FMO DATABASE

FMODB ID: 98932

Calculation Name: 4FR9-A-Xray372

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 4FR9

Chain ID: A

ChEMBL ID:

UniProt ID: Q5LG06

Base Structure: X-ray

Registration Date: 2023-09-23

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	141
LigandCharge	MLY=1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1300708.365875
FMO2-HF: Nuclear repulsion	1244270.572765
FMO2-HF: Total energy	-56437.79311
FMO2-MP2: Total energy	-56603.946986

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:26:ASP)

Summations of interaction energy for fragment #1(A:26:ASP)

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.
106.334	115.854	8.461	-7.464	-10.514	0.068

Interaction energy analysis for fragmet #1(A:26:ASP)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : -1 / q_Mulliken : -0.888 / q_NPA : -0.964

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	28	ASP	-1	-0.942	-0.954	2.507	43.571	47.201	2.576	-2.562	-3.644	0.024
4	A	29	THR	0	-0.101	-0.044	2.320	-31.427	-26.505	2.393	-3.162	-4.152	0.040
5	A	30	GLY	0	-0.030	-0.013	4.178	-9.224	-8.992	0.001	-0.063	-0.169	0.000
6	A	31	TYR	0	-0.016	-0.002	2.129	-7.889	-7.507	3.488	-1.564	-2.305	0.004
7	A	32	LEU	0	-0.001	0.000	3.860	-2.924	-2.841	0.001	-0.045	-0.039	0.000
8	A	33	PRO	0	-0.018	0.008	7.205	0.182	0.182	0.000	0.000	0.000	0.000
9	A	34	PRO	0	0.031	0.030	8.950	-1.663	-1.663	0.000	0.000	0.000	0.000
10	A	35	SER	0	0.042	0.012	11.815	-0.775	-0.775	0.000	0.000	0.000	0.000
11	A	36	GLN	0	0.000	-0.019	15.137	0.589	0.589	0.000	0.000	0.000	0.000
12	A	37	ALA	0	0.005	0.003	17.786	-0.348	-0.348	0.000	0.000	0.000	0.000
13	A	38	ILE	0	0.037	0.025	14.227	-0.559	-0.559	0.000	0.000	0.000	0.000
14	A	39	GLN	0	-0.043	-0.020	14.147	-0.441	-0.441	0.000	0.000	0.000	0.000
15	A	40	ASP	-1	-0.872	-0.946	17.191	13.394	13.394	0.000	0.000	0.000	0.000
16	A	41	ALA	0	-0.072	-0.037	19.895	-0.737	-0.737	0.000	0.000	0.000	0.000
17	A	42	LEU	0	0.049	0.029	16.416	-0.531	-0.531	0.000	0.000	0.000	0.000
18	A	43	MLY	1	0.787	0.929	19.996	-14.334	-14.334	0.000	0.000	0.000	0.000
19	A	44	MLY	1	0.910	0.939	22.192	-12.820	-12.820	0.000	0.000	0.000	0.000
20	A	45	LEU	0	-0.001	0.029	21.919	-0.476	-0.476	0.000	0.000	0.000	0.000
21	A	46	TYR	0	0.035	0.023	21.485	-0.242	-0.242	0.000	0.000	0.000	0.000
22	A	47	PRO	0	0.021	0.011	23.035	0.476	0.476	0.000	0.000	0.000	0.000
23	A	48	ASN	0	-0.069	-0.057	24.961	0.043	0.043	0.000	0.000	0.000	0.000
24	A	49	ALA	0	-0.014	0.009	19.641	0.105	0.105	0.000	0.000	0.000	0.000
25	A	50	THR	0	-0.060	-0.045	19.867	0.030	0.030	0.000	0.000	0.000	0.000
26	A	51	ALA	0	0.012	-0.012	16.773	0.285	0.285	0.000	0.000	0.000	0.000
27	A	52	ILE	0	-0.001	0.016	13.542	0.634	0.634	0.000	0.000	0.000	0.000
28	A	53	MLY	1	0.903	0.974	4.133	-46.640	-46.369	0.002	-0.068	-0.205	0.000
