FMO DATABASE

FMODB ID: 22Y4R

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1397885.80121
FMO2-HF: Nuclear repulsion	1339500.187214
FMO2-HF: Total energy	-58385.613996
FMO2-MP2: Total energy	-58554.034251

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.
-6.137	-2.06	0.032	-1.567	-2.539	-0.003

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 : 0.024 / q_NPA : -0.004

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	61	GLU	-1	-0.749	-0.813	3.397	-0.479	1.610	-0.006	-0.906	-1.176	0.000
4	A	62	MET	0	-0.028	-0.008	3.764	-0.455	0.370	0.007	-0.245	-0.587	0.000
5	A	63	ASP	-1	-0.940	-0.964	3.362	-3.740	-2.758	0.033	-0.409	-0.605	-0.003
6	A	64	HIS	0	-0.078	-0.065	6.291	0.254	0.254	0.000	0.000	0.000	0.000
7	A	65	SER	0	-0.008	-0.010	8.781	0.136	0.136	0.000	0.000	0.000	0.000
8	A	66	GLY	0	0.020	0.026	9.769	0.003	0.003	0.000	0.000	0.000	0.000
9	A	67	SER	0	-0.076	-0.030	10.381	0.014	0.014	0.000	0.000	0.000	0.000
10	A	68	ALA	0	0.007	-0.011	14.242	0.041	0.041	0.000	0.000	0.000	0.000
11	A	69	ASP	-1	-0.906	-0.933	15.597	-0.039	-0.039	0.000	0.000	0.000	0.000
12	A	70	VAL	0	-0.046	-0.043	19.238	0.018	0.018	0.000	0.000	0.000	0.000
13	A	71	PRO	0	-0.016	-0.002	21.615	-0.006	-0.006	0.000	0.000	0.000	0.000
14	A	72	GLU	-1	-0.838	-0.917	24.604	-0.005	-0.005	0.000	0.000	0.000	0.000
15	A	73	GLY	0	-0.066	-0.032	28.172	0.004	0.004	0.000	0.000	0.000	0.000
16	A	74	LEU	0	-0.049	-0.010	24.733	0.006	0.006	0.000	0.000	0.000	0.000
17	A	75	GLN	0	-0.015	-0.020	28.944	-0.002	-0.002	0.000	0.000	0.000	0.000
18	A	76	GLU	-1	-0.896	-0.948	29.381	0.047	0.047	0.000	0.000	0.000	0.000
19	A	77	SER	0	-0.065	-0.070	29.877	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	78	MLY	1	0.778	0.891	31.617	-0.044	-0.044	0.000	0.000	0.000	0.000
21	A	79	ASN	0	-0.078	-0.044	34.423	-0.004	-0.004	0.000	0.000	0.000	0.000
22	A	80	PRO	0	0.030	0.037	29.743	0.004	0.004	0.000	0.000	0.000	0.000
23	A	81	MLY	1	0.877	0.962	29.688	-0.139	-0.139	0.000	0.000	0.000	0.000
24	A	82	TYR	0	-0.083	-0.065	26.590	0.001	0.001	0.000	0.000	0.000	0.000
25	A	83	MLY	1	1.016	1.002	27.673	-0.087	-0.087	0.000	0.000	0.000	0.000
26	A	84	VAL	0	0.054	0.034	25.013	0.010	0.010	0.000	0.000	0.000	0.000
27	A	85	GLY	0	-0.020	-0.002	25.092	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	86	SER	0	-0.093	-0.055	25.811	0.011	0.011	0.000	0.000	0.000	0.000
29	A	87	GLN	0	0.009	-0.007	23.028	0.008	0.008	0.000	0.000	0.000	0.000
30	A	88	VAL	0	-0.012	-0.013	21.202	-0.013	-0.013	0.000	0.000	0.000	0.000
31	A	89	ILE	0	-0.019	0.001	20.628	0.019	0.019	0.000	0.000	0.000	0.000
32	A	90	ILE	0	0.027	0.026	15.844	-0.027	-0.027	0.000	0.000	0.000	0.000
33	A	91	ASN	0	-0.025	-0.008	19.773	0.041	0.041	0.000	0.000	0.000	0.000
34	A	92	THR	0	-0.060	-0.040	18.463	0.018	0.018	0.000	0.000	0.000	0.000
