FMO DATABASE

FMODB ID: JKY59

Calculation Name: 6N1D-A-Xray547

Preferred Name:

Target Type:

Ligand 3-letter code: QUO | MIA | CM0 | G7M | 6MZ | PSU | 5MU | 4SU | SF4 | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6N1D

Chain ID: A

ChEMBL ID:

UniProt ID: P60493

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	127
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-982006.288327
FMO2-HF: Nuclear repulsion	933396.44915
FMO2-HF: Total energy	-48609.839177
FMO2-MP2: Total energy	-48756.096834

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(A:2:GLU)

Summations of interaction energy for fragment #1(A:2:GLU)

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.
9.014	11.607	-0.031	-1.345	-1.217	0.002

Interaction energy analysis for fragmet #1(A:2:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.017

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

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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	4	TYR	0	0.032	0.022	3.871	-3.674	-1.319	-0.030	-1.315	-1.010	0.002
20	A	21	PRO	0	0.024	0.019	4.357	0.148	0.386	-0.001	-0.030	-0.207	0.000
4	A	5	TYR	0	-0.037	-0.031	6.954	1.306	1.306	0.000	0.000	0.000	0.000
5	A	6	GLY	0	0.063	0.048	10.087	0.224	0.224	0.000	0.000	0.000	0.000
6	A	7	THR	0	-0.095	-0.041	13.761	0.263	0.263	0.000	0.000	0.000	0.000
7	A	8	GLY	0	0.101	0.052	16.987	0.062	0.062	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.939	0.961	19.973	1.295	1.295	0.000	0.000	0.000	0.000
9	A	10	ARG	1	0.834	0.901	23.453	0.676	0.676	0.000	0.000	0.000	0.000
10	A	11	LYS	1	0.921	0.945	26.821	0.506	0.506	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.930	-0.965	28.116	-0.540	-0.540	0.000	0.000	0.000	0.000
12	A	13	ALA	0	0.009	0.031	25.042	-0.009	-0.009	0.000	0.000	0.000	0.000
13	A	14	VAL	0	-0.034	-0.023	19.994	-0.071	-0.071	0.000	0.000	0.000	0.000
14	A	15	ALA	0	0.019	0.011	19.243	0.058	0.058	0.000	0.000	0.000	0.000
15	A	16	ARG	1	0.902	0.961	14.350	1.440	1.440	0.000	0.000	0.000	0.000
16	A	17	VAL	0	0.020	0.015	13.186	0.181	0.181	0.000	0.000	0.000	0.000
17	A	18	PHE	0	0.003	-0.007	8.045	-0.245	-0.245	0.000	0.000	0.000	0.000
18	A	19	LEU	0	0.006	0.020	9.110	0.526	0.526	0.000	0.000	0.000	0.000
19	A	20	ARG	1	0.926	0.937	4.975	0.277	0.277	0.000	0.000	0.000	0.000
21	A	22	GLY	0	-0.012	-0.005	7.108	1.254	1.254	0.000	0.000	0.000	0.000
22	A	23	ASN	0	-0.030	-0.024	9.812	0.192	0.192	0.000	0.000	0.000	0.000
23	A	24	GLY	0	0.031	0.022	13.611	-0.117	-0.117	0.000	0.000	0.000	0.000
