FMO DATABASE

FMODB ID: G66N1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1556127.807491
FMO2-HF: Nuclear repulsion	1492896.661737
FMO2-HF: Total energy	-63231.145754
FMO2-MP2: Total energy	-63416.971475

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.
-10.306	-3.849	2.194	-3.954	-4.694	-0.019

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 : 0.036

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	-0.032	-0.011	3.861	0.398	3.114	-0.019	-1.429	-1.268	0.006
4	A	16	TRP	0	0.008	-0.011	6.280	-0.447	-0.447	0.000	0.000	0.000	0.000
5	A	17	VAL	0	0.006	0.014	10.093	-0.064	-0.064	0.000	0.000	0.000	0.000
6	A	18	GLY	0	-0.004	0.004	12.261	0.002	0.002	0.000	0.000	0.000	0.000
7	A	19	ARG	1	0.941	0.959	14.994	0.034	0.034	0.000	0.000	0.000	0.000
8	A	20	PRO	0	0.012	0.014	17.265	-0.020	-0.020	0.000	0.000	0.000	0.000
9	A	21	LEU	0	-0.039	-0.026	18.315	-0.035	-0.035	0.000	0.000	0.000	0.000
10	A	22	PRO	0	-0.006	-0.014	21.195	0.021	0.021	0.000	0.000	0.000	0.000
11	A	23	ASN	0	-0.066	-0.030	22.022	-0.007	-0.007	0.000	0.000	0.000	0.000
12	A	24	ARG	1	0.922	0.938	21.964	-0.108	-0.108	0.000	0.000	0.000	0.000
13	A	25	LYS	1	0.882	0.923	21.330	-0.183	-0.183	0.000	0.000	0.000	0.000
14	A	26	GLN	0	0.062	0.039	23.041	0.012	0.012	0.000	0.000	0.000	0.000
15	A	27	PHE	0	0.000	-0.008	21.549	0.009	0.009	0.000	0.000	0.000	0.000
16	A	28	GLN	0	-0.013	0.003	18.379	0.016	0.016	0.000	0.000	0.000	0.000
17	A	29	GLN	0	-0.006	0.006	15.928	-0.007	-0.007	0.000	0.000	0.000	0.000
18	A	30	MET	0	0.027	0.027	16.345	0.041	0.041	0.000	0.000	0.000	0.000
19	A	31	TYR	0	0.012	-0.002	14.199	-0.013	-0.013	0.000	0.000	0.000	0.000
20	A	32	ARG	1	0.869	0.915	16.302	0.164	0.164	0.000	0.000	0.000	0.000
21	A	33	GLU	-1	-0.765	-0.880	12.915	-0.383	-0.383	0.000	0.000	0.000	0.000
22	A	34	ILE	0	-0.009	0.011	7.590	0.169	0.169	0.000	0.000	0.000	0.000
23	A	35	CYS	0	0.004	0.006	7.355	-0.296	-0.296	0.000	0.000	0.000	0.000
24	A	36	MET	0	0.001	0.011	3.589	0.468	0.688	0.002	-0.084	-0.137	0.000
25	A	37	LYS	1	0.874	0.931	2.504	2.611	3.819	0.645	-0.534	-1.318	0.001
26	A	38	ILE	0	0.024	0.013	2.332	-8.127	-5.858	1.567	-1.906	-1.930	-0.026
27	A	39	ASN	0	0.002	0.000	5.056	0.348	0.392	-0.001	-0.001	-0.041	0.000
28	A	40	ASP	-1	-0.897	-0.946	7.477	-0.824	-0.824	0.000	0.000	0.000	0.000
29	A	41	GLY	0	-0.010	0.007	8.258	0.109	0.109	0.000	0.000	0.000	0.000
