FMO DATABASE

FMODB ID: Y7MN2

Calculation Name: 3C8G-B-Xray547

Preferred Name:

Target Type:

Ligand Name: n-dimethyl-lysine | acetate ion

Ligand 3-letter code: MLY | ACT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3C8G

Chain ID: B

ChEMBL ID:

UniProt ID: Q83Q96

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	166
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1657583.97932
FMO2-HF: Nuclear repulsion	1591672.173044
FMO2-HF: Total energy	-65911.806276
FMO2-MP2: Total energy	-66105.683961

3D Structure Molmil

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(B:3:THR)

Summations of interaction energy for fragment #1(B:3: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.
-242.326	-239.741	7.215	-4.815	-4.985	-0.028

Interaction energy analysis for fragmet #1(B:3:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.778 / q_NPA : 0.878

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	B	5	THR	0	0.011	0.009	3.784	6.972	7.989	-0.018	-0.258	-0.742	-0.001
34	B	36	GLN	0	-0.026	-0.005	2.205	-17.980	-16.412	7.233	-4.557	-4.243	-0.027
4	B	6	GLU	-1	-0.823	-0.909	6.682	-23.232	-23.232	0.000	0.000	0.000	0.000
5	B	7	ASP	-1	-0.936	-0.964	10.169	-21.447	-21.447	0.000	0.000	0.000	0.000
6	B	8	ASP	-1	-0.871	-0.922	5.916	-44.420	-44.420	0.000	0.000	0.000	0.000
7	B	9	VAL	0	-0.020	-0.013	7.598	1.618	1.618	0.000	0.000	0.000	0.000
8	B	10	LEU	0	0.001	-0.008	9.891	2.464	2.464	0.000	0.000	0.000	0.000
9	B	11	GLU	-1	-0.953	-0.962	12.159	-20.913	-20.913	0.000	0.000	0.000	0.000
10	B	12	GLN	0	-0.075	-0.060	6.630	3.314	3.314	0.000	0.000	0.000	0.000
11	B	13	LEU	0	-0.007	-0.007	12.307	1.549	1.549	0.000	0.000	0.000	0.000
12	B	14	ASP	-1	-0.936	-0.967	14.830	-14.356	-14.356	0.000	0.000	0.000	0.000
13	B	15	ALA	0	-0.008	0.003	15.917	1.207	1.207	0.000	0.000	0.000	0.000
14	B	16	GLN	0	-0.058	-0.021	15.033	1.470	1.470	0.000	0.000	0.000	0.000
15	B	17	ASP	-1	-0.903	-0.952	19.111	-12.899	-12.899	0.000	0.000	0.000	0.000
16	B	18	ASN	0	-0.036	-0.029	22.161	0.469	0.469	0.000	0.000	0.000	0.000
17	B	19	LEU	0	0.005	0.008	21.513	-0.858	-0.858	0.000	0.000	0.000	0.000
18	B	20	PHE	0	0.090	0.047	21.365	-0.818	-0.818	0.000	0.000	0.000	0.000
19	B	21	SER	0	-0.014	-0.019	18.808	-0.561	-0.561	0.000	0.000	0.000	0.000
20	B	22	PHE	0	0.031	0.020	17.160	-1.305	-1.305	0.000	0.000	0.000	0.000
21	B	23	MET	0	-0.022	0.001	16.574	-1.318	-1.318	0.000	0.000	0.000	0.000
22	B	24	LYS	1	0.956	0.993	15.390	16.421	16.421	0.000	0.000	0.000	0.000
23	B	25	THR	0	-0.049	-0.030	12.040	-1.584	-1.584	0.000	0.000	0.000	0.000
24	B	26	ALA	0	0.017	0.001	11.961	-2.145	-2.145	0.000	0.000	0.000	0.000
