FMO DATABASE

FMODB ID: 2GMLR

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	155
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1442073.706871
FMO2-HF: Nuclear repulsion	1379318.493268
FMO2-HF: Total energy	-62755.213603
FMO2-MP2: Total energy	-62937.466438

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:ALA)

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

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.
229.968	233.115	-0.032	-1.634	-1.481	-0.007

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.875 / q_NPA : 0.921

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	4	ARG	1	1.056	1.044	3.869	35.487	38.523	-0.031	-1.629	-1.376	-0.007
5	A	6	ARG	1	0.942	0.960	4.640	19.303	19.414	-0.001	-0.005	-0.105	0.000
4	A	5	ARG	1	1.029	1.014	5.938	26.723	26.723	0.000	0.000	0.000	0.000
6	A	7	ALA	0	-0.029	-0.009	4.871	0.753	0.753	0.000	0.000	0.000	0.000
7	A	8	GLU	-1	-0.861	-0.918	6.727	-20.207	-20.207	0.000	0.000	0.000	0.000
8	A	9	VAL	0	-0.076	-0.043	9.767	-1.122	-1.122	0.000	0.000	0.000	0.000
9	A	10	ARG	1	0.970	0.985	11.647	21.724	21.724	0.000	0.000	0.000	0.000
10	A	11	GLN	0	0.052	0.042	13.832	0.320	0.320	0.000	0.000	0.000	0.000
11	A	12	LEU	0	-0.064	-0.041	17.519	-0.303	-0.303	0.000	0.000	0.000	0.000
12	A	13	GLN	0	0.036	0.013	19.726	0.307	0.307	0.000	0.000	0.000	0.000
13	A	14	PRO	0	0.036	0.000	23.404	-0.211	-0.211	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.822	-0.887	25.862	-10.103	-10.103	0.000	0.000	0.000	0.000
15	A	16	LEU	0	-0.005	-0.006	28.496	0.044	0.044	0.000	0.000	0.000	0.000
16	A	17	VAL	0	-0.030	0.003	31.918	0.270	0.270	0.000	0.000	0.000	0.000
17	A	18	TYR	0	0.002	-0.030	31.481	0.316	0.316	0.000	0.000	0.000	0.000
18	A	19	GLY	0	0.047	0.034	31.207	-0.228	-0.228	0.000	0.000	0.000	0.000
19	A	20	ASP	-1	-0.804	-0.903	26.424	-11.285	-11.285	0.000	0.000	0.000	0.000
20	A	21	VAL	0	0.029	0.015	22.361	-0.046	-0.046	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.050	-0.026	23.388	-0.328	-0.328	0.000	0.000	0.000	0.000
22	A	23	VAL	0	0.016	0.022	24.441	-0.106	-0.106	0.000	0.000	0.000	0.000
23	A	24	THR	0	0.019	0.010	22.573	-0.038	-0.038	0.000	0.000	0.000	0.000
24	A	25	ALA	0	-0.055	-0.028	20.314	-0.380	-0.380	0.000	0.000	0.000	0.000
25	A	26	PHE	0	-0.007	0.001	20.995	-0.471	-0.471	0.000	0.000	0.000	0.000
26	A	27	ILE	0	0.044	0.022	23.662	-0.132	-0.132	0.000	0.000	0.000	0.000
27	A	28	ASN	0	-0.052	-0.039	19.759	-0.146	-0.146	0.000	0.000	0.000	0.000
28	A	29	LYS	1	0.892	0.953	17.085	15.453	15.453	0.000	0.000	0.000	0.000
29	A	30	ILE	0	0.009	0.008	21.404	-0.023	-0.023	0.000	0.000	0.000	0.000
30	A	31	MET	0	-0.059	-0.016	21.127	0.473	0.473	0.000	0.000	0.000	0.000
31	A	32	ARG	1	0.892	0.939	22.735	11.209	11.209	0.000	0.000	0.000	0.000
32	A	33	ASP	-1	-0.808	-0.898	23.954	-11.246	-11.246	0.000	0.000	0.000	0.000
33	A	34	GLY	0	0.040	0.034	23.566	0.179	0.179	0.000	0.000	0.000	0.000
34	A	35	LYS	1	0.836	0.902	24.536	10.811	10.811	0.000	0.000	0.000	0.000
