FMO DATABASE

FMODB ID: 74RRK

Calculation Name: 2BNG-A-Xray549

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2BNG

Chain ID: A

ChEMBL ID:

UniProt ID: O33283

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	132
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1136423.096035
FMO2-HF: Nuclear repulsion	1085051.077582
FMO2-HF: Total energy	-51372.018453
FMO2-MP2: Total energy	-51523.381516

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:13:GLU)

Summations of interaction energy for fragment #1(A:13:GLU)

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.
-15.482	-9.414	5.72	-5.734	-6.054	-0.053

Interaction energy analysis for fragmet #1(A:13:GLU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.010 / q_NPA : -0.017

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	15	THR	0	0.027	0.000	3.746	-0.876	0.532	0.001	-0.561	-0.848	0.000
4	A	16	GLU	-1	-0.946	-0.967	2.114	-34.514	-30.484	5.721	-4.945	-4.806	-0.053
5	A	17	ALA	0	0.042	0.027	3.986	5.040	5.512	0.000	-0.178	-0.293	0.000
72	A	84	GLY	0	0.016	0.004	4.270	0.458	0.563	-0.001	-0.010	-0.094	0.000
73	A	85	ALA	0	0.017	0.010	4.306	-2.801	-2.748	-0.001	-0.040	-0.013	0.000
6	A	18	ILE	0	0.022	-0.002	5.833	2.465	2.465	0.000	0.000	0.000	0.000
7	A	19	ARG	1	0.952	0.979	6.621	9.747	9.747	0.000	0.000	0.000	0.000
8	A	20	ALA	0	0.023	0.026	7.633	1.176	1.176	0.000	0.000	0.000	0.000
9	A	21	VAL	0	0.005	0.007	9.306	1.059	1.059	0.000	0.000	0.000	0.000
10	A	22	GLU	-1	-0.908	-0.971	11.542	-3.672	-3.672	0.000	0.000	0.000	0.000
11	A	23	ALA	0	-0.019	-0.001	12.160	0.521	0.521	0.000	0.000	0.000	0.000
12	A	24	PHE	0	0.028	0.008	13.417	0.446	0.446	0.000	0.000	0.000	0.000
13	A	25	LEU	0	-0.002	-0.007	15.341	0.305	0.305	0.000	0.000	0.000	0.000
14	A	26	ASN	0	-0.056	-0.044	16.343	0.402	0.402	0.000	0.000	0.000	0.000
15	A	27	ALA	0	-0.024	0.003	17.673	0.174	0.174	0.000	0.000	0.000	0.000
16	A	28	LEU	0	-0.032	-0.020	19.369	0.179	0.179	0.000	0.000	0.000	0.000
17	A	29	GLN	0	-0.024	0.004	21.470	0.204	0.204	0.000	0.000	0.000	0.000
18	A	30	ASN	0	-0.038	-0.025	21.043	0.147	0.147	0.000	0.000	0.000	0.000
19	A	31	GLU	-1	-0.893	-0.933	23.967	-0.659	-0.659	0.000	0.000	0.000	0.000
20	A	32	ASP	-1	-0.823	-0.871	20.078	-1.290	-1.290	0.000	0.000	0.000	0.000
21	A	33	PHE	0	0.026	-0.027	20.842	-0.092	-0.092	0.000	0.000	0.000	0.000
22	A	34	ASP	-1	-0.832	-0.888	21.386	-0.728	-0.728	0.000	0.000	0.000	0.000
23	A	35	THR	0	-0.038	-0.045	15.612	-0.066	-0.066	0.000	0.000	0.000	0.000
24	A	36	VAL	0	-0.036	-0.010	16.502	-0.148	-0.148	0.000	0.000	0.000	0.000
