FMO DATABASE

FMODB ID: Y16M2

Calculation Name: 2NXP-A-Xray547

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2NXP

Chain ID: A

ChEMBL ID:

UniProt ID: Q15542

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	149
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1619139.380724
FMO2-HF: Nuclear repulsion	1555470.66764
FMO2-HF: Total energy	-63668.713084
FMO2-MP2: Total energy	-63852.775405

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:195:GLN)

Summations of interaction energy for fragment #1(A:195:GLN)

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.
-139.895	-138.319	13.07	-5.508	-9.137	0.027

Interaction energy analysis for fragmet #1(A:195:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.866 / q_NPA : 0.928

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	197	ASP	-1	-0.748	-0.843	2.613	-45.805	-43.516	1.408	-1.533	-2.164	-0.014
4	A	198	VAL	0	0.086	0.029	5.006	2.095	2.204	-0.001	-0.002	-0.105	0.000
104	A	298	LEU	0	-0.076	-0.042	2.356	-4.217	-2.911	1.519	-0.580	-2.245	0.000
105	A	299	ASP	-1	-0.935	-0.949	4.422	-25.297	-25.041	-0.001	-0.014	-0.241	0.000
107	A	301	ARG	1	0.859	0.948	2.005	17.973	15.589	10.145	-3.379	-4.382	0.041
5	A	199	SER	0	-0.099	-0.063	7.248	3.843	3.843	0.000	0.000	0.000	0.000
6	A	200	ALA	0	0.026	-0.002	6.810	2.050	2.050	0.000	0.000	0.000	0.000
7	A	201	VAL	0	-0.048	-0.010	4.803	1.746	1.746	0.000	0.000	0.000	0.000
8	A	202	LEU	0	-0.021	-0.020	7.498	2.750	2.750	0.000	0.000	0.000	0.000
9	A	203	SER	0	-0.112	-0.059	10.463	2.307	2.307	0.000	0.000	0.000	0.000
10	A	204	ALA	0	0.054	0.027	10.895	1.443	1.443	0.000	0.000	0.000	0.000
11	A	205	TYR	0	0.011	0.005	10.784	0.658	0.658	0.000	0.000	0.000	0.000
12	A	206	ASN	0	-0.027	-0.026	15.315	1.359	1.359	0.000	0.000	0.000	0.000
13	A	207	GLN	0	0.012	0.018	17.908	0.964	0.964	0.000	0.000	0.000	0.000
14	A	208	GLN	0	0.021	0.030	20.029	0.371	0.371	0.000	0.000	0.000	0.000
15	A	209	GLY	0	0.053	0.028	22.059	0.274	0.274	0.000	0.000	0.000	0.000
16	A	210	ASP	-1	-0.858	-0.915	24.976	-9.541	-9.541	0.000	0.000	0.000	0.000
17	A	211	PRO	0	-0.009	-0.022	25.859	-0.078	-0.078	0.000	0.000	0.000	0.000
18	A	212	THR	0	-0.076	-0.069	26.952	0.071	0.071	0.000	0.000	0.000	0.000
19	A	213	MET	0	0.019	0.024	29.270	0.236	0.236	0.000	0.000	0.000	0.000
20	A	214	TYR	0	-0.036	-0.049	21.302	0.049	0.049	0.000	0.000	0.000	0.000
21	A	215	GLU	-1	-0.754	-0.858	26.111	-9.776	-9.776	0.000	0.000	0.000	0.000
22	A	216	GLU	-1	-0.840	-0.914	28.253	-9.121	-9.121	0.000	0.000	0.000	0.000
23	A	217	TYR	0	-0.051	-0.014	25.919	0.129	0.129	0.000	0.000	0.000	0.000
24	A	218	TYR	0	0.010	-0.004	20.827	0.163	0.163	0.000	0.000	0.000	0.000
25	A	219	SER	0	-0.009	-0.028	25.851	0.088	0.088	0.000	0.000	0.000	0.000
26	A	220	GLY	0	-0.037	-0.009	29.228	0.217	0.217	0.000	0.000	0.000	0.000
27	A	221	LEU	0	-0.025	-0.014	22.938	0.145	0.145	0.000	0.000	0.000	0.000
28	A	222	LYS	1	0.824	0.907	27.121	9.654	9.654	0.000	0.000	0.000	0.000
