FMO DATABASE

FMODB ID: P2N3R

Calculation Name: 4YX1-A-Xray21

Preferred Name:

Target Type:

Ligand Name: calcium ion

ligand 3-letter code: CA

PDB ID: 4YX1

Chain ID: A

ChEMBL ID:

UniProt ID: P40699

Base Structure: X-ray

Registration Date: 2018-06-07

Reference:

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water	Apo structure with with a 3 angstrom solvent shell.
Procedure	Auto-FMO protocol ver. 1.20180227

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	140
LigandCharge
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-456117.046813
FMO2-HF: Nuclear repulsion	423831.540947
FMO2-HF: Total energy	-32285.505865
FMO2-MP2: Total energy	-32376.587215

3D Structure

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:1:GLY)

Summations of interaction energy for fragment #1(A:1: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.
-139.705	-132.855	7.807	-8.589	-6.069	-0.115

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.774 / q_NPA : 0.866

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	3	VAL	0	0.027	0.027	3.503	6.711	8.484	-0.001	-0.799	-0.973	-0.004
4	A	4	ASP	-1	-0.843	-0.896	1.858	-110.101	-105.010	7.809	-7.776	-5.125	-0.111
5	A	5	VAL	0	0.012	0.012	4.536	-0.924	-0.938	-0.001	-0.014	0.029	0.000
6	A	6	LYS	1	0.929	0.966	7.193	39.123	39.123	0.000	0.000	0.000	0.000
7	A	7	LEU	0	0.024	0.019	9.609	1.369	1.369	0.000	0.000	0.000	0.000
8	A	8	GLU	-1	-0.926	-0.955	13.087	-19.795	-19.795	0.000	0.000	0.000	0.000
9	A	9	PHE	0	0.029	0.013	16.175	0.263	0.263	0.000	0.000	0.000	0.000
10	A	10	VAL	0	-0.014	-0.009	19.093	0.231	0.231	0.000	0.000	0.000	0.000
11	A	11	LEU	0	0.052	0.033	21.679	0.381	0.381	0.000	0.000	0.000	0.000
12	A	12	TYR	0	0.007	-0.022	24.710	0.602	0.602	0.000	0.000	0.000	0.000
13	A	13	ARG	1	0.780	0.856	21.438	13.849	13.849	0.000	0.000	0.000	0.000
14	A	14	LYS	1	0.957	0.977	24.838	10.756	10.756	0.000	0.000	0.000	0.000
15	A	15	ASN	0	-0.042	-0.007	24.990	-0.724	-0.724	0.000	0.000	0.000	0.000
16	A	16	VAL	0	0.043	0.019	27.047	0.428	0.428	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.017	0.004	28.525	-0.116	-0.116	0.000	0.000	0.000	0.000
18	A	18	LEU	0	0.051	-0.002	27.487	-0.083	-0.083	0.000	0.000	0.000	0.000
19	A	19	ALA	0	0.025	0.021	30.659	0.025	0.025	0.000	0.000	0.000	0.000
20	A	20	GLU	-1	-0.753	-0.837	32.081	-9.533	-9.533	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.020	0.019	25.962	0.066	0.066	0.000	0.000	0.000	0.000
22	A	22	GLU	-1	-0.804	-0.848	30.425	-9.467	-9.467	0.000	0.000	0.000	0.000
23	A	23	ALA	0	-0.009	0.011	32.846	0.109	0.109	0.000	0.000	0.000	0.000
24	A	24	MET	0	0.007	0.018	29.072	-0.003	-0.003	0.000	0.000	0.000	0.000
25	A	25	GLY	0	0.032	0.025	31.442	-0.020	-0.020	0.000	0.000	0.000	0.000
26	A	26	GLN	0	0.029	0.055	32.175	0.363	0.363	0.000	0.000	0.000	0.000
27	A	27	GLN	0	0.066	0.091	34.541	0.405	0.405	0.000	0.000	0.000	0.000