24	A	25	LYS	1	0.900	0.964	12.486	-0.090	-0.090	0.000	0.000	0.000	0.000
25	A	26	VAL	0	0.038	0.016	13.266	-0.267	-0.267	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.009	-0.017	14.695	0.156	0.156	0.000	0.000	0.000	0.000
27	A	28	VAL	0	-0.048	-0.035	15.989	-0.192	-0.192	0.000	0.000	0.000	0.000
28	A	29	ASN	0	-0.077	-0.043	17.243	-0.012	-0.012	0.000	0.000	0.000	0.000
29	A	30	GLY	0	0.072	0.057	17.471	0.073	0.073	0.000	0.000	0.000	0.000
30	A	31	GLN	0	-0.012	-0.011	18.905	-0.019	-0.019	0.000	0.000	0.000	0.000
31	A	32	ASP	-1	-0.752	-0.877	19.996	-0.194	-0.194	0.000	0.000	0.000	0.000
32	A	33	PHE	0	-0.060	-0.038	19.060	-0.060	-0.060	0.000	0.000	0.000	0.000
33	A	34	ASN	0	-0.020	-0.012	21.016	-0.060	-0.060	0.000	0.000	0.000	0.000
34	A	35	GLU	-1	-0.890	-0.939	23.746	-0.137	-0.137	0.000	0.000	0.000	0.000
35	A	36	TYR	0	-0.043	-0.032	22.180	-0.005	-0.005	0.000	0.000	0.000	0.000
36	A	37	PHE	0	-0.105	-0.069	23.007	-0.034	-0.034	0.000	0.000	0.000	0.000
37	A	38	GLN	0	0.093	0.055	26.760	-0.012	-0.012	0.000	0.000	0.000	0.000
38	A	39	GLY	0	0.046	0.030	29.410	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.108	-0.039	27.879	-0.015	-0.015	0.000	0.000	0.000	0.000
40	A	41	VAL	0	0.068	0.031	31.626	0.012	0.012	0.000	0.000	0.000	0.000
41	A	42	ARG	1	0.869	0.916	28.916	0.507	0.507	0.000	0.000	0.000	0.000
42	A	43	ALA	0	0.073	0.045	26.176	-0.050	-0.050	0.000	0.000	0.000	0.000
43	A	44	VAL	0	0.061	0.020	24.839	-0.057	-0.057	0.000	0.000	0.000	0.000
44	A	45	ALA	0	-0.007	0.000	24.775	-0.043	-0.043	0.000	0.000	0.000	0.000
45	A	46	ALA	0	-0.035	-0.019	21.917	-0.053	-0.053	0.000	0.000	0.000	0.000
46	A	47	LEU	0	0.037	0.003	19.037	-0.121	-0.121	0.000	0.000	0.000	0.000
47	A	48	GLU	-1	-0.855	-0.917	21.206	-0.527	-0.527	0.000	0.000	0.000	0.000
48	A	49	PRO	0	-0.058	-0.044	18.640	0.051	0.051	0.000	0.000	0.000	0.000
49	A	50	LEU	0	0.019	0.022	15.523	-0.109	-0.109	0.000	0.000	0.000	0.000
50	A	51	ARG	1	0.902	0.947	19.202	0.561	0.561	0.000	0.000	0.000	0.000
51	A	52	ALA	0	-0.019	-0.003	22.634	0.046	0.046	0.000	0.000	0.000	0.000
52	A	53	VAL	0	-0.081	-0.044	17.821	-0.017	-0.017	0.000	0.000	0.000	0.000
53	A	54	ASP	-1	-0.899	-0.934	19.691	-0.389	-0.389	0.000	0.000	0.000	0.000
54	A	55	ALA	0	-0.026	-0.018	15.766	0.069	0.069	0.000	0.000	0.000	0.000
55	A	56	LEU	0	-0.042	-0.020	16.200	-0.126	-0.126	0.000	0.000	0.000	0.000
56	A	57	GLY	0	0.043	0.027	16.655	-0.031	-0.031	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.934	0.963	12.373	0.659	0.659	0.000	0.000	0.000	0.000
58	A	59	PHE	0	-0.029	-0.014	9.966	-0.016	-0.016	0.000	0.000	0.000	0.000
