FMO DATABASE

FMODB ID: 7679K

Calculation Name: 4FR9-A-Xray372

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: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	141
LigandCharge	MLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1304531.46479
FMO2-HF: Nuclear repulsion	1248093.050958
FMO2-HF: Total energy	-56438.413831
FMO2-MP2: Total energy	-56604.649903

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:26:ASP)

Summations of interaction energy for fragment #1(A:26: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.
88.489	82.637	36.033	-16.604	-13.576	0.107

Interaction energy analysis for fragmet #1(A:26:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.877 / q_NPA : -0.928

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	28	ASP	-1	-0.950	-0.968	2.635	45.003	50.395	1.356	-3.137	-3.611	0.000
4	A	29	THR	0	-0.094	-0.078	1.609	-43.393	-56.500	31.845	-11.614	-7.123	0.097
5	A	30	GLY	0	-0.036	-0.009	3.609	-12.117	-11.945	0.026	0.124	-0.321	0.003
6	A	31	TYR	0	-0.084	-0.043	1.930	-8.536	-7.966	2.704	-1.425	-1.849	0.001
7	A	32	LEU	0	-0.012	-0.011	3.980	-2.676	-2.650	-0.001	-0.027	0.002	0.000
8	A	33	PRO	0	0.008	0.016	6.944	-0.619	-0.619	0.000	0.000	0.000	0.000
9	A	34	PRO	0	0.029	0.025	8.512	-1.758	-1.758	0.000	0.000	0.000	0.000
10	A	35	SER	0	0.008	0.001	11.637	-0.824	-0.824	0.000	0.000	0.000	0.000
11	A	36	GLN	0	-0.021	-0.032	14.959	0.396	0.396	0.000	0.000	0.000	0.000
12	A	37	ALA	0	0.021	0.012	17.619	-0.137	-0.137	0.000	0.000	0.000	0.000
13	A	38	ILE	0	0.042	0.021	14.155	-0.591	-0.591	0.000	0.000	0.000	0.000
14	A	39	GLN	0	-0.020	-0.009	13.166	-0.220	-0.220	0.000	0.000	0.000	0.000
15	A	40	ASP	-1	-0.859	-0.930	16.934	13.328	13.328	0.000	0.000	0.000	0.000
16	A	41	ALA	0	-0.057	-0.036	19.512	-0.687	-0.687	0.000	0.000	0.000	0.000
17	A	42	LEU	0	0.049	0.033	16.281	-0.540	-0.540	0.000	0.000	0.000	0.000
18	A	43	MLY	1	0.778	0.915	19.763	-14.368	-14.368	0.000	0.000	0.000	0.000
19	A	44	MLY	1	0.859	0.924	22.060	-13.235	-13.235	0.000	0.000	0.000	0.000
20	A	45	LEU	0	-0.011	0.016	21.846	-0.492	-0.492	0.000	0.000	0.000	0.000
21	A	46	TYR	0	0.018	0.007	21.347	-0.219	-0.219	0.000	0.000	0.000	0.000
22	A	47	PRO	0	-0.003	-0.002	23.023	0.456	0.456	0.000	0.000	0.000	0.000
23	A	48	ASN	0	-0.065	-0.050	24.527	0.049	0.049	0.000	0.000	0.000	0.000
24	A	49	ALA	0	0.006	0.017	19.363	0.103	0.103	0.000	0.000	0.000	0.000
25	A	50	THR	0	-0.072	-0.053	19.473	-0.028	-0.028	0.000	0.000	0.000	0.000
26	A	51	ALA	0	0.013	-0.016	16.593	0.339	0.339	0.000	0.000	0.000	0.000
27	A	52	ILE	0	-0.019	0.009	13.235	0.757	0.757	0.000	0.000	0.000	0.000
28	A	53	MLY	1	0.916	0.976	3.147	-50.956	-49.861	0.103	-0.525	-0.674	0.006
29	A	54	TRP	0	0.006	0.002	9.310	-0.338	-0.338	0.000	0.000	0.000	0.000