28	A	28	GLN	0	0.071	0.056	34.136	-0.295	-0.295	0.000	0.000	0.000	0.000
29	A	29	LEU	0	0.011	0.008	34.601	-0.153	-0.153	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.026	-0.008	31.183	0.222	0.222	0.000	0.000	0.000	0.000
31	A	31	SER	0	-0.028	-0.033	33.484	-0.032	-0.032	0.000	0.000	0.000	0.000
32	A	32	LEU	0	0.020	0.009	29.321	-0.149	-0.149	0.000	0.000	0.000	0.000
33	A	33	PRO	0	-0.009	0.001	31.485	0.335	0.335	0.000	0.000	0.000	0.000
34	A	34	THR	0	0.066	0.014	34.091	-0.162	-0.162	0.000	0.000	0.000	0.000
35	A	35	ASN	0	0.016	0.011	34.669	-0.084	-0.084	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.015	0.025	29.684	-0.175	-0.175	0.000	0.000	0.000	0.000
37	A	37	GLU	-1	-0.826	-0.915	29.543	-9.819	-9.819	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.015	0.008	30.432	-0.150	-0.150	0.000	0.000	0.000	0.000
39	A	39	ASN	0	0.032	0.021	27.420	-0.224	-0.224	0.000	0.000	0.000	0.000
40	A	40	VAL	0	0.030	0.041	23.422	-0.372	-0.372	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.756	-0.835	21.870	-13.475	-13.475	0.000	0.000	0.000	0.000
42	A	42	ILE	0	0.010	0.015	17.787	-0.578	-0.578	0.000	0.000	0.000	0.000
43	A	43	MET	0	-0.013	0.009	16.231	0.313	0.313	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.065	0.024	12.428	-1.109	-1.109	0.000	0.000	0.000	0.000
45	A	45	ASN	0	-0.002	0.003	7.437	-0.582	-0.582	0.000	0.000	0.000	0.000
46	A	46	GLY	0	0.021	0.023	11.012	0.589	0.589	0.000	0.000	0.000	0.000
47	A	47	VAL	0	-0.024	-0.005	14.237	1.640	1.640	0.000	0.000	0.000	0.000
48	A	48	LEU	0	-0.005	-0.002	16.297	-0.621	-0.621	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.002	-0.012	15.355	-0.065	-0.065	0.000	0.000	0.000	0.000
50	A	50	GLY	0	0.056	0.024	19.325	0.469	0.469	0.000	0.000	0.000	0.000
51	A	51	ASN	0	-0.060	-0.004	22.478	-0.098	-0.098	0.000	0.000	0.000	0.000
52	A	52	GLY	0	0.099	0.034	24.962	0.134	0.134	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.859	-0.903	27.305	-9.633	-9.633	0.000	0.000	0.000	0.000
54	A	54	LEU	0	-0.045	-0.022	27.020	-0.290	-0.290	0.000	0.000	0.000	0.000
55	A	55	VAL	0	0.061	0.037	29.426	0.390	0.390	0.000	0.000	0.000	0.000
56	A	56	GLN	0	-0.034	-0.041	30.356	-0.305	-0.305	0.000	0.000	0.000	0.000
57	A	57	MET	0	-0.046	-0.016	28.625	0.132	0.132	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.014	-0.015	32.220	0.222	0.222	0.000	0.000	0.000	0.000
59	A	59	ASP	-1	-0.868	-0.914	30.590	-9.624	-9.624	0.000	0.000	0.000	0.000
60	A	60	THR	0	-0.052	-0.016	26.281	-0.188	-0.188	0.000	0.000	0.000	0.000
61	A	61	LEU	0	0.021	0.008	26.900	0.310	0.310	0.000	0.000	0.000	0.000
62	A	62	GLY	0	-0.005	-0.010	26.078	-0.410	-0.410	0.000	0.000	0.000	0.000
63	A	63	VAL	0	-0.031	-0.019	23.654	0.115	0.115	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.799	-0.846	26.182	-10.108	-10.108	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.026	-0.016	23.265	-0.058	-0.058	0.000	0.000	0.000	0.000