25	B	27	HIS	0	-0.001	0.005	13.009	-1.596	-1.596	0.000	0.000	0.000	0.000
26	B	28	SER	0	-0.018	-0.006	9.988	-1.656	-1.656	0.000	0.000	0.000	0.000
27	B	29	ILE	0	0.022	0.008	8.142	-2.778	-2.778	0.000	0.000	0.000	0.000
28	B	30	LEU	0	0.004	0.001	8.456	-2.068	-2.068	0.000	0.000	0.000	0.000
29	B	31	LEU	0	-0.016	0.002	10.591	-0.176	-0.176	0.000	0.000	0.000	0.000
30	B	32	GLN	0	0.005	-0.014	5.338	-0.164	-0.164	0.000	0.000	0.000	0.000
31	B	33	GLY	0	0.021	0.006	6.306	-2.664	-2.664	0.000	0.000	0.000	0.000
32	B	34	ILE	0	-0.006	-0.003	7.269	0.935	0.935	0.000	0.000	0.000	0.000
33	B	35	ARG	1	0.810	0.899	8.034	26.495	26.495	0.000	0.000	0.000	0.000
35	B	37	PHE	0	0.013	0.022	6.481	1.504	1.504	0.000	0.000	0.000	0.000
36	B	38	LEU	0	0.001	-0.012	9.773	1.815	1.815	0.000	0.000	0.000	0.000
37	B	39	PRO	0	-0.014	-0.012	8.797	1.837	1.837	0.000	0.000	0.000	0.000
38	B	40	SER	0	0.028	0.020	11.666	1.124	1.124	0.000	0.000	0.000	0.000
39	B	41	LEU	0	-0.095	-0.035	13.531	1.416	1.416	0.000	0.000	0.000	0.000
40	B	42	PHE	0	-0.074	-0.039	14.978	1.296	1.296	0.000	0.000	0.000	0.000
41	B	43	VAL	0	-0.009	0.002	16.946	-0.141	-0.141	0.000	0.000	0.000	0.000
42	B	44	ASP	-1	-0.858	-0.932	14.455	-17.592	-17.592	0.000	0.000	0.000	0.000
43	B	45	ASN	0	-0.101	-0.056	16.475	-0.040	-0.040	0.000	0.000	0.000	0.000
44	B	46	ASP	-1	-0.880	-0.944	19.576	-11.846	-11.846	0.000	0.000	0.000	0.000
45	B	47	GLU	-1	-0.918	-0.953	20.062	-13.840	-13.840	0.000	0.000	0.000	0.000
46	B	48	GLU	-1	-0.928	-0.964	20.725	-11.500	-11.500	0.000	0.000	0.000	0.000
47	B	49	ILE	0	-0.021	-0.018	19.985	-0.179	-0.179	0.000	0.000	0.000	0.000
48	B	50	VAL	0	0.022	0.010	15.249	-0.592	-0.592	0.000	0.000	0.000	0.000
49	B	51	GLU	-1	-0.846	-0.898	17.244	-17.334	-17.334	0.000	0.000	0.000	0.000
50	B	52	TYR	0	-0.034	-0.031	19.155	-0.178	-0.178	0.000	0.000	0.000	0.000
51	B	53	ALA	0	-0.035	-0.008	20.268	0.354	0.354	0.000	0.000	0.000	0.000
52	B	54	VAL	0	0.000	-0.004	14.044	-0.398	-0.398	0.000	0.000	0.000	0.000
53	B	55	LYS	1	0.840	0.900	13.944	17.324	17.324	0.000	0.000	0.000	0.000
54	B	56	PRO	0	-0.042	-0.024	15.395	-0.732	-0.732	0.000	0.000	0.000	0.000
55	B	57	LEU	0	-0.021	-0.010	16.927	0.018	0.018	0.000	0.000	0.000	0.000
56	B	58	LEU	0	0.002	-0.006	11.144	-0.318	-0.318	0.000	0.000	0.000	0.000
57	B	59	ALA	0	0.004	0.021	12.364	-1.842	-1.842	0.000	0.000	0.000	0.000
58	B	60	GLN	0	-0.025	-0.020	11.712	-0.702	-0.702	0.000	0.000	0.000	0.000
59	B	61	SER	0	-0.077	-0.047	13.356	1.195	1.195	0.000	0.000	0.000	0.000
60	B	62	GLY	0	0.025	0.033	15.789	1.233	1.233	0.000	0.000	0.000	0.000
61	B	63	PRO	0	-0.052	-0.035	17.616	-0.070	-0.070	0.000	0.000	0.000	0.000
