FMO DATABASE

FMODB ID: NZM9Q

Calculation Name: 2EOC-A-Other547

Preferred Name: Poly [ADP-ribose] polymerase 3

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2EOC

Chain ID: A

ChEMBL ID: CHEMBL5083

UniProt ID: Q9Y6F1

Base Structure: SolutionNMR

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	124
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1052240.970727
FMO2-HF: Nuclear repulsion	1001782.92148
FMO2-HF: Total energy	-50458.049248
FMO2-MP2: Total energy	-50605.720559

3D Structure Molmil

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:34:GLY)

Summations of interaction energy for fragment #1(A:34:GLY)

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.
30.317	31.305	-0.016	-0.404	-0.567	-0.001

Interaction energy analysis for fragmet #1(A:34:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.852 / q_NPA : 0.914

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	36	SER	0	0.063	0.035	3.833	3.590	4.578	-0.016	-0.404	-0.567	-0.001
4	A	37	GLY	0	0.010	0.018	6.393	-2.268	-2.268	0.000	0.000	0.000	0.000
5	A	38	SER	0	-0.015	-0.027	7.243	1.152	1.152	0.000	0.000	0.000	0.000
6	A	39	SER	0	-0.010	-0.001	9.043	0.324	0.324	0.000	0.000	0.000	0.000
7	A	40	GLY	0	0.020	0.024	12.083	-0.390	-0.390	0.000	0.000	0.000	0.000
8	A	41	ALA	0	-0.019	-0.015	14.930	-0.409	-0.409	0.000	0.000	0.000	0.000
9	A	42	GLU	-1	-0.886	-0.935	17.064	-14.471	-14.471	0.000	0.000	0.000	0.000
10	A	43	LYS	1	0.906	0.944	10.992	23.388	23.388	0.000	0.000	0.000	0.000
11	A	44	ARG	1	0.987	0.998	16.118	13.220	13.220	0.000	0.000	0.000	0.000
12	A	45	ILE	0	0.025	0.014	16.380	-0.686	-0.686	0.000	0.000	0.000	0.000
13	A	46	ILE	0	0.002	0.007	19.537	0.931	0.931	0.000	0.000	0.000	0.000
14	A	47	ARG	1	0.936	0.960	21.396	12.760	12.760	0.000	0.000	0.000	0.000
15	A	48	VAL	0	0.018	0.011	23.601	0.243	0.243	0.000	0.000	0.000	0.000
16	A	49	ASP	-1	-0.776	-0.873	25.887	-9.458	-9.458	0.000	0.000	0.000	0.000
17	A	50	PRO	0	0.023	0.005	29.564	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	51	THR	0	-0.047	-0.042	31.669	0.241	0.241	0.000	0.000	0.000	0.000
19	A	52	CYS	0	-0.030	0.010	28.942	0.186	0.186	0.000	0.000	0.000	0.000
20	A	53	PRO	0	0.029	0.020	31.417	-0.183	-0.183	0.000	0.000	0.000	0.000
21	A	54	LEU	0	0.011	-0.019	27.653	-0.097	-0.097	0.000	0.000	0.000	0.000
22	A	55	SER	0	-0.043	-0.031	27.023	-0.409	-0.409	0.000	0.000	0.000	0.000
23	A	56	SER	0	0.011	0.012	27.200	-0.346	-0.346	0.000	0.000	0.000	0.000