66	A	66	HIS	0	0.030	0.046	27.086	0.349	0.349	0.000	0.000	0.000	0.000
67	A	67	GLU	-1	-0.921	-0.964	26.545	-11.257	-11.257	0.000	0.000	0.000	0.000
68	A	68	TRP	0	-0.034	-0.011	19.851	-0.843	-0.843	0.000	0.000	0.000	0.000
69	A	69	LEU	0	-0.015	-0.017	22.001	0.486	0.486	0.000	0.000	0.000	0.000
70	A	0	NME	0	-0.018	-0.005	22.606	-0.412	-0.412	0.000	0.000	0.000	0.000
71	A	101	HOH	0	-0.118	-0.128	30.039	-0.032	-0.032	0.000	0.000	0.000	0.000
72	A	102	HOH	0	0.043	0.049	33.077	-0.156	-0.156	0.000	0.000	0.000	0.000
73	A	103	HOH	0	-0.038	-0.044	39.358	-0.017	-0.017	0.000	0.000	0.000	0.000
74	A	104	HOH	0	-0.048	-0.073	30.817	-0.079	-0.079	0.000	0.000	0.000	0.000
75	A	105	HOH	0	-0.049	-0.077	27.312	0.063	0.063	0.000	0.000	0.000	0.000
76	A	106	HOH	0	0.023	0.029	37.166	0.010	0.010	0.000	0.000	0.000	0.000
77	A	107	HOH	0	0.017	0.025	19.624	0.226	0.226	0.000	0.000	0.000	0.000
78	A	108	HOH	0	-0.050	-0.051	34.129	0.094	0.094	0.000	0.000	0.000	0.000
79	A	109	HOH	0	-0.053	-0.050	34.496	0.052	0.052	0.000	0.000	0.000	0.000
80	A	110	HOH	0	-0.057	-0.050	36.174	0.085	0.085	0.000	0.000	0.000	0.000
81	A	111	HOH	0	0.003	0.024	37.500	-0.014	-0.014	0.000	0.000	0.000	0.000
82	A	112	HOH	0	-0.046	-0.036	33.563	0.112	0.112	0.000	0.000	0.000	0.000
83	A	113	HOH	0	-0.071	-0.048	34.224	0.121	0.121	0.000	0.000	0.000	0.000
84	A	114	HOH	0	-0.053	-0.038	34.933	0.128	0.128	0.000	0.000	0.000	0.000
85	A	115	HOH	0	-0.009	-0.015	17.843	0.380	0.380	0.000	0.000	0.000	0.000
86	A	116	HOH	0	-0.036	-0.031	39.788	0.047	0.047	0.000	0.000	0.000	0.000
87	A	117	HOH	0	-0.044	-0.032	11.776	-0.775	-0.775	0.000	0.000	0.000	0.000
88	A	118	HOH	0	-0.024	-0.023	27.852	0.055	0.055	0.000	0.000	0.000	0.000
89	A	119	HOH	0	-0.055	-0.046	32.338	-0.083	-0.083	0.000	0.000	0.000	0.000
90	A	120	HOH	0	0.005	0.012	31.237	-0.096	-0.096	0.000	0.000	0.000	0.000
91	A	121	HOH	0	-0.035	-0.029	33.566	0.020	0.020	0.000	0.000	0.000	0.000
92	A	122	HOH	0	-0.010	-0.006	27.011	0.127	0.127	0.000	0.000	0.000	0.000
93	A	123	HOH	0	-0.057	-0.046	37.272	0.018	0.018	0.000	0.000	0.000	0.000
94	A	124	HOH	0	-0.034	-0.026	23.698	-0.011	-0.011	0.000	0.000	0.000	0.000
95	A	125	HOH	0	-0.029	-0.027	33.811	-0.010	-0.010	0.000	0.000	0.000	0.000
96	A	126	HOH	0	-0.045	-0.032	33.681	-0.036	-0.036	0.000	0.000	0.000	0.000
97	A	127	HOH	0	-0.012	-0.022	34.946	0.074	0.074	0.000	0.000	0.000	0.000
98	A	128	HOH	0	-0.015	-0.008	37.662	0.070	0.070	0.000	0.000	0.000	0.000
99	A	129	HOH	0	-0.050	-0.040	5.957	2.369	2.369	0.000	0.000	0.000	0.000
100	A	130	HOH	0	-0.047	-0.033	12.737	-0.913	-0.913	0.000	0.000	0.000	0.000
101	A	131	HOH	0	-0.028	-0.024	39.389	0.077	0.077	0.000	0.000	0.000	0.000
102	A	132	HOH	0	-0.034	-0.022	20.128	0.294	0.294	0.000	0.000	0.000	0.000
103	A	133	HOH	0	-0.050	-0.031	33.789	-0.122	-0.122	0.000	0.000	0.000	0.000
