FMO DATABASE

FMODB ID: XRYN8

Calculation Name: 3O4A-C-Xray26

Preferred Name:

Target Type:

Ligand Name: 2-amino-2-hydroxymethyl-propane-1,3-diol

ligand 3-letter code: TRS

PDB ID: 3O4A

Chain ID: C

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2018-07-26

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	142
LigandCharge	TRS=1,SO4=-2
Software	MIZUHO/ABINIT-MP 3.0

Total energy (hartree)

FMO2-HF: Electronic energy	-1120625.158996
FMO2-HF: Nuclear repulsion	1069071.10494
FMO2-HF: Total energy	-51554.054057
FMO2-MP2: Total energy	-51702.277446

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(C:10:ACE)

Summations of interaction energy for fragment #1(C:10:ACE)

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.
-1.096	-0.441	-0.001	-0.342	-0.312	0

Interaction energy analysis for fragmet #1(C:10:ACE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.024

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].
3	C	12	VAL	0	-0.019	0.003	3.852	-0.111	0.464	0.000	-0.335	-0.240
4	C	13	LEU	0	0.010	0.008	6.680	0.286	0.286	0.000	0.000	0.000
5	C	14	LEU	0	-0.001	-0.002	10.202	0.012	0.012	0.000	0.000	0.000
6	C	15	LYS	1	0.905	0.967	13.287	0.333	0.333	0.000	0.000	0.000
7	C	16	SER	0	0.067	0.047	16.137	0.012	0.012	0.000	0.000	0.000
8	C	17	THR	0	-0.061	-0.063	19.241	0.004	0.004	0.000	0.000	0.000
9	C	18	GLU	-1	-0.874	-0.910	21.176	-0.122	-0.122	0.000	0.000	0.000
10	C	19	THR	0	-0.018	-0.001	23.184	0.009	0.009	0.000	0.000	0.000
11	C	20	GLY	0	-0.023	-0.030	20.032	0.009	0.009	0.000	0.000	0.000
12	C	21	GLN	0	-0.065	-0.044	19.444	-0.006	-0.006	0.000	0.000	0.000
13	C	22	TYR	0	0.000	-0.018	13.655	-0.018	-0.018	0.000	0.000	0.000
14	C	23	LEU	0	0.054	0.026	15.313	0.031	0.031	0.000	0.000	0.000
15	C	24	ARG	1	0.777	0.871	15.095	0.140	0.140	0.000	0.000	0.000
16	C	25	ILE	0	-0.014	-0.001	15.788	0.022	0.022	0.000	0.000	0.000
17	C	26	ASN	0	-0.035	-0.014	17.314	-0.015	-0.015	0.000	0.000	0.000
18	C	27	PRO	0	0.000	-0.016	19.342	0.002	0.002	0.000	0.000	0.000
19	C	28	ASP	-1	-0.920	-0.936	20.676	-0.132	-0.132	0.000	0.000	0.000
20	C	29	GLY	0	0.021	0.021	21.853	0.011	0.011	0.000	0.000	0.000
21	C	30	THR	0	-0.033	-0.034	22.812	-0.011	-0.011	0.000	0.000	0.000
22	C	31	VAL	0	-0.020	-0.016	19.311	-0.022	-0.022	0.000	0.000	0.000
23	C	32	ASP	-1	-0.774	-0.859	20.584	-0.182	-0.182	0.000	0.000	0.000
24	C	33	GLY	0	0.021	0.013	19.897	-0.038	-0.038	0.000	0.000	0.000