25	A	37	ASP	-1	-0.856	-0.945	17.660	-0.638	-0.638	0.000	0.000	0.000	0.000
26	A	38	ALA	0	-0.048	-0.013	15.337	0.103	0.103	0.000	0.000	0.000	0.000
27	A	39	ALA	0	0.026	0.025	12.962	-0.051	-0.051	0.000	0.000	0.000	0.000
28	A	40	LEU	0	-0.030	-0.004	13.326	0.004	0.004	0.000	0.000	0.000	0.000
29	A	41	GLY	0	0.042	0.027	14.837	0.143	0.143	0.000	0.000	0.000	0.000
30	A	42	ASP	-1	-0.841	-0.925	15.513	-0.105	-0.105	0.000	0.000	0.000	0.000
31	A	43	ASP	-1	-0.892	-0.950	17.127	0.427	0.427	0.000	0.000	0.000	0.000
32	A	44	LEU	0	-0.056	0.002	16.144	0.035	0.035	0.000	0.000	0.000	0.000
33	A	45	VAL	0	-0.073	-0.041	17.830	0.051	0.051	0.000	0.000	0.000	0.000
34	A	46	TYR	0	0.056	0.031	18.484	-0.068	-0.068	0.000	0.000	0.000	0.000
35	A	47	GLU	-1	-0.807	-0.882	20.808	-0.059	-0.059	0.000	0.000	0.000	0.000
36	A	48	ASN	0	0.050	0.026	22.206	-0.142	-0.142	0.000	0.000	0.000	0.000
37	A	49	VAL	0	0.002	-0.006	23.219	0.075	0.075	0.000	0.000	0.000	0.000
38	A	50	GLY	0	-0.019	-0.007	25.845	-0.007	-0.007	0.000	0.000	0.000	0.000
39	A	51	PHE	0	-0.029	-0.013	28.554	0.026	0.026	0.000	0.000	0.000	0.000
40	A	52	SER	0	0.012	-0.001	26.460	0.005	0.005	0.000	0.000	0.000	0.000
41	A	53	ARG	1	0.807	0.892	23.479	0.041	0.041	0.000	0.000	0.000	0.000
42	A	54	ILE	0	-0.013	0.001	24.184	0.044	0.044	0.000	0.000	0.000	0.000
43	A	55	ARG	1	0.962	0.974	22.159	-0.150	-0.150	0.000	0.000	0.000	0.000
44	A	56	GLY	0	0.045	0.030	21.724	0.019	0.019	0.000	0.000	0.000	0.000
45	A	57	GLY	0	0.035	0.029	19.539	-0.075	-0.075	0.000	0.000	0.000	0.000
46	A	58	ARG	1	0.851	0.911	18.799	0.326	0.326	0.000	0.000	0.000	0.000
47	A	59	ARG	1	0.861	0.928	23.309	0.102	0.102	0.000	0.000	0.000	0.000
48	A	60	THR	0	0.018	0.006	21.195	-0.005	-0.005	0.000	0.000	0.000	0.000
49	A	61	ALA	0	0.069	0.045	20.847	-0.042	-0.042	0.000	0.000	0.000	0.000
50	A	62	THR	0	-0.052	-0.030	22.683	0.003	0.003	0.000	0.000	0.000	0.000
51	A	63	LEU	0	-0.034	-0.021	26.325	0.016	0.016	0.000	0.000	0.000	0.000
52	A	64	LEU	0	-0.008	-0.004	21.722	0.005	0.005	0.000	0.000	0.000	0.000
53	A	65	ARG	1	0.834	0.893	23.525	0.690	0.690	0.000	0.000	0.000	0.000
54	A	66	ARG	1	0.881	0.937	27.015	0.350	0.350	0.000	0.000	0.000	0.000
55	A	67	MET	0	-0.013	0.009	27.576	0.037	0.037	0.000	0.000	0.000	0.000
56	A	68	GLN	0	0.009	0.010	28.958	0.026	0.026	0.000	0.000	0.000	0.000
57	A	69	GLY	0	-0.001	0.003	30.789	0.043	0.043	0.000	0.000	0.000	0.000
58	A	70	ARG	1	0.787	0.892	33.150	0.418	0.418	0.000	0.000	0.000	0.000
59	A	71	VAL	0	-0.010	-0.018	29.976	0.027	0.027	0.000	0.000	0.000	0.000
60	A	72	GLY	0	0.041	0.049	29.541	-0.024	-0.024	0.000	0.000	0.000	0.000
