FMO DATABASE

FMODB ID: 1774Z

Calculation Name: 4DOW-A-Xray372

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 4DOW

Chain ID: A

ChEMBL ID:

UniProt ID: P62806

Base Structure: X-ray

Registration Date: 2023-06-21

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	OptHSide
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	157
LigandCharge	CYM=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1558356.002262
FMO2-HF: Nuclear repulsion	1495125.419334
FMO2-HF: Total energy	-63230.582928
FMO2-MP2: Total energy	-63416.490289

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:13:THR)

Summations of interaction energy for fragment #1(A:13:THR)

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.
-7.171	-0.642	0.605	-3.344	-3.792	-0.005

Interaction energy analysis for fragmet #1(A:13:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.049 / q_NPA : 0.034

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	15	SER	0	-0.024	-0.007	3.804	0.372	3.524	-0.028	-1.656	-1.469	0.009
4	A	16	TRP	0	0.004	-0.012	6.109	-0.425	-0.425	0.000	0.000	0.000	0.000
5	A	17	VAL	0	0.026	0.021	9.733	-0.072	-0.072	0.000	0.000	0.000	0.000
6	A	18	GLY	0	-0.016	-0.003	11.887	0.023	0.023	0.000	0.000	0.000	0.000
7	A	19	ARG	1	0.948	0.960	14.836	0.064	0.064	0.000	0.000	0.000	0.000
8	A	20	PRO	0	0.013	0.015	17.151	-0.020	-0.020	0.000	0.000	0.000	0.000
9	A	21	LEU	0	-0.034	-0.031	18.267	-0.030	-0.030	0.000	0.000	0.000	0.000
10	A	22	PRO	0	-0.012	-0.013	21.146	0.019	0.019	0.000	0.000	0.000	0.000
11	A	23	ASN	0	-0.058	-0.027	22.049	-0.005	-0.005	0.000	0.000	0.000	0.000
12	A	24	ARG	1	0.900	0.932	21.943	-0.096	-0.096	0.000	0.000	0.000	0.000
13	A	25	LYS	1	0.886	0.931	21.522	-0.155	-0.155	0.000	0.000	0.000	0.000
14	A	26	GLN	0	0.062	0.032	23.189	0.008	0.008	0.000	0.000	0.000	0.000
15	A	27	PHE	0	0.009	-0.003	21.241	0.010	0.010	0.000	0.000	0.000	0.000
16	A	28	GLN	0	-0.012	0.006	18.359	0.020	0.020	0.000	0.000	0.000	0.000
17	A	29	GLN	0	-0.020	0.003	15.846	-0.005	-0.005	0.000	0.000	0.000	0.000
18	A	30	MET	0	0.036	0.033	16.357	0.038	0.038	0.000	0.000	0.000	0.000
19	A	31	TYR	0	0.001	0.004	14.116	-0.026	-0.026	0.000	0.000	0.000	0.000
20	A	32	ARG	1	0.901	0.931	16.258	0.188	0.188	0.000	0.000	0.000	0.000
21	A	33	GLU	-1	-0.773	-0.881	13.018	-0.391	-0.391	0.000	0.000	0.000	0.000
22	A	34	ILE	0	-0.011	0.007	7.469	0.163	0.163	0.000	0.000	0.000	0.000
23	A	35	CYS	0	0.004	0.008	7.193	-0.302	-0.302	0.000	0.000	0.000	0.000