104	A	134	HOH	0	-0.033	-0.024	35.993	0.105	0.105	0.000	0.000	0.000	0.000
105	A	135	HOH	0	0.001	0.022	33.994	-0.060	-0.060	0.000	0.000	0.000	0.000
106	A	136	HOH	0	-0.038	-0.025	31.716	-0.081	-0.081	0.000	0.000	0.000	0.000
107	A	137	HOH	0	0.035	0.059	35.004	0.048	0.048	0.000	0.000	0.000	0.000
108	A	138	HOH	0	-0.033	-0.020	29.479	0.160	0.160	0.000	0.000	0.000	0.000
109	A	139	HOH	0	-0.034	-0.033	25.261	-0.009	-0.009	0.000	0.000	0.000	0.000
110	A	140	HOH	0	-0.042	-0.049	33.444	-0.084	-0.084	0.000	0.000	0.000	0.000
111	A	141	HOH	0	-0.019	-0.018	13.050	-0.392	-0.392	0.000	0.000	0.000	0.000
112	A	142	HOH	0	-0.012	-0.015	24.636	-0.044	-0.044	0.000	0.000	0.000	0.000
113	A	143	HOH	0	-0.023	-0.019	29.007	0.036	0.036	0.000	0.000	0.000	0.000
114	A	144	HOH	0	-0.028	-0.018	32.033	0.131	0.131	0.000	0.000	0.000	0.000
115	A	145	HOH	0	0.027	0.018	34.963	-0.009	-0.009	0.000	0.000	0.000	0.000
116	A	146	HOH	0	-0.044	-0.027	5.040	-0.220	-0.220	0.000	0.000	0.000	0.000
117	A	147	HOH	0	0.005	0.005	12.934	-0.062	-0.062	0.000	0.000	0.000	0.000
118	A	148	HOH	0	0.029	0.023	23.963	0.133	0.133	0.000	0.000	0.000	0.000
119	A	149	HOH	0	-0.016	0.015	32.235	-0.044	-0.044	0.000	0.000	0.000	0.000
120	A	150	HOH	0	-0.027	-0.018	16.337	0.477	0.477	0.000	0.000	0.000	0.000
121	A	151	HOH	0	-0.005	0.000	27.721	-0.147	-0.147	0.000	0.000	0.000	0.000
122	A	152	HOH	0	-0.020	-0.010	32.885	-0.110	-0.110	0.000	0.000	0.000	0.000
123	A	153	HOH	0	0.033	0.022	30.094	0.001	0.001	0.000	0.000	0.000	0.000
124	A	154	HOH	0	-0.038	-0.020	30.816	-0.013	-0.013	0.000	0.000	0.000	0.000
125	A	155	HOH	0	-0.063	-0.039	38.373	0.094	0.094	0.000	0.000	0.000	0.000
126	A	156	HOH	0	-0.017	-0.015	19.377	-0.117	-0.117	0.000	0.000	0.000	0.000
127	A	157	HOH	0	-0.029	-0.017	36.577	0.021	0.021	0.000	0.000	0.000	0.000
128	A	158	HOH	0	-0.043	-0.019	29.862	0.068	0.068	0.000	0.000	0.000	0.000
129	A	159	HOH	0	0.058	0.041	22.162	-0.221	-0.221	0.000	0.000	0.000	0.000
130	A	160	HOH	0	0.021	0.015	37.611	-0.093	-0.093	0.000	0.000	0.000	0.000
131	A	161	HOH	0	0.033	0.018	31.862	0.040	0.040	0.000	0.000	0.000	0.000
132	A	162	HOH	0	-0.019	-0.012	38.871	0.007	0.007	0.000	0.000	0.000	0.000
133	A	163	HOH	0	-0.040	-0.010	31.547	0.042	0.042	0.000	0.000	0.000	0.000
134	A	164	HOH	0	-0.027	-0.015	25.367	0.135	0.135	0.000	0.000	0.000	0.000
135	A	165	HOH	0	0.031	0.016	33.814	-0.130	-0.130	0.000	0.000	0.000	0.000
136	A	166	HOH	0	-0.048	-0.023	26.258	0.156	0.156	0.000	0.000	0.000	0.000
137	A	193	HOH	0	-0.009	-0.023	27.987	-0.163	-0.163	0.000	0.000	0.000	0.000
138	B	204	HOH	0	-0.108	-0.125	34.905	-0.013	-0.013	0.000	0.000	0.000	0.000
139	B	216	HOH	0	-0.051	-0.025	35.991	0.081	0.081	0.000	0.000	0.000	0.000
140	B	224	HOH	0	0.033	0.020	25.484	0.144	0.144	0.000	0.000	0.000	0.000

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