61	A	73	PHE	0	-0.003	-0.029	25.123	0.032	0.032	0.000	0.000	0.000	0.000
62	A	74	GLU	-1	-0.785	-0.857	25.518	-0.831	-0.831	0.000	0.000	0.000	0.000
63	A	75	VAL	0	-0.015	-0.015	20.051	0.030	0.030	0.000	0.000	0.000	0.000
64	A	76	LYS	1	0.857	0.941	22.038	1.222	1.222	0.000	0.000	0.000	0.000
65	A	77	ILE	0	0.055	0.020	15.933	0.087	0.087	0.000	0.000	0.000	0.000
66	A	78	HIS	0	-0.058	-0.038	20.016	-0.053	-0.053	0.000	0.000	0.000	0.000
67	A	79	ARG	1	0.858	0.902	17.873	1.087	1.087	0.000	0.000	0.000	0.000
68	A	80	ILE	0	0.010	0.007	12.010	0.112	0.112	0.000	0.000	0.000	0.000
69	A	81	GLY	0	-0.007	0.008	11.374	-0.026	-0.026	0.000	0.000	0.000	0.000
70	A	82	ALA	0	-0.029	-0.022	7.101	-0.117	-0.117	0.000	0.000	0.000	0.000
71	A	83	ASP	-1	-0.953	-0.959	8.234	0.048	0.048	0.000	0.000	0.000	0.000
74	A	86	ALA	0	0.026	0.025	5.742	-0.527	-0.527	0.000	0.000	0.000	0.000
75	A	87	VAL	0	-0.026	-0.025	8.034	-0.844	-0.844	0.000	0.000	0.000	0.000
76	A	88	LEU	0	-0.017	-0.009	10.456	0.569	0.569	0.000	0.000	0.000	0.000
77	A	89	THR	0	-0.024	-0.027	14.099	-0.247	-0.247	0.000	0.000	0.000	0.000
78	A	90	GLU	-1	-0.829	-0.889	16.595	-0.870	-0.870	0.000	0.000	0.000	0.000
79	A	91	ARG	1	0.741	0.807	18.591	1.135	1.135	0.000	0.000	0.000	0.000
80	A	92	THR	0	-0.050	-0.008	22.234	0.119	0.119	0.000	0.000	0.000	0.000
81	A	93	ASP	-1	-0.729	-0.837	23.212	-1.190	-1.190	0.000	0.000	0.000	0.000
82	A	94	ALA	0	-0.024	-0.029	26.002	0.079	0.079	0.000	0.000	0.000	0.000
83	A	95	LEU	0	-0.001	0.009	27.957	-0.033	-0.033	0.000	0.000	0.000	0.000
84	A	96	ILE	0	-0.007	0.000	30.511	0.042	0.042	0.000	0.000	0.000	0.000
85	A	97	ILE	0	0.021	0.012	33.124	0.001	0.001	0.000	0.000	0.000	0.000
86	A	98	GLY	0	0.013	0.002	36.002	0.030	0.030	0.000	0.000	0.000	0.000
87	A	99	PRO	0	-0.018	-0.011	37.187	-0.024	-0.024	0.000	0.000	0.000	0.000
88	A	100	LEU	0	-0.019	-0.003	37.526	-0.006	-0.006	0.000	0.000	0.000	0.000
89	A	101	ARG	1	0.805	0.873	30.053	0.693	0.693	0.000	0.000	0.000	0.000
90	A	102	VAL	0	-0.010	-0.001	33.125	0.019	0.019	0.000	0.000	0.000	0.000
91	A	103	GLN	0	0.017	0.003	29.974	-0.036	-0.036	0.000	0.000	0.000	0.000
92	A	104	PHE	0	0.001	0.000	26.648	0.052	0.052	0.000	0.000	0.000	0.000
93	A	105	TRP	0	-0.006	0.000	24.757	-0.074	-0.074	0.000	0.000	0.000	0.000
94	A	106	VAL	0	-0.012	-0.016	21.627	0.063	0.063	0.000	0.000	0.000	0.000
95	A	107	CYS	0	-0.046	-0.010	20.738	-0.086	-0.086	0.000	0.000	0.000	0.000
96	A	108	GLY	0	0.055	0.019	18.291	0.126	0.126	0.000	0.000	0.000	0.000
97	A	109	VAL	0	-0.039	-0.020	14.972	-0.202	-0.202	0.000	0.000	0.000	0.000
98	A	110	PHE	0	0.002	-0.017	11.831	0.129	0.129	0.000	0.000	0.000	0.000
