FMO DATABASE

FMODB ID: M35RZ

Calculation Name: 4MDW-A-Xray372

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 4MDW

Chain ID: A

ChEMBL ID:

UniProt ID: O05503

Base Structure: X-ray

Registration Date: 2023-06-20

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	OptH
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	147
LigandCharge	MLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1386631.716104
FMO2-HF: Nuclear repulsion	1328246.918633
FMO2-HF: Total energy	-58384.79747
FMO2-MP2: Total energy	-58553.000178

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:59:HIS)

Summations of interaction energy for fragment #1(A:59:HIS)

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.
-2.969	0.138	-0.004	-1.103	-2.002	0

Interaction energy analysis for fragmet #1(A:59:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : -0.009

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].
3	A	61	GLU	-1	-0.847	-0.900	3.073	-0.827	1.528	-0.002	-1.007	-1.346
4	A	62	MET	0	0.001	-0.009	4.092	-0.145	0.232	-0.001	-0.037	-0.340
5	A	63	ASP	-1	-0.913	-0.946	4.378	-1.295	-0.920	-0.001	-0.059	-0.316
6	A	64	HIS	0	-0.084	-0.051	6.698	0.256	0.256	0.000	0.000	0.000
7	A	65	SER	0	-0.035	-0.027	8.784	0.050	0.050	0.000	0.000	0.000
8	A	66	GLY	0	0.038	0.038	9.683	0.012	0.012	0.000	0.000	0.000
9	A	67	SER	0	-0.066	-0.026	10.360	-0.013	-0.013	0.000	0.000	0.000
10	A	68	ALA	0	-0.031	-0.026	14.136	0.024	0.024	0.000	0.000	0.000
11	A	69	ASP	-1	-0.919	-0.948	16.205	0.056	0.056	0.000	0.000	0.000
12	A	70	VAL	0	-0.035	-0.001	19.876	0.014	0.014	0.000	0.000	0.000
13	A	71	PRO	0	-0.004	-0.007	22.132	-0.008	-0.008	0.000	0.000	0.000
14	A	72	GLU	-1	-0.860	-0.929	24.861	0.046	0.046	0.000	0.000	0.000
15	A	73	GLY	0	-0.052	-0.031	28.510	0.003	0.003	0.000	0.000	0.000
16	A	74	LEU	0	-0.023	0.013	25.229	0.003	0.003	0.000	0.000	0.000
17	A	75	GLN	0	-0.035	-0.019	29.355	-0.005	-0.005	0.000	0.000	0.000
18	A	76	GLU	-1	-0.934	-0.969	29.927	0.081	0.081	0.000	0.000	0.000
19	A	77	SER	0	-0.031	-0.032	30.362	-0.006	-0.006	0.000	0.000	0.000
20	A	78	MLY	1	0.820	0.920	32.138	-0.073	-0.073	0.000	0.000	0.000
21	A	79	ASN	0	-0.053	-0.037	35.228	-0.002	-0.002	0.000	0.000	0.000
22	A	80	PRO	0	0.038	0.044	29.975	0.002	0.002	0.000	0.000	0.000
23	A	81	MLY	1	0.937	0.987	30.219	-0.138	-0.138	0.000	0.000	0.000
24	A	82	TYR	0	-0.067	-0.038	26.933	-0.003	-0.003	0.000	0.000	0.000
25	A	83	MLY	1	1.008	1.002	28.316	-0.093	-0.093	0.000	0.000	0.000
26	A	84	VAL	0	0.059	0.020	25.530	0.010	0.010	0.000	0.000	0.000
27	A	85	GLY	0	-0.022	-0.007	25.401	-0.008	-0.008	0.000	0.000	0.000
28	A	86	SER	0	-0.099	-0.038	26.241	0.004	0.004	0.000	0.000	0.000
