FMO DATABASE

FMODB ID: 7G9YK

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1388686.519919
FMO2-HF: Nuclear repulsion	1330301.257807
FMO2-HF: Total energy	-58385.262112
FMO2-MP2: Total energy	-58553.554809

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.
-3.711	-0.452	-0.003	-1.086	-2.169	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 : 0.022 / 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	-0.789	-0.873	3.038	-0.267	2.069	0.000	-1.002	-1.334
4	A	62	MET	0	0.010	0.001	4.096	-0.269	0.143	0.000	-0.042	-0.370
5	A	63	ASP	-1	-0.925	-0.948	4.403	-1.759	-1.417	-0.001	-0.040	-0.301
6	A	64	HIS	0	-0.099	-0.067	6.706	0.178	0.178	0.000	0.000	0.000
7	A	65	SER	0	-0.040	-0.027	8.800	0.085	0.085	0.000	0.000	0.000
8	A	66	GLY	0	0.040	0.035	9.706	0.000	0.000	0.000	0.000	0.000
9	A	67	SER	0	-0.078	-0.023	10.383	-0.015	-0.015	0.000	0.000	0.000
10	A	68	ALA	0	-0.021	-0.030	14.160	0.031	0.031	0.000	0.000	0.000
11	A	69	ASP	-1	-0.928	-0.955	16.224	0.003	0.003	0.000	0.000	0.000
12	A	70	VAL	0	-0.036	-0.004	19.897	0.014	0.014	0.000	0.000	0.000
13	A	71	PRO	0	-0.003	-0.006	22.102	-0.007	-0.007	0.000	0.000	0.000
14	A	72	GLU	-1	-0.860	-0.932	24.882	0.020	0.020	0.000	0.000	0.000
15	A	73	GLY	0	-0.054	-0.030	28.532	0.004	0.004	0.000	0.000	0.000
16	A	74	LEU	0	-0.033	0.010	25.262	0.005	0.005	0.000	0.000	0.000
17	A	75	GLN	0	-0.055	-0.038	29.371	-0.005	-0.005	0.000	0.000	0.000
18	A	76	GLU	-1	-0.910	-0.960	29.928	0.067	0.067	0.000	0.000	0.000
19	A	77	SER	0	-0.055	-0.057	30.368	-0.004	-0.004	0.000	0.000	0.000
20	A	78	MLY	1	0.789	0.905	32.146	-0.062	-0.062	0.000	0.000	0.000
21	A	79	ASN	0	-0.052	-0.033	35.220	-0.004	-0.004	0.000	0.000	0.000
22	A	80	PRO	0	0.028	0.032	29.961	0.002	0.002	0.000	0.000	0.000
23	A	81	MLY	1	0.915	0.975	30.087	-0.151	-0.151	0.000	0.000	0.000
24	A	82	TYR	0	-0.090	-0.061	26.919	-0.002	-0.002	0.000	0.000	0.000
25	A	83	MLY	1	1.005	1.000	28.303	-0.096	-0.096	0.000	0.000	0.000
26	A	84	VAL	0	0.070	0.039	25.519	0.011	0.011	0.000	0.000	0.000
27	A	85	GLY	0	-0.019	-0.006	25.399	-0.008	-0.008	0.000	0.000	0.000
28	A	86	SER	0	-0.102	-0.054	26.241	0.007	0.007	0.000	0.000	0.000
29	A	87	GLN	0	0.004	-0.010	23.053	0.005	0.005	0.000	0.000	0.000
30	A	88	VAL	0	-0.006	-0.015	21.363	-0.012	-0.012	0.000	0.000	0.000
31	A	89	ILE	0	-0.016	0.000	20.802	0.017	0.017	0.000	0.000	0.000
32	A	90	ILE	0	0.052	0.036	15.913	-0.024	-0.024	0.000	0.000	0.000
33	A	91	ASN	0	-0.029	-0.027	19.638	0.035	0.035	0.000	0.000	0.000
34	A	92	THR	0	-0.050	-0.040	18.178	0.012	0.012	0.000	0.000	0.000
