FMO DATABASE

FMODB ID: P3N8L

Calculation Name: 4FR9-A-Xray13

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 4FR9

Chain ID: A

ChEMBL ID:

UniProt ID: Q5LG06

Base Structure: X-ray

Registration Date: 2018-03-01

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	No
Procedure	Auto-FMO protocol ver. 1.20181228

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	142
LigandCharge	MLY=1
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-1305472.984839
FMO2-HF: Nuclear repulsion	1248884.284746
FMO2-HF: Total energy	-56588.700093
FMO2-MP2: Total energy	-56755.290601

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:25:ACE)

Summations of interaction energy for fragment #1(A:25: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.
2.897	5.145	2.159	-2.079	-2.329	-0.005

Interaction energy analysis for fragmet #1(A:25:ACE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / 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

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	27	ASP	-1	-0.924	-0.974	3.852	0.021	0.960	-0.012	-0.427	-0.501	-0.001
4	A	28	ASP	-1	-0.941	-0.954	6.544	-0.566	-0.566	0.000	0.000	0.000	0.000
5	A	29	THR	0	-0.103	-0.044	3.626	0.722	0.905	0.002	-0.054	-0.132	0.000
6	A	30	GLY	0	-0.031	-0.013	6.252	0.311	0.311	0.000	0.000	0.000	0.000
7	A	31	TYR	0	-0.016	-0.002	2.624	-0.467	0.259	1.491	-0.988	-1.228	-0.007
8	A	32	LEU	0	0.000	0.002	4.598	-0.354	-0.370	-0.001	-0.008	0.025	0.000
9	A	33	PRO	0	-0.020	0.008	6.688	0.251	0.251	0.000	0.000	0.000	0.000
10	A	34	PRO	0	0.036	0.035	7.705	-0.031	-0.031	0.000	0.000	0.000	0.000
11	A	35	SER	0	0.047	0.015	10.201	-0.080	-0.080	0.000	0.000	0.000	0.000
12	A	36	GLN	0	-0.021	-0.035	13.796	0.011	0.011	0.000	0.000	0.000	0.000
13	A	37	ALA	0	0.007	0.003	16.239	0.004	0.004	0.000	0.000	0.000	0.000
14	A	38	ILE	0	0.055	0.036	12.188	-0.009	-0.009	0.000	0.000	0.000	0.000
15	A	39	GLN	0	-0.032	-0.020	12.598	-0.012	-0.012	0.000	0.000	0.000	0.000
16	A	40	ASP	-1	-0.894	-0.957	15.128	0.094	0.094	0.000	0.000	0.000	0.000
17	A	41	ALA	0	-0.054	-0.029	17.589	-0.015	-0.015	0.000	0.000	0.000	0.000
18	A	42	LEU	0	0.053	0.031	13.984	-0.011	-0.011	0.000	0.000	0.000	0.000
19	A	43	MLY	1	0.894	0.961	15.799	-0.130	-0.130	0.000	0.000	0.000	0.000
20	A	44	MLY	1	0.880	0.939	19.960	-0.134	-0.134	0.000	0.000	0.000	0.000
21	A	45	LEU	0	-0.007	0.024	19.261	-0.012	-0.012	0.000	0.000	0.000	0.000
22	A	46	TYR	0	0.020	0.012	18.807	-0.002	-0.002	0.000	0.000	0.000	0.000
23	A	47	PRO	0	0.001	0.009	20.512	0.002	0.002	0.000	0.000	0.000	0.000
24	A	48	ASN	0	-0.094	-0.060	22.571	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	49	ALA	0	-0.011	0.008	16.915	-0.004	-0.004	0.000	0.000	0.000	0.000
26	A	50	THR	0	-0.071	-0.039	17.398	-0.017	-0.017	0.000	0.000	0.000	0.000
27	A	51	ALA	0	-0.003	-0.021	14.281	0.020	0.020	0.000	0.000	0.000	0.000
