FMO DATABASE

FMODB ID: PGYN1

Calculation Name: 2NLD-A-Xray28

Preferred Name:

Target Type:

Ligand Name: acetate ion

ligand 3-letter code: ACT

PDB ID: 2NLD

Chain ID: A

ChEMBL ID:

UniProt ID: P60022

Base Structure: X-ray

Registration Date: 2018-07-26

Reference:

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water	Apo structure with with a 3 angstrom solvent shell.
Procedure	Auto-FMO protocol ver. 1.20180227

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	88
LigandCharge	SO4=-2
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-213451.964335
FMO2-HF: Nuclear repulsion	193018.432167
FMO2-HF: Total energy	-20433.532168
FMO2-MP2: Total energy	-20484.2675

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:1:ASP)

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

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.
-62.753	-64.953	51.099	-26.186	-22.714	-0.013

Interaction energy analysis for fragmet #1(A:1:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.079 / q_NPA : -0.039

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	3	TYR	0	0.069	0.049	3.010	-4.970	-1.463	0.572	-1.633	-2.445	0.010
4	A	4	ASN	0	0.055	0.103	1.900	-16.295	-15.907	7.600	-3.691	-4.298	0.042
5	A	34	CYS	0	-0.085	-0.006	3.458	-5.588	-4.265	0.021	-0.584	-0.760	0.003
6	A	6	VAL	0	0.034	0.030	4.742	0.957	1.097	-0.001	-0.015	-0.124	0.000
7	A	7	SER	0	-0.010	0.040	6.051	-0.805	-0.805	0.000	0.000	0.000	0.000
8	A	8	SER	0	0.003	-0.007	6.996	-0.235	-0.235	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.004	0.008	9.347	-0.471	-0.471	0.000	0.000	0.000	0.000
10	A	10	GLY	0	0.021	0.002	8.292	-0.221	-0.221	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.008	-0.016	9.184	0.751	0.751	0.000	0.000	0.000	0.000
12	A	27	CYS	0	0.017	0.052	2.440	-18.497	-16.449	1.744	-2.194	-1.598	-0.017
13	A	13	LEU	0	0.001	0.003	8.079	1.430	1.430	0.000	0.000	0.000	0.000
14	A	14	TYR	0	0.082	0.025	10.560	-0.835	-0.835	0.000	0.000	0.000	0.000
15	A	15	SER	0	-0.029	0.009	12.520	0.135	0.135	0.000	0.000	0.000	0.000
16	A	16	ALA	0	0.036	0.014	14.292	-0.416	-0.416	0.000	0.000	0.000	0.000
17	A	35	CYS	0	-0.097	-0.021	6.562	0.585	0.585	0.000	0.000	0.000	0.000
18	A	18	PRO	0	0.075	0.047	14.357	0.271	0.271	0.000	0.000	0.000	0.000
19	A	19	ILE	0	0.021	-0.006	17.125	-0.142	-0.142	0.000	0.000	0.000	0.000
20	A	20	PHE	0	-0.017	-0.019	18.462	0.030	0.030	0.000	0.000	0.000	0.000
21	A	21	THR	0	0.017	0.033	12.918	-0.187	-0.187	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.927	0.981	12.966	2.855	2.855	0.000	0.000	0.000	0.000
23	A	23	ILE	0	0.036	0.011	9.367	-0.527	-0.527	0.000	0.000	0.000	0.000
24	A	24	GLN	0	-0.054	-0.020	8.316	0.950	0.950	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.068	0.040	4.834	-1.936	-1.936	0.000	0.000	0.000	0.000
26	A	26	THR	0	-0.063	-0.027	4.036	0.920	1.275	-0.001	-0.044	-0.310	0.000
27	A	28	TYR	0	0.045	0.027	3.487	2.375	2.446	0.007	0.116	-0.194	0.000
28	A	29	ARG	1	0.917	0.942	4.929	-1.451	-1.451	0.000	0.000	0.000	0.000
29	A	30	GLY	0	0.036	0.016	5.248	1.246	1.246	0.000	0.000	0.000	0.000
30	A	31	LYS	1	0.855	0.933	6.862	3.137	3.137	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.072	0.060	7.180	0.950	0.950	0.000	0.000	0.000	0.000
32	A	33	LYS	1	0.917	0.943	6.861	3.275	3.275	0.000	0.000	0.000	0.000
33	A	36	LYS	0	0.195	0.131	8.581	0.201	0.201	0.000	0.000	0.000	0.000
34	A	201	SO4	-2	-1.770	-1.865	4.192	33.480	33.693	0.002	-0.031	-0.183	0.000
35	A	202	SO4	-2	-1.622	-1.760	2.471	-11.597	-9.623	2.569	-1.890	-2.654	-0.026
36	A	203	HOH	0	-0.045	-0.032	10.938	0.245	0.245	0.000	0.000	0.000	0.000
37	A	204	HOH	0	-0.008	-0.007	11.190	0.241	0.241	0.000	0.000	0.000	0.000
38	A	205	HOH	0	0.032	0.021	14.461	-0.130	-0.130	0.000	0.000	0.000	0.000
