FMO DATABASE

FMODB ID: N6Y9Q

Calculation Name: 1NGN-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1NGN

Chain ID: A

ChEMBL ID:

UniProt ID: Q9Z2D7

Base Structure: X-ray

Registration Date: 2025-10-11

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	OptH
Protonation	MOE:Protonate 3D
Complement	ac.sh, 23 2024 Oct
Water	No
Procedure	Manual calculation
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	144
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1497488.588191
FMO2-HF: Nuclear repulsion	1438283.734798
FMO2-HF: Total energy	-59204.853393
FMO2-MP2: Total energy	-59382.390756

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:411:LYS)

Summations of interaction energy for fragment #1(A:411:LYS)

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.
-35.395	-33.23	0.03	-1.134	-1.061	-0.006

Interaction energy analysis for fragmet #1(A:411:LYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 2 / q_Mulliken : 1.829 / q_NPA : 1.897

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	413	THR	0	0.018	0.007	3.182	-13.215	-11.050	0.030	-1.134	-1.061	-0.006
4	A	414	PRO	0	0.007	0.036	5.498	5.240	5.240	0.000	0.000	0.000	0.000
5	A	415	PRO	0	0.043	0.041	9.092	1.246	1.246	0.000	0.000	0.000	0.000
6	A	416	ARG	1	0.821	0.902	10.003	45.077	45.077	0.000	0.000	0.000	0.000
7	A	417	SER	0	-0.001	-0.019	14.500	1.643	1.643	0.000	0.000	0.000	0.000
8	A	418	PRO	0	0.022	0.008	17.640	0.417	0.417	0.000	0.000	0.000	0.000
9	A	419	PHE	0	0.013	-0.011	20.297	1.423	1.423	0.000	0.000	0.000	0.000
10	A	420	ASN	0	-0.020	0.003	18.404	0.012	0.012	0.000	0.000	0.000	0.000
11	A	421	LEU	0	-0.056	-0.027	16.866	1.465	1.465	0.000	0.000	0.000	0.000
12	A	422	VAL	0	0.042	0.023	17.079	-1.106	-1.106	0.000	0.000	0.000	0.000
13	A	423	GLN	0	0.048	0.006	14.134	-0.653	-0.653	0.000	0.000	0.000	0.000
14	A	424	GLU	-1	-0.752	-0.837	12.607	-37.285	-37.285	0.000	0.000	0.000	0.000
15	A	425	ILE	0	-0.025	-0.010	12.508	-2.124	-2.124	0.000	0.000	0.000	0.000
16	A	426	LEU	0	-0.013	-0.010	13.315	-0.341	-0.341	0.000	0.000	0.000	0.000
17	A	427	PHE	0	-0.016	-0.010	5.487	-0.613	-0.613	0.000	0.000	0.000	0.000
18	A	428	HIS	0	-0.041	-0.012	7.530	-4.903	-4.903	0.000	0.000	0.000	0.000
19	A	429	ASP	-1	-0.785	-0.900	8.577	-39.072	-39.072	0.000	0.000	0.000	0.000
20	A	430	PRO	0	0.017	-0.023	9.500	2.706	2.706	0.000	0.000	0.000	0.000
21	A	431	TRP	0	0.008	0.024	12.240	1.813	1.813	0.000	0.000	0.000	0.000
22	A	432	LYS	1	0.934	0.980	15.050	33.753	33.753	0.000	0.000	0.000	0.000
23	A	433	LEU	0	-0.072	-0.013	12.335	1.856	1.856	0.000	0.000	0.000	0.000
24	A	434	LEU	0	-0.009	-0.003	15.088	1.671	1.671	0.000	0.000	0.000	0.000
25	A	435	ILE	0	0.058	0.038	17.459	1.827	1.827	0.000	0.000	0.000	0.000
26	A	436	ALA	0	0.010	0.002	18.226	1.516	1.516	0.000	0.000	0.000	0.000
27	A	437	THR	0	-0.105	-0.061	18.218	0.964	0.964	0.000	0.000	0.000	0.000
28	A	438	ILE	0	0.006	0.000	20.934	1.239	1.239	0.000	0.000	0.000	0.000
