FMO DATABASE

FMODB ID: 3KGML

Calculation Name: 1EQ3-A-Other547

Preferred Name: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 2

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1EQ3

Chain ID: A

ChEMBL ID: CHEMBL4923

UniProt ID: Q9Y237

Base Structure: SolutionNMR

Registration Date: 2025-09-02

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	96
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-682646.35639
FMO2-HF: Nuclear repulsion	643838.356478
FMO2-HF: Total energy	-38807.999912
FMO2-MP2: Total energy	-38916.337134

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:36:ASN)

Summations of interaction energy for fragment #1(A:36:ASN)

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.
-15.472	-7.424	11.936	-9.998	-9.984	-0.085

Interaction energy analysis for fragmet #1(A:36:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.778 / q_NPA : 0.872

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	38	VAL	0	0.021	0.025	3.847	-6.009	-4.004	0.003	-1.025	-0.983	0.000
51	A	86	THR	0	0.021	-0.005	2.577	-6.200	-4.177	1.121	-1.037	-2.107	0.012
52	A	87	ARG	1	0.946	0.976	3.894	24.173	24.287	0.001	0.015	-0.129	0.000
96	A	131	LYS	0	0.176	0.109	1.940	-67.809	-63.903	10.811	-7.951	-6.765	-0.097
4	A	39	LYS	1	0.822	0.912	6.858	27.004	27.004	0.000	0.000	0.000	0.000
5	A	40	VAL	0	0.001	-0.003	9.744	1.183	1.183	0.000	0.000	0.000	0.000
6	A	41	ARG	1	0.850	0.905	12.960	18.289	18.289	0.000	0.000	0.000	0.000
7	A	42	HIS	0	-0.043	-0.048	16.568	0.326	0.326	0.000	0.000	0.000	0.000
8	A	43	ILE	0	0.035	0.039	19.533	0.341	0.341	0.000	0.000	0.000	0.000
9	A	44	LEU	0	-0.051	-0.016	22.291	-0.189	-0.189	0.000	0.000	0.000	0.000
10	A	45	CYS	0	0.049	0.039	24.693	0.502	0.502	0.000	0.000	0.000	0.000
11	A	46	GLU	-1	-0.826	-0.909	28.399	-10.515	-10.515	0.000	0.000	0.000	0.000
12	A	47	LYS	1	0.910	0.957	30.668	9.666	9.666	0.000	0.000	0.000	0.000
13	A	48	HIS	0	0.075	0.019	32.005	0.269	0.269	0.000	0.000	0.000	0.000
14	A	49	GLY	0	-0.030	-0.011	33.761	0.191	0.191	0.000	0.000	0.000	0.000
15	A	50	LYS	1	0.903	0.987	29.937	10.220	10.220	0.000	0.000	0.000	0.000
16	A	51	ILE	0	-0.051	-0.046	28.373	-0.206	-0.206	0.000	0.000	0.000	0.000
17	A	52	MET	0	0.062	0.025	30.157	-0.280	-0.280	0.000	0.000	0.000	0.000
18	A	53	GLU	-1	-0.823	-0.915	32.060	-8.940	-8.940	0.000	0.000	0.000	0.000
19	A	54	ALA	0	-0.010	-0.009	28.721	-0.082	-0.082	0.000	0.000	0.000	0.000
20	A	55	MET	0	0.032	0.015	27.349	-0.171	-0.171	0.000	0.000	0.000	0.000
21	A	56	GLU	-1	-0.932	-0.955	28.369	-9.059	-9.059	0.000	0.000	0.000	0.000
22	A	57	LYS	1	0.865	0.929	31.173	8.934	8.934	0.000	0.000	0.000	0.000
