216	GLU	-1	-0.900	-0.920	29.197	-0.210	-0.210	0.000	0.000	0.000	0.000
75	A	217	LEU	0	-0.083	-0.038	26.673	0.002	0.002	0.000	0.000	0.000	0.000
76	A	218	ASP	-1	-0.881	-0.952	30.077	-0.117	-0.117	0.000	0.000	0.000	0.000
77	A	219	PRO	0	0.009	0.009	31.911	0.000	0.000	0.000	0.000	0.000	0.000
78	A	220	GLU	-1	-0.905	-0.956	35.210	-0.094	-0.094	0.000	0.000	0.000	0.000
79	A	221	HIS	0	0.010	0.037	28.348	0.012	0.012	0.000	0.000	0.000	0.000
80	A	222	GLN	0	-0.014	-0.010	33.392	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	223	ARG	1	0.797	0.858	27.996	0.124	0.124	0.000	0.000	0.000	0.000
82	A	224	ALA	0	0.051	0.036	30.648	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	225	ASN	0	-0.019	-0.033	32.234	0.000	0.000	0.000	0.000	0.000	0.000
84	A	226	GLY	0	-0.053	-0.020	35.463	0.005	0.005	0.000	0.000	0.000	0.000
85	A	227	ASN	0	0.012	-0.012	29.540	0.014	0.014	0.000	0.000	0.000	0.000
86	A	228	LEU	0	0.009	0.022	33.545	-0.002	-0.002	0.000	0.000	0.000	0.000
87	A	229	LYS	1	0.952	0.970	35.272	0.088	0.088	0.000	0.000	0.000	0.000
88	A	230	TYR	0	-0.076	-0.026	33.267	0.009	0.009	0.000	0.000	0.000	0.000
89	A	231	PHE	0	0.058	0.004	29.671	0.004	0.004	0.000	0.000	0.000	0.000
90	A	232	GLU	-1	-0.780	-0.890	35.033	-0.123	-0.123	0.000	0.000	0.000	0.000
91	A	233	TYR	0	-0.055	-0.023	38.058	0.007	0.007	0.000	0.000	0.000	0.000
92	A	234	ILE	0	-0.025	-0.017	34.965	0.006	0.006	0.000	0.000	0.000	0.000
93	A	235	MET	0	-0.016	-0.005	34.500	0.003	0.003	0.000	0.000	0.000	0.000
94	A	236	ALA	0	-0.042	-0.003	38.192	0.002	0.002	0.000	0.000	0.000	0.000
95	A	237	LYS	1	0.828	0.932	40.993	0.083	0.083	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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