59	A	60	ASP	-1	-0.732	-0.852	9.459	0.161	0.161	0.000	0.000	0.000	0.000
60	A	61	ALA	0	-0.034	-0.037	10.296	-0.747	-0.747	0.000	0.000	0.000	0.000
61	A	62	TYR	0	0.002	0.013	10.011	0.389	0.389	0.000	0.000	0.000	0.000
62	A	63	ILE	0	0.005	-0.005	11.754	-0.324	-0.324	0.000	0.000	0.000	0.000
63	A	64	THR	0	-0.007	-0.006	14.997	0.152	0.152	0.000	0.000	0.000	0.000
64	A	65	VAL	0	0.004	0.013	16.897	-0.085	-0.085	0.000	0.000	0.000	0.000
65	A	66	ARG	1	0.908	0.935	20.401	0.838	0.838	0.000	0.000	0.000	0.000
66	A	67	GLY	0	0.081	0.042	22.839	-0.017	-0.017	0.000	0.000	0.000	0.000
67	A	68	GLY	0	0.064	0.031	26.135	-0.033	-0.033	0.000	0.000	0.000	0.000
68	A	69	GLY	0	0.018	0.014	28.408	0.027	0.027	0.000	0.000	0.000	0.000
69	A	70	LYS	1	0.940	0.960	26.291	0.488	0.488	0.000	0.000	0.000	0.000
70	A	71	SER	0	0.038	0.017	27.625	-0.040	-0.040	0.000	0.000	0.000	0.000
71	A	72	GLY	0	0.003	0.001	27.856	-0.028	-0.028	0.000	0.000	0.000	0.000
72	A	73	GLN	0	0.001	-0.008	23.947	-0.056	-0.056	0.000	0.000	0.000	0.000
73	A	74	ILE	0	0.033	0.029	22.998	-0.087	-0.087	0.000	0.000	0.000	0.000
74	A	75	ASP	-1	-0.871	-0.927	23.424	-0.777	-0.777	0.000	0.000	0.000	0.000
75	A	76	ALA	0	-0.034	-0.017	21.996	-0.060	-0.060	0.000	0.000	0.000	0.000
76	A	77	ILE	0	0.016	0.008	18.198	-0.150	-0.150	0.000	0.000	0.000	0.000
77	A	78	LYS	1	0.952	0.996	19.090	0.582	0.582	0.000	0.000	0.000	0.000
78	A	79	LEU	0	-0.067	-0.015	20.577	-0.031	-0.031	0.000	0.000	0.000	0.000
79	A	80	GLY	0	-0.008	-0.025	17.147	-0.122	-0.122	0.000	0.000	0.000	0.000
80	A	81	ILE	0	0.026	0.010	14.828	-0.342	-0.342	0.000	0.000	0.000	0.000
81	A	82	ALA	0	0.034	0.007	14.410	-0.237	-0.237	0.000	0.000	0.000	0.000
82	A	83	ARG	1	0.834	0.915	15.999	1.631	1.631	0.000	0.000	0.000	0.000
83	A	84	ALA	0	0.044	0.042	10.690	-0.200	-0.200	0.000	0.000	0.000	0.000
84	A	85	LEU	0	0.005	0.016	9.688	0.348	0.348	0.000	0.000	0.000	0.000
85	A	86	VAL	0	0.017	-0.005	10.403	-0.268	-0.268	0.000	0.000	0.000	0.000
86	A	87	GLN	0	-0.034	-0.031	8.898	-0.131	-0.131	0.000	0.000	0.000	0.000
87	A	88	TYR	0	0.023	0.006	7.496	-0.411	-0.411	0.000	0.000	0.000	0.000
88	A	89	ASN	0	-0.038	0.007	8.411	0.854	0.854	0.000	0.000	0.000	0.000
89	A	90	PRO	0	0.018	0.002	11.832	0.133	0.133	0.000	0.000	0.000	0.000
90	A	91	ASP	-1	-0.839	-0.926	14.934	-1.123	-1.123	0.000	0.000	0.000	0.000
91	A	92	TYR	0	0.021	0.025	14.579	0.151	0.151	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.887	0.926	17.292	1.249	1.249	0.000	0.000	0.000	0.000
93	A	94	ALA	0	0.031	0.013	20.216	0.064	0.064	0.000	0.000	0.000	0.000