24	A	57	ASN	0	-0.017	0.004	26.941	0.092	0.092	0.000	0.000	0.000	0.000
25	A	58	PRO	0	0.045	0.022	23.388	-0.420	-0.420	0.000	0.000	0.000	0.000
26	A	59	GLY	0	-0.007	-0.007	19.910	-0.111	-0.111	0.000	0.000	0.000	0.000
27	A	60	THR	0	-0.038	-0.020	20.187	-0.540	-0.540	0.000	0.000	0.000	0.000
28	A	61	GLN	0	-0.059	-0.027	16.445	-0.675	-0.675	0.000	0.000	0.000	0.000
29	A	62	VAL	0	-0.026	-0.026	21.089	0.484	0.484	0.000	0.000	0.000	0.000
30	A	63	TYR	0	-0.082	-0.057	17.964	-0.594	-0.594	0.000	0.000	0.000	0.000
31	A	64	GLU	-1	-0.816	-0.912	16.830	-15.597	-15.597	0.000	0.000	0.000	0.000
32	A	65	ASP	-1	-0.894	-0.945	18.369	-15.863	-15.863	0.000	0.000	0.000	0.000
33	A	66	TYR	0	-0.049	-0.012	20.818	0.760	0.760	0.000	0.000	0.000	0.000
34	A	67	ASN	0	0.005	-0.038	23.330	-0.024	-0.024	0.000	0.000	0.000	0.000
35	A	68	CYS	0	-0.043	0.001	26.283	0.008	0.008	0.000	0.000	0.000	0.000
36	A	69	THR	0	0.050	0.032	29.549	0.188	0.188	0.000	0.000	0.000	0.000
37	A	70	LEU	0	-0.025	-0.014	32.744	0.063	0.063	0.000	0.000	0.000	0.000
38	A	71	ASN	0	0.033	0.006	35.877	0.153	0.153	0.000	0.000	0.000	0.000
39	A	72	GLN	0	0.022	0.025	39.464	-0.027	-0.027	0.000	0.000	0.000	0.000
40	A	73	THR	0	-0.009	-0.014	43.046	0.013	0.013	0.000	0.000	0.000	0.000
41	A	74	ASN	0	-0.014	-0.002	46.336	-0.109	-0.109	0.000	0.000	0.000	0.000
42	A	75	ILE	0	0.001	0.010	49.994	-0.001	-0.001	0.000	0.000	0.000	0.000
43	A	76	GLU	-1	-0.872	-0.940	52.842	-5.825	-5.825	0.000	0.000	0.000	0.000
44	A	77	ASN	0	-0.041	-0.034	53.456	-0.036	-0.036	0.000	0.000	0.000	0.000
45	A	78	ASN	0	0.013	0.011	50.090	-0.122	-0.122	0.000	0.000	0.000	0.000
46	A	79	ASN	0	-0.015	0.008	49.803	-0.146	-0.146	0.000	0.000	0.000	0.000
47	A	80	ASN	0	0.035	0.012	44.993	-0.105	-0.105	0.000	0.000	0.000	0.000
48	A	81	LYS	1	0.928	0.954	43.021	6.798	6.798	0.000	0.000	0.000	0.000
49	A	82	PHE	0	0.015	0.026	36.780	-0.072	-0.072	0.000	0.000	0.000	0.000
50	A	83	TYR	0	-0.057	-0.066	35.439	0.263	0.263	0.000	0.000	0.000	0.000
51	A	84	ILE	0	0.002	0.013	31.212	-0.122	-0.122	0.000	0.000	0.000	0.000
52	A	85	ILE	0	-0.022	-0.015	29.913	0.177	0.177	0.000	0.000	0.000	0.000
53	A	86	GLN	0	0.015	0.001	26.024	0.036	0.036	0.000	0.000	0.000	0.000
54	A	87	LEU	0	-0.012	0.015	23.234	0.327	0.327	0.000	0.000	0.000	0.000
55	A	88	LEU	0	-0.008	0.007	23.564	-0.451	-0.451	0.000	0.000	0.000	0.000
56	A	89	GLN	0	0.031	0.004	18.144	-0.196	-0.196	0.000	0.000	0.000	0.000
57	A	90	ASP	-1	-0.785	-0.887	21.999	-12.755	-12.755	0.000	0.000	0.000	0.000