29	A	439	PHE	0	-0.039	-0.018	23.315	1.142	1.142	0.000	0.000	0.000	0.000
30	A	440	LEU	0	0.002	-0.014	21.623	0.998	0.998	0.000	0.000	0.000	0.000
31	A	441	ASN	0	-0.007	0.016	25.025	0.651	0.651	0.000	0.000	0.000	0.000
32	A	442	ARG	1	0.919	0.968	26.372	19.689	19.689	0.000	0.000	0.000	0.000
33	A	443	THR	0	-0.006	0.005	28.199	1.042	1.042	0.000	0.000	0.000	0.000
34	A	444	SER	0	0.013	0.010	28.088	-0.781	-0.781	0.000	0.000	0.000	0.000
35	A	445	GLY	0	0.085	0.032	26.360	0.009	0.009	0.000	0.000	0.000	0.000
36	A	446	LYS	1	0.943	0.971	27.039	16.990	16.990	0.000	0.000	0.000	0.000
37	A	447	MET	0	0.002	0.001	29.738	0.299	0.299	0.000	0.000	0.000	0.000
38	A	448	ALA	0	0.052	0.011	26.436	-0.005	-0.005	0.000	0.000	0.000	0.000
39	A	449	ILE	0	-0.019	-0.003	23.065	-0.448	-0.448	0.000	0.000	0.000	0.000
40	A	450	PRO	0	-0.013	-0.010	25.022	-0.494	-0.494	0.000	0.000	0.000	0.000
41	A	451	VAL	0	0.068	0.037	27.257	-0.239	-0.239	0.000	0.000	0.000	0.000
42	A	452	LEU	0	-0.011	0.012	20.369	-0.237	-0.237	0.000	0.000	0.000	0.000
43	A	453	TRP	0	-0.010	-0.020	18.036	-1.104	-1.104	0.000	0.000	0.000	0.000
44	A	454	GLU	-1	-0.891	-0.947	24.022	-18.914	-18.914	0.000	0.000	0.000	0.000
45	A	455	PHE	0	-0.018	-0.017	22.892	0.221	0.221	0.000	0.000	0.000	0.000
46	A	456	LEU	0	-0.046	-0.037	19.017	-0.351	-0.351	0.000	0.000	0.000	0.000
47	A	457	GLU	-1	-0.971	-0.970	22.404	-21.804	-21.804	0.000	0.000	0.000	0.000
48	A	458	LYS	1	0.924	0.966	24.945	19.353	19.353	0.000	0.000	0.000	0.000
49	A	459	TYR	0	-0.022	-0.015	24.974	0.422	0.422	0.000	0.000	0.000	0.000
50	A	460	PRO	0	0.008	0.010	21.029	-0.938	-0.938	0.000	0.000	0.000	0.000
51	A	461	SER	0	-0.049	-0.068	19.060	-1.288	-1.288	0.000	0.000	0.000	0.000
52	A	462	ALA	0	0.052	0.030	18.666	1.250	1.250	0.000	0.000	0.000	0.000
53	A	463	GLU	-1	-0.831	-0.914	19.333	-28.687	-28.687	0.000	0.000	0.000	0.000
54	A	464	VAL	0	-0.023	-0.005	23.008	1.141	1.141	0.000	0.000	0.000	0.000
55	A	465	ALA	0	0.001	0.001	23.300	0.972	0.972	0.000	0.000	0.000	0.000
56	A	466	ARG	1	0.806	0.879	23.796	23.623	23.623	0.000	0.000	0.000	0.000
57	A	467	ALA	0	-0.038	-0.010	26.201	0.596	0.596	0.000	0.000	0.000	0.000
58	A	468	ALA	0	-0.017	0.007	28.791	0.678	0.678	0.000	0.000	0.000	0.000
59	A	469	ASP	-1	-0.841	-0.915	30.511	-16.439	-16.439	0.000	0.000	0.000	0.000
60	A	470	TRP	0	0.009	-0.030	32.608	-0.208	-0.208	0.000	0.000	0.000	0.000
61	A	471	ARG	1	0.908	0.950	33.607	15.318	15.318	0.000	0.000	0.000	0.000
62	A	472	ASP	-1	-0.856	-0.922	33.873	-16.662	-16.662	0.000	0.000	0.000	0.000
63	A	473	VAL	0	-0.014	0.002	29.063	-0.235	-0.235	0.000	0.000	0.000	0.000
64	A	474	SER	0	-0.071	-0.058	31.831	-0.184	-0.184	0.000	0.000	0.000	0.000
65	A	475	GLU	-1	-0.820	-0.901	34.233	-15.210	-15.210	0.000	0.000	0.000	0.000
66	A	476	LEU	0	-0.014	0.003	29.142	0.091	0.091	0.000	0.000	0.000	0.000
67	A	477	LEU	0	0.006	-0.016	28.543	-0.173	-0.173	0.000	0.000	0.000	0.000
