FMO DATABASE

FMODB ID: 3JK7L

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

Total energy (hartree)

FMO2-HF: Electronic energy	-727654.085144
FMO2-HF: Nuclear repulsion	688756.780748
FMO2-HF: Total energy	-38897.304397
FMO2-MP2: Total energy	-39010.988849

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.
-3.097	-0.114	-0.023	-1.665	-1.296	0.002

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 : -0.026 / q_NPA : -0.020

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	0.005	0.013	3.859	-1.128	1.855	-0.023	-1.665	-1.296	0.002
4	A	146	THR	0	0.038	0.006	6.458	-0.168	-0.168	0.000	0.000	0.000	0.000
5	A	147	ALA	0	0.020	0.009	9.570	-0.051	-0.051	0.000	0.000	0.000	0.000
6	A	148	GLU	-1	-0.881	-0.918	12.852	-0.060	-0.060	0.000	0.000	0.000	0.000
7	A	149	ASP	-1	-0.799	-0.877	8.803	-0.048	-0.048	0.000	0.000	0.000	0.000
8	A	150	SER	0	-0.082	-0.061	9.924	0.016	0.016	0.000	0.000	0.000	0.000
9	A	151	PHE	0	0.049	0.014	11.337	0.074	0.074	0.000	0.000	0.000	0.000
10	A	152	GLU	-1	-1.007	-1.002	13.543	0.123	0.123	0.000	0.000	0.000	0.000
11	A	153	LEU	0	0.012	-0.012	9.265	0.028	0.028	0.000	0.000	0.000	0.000
12	A	154	GLY	0	0.011	0.002	13.609	0.014	0.014	0.000	0.000	0.000	0.000
13	A	155	LYS	1	0.916	0.966	15.843	0.135	0.135	0.000	0.000	0.000	0.000
14	A	156	VAL	0	0.005	0.009	16.501	0.018	0.018	0.000	0.000	0.000	0.000
15	A	157	ALA	0	0.051	0.031	16.278	0.012	0.012	0.000	0.000	0.000	0.000
16	A	158	TYR	0	-0.007	0.004	18.275	0.023	0.023	0.000	0.000	0.000	0.000
17	A	159	THR	0	-0.111	-0.072	21.305	0.018	0.018	0.000	0.000	0.000	0.000
18	A	160	GLU	-1	-1.015	-1.009	18.793	-0.003	-0.003	0.000	0.000	0.000	0.000
19	A	161	ALA	0	-0.014	0.025	22.481	0.009	0.009	0.000	0.000	0.000	0.000
20	A	162	ASP	-1	-0.846	-0.917	18.471	-0.239	-0.239	0.000	0.000	0.000	0.000
21	A	163	TYR	0	0.055	0.012	19.441	-0.033	-0.033	0.000	0.000	0.000	0.000
22	A	164	TYR	0	0.035	0.038	15.113	-0.052	-0.052	0.000	0.000	0.000	0.000
23	A	165	HIS	0	-0.062	-0.064	13.406	-0.119	-0.119	0.000	0.000	0.000	0.000
24	A	166	THR	0	-0.066	-0.046	15.280	-0.044	-0.044	0.000	0.000	0.000	0.000
25	A	167	GLU	-1	-0.840	-0.924	17.212	-0.453	-0.453	0.000	0.000	0.000	0.000
26	A	168	LEU	0	-0.035	-0.011	10.927	-0.077	-0.077	0.000	0.000	0.000	0.000
27	A	169	TRP	0	-0.018	-0.023	9.391	-0.089	-0.089	0.000	0.000	0.000	0.000
28	A	170	MET	0	0.006	0.017	13.030	-0.051	-0.051	0.000	0.000	0.000	0.000
29	A	171	GLU	-1	-0.821	-0.919	14.705	-0.575	-0.575	0.000	0.000	0.000	0.000