24	A	36	MET	0	0.001	0.005	3.769	0.248	0.389	0.000	-0.055	-0.086	0.000
25	A	37	LYS	1	0.885	0.938	2.739	2.478	3.763	0.254	-0.471	-1.068	-0.001
26	A	38	ILE	0	0.029	0.025	2.745	-4.743	-2.840	0.380	-1.160	-1.124	-0.013
27	A	39	ASN	0	-0.038	-0.024	5.428	0.122	0.122	0.000	0.000	0.000	0.000
28	A	40	ASP	-1	-0.857	-0.929	7.552	-0.631	-0.631	0.000	0.000	0.000	0.000
29	A	41	GLY	0	-0.046	-0.022	7.994	0.084	0.084	0.000	0.000	0.000	0.000
30	A	42	SER	0	0.006	0.002	8.327	-0.132	-0.132	0.000	0.000	0.000	0.000
31	A	43	GLU	-1	-0.899	-0.952	6.630	-2.134	-2.134	0.000	0.000	0.000	0.000
32	A	44	ILE	0	0.006	0.007	7.694	0.439	0.439	0.000	0.000	0.000	0.000
33	A	45	HIS	0	-0.048	-0.034	8.883	-0.198	-0.198	0.000	0.000	0.000	0.000
34	A	46	ILE	0	-0.009	-0.003	8.418	0.094	0.094	0.000	0.000	0.000	0.000
35	A	47	LYS	1	0.834	0.912	11.998	0.536	0.536	0.000	0.000	0.000	0.000
36	A	48	VAL	0	0.021	0.002	15.245	0.009	0.009	0.000	0.000	0.000	0.000
37	A	49	GLY	0	-0.057	-0.026	17.454	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	50	GLN	0	0.017	0.016	15.305	-0.038	-0.038	0.000	0.000	0.000	0.000
39	A	51	PHE	0	0.034	0.010	16.673	0.043	0.043	0.000	0.000	0.000	0.000
40	A	52	VAL	0	0.009	0.005	11.418	-0.076	-0.076	0.000	0.000	0.000	0.000
41	A	53	LEU	0	0.009	0.009	12.781	0.092	0.092	0.000	0.000	0.000	0.000
42	A	54	ILE	0	-0.002	-0.010	11.749	-0.057	-0.057	0.000	0.000	0.000	0.000
43	A	55	GLN	0	-0.014	-0.026	11.334	-0.042	-0.042	0.000	0.000	0.000	0.000
44	A	56	GLY	0	0.038	0.018	13.203	0.045	0.045	0.000	0.000	0.000	0.000
45	A	57	GLU	-1	-0.821	-0.892	16.277	0.152	0.152	0.000	0.000	0.000	0.000
46	A	58	ASP	-1	-0.870	-0.938	16.978	0.219	0.219	0.000	0.000	0.000	0.000
47	A	59	ASN	0	-0.066	-0.030	18.461	-0.020	-0.020	0.000	0.000	0.000	0.000
48	A	60	LYS	1	0.790	0.884	20.104	-0.118	-0.118	0.000	0.000	0.000	0.000
49	A	61	LYS	1	0.926	0.959	19.070	0.020	0.020	0.000	0.000	0.000	0.000
50	A	62	PRO	0	0.050	0.034	14.664	0.018	0.018	0.000	0.000	0.000	0.000
51	A	63	TYR	0	0.039	0.038	16.625	-0.013	-0.013	0.000	0.000	0.000	0.000
52	A	64	VAL	0	0.006	0.002	16.486	-0.033	-0.033	0.000	0.000	0.000	0.000
53	A	65	ALA	0	0.004	0.001	16.635	0.031	0.031	0.000	0.000	0.000	0.000
54	A	66	LYS	1	0.950	0.999	17.145	0.027	0.027	0.000	0.000	0.000	0.000
55	A	67	LEU	0	-0.004	0.006	12.628	0.047	0.047	0.000	0.000	0.000	0.000
56	A	68	ILE	0	-0.020	-0.026	17.030	-0.015	-0.015	0.000	0.000	0.000	0.000
57	A	69	GLU	-1	-0.834	-0.890	17.751	0.147	0.147	0.000	0.000	0.000	0.000
58	A	70	LEU	0	0.014	0.018	11.382	0.012	0.012	0.000	0.000	0.000	0.000