30	A	55	GLU	-1	-0.868	-0.942	6.136	41.767	41.767	0.000	0.000	0.000	0.000
31	A	56	GLN	0	0.013	-0.002	6.772	-1.052	-1.052	0.000	0.000	0.000	0.000
32	A	57	MLY	1	0.872	0.970	8.287	-24.138	-24.138	0.000	0.000	0.000	0.000
33	A	58	GLY	0	0.019	0.003	10.934	-2.609	-2.609	0.000	0.000	0.000	0.000
34	A	59	VAL	0	-0.054	-0.035	12.213	0.527	0.527	0.000	0.000	0.000	0.000
35	A	60	TYR	0	-0.032	-0.022	13.737	-1.163	-1.163	0.000	0.000	0.000	0.000
36	A	61	TYR	0	-0.050	-0.038	8.758	1.085	1.085	0.000	0.000	0.000	0.000
37	A	62	VAL	0	-0.009	-0.005	11.055	-1.849	-1.849	0.000	0.000	0.000	0.000
38	A	63	ALA	0	-0.020	-0.018	11.229	2.261	2.261	0.000	0.000	0.000	0.000
39	A	64	ASP	-1	-0.831	-0.894	11.969	20.914	20.914	0.000	0.000	0.000	0.000
40	A	65	CYS	0	-0.090	-0.045	13.754	-0.006	-0.006	0.000	0.000	0.000	0.000
41	A	66	GLN	0	0.004	-0.003	16.556	-0.979	-0.979	0.000	0.000	0.000	0.000
42	A	67	ALA	0	0.019	-0.001	20.159	-0.133	-0.133	0.000	0.000	0.000	0.000
43	A	68	ASP	-1	-0.867	-0.931	23.165	11.812	11.812	0.000	0.000	0.000	0.000
44	A	69	GLY	0	-0.034	-0.009	25.994	-0.365	-0.365	0.000	0.000	0.000	0.000
45	A	70	ARG	1	0.787	0.885	24.254	-11.698	-11.698	0.000	0.000	0.000	0.000
46	A	71	GLU	-1	-0.770	-0.866	19.107	15.432	15.432	0.000	0.000	0.000	0.000
47	A	72	MLY	1	0.794	0.888	18.871	-13.434	-13.434	0.000	0.000	0.000	0.000
48	A	73	GLU	-1	-0.782	-0.888	13.705	23.401	23.401	0.000	0.000	0.000	0.000
49	A	74	VAL	0	-0.054	-0.034	16.368	-1.045	-1.045	0.000	0.000	0.000	0.000
50	A	75	TRP	0	0.038	0.015	15.346	1.672	1.672	0.000	0.000	0.000	0.000
51	A	76	PHE	0	0.009	-0.022	15.849	-1.454	-1.454	0.000	0.000	0.000	0.000
52	A	77	ASP	-1	-0.722	-0.850	15.976	15.818	15.818	0.000	0.000	0.000	0.000
53	A	78	ALA	0	0.022	0.011	15.911	0.245	0.245	0.000	0.000	0.000	0.000
54	A	79	ASN	0	-0.165	-0.095	16.884	-0.373	-0.373	0.000	0.000	0.000	0.000
55	A	80	ALA	0	-0.038	-0.015	18.420	-0.615	-0.615	0.000	0.000	0.000	0.000
56	A	81	ASN	0	-0.080	-0.040	19.396	-0.847	-0.847	0.000	0.000	0.000	0.000
57	A	82	TRP	0	-0.012	-0.016	20.293	0.326	0.326	0.000	0.000	0.000	0.000
58	A	83	LEU	0	-0.045	-0.039	19.497	-0.629	-0.629	0.000	0.000	0.000	0.000
59	A	84	MET	0	-0.012	0.008	19.404	-0.656	-0.656	0.000	0.000	0.000	0.000
60	A	85	THR	0	-0.026	-0.017	20.219	0.983	0.983	0.000	0.000	0.000	0.000
61	A	86	GLU	-1	-0.804	-0.893	19.389	15.295	15.295	0.000	0.000	0.000	0.000
62	A	87	THR	0	-0.041	-0.041	20.501	0.705	0.705	0.000	0.000	0.000	0.000
63	A	88	GLH	0	0.002	-0.021	21.462	-0.279	-0.279	0.000	0.000	0.000	0.000
64	A	89	LEU	0	-0.056	-0.045	23.480	-0.551	-0.551	0.000	0.000	0.000	0.000
65	A	90	ASN	0	-0.005	0.005	26.835	0.188	0.188	0.000	0.000	0.000	0.000
66	A	91	SER	0	0.026	0.010	28.520	-0.065	-0.065	0.000	0.000	0.000	0.000
67	A	92	ILE	0	0.129	0.055	30.961	0.013	0.013	0.000	0.000	0.000	0.000