62	B	64	LEU	0	0.010	-0.004	15.177	0.547	0.547	0.000	0.000	0.000	0.000
63	B	65	ASP	-1	-0.834	-0.909	12.590	-25.742	-25.742	0.000	0.000	0.000	0.000
64	B	66	ASP	-1	-0.823	-0.909	14.530	-15.585	-15.585	0.000	0.000	0.000	0.000
65	B	67	ILE	0	0.024	0.003	13.754	-0.075	-0.075	0.000	0.000	0.000	0.000
66	B	68	ASP	-1	-0.741	-0.824	15.566	-14.718	-14.718	0.000	0.000	0.000	0.000
67	B	69	VAL	0	-0.092	-0.042	18.245	0.730	0.730	0.000	0.000	0.000	0.000
68	B	70	ALA	0	0.016	0.022	14.285	0.369	0.369	0.000	0.000	0.000	0.000
69	B	71	LEU	0	0.028	0.014	15.833	0.187	0.187	0.000	0.000	0.000	0.000
70	B	72	ARG	1	0.867	0.913	17.575	13.816	13.816	0.000	0.000	0.000	0.000
71	B	73	LEU	0	0.008	0.012	17.762	0.674	0.674	0.000	0.000	0.000	0.000
72	B	74	ILE	0	0.037	0.022	13.826	0.518	0.518	0.000	0.000	0.000	0.000
73	B	75	TYR	0	-0.049	-0.020	18.395	0.733	0.733	0.000	0.000	0.000	0.000
74	B	76	ALA	0	-0.028	-0.014	21.567	0.557	0.557	0.000	0.000	0.000	0.000
75	B	77	LEU	0	-0.036	-0.011	19.517	0.562	0.562	0.000	0.000	0.000	0.000
76	B	78	GLY	0	-0.047	-0.023	22.397	0.019	0.019	0.000	0.000	0.000	0.000
77	B	79	LYS	1	0.876	0.938	17.777	14.230	14.230	0.000	0.000	0.000	0.000
78	B	80	MET	0	0.052	0.042	15.485	-0.597	-0.597	0.000	0.000	0.000	0.000
79	B	81	ASP	-1	-0.847	-0.917	19.779	-12.694	-12.694	0.000	0.000	0.000	0.000
80	B	82	LYS	1	0.928	0.946	22.068	10.059	10.059	0.000	0.000	0.000	0.000
81	B	83	TRP	0	-0.019	-0.015	19.430	0.306	0.306	0.000	0.000	0.000	0.000
82	B	84	LEU	0	0.089	0.063	15.753	-0.024	-0.024	0.000	0.000	0.000	0.000
83	B	85	TYR	0	0.041	0.003	18.843	-0.494	-0.494	0.000	0.000	0.000	0.000
84	B	86	ALA	0	-0.042	-0.012	20.500	-0.146	-0.146	0.000	0.000	0.000	0.000
85	B	87	ASP	-1	-0.696	-0.818	19.620	-13.822	-13.822	0.000	0.000	0.000	0.000
86	B	88	ILE	0	0.044	0.017	14.386	-0.188	-0.188	0.000	0.000	0.000	0.000
87	B	89	THR	0	-0.020	-0.015	17.893	-0.112	-0.112	0.000	0.000	0.000	0.000
88	B	90	HIS	0	-0.060	-0.037	20.722	0.454	0.454	0.000	0.000	0.000	0.000
89	B	91	PHE	0	0.014	0.000	17.589	0.152	0.152	0.000	0.000	0.000	0.000
90	B	92	SER	0	-0.052	-0.046	18.120	-0.118	-0.118	0.000	0.000	0.000	0.000
91	B	93	GLN	0	-0.027	-0.018	19.485	0.407	0.407	0.000	0.000	0.000	0.000
92	B	94	TYR	0	0.050	0.023	22.831	0.344	0.344	0.000	0.000	0.000	0.000
93	B	95	TRP	0	0.033	0.016	17.970	0.197	0.197	0.000	0.000	0.000	0.000
94	B	96	HIS	1	0.756	0.830	21.133	14.215	14.215	0.000	0.000	0.000	0.000
95	B	97	TYR	0	-0.069	-0.038	23.304	0.392	0.392	0.000	0.000	0.000	0.000
96	B	98	LEU	0	-0.010	-0.011	22.465	0.225	0.225	0.000	0.000	0.000	0.000
97	B	99	ASN	0	-0.042	-0.019	21.694	-0.019	-0.019	0.000	0.000	0.000	0.000