59	A	71	PHE	0	-0.014	-0.030	13.671	-0.023	-0.023	0.000	0.000	0.000	0.000
60	A	72	GLN	0	0.082	0.068	11.018	0.192	0.192	0.000	0.000	0.000	0.000
61	A	73	ASN	0	0.015	-0.022	13.821	-0.167	-0.167	0.000	0.000	0.000	0.000
62	A	74	GLY	0	0.000	-0.022	15.647	0.060	0.060	0.000	0.000	0.000	0.000
63	A	75	ALA	0	-0.045	-0.019	17.706	-0.019	-0.019	0.000	0.000	0.000	0.000
64	A	76	GLU	-1	-0.833	-0.880	14.967	0.578	0.578	0.000	0.000	0.000	0.000
65	A	77	VAL	0	-0.022	0.008	16.314	0.014	0.014	0.000	0.000	0.000	0.000
66	A	78	PRO	0	0.038	-0.020	12.449	-0.038	-0.038	0.000	0.000	0.000	0.000
67	A	79	PRO	0	-0.012	0.001	12.580	0.032	0.032	0.000	0.000	0.000	0.000
68	A	80	LYS	1	0.849	0.920	8.942	-1.440	-1.440	0.000	0.000	0.000	0.000
69	A	81	LYS	1	0.824	0.928	5.194	-3.431	-3.383	-0.001	-0.002	-0.045	0.000
70	A	82	CYM	-1	-0.714	-0.795	9.909	0.731	0.731	0.000	0.000	0.000	0.000
71	A	83	ALA	0	0.011	-0.009	12.283	-0.083	-0.083	0.000	0.000	0.000	0.000
72	A	84	ARG	1	0.810	0.911	14.100	-0.168	-0.168	0.000	0.000	0.000	0.000
73	A	85	VAL	0	-0.005	-0.009	15.847	-0.041	-0.041	0.000	0.000	0.000	0.000
74	A	86	GLN	0	-0.058	-0.022	18.822	0.021	0.021	0.000	0.000	0.000	0.000
75	A	87	TRP	0	0.028	-0.008	17.105	-0.029	-0.029	0.000	0.000	0.000	0.000
76	A	88	PHE	0	0.026	0.010	21.174	-0.010	-0.010	0.000	0.000	0.000	0.000
77	A	89	VAL	0	0.012	0.025	22.566	0.010	0.010	0.000	0.000	0.000	0.000
78	A	90	ARG	1	0.924	0.950	18.729	0.047	0.047	0.000	0.000	0.000	0.000
79	A	91	PHE	0	0.109	0.039	25.320	0.010	0.010	0.000	0.000	0.000	0.000
80	A	92	LEU	0	-0.070	-0.051	26.691	0.005	0.005	0.000	0.000	0.000	0.000
81	A	93	GLU	-1	-0.876	-0.944	23.701	0.057	0.057	0.000	0.000	0.000	0.000
82	A	94	ILE	0	-0.029	0.012	27.447	0.006	0.006	0.000	0.000	0.000	0.000
83	A	95	PRO	0	0.030	0.013	30.855	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	96	VAL	0	0.087	0.027	33.644	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	97	SER	0	-0.025	-0.014	35.576	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	98	LYS	1	0.788	0.888	35.782	-0.023	-0.023	0.000	0.000	0.000	0.000
87	A	99	ARG	1	0.887	0.964	31.192	-0.024	-0.024	0.000	0.000	0.000	0.000
88	A	100	HIS	0	-0.010	-0.007	36.202	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	101	LEU	0	0.014	0.008	38.350	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	102	LEU	0	-0.045	0.005	33.665	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	103	GLY	0	0.003	0.000	37.672	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	104	ARG	1	0.779	0.846	33.464	0.028	0.028	0.000	0.000	0.000	0.000