35	A	93	SER	0	-0.011	-0.026	16.450	0.030	0.030	0.000	0.000	0.000
36	A	94	HIS	1	0.804	0.897	15.364	-0.297	-0.297	0.000	0.000	0.000
37	A	95	MET	0	0.056	0.040	7.925	0.129	0.129	0.000	0.000	0.000
38	A	96	MLY	1	0.873	0.934	4.544	-3.522	-3.453	-0.001	-0.002	-0.066
39	A	97	GLY	0	0.052	0.037	9.378	0.082	0.082	0.000	0.000	0.000
40	A	98	MET	0	0.002	0.017	10.781	-0.096	-0.096	0.000	0.000	0.000
41	A	99	MLY	1	0.899	0.959	13.681	-0.446	-0.446	0.000	0.000	0.000
42	A	100	GLY	0	-0.036	-0.026	16.718	0.021	0.021	0.000	0.000	0.000
43	A	101	ALA	0	-0.015	0.014	14.525	-0.008	-0.008	0.000	0.000	0.000
44	A	102	GLU	-1	-0.811	-0.889	16.474	0.241	0.241	0.000	0.000	0.000
45	A	103	ALA	0	0.027	-0.001	16.855	0.029	0.029	0.000	0.000	0.000
46	A	104	THR	0	-0.081	-0.042	18.689	-0.024	-0.024	0.000	0.000	0.000
47	A	105	VAL	0	0.024	0.030	20.169	0.007	0.007	0.000	0.000	0.000
48	A	106	THR	0	-0.059	-0.056	19.442	-0.010	-0.010	0.000	0.000	0.000
49	A	107	GLY	0	0.025	0.019	22.380	-0.017	-0.017	0.000	0.000	0.000
50	A	108	ALA	0	0.004	0.002	24.181	0.015	0.015	0.000	0.000	0.000
51	A	109	TYR	0	0.025	0.010	23.710	-0.007	-0.007	0.000	0.000	0.000
52	A	110	ASP	-1	-0.771	-0.850	28.516	0.095	0.095	0.000	0.000	0.000
53	A	111	THR	0	0.006	-0.034	27.175	-0.006	-0.006	0.000	0.000	0.000
54	A	112	THR	0	-0.064	-0.034	30.036	0.003	0.003	0.000	0.000	0.000
55	A	113	ALA	0	0.009	0.011	25.413	-0.002	-0.002	0.000	0.000	0.000
56	A	114	TYR	0	-0.009	-0.043	25.734	-0.003	-0.003	0.000	0.000	0.000
57	A	115	VAL	0	-0.086	-0.017	23.720	0.012	0.012	0.000	0.000	0.000
58	A	116	VAL	0	-0.011	0.001	21.873	-0.017	-0.017	0.000	0.000	0.000
59	A	117	SER	0	0.068	0.033	22.616	0.028	0.028	0.000	0.000	0.000
60	A	118	TYR	0	0.008	-0.002	16.462	-0.032	-0.032	0.000	0.000	0.000
61	A	119	THR	0	0.003	0.001	20.613	0.027	0.027	0.000	0.000	0.000
62	A	120	PRO	0	0.025	0.028	15.896	-0.021	-0.021	0.000	0.000	0.000
63	A	121	THR	0	0.018	0.007	18.071	-0.015	-0.015	0.000	0.000	0.000
64	A	122	ASN	0	-0.067	-0.033	13.888	-0.027	-0.027	0.000	0.000	0.000
65	A	123	GLY	0	-0.014	0.001	17.020	-0.015	-0.015	0.000	0.000	0.000
66	A	124	GLY	0	-0.013	-0.015	16.148	0.011	0.011	0.000	0.000	0.000
67	A	125	GLN	0	-0.042	-0.035	16.477	0.026	0.026	0.000	0.000	0.000
68	A	126	ARG	1	0.960	0.983	17.629	-0.117	-0.117	0.000	0.000	0.000
69	A	127	VAL	0	-0.011	0.000	16.471	0.034	0.034	0.000	0.000	0.000
70	A	128	ASP	-1	-0.906	-0.951	18.960	0.169	0.169	0.000	0.000	0.000
71	A	129	HIS	0	-0.060	-0.046	21.056	0.016	0.016	0.000	0.000	0.000
72	A	130	HIS	0	-0.016	-0.001	15.774	0.049	0.049	0.000	0.000	0.000