28	A	52	ILE	0	-0.001	0.017	11.240	0.020	0.020	0.000	0.000	0.000	0.000
29	A	53	MLY	1	0.877	0.970	2.547	-0.492	-0.135	0.620	-0.444	-0.533	0.003
30	A	54	TRP	0	-0.022	-0.012	7.031	0.019	0.019	0.000	0.000	0.000	0.000
31	A	55	GLU	-1	-0.906	-0.960	3.281	3.084	3.206	0.060	-0.139	-0.044	0.000
32	A	56	GLN	0	0.002	-0.003	4.019	-1.076	-1.139	-0.001	-0.019	0.084	0.000
33	A	57	MLY	1	0.971	0.995	5.954	-0.612	-0.612	0.000	0.000	0.000	0.000
34	A	58	GLY	0	0.020	0.018	8.763	-0.174	-0.174	0.000	0.000	0.000	0.000
35	A	59	VAL	0	-0.052	-0.038	10.681	0.036	0.036	0.000	0.000	0.000	0.000
36	A	60	TYR	0	-0.052	-0.051	11.474	-0.050	-0.050	0.000	0.000	0.000	0.000
37	A	61	TYR	0	-0.083	-0.067	6.933	0.148	0.148	0.000	0.000	0.000	0.000
38	A	62	VAL	0	0.015	0.002	8.413	-0.173	-0.173	0.000	0.000	0.000	0.000
39	A	63	ALA	0	-0.045	-0.030	8.583	0.205	0.205	0.000	0.000	0.000	0.000
40	A	64	ASP	-1	-0.869	-0.915	9.263	0.358	0.358	0.000	0.000	0.000	0.000
41	A	65	CYS	0	-0.054	-0.047	10.987	-0.052	-0.052	0.000	0.000	0.000	0.000
42	A	66	GLN	0	0.031	0.041	14.038	-0.021	-0.021	0.000	0.000	0.000	0.000
43	A	67	ALA	0	0.013	-0.021	17.614	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	68	ASP	-1	-0.904	-0.943	20.547	0.106	0.106	0.000	0.000	0.000	0.000
45	A	69	GLY	0	-0.042	-0.022	23.236	-0.004	-0.004	0.000	0.000	0.000	0.000
46	A	70	ARG	1	0.864	0.935	21.468	-0.105	-0.105	0.000	0.000	0.000	0.000
47	A	71	GLU	-1	-0.828	-0.914	15.945	0.159	0.159	0.000	0.000	0.000	0.000
48	A	72	MLY	1	0.877	0.934	16.127	-0.169	-0.169	0.000	0.000	0.000	0.000
49	A	73	GLU	-1	-0.853	-0.908	11.816	0.501	0.501	0.000	0.000	0.000	0.000
50	A	74	VAL	0	-0.065	-0.037	13.418	-0.046	-0.046	0.000	0.000	0.000	0.000
51	A	75	TRP	0	0.047	0.019	12.745	0.117	0.117	0.000	0.000	0.000	0.000
52	A	76	PHE	0	-0.002	-0.018	13.329	-0.085	-0.085	0.000	0.000	0.000	0.000
53	A	77	ASP	-1	-0.759	-0.879	13.613	0.298	0.298	0.000	0.000	0.000	0.000
54	A	78	ALA	0	0.016	-0.009	14.581	0.001	0.001	0.000	0.000	0.000	0.000
55	A	79	ASN	0	-0.120	-0.055	15.508	-0.031	-0.031	0.000	0.000	0.000	0.000
56	A	80	ALA	0	-0.082	-0.037	16.506	-0.019	-0.019	0.000	0.000	0.000	0.000
57	A	81	ASN	0	-0.039	-0.017	17.505	-0.022	-0.022	0.000	0.000	0.000	0.000
58	A	82	TRP	0	-0.004	-0.013	18.020	0.015	0.015	0.000	0.000	0.000	0.000
59	A	83	LEU	0	-0.026	-0.023	16.975	-0.023	-0.023	0.000	0.000	0.000	0.000
60	A	84	MET	0	0.003	0.005	16.856	-0.026	-0.026	0.000	0.000	0.000	0.000
61	A	85	THR	0	-0.034	-0.023	17.541	0.043	0.043	0.000	0.000	0.000	0.000
62	A	86	GLU	-1	-0.802	-0.901	16.622	0.250	0.250	0.000	0.000	0.000	0.000
63	A	87	THR	0	-0.038	-0.028	17.611	0.011	0.011	0.000	0.000	0.000	0.000
64	A	88	GLH	0	-0.003	-0.053	18.603	-0.002	-0.002	0.000	0.000	0.000	0.000
65	A	89	LEU	0	-0.106	-0.060	20.524	-0.016	-0.016	0.000	0.000	0.000	0.000
66	A	90	ASN	0	0.006	-0.004	23.959	0.005	0.005	0.000	0.000	0.000	0.000
67	A	91	SER	0	0.013	-0.002	25.747	-0.005	-0.005	0.000	0.000	0.000	0.000