29	A	54	TRP	0	-0.013	-0.007	9.160	-1.079	-1.079	0.000	0.000	0.000	0.000
30	A	55	GLU	-1	-0.902	-0.954	5.601	44.648	44.648	0.000	0.000	0.000	0.000
31	A	56	GLN	0	0.010	0.001	6.244	-1.912	-1.912	0.000	0.000	0.000	0.000
32	A	57	MLY	1	0.976	0.998	7.689	-23.920	-23.920	0.000	0.000	0.000	0.000
33	A	58	GLY	0	0.017	0.016	10.406	-2.376	-2.376	0.000	0.000	0.000	0.000
34	A	59	VAL	0	-0.058	-0.041	11.707	0.809	0.809	0.000	0.000	0.000	0.000
35	A	60	TYR	0	-0.043	-0.044	13.128	-1.136	-1.136	0.000	0.000	0.000	0.000
36	A	61	TYR	0	-0.064	-0.054	8.659	1.131	1.131	0.000	0.000	0.000	0.000
37	A	62	VAL	0	0.010	-0.001	10.991	-2.030	-2.030	0.000	0.000	0.000	0.000
38	A	63	ALA	0	-0.039	-0.026	11.292	2.228	2.228	0.000	0.000	0.000	0.000
39	A	64	ASP	-1	-0.868	-0.914	12.156	20.760	20.760	0.000	0.000	0.000	0.000
40	A	65	CYS	0	-0.059	-0.049	13.908	-0.075	-0.075	0.000	0.000	0.000	0.000
41	A	66	GLN	0	0.029	0.036	16.896	-1.018	-1.018	0.000	0.000	0.000	0.000
42	A	67	ALA	0	0.007	-0.023	20.443	-0.112	-0.112	0.000	0.000	0.000	0.000
43	A	68	ASP	-1	-0.903	-0.942	23.408	11.273	11.273	0.000	0.000	0.000	0.000
44	A	69	GLY	0	-0.038	-0.020	26.065	-0.331	-0.331	0.000	0.000	0.000	0.000
45	A	70	ARG	1	0.868	0.939	24.335	-11.445	-11.445	0.000	0.000	0.000	0.000
46	A	71	GLU	-1	-0.820	-0.908	18.705	16.384	16.384	0.000	0.000	0.000	0.000
47	A	72	MLY	1	0.876	0.933	19.030	-13.430	-13.430	0.000	0.000	0.000	0.000
48	A	73	GLU	-1	-0.850	-0.906	14.651	21.156	21.156	0.000	0.000	0.000	0.000
49	A	74	VAL	0	-0.067	-0.037	16.254	-1.102	-1.102	0.000	0.000	0.000	0.000
50	A	75	TRP	0	0.046	0.018	14.802	1.636	1.636	0.000	0.000	0.000	0.000
51	A	76	PHE	0	0.005	-0.014	15.760	-1.406	-1.406	0.000	0.000	0.000	0.000
52	A	77	ASP	-1	-0.788	-0.896	15.759	15.611	15.611	0.000	0.000	0.000	0.000
53	A	78	ALA	0	0.024	-0.005	16.091	0.205	0.205	0.000	0.000	0.000	0.000
54	A	79	ASN	0	-0.116	-0.052	17.013	-0.102	-0.102	0.000	0.000	0.000	0.000
55	A	80	ALA	0	-0.069	-0.029	18.552	-0.495	-0.495	0.000	0.000	0.000	0.000
56	A	81	ASN	0	-0.037	-0.016	19.498	-0.607	-0.607	0.000	0.000	0.000	0.000
57	A	82	TRP	0	0.002	-0.010	20.367	0.318	0.318	0.000	0.000	0.000	0.000
58	A	83	LEU	0	-0.044	-0.034	19.079	-0.615	-0.615	0.000	0.000	0.000	0.000
59	A	84	MET	0	0.001	0.003	19.262	-0.651	-0.651	0.000	0.000	0.000	0.000
60	A	85	THR	0	-0.029	-0.020	20.178	0.972	0.972	0.000	0.000	0.000	0.000
61	A	86	GLU	-1	-0.802	-0.900	19.347	15.201	15.201	0.000	0.000	0.000	0.000
62	A	87	THR	0	-0.038	-0.028	20.455	0.501	0.501	0.000	0.000	0.000	0.000
63	A	88	GLH	0	-0.002	-0.052	21.329	-0.147	-0.147	0.000	0.000	0.000	0.000
64	A	89	LEU	0	-0.106	-0.060	23.284	-0.519	-0.519	0.000	0.000	0.000	0.000
65	A	90	ASN	0	0.007	-0.003	26.592	0.459	0.459	0.000	0.000	0.000	0.000
66	A	91	SER	0	0.015	-0.001	28.353	-0.123	-0.123	0.000	0.000	0.000	0.000
