FMO DATABASE

FMODB ID: JK529

Calculation Name: 1NP6-A-Xray549

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1NP6

Chain ID: A

ChEMBL ID:

UniProt ID: P32125

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	158
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1412889.397663
FMO2-HF: Nuclear repulsion	1351622.466339
FMO2-HF: Total energy	-61266.931324
FMO2-MP2: Total energy	-61445.890501

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:6:MET)

Summations of interaction energy for fragment #1(A:6:MET)

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.
-142.782	-138.846	0.62	-1.819	-2.735	-0.008

Interaction energy analysis for fragmet #1(A:6:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.837 / q_NPA : 0.907

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	8	PRO	0	0.027	0.021	3.648	-5.198	-3.540	0.000	-0.761	-0.897	0.000
82	A	99	THR	0	0.010	-0.019	3.027	-4.505	-2.866	0.586	-0.732	-1.492	-0.006
83	A	100	SER	0	-0.073	-0.050	3.373	-3.717	-3.104	0.035	-0.325	-0.323	-0.002
84	A	101	LYS	1	0.815	0.888	4.978	25.348	25.374	-0.001	-0.001	-0.023	0.000
4	A	9	LEU	0	0.014	0.006	5.872	1.881	1.881	0.000	0.000	0.000	0.000
5	A	10	LEU	0	-0.019	-0.005	7.994	1.529	1.529	0.000	0.000	0.000	0.000
6	A	11	ALA	0	0.010	0.010	11.790	0.757	0.757	0.000	0.000	0.000	0.000
7	A	12	PHE	0	0.017	0.002	14.708	0.936	0.936	0.000	0.000	0.000	0.000
8	A	13	ALA	0	0.013	0.004	18.199	0.395	0.395	0.000	0.000	0.000	0.000
9	A	14	ALA	0	0.016	-0.014	21.120	0.360	0.360	0.000	0.000	0.000	0.000
10	A	15	TRP	0	0.029	0.035	24.771	-0.112	-0.112	0.000	0.000	0.000	0.000
11	A	16	SER	0	-0.013	-0.009	28.034	-0.132	-0.132	0.000	0.000	0.000	0.000
12	A	17	GLY	0	0.021	0.010	29.560	0.213	0.213	0.000	0.000	0.000	0.000
13	A	18	THR	0	-0.005	-0.011	27.567	0.223	0.223	0.000	0.000	0.000	0.000
14	A	19	GLY	0	0.006	0.005	28.253	-0.098	-0.098	0.000	0.000	0.000	0.000
15	A	20	LYS	1	0.918	0.952	20.445	14.305	14.305	0.000	0.000	0.000	0.000
16	A	21	THR	0	0.025	0.006	22.888	-0.173	-0.173	0.000	0.000	0.000	0.000
17	A	22	THR	0	-0.061	-0.051	23.966	-0.146	-0.146	0.000	0.000	0.000	0.000
18	A	23	LEU	0	0.042	0.038	22.761	0.108	0.108	0.000	0.000	0.000	0.000
19	A	24	LEU	0	0.053	0.030	17.909	-0.101	-0.101	0.000	0.000	0.000	0.000
20	A	25	LYS	1	0.895	0.946	20.969	11.482	11.482	0.000	0.000	0.000	0.000
21	A	26	LYS	1	0.916	0.969	23.336	11.419	11.419	0.000	0.000	0.000	0.000
22	A	27	LEU	0	0.075	0.036	18.133	0.054	0.054	0.000	0.000	0.000	0.000