68	A	92	ILE	0	0.140	0.066	28.631	0.003	0.003	0.000	0.000	0.000	0.000
69	A	93	ASN	0	-0.044	-0.017	31.112	-0.001	-0.001	0.000	0.000	0.000	0.000
70	A	94	ASN	0	-0.096	-0.053	28.122	0.000	0.000	0.000	0.000	0.000	0.000
71	A	95	LEU	0	0.044	0.041	28.963	0.005	0.005	0.000	0.000	0.000	0.000
72	A	96	PRO	0	0.016	0.017	30.890	-0.006	-0.006	0.000	0.000	0.000	0.000
73	A	97	PRO	0	0.019	-0.009	33.957	-0.001	-0.001	0.000	0.000	0.000	0.000
74	A	98	ALA	0	0.016	0.019	37.106	-0.002	-0.002	0.000	0.000	0.000	0.000
75	A	99	VAL	0	0.024	0.014	31.442	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	100	LEU	0	-0.015	0.002	34.478	-0.001	-0.001	0.000	0.000	0.000	0.000
77	A	101	THR	0	-0.039	-0.025	35.612	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	102	ALA	0	0.047	0.033	36.311	-0.002	-0.002	0.000	0.000	0.000	0.000
79	A	103	PHE	0	0.008	0.003	33.243	-0.001	-0.001	0.000	0.000	0.000	0.000
80	A	104	MET	0	-0.041	-0.030	35.912	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	105	GLU	-1	-0.960	-0.976	38.788	0.045	0.045	0.000	0.000	0.000	0.000
82	A	106	SER	0	-0.067	-0.024	36.907	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	107	SER	0	-0.030	-0.041	38.728	-0.003	-0.003	0.000	0.000	0.000	0.000
84	A	108	TYR	0	-0.042	-0.049	34.012	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	109	ASN	0	-0.089	-0.015	35.676	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	110	ASN	0	-0.007	-0.009	37.515	0.001	0.001	0.000	0.000	0.000	0.000
87	A	111	TRP	0	-0.058	-0.032	32.161	-0.002	-0.002	0.000	0.000	0.000	0.000
88	A	112	VAL	0	-0.004	0.009	29.972	-0.001	-0.001	0.000	0.000	0.000	0.000
89	A	113	VAL	0	-0.031	-0.019	28.061	0.004	0.004	0.000	0.000	0.000	0.000
90	A	114	ASP	-1	-0.845	-0.929	24.644	0.077	0.077	0.000	0.000	0.000	0.000
91	A	115	ASP	-1	-0.803	-0.844	20.692	0.147	0.147	0.000	0.000	0.000	0.000
92	A	116	VAL	0	-0.093	-0.058	23.855	-0.008	-0.008	0.000	0.000	0.000	0.000
93	A	117	VAL	0	0.059	0.048	19.953	0.001	0.001	0.000	0.000	0.000	0.000
94	A	118	ILE	0	-0.056	-0.030	22.485	-0.014	-0.014	0.000	0.000	0.000	0.000
95	A	119	LEU	0	-0.015	0.002	19.924	0.019	0.019	0.000	0.000	0.000	0.000
96	A	120	GLU	-1	-0.944	-0.968	21.911	0.131	0.131	0.000	0.000	0.000	0.000
97	A	121	TYR	0	-0.036	-0.054	21.828	0.029	0.029	0.000	0.000	0.000	0.000
98	A	122	PRO	0	-0.023	-0.002	22.496	-0.016	-0.016	0.000	0.000	0.000	0.000
99	A	123	ASN	0	-0.039	-0.016	25.487	-0.005	-0.005	0.000	0.000	0.000	0.000
100	A	124	GLU	-1	-0.841	-0.918	28.075	0.102	0.102	0.000	0.000	0.000	0.000
101	A	125	PRO	0	-0.057	-0.048	29.817	0.000	0.000	0.000	0.000	0.000	0.000
102	A	126	SER	0	0.003	0.000	27.761	0.009	0.009	0.000	0.000	0.000	0.000
103	A	127	THR	0	0.038	0.034	26.717	0.012	0.012	0.000	0.000	0.000	0.000
104	A	128	GLU	-1	-0.895	-0.922	25.281	0.139	0.139	0.000	0.000	0.000	0.000
105	A	129	PHE	0	-0.002	-0.017	25.909	0.008	0.008	0.000	0.000	0.000	0.000