58	A	91	SER	0	0.003	-0.017	20.399	-0.737	-0.737	0.000	0.000	0.000	0.000
59	A	92	ASN	0	-0.080	-0.036	21.414	-0.411	-0.411	0.000	0.000	0.000	0.000
60	A	93	ARG	1	0.898	0.951	20.469	14.736	14.736	0.000	0.000	0.000	0.000
61	A	94	PHE	0	-0.008	0.011	22.525	0.260	0.260	0.000	0.000	0.000	0.000
62	A	95	PHE	0	0.046	0.017	20.434	-0.397	-0.397	0.000	0.000	0.000	0.000
63	A	96	THR	0	-0.007	-0.004	25.540	0.664	0.664	0.000	0.000	0.000	0.000
64	A	97	CYS	0	-0.046	-0.001	27.531	-0.393	-0.393	0.000	0.000	0.000	0.000
65	A	98	TRP	0	0.013	0.015	29.426	0.378	0.378	0.000	0.000	0.000	0.000
66	A	99	ASN	0	-0.008	-0.019	31.184	0.200	0.200	0.000	0.000	0.000	0.000
67	A	100	ARG	1	0.889	0.955	34.353	8.911	8.911	0.000	0.000	0.000	0.000
68	A	101	TRP	0	0.005	0.005	36.441	-0.093	-0.093	0.000	0.000	0.000	0.000
69	A	102	GLY	0	0.023	0.005	39.620	0.085	0.085	0.000	0.000	0.000	0.000
70	A	103	ARG	1	0.918	0.966	42.792	6.517	6.517	0.000	0.000	0.000	0.000
71	A	104	VAL	0	-0.013	-0.011	41.012	-0.164	-0.164	0.000	0.000	0.000	0.000
72	A	105	GLY	0	0.032	0.023	41.395	0.146	0.146	0.000	0.000	0.000	0.000
73	A	106	GLU	-1	-0.909	-0.942	42.571	-6.889	-6.889	0.000	0.000	0.000	0.000
74	A	107	VAL	0	0.020	0.001	39.045	-0.196	-0.196	0.000	0.000	0.000	0.000
75	A	108	GLY	0	0.017	0.008	39.703	-0.194	-0.194	0.000	0.000	0.000	0.000
76	A	109	GLN	0	-0.013	0.001	41.635	0.033	0.033	0.000	0.000	0.000	0.000
77	A	110	SER	0	0.018	0.000	37.081	-0.169	-0.169	0.000	0.000	0.000	0.000
78	A	111	LYS	1	0.879	0.944	36.683	8.081	8.081	0.000	0.000	0.000	0.000
79	A	112	ILE	0	0.014	0.008	30.915	-0.225	-0.225	0.000	0.000	0.000	0.000
80	A	113	ASN	0	-0.019	0.000	32.737	0.417	0.417	0.000	0.000	0.000	0.000
81	A	114	HIS	0	0.014	-0.005	30.065	-0.061	-0.061	0.000	0.000	0.000	0.000
82	A	115	PHE	0	0.014	-0.002	28.550	0.280	0.280	0.000	0.000	0.000	0.000
83	A	116	THR	0	0.019	0.006	27.917	-0.405	-0.405	0.000	0.000	0.000	0.000
84	A	117	ARG	1	0.958	0.980	26.176	10.143	10.143	0.000	0.000	0.000	0.000
85	A	118	LEU	0	0.054	0.037	20.130	0.342	0.342	0.000	0.000	0.000	0.000
86	A	119	GLU	-1	-0.924	-0.981	24.255	-11.601	-11.601	0.000	0.000	0.000	0.000
87	A	120	ASP	-1	-0.951	-0.975	26.336	-9.597	-9.597	0.000	0.000	0.000	0.000
88	A	121	ALA	0	0.071	0.039	26.335	0.245	0.245	0.000	0.000	0.000	0.000
89	A	122	LYS	1	0.947	0.972	22.042	13.201	13.201	0.000	0.000	0.000	0.000
90	A	123	LYS	1	0.933	0.978	26.863	10.069	10.069	0.000	0.000	0.000	0.000
91	A	124	ASP	-1	-0.905	-0.951	30.345	-9.065	-9.065	0.000	0.000	0.000	0.000