30	A	42	SER	0	-0.022	-0.023	8.111	-0.155	-0.155	0.000	0.000	0.000	0.000
31	A	43	GLU	-1	-0.889	-0.958	6.317	-2.098	-2.098	0.000	0.000	0.000	0.000
32	A	44	ILE	0	0.000	0.002	7.667	0.444	0.444	0.000	0.000	0.000	0.000
33	A	45	HIS	0	-0.021	-0.010	8.854	-0.161	-0.161	0.000	0.000	0.000	0.000
34	A	46	ILE	0	-0.029	-0.015	8.243	0.095	0.095	0.000	0.000	0.000	0.000
35	A	47	LYS	1	0.828	0.912	12.072	0.542	0.542	0.000	0.000	0.000	0.000
36	A	48	VAL	0	0.008	-0.001	15.296	0.001	0.001	0.000	0.000	0.000	0.000
37	A	49	GLY	0	-0.036	-0.017	17.511	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	50	GLN	0	0.030	0.018	15.206	-0.026	-0.026	0.000	0.000	0.000	0.000
39	A	51	PHE	0	0.032	0.011	16.605	0.049	0.049	0.000	0.000	0.000	0.000
40	A	52	VAL	0	0.004	0.000	11.439	-0.082	-0.082	0.000	0.000	0.000	0.000
41	A	53	LEU	0	0.013	0.019	12.470	0.096	0.096	0.000	0.000	0.000	0.000
42	A	54	ILE	0	-0.011	-0.012	11.389	-0.068	-0.068	0.000	0.000	0.000	0.000
43	A	55	GLN	0	0.004	-0.012	11.085	-0.052	-0.052	0.000	0.000	0.000	0.000
44	A	56	GLY	0	0.026	0.004	12.966	0.039	0.039	0.000	0.000	0.000	0.000
45	A	57	GLU	-1	-0.803	-0.874	16.032	0.152	0.152	0.000	0.000	0.000	0.000
46	A	58	ASP	-1	-0.897	-0.949	16.828	0.210	0.210	0.000	0.000	0.000	0.000
47	A	59	ASN	0	-0.071	-0.037	18.294	-0.031	-0.031	0.000	0.000	0.000	0.000
48	A	60	LYS	1	0.800	0.886	19.848	-0.109	-0.109	0.000	0.000	0.000	0.000
49	A	61	LYS	1	0.938	0.970	18.794	0.037	0.037	0.000	0.000	0.000	0.000
50	A	62	PRO	0	0.044	0.028	14.384	0.018	0.018	0.000	0.000	0.000	0.000
51	A	63	TYR	0	0.043	0.040	16.512	-0.018	-0.018	0.000	0.000	0.000	0.000
52	A	64	VAL	0	0.018	0.002	16.173	-0.039	-0.039	0.000	0.000	0.000	0.000
53	A	65	ALA	0	-0.009	0.001	16.577	0.036	0.036	0.000	0.000	0.000	0.000
54	A	66	LYS	1	0.934	0.995	16.754	0.035	0.035	0.000	0.000	0.000	0.000
55	A	67	LEU	0	0.019	0.009	12.497	0.049	0.049	0.000	0.000	0.000	0.000
56	A	68	ILE	0	-0.036	-0.023	16.937	-0.017	-0.017	0.000	0.000	0.000	0.000
57	A	69	GLU	-1	-0.844	-0.890	17.952	0.173	0.173	0.000	0.000	0.000	0.000
58	A	70	LEU	0	0.037	0.026	11.391	0.004	0.004	0.000	0.000	0.000	0.000
59	A	71	PHE	0	-0.023	-0.028	13.595	-0.028	-0.028	0.000	0.000	0.000	0.000
60	A	72	GLN	0	0.075	0.058	10.918	0.179	0.179	0.000	0.000	0.000	0.000
61	A	73	ASN	0	-0.004	-0.023	13.690	-0.178	-0.178	0.000	0.000	0.000	0.000
62	A	74	GLY	0	0.018	-0.008	15.193	0.082	0.082	0.000	0.000	0.000	0.000