35	A	36	LYS	1	1.007	0.991	24.692	11.946	11.946	0.000	0.000	0.000	0.000
36	A	37	ASN	0	0.026	0.002	26.955	-0.229	-0.229	0.000	0.000	0.000	0.000
37	A	38	LEU	0	0.021	0.008	30.444	0.178	0.178	0.000	0.000	0.000	0.000
38	A	39	ALA	0	0.016	0.017	27.181	0.188	0.188	0.000	0.000	0.000	0.000
39	A	40	ALA	0	0.027	0.004	29.137	0.080	0.080	0.000	0.000	0.000	0.000
40	A	41	ARG	1	0.924	0.972	30.371	8.466	8.466	0.000	0.000	0.000	0.000
41	A	42	ILE	0	-0.039	-0.012	29.805	0.209	0.209	0.000	0.000	0.000	0.000
42	A	43	PHE	0	0.040	0.014	29.269	0.108	0.108	0.000	0.000	0.000	0.000
43	A	44	TYR	0	-0.009	-0.047	31.020	0.302	0.302	0.000	0.000	0.000	0.000
44	A	45	ASP	-1	-0.812	-0.902	34.805	-7.964	-7.964	0.000	0.000	0.000	0.000
45	A	46	ALA	0	-0.023	-0.015	33.998	0.176	0.176	0.000	0.000	0.000	0.000
46	A	47	CYS	0	-0.081	-0.045	33.818	0.086	0.086	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.899	0.957	36.636	8.197	8.197	0.000	0.000	0.000	0.000
48	A	49	ILE	0	0.072	0.049	38.382	0.131	0.131	0.000	0.000	0.000	0.000
49	A	50	ILE	0	-0.045	-0.037	36.794	0.122	0.122	0.000	0.000	0.000	0.000
50	A	51	GLN	0	-0.015	-0.008	40.463	-0.026	-0.026	0.000	0.000	0.000	0.000
51	A	52	GLU	-1	-0.925	-0.949	42.605	-6.798	-6.798	0.000	0.000	0.000	0.000
52	A	53	LYS	1	0.869	0.951	42.500	7.033	7.033	0.000	0.000	0.000	0.000
53	A	54	THR	0	-0.047	-0.056	42.895	0.192	0.192	0.000	0.000	0.000	0.000
54	A	55	GLY	0	0.062	0.052	44.455	-0.065	-0.065	0.000	0.000	0.000	0.000
55	A	56	GLN	0	-0.019	-0.002	39.837	0.015	0.015	0.000	0.000	0.000	0.000
56	A	57	GLU	-1	-0.803	-0.911	38.568	-7.681	-7.681	0.000	0.000	0.000	0.000
57	A	58	PRO	0	-0.007	-0.004	35.680	-0.210	-0.210	0.000	0.000	0.000	0.000
58	A	59	LEU	0	-0.017	-0.013	30.081	-0.269	-0.269	0.000	0.000	0.000	0.000
59	A	60	LYS	1	0.890	0.940	32.774	7.437	7.437	0.000	0.000	0.000	0.000
60	A	61	VAL	0	0.062	0.035	34.944	-0.038	-0.038	0.000	0.000	0.000	0.000
61	A	62	PHE	0	-0.021	-0.003	27.406	-0.254	-0.254	0.000	0.000	0.000	0.000
62	A	63	LYS	1	0.884	0.909	27.765	10.247	10.247	0.000	0.000	0.000	0.000
63	A	64	GLN	0	0.057	0.043	29.470	-0.321	-0.321	0.000	0.000	0.000	0.000
64	A	65	ALA	0	0.033	0.038	30.735	-0.134	-0.134	0.000	0.000	0.000	0.000
65	A	66	VAL	0	-0.047	-0.032	24.621	-0.369	-0.369	0.000	0.000	0.000	0.000
66	A	67	GLU	-1	-0.886	-0.943	26.065	-11.671	-11.671	0.000	0.000	0.000	0.000
67	A	68	ASN	0	-0.010	-0.002	27.904	0.010	0.010	0.000	0.000	0.000	0.000
68	A	69	VAL	0	-0.041	-0.022	24.152	-0.117	-0.117	0.000	0.000	0.000	0.000
69	A	70	LYS	1	0.823	0.904	22.219	11.395	11.395	0.000	0.000	0.000	0.000
70	A	71	PRO	0	0.006	0.018	20.791	0.306	0.306	0.000	0.000	0.000	0.000
71	A	72	ARG	1	0.968	0.990	22.980	10.469	10.469	0.000	0.000	0.000	0.000
72	A	73	MET	0	-0.034	-0.023	21.286	-0.411	-0.411	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.800	-0.870	16.002	-17.409	-17.409	0.000	0.000	0.000	0.000
74	A	75	VAL	0	0.019	0.019	18.946	-0.102	-0.102	0.000	0.000	0.000	0.000
75	A	76	ARG	1	0.888	0.935	11.187	21.165	21.165	0.000	0.000	0.000	0.000