94	A	95	LYS	1	1.034	1.012	22.229	0.520	0.520	0.000	0.000	0.000	0.000
95	A	96	LEU	0	0.011	0.010	18.792	0.000	0.000	0.000	0.000	0.000	0.000
96	A	97	LYS	1	0.921	0.950	22.989	0.811	0.811	0.000	0.000	0.000	0.000
97	A	98	PRO	0	-0.009	-0.011	24.849	0.022	0.022	0.000	0.000	0.000	0.000
98	A	99	LEU	0	0.044	0.032	26.088	0.036	0.036	0.000	0.000	0.000	0.000
99	A	100	GLY	0	0.002	0.028	27.138	0.020	0.020	0.000	0.000	0.000	0.000
100	A	101	PHE	0	0.005	-0.021	22.510	0.001	0.001	0.000	0.000	0.000	0.000
101	A	102	LEU	0	-0.030	0.006	19.753	-0.055	-0.055	0.000	0.000	0.000	0.000
102	A	103	THR	0	-0.048	-0.046	22.915	0.047	0.047	0.000	0.000	0.000	0.000
103	A	104	ARG	1	0.885	0.939	25.281	0.867	0.867	0.000	0.000	0.000	0.000
104	A	105	ASP	-1	-0.729	-0.846	26.200	-0.558	-0.558	0.000	0.000	0.000	0.000
105	A	106	ALA	0	-0.022	-0.015	29.386	0.014	0.014	0.000	0.000	0.000	0.000
106	A	107	ARG	1	0.895	0.943	30.755	0.525	0.525	0.000	0.000	0.000	0.000
107	A	108	VAL	0	-0.004	-0.003	32.237	0.002	0.002	0.000	0.000	0.000	0.000
108	A	109	VAL	0	0.018	0.007	34.458	0.022	0.022	0.000	0.000	0.000	0.000
109	A	110	GLU	-1	-0.794	-0.871	37.610	-0.336	-0.336	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.960	0.979	40.666	0.341	0.341	0.000	0.000	0.000	0.000
111	A	112	LYS	1	0.920	0.946	41.864	0.261	0.261	0.000	0.000	0.000	0.000
112	A	113	LYS	1	0.858	0.939	44.826	0.308	0.308	0.000	0.000	0.000	0.000
113	A	114	TYR	0	0.089	0.044	48.227	0.001	0.001	0.000	0.000	0.000	0.000
114	A	115	GLY	0	0.065	0.027	51.705	-0.002	-0.002	0.000	0.000	0.000	0.000
115	A	116	LYS	1	0.852	0.931	50.638	0.248	0.248	0.000	0.000	0.000	0.000
116	A	117	HIS	0	0.084	0.042	50.812	-0.009	-0.009	0.000	0.000	0.000	0.000
117	A	118	LYS	1	0.995	0.990	45.027	0.255	0.255	0.000	0.000	0.000	0.000
118	A	119	ALA	0	-0.005	0.006	44.491	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	120	ARG	1	0.896	0.916	43.968	0.324	0.324	0.000	0.000	0.000	0.000
120	A	121	ARG	1	0.875	0.942	48.716	0.203	0.203	0.000	0.000	0.000	0.000
121	A	122	ALA	0	0.066	0.034	51.359	-0.003	-0.003	0.000	0.000	0.000	0.000
122	A	123	PRO	0	0.052	0.026	54.458	-0.001	-0.001	0.000	0.000	0.000	0.000
123	A	124	GLN	0	0.029	0.011	56.907	-0.006	-0.006	0.000	0.000	0.000	0.000
124	A	125	TYR	0	0.009	0.012	59.790	0.001	0.001	0.000	0.000	0.000	0.000
125	A	126	SER	0	-0.013	-0.019	62.352	0.001	0.001	0.000	0.000	0.000	0.000
126	A	127	LYS	1	0.945	0.981	66.141	0.125	0.125	0.000	0.000	0.000	0.000
127	A	128	ARG	0	0.112	0.071	68.873	-0.009	-0.009	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:GLU)