68	A	93	ASN	0	-0.059	-0.027	33.569	-0.048	-0.048	0.000	0.000	0.000	0.000
69	A	94	ASN	0	-0.048	-0.027	30.644	0.217	0.217	0.000	0.000	0.000	0.000
70	A	95	LEU	0	0.048	0.058	31.569	0.171	0.171	0.000	0.000	0.000	0.000
71	A	96	PRO	0	0.007	0.017	33.872	-0.266	-0.266	0.000	0.000	0.000	0.000
72	A	97	PRO	0	0.018	-0.017	36.758	-0.044	-0.044	0.000	0.000	0.000	0.000
73	A	98	ALA	0	0.000	0.024	39.903	-0.095	-0.095	0.000	0.000	0.000	0.000
74	A	99	VAL	0	0.032	0.024	33.992	-0.084	-0.084	0.000	0.000	0.000	0.000
75	A	100	LEU	0	-0.027	0.001	36.991	0.029	0.029	0.000	0.000	0.000	0.000
76	A	101	THR	0	-0.046	-0.040	38.027	-0.107	-0.107	0.000	0.000	0.000	0.000
77	A	102	ALA	0	0.055	0.028	38.997	-0.070	-0.070	0.000	0.000	0.000	0.000
78	A	103	PHE	0	0.013	0.009	34.709	-0.018	-0.018	0.000	0.000	0.000	0.000
79	A	104	MET	0	-0.042	-0.021	38.003	-0.044	-0.044	0.000	0.000	0.000	0.000
80	A	105	GLU	-1	-0.952	-0.978	40.835	7.066	7.066	0.000	0.000	0.000	0.000
81	A	106	SER	0	-0.049	-0.023	38.513	-0.055	-0.055	0.000	0.000	0.000	0.000
82	A	107	SER	0	-0.046	-0.043	39.672	-0.126	-0.126	0.000	0.000	0.000	0.000
83	A	108	TYR	0	-0.012	-0.041	34.772	0.045	0.045	0.000	0.000	0.000	0.000
84	A	109	ASN	0	-0.087	-0.021	36.992	0.126	0.126	0.000	0.000	0.000	0.000
85	A	110	ASN	0	-0.046	-0.026	39.032	-0.039	-0.039	0.000	0.000	0.000	0.000
86	A	111	TRP	0	-0.057	-0.016	33.152	0.044	0.044	0.000	0.000	0.000	0.000
87	A	112	VAL	0	-0.006	0.004	30.668	-0.075	-0.075	0.000	0.000	0.000	0.000
88	A	113	VAL	0	-0.017	-0.016	29.807	0.084	0.084	0.000	0.000	0.000	0.000
89	A	114	ASP	-1	-0.871	-0.941	25.535	11.665	11.665	0.000	0.000	0.000	0.000
90	A	115	ASP	-1	-0.797	-0.881	22.750	14.063	14.063	0.000	0.000	0.000	0.000
91	A	116	VAL	0	-0.074	-0.049	25.884	-0.591	-0.591	0.000	0.000	0.000	0.000
92	A	117	VAL	0	0.026	0.032	22.391	0.151	0.151	0.000	0.000	0.000	0.000
93	A	118	ILE	0	-0.063	-0.033	25.426	-0.651	-0.651	0.000	0.000	0.000	0.000
94	A	119	LEU	0	0.026	0.024	22.532	0.598	0.598	0.000	0.000	0.000	0.000
95	A	120	GLU	-1	-0.804	-0.887	24.519	11.995	11.995	0.000	0.000	0.000	0.000
96	A	121	TYR	0	0.001	-0.041	24.499	0.833	0.833	0.000	0.000	0.000	0.000
97	A	122	PRO	0	-0.031	-0.004	24.919	-0.483	-0.483	0.000	0.000	0.000	0.000
98	A	123	ASN	0	-0.045	-0.032	27.839	-0.216	-0.216	0.000	0.000	0.000	0.000
99	A	124	GLU	-1	-0.796	-0.875	30.535	9.481	9.481	0.000	0.000	0.000	0.000
100	A	125	PRO	0	-0.038	-0.028	32.442	0.025	0.025	0.000	0.000	0.000	0.000
101	A	126	SER	0	-0.010	-0.016	30.585	0.347	0.347	0.000	0.000	0.000	0.000
102	A	127	THR	0	-0.043	-0.033	29.432	0.508	0.508	0.000	0.000	0.000	0.000
103	A	128	GLU	-1	-0.864	-0.900	28.250	10.892	10.892	0.000	0.000	0.000	0.000
104	A	129	PHE	0	0.036	0.008	28.381	0.356	0.356	0.000	0.000	0.000	0.000
105	A	130	VAL	0	-0.016	-0.006	26.136	-0.330	-0.330	0.000	0.000	0.000	0.000