76	A	77	SER	0	0.039	0.019	15.949	-0.014	-0.014	0.000	0.000	0.000	0.000
77	A	78	ARG	1	0.921	0.960	14.363	16.630	16.630	0.000	0.000	0.000	0.000
78	A	79	ARG	1	0.970	0.999	15.356	17.033	17.033	0.000	0.000	0.000	0.000
79	A	80	VAL	0	-0.012	-0.015	17.165	-0.620	-0.620	0.000	0.000	0.000	0.000
80	A	81	GLY	0	0.030	0.019	20.035	0.431	0.431	0.000	0.000	0.000	0.000
81	A	82	GLY	0	0.070	0.038	22.960	-0.190	-0.190	0.000	0.000	0.000	0.000
82	A	83	ALA	0	-0.009	0.005	22.776	0.117	0.117	0.000	0.000	0.000	0.000
83	A	84	ASN	0	-0.075	-0.062	17.676	-1.027	-1.027	0.000	0.000	0.000	0.000
84	A	85	TYR	0	0.075	0.051	19.961	0.633	0.633	0.000	0.000	0.000	0.000
85	A	86	GLN	0	-0.009	-0.019	18.984	-1.197	-1.197	0.000	0.000	0.000	0.000
86	A	87	VAL	0	-0.028	-0.005	17.801	0.587	0.587	0.000	0.000	0.000	0.000
87	A	88	PRO	0	0.040	0.025	18.562	-0.789	-0.789	0.000	0.000	0.000	0.000
88	A	89	MET	0	-0.046	-0.021	14.112	-0.713	-0.713	0.000	0.000	0.000	0.000
89	A	90	GLU	-1	-0.831	-0.921	19.314	-12.620	-12.620	0.000	0.000	0.000	0.000
90	A	91	VAL	0	0.000	0.003	16.862	-0.943	-0.943	0.000	0.000	0.000	0.000
91	A	92	SER	0	-0.005	0.002	12.911	0.588	0.588	0.000	0.000	0.000	0.000
92	A	93	PRO	0	0.124	0.051	15.750	-0.398	-0.398	0.000	0.000	0.000	0.000
93	A	94	ARG	1	0.953	0.971	12.618	19.580	19.580	0.000	0.000	0.000	0.000
94	A	95	ARG	1	0.814	0.887	12.185	19.403	19.403	0.000	0.000	0.000	0.000
95	A	96	GLN	0	0.032	0.001	14.668	0.006	0.006	0.000	0.000	0.000	0.000
96	A	97	GLN	0	0.040	0.022	18.354	0.906	0.906	0.000	0.000	0.000	0.000
97	A	98	SER	0	-0.060	-0.050	14.838	0.137	0.137	0.000	0.000	0.000	0.000
98	A	99	LEU	0	-0.092	-0.038	16.115	-0.295	-0.295	0.000	0.000	0.000	0.000
99	A	100	ALA	0	0.081	0.050	18.156	0.381	0.381	0.000	0.000	0.000	0.000
100	A	101	LEU	0	-0.010	-0.013	19.003	0.311	0.311	0.000	0.000	0.000	0.000
101	A	102	ARG	1	0.886	0.928	15.658	17.366	17.366	0.000	0.000	0.000	0.000
102	A	103	TRP	0	-0.003	-0.003	19.834	0.262	0.262	0.000	0.000	0.000	0.000
103	A	104	LEU	0	0.060	0.035	23.090	0.391	0.391	0.000	0.000	0.000	0.000
104	A	105	VAL	0	-0.030	-0.010	22.992	0.386	0.386	0.000	0.000	0.000	0.000
105	A	106	GLN	0	-0.043	-0.037	20.045	-0.433	-0.433	0.000	0.000	0.000	0.000
106	A	107	ALA	0	-0.005	0.021	24.812	0.169	0.169	0.000	0.000	0.000	0.000
107	A	108	ALA	0	0.059	0.035	28.044	0.351	0.351	0.000	0.000	0.000	0.000
108	A	109	ASN	0	-0.068	-0.045	28.123	-0.060	-0.060	0.000	0.000	0.000	0.000
109	A	110	GLN	0	0.032	0.037	30.136	-0.027	-0.027	0.000	0.000	0.000	0.000
110	A	111	ARG	1	0.871	0.954	31.754	8.619	8.619	0.000	0.000	0.000	0.000
111	A	112	PRO	0	0.004	0.008	34.521	-0.040	-0.040	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.814	-0.920	36.896	-7.713	-7.713	0.000	0.000	0.000	0.000
113	A	114	ARG	1	0.984	0.984	37.413	7.028	7.028	0.000	0.000	0.000	0.000
114	A	115	ARG	1	0.912	0.951	38.273	7.878	7.878	0.000	0.000	0.000	0.000
115	A	116	ALA	0	-0.005	-0.014	33.694	-0.169	-0.169	0.000	0.000	0.000	0.000
116	A	117	ALA	0	0.049	0.020	34.157	-0.160	-0.160	0.000	0.000	0.000	0.000