35	A	93	SER	0	0.005	-0.026	16.553	0.029	0.029	0.000	0.000	0.000	0.000
36	A	94	HIS	1	0.792	0.899	15.618	-0.237	-0.237	0.000	0.000	0.000	0.000
37	A	95	MET	0	0.044	0.046	8.160	0.122	0.122	0.000	0.000	0.000	0.000
38	A	96	MLY	1	0.861	0.919	4.377	-3.814	-3.728	-0.001	-0.005	-0.079	0.000
39	A	97	GLY	0	0.048	0.034	9.749	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	98	MET	0	-0.016	0.004	10.873	-0.114	-0.114	0.000	0.000	0.000	0.000
41	A	99	MLY	1	0.905	0.968	13.639	-0.425	-0.425	0.000	0.000	0.000	0.000
42	A	100	GLY	0	-0.053	-0.037	16.389	0.036	0.036	0.000	0.000	0.000	0.000
43	A	101	ALA	0	-0.010	0.011	14.378	-0.013	-0.013	0.000	0.000	0.000	0.000
44	A	102	GLU	-1	-0.775	-0.876	16.278	0.243	0.243	0.000	0.000	0.000	0.000
45	A	103	ALA	0	0.030	0.018	16.825	0.022	0.022	0.000	0.000	0.000	0.000
46	A	104	THR	0	-0.075	-0.055	18.609	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	105	VAL	0	0.011	0.029	20.120	0.003	0.003	0.000	0.000	0.000	0.000
48	A	106	THR	0	-0.036	-0.043	18.712	-0.007	-0.007	0.000	0.000	0.000	0.000
49	A	107	GLY	0	0.007	0.008	21.712	-0.017	-0.017	0.000	0.000	0.000	0.000
50	A	108	ALA	0	0.007	0.008	23.666	0.013	0.013	0.000	0.000	0.000	0.000
51	A	109	TYR	0	0.031	0.013	23.270	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	110	ASP	-1	-0.758	-0.824	28.275	0.077	0.077	0.000	0.000	0.000	0.000
53	A	111	THR	0	-0.003	-0.027	27.220	-0.006	-0.006	0.000	0.000	0.000	0.000
54	A	112	THR	0	-0.064	-0.034	30.448	0.007	0.007	0.000	0.000	0.000	0.000
55	A	113	ALA	0	0.019	0.018	25.578	-0.005	-0.005	0.000	0.000	0.000	0.000
56	A	114	TYR	0	-0.017	-0.043	25.472	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	115	VAL	0	-0.085	-0.017	23.788	0.008	0.008	0.000	0.000	0.000	0.000
58	A	116	VAL	0	-0.027	-0.013	21.802	-0.014	-0.014	0.000	0.000	0.000	0.000
59	A	117	SER	0	0.044	0.002	22.320	0.025	0.025	0.000	0.000	0.000	0.000
60	A	118	TYR	0	0.021	-0.008	16.355	-0.030	-0.030	0.000	0.000	0.000	0.000
61	A	119	THR	0	0.003	-0.002	20.276	0.024	0.024	0.000	0.000	0.000	0.000
62	A	120	PRO	0	0.005	0.015	15.652	-0.021	-0.021	0.000	0.000	0.000	0.000
63	A	121	THR	0	0.016	0.009	17.836	-0.015	-0.015	0.000	0.000	0.000	0.000
64	A	122	ASN	0	-0.080	-0.036	13.931	-0.050	-0.050	0.000	0.000	0.000	0.000
65	A	123	GLY	0	-0.003	0.002	17.034	-0.012	-0.012	0.000	0.000	0.000	0.000
66	A	124	GLY	0	-0.002	-0.010	16.204	-0.008	-0.008	0.000	0.000	0.000	0.000
67	A	125	GLN	0	-0.040	-0.032	16.662	0.028	0.028	0.000	0.000	0.000	0.000
68	A	126	ARG	1	0.772	0.878	17.755	-0.100	-0.100	0.000	0.000	0.000	0.000
69	A	127	VAL	0	-0.004	0.011	15.971	0.035	0.035	0.000	0.000	0.000	0.000
70	A	128	ASP	-1	-0.806	-0.911	18.698	0.113	0.113	0.000	0.000	0.000	0.000
71	A	129	HIS	0	-0.054	-0.039	20.965	0.023	0.023	0.000	0.000	0.000	0.000
72	A	130	HIS	0	-0.022	0.003	16.059	0.049	0.049	0.000	0.000	0.000	0.000