73	A	131	MLY	1	0.922	0.981	19.504	-0.262	-0.262	0.000	0.000	0.000
74	A	132	TRP	0	-0.044	-0.071	18.452	0.033	0.033	0.000	0.000	0.000
75	A	133	VAL	0	-0.011	0.015	20.250	0.000	0.000	0.000	0.000	0.000
76	A	134	ILE	0	-0.003	-0.002	22.627	0.005	0.005	0.000	0.000	0.000
77	A	135	GLN	0	0.010	0.004	25.594	0.000	0.000	0.000	0.000	0.000
78	A	136	GLU	-1	-0.740	-0.867	26.784	0.066	0.066	0.000	0.000	0.000
79	A	137	GLU	-1	-0.801	-0.882	20.899	0.087	0.087	0.000	0.000	0.000
80	A	138	ILE	0	-0.007	0.006	24.472	-0.002	-0.002	0.000	0.000	0.000
81	A	139	MLY	1	0.901	0.940	27.083	0.001	0.001	0.000	0.000	0.000
82	A	140	ASP	-1	-0.919	-0.966	28.561	0.007	0.007	0.000	0.000	0.000
83	A	141	ALA	0	-0.002	0.018	30.841	0.001	0.001	0.000	0.000	0.000
84	A	142	GLY	0	-0.012	0.003	32.646	0.000	0.000	0.000	0.000	0.000
85	A	143	ASP	-1	-0.870	-0.936	33.467	0.044	0.044	0.000	0.000	0.000
86	A	144	MLY	1	0.828	0.925	35.766	-0.045	-0.045	0.000	0.000	0.000
87	A	145	THR	0	-0.019	-0.013	34.127	0.001	0.001	0.000	0.000	0.000
88	A	146	LEU	0	0.005	0.010	31.043	-0.004	-0.004	0.000	0.000	0.000
89	A	147	GLN	0	-0.044	-0.046	33.820	0.003	0.003	0.000	0.000	0.000
90	A	148	PRO	0	-0.003	-0.014	32.528	-0.001	-0.001	0.000	0.000	0.000
91	A	149	GLY	0	0.023	0.023	32.101	-0.005	-0.005	0.000	0.000	0.000
92	A	150	ASP	-1	-0.876	-0.926	32.727	0.054	0.054	0.000	0.000	0.000
93	A	151	GLN	0	-0.087	-0.054	29.811	0.004	0.004	0.000	0.000	0.000
94	A	152	VAL	0	0.004	0.001	26.943	-0.007	-0.007	0.000	0.000	0.000
95	A	153	ILE	0	-0.025	0.002	25.499	0.001	0.001	0.000	0.000	0.000
96	A	154	LEU	0	0.010	0.015	20.879	0.003	0.003	0.000	0.000	0.000
97	A	155	GLU	-1	-0.827	-0.936	23.067	-0.025	-0.025	0.000	0.000	0.000
98	A	156	ALA	0	0.000	0.010	19.309	-0.010	-0.010	0.000	0.000	0.000
99	A	157	SER	0	-0.015	-0.028	16.157	-0.005	-0.005	0.000	0.000	0.000
100	A	158	HIS	0	-0.044	-0.043	14.620	-0.012	-0.012	0.000	0.000	0.000
101	A	159	MET	0	0.049	0.039	11.144	0.005	0.005	0.000	0.000	0.000
102	A	160	MLY	1	0.957	0.963	9.577	0.392	0.392	0.000	0.000	0.000
103	A	161	GLY	0	0.014	0.016	12.093	0.046	0.046	0.000	0.000	0.000
104	A	162	MET	0	-0.009	0.023	15.382	0.011	0.011	0.000	0.000	0.000
105	A	163	MLY	1	0.874	0.938	17.302	0.035	0.035	0.000	0.000	0.000
106	A	164	GLY	0	-0.025	-0.020	19.393	-0.016	-0.016	0.000	0.000	0.000
107	A	165	ALA	0	-0.041	-0.009	20.185	-0.002	-0.002	0.000	0.000	0.000
108	A	166	THR	0	-0.035	-0.028	22.273	0.001	0.001	0.000	0.000	0.000
109	A	167	ALA	0	-0.034	-0.029	23.683	0.008	0.008	0.000	0.000	0.000
110	A	168	GLU	-1	-0.881	-0.934	25.390	0.081	0.081	0.000	0.000	0.000