23	A	28	ILE	0	0.015	0.012	17.044	-0.451	-0.451	0.000	0.000	0.000	0.000
24	A	29	PRO	0	-0.018	-0.013	18.368	-0.423	-0.423	0.000	0.000	0.000	0.000
25	A	30	ALA	0	0.064	0.044	20.435	-0.062	-0.062	0.000	0.000	0.000	0.000
26	A	31	LEU	0	0.006	-0.003	14.865	-0.181	-0.181	0.000	0.000	0.000	0.000
27	A	32	CYS	0	-0.058	-0.028	16.104	-0.621	-0.621	0.000	0.000	0.000	0.000
28	A	33	ALA	0	-0.047	-0.021	17.159	0.063	0.063	0.000	0.000	0.000	0.000
29	A	34	ARG	1	0.762	0.858	17.141	15.051	15.051	0.000	0.000	0.000	0.000
30	A	35	GLY	0	-0.019	-0.003	15.180	-0.493	-0.493	0.000	0.000	0.000	0.000
31	A	36	ILE	0	-0.019	-0.002	10.835	-1.308	-1.308	0.000	0.000	0.000	0.000
32	A	37	ARG	1	0.818	0.892	6.657	29.472	29.472	0.000	0.000	0.000	0.000
33	A	38	PRO	0	-0.004	-0.003	9.785	-2.842	-2.842	0.000	0.000	0.000	0.000
34	A	39	GLY	0	0.021	0.011	10.616	1.423	1.423	0.000	0.000	0.000	0.000
35	A	40	LEU	0	-0.058	-0.036	11.533	0.262	0.262	0.000	0.000	0.000	0.000
36	A	41	ILE	0	0.008	0.013	9.263	0.584	0.584	0.000	0.000	0.000	0.000
37	A	42	LYS	1	0.922	0.959	13.513	14.370	14.370	0.000	0.000	0.000	0.000
38	A	43	HIS	1	0.848	0.932	17.159	14.538	14.538	0.000	0.000	0.000	0.000
39	A	44	THR	0	-0.064	-0.042	19.475	0.162	0.162	0.000	0.000	0.000	0.000
40	A	45	HIS	0	-0.026	-0.030	23.141	-0.307	-0.307	0.000	0.000	0.000	0.000
41	A	46	HIS	-1	-0.912	-0.932	26.425	-11.130	-11.130	0.000	0.000	0.000	0.000
42	A	59	GLU	-1	-0.956	-0.984	33.357	-8.447	-8.447	0.000	0.000	0.000	0.000
43	A	60	LEU	0	0.035	-0.003	31.466	0.055	0.055	0.000	0.000	0.000	0.000
44	A	61	ARG	1	0.919	0.947	25.861	11.596	11.596	0.000	0.000	0.000	0.000
45	A	62	LYS	1	0.956	0.983	30.060	8.427	8.427	0.000	0.000	0.000	0.000
46	A	63	ALA	0	-0.018	-0.007	33.210	0.201	0.201	0.000	0.000	0.000	0.000
47	A	64	GLY	0	0.029	0.021	31.620	0.155	0.155	0.000	0.000	0.000	0.000
48	A	65	ALA	0	-0.059	-0.020	27.919	-0.205	-0.205	0.000	0.000	0.000	0.000
49	A	66	ALA	0	0.042	0.018	25.394	-0.246	-0.246	0.000	0.000	0.000	0.000
50	A	67	GLN	0	0.003	0.010	19.611	-0.903	-0.903	0.000	0.000	0.000	0.000
51	A	68	THR	0	-0.039	-0.028	22.688	0.772	0.772	0.000	0.000	0.000	0.000
52	A	69	ILE	0	0.006	0.017	19.249	-0.525	-0.525	0.000	0.000	0.000	0.000
53	A	70	VAL	0	-0.005	0.002	22.772	0.679	0.679	0.000	0.000	0.000	0.000
54	A	71	ALA	0	0.008	-0.006	22.380	-0.641	-0.641	0.000	0.000	0.000	0.000
55	A	72	SER	0	-0.047	-0.035	23.328	0.664	0.664	0.000	0.000	0.000	0.000
56	A	73	GLN	0	0.019	-0.005	23.370	-0.422	-0.422	0.000	0.000	0.000	0.000