68	A	478	LYS	1	0.827	0.910	32.319	15.188	15.188	0.000	0.000	0.000	0.000
69	A	479	PRO	0	-0.021	-0.009	33.330	0.283	0.283	0.000	0.000	0.000	0.000
70	A	480	LEU	0	-0.041	-0.007	28.978	-0.092	-0.092	0.000	0.000	0.000	0.000
71	A	481	GLY	0	0.022	0.023	33.271	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	482	LEU	0	-0.024	-0.030	34.075	-0.451	-0.451	0.000	0.000	0.000	0.000
73	A	483	TYR	0	0.057	0.038	33.636	-0.328	-0.328	0.000	0.000	0.000	0.000
74	A	484	ASP	-1	-0.790	-0.900	33.458	-16.416	-16.416	0.000	0.000	0.000	0.000
75	A	485	LEU	0	-0.045	-0.015	32.535	-0.270	-0.270	0.000	0.000	0.000	0.000
76	A	486	ARG	1	0.830	0.919	29.053	18.699	18.699	0.000	0.000	0.000	0.000
77	A	487	ALA	0	0.057	0.030	28.989	-0.710	-0.710	0.000	0.000	0.000	0.000
78	A	488	LYS	1	0.916	0.969	29.465	16.045	16.045	0.000	0.000	0.000	0.000
79	A	489	THR	0	-0.048	-0.025	26.309	-0.396	-0.396	0.000	0.000	0.000	0.000
80	A	490	ILE	0	0.008	0.005	24.572	-0.790	-0.790	0.000	0.000	0.000	0.000
81	A	491	ILE	0	0.006	0.033	24.764	-0.949	-0.949	0.000	0.000	0.000	0.000
82	A	492	LYS	1	0.884	0.931	26.107	20.139	20.139	0.000	0.000	0.000	0.000
83	A	493	PHE	0	-0.016	-0.008	17.954	-0.595	-0.595	0.000	0.000	0.000	0.000
84	A	494	SER	0	0.001	-0.021	21.478	-1.391	-1.391	0.000	0.000	0.000	0.000
85	A	495	ASP	-1	-0.813	-0.885	22.146	-23.084	-23.084	0.000	0.000	0.000	0.000
86	A	496	GLU	-1	-0.798	-0.877	23.276	-23.500	-23.500	0.000	0.000	0.000	0.000
87	A	497	TYR	0	-0.024	-0.019	13.840	-1.432	-1.432	0.000	0.000	0.000	0.000
88	A	498	LEU	0	0.007	0.002	18.126	-1.533	-1.533	0.000	0.000	0.000	0.000
89	A	499	THR	0	-0.056	-0.031	20.304	0.158	0.158	0.000	0.000	0.000	0.000
90	A	500	LYS	1	0.833	0.916	21.711	26.419	26.419	0.000	0.000	0.000	0.000
91	A	501	GLN	0	0.012	0.011	19.721	-0.364	-0.364	0.000	0.000	0.000	0.000
92	A	502	TRP	0	-0.066	-0.045	13.285	0.486	0.486	0.000	0.000	0.000	0.000
93	A	503	ARG	1	0.892	0.950	15.351	33.020	33.020	0.000	0.000	0.000	0.000
94	A	504	TYR	0	-0.081	-0.072	13.389	-1.542	-1.542	0.000	0.000	0.000	0.000
95	A	505	PRO	0	0.054	0.025	14.574	1.710	1.710	0.000	0.000	0.000	0.000
96	A	506	ILE	0	-0.047	-0.025	17.427	1.263	1.263	0.000	0.000	0.000	0.000
97	A	507	GLU	-1	-0.837	-0.909	19.062	-29.120	-29.120	0.000	0.000	0.000	0.000
98	A	508	LEU	0	-0.031	0.010	18.274	0.770	0.770	0.000	0.000	0.000	0.000
99	A	509	HIS	0	-0.008	-0.016	22.396	0.472	0.472	0.000	0.000	0.000	0.000
100	A	510	GLY	0	0.035	0.002	24.166	-0.452	-0.452	0.000	0.000	0.000	0.000
101	A	511	ILE	0	-0.066	-0.009	18.977	-0.142	-0.142	0.000	0.000	0.000	0.000
102	A	512	GLY	0	0.051	0.026	22.312	0.515	0.515	0.000	0.000	0.000	0.000
103	A	513	LYS	1	0.817	0.878	21.356	24.504	24.504	0.000	0.000	0.000	0.000
104	A	514	TYR	0	0.031	0.023	20.334	-1.350	-1.350	0.000	0.000	0.000	0.000
105	A	515	GLY	0	0.085	0.042	18.494	-1.128	-1.128	0.000	0.000	0.000	0.000
106	A	516	ASN	0	0.034	0.003	16.615	-3.173	-3.173	0.000	0.000	0.000	0.000