92	A	125	PHE	0	0.020	0.005	27.278	0.245	0.245	0.000	0.000	0.000	0.000
93	A	126	GLU	-1	-0.900	-0.966	27.296	-11.028	-11.028	0.000	0.000	0.000	0.000
94	A	127	LYS	1	0.827	0.923	30.558	8.678	8.678	0.000	0.000	0.000	0.000
95	A	128	LYS	1	0.931	0.973	33.615	8.705	8.705	0.000	0.000	0.000	0.000
96	A	129	PHE	0	0.065	0.016	31.625	0.233	0.233	0.000	0.000	0.000	0.000
97	A	130	ARG	1	0.928	0.981	33.668	8.772	8.772	0.000	0.000	0.000	0.000
98	A	131	GLU	-1	-0.869	-0.923	35.505	-7.777	-7.777	0.000	0.000	0.000	0.000
99	A	132	LYS	1	0.845	0.945	36.712	8.168	8.168	0.000	0.000	0.000	0.000
100	A	133	THR	0	0.050	0.006	34.967	0.206	0.206	0.000	0.000	0.000	0.000
101	A	134	LYS	1	0.879	0.953	37.868	7.394	7.394	0.000	0.000	0.000	0.000
102	A	135	ASN	0	-0.011	0.000	34.584	0.019	0.019	0.000	0.000	0.000	0.000
103	A	136	ASN	0	0.052	0.010	31.443	0.179	0.179	0.000	0.000	0.000	0.000
104	A	137	TRP	0	0.016	0.014	24.318	0.312	0.312	0.000	0.000	0.000	0.000
105	A	138	ALA	0	0.039	0.009	26.533	-0.144	-0.144	0.000	0.000	0.000	0.000
106	A	139	GLU	-1	-0.893	-0.943	27.547	-9.452	-9.452	0.000	0.000	0.000	0.000
107	A	140	ARG	1	0.931	0.960	26.097	11.451	11.451	0.000	0.000	0.000	0.000
108	A	141	ASP	-1	-0.933	-0.944	29.453	-9.920	-9.920	0.000	0.000	0.000	0.000
109	A	142	HIS	1	0.878	0.937	31.142	9.297	9.297	0.000	0.000	0.000	0.000
110	A	143	PHE	0	-0.029	-0.020	33.622	0.216	0.216	0.000	0.000	0.000	0.000
111	A	144	VAL	0	0.006	0.005	35.458	0.174	0.174	0.000	0.000	0.000	0.000
112	A	145	SER	0	0.009	-0.003	39.258	-0.046	-0.046	0.000	0.000	0.000	0.000
113	A	146	HIS	0	-0.003	-0.005	40.340	0.367	0.367	0.000	0.000	0.000	0.000
114	A	147	PRO	0	0.049	0.025	43.599	-0.072	-0.072	0.000	0.000	0.000	0.000
115	A	148	GLY	0	0.037	0.020	45.963	0.083	0.083	0.000	0.000	0.000	0.000
116	A	149	LYS	1	0.750	0.871	41.656	7.424	7.424	0.000	0.000	0.000	0.000
117	A	150	TYR	0	-0.041	-0.035	38.323	0.006	0.006	0.000	0.000	0.000	0.000
118	A	151	THR	0	0.024	0.007	38.401	-0.149	-0.149	0.000	0.000	0.000	0.000
119	A	152	LEU	0	0.001	-0.004	30.422	-0.082	-0.082	0.000	0.000	0.000	0.000
120	A	153	ILE	0	-0.043	-0.020	33.702	0.122	0.122	0.000	0.000	0.000	0.000
121	A	154	GLU	-1	-0.945	-0.977	29.193	-10.402	-10.402	0.000	0.000	0.000	0.000
122	A	155	VAL	0	-0.079	-0.034	29.624	-0.231	-0.231	0.000	0.000	0.000	0.000
123	A	156	GLN	0	-0.023	-0.016	32.401	0.135	0.135	0.000	0.000	0.000	0.000
124	A	157	ALA	-1	-0.908	-0.937	29.431	-9.564	-9.564	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:34:GLY)