93	A	105	SER	0	0.000	0.000	35.031	0.004	0.004	0.000	0.000	0.000	0.000
94	A	106	PRO	0	-0.042	-0.001	30.942	-0.004	-0.004	0.000	0.000	0.000	0.000
95	A	107	PRO	0	0.047	0.025	29.994	0.002	0.002	0.000	0.000	0.000	0.000
96	A	108	ALA	0	-0.016	-0.025	26.068	0.001	0.001	0.000	0.000	0.000	0.000
97	A	109	GLN	0	-0.015	-0.015	24.736	0.008	0.008	0.000	0.000	0.000	0.000
98	A	110	GLU	-1	-0.775	-0.838	25.504	-0.047	-0.047	0.000	0.000	0.000	0.000
99	A	111	ILE	0	-0.093	-0.043	22.065	0.008	0.008	0.000	0.000	0.000	0.000
100	A	112	PHE	0	0.026	-0.009	26.060	-0.001	-0.001	0.000	0.000	0.000	0.000
101	A	113	TRP	0	0.029	0.016	25.794	-0.002	-0.002	0.000	0.000	0.000	0.000
102	A	114	TYR	0	-0.065	-0.053	25.445	0.003	0.003	0.000	0.000	0.000	0.000
103	A	115	ASP	-1	-0.932	-0.963	27.206	0.023	0.023	0.000	0.000	0.000	0.000
104	A	116	CYS	0	-0.074	-0.059	28.688	0.002	0.002	0.000	0.000	0.000	0.000
105	A	117	SER	0	-0.001	-0.003	27.812	0.000	0.000	0.000	0.000	0.000	0.000
106	A	118	ASP	-1	-0.742	-0.818	27.890	0.082	0.082	0.000	0.000	0.000	0.000
107	A	119	TRP	0	-0.016	0.004	23.633	0.016	0.016	0.000	0.000	0.000	0.000
108	A	120	ASP	-1	-0.764	-0.888	20.532	0.202	0.202	0.000	0.000	0.000	0.000
109	A	121	ASN	0	-0.017	-0.001	20.312	0.020	0.020	0.000	0.000	0.000	0.000
110	A	122	LYS	1	0.724	0.800	14.336	-0.533	-0.533	0.000	0.000	0.000	0.000
111	A	123	ILE	0	-0.015	-0.001	12.699	0.005	0.005	0.000	0.000	0.000	0.000
112	A	124	ASN	0	0.067	0.028	9.881	-0.073	-0.073	0.000	0.000	0.000	0.000
113	A	125	VAL	0	0.006	-0.003	6.002	-0.054	-0.054	0.000	0.000	0.000	0.000
114	A	126	GLU	-1	-0.853	-0.911	4.901	1.966	1.966	0.000	0.000	0.000	0.000
115	A	127	THR	0	-0.041	-0.024	6.498	-0.122	-0.122	0.000	0.000	0.000	0.000
116	A	128	ILE	0	-0.064	-0.018	7.693	-0.103	-0.103	0.000	0.000	0.000	0.000
117	A	129	ILE	0	0.019	0.008	7.025	-0.173	-0.173	0.000	0.000	0.000	0.000
118	A	130	GLY	0	0.031	0.002	7.953	-0.342	-0.342	0.000	0.000	0.000	0.000
119	A	131	PRO	0	-0.048	-0.019	9.529	0.181	0.181	0.000	0.000	0.000	0.000
120	A	132	VAL	0	0.017	0.011	12.636	0.012	0.012	0.000	0.000	0.000	0.000
121	A	133	GLN	0	-0.003	0.012	16.061	-0.004	-0.004	0.000	0.000	0.000	0.000
122	A	134	VAL	0	0.001	-0.013	19.389	0.019	0.019	0.000	0.000	0.000	0.000
123	A	135	VAL	0	-0.020	-0.016	21.871	-0.005	-0.005	0.000	0.000	0.000	0.000
124	A	136	ALA	0	-0.031	-0.008	25.466	0.010	0.010	0.000	0.000	0.000	0.000