67	A	92	ILE	0	0.140	0.066	31.101	0.018	0.018	0.000	0.000	0.000	0.000
68	A	93	ASN	0	-0.041	-0.015	33.694	-0.248	-0.248	0.000	0.000	0.000	0.000
69	A	94	ASN	0	-0.096	-0.053	30.843	0.110	0.110	0.000	0.000	0.000	0.000
70	A	95	LEU	0	0.042	0.040	31.614	0.145	0.145	0.000	0.000	0.000	0.000
71	A	96	PRO	0	0.016	0.017	33.698	-0.265	-0.265	0.000	0.000	0.000	0.000
72	A	97	PRO	0	0.021	-0.008	36.767	-0.042	-0.042	0.000	0.000	0.000	0.000
73	A	98	ALA	0	0.017	0.020	39.838	-0.077	-0.077	0.000	0.000	0.000	0.000
74	A	99	VAL	0	0.022	0.013	34.094	-0.067	-0.067	0.000	0.000	0.000	0.000
75	A	100	LEU	0	-0.015	0.001	37.105	0.013	0.013	0.000	0.000	0.000	0.000
76	A	101	THR	0	-0.037	-0.024	38.259	-0.116	-0.116	0.000	0.000	0.000	0.000
77	A	102	ALA	0	0.047	0.032	38.861	-0.086	-0.086	0.000	0.000	0.000	0.000
78	A	103	PHE	0	0.007	0.002	35.276	-0.028	-0.028	0.000	0.000	0.000	0.000
79	A	104	MET	0	-0.040	-0.029	38.368	-0.061	-0.061	0.000	0.000	0.000	0.000
80	A	105	GLU	-1	-0.958	-0.974	41.145	7.046	7.046	0.000	0.000	0.000	0.000
81	A	106	SER	0	-0.069	-0.025	39.034	-0.073	-0.073	0.000	0.000	0.000	0.000
82	A	107	SER	0	-0.028	-0.040	40.495	-0.120	-0.120	0.000	0.000	0.000	0.000
83	A	108	TYR	0	-0.043	-0.050	35.485	0.035	0.035	0.000	0.000	0.000	0.000
84	A	109	ASN	0	-0.089	-0.015	37.428	0.156	0.156	0.000	0.000	0.000	0.000
85	A	110	ASN	0	-0.005	-0.008	39.341	0.035	0.035	0.000	0.000	0.000	0.000
86	A	111	TRP	0	-0.059	-0.032	33.317	0.029	0.029	0.000	0.000	0.000	0.000
87	A	112	VAL	0	-0.003	0.010	31.167	-0.118	-0.118	0.000	0.000	0.000	0.000
88	A	113	VAL	0	-0.032	-0.019	30.018	0.146	0.146	0.000	0.000	0.000	0.000
89	A	114	ASP	-1	-0.843	-0.928	25.991	11.545	11.545	0.000	0.000	0.000	0.000
90	A	115	ASP	-1	-0.803	-0.844	22.904	13.937	13.937	0.000	0.000	0.000	0.000
91	A	116	VAL	0	-0.091	-0.057	26.246	-0.611	-0.611	0.000	0.000	0.000	0.000
92	A	117	VAL	0	0.057	0.047	22.522	0.153	0.153	0.000	0.000	0.000	0.000
93	A	118	ILE	0	-0.053	-0.028	25.237	-0.617	-0.617	0.000	0.000	0.000	0.000
94	A	119	LEU	0	-0.017	0.000	22.457	0.622	0.622	0.000	0.000	0.000	0.000
95	A	120	GLU	-1	-0.941	-0.966	24.602	11.031	11.031	0.000	0.000	0.000	0.000
96	A	121	TYR	0	-0.044	-0.059	24.166	0.822	0.822	0.000	0.000	0.000	0.000
97	A	122	PRO	0	-0.025	-0.003	24.989	-0.476	-0.476	0.000	0.000	0.000	0.000
98	A	123	ASN	0	-0.041	-0.018	27.967	-0.172	-0.172	0.000	0.000	0.000	0.000
99	A	124	GLU	-1	-0.834	-0.914	30.521	9.392	9.392	0.000	0.000	0.000	0.000
100	A	125	PRO	0	-0.055	-0.046	32.138	0.000	0.000	0.000	0.000	0.000	0.000
101	A	126	SER	0	0.000	-0.001	30.304	0.364	0.364	0.000	0.000	0.000	0.000
102	A	127	THR	0	0.039	0.035	29.348	0.467	0.467	0.000	0.000	0.000	0.000
103	A	128	GLU	-1	-0.894	-0.921	27.661	10.995	10.995	0.000	0.000	0.000	0.000
104	A	129	PHE	0	0.000	-0.016	28.547	0.318	0.318	0.000	0.000	0.000	0.000