23	A	58	LEU	0	0.003	0.006	23.454	0.031	0.031	0.000	0.000	0.000	0.000
24	A	59	LYS	1	0.857	0.936	27.467	9.610	9.610	0.000	0.000	0.000	0.000
25	A	60	SER	0	0.047	0.008	24.496	-0.306	-0.306	0.000	0.000	0.000	0.000
26	A	61	GLY	0	0.031	0.005	23.055	0.014	0.014	0.000	0.000	0.000	0.000
27	A	62	MET	0	-0.034	-0.010	23.660	0.161	0.161	0.000	0.000	0.000	0.000
28	A	63	ARG	1	0.896	0.950	27.295	9.733	9.733	0.000	0.000	0.000	0.000
29	A	64	PHE	0	0.003	0.017	20.309	0.051	0.051	0.000	0.000	0.000	0.000
30	A	65	ASN	0	0.036	0.007	25.047	-0.240	-0.240	0.000	0.000	0.000	0.000
31	A	66	GLU	-1	-0.854	-0.919	26.873	-9.488	-9.488	0.000	0.000	0.000	0.000
32	A	67	VAL	0	-0.010	-0.022	27.403	0.194	0.194	0.000	0.000	0.000	0.000
33	A	68	ALA	0	0.016	0.002	24.691	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	69	ALA	0	-0.031	-0.015	26.599	0.112	0.112	0.000	0.000	0.000	0.000
35	A	70	GLN	0	-0.003	-0.009	29.562	0.121	0.121	0.000	0.000	0.000	0.000
36	A	71	TYR	0	-0.043	-0.022	27.901	0.169	0.169	0.000	0.000	0.000	0.000
37	A	72	SER	0	0.013	0.008	26.479	-0.564	-0.564	0.000	0.000	0.000	0.000
38	A	73	GLU	-1	-0.896	-0.946	27.511	-9.671	-9.671	0.000	0.000	0.000	0.000
39	A	74	ASP	-1	-0.889	-0.941	22.324	-13.097	-13.097	0.000	0.000	0.000	0.000
40	A	75	LYS	1	0.990	0.997	23.868	10.900	10.900	0.000	0.000	0.000	0.000
41	A	76	ALA	0	-0.008	-0.003	24.620	-0.144	-0.144	0.000	0.000	0.000	0.000
42	A	77	ARG	1	0.895	0.950	21.215	12.728	12.728	0.000	0.000	0.000	0.000
43	A	78	GLN	0	-0.053	-0.044	18.549	-1.405	-1.405	0.000	0.000	0.000	0.000
44	A	79	GLY	0	0.044	0.032	19.123	0.589	0.589	0.000	0.000	0.000	0.000
45	A	80	GLY	0	0.043	0.041	20.506	0.293	0.293	0.000	0.000	0.000	0.000
46	A	81	ASP	-1	-0.906	-0.949	15.939	-17.679	-17.679	0.000	0.000	0.000	0.000
47	A	82	LEU	0	-0.008	-0.006	12.125	0.486	0.486	0.000	0.000	0.000	0.000
48	A	83	GLY	0	0.002	0.011	11.813	-0.883	-0.883	0.000	0.000	0.000	0.000
49	A	84	TRP	0	-0.007	-0.016	5.082	-1.197	-1.197	0.000	0.000	0.000	0.000
50	A	85	MET	0	0.004	0.013	6.997	1.391	1.391	0.000	0.000	0.000	0.000
53	A	88	GLY	0	0.081	0.053	7.164	0.620	0.620	0.000	0.000	0.000	0.000
54	A	89	SER	0	-0.039	-0.035	10.143	0.359	0.359	0.000	0.000	0.000	0.000
55	A	90	MET	0	-0.004	0.007	13.522	0.383	0.383	0.000	0.000	0.000	0.000
56	A	91	VAL	0	-0.007	-0.009	16.686	0.860	0.860	0.000	0.000	0.000	0.000
57	A	92	GLY	0	0.101	0.046	17.259	0.336	0.336	0.000	0.000	0.000	0.000
58	A	93	PRO	0	-0.012	0.013	16.728	-0.900	-0.900	0.000	0.000	0.000	0.000
59	A	94	PHE	0	-0.023	-0.018	15.649	-0.453	-0.453	0.000	0.000	0.000	0.000
60	A	95	GLN	0	-0.025	-0.016	10.595	0.864	0.864	0.000	0.000	0.000	0.000