39	A	206	HOH	0	-0.035	-0.029	4.135	-1.867	-1.810	0.000	-0.011	-0.046	0.000
40	A	207	HOH	0	0.018	0.014	13.283	-0.127	-0.127	0.000	0.000	0.000	0.000
41	A	208	HOH	0	-0.036	-0.024	18.243	0.016	0.016	0.000	0.000	0.000	0.000
42	A	209	HOH	0	0.025	0.025	9.915	-0.016	-0.016	0.000	0.000	0.000	0.000
43	A	210	HOH	0	0.019	0.005	10.544	-0.095	-0.095	0.000	0.000	0.000	0.000
44	A	211	HOH	0	0.000	-0.010	2.513	-2.461	-0.920	0.794	-1.085	-1.250	-0.006
45	A	212	HOH	0	-0.049	-0.034	11.150	0.122	0.122	0.000	0.000	0.000	0.000
46	A	213	HOH	0	0.028	0.020	20.112	-0.063	-0.063	0.000	0.000	0.000	0.000
47	A	214	HOH	0	-0.040	-0.041	4.876	-0.434	-0.434	0.000	0.000	0.000	0.000
48	A	215	HOH	0	-0.050	-0.026	4.670	-1.919	-1.883	-0.001	-0.003	-0.032	0.000
49	A	216	HOH	0	-0.032	-0.020	10.019	-0.339	-0.339	0.000	0.000	0.000	0.000
50	A	217	HOH	0	-0.009	-0.017	1.721	-18.436	-24.083	14.808	-6.172	-2.990	0.053
51	A	218	HOH	0	0.028	0.025	21.171	-0.053	-0.053	0.000	0.000	0.000	0.000
52	A	219	HOH	0	-0.009	-0.031	11.364	0.048	0.048	0.000	0.000	0.000	0.000
53	A	220	HOH	0	0.014	0.014	2.862	1.949	2.472	0.065	-0.321	-0.266	-0.002
54	A	221	HOH	0	0.017	0.014	9.375	-0.296	-0.296	0.000	0.000	0.000	0.000
55	A	222	HOH	0	-0.069	-0.051	12.622	0.170	0.170	0.000	0.000	0.000	0.000
56	A	223	HOH	0	-0.023	-0.021	17.352	0.077	0.077	0.000	0.000	0.000	0.000
57	A	224	HOH	0	-0.038	-0.035	9.881	0.127	0.127	0.000	0.000	0.000	0.000
58	A	225	HOH	0	-0.071	-0.064	16.653	0.042	0.042	0.000	0.000	0.000	0.000
59	A	226	HOH	0	-0.040	-0.027	11.950	0.052	0.052	0.000	0.000	0.000	0.000
60	A	229	HOH	0	-0.078	-0.050	14.206	0.033	0.033	0.000	0.000	0.000	0.000
61	A	230	HOH	0	0.020	0.024	9.679	0.190	0.190	0.000	0.000	0.000	0.000
62	A	232	HOH	0	-0.031	-0.017	10.829	0.096	0.096	0.000	0.000	0.000	0.000
63	A	233	HOH	0	-0.016	-0.006	12.358	0.241	0.241	0.000	0.000	0.000	0.000
64	A	235	HOH	0	0.026	0.018	10.345	0.060	0.060	0.000	0.000	0.000	0.000
65	A	237	HOH	0	-0.028	-0.031	12.396	0.189	0.189	0.000	0.000	0.000	0.000
66	A	238	HOH	0	-0.061	-0.066	5.183	-0.922	-0.922	0.000	0.000	0.000	0.000
67	A	240	HOH	0	-0.021	-0.013	14.681	0.055	0.055	0.000	0.000	0.000	0.000
68	A	241	HOH	0	0.012	-0.001	1.708	-10.343	-19.011	15.982	-5.057	-2.258	-0.035
69	A	249	HOH	0	-0.064	-0.086	6.275	0.016	0.016	0.000	0.000	0.000	0.000
70	A	250	HOH	0	-0.015	-0.021	12.576	-0.034	-0.034	0.000	0.000	0.000	0.000
71	A	254	HOH	0	-0.024	-0.014	14.462	0.011	0.011	0.000	0.000	0.000	0.000
72	A	255	HOH	0	-0.061	-0.037	2.856	-3.895	-2.858	0.263	-0.708	-0.593	-0.003
73	A	256	HOH	0	0.028	0.015	9.366	-0.404	-0.404	0.000	0.000	0.000	0.000
74	A	257	HOH	0	-0.026	-0.013	13.287	0.038	0.038	0.000	0.000	0.000	0.000
75	A	258	HOH	0	-0.034	-0.026	9.260	-0.403	-0.403	0.000	0.000	0.000	0.000
76	A	260	HOH	0	0.013	0.014	2.632	0.346	0.952	0.164	-0.370	-0.399	-0.002
77	A	261	HOH	0	-0.098	-0.079	9.550	0.121	0.121	0.000	0.000	0.000	0.000
78	A	262	HOH	0	-0.014	-0.013	9.865	0.066	0.066	0.000	0.000	0.000	0.000
79	A	265	HOH	0	0.033	0.017	13.650	-0.171	-0.171	0.000	0.000	0.000	0.000
80	A	268	HOH	0	-0.017	-0.007	11.675	0.139	0.139	0.000	0.000	0.000	0.000
81	A	269	HOH	0	0.008	0.002	8.484	-0.086	-0.086	0.000	0.000	0.000	0.000
82	A	270	HOH	0	-0.012	-0.023	6.469	0.822	0.822	0.000	0.000	0.000	0.000
83	A	274	HOH	0	0.014	0.002	7.099	0.725	0.725	0.000	0.000	0.000	0.000
84	A	275	HOH	0	0.033	0.021	1.918	-15.621	-17.325	6.511	-2.493	-2.314	-0.030
85	A	276	HOH	0	-0.008	-0.016	11.875	0.097	0.097	0.000	0.000	0.000	0.000
86	A	283	HOH	0	-0.012	-0.010	10.053	-0.350	-0.350	0.000	0.000	0.000	0.000
87	A	284	HOH	0	0.035	0.057	7.911	0.552	0.552	0.000	0.000	0.000	0.000
88	A	285	HOH	0	-0.019	-0.028	7.822	-0.549	-0.549	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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