25	C	34	THR	0	0.025	0.014	17.931	0.035	0.035	0.000	0.000	0.000
26	C	35	ARG	1	0.875	0.927	18.824	0.132	0.132	0.000	0.000	0.000
27	C	36	ASP	-1	-0.878	-0.913	18.815	-0.159	-0.159	0.000	0.000	0.000
28	C	37	ARG	1	0.900	0.946	10.386	0.359	0.359	0.000	0.000	0.000
29	C	38	SER	0	-0.108	-0.059	13.904	-0.020	-0.020	0.000	0.000	0.000
30	C	39	ASP	-1	-0.779	-0.887	15.790	-0.211	-0.211	0.000	0.000	0.000
31	C	40	GLN	0	0.042	0.022	10.082	-0.052	-0.052	0.000	0.000	0.000
32	C	41	HIS	0	-0.101	-0.064	11.944	-0.074	-0.074	0.000	0.000	0.000
33	C	42	ILE	0	-0.031	-0.009	11.757	-0.026	-0.026	0.000	0.000	0.000
34	C	43	GLN	0	-0.019	0.004	6.642	-0.050	-0.050	0.000	0.000	0.000
35	C	44	PHE	0	-0.001	-0.001	8.372	0.151	0.151	0.000	0.000	0.000
36	C	45	GLN	0	-0.032	-0.026	6.284	-0.756	-0.756	0.000	0.000	0.000
37	C	46	ILE	0	0.015	0.014	7.469	0.324	0.324	0.000	0.000	0.000
38	C	47	SER	0	-0.059	-0.034	8.872	-0.007	-0.007	0.000	0.000	0.000
39	C	48	PRO	0	-0.006	-0.011	11.168	0.016	0.016	0.000	0.000	0.000
40	C	49	GLU	-1	-0.742	-0.832	14.359	-0.144	-0.144	0.000	0.000	0.000
41	C	50	GLY	0	-0.007	-0.004	17.586	0.012	0.012	0.000	0.000	0.000
42	C	51	GLY	0	-0.042	-0.029	18.351	-0.005	-0.005	0.000	0.000	0.000
43	C	52	GLY	0	-0.034	-0.022	18.826	0.007	0.007	0.000	0.000	0.000
44	C	53	GLU	-1	-0.856	-0.922	18.748	-0.174	-0.174	0.000	0.000	0.000
45	C	54	VAL	0	-0.066	-0.037	13.362	-0.011	-0.011	0.000	0.000	0.000
46	C	55	LEU	0	0.017	0.022	13.994	0.026	0.026	0.000	0.000	0.000
47	C	56	LEU	0	0.008	0.001	12.349	-0.111	-0.111	0.000	0.000	0.000
48	C	57	LYS	1	0.935	0.973	10.186	0.446	0.446	0.000	0.000	0.000
49	C	58	SER	0	0.073	0.064	10.483	-0.169	-0.169	0.000	0.000	0.000
50	C	59	THR	0	-0.063	-0.061	6.406	0.096	0.096	0.000	0.000	0.000
51	C	60	GLU	-1	-0.875	-0.939	9.602	-0.086	-0.086	0.000	0.000	0.000
52	C	61	THR	0	-0.007	0.002	12.449	0.076	0.076	0.000	0.000	0.000
53	C	62	GLY	0	-0.019	-0.022	13.390	0.050	0.050	0.000	0.000	0.000
54	C	63	GLN	0	-0.085	-0.050	14.412	0.036	0.036	0.000	0.000	0.000
55	C	64	TYR	0	-0.012	-0.015	14.062	-0.054	-0.054	0.000	0.000	0.000
56	C	65	LEU	0	0.031	0.017	16.259	0.029	0.029	0.000	0.000	0.000
57	C	66	ARG	1	0.788	0.870	18.109	0.147	0.147	0.000	0.000	0.000
58	C	67	ILE	0	-0.003	0.006	21.707	-0.001	-0.001	0.000	0.000	0.000
59	C	68	ASN	0	-0.038	-0.015	24.312	0.011	0.011	0.000	0.000	0.000
60	C	69	PRO	0	0.001	-0.022	27.704	0.001	0.001	0.000	0.000	0.000