61	A	96	GLU	-1	-0.869	-0.937	12.477	-22.505	-22.505	0.000	0.000	0.000	0.000
62	A	97	ALA	0	-0.020	-0.017	12.937	-1.131	-1.131	0.000	0.000	0.000	0.000
63	A	98	ALA	0	-0.023	-0.008	11.911	-0.469	-0.469	0.000	0.000	0.000	0.000
64	A	99	PHE	0	-0.074	-0.048	5.663	-3.003	-3.003	0.000	0.000	0.000	0.000
65	A	100	ALA	0	-0.026	-0.003	9.086	-1.950	-1.950	0.000	0.000	0.000	0.000
66	A	101	LEU	0	-0.009	0.008	11.535	1.665	1.665	0.000	0.000	0.000	0.000
67	A	102	PRO	0	-0.020	-0.005	12.338	-1.167	-1.167	0.000	0.000	0.000	0.000
68	A	103	VAL	0	-0.010	-0.023	11.796	0.063	0.063	0.000	0.000	0.000	0.000
69	A	104	SER	0	-0.019	-0.001	14.478	0.434	0.434	0.000	0.000	0.000	0.000
70	A	105	GLY	0	0.017	-0.012	18.319	0.355	0.355	0.000	0.000	0.000	0.000
71	A	106	MET	0	-0.033	-0.016	20.312	-0.297	-0.297	0.000	0.000	0.000	0.000
72	A	107	ASP	-1	-0.876	-0.939	21.741	-13.500	-13.500	0.000	0.000	0.000	0.000
73	A	108	LYS	1	0.912	0.956	17.288	14.907	14.907	0.000	0.000	0.000	0.000
74	A	109	PRO	0	-0.049	-0.007	15.338	-1.194	-1.194	0.000	0.000	0.000	0.000
75	A	110	VAL	0	0.048	0.014	16.044	-0.395	-0.395	0.000	0.000	0.000	0.000
76	A	111	PHE	0	0.032	0.017	16.882	-0.937	-0.937	0.000	0.000	0.000	0.000
77	A	112	THR	0	-0.041	-0.024	16.836	-0.261	-0.261	0.000	0.000	0.000	0.000
78	A	113	ASP	-1	-0.818	-0.875	19.255	-12.747	-12.747	0.000	0.000	0.000	0.000
79	A	114	PRO	0	-0.088	-0.074	22.793	-0.134	-0.134	0.000	0.000	0.000	0.000
80	A	115	PRO	0	0.035	0.027	22.579	-0.398	-0.398	0.000	0.000	0.000	0.000
81	A	116	VAL	0	0.001	0.004	20.027	0.442	0.442	0.000	0.000	0.000	0.000
82	A	117	LYS	1	0.951	0.970	23.260	10.456	10.456	0.000	0.000	0.000	0.000
83	A	118	THR	0	-0.064	-0.037	23.354	-0.303	-0.303	0.000	0.000	0.000	0.000
84	A	119	LYS	1	0.950	0.957	26.806	10.349	10.349	0.000	0.000	0.000	0.000
85	A	120	PHE	0	0.052	0.037	22.277	0.320	0.320	0.000	0.000	0.000	0.000
86	A	121	GLY	0	0.126	0.055	26.367	-0.328	-0.328	0.000	0.000	0.000	0.000
87	A	122	TYR	0	-0.127	-0.065	26.282	-0.073	-0.073	0.000	0.000	0.000	0.000
88	A	123	HIS	1	0.872	0.924	21.516	13.062	13.062	0.000	0.000	0.000	0.000
89	A	124	ILE	0	0.033	0.026	21.712	-0.001	-0.001	0.000	0.000	0.000	0.000
90	A	125	ILE	0	-0.012	-0.002	16.171	-0.014	-0.014	0.000	0.000	0.000	0.000
91	A	126	MET	0	-0.007	0.008	15.674	0.204	0.204	0.000	0.000	0.000	0.000
92	A	127	VAL	0	-0.018	-0.011	10.536	-1.008	-1.008	0.000	0.000	0.000	0.000
93	A	128	GLU	-1	-0.832	-0.904	12.287	-20.329	-20.329	0.000	0.000	0.000	0.000
94	A	129	GLY	0	-0.002	-0.008	8.496	0.128	0.128	0.000	0.000	0.000	0.000
95	A	130	ARG	1	0.931	0.968	6.456	28.675	28.675	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:36:ASN)