73	A	131	MLY	1	0.879	0.950	18.976	-0.224	-0.224	0.000	0.000	0.000	0.000
74	A	132	TRP	0	-0.060	-0.063	18.272	0.028	0.028	0.000	0.000	0.000	0.000
75	A	133	VAL	0	0.001	0.014	19.871	-0.009	-0.009	0.000	0.000	0.000	0.000
76	A	134	ILE	0	0.006	0.001	22.452	0.012	0.012	0.000	0.000	0.000	0.000
77	A	135	GLN	0	0.021	0.016	25.515	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	136	GLU	-1	-0.755	-0.876	26.390	0.033	0.033	0.000	0.000	0.000	0.000
79	A	137	GLU	-1	-0.781	-0.880	20.690	0.023	0.023	0.000	0.000	0.000	0.000
80	A	138	ILE	0	-0.005	0.001	23.930	-0.005	-0.005	0.000	0.000	0.000	0.000
81	A	139	MLY	1	0.891	0.942	26.685	0.040	0.040	0.000	0.000	0.000	0.000
82	A	140	ASP	-1	-0.894	-0.960	28.235	-0.023	-0.023	0.000	0.000	0.000	0.000
83	A	141	ALA	0	-0.006	0.013	30.857	0.002	0.002	0.000	0.000	0.000	0.000
84	A	142	GLY	0	0.002	0.007	32.598	0.003	0.003	0.000	0.000	0.000	0.000
85	A	143	ASP	-1	-0.892	-0.948	33.267	0.019	0.019	0.000	0.000	0.000	0.000
86	A	144	MLY	1	0.828	0.931	35.564	-0.025	-0.025	0.000	0.000	0.000	0.000
87	A	145	THR	0	-0.013	-0.004	33.748	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	146	LEU	0	-0.015	0.001	30.620	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	147	GLN	0	-0.064	-0.067	33.631	0.005	0.005	0.000	0.000	0.000	0.000
90	A	148	PRO	0	0.006	-0.013	32.485	-0.002	-0.002	0.000	0.000	0.000	0.000
91	A	149	GLY	0	0.019	0.022	32.072	-0.003	-0.003	0.000	0.000	0.000	0.000
92	A	150	ASP	-1	-0.828	-0.886	32.538	0.030	0.030	0.000	0.000	0.000	0.000
93	A	151	GLN	0	-0.090	-0.058	30.030	0.001	0.001	0.000	0.000	0.000	0.000
94	A	152	VAL	0	-0.016	-0.008	26.670	-0.006	-0.006	0.000	0.000	0.000	0.000
95	A	153	ILE	0	-0.017	-0.009	24.912	-0.003	-0.003	0.000	0.000	0.000	0.000
96	A	154	LEU	0	-0.004	0.011	20.372	0.006	0.006	0.000	0.000	0.000	0.000
97	A	155	GLU	-1	-0.819	-0.933	22.352	-0.079	-0.079	0.000	0.000	0.000	0.000
98	A	156	ALA	0	-0.005	0.008	19.181	-0.012	-0.012	0.000	0.000	0.000	0.000
99	A	157	SER	0	0.009	-0.014	15.852	-0.013	-0.013	0.000	0.000	0.000	0.000
100	A	158	HIS	0	-0.053	-0.053	14.131	-0.033	-0.033	0.000	0.000	0.000	0.000
101	A	159	MET	0	0.041	0.041	10.712	-0.011	-0.011	0.000	0.000	0.000	0.000
102	A	160	MLY	1	0.971	0.974	9.485	0.601	0.601	0.000	0.000	0.000	0.000
103	A	161	GLY	0	0.002	0.007	11.549	0.056	0.056	0.000	0.000	0.000	0.000
104	A	162	MET	0	-0.026	0.019	14.837	0.021	0.021	0.000	0.000	0.000	0.000
105	A	163	MLY	1	0.876	0.948	16.806	0.104	0.104	0.000	0.000	0.000	0.000
106	A	164	GLY	0	-0.037	-0.029	18.998	-0.019	-0.019	0.000	0.000	0.000	0.000
107	A	165	ALA	0	-0.023	-0.006	19.897	0.002	0.002	0.000	0.000	0.000	0.000
108	A	166	THR	0	-0.012	-0.016	21.955	0.004	0.004	0.000	0.000	0.000	0.000
109	A	167	ALA	0	-0.033	-0.020	23.410	0.006	0.006	0.000	0.000	0.000	0.000
110	A	168	GLU	-1	-0.805	-0.874	25.226	0.059	0.059	0.000	0.000	0.000	0.000