61	C	70	ASP	-1	-0.922	-0.944	30.774	-0.107	-0.107	0.000	0.000	0.000
62	C	71	GLY	0	0.060	0.047	28.949	0.004	0.004	0.000	0.000	0.000
63	C	72	THR	0	-0.041	-0.034	27.990	-0.012	-0.012	0.000	0.000	0.000
64	C	73	VAL	0	-0.017	-0.012	21.479	-0.006	-0.006	0.000	0.000	0.000
65	C	74	ASP	-1	-0.798	-0.872	22.941	-0.152	-0.152	0.000	0.000	0.000
66	C	75	GLY	0	0.003	0.005	19.961	-0.026	-0.026	0.000	0.000	0.000
67	C	76	THR	0	0.027	0.015	19.807	0.031	0.031	0.000	0.000	0.000
68	C	76	ARG	1	0.856	0.911	17.794	0.134	0.134	0.000	0.000	0.000
69	C	77	ASP	-1	-0.876	-0.904	20.112	-0.094	-0.094	0.000	0.000	0.000
70	C	78	ARG	1	0.773	0.856	17.157	0.150	0.150	0.000	0.000	0.000
71	C	79	SER	0	-0.107	-0.076	20.946	0.000	0.000	0.000	0.000	0.000
72	C	80	ASP	-1	-0.798	-0.893	22.801	-0.136	-0.136	0.000	0.000	0.000
73	C	81	GLN	0	0.010	-0.008	23.291	-0.016	-0.016	0.000	0.000	0.000
74	C	82	HIS	0	0.008	0.020	24.285	-0.005	-0.005	0.000	0.000	0.000
75	C	83	ILE	0	-0.040	-0.023	18.534	-0.018	-0.018	0.000	0.000	0.000
76	C	84	GLN	0	-0.014	0.004	18.589	-0.043	-0.043	0.000	0.000	0.000
77	C	85	PHE	0	0.014	0.000	17.241	0.005	0.005	0.000	0.000	0.000
78	C	86	GLN	0	-0.023	-0.023	18.538	0.002	0.002	0.000	0.000	0.000
79	C	87	ILE	0	-0.001	0.006	13.442	-0.008	-0.008	0.000	0.000	0.000
80	C	88	SER	0	-0.024	-0.017	17.726	0.023	0.023	0.000	0.000	0.000
81	C	89	PRO	0	-0.042	-0.035	19.103	-0.010	-0.010	0.000	0.000	0.000
82	C	90	GLU	-1	-0.791	-0.885	20.583	-0.137	-0.137	0.000	0.000	0.000
83	C	91	GLY	0	-0.051	-0.010	21.805	0.017	0.017	0.000	0.000	0.000
84	C	92	GLY	0	0.008	-0.005	22.090	-0.001	-0.001	0.000	0.000	0.000
85	C	93	GLY	0	-0.077	-0.043	17.870	-0.005	-0.005	0.000	0.000	0.000
86	C	94	GLU	-1	-0.855	-0.912	17.075	-0.226	-0.226	0.000	0.000	0.000
87	C	95	VAL	0	-0.051	-0.037	15.565	0.012	0.012	0.000	0.000	0.000
88	C	96	LEU	0	0.036	0.034	18.777	-0.005	-0.005	0.000	0.000	0.000
89	C	97	LEU	0	-0.021	-0.016	15.542	-0.022	-0.022	0.000	0.000	0.000
90	C	98	LYS	1	0.965	0.988	19.365	0.164	0.164	0.000	0.000	0.000
91	C	99	SER	0	0.027	0.025	21.571	-0.004	-0.004	0.000	0.000	0.000
92	C	100	THR	0	-0.070	-0.061	21.927	0.014	0.014	0.000	0.000	0.000
93	C	101	GLU	-1	-0.890	-0.923	24.662	-0.097	-0.097	0.000	0.000	0.000
94	C	102	THR	0	-0.009	-0.002	26.855	0.010	0.010	0.000	0.000	0.000
95	C	103	GLY	0	-0.016	-0.014	27.216	0.009	0.009	0.000	0.000	0.000
96	C	107	GLN	0	-0.065	-0.040	26.484	0.005	0.005	0.000	0.000	0.000