57	A	74	GLN	0	-0.004	-0.003	23.372	-0.332	-0.332	0.000	0.000	0.000	0.000
58	A	75	ARG	1	0.966	0.989	20.030	12.086	12.086	0.000	0.000	0.000	0.000
59	A	76	TRP	0	0.000	0.019	14.398	0.943	0.943	0.000	0.000	0.000	0.000
60	A	77	ALA	0	0.012	0.014	19.091	-0.635	-0.635	0.000	0.000	0.000	0.000
61	A	78	LEU	0	0.029	0.013	16.834	0.526	0.526	0.000	0.000	0.000	0.000
62	A	79	MET	0	-0.040	-0.020	19.198	0.048	0.048	0.000	0.000	0.000	0.000
63	A	80	THR	0	0.014	-0.015	19.277	-0.057	-0.057	0.000	0.000	0.000	0.000
64	A	81	GLU	-1	-0.876	-0.919	21.320	-11.674	-11.674	0.000	0.000	0.000	0.000
65	A	82	THR	0	-0.044	-0.028	20.448	-0.291	-0.291	0.000	0.000	0.000	0.000
66	A	83	PRO	0	-0.051	-0.015	23.818	0.097	0.097	0.000	0.000	0.000	0.000
67	A	84	ASP	-1	-0.914	-0.966	26.778	-10.452	-10.452	0.000	0.000	0.000	0.000
68	A	85	GLU	-1	-0.934	-0.962	21.898	-13.102	-13.102	0.000	0.000	0.000	0.000
69	A	86	GLU	-1	-0.894	-0.926	21.079	-13.887	-13.887	0.000	0.000	0.000	0.000
70	A	87	GLU	-1	-0.864	-0.941	15.762	-19.228	-19.228	0.000	0.000	0.000	0.000
71	A	88	LEU	0	-0.049	-0.039	16.668	-0.058	-0.058	0.000	0.000	0.000	0.000
72	A	89	ASP	-1	-0.847	-0.905	11.531	-25.757	-25.757	0.000	0.000	0.000	0.000
73	A	90	LEU	0	0.013	-0.013	10.402	-1.241	-1.241	0.000	0.000	0.000	0.000
74	A	91	GLN	0	0.002	0.007	6.063	-7.603	-7.603	0.000	0.000	0.000	0.000
75	A	92	PHE	0	-0.006	0.006	7.591	-3.466	-3.466	0.000	0.000	0.000	0.000
76	A	93	LEU	0	0.010	0.000	9.993	-0.847	-0.847	0.000	0.000	0.000	0.000
77	A	94	ALA	0	0.014	0.005	5.483	-0.031	-0.031	0.000	0.000	0.000	0.000
78	A	95	SER	0	-0.099	-0.043	6.362	-0.886	-0.886	0.000	0.000	0.000	0.000
79	A	96	ARG	1	0.858	0.925	7.165	28.271	28.271	0.000	0.000	0.000	0.000
80	A	97	MET	0	-0.034	-0.003	7.865	1.817	1.817	0.000	0.000	0.000	0.000
81	A	98	ASP	-1	-0.768	-0.845	7.511	-30.975	-30.975	0.000	0.000	0.000	0.000
85	A	102	LEU	0	-0.013	-0.003	6.291	2.477	2.477	0.000	0.000	0.000	0.000
86	A	103	ASP	-1	-0.766	-0.867	5.287	-33.060	-33.060	0.000	0.000	0.000	0.000
87	A	104	LEU	0	-0.004	-0.009	6.590	-2.678	-2.678	0.000	0.000	0.000	0.000
88	A	105	ILE	0	-0.024	-0.006	5.695	1.979	1.979	0.000	0.000	0.000	0.000
89	A	106	LEU	0	0.015	0.009	8.950	0.319	0.319	0.000	0.000	0.000	0.000
90	A	107	VAL	0	0.010	-0.001	10.956	-0.320	-0.320	0.000	0.000	0.000	0.000
91	A	108	GLU	-1	-0.837	-0.925	13.661	-13.972	-13.972	0.000	0.000	0.000	0.000
92	A	109	GLY	0	-0.002	0.000	17.375	0.228	0.228	0.000	0.000	0.000	0.000
93	A	110	PHE	0	0.018	-0.001	15.548	0.613	0.613	0.000	0.000	0.000	0.000