125	A	137	LEU	0	-0.024	0.000	28.487	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	138	ALA	0	0.027	0.009	31.698	0.006	0.006	0.000	0.000	0.000	0.000
127	A	139	PRO	0	0.000	-0.019	35.147	-0.001	-0.001	0.000	0.000	0.000	0.000
128	A	140	GLU	-1	-0.907	-0.958	36.631	-0.041	-0.041	0.000	0.000	0.000	0.000
129	A	141	GLU	-1	-0.848	-0.901	34.095	-0.072	-0.072	0.000	0.000	0.000	0.000
130	A	142	VAL	0	-0.039	-0.027	35.390	0.003	0.003	0.000	0.000	0.000	0.000
131	A	143	ILE	0	-0.016	-0.011	29.349	-0.004	-0.004	0.000	0.000	0.000	0.000
132	A	144	PRO	0	0.068	0.028	30.002	0.005	0.005	0.000	0.000	0.000	0.000
133	A	145	VAL	0	-0.084	-0.050	29.177	-0.006	-0.006	0.000	0.000	0.000	0.000
134	A	146	ASP	-1	-0.860	-0.900	30.563	-0.093	-0.093	0.000	0.000	0.000	0.000
135	A	147	GLN	0	-0.018	-0.031	29.253	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	148	LYS	1	0.847	0.904	23.383	0.187	0.187	0.000	0.000	0.000	0.000
137	A	149	SER	0	-0.036	-0.019	24.350	-0.009	-0.009	0.000	0.000	0.000	0.000
138	A	150	GLU	-1	-0.808	-0.880	23.865	-0.168	-0.168	0.000	0.000	0.000	0.000
139	A	151	GLU	-1	-0.908	-0.945	17.565	-0.290	-0.290	0.000	0.000	0.000	0.000
140	A	152	THR	0	-0.124	-0.065	20.035	-0.021	-0.021	0.000	0.000	0.000	0.000
141	A	153	LEU	0	-0.040	-0.011	19.828	0.022	0.022	0.000	0.000	0.000	0.000
142	A	154	PHE	0	0.044	0.012	23.273	-0.007	-0.007	0.000	0.000	0.000	0.000
143	A	155	VAL	0	-0.032	-0.020	25.925	0.010	0.010	0.000	0.000	0.000	0.000
144	A	156	LYS	1	0.847	0.937	27.807	0.045	0.045	0.000	0.000	0.000	0.000
145	A	157	LEU	0	-0.026	-0.020	31.004	0.003	0.003	0.000	0.000	0.000	0.000
146	A	158	SER	0	-0.013	-0.015	30.008	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	159	TRP	0	0.012	0.002	29.957	0.001	0.001	0.000	0.000	0.000	0.000
148	A	160	ASN	0	0.104	0.050	30.690	0.005	0.005	0.000	0.000	0.000	0.000
149	A	161	LYS	1	0.812	0.894	30.233	-0.059	-0.059	0.000	0.000	0.000	0.000
150	A	162	LYS	1	0.844	0.924	33.891	-0.031	-0.031	0.000	0.000	0.000	0.000
151	A	163	ASP	-1	-0.750	-0.901	36.720	0.006	0.006	0.000	0.000	0.000	0.000
152	A	164	PHE	0	-0.015	-0.011	32.205	0.001	0.001	0.000	0.000	0.000	0.000
153	A	165	ALA	0	-0.007	0.008	34.718	0.001	0.001	0.000	0.000	0.000	0.000
154	A	166	PRO	0	0.054	0.011	34.579	-0.003	-0.003	0.000	0.000	0.000	0.000
155	A	167	LEU	0	0.020	0.023	28.684	0.005	0.005	0.000	0.000	0.000	0.000
156	A	168	PRO	0	0.015	0.014	30.412	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	169	PRO	0	-0.036	-0.007	30.759	-0.008	-0.008	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:13:THR)