FMO DATABASE

FMODB ID: 97MQ2

Calculation Name: 3NPP-A-Xray547

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3NPP

Chain ID: A

ChEMBL ID:

UniProt ID: P54940

Base Structure: X-ray

Registration Date: 2025-10-04

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	87
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-591854.822581
FMO2-HF: Nuclear repulsion	557111.34193
FMO2-HF: Total energy	-34743.480652
FMO2-MP2: Total energy	-34846.541094

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:0:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

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.
5.379	6.908	0.021	-0.749	-0.8	-0.004

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.888 / q_NPA : 0.933

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	31	PHE	0	0.057	0.031	3.625	-0.560	0.969	0.021	-0.749	-0.800	-0.004
4	A	32	ASN	0	-0.017	-0.010	6.650	2.792	2.792	0.000	0.000	0.000	0.000
5	A	33	PRO	0	0.072	0.037	10.424	-0.192	-0.192	0.000	0.000	0.000	0.000
6	A	34	PHE	0	-0.001	-0.001	13.501	1.293	1.293	0.000	0.000	0.000	0.000
7	A	35	ILE	0	-0.017	-0.016	13.838	-0.313	-0.313	0.000	0.000	0.000	0.000
8	A	36	HIS	0	0.034	0.031	16.177	0.958	0.958	0.000	0.000	0.000	0.000
9	A	37	GLN	0	-0.029	-0.028	17.947	-0.837	-0.837	0.000	0.000	0.000	0.000
10	A	38	GLN	0	-0.043	-0.020	19.513	0.838	0.838	0.000	0.000	0.000	0.000
11	A	39	ASP	-1	-0.800	-0.895	22.684	-11.878	-11.878	0.000	0.000	0.000	0.000
12	A	40	VAL	0	-0.016	-0.023	23.744	0.167	0.167	0.000	0.000	0.000	0.000
13	A	41	TYR	0	0.022	0.008	26.741	0.011	0.011	0.000	0.000	0.000	0.000
14	A	42	VAL	0	0.018	0.002	29.019	-0.092	-0.092	0.000	0.000	0.000	0.000
15	A	43	GLN	0	0.065	0.026	31.877	0.350	0.350	0.000	0.000	0.000	0.000
16	A	44	ILE	0	-0.037	0.002	33.200	-0.205	-0.205	0.000	0.000	0.000	0.000
17	A	45	ASP	-1	-0.778	-0.875	35.256	-8.549	-8.549	0.000	0.000	0.000	0.000
18	A	46	ARG	1	0.772	0.863	33.314	9.030	9.030	0.000	0.000	0.000	0.000
19	A	47	ASP	-1	-0.883	-0.931	35.980	-7.975	-7.975	0.000	0.000	0.000	0.000
20	A	48	GLY	0	0.024	0.010	32.970	-0.266	-0.266	0.000	0.000	0.000	0.000
21	A	49	ARG	1	0.904	0.955	28.677	10.629	10.629	0.000	0.000	0.000	0.000
22	A	50	HIS	0	0.007	0.007	31.681	-0.268	-0.268	0.000	0.000	0.000	0.000
23	A	51	LEU	0	0.013	0.000	26.134	-0.158	-0.158	0.000	0.000	0.000	0.000
24	A	52	SER	0	-0.026	0.016	30.571	0.139	0.139	0.000	0.000	0.000	0.000
25	A	53	PRO	0	-0.033	-0.029	29.563	-0.264	-0.264	0.000	0.000	0.000	0.000
26	A	54	GLY	0	0.045	-0.005	31.620	-0.153	-0.153	0.000	0.000	0.000	0.000
27	A	55	GLY	0	0.004	0.021	30.038	0.043	0.043	0.000	0.000	0.000	0.000
28	A	56	THR	0	-0.052	-0.028	30.927	0.339	0.339	0.000	0.000	0.000	0.000
29	A	57	GLU	-1	-0.929	-0.968	25.782	-11.872	-11.872	0.000	0.000	0.000	0.000
30	A	58	TYR	0	0.059	0.020	28.097	0.498	0.498	0.000	0.000	0.000	0.000
31	A	59	THR	0	0.030	0.029	25.582	-0.608	-0.608	0.000	0.000	0.000	0.000
32	A	60	LEU	0	-0.053	-0.020	27.510	0.393	0.393	0.000	0.000	0.000	0.000
33	A	61	ASP	-1	-0.813	-0.896	27.735	-10.749	-10.749	0.000	0.000	0.000	0.000
34	A	62	GLY	0	0.000	-0.010	28.559	0.295	0.295	0.000	0.000	0.000	0.000
35	A	63	TYR	0	-0.023	-0.015	28.708	-0.160	-0.160	0.000	0.000	0.000	0.000
36	A	64	ASN	0	0.034	0.043	24.033	0.560	0.560	0.000	0.000	0.000	0.000
37	A	65	ALA	0	0.054	0.024	27.149	0.376	0.376	0.000	0.000	0.000	0.000
38	A	66	SER	0	-0.086	-0.045	27.162	0.164	0.164	0.000	0.000	0.000	0.000
39	A	67	GLY	0	0.022	0.008	29.432	0.203	0.203	0.000	0.000	0.000	0.000