94	A	111	LYS	1	0.948	0.963	18.484	12.534	12.534	0.000	0.000	0.000	0.000
95	A	112	HIS	0	0.042	0.024	17.696	0.629	0.629	0.000	0.000	0.000	0.000
96	A	113	GLU	-1	-0.833	-0.914	15.104	-18.884	-18.884	0.000	0.000	0.000	0.000
97	A	114	GLU	-1	-0.874	-0.927	14.408	-16.896	-16.896	0.000	0.000	0.000	0.000
98	A	115	ILE	0	-0.033	-0.025	9.828	-1.863	-1.863	0.000	0.000	0.000	0.000
99	A	116	ALA	0	0.030	0.023	11.684	1.672	1.672	0.000	0.000	0.000	0.000
100	A	117	LYS	1	0.840	0.919	13.443	16.273	16.273	0.000	0.000	0.000	0.000
101	A	118	ILE	0	0.030	0.023	16.516	0.698	0.698	0.000	0.000	0.000	0.000
102	A	119	VAL	0	0.005	0.002	19.247	0.021	0.021	0.000	0.000	0.000	0.000
103	A	120	LEU	0	-0.056	-0.026	22.433	0.188	0.188	0.000	0.000	0.000	0.000
104	A	121	PHE	0	0.010	-0.004	25.205	0.129	0.129	0.000	0.000	0.000	0.000
105	A	122	ARG	1	0.832	0.899	28.838	10.521	10.521	0.000	0.000	0.000	0.000
106	A	123	ASP	-1	-0.893	-0.937	32.158	-8.491	-8.491	0.000	0.000	0.000	0.000
107	A	124	GLY	0	0.005	0.005	35.598	0.188	0.188	0.000	0.000	0.000	0.000
108	A	125	ALA	0	-0.062	-0.031	32.834	0.133	0.133	0.000	0.000	0.000	0.000
109	A	126	GLY	0	-0.027	-0.010	34.543	-0.133	-0.133	0.000	0.000	0.000	0.000
110	A	127	HIS	1	0.837	0.913	33.115	9.537	9.537	0.000	0.000	0.000	0.000
111	A	128	ARG	1	0.952	0.997	35.418	7.903	7.903	0.000	0.000	0.000	0.000
112	A	129	PRO	0	0.034	0.020	32.976	-0.264	-0.264	0.000	0.000	0.000	0.000
113	A	130	GLU	-1	-0.872	-0.958	32.702	-8.770	-8.770	0.000	0.000	0.000	0.000
114	A	131	GLU	-1	-0.914	-0.966	33.202	-9.011	-9.011	0.000	0.000	0.000	0.000
115	A	132	LEU	0	-0.049	-0.020	27.521	-0.311	-0.311	0.000	0.000	0.000	0.000
116	A	133	VAL	0	-0.023	-0.008	25.430	0.087	0.087	0.000	0.000	0.000	0.000
117	A	134	ILE	0	0.003	0.004	23.773	-0.543	-0.543	0.000	0.000	0.000	0.000
118	A	135	ASP	-1	-0.796	-0.893	19.787	-15.483	-15.483	0.000	0.000	0.000	0.000
119	A	136	ARG	1	0.914	0.935	17.414	16.084	16.084	0.000	0.000	0.000	0.000
120	A	137	HIS	0	-0.073	-0.027	15.492	-1.002	-1.002	0.000	0.000	0.000	0.000
121	A	138	VAL	0	-0.068	-0.030	16.618	-0.971	-0.971	0.000	0.000	0.000	0.000
122	A	139	ILE	0	-0.013	-0.004	14.852	0.373	0.373	0.000	0.000	0.000	0.000
123	A	140	ALA	0	-0.010	-0.010	18.630	0.476	0.476	0.000	0.000	0.000	0.000
124	A	141	VAL	0	0.000	0.004	21.513	-0.245	-0.245	0.000	0.000	0.000	0.000
125	A	142	ALA	0	0.002	0.009	23.839	0.243	0.243	0.000	0.000	0.000	0.000
126	A	143	SER	0	0.009	-0.032	25.594	0.152	0.152	0.000	0.000	0.000	0.000