29	A	87	GLN	0	0.006	-0.010	22.568	0.000	0.000	0.000	0.000	0.000
30	A	88	VAL	0	-0.008	-0.015	21.326	-0.011	-0.011	0.000	0.000	0.000
31	A	89	ILE	0	-0.014	0.000	20.797	0.013	0.013	0.000	0.000	0.000
32	A	90	ILE	0	0.053	0.040	16.155	-0.018	-0.018	0.000	0.000	0.000
33	A	91	ASN	0	-0.006	-0.009	19.662	0.026	0.026	0.000	0.000	0.000
34	A	92	THR	0	-0.060	-0.020	18.211	0.007	0.007	0.000	0.000	0.000
35	A	93	SER	0	-0.016	-0.027	16.496	0.023	0.023	0.000	0.000	0.000
36	A	94	HIS	1	0.811	0.904	15.365	-0.293	-0.293	0.000	0.000	0.000
37	A	95	MET	0	0.061	0.042	8.068	0.111	0.111	0.000	0.000	0.000
38	A	96	MLY	1	0.954	0.965	5.380	-2.612	-2.612	0.000	0.000	0.000
39	A	97	GLY	0	0.056	0.039	9.411	0.081	0.081	0.000	0.000	0.000
40	A	98	MET	0	0.021	0.026	10.807	-0.086	-0.086	0.000	0.000	0.000
41	A	99	MLY	1	0.917	0.967	13.710	-0.399	-0.399	0.000	0.000	0.000
42	A	100	GLY	0	-0.045	-0.030	16.745	0.015	0.015	0.000	0.000	0.000
43	A	101	ALA	0	-0.011	0.014	14.529	-0.009	-0.009	0.000	0.000	0.000
44	A	102	GLU	-1	-0.843	-0.922	16.489	0.218	0.218	0.000	0.000	0.000
45	A	103	ALA	0	0.024	-0.001	16.862	0.028	0.028	0.000	0.000	0.000
46	A	104	THR	0	-0.092	-0.047	18.698	-0.027	-0.027	0.000	0.000	0.000
47	A	105	VAL	0	0.022	0.028	20.175	0.011	0.011	0.000	0.000	0.000
48	A	106	THR	0	-0.052	-0.045	19.517	-0.012	-0.012	0.000	0.000	0.000
49	A	107	GLY	0	0.028	0.021	22.378	-0.015	-0.015	0.000	0.000	0.000
50	A	108	ALA	0	0.005	0.001	24.176	0.012	0.012	0.000	0.000	0.000
51	A	109	TYR	0	0.024	0.009	23.665	-0.006	-0.006	0.000	0.000	0.000
52	A	110	ASP	-1	-0.826	-0.909	28.507	0.102	0.102	0.000	0.000	0.000
53	A	111	THR	0	-0.007	-0.039	27.088	-0.005	-0.005	0.000	0.000	0.000
54	A	112	THR	0	-0.057	-0.025	30.017	0.001	0.001	0.000	0.000	0.000
55	A	113	ALA	0	0.007	0.006	25.383	0.001	0.001	0.000	0.000	0.000
56	A	114	TYR	0	-0.009	-0.037	25.743	-0.006	-0.006	0.000	0.000	0.000
57	A	115	VAL	0	-0.079	-0.018	23.778	0.013	0.013	0.000	0.000	0.000
58	A	116	VAL	0	-0.013	0.000	21.912	-0.015	-0.015	0.000	0.000	0.000
59	A	117	SER	0	0.062	0.025	22.616	0.026	0.026	0.000	0.000	0.000
60	A	118	TYR	0	-0.004	-0.008	16.405	-0.024	-0.024	0.000	0.000	0.000
61	A	119	THR	0	0.004	0.008	20.508	0.023	0.023	0.000	0.000	0.000
62	A	120	PRO	0	0.023	0.029	15.828	-0.017	-0.017	0.000	0.000	0.000
63	A	121	THR	0	0.002	0.001	17.999	-0.014	-0.014	0.000	0.000	0.000
64	A	122	ASN	0	-0.040	-0.024	12.924	-0.002	-0.002	0.000	0.000	0.000
65	A	123	GLY	0	-0.015	0.004	16.944	-0.014	-0.014	0.000	0.000	0.000
66	A	124	GLY	0	-0.004	-0.010	16.209	0.014	0.014	0.000	0.000	0.000
67	A	125	GLN	0	-0.040	-0.035	16.528	0.019	0.019	0.000	0.000	0.000
68	A	126	ARG	1	0.941	0.966	17.690	-0.123	-0.123	0.000	0.000	0.000
69	A	127	VAL	0	-0.009	0.000	16.293	0.028	0.028	0.000	0.000	0.000