29	A	223	HIS	0	0.026	0.014	28.064	0.088	0.088	0.000	0.000	0.000	0.000
30	A	224	PHE	0	0.025	0.007	27.360	0.149	0.149	0.000	0.000	0.000	0.000
31	A	225	ILE	0	-0.008	0.008	24.448	0.130	0.130	0.000	0.000	0.000	0.000
32	A	226	GLU	-1	-0.882	-0.942	28.770	-9.194	-9.194	0.000	0.000	0.000	0.000
33	A	227	CYS	0	-0.074	-0.038	31.186	0.315	0.315	0.000	0.000	0.000	0.000
34	A	228	SER	0	-0.073	-0.030	30.533	0.126	0.126	0.000	0.000	0.000	0.000
35	A	229	LEU	0	0.003	-0.004	32.667	0.083	0.083	0.000	0.000	0.000	0.000
36	A	230	ASP	-1	-0.866	-0.937	31.890	-8.662	-8.662	0.000	0.000	0.000	0.000
37	A	231	CYS	0	-0.054	-0.015	30.224	-0.194	-0.194	0.000	0.000	0.000	0.000
38	A	232	HIS	0	0.018	-0.018	28.560	-0.238	-0.238	0.000	0.000	0.000	0.000
39	A	233	ARG	1	0.948	0.984	27.371	8.808	8.808	0.000	0.000	0.000	0.000
40	A	234	ALA	0	-0.021	0.003	26.457	-0.338	-0.338	0.000	0.000	0.000	0.000
41	A	235	GLU	-1	-0.782	-0.820	23.779	-11.573	-11.573	0.000	0.000	0.000	0.000
42	A	236	LEU	0	0.016	-0.006	22.541	-0.573	-0.573	0.000	0.000	0.000	0.000
43	A	237	SER	0	-0.008	-0.020	22.625	-0.216	-0.216	0.000	0.000	0.000	0.000
44	A	238	GLN	0	-0.055	-0.043	18.324	-0.831	-0.831	0.000	0.000	0.000	0.000
45	A	239	LEU	0	-0.011	-0.011	17.827	-0.651	-0.651	0.000	0.000	0.000	0.000
46	A	240	PHE	0	0.019	0.016	18.657	-0.316	-0.316	0.000	0.000	0.000	0.000
47	A	241	TYR	0	0.103	0.066	12.780	-0.368	-0.368	0.000	0.000	0.000	0.000
48	A	242	PRO	0	-0.001	-0.001	13.158	-0.337	-0.337	0.000	0.000	0.000	0.000
49	A	243	LEU	0	0.013	0.007	14.621	-0.320	-0.320	0.000	0.000	0.000	0.000
50	A	244	PHE	0	-0.011	0.009	17.590	0.057	0.057	0.000	0.000	0.000	0.000
51	A	245	VAL	0	0.012	0.000	11.969	0.055	0.055	0.000	0.000	0.000	0.000
52	A	246	HIS	0	-0.001	0.011	14.195	-1.002	-1.002	0.000	0.000	0.000	0.000
53	A	247	MET	0	-0.033	-0.014	15.324	0.184	0.184	0.000	0.000	0.000	0.000
54	A	248	TYR	0	0.001	-0.003	17.033	0.570	0.570	0.000	0.000	0.000	0.000
55	A	249	LEU	0	0.021	0.004	12.446	0.183	0.183	0.000	0.000	0.000	0.000
56	A	250	GLU	-1	-0.785	-0.853	16.600	-14.613	-14.613	0.000	0.000	0.000	0.000
57	A	251	LEU	0	-0.023	0.006	18.164	0.463	0.463	0.000	0.000	0.000	0.000
58	A	252	VAL	0	0.008	0.014	18.653	0.332	0.332	0.000	0.000	0.000	0.000
59	A	253	TYR	0	0.017	-0.006	15.574	-0.120	-0.120	0.000	0.000	0.000	0.000
60	A	254	ASN	0	-0.129	-0.079	18.710	0.295	0.295	0.000	0.000	0.000	0.000
61	A	255	GLN	0	-0.042	-0.026	21.961	0.299	0.299	0.000	0.000	0.000	0.000
62	A	256	HIS	1	0.877	0.952	23.754	11.765	11.765	0.000	0.000	0.000	0.000
63	A	257	GLU	-1	-0.862	-0.943	24.544	-11.287	-11.287	0.000	0.000	0.000	0.000
64	A	258	ASN	0	-0.046	-0.019	25.864	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	259	GLU	-1	-0.844	-0.934	26.596	-10.135	-10.135	0.000	0.000	0.000	0.000
66	A	260	ALA	0	0.008	0.005	22.080	-0.075	-0.075	0.000	0.000	0.000	0.000
67	A	261	LYS	1	0.799	0.889	23.732	9.548	9.548	0.000	0.000	0.000	0.000