111	A	169	ILE	0	-0.029	-0.015	26.886	0.012	0.012	0.000	0.000	0.000
112	A	170	ASP	-1	-0.775	-0.882	25.678	0.143	0.143	0.000	0.000	0.000
113	A	171	SER	0	-0.047	-0.044	28.401	0.000	0.000	0.000	0.000	0.000
114	A	172	ALA	0	0.016	0.008	28.891	0.001	0.001	0.000	0.000	0.000
115	A	173	GLU	-1	-0.922	-0.963	28.059	0.155	0.155	0.000	0.000	0.000
116	A	174	MLY	1	0.901	0.963	30.366	-0.072	-0.072	0.000	0.000	0.000
117	A	175	THR	0	-0.008	-0.006	28.012	0.002	0.002	0.000	0.000	0.000
118	A	176	THR	0	0.016	0.023	28.050	-0.006	-0.006	0.000	0.000	0.000
119	A	177	VAL	0	-0.015	-0.007	24.150	0.014	0.014	0.000	0.000	0.000
120	A	178	TYR	0	-0.066	-0.084	22.792	-0.013	-0.013	0.000	0.000	0.000
121	A	179	MET	0	-0.012	0.019	18.621	0.010	0.010	0.000	0.000	0.000
122	A	180	VAL	0	0.009	-0.007	16.770	-0.006	-0.006	0.000	0.000	0.000
123	A	181	ASP	-1	-0.740	-0.825	15.622	0.238	0.238	0.000	0.000	0.000
124	A	182	TYR	0	-0.001	-0.021	9.782	-0.050	-0.050	0.000	0.000	0.000
125	A	183	THR	0	-0.021	0.002	12.591	0.018	0.018	0.000	0.000	0.000
126	A	184	SER	0	-0.039	-0.045	7.649	-0.054	-0.054	0.000	0.000	0.000
127	A	185	THR	0	-0.011	-0.020	10.650	0.038	0.038	0.000	0.000	0.000
128	A	186	THR	0	-0.067	-0.026	7.854	-0.119	-0.119	0.000	0.000	0.000
129	A	187	SER	0	-0.007	-0.017	6.043	-0.069	-0.069	0.000	0.000	0.000
130	A	188	GLY	0	-0.003	0.006	8.128	-0.101	-0.101	0.000	0.000	0.000
131	A	189	GLU	-1	-0.947	-0.973	5.106	1.787	1.887	-0.001	0.000	-0.098
132	A	190	MLY	1	0.817	0.890	9.384	-0.324	-0.324	0.000	0.000	0.000
133	A	191	VAL	0	0.043	0.027	8.344	-0.003	-0.003	0.000	0.000	0.000
134	A	192	MLY	1	0.808	0.876	10.860	-0.226	-0.226	0.000	0.000	0.000
135	A	193	ASN	0	-0.004	-0.009	13.534	-0.010	-0.010	0.000	0.000	0.000
136	A	194	HIS	0	0.073	0.046	13.393	-0.014	-0.014	0.000	0.000	0.000
137	A	195	LYS	1	0.865	0.938	15.000	-0.086	-0.086	0.000	0.000	0.000
138	A	196	TRP	0	-0.012	-0.036	16.606	0.009	0.009	0.000	0.000	0.000
139	A	197	VAL	0	-0.058	-0.024	18.163	0.028	0.028	0.000	0.000	0.000
140	A	198	THR	0	0.062	0.040	20.859	-0.013	-0.013	0.000	0.000	0.000
141	A	199	GLU	-1	-0.771	-0.884	24.400	0.143	0.143	0.000	0.000	0.000
142	A	200	ASP	-1	-0.912	-0.955	26.930	0.161	0.161	0.000	0.000	0.000
143	A	201	GLU	-1	-0.802	-0.860	21.594	0.285	0.285	0.000	0.000	0.000
144	A	202	LEU	0	-0.009	0.009	20.889	0.029	0.029	0.000	0.000	0.000
145	A	203	SER	0	-0.024	0.001	23.972	-0.024	-0.024	0.000	0.000	0.000
146	A	204	ALA	0	0.020	0.007	25.169	0.007	0.007	0.000	0.000	0.000
147	A	205	MLY	1	0.822	0.906	22.834	-0.247	-0.247	0.000	0.000	0.000

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