98	B	100	GLU	-1	-0.912	-0.930	23.616	-12.850	-12.850	0.000	0.000	0.000	0.000
99	B	101	GLN	0	-0.094	-0.041	26.852	0.629	0.629	0.000	0.000	0.000	0.000
100	B	102	ASP	-1	-0.803	-0.885	28.374	-9.795	-9.795	0.000	0.000	0.000	0.000
101	B	103	GLU	-1	-0.900	-0.956	25.540	-11.056	-11.056	0.000	0.000	0.000	0.000
102	B	104	THR	0	-0.121	-0.075	26.777	-0.161	-0.161	0.000	0.000	0.000	0.000
103	B	105	PRO	0	-0.036	-0.005	27.740	0.022	0.022	0.000	0.000	0.000	0.000
104	B	106	GLY	0	0.049	0.017	26.998	-0.516	-0.516	0.000	0.000	0.000	0.000
105	B	107	PHE	0	-0.034	-0.039	21.602	0.129	0.129	0.000	0.000	0.000	0.000
106	B	108	ALA	0	0.000	0.001	27.104	0.051	0.051	0.000	0.000	0.000	0.000
107	B	109	ASP	-1	-0.830	-0.902	30.330	-9.637	-9.637	0.000	0.000	0.000	0.000
108	B	110	ASP	-1	-0.867	-0.934	31.001	-9.124	-9.124	0.000	0.000	0.000	0.000
109	B	111	ILE	0	0.022	0.015	29.262	-0.125	-0.125	0.000	0.000	0.000	0.000
110	B	112	THR	0	-0.029	-0.014	26.495	-0.407	-0.407	0.000	0.000	0.000	0.000
111	B	113	TRP	0	0.023	0.001	27.712	-0.356	-0.356	0.000	0.000	0.000	0.000
112	B	114	ASP	-1	-0.880	-0.940	29.944	-9.547	-9.547	0.000	0.000	0.000	0.000
113	B	115	PHE	0	-0.012	-0.006	20.983	-0.064	-0.064	0.000	0.000	0.000	0.000
114	B	116	ILE	0	-0.004	-0.014	24.258	-0.208	-0.208	0.000	0.000	0.000	0.000
115	B	117	SER	0	-0.036	-0.024	26.210	0.003	0.003	0.000	0.000	0.000	0.000
116	B	118	ASN	0	-0.082	-0.037	27.586	0.364	0.364	0.000	0.000	0.000	0.000
117	B	119	VAL	0	-0.019	0.018	21.463	-0.306	-0.306	0.000	0.000	0.000	0.000
118	B	120	ASN	0	-0.061	-0.057	23.481	0.676	0.676	0.000	0.000	0.000	0.000
119	B	121	SER	0	-0.038	-0.038	20.256	0.269	0.269	0.000	0.000	0.000	0.000
120	B	122	ILE	0	-0.034	-0.004	22.211	-0.003	-0.003	0.000	0.000	0.000	0.000
121	B	123	THR	0	-0.011	-0.023	24.591	0.348	0.348	0.000	0.000	0.000	0.000
122	B	124	ARG	1	0.870	0.938	24.063	12.675	12.675	0.000	0.000	0.000	0.000
123	B	125	ASN	0	-0.022	0.006	24.078	0.658	0.658	0.000	0.000	0.000	0.000
124	B	126	ALA	0	0.032	0.014	27.163	0.087	0.087	0.000	0.000	0.000	0.000
125	B	127	THR	0	-0.008	-0.004	29.125	0.166	0.166	0.000	0.000	0.000	0.000
126	B	128	LEU	0	0.020	0.019	25.496	0.161	0.161	0.000	0.000	0.000	0.000
127	B	129	TYR	0	0.058	0.005	28.811	0.260	0.260	0.000	0.000	0.000	0.000
128	B	130	ASP	-1	-0.867	-0.947	30.101	-8.923	-8.923	0.000	0.000	0.000	0.000
129	B	131	ALA	0	-0.023	-0.003	31.341	0.275	0.275	0.000	0.000	0.000	0.000
130	B	132	LEU	0	-0.009	-0.006	27.233	0.168	0.168	0.000	0.000	0.000	0.000
131	B	133	LYS	1	0.872	0.941	31.707	9.253	9.253	0.000	0.000	0.000	0.000
132	B	134	ALA	0	-0.048	-0.027	34.864	0.260	0.260	0.000	0.000	0.000	0.000