99	A	111	GLU	-1	-0.936	-0.957	9.854	-0.017	-0.017	0.000	0.000	0.000	0.000
100	A	112	VAL	0	-0.050	-0.025	6.232	-0.252	-0.252	0.000	0.000	0.000	0.000
101	A	113	ASP	-1	-0.920	-0.951	6.650	3.401	3.401	0.000	0.000	0.000	0.000
102	A	114	ASP	-1	-0.855	-0.931	6.548	3.209	3.209	0.000	0.000	0.000	0.000
103	A	115	GLY	0	-0.060	-0.032	6.461	-1.275	-1.275	0.000	0.000	0.000	0.000
104	A	116	ARG	1	0.777	0.884	7.349	0.639	0.639	0.000	0.000	0.000	0.000
105	A	117	ILE	0	0.006	-0.002	10.505	0.208	0.208	0.000	0.000	0.000	0.000
106	A	118	THR	0	0.006	-0.008	11.810	0.119	0.119	0.000	0.000	0.000	0.000
107	A	119	LEU	0	-0.030	-0.007	13.217	0.198	0.198	0.000	0.000	0.000	0.000
108	A	120	TRP	0	0.017	-0.010	14.159	-0.308	-0.308	0.000	0.000	0.000	0.000
109	A	121	ARG	1	0.863	0.917	16.823	0.449	0.449	0.000	0.000	0.000	0.000
110	A	122	ASP	-1	-0.746	-0.825	18.960	-1.202	-1.202	0.000	0.000	0.000	0.000
111	A	123	TYR	0	-0.032	-0.030	19.700	0.139	0.139	0.000	0.000	0.000	0.000
112	A	124	PHE	0	0.050	0.020	23.817	-0.063	-0.063	0.000	0.000	0.000	0.000
113	A	125	ASP	-1	-0.798	-0.897	26.958	-0.329	-0.329	0.000	0.000	0.000	0.000
114	A	126	VAL	0	0.028	0.012	30.619	-0.017	-0.017	0.000	0.000	0.000	0.000
115	A	127	TYR	0	-0.007	-0.012	33.655	0.000	0.000	0.000	0.000	0.000	0.000
116	A	128	ASP	-1	-0.892	-0.980	30.976	-0.543	-0.543	0.000	0.000	0.000	0.000
117	A	129	MET	0	0.030	0.023	29.159	0.010	0.010	0.000	0.000	0.000	0.000
118	A	130	PHE	0	-0.018	0.002	33.477	0.007	0.007	0.000	0.000	0.000	0.000
119	A	131	LYS	1	0.872	0.958	34.489	0.432	0.432	0.000	0.000	0.000	0.000
120	A	132	GLY	0	0.045	0.027	34.607	0.002	0.002	0.000	0.000	0.000	0.000
121	A	133	LEU	0	-0.028	-0.015	35.629	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	134	LEU	0	-0.013	-0.008	37.879	0.009	0.009	0.000	0.000	0.000	0.000
123	A	135	ARG	1	0.904	0.951	37.651	0.464	0.464	0.000	0.000	0.000	0.000
124	A	136	GLY	0	0.059	0.035	38.394	-0.003	-0.003	0.000	0.000	0.000	0.000
125	A	137	LEU	0	-0.041	-0.039	39.087	0.011	0.011	0.000	0.000	0.000	0.000
126	A	138	VAL	0	-0.030	-0.007	42.580	0.014	0.014	0.000	0.000	0.000	0.000
127	A	139	ALA	0	0.006	0.009	40.340	0.009	0.009	0.000	0.000	0.000	0.000
128	A	140	LEU	0	-0.042	-0.022	41.193	0.001	0.001	0.000	0.000	0.000	0.000
129	A	141	VAL	0	-0.060	-0.021	43.951	0.014	0.014	0.000	0.000	0.000	0.000
130	A	142	VAL	0	-0.049	-0.030	45.955	0.013	0.013	0.000	0.000	0.000	0.000
131	A	143	PRO	0	-0.024	-0.012	43.268	-0.013	-0.013	0.000	0.000	0.000	0.000
132	A	144	SER	-1	-0.935	-0.950	40.725	-0.442	-0.442	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:13:GLU)