111	A	169	ILE	0	-0.006	-0.005	26.613	0.010	0.010	0.000	0.000	0.000	0.000
112	A	170	ASP	-1	-0.752	-0.851	25.421	0.112	0.112	0.000	0.000	0.000	0.000
113	A	171	SER	0	-0.065	-0.047	28.409	0.002	0.002	0.000	0.000	0.000	0.000
114	A	172	ALA	0	0.026	0.007	28.642	0.000	0.000	0.000	0.000	0.000	0.000
115	A	173	GLU	-1	-0.865	-0.934	27.898	0.134	0.134	0.000	0.000	0.000	0.000
116	A	174	MLY	1	0.883	0.950	30.389	-0.054	-0.054	0.000	0.000	0.000	0.000
117	A	175	THR	0	-0.017	-0.011	28.122	0.003	0.003	0.000	0.000	0.000	0.000
118	A	176	THR	0	0.015	0.008	28.323	-0.007	-0.007	0.000	0.000	0.000	0.000
119	A	177	VAL	0	-0.026	-0.013	24.271	0.014	0.014	0.000	0.000	0.000	0.000
120	A	178	TYR	0	-0.053	-0.077	22.840	-0.009	-0.009	0.000	0.000	0.000	0.000
121	A	179	MET	0	-0.022	0.014	18.401	0.003	0.003	0.000	0.000	0.000	0.000
122	A	180	VAL	0	-0.009	-0.016	16.641	0.001	0.001	0.000	0.000	0.000	0.000
123	A	181	ASP	-1	-0.719	-0.818	15.442	0.189	0.189	0.000	0.000	0.000	0.000
124	A	182	TYR	0	-0.024	-0.034	9.909	-0.046	-0.046	0.000	0.000	0.000	0.000
125	A	183	THR	0	-0.029	-0.016	12.629	0.016	0.016	0.000	0.000	0.000	0.000
126	A	184	SER	0	-0.038	-0.045	7.975	-0.056	-0.056	0.000	0.000	0.000	0.000
127	A	185	THR	0	-0.008	-0.017	10.887	0.079	0.079	0.000	0.000	0.000	0.000
128	A	186	THR	0	-0.067	-0.049	8.184	-0.139	-0.139	0.000	0.000	0.000	0.000
129	A	187	SER	0	-0.022	-0.022	6.254	0.114	0.114	0.000	0.000	0.000	0.000
130	A	188	GLY	0	-0.028	-0.004	8.238	-0.075	-0.075	0.000	0.000	0.000	0.000
131	A	189	GLU	-1	-0.935	-0.968	4.766	1.744	1.839	-0.001	-0.002	-0.092	0.000
132	A	190	MLY	1	0.806	0.890	9.147	-0.337	-0.337	0.000	0.000	0.000	0.000
133	A	191	VAL	0	0.054	0.034	8.381	-0.036	-0.036	0.000	0.000	0.000	0.000
134	A	192	MLY	1	0.813	0.879	10.649	-0.159	-0.159	0.000	0.000	0.000	0.000
135	A	193	ASN	0	0.005	-0.004	13.142	-0.012	-0.012	0.000	0.000	0.000	0.000
136	A	194	HIS	0	0.054	0.032	13.563	-0.027	-0.027	0.000	0.000	0.000	0.000
137	A	195	LYS	1	0.841	0.931	14.812	-0.015	-0.015	0.000	0.000	0.000	0.000
138	A	196	TRP	0	-0.010	-0.030	16.308	0.005	0.005	0.000	0.000	0.000	0.000
139	A	197	VAL	0	-0.063	-0.032	18.430	0.033	0.033	0.000	0.000	0.000	0.000
140	A	198	THR	0	0.024	0.020	21.089	-0.013	-0.013	0.000	0.000	0.000	0.000
141	A	199	GLU	-1	-0.765	-0.879	24.719	0.127	0.127	0.000	0.000	0.000	0.000
142	A	200	ASP	-1	-0.880	-0.945	26.833	0.147	0.147	0.000	0.000	0.000	0.000
143	A	201	GLU	-1	-0.754	-0.851	21.830	0.249	0.249	0.000	0.000	0.000	0.000
144	A	202	LEU	0	0.005	0.011	20.729	0.029	0.029	0.000	0.000	0.000	0.000
145	A	203	SER	0	-0.021	-0.002	23.932	-0.024	-0.024	0.000	0.000	0.000	0.000
146	A	204	ALA	0	0.030	0.012	25.011	0.006	0.006	0.000	0.000	0.000	0.000
147	A	205	MLY	1	0.787	0.891	22.639	-0.248	-0.248	0.000	0.000	0.000	0.000

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