Data S3 - list of the atoms used in aech cofactor to calculate the center cofactor id - the PDB name of this cofactor "cofactor type - metal, nucleotide, iron-sulfar etc." center atoms - the atoms used in aech cofactor to calculate the center nucleotide - If another microenvironments generated from the nucleotid part of the cofactor than the atoms used in aech cofactor to calculate this center cofactor id cofactor type center atoms nucleotide Chlorophyll BCB Chl C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Chlorophyll CLA Chl C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Chlorophyll CHL Chl C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Chlorophyll BCL Chl C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Chlorophyll CL0 Chl C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Chlorophyll PMR Chl C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Chlorophyll PHO Chl C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Chlorophyll BPB Chl C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Chlorophyll BPH Chl C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Chlorophyll 68G Chl C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Chlorophyll CL7 Chl C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Chlorophyll AOH chl C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Chlorophyll GB0 Chl C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Chlorophyll GBF Chl C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme HEA Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme HAS Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme 2FH Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme 522 Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme 89R Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme DDH Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme DHE Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme HES Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme HDD Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme HDE Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme HDM Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme HEB Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme HEC Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme HEM Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme HEO Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme HEV Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme HP5 Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme MH0 Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme N7H Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme NTE Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme OBV Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme SRM Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme VER Heme C2A;C3A;C2B;C3B;C2C;C3C;C2;C3D na Heme B12 Heme C13;C18;C7;N21 na Co-A 52O Nuc S1 O1;N4 Co-A BCO Nuc S1 O1;N4 Co-A IVC Nuc S1 O1;N4 Co-A 1VU Nuc S O11;N5 Co-A 2CP Nuc S O4';N1 Co-A 3CP Nuc S O4';N1 Co-A COW Nuc S O4';N1 Co-A HXC Nuc S O4';N1 Co-A MCA Nuc S O4';N1 Co-A MLC Nuc S O4';N1 Co-A OXK Nuc S O4';N1 Co-A SCA Nuc S O4';N1 Co-A SOP Nuc S O4';N1 Co-A UCC Nuc S O4';N1 Co-A 01A Nuc S1P O4A';N1A Co-A JBT Nuc S1P O4B;N1 Co-A 2MC Nuc S1P O4B;N1A Co-A 3HC Nuc S1P O4B;N1A Co-A 3KK Nuc S1P O4B;N1A Co-A 4BN Nuc S1P O4B;N1A Co-A CAA Nuc S1P O4B;N1A Co-A CAO Nuc S1P O4B;N1A Co-A CO6 Nuc S1P O4B;N1A Co-A CO8 Nuc S1P O4B;N1A Co-A COA Nuc S1P O4B;N1A Co-A COF Nuc S1P O4B;N1A Co-A COK Nuc S1P O4B;N1A Co-A COS Nuc S1P O4B;N1A Co-A COZ Nuc S1P O4B;N1A Co-A CS8 Nuc S1P O4B;N1A Co-A FRE Nuc S1P O4B;N1A Co-A HDC Nuc S1P O4B;N1A Co-A HMG Nuc S1P O4B;N1A Co-A MDE Nuc S1P O4B;N1A Co-A MRR Nuc S1P O4B;N1A Co-A MRS Nuc S1P O4B;N1A Co-A RFC Nuc S1P O4B;N1A Co-A SFC Nuc S1P O4B;N1A Co-A SPF Nuc S1P O4B;N1A Co-A ST9 Nuc S1P O4B;N1A Co-A 0FQ Nuc S1P O4D;N1A Co-A 4CA Nuc S1P O4D;N1A Co-A 4CO Nuc S1P O4D;N1A Co-A BCA Nuc S1P O4D;N1A Co-A BYC Nuc S1P O4D;N1A Co-A FAQ Nuc S1P O4D;N1A Co-A HFQ Nuc S1P O4D;N1A Co-A COO Nuc S1 