63	A	75	ALA	0	-0.040	-0.013	17.707	-0.032	-0.032	0.000	0.000	0.000	0.000
64	A	76	GLU	-1	-0.824	-0.895	14.835	0.627	0.627	0.000	0.000	0.000	0.000
65	A	77	VAL	0	-0.008	0.005	16.580	0.017	0.017	0.000	0.000	0.000	0.000
66	A	78	PRO	0	0.019	-0.001	12.452	-0.040	-0.040	0.000	0.000	0.000	0.000
67	A	79	PRO	0	-0.006	0.008	13.136	0.047	0.047	0.000	0.000	0.000	0.000
68	A	80	LYS	1	0.835	0.904	9.372	-1.358	-1.358	0.000	0.000	0.000	0.000
69	A	81	LYS	1	0.835	0.936	5.423	-3.296	-3.296	0.000	0.000	0.000	0.000
70	A	82	CYM	-1	-0.748	-0.816	9.316	0.857	0.857	0.000	0.000	0.000	0.000
71	A	83	ALA	0	0.025	-0.003	11.863	-0.092	-0.092	0.000	0.000	0.000	0.000
72	A	84	ARG	1	0.782	0.879	14.055	-0.182	-0.182	0.000	0.000	0.000	0.000
73	A	85	VAL	0	0.008	0.002	15.625	-0.039	-0.039	0.000	0.000	0.000	0.000
74	A	86	GLN	0	-0.050	-0.016	18.829	0.022	0.022	0.000	0.000	0.000	0.000
75	A	87	TRP	0	0.044	-0.008	16.764	-0.034	-0.034	0.000	0.000	0.000	0.000
76	A	88	PHE	0	-0.002	-0.004	21.021	-0.007	-0.007	0.000	0.000	0.000	0.000
77	A	89	VAL	0	0.006	0.031	21.922	0.000	0.000	0.000	0.000	0.000	0.000
78	A	90	ARG	1	0.910	0.941	18.517	0.062	0.062	0.000	0.000	0.000	0.000
79	A	91	PHE	0	0.084	0.023	25.006	0.011	0.011	0.000	0.000	0.000	0.000
80	A	92	LEU	0	-0.070	-0.051	25.957	0.005	0.005	0.000	0.000	0.000	0.000
81	A	93	GLU	-1	-0.851	-0.927	23.315	0.044	0.044	0.000	0.000	0.000	0.000
82	A	94	ILE	0	-0.004	0.025	27.048	0.008	0.008	0.000	0.000	0.000	0.000
83	A	95	PRO	0	0.021	0.007	30.257	-0.001	-0.001	0.000	0.000	0.000	0.000
84	A	96	VAL	0	0.047	0.010	33.114	-0.005	-0.005	0.000	0.000	0.000	0.000
85	A	97	SER	0	-0.003	0.001	34.924	-0.004	-0.004	0.000	0.000	0.000	0.000
86	A	98	LYS	1	0.867	0.926	35.888	-0.019	-0.019	0.000	0.000	0.000	0.000
87	A	99	ARG	1	0.856	0.945	30.416	-0.019	-0.019	0.000	0.000	0.000	0.000
88	A	100	HIS	0	-0.017	-0.017	35.593	-0.005	-0.005	0.000	0.000	0.000	0.000
89	A	101	LEU	0	0.006	0.009	38.358	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	102	LEU	0	-0.038	0.006	33.070	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	103	GLY	0	0.004	0.000	37.100	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	104	ARG	1	0.768	0.846	33.008	0.036	0.036	0.000	0.000	0.000	0.000
93	A	105	SER	0	0.001	0.002	33.862	0.004	0.004	0.000	0.000	0.000	0.000
94	A	106	PRO	0	-0.018	0.008	30.289	-0.003	-0.003	0.000	0.000	0.000	0.000