106	A	130	VAL	0	-0.007	-0.007	23.908	-0.008	-0.008	0.000	0.000	0.000	0.000
107	A	131	VAL	0	-0.013	-0.002	25.606	0.002	0.002	0.000	0.000	0.000	0.000
108	A	132	THR	0	0.011	-0.005	24.143	0.000	0.000	0.000	0.000	0.000	0.000
109	A	133	VAL	0	-0.036	-0.020	26.567	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	134	GLU	-1	-0.901	-0.961	27.942	0.068	0.068	0.000	0.000	0.000	0.000
111	A	135	GLN	0	-0.033	-0.029	30.597	-0.007	-0.007	0.000	0.000	0.000	0.000
112	A	136	GLY	0	-0.069	-0.025	32.798	-0.002	-0.002	0.000	0.000	0.000	0.000
113	A	137	MLY	1	0.852	0.948	30.533	-0.066	-0.066	0.000	0.000	0.000	0.000
114	A	138	MLY	1	0.957	0.983	21.715	-0.107	-0.107	0.000	0.000	0.000	0.000
115	A	139	VAL	0	-0.057	-0.037	28.018	0.002	0.002	0.000	0.000	0.000	0.000
116	A	140	ASP	-1	-0.759	-0.856	23.376	0.145	0.145	0.000	0.000	0.000	0.000
117	A	141	LEU	0	-0.052	-0.035	26.993	-0.003	-0.003	0.000	0.000	0.000	0.000
118	A	142	TYR	0	0.046	0.019	23.722	0.008	0.008	0.000	0.000	0.000	0.000
119	A	143	PHE	0	0.011	-0.008	29.099	-0.008	-0.008	0.000	0.000	0.000	0.000
120	A	144	SER	0	0.044	0.022	30.436	0.006	0.006	0.000	0.000	0.000	0.000
121	A	145	GLU	-1	-0.864	-0.951	31.499	0.086	0.086	0.000	0.000	0.000	0.000
122	A	146	GLY	0	-0.061	-0.033	33.395	-0.004	-0.004	0.000	0.000	0.000	0.000
123	A	147	GLY	0	-0.022	-0.002	35.319	-0.004	-0.004	0.000	0.000	0.000	0.000
124	A	148	GLY	0	-0.020	-0.008	36.019	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	149	LEU	0	-0.003	-0.003	32.842	0.005	0.005	0.000	0.000	0.000	0.000
126	A	150	LEU	0	-0.052	-0.029	30.657	-0.003	-0.003	0.000	0.000	0.000	0.000
127	A	151	HIS	0	-0.013	-0.015	28.958	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	152	GLU	-1	-0.858	-0.896	30.816	0.070	0.070	0.000	0.000	0.000	0.000
129	A	153	MLY	1	0.871	0.954	23.963	-0.147	-0.147	0.000	0.000	0.000	0.000
130	A	154	ASP	-1	-0.859	-0.915	27.558	0.082	0.082	0.000	0.000	0.000	0.000
131	A	155	VAL	0	0.050	0.019	23.028	0.004	0.004	0.000	0.000	0.000	0.000
132	A	156	THR	0	-0.052	-0.045	23.950	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	157	ASN	0	-0.081	-0.042	23.584	-0.007	-0.007	0.000	0.000	0.000	0.000
134	A	158	GLY	0	-0.030	-0.016	20.100	0.003	0.003	0.000	0.000	0.000	0.000
135	A	159	ASP	-1	-0.822	-0.899	16.097	0.299	0.299	0.000	0.000	0.000	0.000
136	A	160	ASP	-1	-0.904	-0.941	18.132	0.178	0.178	0.000	0.000	0.000	0.000
137	A	161	THR	0	-0.060	-0.033	14.310	0.019	0.019	0.000	0.000	0.000	0.000
138	A	162	HIS	1	0.842	0.932	16.778	-0.232	-0.232	0.000	0.000	0.000	0.000
139	A	163	TRP	0	-0.022	-0.018	11.741	0.090	0.090	0.000	0.000	0.000	0.000
140	A	164	PRO	0	-0.003	-0.012	15.823	-0.039	-0.039	0.000	0.000	0.000	0.000
141	A	165	ARG	1	0.766	0.873	18.914	-0.159	-0.159	0.000	0.000	0.000	0.000
142	A	166	VAL	-1	-0.889	-0.899	19.299	0.231	0.231	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:25:ACE)