40	A	68	LYS	1	0.899	0.959	22.225	13.520	13.520	0.000	0.000	0.000	0.000
41	A	69	LYS	1	0.881	0.935	28.000	10.008	10.008	0.000	0.000	0.000	0.000
42	A	70	GLU	-1	-0.940	-0.982	23.095	-13.517	-13.517	0.000	0.000	0.000	0.000
43	A	71	GLU	-1	-0.929	-0.958	23.634	-12.197	-12.197	0.000	0.000	0.000	0.000
44	A	72	VAL	0	-0.042	-0.030	22.844	-0.648	-0.648	0.000	0.000	0.000	0.000
45	A	73	THR	0	0.028	0.008	22.145	0.351	0.351	0.000	0.000	0.000	0.000
46	A	74	PHE	0	-0.052	-0.036	22.890	-0.476	-0.476	0.000	0.000	0.000	0.000
47	A	75	PHE	0	0.048	0.012	22.660	0.291	0.291	0.000	0.000	0.000	0.000
48	A	76	ALA	0	-0.014	0.008	27.130	-0.073	-0.073	0.000	0.000	0.000	0.000
49	A	77	GLY	0	-0.007	-0.010	30.235	0.017	0.017	0.000	0.000	0.000	0.000
50	A	78	LYS	1	0.946	0.961	32.204	8.721	8.721	0.000	0.000	0.000	0.000
51	A	79	GLU	-1	-0.901	-0.931	34.226	-8.367	-8.367	0.000	0.000	0.000	0.000
52	A	80	LEU	0	-0.049	-0.030	32.116	0.180	0.180	0.000	0.000	0.000	0.000
53	A	81	ARG	1	0.942	0.970	36.550	7.253	7.253	0.000	0.000	0.000	0.000
54	A	82	LYS	1	0.954	0.965	38.665	7.659	7.659	0.000	0.000	0.000	0.000
55	A	83	ASN	0	-0.038	-0.037	39.317	0.070	0.070	0.000	0.000	0.000	0.000
56	A	84	ALA	0	-0.004	0.025	37.581	0.100	0.100	0.000	0.000	0.000	0.000
57	A	85	TYR	0	0.029	0.010	35.898	-0.156	-0.156	0.000	0.000	0.000	0.000
58	A	86	LEU	0	-0.009	-0.010	30.371	0.021	0.021	0.000	0.000	0.000	0.000
59	A	87	LYS	1	0.842	0.948	28.685	10.368	10.368	0.000	0.000	0.000	0.000
60	A	88	VAL	0	-0.001	-0.014	24.406	-0.028	-0.028	0.000	0.000	0.000	0.000
61	A	89	LYS	1	0.908	0.979	22.992	12.206	12.206	0.000	0.000	0.000	0.000
62	A	90	ALA	0	0.033	0.005	19.141	-0.239	-0.239	0.000	0.000	0.000	0.000
63	A	91	LYS	1	0.841	0.912	16.476	15.302	15.302	0.000	0.000	0.000	0.000
64	A	92	GLY	0	-0.012	-0.015	14.474	-1.146	-1.146	0.000	0.000	0.000	0.000
65	A	93	LYS	1	0.917	0.946	14.032	20.233	20.233	0.000	0.000	0.000	0.000
66	A	94	TYR	0	0.004	0.020	14.559	0.247	0.247	0.000	0.000	0.000	0.000
67	A	95	VAL	0	0.041	0.016	16.500	0.363	0.363	0.000	0.000	0.000	0.000
68	A	96	GLU	-1	-0.862	-0.917	19.332	-15.155	-15.155	0.000	0.000	0.000	0.000
69	A	97	THR	0	-0.011	-0.016	21.835	0.317	0.317	0.000	0.000	0.000	0.000
70	A	98	TRP	0	-0.006	0.000	25.646	0.044	0.044	0.000	0.000	0.000	0.000
71	A	99	GLU	-1	-0.871	-0.937	28.616	-9.657	-9.657	0.000	0.000	0.000	0.000
72	A	100	GLU	-1	-0.936	-0.963	31.994	-7.995	-7.995	0.000	0.000	0.000	0.000
73	A	101	VAL	0	-0.027	-0.009	33.898	-0.012	-0.012	0.000	0.000	0.000	0.000
74	A	102	LYS	1	0.901	0.953	36.634	7.654	7.654	0.000	0.000	0.000	0.000
75	A	103	PHE	0	0.000	-0.001	38.623	-0.196	-0.196	0.000	0.000	0.000	0.000
76	A	104	GLU	-1	-0.864	-0.959	39.393	-7.460	-7.460	0.000	0.000	0.000	0.000
77	A	105	ASP	-1	-0.885	-0.935	38.042	-7.802	-7.802	0.000	0.000	0.000	0.000
78	A	106	MET	0	-0.106	-0.031	35.198	-0.428	-0.428	0.000	0.000	0.000	0.000
79	A	107	PRO	0	0.031	0.018	32.211	0.193	0.193	0.000	0.000	0.000	0.000
80	A	108	ASP	-1	-0.802	-0.885	35.551	-7.941	-7.941	0.000	0.000	0.000	0.000
81	A	109	SER	0	-0.055	-0.040	34.440	0.072	0.072	0.000	0.000	0.000	0.000
82	A	110	VAL	0	-0.037	-0.020	32.091	-0.116	-0.116	0.000	0.000	0.000	0.000
83	A	111	GLN	0	0.010	0.002	34.887	0.233	0.233	0.000	0.000	0.000	0.000
84	A	112	SER	0	-0.074	-0.052	38.134	0.218	0.218	0.000	0.000	0.000	0.000
85	A	113	LYS	1	0.813	0.900	32.644	9.481	9.481	0.000	0.000	0.000	0.000
86	A	114	LEU	0	-0.035	-0.009	33.196	-0.146	-0.146	0.000	0.000	0.000	0.000
87	A	115	LYS	0	0.002	0.021	37.414	0.033	0.033	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)