106	A	131	VAL	0	-0.014	-0.004	28.096	0.141	0.141	0.000	0.000	0.000	0.000
107	A	132	THR	0	0.003	-0.003	24.910	-0.190	-0.190	0.000	0.000	0.000	0.000
108	A	133	VAL	0	-0.012	-0.007	27.871	-0.177	-0.177	0.000	0.000	0.000	0.000
109	A	134	GLU	-1	-0.872	-0.949	28.164	11.293	11.293	0.000	0.000	0.000	0.000
110	A	135	GLN	0	-0.020	-0.013	31.290	-0.436	-0.436	0.000	0.000	0.000	0.000
111	A	136	GLY	0	-0.050	-0.013	33.002	-0.250	-0.250	0.000	0.000	0.000	0.000
112	A	137	MLY	1	0.840	0.924	30.982	-9.496	-9.496	0.000	0.000	0.000	0.000
113	A	138	MLY	1	0.892	0.937	23.966	-12.714	-12.714	0.000	0.000	0.000	0.000
114	A	139	VAL	0	-0.048	-0.034	29.066	0.033	0.033	0.000	0.000	0.000	0.000
115	A	140	ASP	-1	-0.715	-0.809	25.044	12.960	12.960	0.000	0.000	0.000	0.000
116	A	141	LEU	0	-0.050	-0.027	28.285	-0.331	-0.331	0.000	0.000	0.000	0.000
117	A	142	TYR	0	0.009	-0.031	25.174	0.152	0.152	0.000	0.000	0.000	0.000
118	A	143	PHE	0	0.006	-0.013	31.056	-0.412	-0.412	0.000	0.000	0.000	0.000
119	A	144	SER	0	0.037	0.015	32.983	0.222	0.222	0.000	0.000	0.000	0.000
120	A	145	GLU	-1	-0.844	-0.923	33.608	9.258	9.258	0.000	0.000	0.000	0.000
121	A	146	GLY	0	-0.052	-0.027	36.131	-0.144	-0.144	0.000	0.000	0.000	0.000
122	A	147	GLY	0	-0.007	-0.005	38.068	-0.226	-0.226	0.000	0.000	0.000	0.000
123	A	148	GLY	0	-0.017	-0.007	38.828	-0.080	-0.080	0.000	0.000	0.000	0.000
124	A	149	LEU	0	-0.009	-0.003	34.622	0.225	0.225	0.000	0.000	0.000	0.000
125	A	150	LEU	0	-0.057	-0.021	33.226	-0.201	-0.201	0.000	0.000	0.000	0.000
126	A	151	HIS	0	-0.050	-0.040	30.849	-0.050	-0.050	0.000	0.000	0.000	0.000
127	A	152	GLU	-1	-0.857	-0.892	32.241	8.958	8.958	0.000	0.000	0.000	0.000
128	A	153	MLY	1	0.852	0.938	25.716	-11.912	-11.912	0.000	0.000	0.000	0.000
129	A	154	ASP	-1	-0.832	-0.879	28.593	10.857	10.857	0.000	0.000	0.000	0.000
130	A	155	VAL	0	0.050	0.022	23.849	0.205	0.205	0.000	0.000	0.000	0.000
131	A	156	THR	0	-0.052	-0.046	24.732	0.191	0.191	0.000	0.000	0.000	0.000
132	A	157	ASN	0	-0.085	-0.048	23.979	0.252	0.252	0.000	0.000	0.000	0.000
133	A	158	GLY	0	-0.019	-0.005	21.103	-0.300	-0.300	0.000	0.000	0.000	0.000
134	A	159	ASP	-1	-0.833	-0.881	17.360	19.055	19.055	0.000	0.000	0.000	0.000
135	A	160	ASP	-1	-0.919	-0.956	19.048	15.520	15.520	0.000	0.000	0.000	0.000
136	A	161	THR	0	-0.071	-0.048	15.284	-0.067	-0.067	0.000	0.000	0.000	0.000
137	A	162	HIS	1	0.847	0.919	18.555	-15.417	-15.417	0.000	0.000	0.000	0.000
138	A	163	TRP	0	-0.022	-0.019	13.535	1.385	1.385	0.000	0.000	0.000	0.000
139	A	164	PRO	0	0.013	-0.003	18.531	-0.982	-0.982	0.000	0.000	0.000	0.000
140	A	165	ARG	1	0.772	0.873	21.459	-11.230	-11.230	0.000	0.000	0.000	0.000
141	A	166	VAL	0	-0.025	0.021	21.636	-0.158	-0.158	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:26:ASP)