30	A	172	GLN	0	-0.062	-0.025	8.655	-0.168	-0.168	0.000	0.000	0.000	0.000
31	A	173	ALA	0	0.021	0.016	12.129	-0.013	-0.013	0.000	0.000	0.000	0.000
32	A	174	LEU	0	-0.028	-0.015	14.010	0.051	0.051	0.000	0.000	0.000	0.000
33	A	175	ARG	1	0.901	0.956	10.345	1.508	1.508	0.000	0.000	0.000	0.000
34	A	176	GLN	0	-0.035	-0.021	9.742	-0.231	-0.231	0.000	0.000	0.000	0.000
35	A	177	LEU	0	-0.010	-0.015	13.279	0.092	0.092	0.000	0.000	0.000	0.000
36	A	178	ASP	-1	-0.842	-0.891	16.946	-0.367	-0.367	0.000	0.000	0.000	0.000
37	A	179	GLU	-1	-0.996	-0.997	12.246	-1.043	-1.043	0.000	0.000	0.000	0.000
38	A	180	GLY	0	-0.051	-0.016	16.163	0.045	0.045	0.000	0.000	0.000	0.000
39	A	181	GLU	-1	-0.846	-0.912	11.600	-0.655	-0.655	0.000	0.000	0.000	0.000
40	A	182	ILE	0	-0.046	-0.027	15.643	0.038	0.038	0.000	0.000	0.000	0.000
41	A	183	SER	0	0.025	0.001	15.371	0.008	0.008	0.000	0.000	0.000	0.000
42	A	184	THR	0	-0.088	-0.054	17.661	0.013	0.013	0.000	0.000	0.000	0.000
43	A	185	ILE	0	-0.036	0.000	16.130	0.004	0.004	0.000	0.000	0.000	0.000
44	A	186	ASP	-1	-0.726	-0.844	19.258	-0.229	-0.229	0.000	0.000	0.000	0.000
45	A	187	LYS	1	0.846	0.882	20.999	0.351	0.351	0.000	0.000	0.000	0.000
46	A	188	VAL	0	-0.005	-0.016	21.995	-0.015	-0.015	0.000	0.000	0.000	0.000
47	A	189	SER	0	-0.025	-0.030	22.007	0.007	0.007	0.000	0.000	0.000	0.000
48	A	190	VAL	0	-0.013	-0.006	17.709	0.006	0.006	0.000	0.000	0.000	0.000
49	A	191	LEU	0	-0.007	-0.007	20.617	-0.012	-0.012	0.000	0.000	0.000	0.000
50	A	192	ASP	-1	-0.796	-0.870	23.317	-0.154	-0.154	0.000	0.000	0.000	0.000
51	A	193	TYR	0	-0.040	-0.022	20.916	0.013	0.013	0.000	0.000	0.000	0.000
52	A	194	LEU	0	-0.016	0.009	18.818	0.009	0.009	0.000	0.000	0.000	0.000
53	A	195	SER	0	-0.028	-0.016	21.734	0.011	0.011	0.000	0.000	0.000	0.000
54	A	196	TYR	0	-0.050	-0.040	25.248	0.013	0.013	0.000	0.000	0.000	0.000
55	A	197	ALA	0	0.014	-0.005	21.096	0.015	0.015	0.000	0.000	0.000	0.000
56	A	198	VAL	0	0.019	0.027	21.888	0.003	0.003	0.000	0.000	0.000	0.000
57	A	199	TYR	0	0.023	0.015	24.030	0.020	0.020	0.000	0.000	0.000	0.000
58	A	200	GLN	0	-0.079	-0.014	25.522	0.023	0.023	0.000	0.000	0.000	0.000
59	A	201	GLN	0	-0.069	-0.059	20.944	0.008	0.008	0.000	0.000	0.000	0.000
60	A	202	GLY	0	-0.037	-0.014	25.897	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	203	ASP	-1	-0.882	-0.932	25.488	-0.253	-0.253	0.000	0.000	0.000	0.000
62	A	204	LEU	0	0.009	-0.024	27.828	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	205	ASP	-1	-0.890	-0.941	30.054	-0.176	-0.176	0.000	0.000	0.000	0.000