133	B	135	MET	0	-0.028	-0.017	32.811	0.108	0.108	0.000	0.000	0.000	0.000
134	B	136	LYS	1	0.849	0.937	33.451	9.233	9.233	0.000	0.000	0.000	0.000
135	B	137	PHE	0	-0.034	-0.018	35.113	0.189	0.189	0.000	0.000	0.000	0.000
136	B	138	ALA	0	-0.060	-0.023	39.304	0.215	0.215	0.000	0.000	0.000	0.000
137	B	139	ASP	-1	-0.829	-0.918	38.873	-8.055	-8.055	0.000	0.000	0.000	0.000
138	B	140	PHE	0	-0.041	-0.033	41.045	0.076	0.076	0.000	0.000	0.000	0.000
139	B	141	ALA	0	-0.057	-0.031	43.804	0.099	0.099	0.000	0.000	0.000	0.000
140	B	142	VAL	0	-0.037	-0.010	40.116	0.065	0.065	0.000	0.000	0.000	0.000
141	B	143	TRP	0	0.016	0.028	34.839	-0.124	-0.124	0.000	0.000	0.000	0.000
142	B	144	SER	0	-0.029	-0.017	35.707	-0.041	-0.041	0.000	0.000	0.000	0.000
143	B	145	GLU	-1	-0.864	-0.929	32.691	-9.538	-9.538	0.000	0.000	0.000	0.000
144	B	146	ALA	0	0.029	0.019	30.912	-0.350	-0.350	0.000	0.000	0.000	0.000
145	B	147	ARG	1	0.936	0.967	29.845	9.156	9.156	0.000	0.000	0.000	0.000
146	B	148	PHE	0	0.035	0.017	29.959	-0.356	-0.356	0.000	0.000	0.000	0.000
147	B	149	SER	0	0.028	0.000	27.613	-0.350	-0.350	0.000	0.000	0.000	0.000
148	B	150	GLY	0	0.011	0.016	25.660	-0.522	-0.522	0.000	0.000	0.000	0.000
149	B	151	MET	0	-0.048	-0.019	25.155	-0.415	-0.415	0.000	0.000	0.000	0.000
150	B	152	VAL	0	0.028	0.024	24.920	-0.429	-0.429	0.000	0.000	0.000	0.000
151	B	153	LYS	1	0.898	0.959	20.646	14.253	14.253	0.000	0.000	0.000	0.000
152	B	154	THR	0	-0.027	-0.015	20.834	-0.899	-0.899	0.000	0.000	0.000	0.000
153	B	155	ALA	0	-0.018	-0.013	21.395	-0.584	-0.584	0.000	0.000	0.000	0.000
154	B	156	LEU	0	0.003	-0.003	19.623	-0.365	-0.365	0.000	0.000	0.000	0.000
155	B	157	THR	0	-0.007	-0.013	16.046	-1.086	-1.086	0.000	0.000	0.000	0.000
156	B	158	LEU	0	-0.045	-0.017	16.735	-0.948	-0.948	0.000	0.000	0.000	0.000
157	B	159	ALA	0	0.048	0.034	18.012	-0.483	-0.483	0.000	0.000	0.000	0.000
158	B	160	VAL	0	0.020	0.020	12.331	-0.471	-0.471	0.000	0.000	0.000	0.000
159	B	161	THR	0	0.011	0.006	12.925	-1.852	-1.852	0.000	0.000	0.000	0.000
160	B	162	THR	0	-0.074	-0.059	13.623	-0.415	-0.415	0.000	0.000	0.000	0.000
161	B	163	THR	0	-0.032	-0.026	13.583	0.171	0.171	0.000	0.000	0.000	0.000
162	B	164	LEU	0	-0.014	-0.017	8.510	-0.550	-0.550	0.000	0.000	0.000	0.000
163	B	165	LYS	1	0.839	0.916	10.928	22.193	22.193	0.000	0.000	0.000	0.000
164	B	166	GLU	-1	-0.931	-0.972	12.912	-15.805	-15.805	0.000	0.000	0.000	0.000
165	B	167	LEU	0	-0.102	-0.044	10.659	0.710	0.710	0.000	0.000	0.000	0.000
166	B	168	THR	-1	-0.981	-0.978	8.948	-23.679	-23.679	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(B:3:THR)