127	A	144	ASP	-1	-0.835	-0.918	29.364	-9.716	-9.716	0.000	0.000	0.000	0.000
128	A	145	VAL	0	-0.007	0.010	32.651	0.331	0.331	0.000	0.000	0.000	0.000
129	A	146	PRO	0	0.002	-0.001	32.785	-0.345	-0.345	0.000	0.000	0.000	0.000
130	A	147	LEU	0	-0.007	0.007	29.256	0.151	0.151	0.000	0.000	0.000	0.000
131	A	148	ASN	0	-0.031	-0.016	31.915	-0.122	-0.122	0.000	0.000	0.000	0.000
132	A	149	LEU	0	-0.012	-0.016	26.690	-0.094	-0.094	0.000	0.000	0.000	0.000
133	A	150	ASP	-1	-0.900	-0.931	26.538	-10.800	-10.800	0.000	0.000	0.000	0.000
134	A	151	VAL	0	-0.041	-0.024	22.384	-0.477	-0.477	0.000	0.000	0.000	0.000
135	A	152	ALA	0	-0.001	0.003	22.109	0.481	0.481	0.000	0.000	0.000	0.000
136	A	153	LEU	0	-0.003	0.005	24.036	-0.129	-0.129	0.000	0.000	0.000	0.000
137	A	154	LEU	0	-0.010	-0.011	21.663	-0.024	-0.024	0.000	0.000	0.000	0.000
138	A	155	ASP	-1	-0.796	-0.896	26.362	-10.190	-10.190	0.000	0.000	0.000	0.000
139	A	156	ILE	0	-0.079	-0.044	26.138	-0.424	-0.424	0.000	0.000	0.000	0.000
140	A	157	ASN	0	-0.065	-0.044	27.729	-0.159	-0.159	0.000	0.000	0.000	0.000
141	A	158	ASP	-1	-0.842	-0.906	27.621	-11.551	-11.551	0.000	0.000	0.000	0.000
142	A	159	VAL	0	-0.046	-0.042	23.658	-0.455	-0.455	0.000	0.000	0.000	0.000
143	A	160	GLU	-1	-0.870	-0.919	23.234	-13.732	-13.732	0.000	0.000	0.000	0.000
144	A	161	GLY	0	0.079	0.050	22.976	-0.550	-0.550	0.000	0.000	0.000	0.000
145	A	162	LEU	0	-0.077	-0.041	20.513	-0.567	-0.567	0.000	0.000	0.000	0.000
146	A	163	ALA	0	-0.018	-0.026	19.111	-0.996	-0.996	0.000	0.000	0.000	0.000
147	A	164	ASP	-1	-0.826	-0.888	18.380	-14.581	-14.581	0.000	0.000	0.000	0.000
148	A	165	PHE	0	-0.008	0.000	18.176	-0.951	-0.951	0.000	0.000	0.000	0.000
149	A	166	VAL	0	-0.012	-0.016	14.415	-1.008	-1.008	0.000	0.000	0.000	0.000
150	A	167	VAL	0	0.011	0.006	13.992	-1.996	-1.996	0.000	0.000	0.000	0.000
151	A	168	GLU	-1	-0.874	-0.953	13.889	-17.810	-17.810	0.000	0.000	0.000	0.000
152	A	169	TRP	0	-0.048	-0.023	9.863	-1.332	-1.332	0.000	0.000	0.000	0.000
153	A	170	MET	0	-0.039	-0.019	8.850	-0.948	-0.948	0.000	0.000	0.000	0.000
154	A	171	GLN	0	-0.004	0.011	9.789	-1.591	-1.591	0.000	0.000	0.000	0.000
155	A	172	LYS	1	0.865	0.945	12.039	23.646	23.646	0.000	0.000	0.000	0.000
156	A	173	GLN	0	-0.061	-0.037	7.985	3.390	3.390	0.000	0.000	0.000	0.000
157	A	174	ASN	0	-0.046	-0.030	6.693	-4.728	-4.728	0.000	0.000	0.000	0.000
158	A	175	GLY	-1	-0.952	-0.951	5.041	-43.426	-43.426	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:MET)