68	A	262	SER	0	-0.020	-0.023	25.773	0.120	0.120	0.000	0.000	0.000	0.000
69	A	263	PHE	0	0.014	0.002	20.643	0.108	0.108	0.000	0.000	0.000	0.000
70	A	264	PHE	0	0.013	-0.008	19.196	-0.088	-0.088	0.000	0.000	0.000	0.000
71	A	265	GLU	-1	-0.855	-0.923	23.585	-9.561	-9.561	0.000	0.000	0.000	0.000
72	A	266	LYS	1	0.837	0.926	27.020	9.351	9.351	0.000	0.000	0.000	0.000
73	A	267	PHE	0	0.001	-0.005	23.774	0.227	0.227	0.000	0.000	0.000	0.000
74	A	268	HIS	0	-0.046	-0.018	22.091	-0.122	-0.122	0.000	0.000	0.000	0.000
75	A	269	GLY	0	0.014	0.012	22.968	-0.196	-0.196	0.000	0.000	0.000	0.000
76	A	270	ASP	-1	-0.857	-0.931	25.589	-9.579	-9.579	0.000	0.000	0.000	0.000
77	A	271	GLN	0	-0.087	-0.048	19.783	-0.611	-0.611	0.000	0.000	0.000	0.000
78	A	272	GLU	-1	-0.866	-0.943	19.504	-11.235	-11.235	0.000	0.000	0.000	0.000
79	A	273	CYS	0	-0.033	-0.020	20.489	-0.361	-0.361	0.000	0.000	0.000	0.000
80	A	274	TYR	0	-0.045	-0.031	16.954	0.205	0.205	0.000	0.000	0.000	0.000
81	A	275	TYR	0	0.045	0.041	14.119	-0.517	-0.517	0.000	0.000	0.000	0.000
82	A	276	GLN	0	-0.023	-0.030	17.484	-0.237	-0.237	0.000	0.000	0.000	0.000
83	A	277	ASP	-1	-0.920	-0.950	17.185	-13.742	-13.742	0.000	0.000	0.000	0.000
84	A	278	ASP	-1	-0.896	-0.959	12.298	-17.367	-17.367	0.000	0.000	0.000	0.000
85	A	279	LEU	0	-0.028	-0.018	14.926	-0.363	-0.363	0.000	0.000	0.000	0.000
86	A	280	ARG	1	0.961	0.988	17.723	12.775	12.775	0.000	0.000	0.000	0.000
87	A	281	VAL	0	-0.027	0.000	12.882	0.205	0.205	0.000	0.000	0.000	0.000
88	A	282	LEU	0	0.009	0.020	14.094	-0.015	-0.015	0.000	0.000	0.000	0.000
89	A	283	SER	0	-0.055	-0.032	16.056	0.280	0.280	0.000	0.000	0.000	0.000
90	A	284	SER	0	-0.065	-0.040	16.908	0.330	0.330	0.000	0.000	0.000	0.000
91	A	285	LEU	0	-0.038	-0.017	13.146	0.077	0.077	0.000	0.000	0.000	0.000
92	A	286	THR	0	0.024	0.016	17.793	0.177	0.177	0.000	0.000	0.000	0.000
93	A	287	LYS	1	0.943	0.975	20.484	11.849	11.849	0.000	0.000	0.000	0.000
94	A	288	LYS	1	0.915	0.959	18.402	13.437	13.437	0.000	0.000	0.000	0.000
95	A	289	GLU	-1	-0.961	-0.993	17.633	-13.183	-13.183	0.000	0.000	0.000	0.000
96	A	290	HIS	0	0.003	0.012	17.284	-0.622	-0.622	0.000	0.000	0.000	0.000
97	A	291	MET	0	0.007	0.022	13.917	-0.564	-0.564	0.000	0.000	0.000	0.000
98	A	292	LYS	1	0.895	0.936	12.719	16.333	16.333	0.000	0.000	0.000	0.000
99	A	293	GLY	0	0.001	0.008	12.369	0.790	0.790	0.000	0.000	0.000	0.000
100	A	294	ASN	0	0.002	0.026	11.593	-1.020	-1.020	0.000	0.000	0.000	0.000
101	A	295	GLU	-1	-0.857	-0.951	6.319	-36.478	-36.478	0.000	0.000	0.000	0.000
102	A	296	THR	0	0.000	-0.014	6.649	-2.403	-2.403	0.000	0.000	0.000	0.000
103	A	297	MET	0	-0.012	-0.002	8.519	1.081	1.081	0.000	0.000	0.000	0.000
106	A	300	PHE	0	0.024	-0.002	6.566	1.626	1.626	0.000	0.000	0.000	0.000
108	A	302	THR	0	0.020	-0.016	7.557	-0.082	-0.082	0.000	0.000	0.000	0.000
109	A	303	SER	0	0.039	0.020	6.499	0.333	0.333	0.000	0.000	0.000	0.000
110	A	304	LYS	1	0.802	0.896	5.328	21.068	21.068	0.000	0.000	0.000	0.000