70	A	128	ASP	-1	-0.927	-0.971	19.005	0.175	0.175	0.000	0.000	0.000
71	A	129	HIS	0	-0.030	-0.020	21.056	0.014	0.014	0.000	0.000	0.000
72	A	130	HIS	0	-0.015	-0.006	15.417	0.037	0.037	0.000	0.000	0.000
73	A	131	MLY	1	0.938	0.983	19.525	-0.254	-0.254	0.000	0.000	0.000
74	A	132	TRP	0	-0.050	-0.070	18.486	0.029	0.029	0.000	0.000	0.000
75	A	133	VAL	0	-0.017	0.013	20.250	0.005	0.005	0.000	0.000	0.000
76	A	134	ILE	0	-0.011	-0.005	22.627	0.000	0.000	0.000	0.000	0.000
77	A	135	GLN	0	0.027	0.018	25.577	0.001	0.001	0.000	0.000	0.000
78	A	136	GLU	-1	-0.760	-0.876	26.878	0.084	0.084	0.000	0.000	0.000
79	A	137	GLU	-1	-0.809	-0.884	20.839	0.132	0.132	0.000	0.000	0.000
80	A	138	ILE	0	-0.008	0.004	24.453	0.001	0.001	0.000	0.000	0.000
81	A	139	MLY	1	0.938	0.962	27.102	-0.033	-0.033	0.000	0.000	0.000
82	A	140	ASP	-1	-0.948	-0.981	28.541	0.035	0.035	0.000	0.000	0.000
83	A	141	ALA	0	-0.014	0.009	30.810	-0.001	-0.001	0.000	0.000	0.000
84	A	142	GLY	0	-0.021	-0.003	32.624	-0.002	-0.002	0.000	0.000	0.000
85	A	143	ASP	-1	-0.849	-0.931	33.445	0.062	0.062	0.000	0.000	0.000
86	A	144	MLY	1	0.853	0.933	35.745	-0.055	-0.055	0.000	0.000	0.000
87	A	145	THR	0	-0.032	-0.018	34.198	0.001	0.001	0.000	0.000	0.000
88	A	146	LEU	0	-0.005	0.004	30.843	-0.004	-0.004	0.000	0.000	0.000
89	A	147	GLN	0	-0.058	-0.048	33.820	0.002	0.002	0.000	0.000	0.000
90	A	148	PRO	0	-0.003	-0.013	32.527	0.000	0.000	0.000	0.000	0.000
91	A	149	GLY	0	0.022	0.022	32.102	-0.006	-0.006	0.000	0.000	0.000
92	A	150	ASP	-1	-0.884	-0.932	32.671	0.067	0.067	0.000	0.000	0.000
93	A	151	GLN	0	-0.069	-0.038	29.835	0.005	0.005	0.000	0.000	0.000
94	A	152	VAL	0	0.010	0.004	26.809	-0.006	-0.006	0.000	0.000	0.000
95	A	153	ILE	0	-0.030	-0.003	25.553	0.002	0.002	0.000	0.000	0.000
96	A	154	LEU	0	0.004	0.012	20.748	0.002	0.002	0.000	0.000	0.000
97	A	155	GLU	-1	-0.893	-0.966	23.040	0.030	0.030	0.000	0.000	0.000
98	A	156	ALA	0	0.001	0.012	19.269	-0.004	-0.004	0.000	0.000	0.000
99	A	157	SER	0	-0.021	-0.033	16.104	-0.004	-0.004	0.000	0.000	0.000
100	A	158	HIS	0	-0.059	-0.045	14.571	0.005	0.005	0.000	0.000	0.000
101	A	159	MET	0	0.049	0.037	11.076	0.009	0.009	0.000	0.000	0.000
102	A	160	MLY	1	0.955	0.960	9.666	0.151	0.151	0.000	0.000	0.000
103	A	161	GLY	0	-0.009	0.007	12.055	0.030	0.030	0.000	0.000	0.000
104	A	162	MET	0	0.016	0.033	15.338	0.000	0.000	0.000	0.000	0.000
105	A	163	MLY	1	0.954	0.975	17.266	-0.031	-0.031	0.000	0.000	0.000
106	A	164	GLY	0	-0.036	-0.024	19.368	-0.012	-0.012	0.000	0.000	0.000
107	A	165	ALA	0	-0.035	-0.008	20.158	-0.005	-0.005	0.000	0.000	0.000
108	A	166	THR	0	-0.031	-0.024	22.222	-0.001	-0.001	0.000	0.000	0.000