107	A	517	ASP	-1	-0.787	-0.893	15.693	-30.494	-30.494	0.000	0.000	0.000	0.000
108	A	518	SER	0	-0.006	-0.015	15.368	-1.589	-1.589	0.000	0.000	0.000	0.000
109	A	519	TYR	0	0.049	0.010	11.001	-3.032	-3.032	0.000	0.000	0.000	0.000
110	A	520	ARG	1	0.850	0.906	10.935	31.878	31.878	0.000	0.000	0.000	0.000
111	A	521	ILE	0	0.007	0.015	12.089	-1.116	-1.116	0.000	0.000	0.000	0.000
112	A	522	PHE	0	-0.018	-0.023	9.991	-3.387	-3.387	0.000	0.000	0.000	0.000
113	A	523	CYS	0	-0.032	-0.006	7.520	-3.059	-3.059	0.000	0.000	0.000	0.000
114	A	524	VAL	0	-0.016	-0.001	6.233	-8.830	-8.830	0.000	0.000	0.000	0.000
115	A	525	ASN	0	-0.021	0.004	6.429	7.599	7.599	0.000	0.000	0.000	0.000
116	A	526	GLU	-1	-0.762	-0.849	8.304	-40.861	-40.861	0.000	0.000	0.000	0.000
117	A	527	TRP	0	0.038	0.017	10.867	4.942	4.942	0.000	0.000	0.000	0.000
118	A	528	LYS	1	0.796	0.908	13.671	39.638	39.638	0.000	0.000	0.000	0.000
119	A	529	GLN	0	-0.014	-0.012	13.625	3.109	3.109	0.000	0.000	0.000	0.000
120	A	530	VAL	0	-0.091	-0.026	15.179	1.530	1.530	0.000	0.000	0.000	0.000
121	A	531	HIS	0	0.059	0.025	17.936	0.767	0.767	0.000	0.000	0.000	0.000
122	A	532	PRO	0	-0.010	0.007	19.151	0.647	0.647	0.000	0.000	0.000	0.000
123	A	533	GLU	-1	-0.848	-0.921	21.800	-21.546	-21.546	0.000	0.000	0.000	0.000
124	A	534	ASP	-1	-0.841	-0.923	22.329	-24.265	-24.265	0.000	0.000	0.000	0.000
125	A	535	HIS	0	0.020	0.005	23.810	-0.607	-0.607	0.000	0.000	0.000	0.000
126	A	536	LYS	1	0.833	0.909	21.404	25.478	25.478	0.000	0.000	0.000	0.000
127	A	537	LEU	0	-0.009	-0.011	17.207	-0.872	-0.872	0.000	0.000	0.000	0.000
128	A	538	ASN	0	-0.011	-0.014	19.734	-1.483	-1.483	0.000	0.000	0.000	0.000
129	A	539	LYS	1	0.935	0.987	21.831	22.069	22.069	0.000	0.000	0.000	0.000
130	A	540	TYR	0	-0.050	-0.043	12.689	-0.878	-0.878	0.000	0.000	0.000	0.000
131	A	541	HIS	0	-0.021	-0.023	16.702	-0.427	-0.427	0.000	0.000	0.000	0.000
132	A	542	ASP	-1	-0.863	-0.929	18.742	-25.523	-25.523	0.000	0.000	0.000	0.000
133	A	543	TRP	0	-0.010	-0.007	15.232	-0.545	-0.545	0.000	0.000	0.000	0.000
134	A	544	LEU	0	0.000	0.004	12.916	-0.628	-0.628	0.000	0.000	0.000	0.000
135	A	545	TRP	0	0.004	-0.019	17.046	-1.537	-1.537	0.000	0.000	0.000	0.000
136	A	546	GLU	-1	-0.882	-0.925	19.053	-25.579	-25.579	0.000	0.000	0.000	0.000
137	A	547	ASN	0	-0.052	-0.043	18.319	1.026	1.026	0.000	0.000	0.000	0.000
138	A	548	HIS	1	0.806	0.878	14.047	33.767	33.767	0.000	0.000	0.000	0.000
139	A	549	GLU	-1	-0.863	-0.918	14.675	-30.756	-30.756	0.000	0.000	0.000	0.000
140	A	550	LYS	1	0.807	0.904	17.145	26.810	26.810	0.000	0.000	0.000	0.000
141	A	551	LEU	0	-0.030	-0.006	13.421	-0.220	-0.220	0.000	0.000	0.000	0.000
142	A	552	SER	0	-0.017	-0.014	9.668	-0.282	-0.282	0.000	0.000	0.000	0.000
143	A	553	LEU	0	-0.082	-0.032	8.283	-4.152	-4.152	0.000	0.000	0.000	0.000
144	A	554	SER	-1	-0.757	-0.859	9.829	-38.079	-38.079	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:411:LYS)