117	A	118	VAL	0	0.049	0.034	35.015	-0.135	-0.135	0.000	0.000	0.000	0.000
118	A	119	ARG	1	0.912	0.972	31.869	9.231	9.231	0.000	0.000	0.000	0.000
119	A	120	ILE	0	-0.043	-0.015	28.805	-0.301	-0.301	0.000	0.000	0.000	0.000
120	A	121	ALA	0	0.060	0.012	31.984	-0.089	-0.089	0.000	0.000	0.000	0.000
121	A	122	HIS	0	-0.038	-0.017	34.871	0.097	0.097	0.000	0.000	0.000	0.000
122	A	123	GLU	-1	-0.843	-0.932	30.803	-9.442	-9.442	0.000	0.000	0.000	0.000
123	A	124	LEU	0	-0.088	-0.040	29.018	-0.203	-0.203	0.000	0.000	0.000	0.000
124	A	125	MET	0	-0.002	-0.011	32.317	0.052	0.052	0.000	0.000	0.000	0.000
125	A	126	ASP	-1	-0.818	-0.896	35.289	-8.160	-8.160	0.000	0.000	0.000	0.000
126	A	127	ALA	0	-0.077	-0.053	30.767	-0.010	-0.010	0.000	0.000	0.000	0.000
127	A	128	ALA	0	-0.052	-0.031	32.727	-0.147	-0.147	0.000	0.000	0.000	0.000
128	A	129	GLU	-1	-0.891	-0.935	34.643	-7.698	-7.698	0.000	0.000	0.000	0.000
129	A	130	GLY	0	0.033	0.030	33.616	0.017	0.017	0.000	0.000	0.000	0.000
130	A	131	LYS	1	0.856	0.919	34.694	7.835	7.835	0.000	0.000	0.000	0.000
131	A	132	GLY	0	0.088	0.059	32.701	0.106	0.106	0.000	0.000	0.000	0.000
132	A	133	GLY	0	0.012	-0.010	30.887	-0.156	-0.156	0.000	0.000	0.000	0.000
133	A	134	ALA	0	-0.024	-0.026	26.558	-0.281	-0.281	0.000	0.000	0.000	0.000
134	A	135	VAL	0	0.020	0.028	26.955	-0.406	-0.406	0.000	0.000	0.000	0.000
135	A	136	LYS	1	0.981	0.994	28.709	9.258	9.258	0.000	0.000	0.000	0.000
136	A	137	LYS	1	0.947	0.963	24.392	11.737	11.737	0.000	0.000	0.000	0.000
137	A	138	LYS	1	0.832	0.928	24.153	10.561	10.561	0.000	0.000	0.000	0.000
138	A	139	GLU	-1	-0.823	-0.924	25.044	-9.953	-9.953	0.000	0.000	0.000	0.000
139	A	140	ASP	-1	-0.848	-0.910	25.993	-10.897	-10.897	0.000	0.000	0.000	0.000
140	A	141	VAL	0	-0.036	-0.018	20.261	-0.179	-0.179	0.000	0.000	0.000	0.000
141	A	142	GLU	-1	-0.782	-0.878	23.684	-11.416	-11.416	0.000	0.000	0.000	0.000
142	A	143	ARG	1	0.773	0.876	25.856	10.218	10.218	0.000	0.000	0.000	0.000
143	A	144	MET	0	-0.020	-0.013	22.852	0.090	0.090	0.000	0.000	0.000	0.000
144	A	145	ALA	0	-0.036	-0.003	22.859	-0.355	-0.355	0.000	0.000	0.000	0.000
145	A	146	GLU	-1	-0.952	-0.983	24.551	-10.067	-10.067	0.000	0.000	0.000	0.000
146	A	147	ALA	0	0.044	0.026	27.719	0.286	0.286	0.000	0.000	0.000	0.000
147	A	148	ASN	0	-0.076	-0.037	25.224	0.352	0.352	0.000	0.000	0.000	0.000
148	A	149	ARG	1	0.968	0.978	26.839	9.284	9.284	0.000	0.000	0.000	0.000
149	A	150	ALA	0	0.035	0.028	28.704	-0.009	-0.009	0.000	0.000	0.000	0.000
150	A	151	TYR	0	0.003	-0.006	21.722	0.046	0.046	0.000	0.000	0.000	0.000
151	A	152	ALA	0	-0.022	-0.011	24.901	-0.603	-0.603	0.000	0.000	0.000	0.000
152	A	153	HIS	1	0.877	0.941	24.063	12.711	12.711	0.000	0.000	0.000	0.000
153	A	154	TYR	0	-0.030	-0.016	19.942	-0.273	-0.273	0.000	0.000	0.000	0.000
154	A	155	ARG	1	0.947	0.979	21.042	12.433	12.433	0.000	0.000	0.000	0.000
155	A	156	TRP	-1	-0.898	-0.944	12.575	-16.738	-16.738	0.000	0.000	0.000	0.000

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