95	A	107	PRO	0	0.035	0.020	29.351	0.002	0.002	0.000	0.000	0.000	0.000
96	A	108	ALA	0	-0.028	-0.036	25.808	0.001	0.001	0.000	0.000	0.000	0.000
97	A	109	GLN	0	-0.030	-0.020	24.360	0.007	0.007	0.000	0.000	0.000	0.000
98	A	110	GLU	-1	-0.792	-0.853	24.886	-0.056	-0.056	0.000	0.000	0.000	0.000
99	A	111	ILE	0	-0.075	-0.032	21.608	0.009	0.009	0.000	0.000	0.000	0.000
100	A	112	PHE	0	0.025	-0.008	25.576	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	113	TRP	0	0.018	0.014	25.581	0.000	0.000	0.000	0.000	0.000	0.000
102	A	114	TYR	0	-0.045	-0.064	25.025	0.002	0.002	0.000	0.000	0.000	0.000
103	A	115	ASP	-1	-0.908	-0.947	26.795	0.022	0.022	0.000	0.000	0.000	0.000
104	A	116	CYS	0	-0.087	-0.049	28.436	0.003	0.003	0.000	0.000	0.000	0.000
105	A	117	SER	0	-0.010	-0.020	27.255	-0.001	-0.001	0.000	0.000	0.000	0.000
106	A	118	ASP	-1	-0.732	-0.813	28.065	0.086	0.086	0.000	0.000	0.000	0.000
107	A	119	TRP	0	-0.037	-0.004	23.314	0.017	0.017	0.000	0.000	0.000	0.000
108	A	120	ASP	-1	-0.746	-0.858	20.509	0.209	0.209	0.000	0.000	0.000	0.000
109	A	121	ASN	0	0.005	0.003	19.797	0.018	0.018	0.000	0.000	0.000	0.000
110	A	122	LYS	1	0.739	0.805	13.739	-0.605	-0.605	0.000	0.000	0.000	0.000
111	A	123	ILE	0	-0.002	0.005	12.386	-0.011	-0.011	0.000	0.000	0.000	0.000
112	A	124	ASN	0	0.051	0.016	9.412	-0.149	-0.149	0.000	0.000	0.000	0.000
113	A	125	VAL	0	-0.012	-0.017	5.718	-0.061	-0.061	0.000	0.000	0.000	0.000
114	A	126	GLU	-1	-0.845	-0.905	5.244	1.753	1.753	0.000	0.000	0.000	0.000
115	A	127	THR	0	-0.023	-0.011	6.354	-0.081	-0.081	0.000	0.000	0.000	0.000
116	A	128	ILE	0	-0.069	-0.022	7.523	-0.092	-0.092	0.000	0.000	0.000	0.000
117	A	129	ILE	0	0.025	0.003	6.618	-0.282	-0.282	0.000	0.000	0.000	0.000
118	A	130	GLY	0	0.035	0.010	7.874	-0.353	-0.353	0.000	0.000	0.000	0.000
119	A	131	PRO	0	-0.046	-0.023	9.159	0.215	0.215	0.000	0.000	0.000	0.000
120	A	132	VAL	0	0.010	0.004	12.310	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	133	GLN	0	0.013	0.019	15.709	0.003	0.003	0.000	0.000	0.000	0.000
122	A	134	VAL	0	-0.001	-0.012	19.133	0.019	0.019	0.000	0.000	0.000	0.000
123	A	135	VAL	0	-0.031	-0.012	21.632	-0.002	-0.002	0.000	0.000	0.000	0.000
124	A	136	ALA	0	-0.020	-0.016	25.277	0.010	0.010	0.000	0.000	0.000	0.000
125	A	137	LEU	0	-0.027	-0.006	28.037	-0.006	-0.006	0.000	0.000	0.000	0.000
126	A	138	ALA	0	0.031	0.016	31.461	0.007	0.007	0.000	0.000	0.000	0.000