105	A	130	VAL	0	-0.009	-0.008	26.311	-0.342	-0.342	0.000	0.000	0.000	0.000
106	A	131	VAL	0	-0.011	-0.001	28.096	0.191	0.191	0.000	0.000	0.000	0.000
107	A	132	THR	0	0.010	-0.005	25.670	-0.130	-0.130	0.000	0.000	0.000	0.000
108	A	133	VAL	0	-0.035	-0.019	28.439	-0.159	-0.159	0.000	0.000	0.000	0.000
109	A	134	GLU	-1	-0.901	-0.961	28.646	11.162	11.162	0.000	0.000	0.000	0.000
110	A	135	GLN	0	-0.031	-0.028	31.639	-0.431	-0.431	0.000	0.000	0.000	0.000
111	A	136	GLY	0	-0.068	-0.024	33.264	-0.237	-0.237	0.000	0.000	0.000	0.000
112	A	137	MLY	1	0.846	0.942	31.254	-9.196	-9.196	0.000	0.000	0.000	0.000
113	A	138	MLY	1	0.959	0.986	22.416	-13.236	-13.236	0.000	0.000	0.000	0.000
114	A	139	VAL	0	-0.055	-0.036	29.227	0.045	0.045	0.000	0.000	0.000	0.000
115	A	140	ASP	-1	-0.762	-0.857	25.314	12.677	12.677	0.000	0.000	0.000	0.000
116	A	141	LEU	0	-0.050	-0.034	28.908	-0.272	-0.272	0.000	0.000	0.000	0.000
117	A	142	TYR	0	0.042	0.017	25.835	0.301	0.301	0.000	0.000	0.000	0.000
118	A	143	PHE	0	0.014	-0.006	31.446	-0.394	-0.394	0.000	0.000	0.000	0.000
119	A	144	SER	0	0.041	0.020	32.997	0.235	0.235	0.000	0.000	0.000	0.000
120	A	145	GLU	-1	-0.865	-0.952	34.248	9.022	9.022	0.000	0.000	0.000	0.000
121	A	146	GLY	0	-0.059	-0.031	36.098	-0.152	-0.152	0.000	0.000	0.000	0.000
122	A	147	GLY	0	-0.020	-0.001	37.955	-0.213	-0.213	0.000	0.000	0.000	0.000
123	A	148	GLY	0	-0.018	-0.007	38.570	-0.139	-0.139	0.000	0.000	0.000	0.000
124	A	149	LEU	0	-0.001	-0.003	35.134	0.235	0.235	0.000	0.000	0.000	0.000
125	A	150	LEU	0	-0.054	-0.029	33.084	-0.182	-0.182	0.000	0.000	0.000	0.000
126	A	151	HIS	0	-0.016	-0.017	31.177	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	152	GLU	-1	-0.854	-0.894	32.799	8.779	8.779	0.000	0.000	0.000	0.000
128	A	153	MLY	1	0.866	0.952	26.017	-11.754	-11.754	0.000	0.000	0.000	0.000
129	A	154	ASP	-1	-0.850	-0.909	29.208	10.763	10.763	0.000	0.000	0.000	0.000
130	A	155	VAL	0	0.046	0.016	24.363	0.167	0.167	0.000	0.000	0.000	0.000
131	A	156	THR	0	-0.049	-0.043	24.960	0.218	0.218	0.000	0.000	0.000	0.000
132	A	157	ASN	0	-0.077	-0.040	24.118	0.376	0.376	0.000	0.000	0.000	0.000
133	A	158	GLY	0	-0.029	-0.015	20.773	-0.139	-0.139	0.000	0.000	0.000	0.000
134	A	159	ASP	-1	-0.822	-0.899	17.715	18.509	18.509	0.000	0.000	0.000	0.000
135	A	160	ASP	-1	-0.900	-0.938	19.366	15.374	15.374	0.000	0.000	0.000	0.000
136	A	161	THR	0	-0.058	-0.032	15.941	-0.037	-0.037	0.000	0.000	0.000	0.000
137	A	162	HIS	1	0.845	0.934	18.968	-14.852	-14.852	0.000	0.000	0.000	0.000
138	A	163	TRP	0	-0.019	-0.017	13.540	1.364	1.364	0.000	0.000	0.000	0.000
139	A	164	PRO	0	0.006	-0.008	18.029	-0.957	-0.957	0.000	0.000	0.000	0.000
140	A	165	ARG	1	0.793	0.890	21.081	-11.280	-11.280	0.000	0.000	0.000	0.000
141	A	166	VAL	0	-0.003	0.040	21.066	-0.118	-0.118	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:26:ASP)