111	A	305	PHE	0	-0.003	0.003	6.909	0.446	0.446	0.000	0.000	0.000	0.000
112	A	306	VAL	0	-0.035	-0.008	10.185	0.255	0.255	0.000	0.000	0.000	0.000
113	A	307	LEU	0	-0.014	0.000	12.537	0.895	0.895	0.000	0.000	0.000	0.000
114	A	308	ARG	1	0.922	0.957	15.130	16.716	16.716	0.000	0.000	0.000	0.000
115	A	309	ILE	0	-0.025	0.013	19.409	0.407	0.407	0.000	0.000	0.000	0.000
116	A	310	SER	0	0.041	-0.016	22.977	-0.078	-0.078	0.000	0.000	0.000	0.000
117	A	311	ARG	1	0.812	0.861	26.184	10.855	10.855	0.000	0.000	0.000	0.000
118	A	312	ASP	-1	-0.858	-0.929	27.465	-9.036	-9.036	0.000	0.000	0.000	0.000
119	A	313	SER	0	0.030	-0.032	26.342	0.333	0.333	0.000	0.000	0.000	0.000
120	A	314	TYR	0	0.038	0.020	22.886	0.179	0.179	0.000	0.000	0.000	0.000
121	A	315	GLN	0	-0.086	-0.042	26.636	0.063	0.063	0.000	0.000	0.000	0.000
122	A	316	LEU	0	-0.060	-0.018	30.051	0.205	0.205	0.000	0.000	0.000	0.000
123	A	317	LEU	0	0.031	0.019	22.835	0.113	0.113	0.000	0.000	0.000	0.000
124	A	318	LYS	1	0.920	0.971	26.947	10.673	10.673	0.000	0.000	0.000	0.000
125	A	319	ARG	1	0.938	0.978	28.028	8.852	8.852	0.000	0.000	0.000	0.000
126	A	320	HIS	0	0.040	0.025	27.780	0.292	0.292	0.000	0.000	0.000	0.000
127	A	321	LEU	0	-0.047	-0.035	23.961	0.036	0.036	0.000	0.000	0.000	0.000
128	A	322	GLN	0	-0.038	-0.030	28.270	0.045	0.045	0.000	0.000	0.000	0.000
129	A	323	GLU	-1	-0.922	-0.944	30.667	-8.299	-8.299	0.000	0.000	0.000	0.000
130	A	324	LYS	1	0.801	0.900	30.729	9.530	9.530	0.000	0.000	0.000	0.000
131	A	325	GLN	0	0.026	-0.003	30.806	-0.459	-0.459	0.000	0.000	0.000	0.000
132	A	326	ASN	0	-0.017	-0.011	26.220	-0.106	-0.106	0.000	0.000	0.000	0.000
133	A	327	ASN	0	0.027	0.022	26.474	-0.365	-0.365	0.000	0.000	0.000	0.000
134	A	328	GLN	0	0.027	0.006	20.338	0.218	0.218	0.000	0.000	0.000	0.000
135	A	329	ILE	0	0.001	-0.001	21.580	-0.545	-0.545	0.000	0.000	0.000	0.000
136	A	330	TRP	0	-0.030	-0.013	21.656	-0.377	-0.377	0.000	0.000	0.000	0.000
137	A	331	ASN	0	0.015	0.002	21.309	-0.226	-0.226	0.000	0.000	0.000	0.000
138	A	332	ILE	0	0.005	0.002	16.315	-0.674	-0.674	0.000	0.000	0.000	0.000
139	A	333	VAL	0	-0.036	-0.025	17.081	-0.837	-0.837	0.000	0.000	0.000	0.000
140	A	334	GLN	0	-0.061	-0.028	18.701	0.085	0.085	0.000	0.000	0.000	0.000
141	A	335	GLU	-1	-0.961	-0.965	16.398	-15.740	-15.740	0.000	0.000	0.000	0.000
142	A	336	HIS	0	-0.023	-0.024	13.019	-2.405	-2.405	0.000	0.000	0.000	0.000
143	A	337	LEU	0	-0.034	-0.011	12.249	-1.252	-1.252	0.000	0.000	0.000	0.000
144	A	338	TYR	0	-0.025	-0.004	9.062	-1.168	-1.168	0.000	0.000	0.000	0.000
145	A	339	ILE	0	-0.033	-0.020	12.826	0.592	0.592	0.000	0.000	0.000	0.000
146	A	340	ASP	-1	-0.896	-0.929	15.885	-17.786	-17.786	0.000	0.000	0.000	0.000
147	A	341	ILE	0	-0.064	-0.057	18.340	0.547	0.547	0.000	0.000	0.000	0.000
148	A	342	PHE	0	-0.052	-0.024	18.969	-0.235	-0.235	0.000	0.000	0.000	0.000
149	A	343	ASP	-2	-1.700	-1.807	24.672	-20.816	-20.816	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:195:GLN)