127	A	139	PRO	0	-0.013	-0.029	34.961	-0.002	-0.002	0.000	0.000	0.000	0.000
128	A	140	GLU	-1	-0.867	-0.930	36.622	-0.044	-0.044	0.000	0.000	0.000	0.000
129	A	141	GLU	-1	-0.871	-0.916	33.975	-0.077	-0.077	0.000	0.000	0.000	0.000
130	A	142	VAL	0	-0.024	-0.014	34.864	0.002	0.002	0.000	0.000	0.000	0.000
131	A	143	ILE	0	-0.001	0.002	28.965	-0.004	-0.004	0.000	0.000	0.000	0.000
132	A	144	PRO	0	0.038	0.024	28.774	0.004	0.004	0.000	0.000	0.000	0.000
133	A	145	VAL	0	-0.045	-0.028	28.568	-0.008	-0.008	0.000	0.000	0.000	0.000
134	A	146	ASP	-1	-0.843	-0.901	30.179	-0.108	-0.108	0.000	0.000	0.000	0.000
135	A	147	GLN	0	-0.033	-0.036	29.172	-0.016	-0.016	0.000	0.000	0.000	0.000
136	A	148	LYS	1	0.821	0.889	23.588	0.201	0.201	0.000	0.000	0.000	0.000
137	A	149	SER	0	-0.064	-0.030	24.017	-0.013	-0.013	0.000	0.000	0.000	0.000
138	A	150	GLU	-1	-0.767	-0.851	23.701	-0.204	-0.204	0.000	0.000	0.000	0.000
139	A	151	GLU	-1	-0.902	-0.939	17.186	-0.350	-0.350	0.000	0.000	0.000	0.000
140	A	152	THR	0	-0.148	-0.085	20.044	-0.014	-0.014	0.000	0.000	0.000	0.000
141	A	153	LEU	0	-0.019	-0.002	19.287	0.026	0.026	0.000	0.000	0.000	0.000
142	A	154	PHE	0	0.037	-0.001	22.789	-0.006	-0.006	0.000	0.000	0.000	0.000
143	A	155	VAL	0	-0.016	-0.008	25.517	0.010	0.010	0.000	0.000	0.000	0.000
144	A	156	LYS	1	0.841	0.914	27.636	0.052	0.052	0.000	0.000	0.000	0.000
145	A	157	LEU	0	-0.054	-0.020	30.374	0.004	0.004	0.000	0.000	0.000	0.000
146	A	158	SER	0	-0.033	-0.034	29.609	-0.002	-0.002	0.000	0.000	0.000	0.000
147	A	159	TRP	0	0.013	0.002	29.380	0.001	0.001	0.000	0.000	0.000	0.000
148	A	160	ASN	0	0.096	0.056	30.113	0.006	0.006	0.000	0.000	0.000	0.000
149	A	161	LYS	1	0.813	0.882	29.447	-0.063	-0.063	0.000	0.000	0.000	0.000
150	A	162	LYS	1	0.863	0.944	33.239	-0.032	-0.032	0.000	0.000	0.000	0.000
151	A	163	ASP	-1	-0.805	-0.941	36.070	0.007	0.007	0.000	0.000	0.000	0.000
152	A	164	PHE	0	0.009	0.013	32.025	0.001	0.001	0.000	0.000	0.000	0.000
153	A	165	ALA	0	0.002	0.014	34.311	0.001	0.001	0.000	0.000	0.000	0.000
154	A	166	PRO	0	0.059	0.018	34.144	-0.004	-0.004	0.000	0.000	0.000	0.000
155	A	167	LEU	0	0.034	0.033	28.156	0.004	0.004	0.000	0.000	0.000	0.000
156	A	168	PRO	0	0.021	0.024	29.997	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	169	PRO	0	-0.062	-0.025	30.048	-0.006	-0.006	0.000	0.000	0.000	0.000

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