109	A	167	ALA	0	-0.040	-0.031	23.677	0.008	0.008	0.000	0.000	0.000
110	A	168	GLU	-1	-0.912	-0.957	25.329	0.093	0.093	0.000	0.000	0.000
111	A	169	ILE	0	-0.033	-0.011	26.841	0.012	0.012	0.000	0.000	0.000
112	A	170	ASP	-1	-0.760	-0.864	25.900	0.146	0.146	0.000	0.000	0.000
113	A	171	SER	0	-0.061	-0.050	28.222	-0.002	-0.002	0.000	0.000	0.000
114	A	172	ALA	0	0.025	0.006	28.891	0.003	0.003	0.000	0.000	0.000
115	A	173	GLU	-1	-0.943	-0.970	28.528	0.149	0.149	0.000	0.000	0.000
116	A	174	MLY	1	0.922	0.977	30.395	-0.079	-0.079	0.000	0.000	0.000
117	A	175	THR	0	-0.010	-0.007	28.022	0.000	0.000	0.000	0.000	0.000
118	A	176	THR	0	0.017	0.024	28.026	-0.005	-0.005	0.000	0.000	0.000
119	A	177	VAL	0	-0.017	-0.011	24.150	0.012	0.012	0.000	0.000	0.000
120	A	178	TYR	0	-0.078	-0.066	22.694	-0.011	-0.011	0.000	0.000	0.000
121	A	179	MET	0	-0.013	0.015	18.588	0.013	0.013	0.000	0.000	0.000
122	A	180	VAL	0	0.007	-0.005	16.761	-0.009	-0.009	0.000	0.000	0.000
123	A	181	ASP	-1	-0.786	-0.863	15.617	0.250	0.250	0.000	0.000	0.000
124	A	182	TYR	0	-0.007	-0.023	10.509	0.011	0.011	0.000	0.000	0.000
125	A	183	THR	0	-0.037	-0.008	12.575	0.021	0.021	0.000	0.000	0.000
126	A	184	SER	0	-0.021	-0.032	7.930	-0.054	-0.054	0.000	0.000	0.000
127	A	185	THR	0	-0.014	-0.022	10.659	0.027	0.027	0.000	0.000	0.000
128	A	186	THR	0	-0.080	-0.037	7.937	0.001	0.001	0.000	0.000	0.000
129	A	187	SER	0	-0.008	-0.017	6.080	-0.042	-0.042	0.000	0.000	0.000
130	A	188	GLY	0	0.004	0.015	8.126	-0.099	-0.099	0.000	0.000	0.000
131	A	189	GLU	-1	-0.952	-0.971	5.245	1.447	1.447	0.000	0.000	0.000
132	A	190	MLY	1	0.892	0.940	9.370	-0.304	-0.304	0.000	0.000	0.000
133	A	191	VAL	0	0.042	0.024	8.321	0.016	0.016	0.000	0.000	0.000
134	A	192	MLY	1	0.811	0.883	10.860	-0.262	-0.262	0.000	0.000	0.000
135	A	193	ASN	0	-0.004	-0.021	13.527	-0.010	-0.010	0.000	0.000	0.000
136	A	194	HIS	0	0.078	0.039	13.355	-0.005	-0.005	0.000	0.000	0.000
137	A	195	LYS	1	0.866	0.925	14.993	-0.150	-0.150	0.000	0.000	0.000
138	A	196	TRP	0	-0.004	-0.018	16.593	0.012	0.012	0.000	0.000	0.000
139	A	197	VAL	0	-0.074	-0.033	18.211	0.025	0.025	0.000	0.000	0.000
140	A	198	THR	0	0.066	0.036	20.884	-0.012	-0.012	0.000	0.000	0.000
141	A	199	GLU	-1	-0.783	-0.904	24.425	0.139	0.139	0.000	0.000	0.000
142	A	200	ASP	-1	-0.914	-0.953	26.954	0.153	0.153	0.000	0.000	0.000
143	A	201	GLU	-1	-0.802	-0.880	21.598	0.267	0.267	0.000	0.000	0.000
144	A	202	LEU	0	-0.015	0.002	20.905	0.026	0.026	0.000	0.000	0.000
145	A	203	SER	0	-0.044	-0.036	23.995	-0.022	-0.022	0.000	0.000	0.000
146	A	204	ALA	0	0.021	0.006	25.185	0.006	0.006	0.000	0.000	0.000
147	A	205	MLY	1	0.862	0.942	23.109	-0.210	-0.210	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:59:HIS)