FMO DATABASE

FMODB ID: XRYY8

Calculation Name: 3NGG-A-Xray29

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NGG

Chain ID: A

ChEMBL ID:

UniProt ID: P83952

Base Structure: X-ray

Registration Date: 2018-09-06

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	87
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-277586.373244
FMO2-HF: Nuclear repulsion	254220.604343
FMO2-HF: Total energy	-23365.768901
FMO2-MP2: Total energy	-23425.627676

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:4:ACE)

Summations of interaction energy for fragment #1(A:4:ACE)

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.
0.667	1.418	-0.012	-0.333	-0.406	0.001

Interaction energy analysis for fragmet #1(A:4:ACE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.004

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

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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	6	LYS	1	0.851	0.939	3.827	1.719	2.424	-0.011	-0.316	-0.378	0.001
4	A	7	PRO	0	0.010	0.004	7.048	-0.077	-0.077	0.000	0.000	0.000	0.000
5	A	8	GLY	0	0.065	0.033	9.005	0.011	0.011	0.000	0.000	0.000	0.000
6	A	9	LEU	0	-0.020	-0.002	11.344	-0.124	-0.124	0.000	0.000	0.000	0.000
7	A	35	CYS	0	-0.007	-0.004	12.030	-0.115	-0.115	0.000	0.000	0.000	0.000
8	A	11	PRO	0	0.016	0.033	15.468	0.034	0.034	0.000	0.000	0.000	0.000
9	A	12	PRO	0	0.050	0.029	19.220	-0.013	-0.013	0.000	0.000	0.000	0.000
10	A	13	ARG	1	0.770	0.848	20.793	0.202	0.202	0.000	0.000	0.000	0.000
11	A	14	PRO	0	0.026	0.025	23.285	0.003	0.003	0.000	0.000	0.000	0.000
12	A	15	GLN	0	0.024	0.016	23.058	-0.005	-0.005	0.000	0.000	0.000	0.000
13	A	16	LYS	1	0.958	1.001	24.691	0.103	0.103	0.000	0.000	0.000	0.000
14	A	17	PRO	0	0.020	-0.009	25.731	0.001	0.001	0.000	0.000	0.000	0.000
15	A	39	CYS	0	-0.122	-0.089	20.484	-0.018	-0.018	0.000	0.000	0.000	0.000
16	A	19	VAL	0	0.004	0.027	21.945	0.001	0.001	0.000	0.000	0.000	0.000
17	A	20	LYS	1	1.002	0.997	16.490	0.263	0.263	0.000	0.000	0.000	0.000
18	A	21	GLU	-1	-0.755	-0.862	18.233	-0.230	-0.230	0.000	0.000	0.000	0.000
19	A	34	CYS	0	-0.064	-0.027	10.781	0.159	0.159	0.000	0.000	0.000	0.000
20	A	23	LYS	1	0.878	0.941	11.653	0.320	0.320	0.000	0.000	0.000	0.000
21	A	24	ASN	0	0.004	-0.022	7.937	-0.040	-0.040	0.000	0.000	0.000	0.000
22	A	25	ASP	-1	-0.620	-0.821	6.913	-1.439	-1.439	0.000	0.000	0.000	0.000
23	A	26	ASP	-1	-0.816	-0.887	7.025	-0.678	-0.678	0.000	0.000	0.000	0.000
24	A	27	SER	0	-0.094	-0.044	9.081	0.180	0.180	0.000	0.000	0.000	0.000
25	A	43	CYS	0	-0.057	-0.001	11.795	0.034	0.034	0.000	0.000	0.000	0.000
26	A	29	PRO	0	0.070	0.044	12.628	-0.037	-0.037	0.000	0.000	0.000	0.000
27	A	30	GLY	0	0.057	0.019	14.445	-0.022	-0.022	0.000	0.000	0.000	0.000
28	A	31	GLN	0	0.059	0.063	12.160	-0.062	-0.062	0.000	0.000	0.000	0.000
29	A	32	GLN	0	-0.009	-0.001	12.485	-0.083	-0.083	0.000	0.000	0.000	0.000
30	A	33	LYS	1	0.757	0.882	8.284	1.145	1.145	0.000	0.000	0.000	0.000
31	A	36	ASN	0	0.020	-0.001	14.477	0.072	0.072	0.000	0.000	0.000	0.000
32	A	37	TYR	0	-0.022	-0.028	16.437	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	38	GLY	0	0.033	0.027	19.404	0.036	0.036	0.000	0.000	0.000	0.000
34	A	40	LYS	1	0.844	0.956	20.419	0.205	0.205	0.000	0.000	0.000	0.000
35	A	41	ASP	-1	-0.820	-0.909	15.998	-0.386	-0.386	0.000	0.000	0.000	0.000
36	A	42	GLU	-1	-0.747	-0.835	17.103	-0.196	-0.196	0.000	0.000	0.000	0.000
37	A	44	ARG	1	0.804	0.891	15.378	0.297	0.297	0.000	0.000	0.000	0.000
38	A	45	ASP	-1	-0.798	-0.890	15.310	-0.288	-0.288	0.000	0.000	0.000	0.000
39	A	46	PRO	0	-0.066	-0.009	13.300	0.009	0.009	0.000	0.000	0.000	0.000