O4X;N1A Co-A GRA Nuc S1 O4X;N1A Co-A 01K Nuc S20 O60;N57 Co-A LYX Nuc S20 O61;N58 Co-A COD Nuc O17 S44;N1 Flavin adenine dinucleotide FAD Nuc N5;C5A;C6;C7;C8;C9;C9A;N10;C10;N1;C2;02;N3;C4;04;C4A O4B;N1A Flavin mononucleotide FMN Nuc N5;C5X;C6;C7;C8;C9;C9A;N10;C10;N1;C2;02;N3;C4;04;C4X na Molybdopterin 2MD Nuc C7;011;C11;C12;S12;C13;S13;C14;N15;C16;C15;O14;N17;C17;16;N18;C20;N8 O11;N1 Molybdopterin MGD Nuc C11;C12;S12;C13;S13;C14;N15;C16;C17;O17;N18;C19;N19;N20;C21;N22;C23;O11 O4';N1 Molybdopterin PCD Nuc "N1';C2';N2';N3',C4';O4';C4A;N5';C6';C7';S7';MO;OR1;OM2;OM1;S8';C8';C9'O9';C7;N8';C4B" O4D Molybdopterin MSS Nuc C1';S1';MOM1;OM1;S2';C2';C3';C3';C7;N8;C10;N1;C2;N2;N3;C4;O4;C9;N5;C6 na Molybdopterin MTQ Nuc C1';S1';MOM1;OM2;OM1;S2';C2';C3';O3';C7;N8;C10;N1;C2;N2;N3;C4;O4;C9;N5;C6 na Molybdopterin MTV Nuc C1';S1';MOM1;OM2;OM1;S2';C2';C3';O3';C7;N8';C10;N1;C2;N2;N3;C4;O4;C9;N5;C6 na Molybdopterin MTE Nuc N1;C2;N2;N3;C4;O4;C9;C10;N5;C6;C1';S1';C2';S2';C3';O3';C7;N8; na Molybdopterin PGD Nuc "N1';C2';N2';N3',C4';O4';C4A;N5';C6';C7';S7';MO;OR1;OM2;OM1;S8';C8';C9'O9';C7;N8';C4B" O4D Molybdopterin MCN Nuc "N1';C2';N2';N3',C4';O4';C4A;N5';C6';C7';S7';MO;OR1;OM2;OM1;S8';C8';C9'O9';C7;N8';C4B" O4D Nicotinamide-adenine dinucleotide NAD Nuc N1N;C2N;C3N;C7N;N7N;O7N;C4N;C5N;C6N O4B;N1A Nicotinamide-adenine dinucleotide NAP Nuc N1N;C2N;C3N;C7N;N7N;O7N;C4N;C5N;C6N O4B;N1A Nicotinamide-adenine dinucleotide NDP Nuc N1N;C2N;C3N;C7N;N7N;O7N;C4N;C5N;C6N O4B;N1A Nicotinamide-adenine dinucleotide NJP Nuc N1N;C2N;C3N;C7N;N7N;O7N;C4N;C5N;C6N;O8N O4B;N1A Nicotinamide-adenine dinucleotide NZQ Nuc N1N;C2N;C3N;C7N;N7N;O7N;C4N;C5N;C6N;O5N;O6N O4B;N1A Ascorbic acid ASC Organic all na Ascorbic acid ISD Organic all na Biopterin 4AB Organic all na Biopterin 7AP Organic all na Biopterin BHS Organic all na Biopterin BIO Organic all na Biopterin H2B Organic all na Biopterin H4B Organic all na Biopterin HBI Organic all na Biotin BT5 Organic S1B O4';N1 Biotin 41M Organic S7 na Biotin B1R Organic S1 na Biotin B4F Organic S1 na Biotin B9P Organic S1 na Biotin BC4 Organic SAK na Biotin BH7 Organic S7 na Biotin BNI Organic S1 na Biotin BSO Organic S1 na Biotin BTN Organic S1 na Biotin BTQ Organic S1 na Biotin BTX Organic S1B na Biotin BYY Organic S1 na Biotin GBO Organic S1 na Biotin IMI Organic S1 na Biotin SHM Organic S7 na Biotin SNR Organic S7 na Co-B TP7 Organic S7 na Co-M COM Organic S2 na Glutathione GSH Organic SG2 na MIO-factor MDO Organic C1;N3;C2;CA2;N2 na Phosphopantetheine H2V Organic S na Phosphopantetheine PN2 Organic S1 na Phosphopantetheine PNS Organic S44 na Pyridoxial 5'-phosphate PLP Organic N1;C2;C3;O3;C4;C4A;O4A;C5;C6 na Sam SAM Organic SD na Menaquinone MQ7 Quinone O1;C1;C10;C9;C8;C7;C6;C5;C4;O4;C3;C2 na Menaquinone MQ8 Quinone O1;C1;C10;C9;C8;C7;C6;C5;C4;O4;C3;C2 na Menaquinone MQ9 Quinone C1;O1;C2;C3D;C3C;C3B;C3A;C3;C4;O4;C5;C6 na Pyrroloquinoline Quinone PQQ Quinone all na Quinone 4YP Quinone CAS;CAV;OAH;CATOAN;CAR;NAF;CAU;OAG;CAQ na Quinone DCQ Quinone C1;C2;C3;C4;C5;C6;O2;O5 na Quinone EMO Quinone C1;C2;C3;C4;C5;C6;C7;C8;C9;C16;C17;C18;C19;C20;O1;O3;O6;O17;O19 na Quinone FLV Quinone CAJ;CAG;CAL;CAO;CAK;CAF;CAI;CAH;CAN;CAM;OAB;OAD;OAA;OAE;OAC na Quinone PL9 Quinone C1;C2;C3;C4;C5;C6;O1;O2 na Quinone PLQ Quinone C1;C2;C3;C4;C5;C6;O2;O5 na Quinone PQ9 Quinone C1;C2;C3;C4;C5;C10;O1;O4 na Quinone PQQ Quinone all na Quinone PQN Quinone C1;C2;C3;C4;C5;C10;O1;O4 na Quinone TPQ Quinone C1;C2;C3;C4;C5;C6;O2;O5;O4 na Topaquinone 1TY Quinone CD1;CD2;CG;OX1;CE2;NX1;CZ;OH;CE1 na Topaquinone 2TY Quinone CD1;CD2;CG;OX1;CE2;NX1;CZ;OH;CE1 na Tryptophan tryptophylquinone TRQ Quinone CD1;CG;CD2;CE3;CZ3;CH2;O6;CZ2;O7;CE2;NE1 na Ubiquinone DCQ Quinone C1;C2;C3;C4;C5;C6;O2;O5 na Ubiquinone U10 Quinone C1;C2;C3;C4;C5;C6;O2;O5 na Ubiquinone UQ1 Quinone C1;C2;C3;C4;C5;C10;O1;O4 na Ubiquinone UQ2 Quinone C1;C2;C3;C4;C5;C10;O1;O4 na Ubiquinone UQ7 Quinone C1;C2;C3;C4;C5;C10;O1;O4 na Ubiquinone UQ8 Quinone C1;C2;C3;C4;C5;C6;O2;O5 na Ubiquinone UQ9 Quinone C1;C2;C3;C4;C5;C6;O2;O5 na