64	A	206	LYS	1	0.831	0.911	19.947	0.435	0.435	0.000	0.000	0.000	0.000
65	A	207	ALA	0	0.023	0.018	26.943	-0.007	-0.007	0.000	0.000	0.000	0.000
66	A	208	LEU	0	-0.014	0.004	27.854	0.005	0.005	0.000	0.000	0.000	0.000
67	A	209	LEU	0	-0.014	0.001	26.063	0.005	0.005	0.000	0.000	0.000	0.000
68	A	210	LEU	0	0.024	0.000	22.733	0.001	0.001	0.000	0.000	0.000	0.000
69	A	211	THR	0	-0.031	-0.025	26.773	0.007	0.007	0.000	0.000	0.000	0.000
70	A	212	LYS	1	0.834	0.906	29.730	0.162	0.162	0.000	0.000	0.000	0.000
71	A	213	LYS	1	0.855	0.922	25.327	0.260	0.260	0.000	0.000	0.000	0.000
72	A	214	LEU	0	-0.021	-0.005	26.849	0.004	0.004	0.000	0.000	0.000	0.000
73	A	215	LEU	0	-0.022	-0.022	28.476	0.008	0.008	0.000	0.000	0.000	0.000
74	A	216	GLU	-1	-0.894	-0.922	29.832	-0.202	-0.202	0.000	0.000	0.000	0.000
75	A	217	LEU	0	-0.087	-0.039	26.583	0.004	0.004	0.000	0.000	0.000	0.000
76	A	218	ASP	-1	-0.891	-0.961	30.082	-0.124	-0.124	0.000	0.000	0.000	0.000
77	A	219	PRO	0	-0.008	0.003	31.920	0.002	0.002	0.000	0.000	0.000	0.000
78	A	220	GLU	-1	-0.900	-0.963	35.166	-0.094	-0.094	0.000	0.000	0.000	0.000
79	A	221	HIS	0	0.002	0.039	28.354	0.014	0.014	0.000	0.000	0.000	0.000
80	A	222	GLN	0	-0.014	-0.017	33.434	0.001	0.001	0.000	0.000	0.000	0.000
81	A	223	ARG	1	0.799	0.864	28.133	0.137	0.137	0.000	0.000	0.000	0.000
82	A	224	ALA	0	0.048	0.027	30.575	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	225	ASN	0	-0.016	-0.016	32.347	0.000	0.000	0.000	0.000	0.000	0.000
84	A	226	GLY	0	-0.039	-0.017	36.010	0.003	0.003	0.000	0.000	0.000	0.000
85	A	227	ASN	0	0.026	-0.002	30.027	0.013	0.013	0.000	0.000	0.000	0.000
86	A	228	LEU	0	0.018	0.031	33.965	-0.004	-0.004	0.000	0.000	0.000	0.000
87	A	229	LYS	1	0.917	0.951	35.550	0.092	0.092	0.000	0.000	0.000	0.000
88	A	230	TYR	0	-0.078	-0.033	33.283	0.007	0.007	0.000	0.000	0.000	0.000
89	A	231	PHE	0	0.060	0.004	29.738	0.004	0.004	0.000	0.000	0.000	0.000
90	A	232	GLU	-1	-0.791	-0.891	35.143	-0.127	-0.127	0.000	0.000	0.000	0.000
91	A	233	TYR	0	-0.049	-0.020	38.008	0.007	0.007	0.000	0.000	0.000	0.000
92	A	234	ILE	0	-0.039	-0.020	34.833	0.005	0.005	0.000	0.000	0.000	0.000
93	A	235	MET	0	-0.012	-0.004	34.412	0.003	0.003	0.000	0.000	0.000	0.000
94	A	236	ALA	0	-0.030	0.004	37.925	0.003	0.003	0.000	0.000	0.000	0.000
95	A	237	LYS	1	0.849	0.944	40.885	0.085	0.085	0.000	0.000	0.000	0.000

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