40	A	47	ILE	0	0.039	0.014	15.467	0.045	0.045	0.000	0.000	0.000	0.000
41	A	48	PHE	0	-0.039	-0.031	12.776	-0.034	-0.034	0.000	0.000	0.000	0.000
42	A	49	VAL	0	-0.049	-0.034	15.990	0.012	0.012	0.000	0.000	0.000	0.000
43	A	50	GLY	-1	-0.908	-0.930	17.873	-0.058	-0.058	0.000	0.000	0.000	0.000
44	A	51	HOH	0	-0.049	-0.032	18.240	0.013	0.013	0.000	0.000	0.000	0.000
45	A	52	HOH	0	0.033	0.023	29.004	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	53	HOH	0	-0.002	0.004	25.813	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	54	HOH	0	-0.019	-0.012	22.443	0.002	0.002	0.000	0.000	0.000	0.000
48	A	55	HOH	0	0.014	0.005	21.477	-0.003	-0.003	0.000	0.000	0.000	0.000
49	A	56	HOH	0	0.038	0.025	13.165	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	57	HOH	0	-0.020	-0.030	11.124	0.021	0.021	0.000	0.000	0.000	0.000
51	A	59	HOH	0	-0.020	-0.018	9.491	-0.006	-0.006	0.000	0.000	0.000	0.000
52	A	60	HOH	0	-0.021	-0.020	23.481	0.004	0.004	0.000	0.000	0.000	0.000
53	A	61	HOH	0	0.025	0.013	23.004	0.000	0.000	0.000	0.000	0.000	0.000
54	A	62	HOH	0	0.050	0.029	20.197	-0.009	-0.009	0.000	0.000	0.000	0.000
55	A	63	HOH	0	0.035	0.025	5.842	0.204	0.204	0.000	0.000	0.000	0.000
56	A	66	HOH	0	0.048	0.033	10.222	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	67	HOH	0	-0.004	-0.014	23.412	0.004	0.004	0.000	0.000	0.000	0.000
58	A	68	HOH	0	0.033	0.022	28.188	-0.004	-0.004	0.000	0.000	0.000	0.000
59	A	69	HOH	0	0.039	0.024	8.647	0.006	0.006	0.000	0.000	0.000	0.000
60	A	71	HOH	0	0.000	-0.007	10.083	-0.103	-0.103	0.000	0.000	0.000	0.000
61	A	72	HOH	0	-0.013	-0.013	19.680	0.010	0.010	0.000	0.000	0.000	0.000
62	A	74	HOH	0	-0.039	-0.023	14.282	-0.019	-0.019	0.000	0.000	0.000	0.000
63	A	76	HOH	0	-0.004	0.001	24.555	-0.001	-0.001	0.000	0.000	0.000	0.000
64	A	77	HOH	0	-0.032	-0.032	26.364	0.003	0.003	0.000	0.000	0.000	0.000
65	A	78	HOH	0	0.037	0.023	19.362	-0.008	-0.008	0.000	0.000	0.000	0.000
66	A	79	HOH	0	-0.036	-0.021	11.292	0.034	0.034	0.000	0.000	0.000	0.000
67	A	80	HOH	0	0.001	-0.008	19.098	0.003	0.003	0.000	0.000	0.000	0.000
68	A	83	HOH	0	0.020	0.002	24.746	-0.003	-0.003	0.000	0.000	0.000	0.000
69	A	84	HOH	0	-0.029	-0.016	13.256	-0.031	-0.031	0.000	0.000	0.000	0.000
70	A	87	HOH	0	-0.003	-0.007	24.740	-0.004	-0.004	0.000	0.000	0.000	0.000
71	A	90	HOH	0	-0.037	-0.031	4.897	-0.339	-0.339	-0.001	-0.003	0.003	0.000
72	A	91	HOH	0	0.034	0.019	12.792	-0.016	-0.016	0.000	0.000	0.000	0.000
73	A	94	HOH	0	0.013	0.013	20.620	0.000	0.000	0.000	0.000	0.000	0.000
74	A	95	HOH	0	0.062	0.042	23.976	0.000	0.000	0.000	0.000	0.000	0.000
75	A	99	HOH	0	-0.052	-0.032	19.793	0.003	0.003	0.000	0.000	0.000	0.000
76	A	102	HOH	0	-0.022	-0.014	15.200	0.013	0.013	0.000	0.000	0.000	0.000
77	A	104	HOH	0	-0.012	-0.020	9.511	-0.077	-0.077	0.000	0.000	0.000	0.000
78	A	106	HOH	0	0.018	0.007	10.215	0.008	0.008	0.000	0.000	0.000	0.000
79	A	108	HOH	0	-0.009	-0.009	9.003	-0.060	-0.060	0.000	0.000	0.000	0.000
80	A	109	HOH	0	-0.054	-0.059	17.460	0.012	0.012	0.000	0.000	0.000	0.000
81	A	110	HOH	0	-0.069	-0.062	22.334	0.008	0.008	0.000	0.000	0.000	0.000
82	A	114	HOH	0	-0.032	-0.027	23.255	0.004	0.004	0.000	0.000	0.000	0.000
83	A	115	HOH	0	0.001	0.008	19.112	0.004	0.004	0.000	0.000	0.000	0.000
84	A	118	HOH	0	0.030	0.020	14.974	-0.012	-0.012	0.000	0.000	0.000	0.000
85	A	127	HOH	0	-0.065	-0.057	19.033	0.006	0.006	0.000	0.000	0.000	0.000
86	A	135	HOH	0	-0.029	-0.018	7.113	-0.028	-0.028	0.000	0.000	0.000	0.000
87	A	140	HOH	0	-0.061	-0.030	4.000	0.097	0.143	0.000	-0.014	-0.031	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:4:ACE)