97	C	108	TYR	0	-0.005	-0.021	23.456	-0.014	-0.014	0.000	0.000	0.000
98	C	109	LEU	0	0.004	0.003	18.381	0.005	0.005	0.000	0.000	0.000
99	C	110	ARG	1	0.801	0.879	22.279	0.125	0.125	0.000	0.000	0.000
100	C	111	ILE	0	-0.058	-0.026	18.834	-0.009	-0.009	0.000	0.000	0.000
101	C	112	ASN	0	0.009	0.006	23.464	0.008	0.008	0.000	0.000	0.000
102	C	113	PRO	0	-0.008	-0.025	26.158	-0.006	-0.006	0.000	0.000	0.000
103	C	114	ASP	-1	-0.917	-0.932	27.817	-0.125	-0.125	0.000	0.000	0.000
104	C	115	GLY	0	0.009	0.020	24.634	0.004	0.004	0.000	0.000	0.000
105	C	116	THR	0	-0.039	-0.039	24.435	-0.014	-0.014	0.000	0.000	0.000
106	C	117	VAL	0	-0.024	-0.018	21.104	-0.011	-0.011	0.000	0.000	0.000
107	C	118	ASP	-1	-0.822	-0.885	24.266	-0.139	-0.139	0.000	0.000	0.000
108	C	119	GLY	0	0.006	0.002	24.925	-0.017	-0.017	0.000	0.000	0.000
109	C	123	THR	0	0.096	0.054	26.640	0.015	0.015	0.000	0.000	0.000
110	C	123	ARG	1	0.846	0.906	27.940	0.100	0.100	0.000	0.000	0.000
111	C	124	ASP	-1	-0.790	-0.854	30.369	-0.100	-0.100	0.000	0.000	0.000
112	C	125	ARG	1	0.813	0.892	25.440	0.133	0.133	0.000	0.000	0.000
113	C	126	SER	0	-0.092	-0.065	28.717	-0.003	-0.003	0.000	0.000	0.000
114	C	127	ASP	-1	-0.709	-0.825	28.188	-0.134	-0.134	0.000	0.000	0.000
115	C	128	GLN	0	-0.043	-0.033	27.721	-0.009	-0.009	0.000	0.000	0.000
116	C	129	HIS	0	-0.002	0.004	25.143	-0.014	-0.014	0.000	0.000	0.000
117	C	130	ILE	0	-0.034	-0.015	23.114	-0.018	-0.018	0.000	0.000	0.000
118	C	131	GLN	0	-0.007	0.006	21.590	-0.024	-0.024	0.000	0.000	0.000
119	C	132	PHE	0	0.000	-0.014	16.325	-0.021	-0.021	0.000	0.000	0.000
120	C	133	GLN	0	0.002	0.002	14.277	-0.002	-0.002	0.000	0.000	0.000
121	C	134	ILE	0	-0.009	-0.005	9.505	-0.055	-0.055	0.000	0.000	0.000
122	C	135	SER	0	-0.057	-0.031	10.125	0.084	0.084	0.000	0.000	0.000
123	C	136	PRO	0	0.000	-0.017	5.488	-0.233	-0.233	0.000	0.000	0.000
124	C	137	GLU	-1	-0.958	-0.968	5.106	-0.099	-0.099	0.000	0.000	0.000
125	C	138	NME	0	-0.004	0.005	4.280	0.336	0.416	-0.001	-0.007	-0.072
126	B	144	SO4	-2	-1.919	-1.965	51.576	-0.078	-0.078	0.000	0.000	0.000
127	C	141	TRS	1	0.882	0.892	43.720	0.054	0.054	0.000	0.000	0.000
128	C	142	SO4	-2	-1.872	-1.907	51.775	-0.078	-0.078	0.000	0.000	0.000
129	C	143	SO4	-2	-1.932	-1.956	54.527	-0.073	-0.073	0.000	0.000	0.000
130	C	144	SO4	-2	-1.806	-1.897	32.973	-0.199	-0.199	0.000	0.000	0.000
131	A	157	HOH	0	-0.061	-0.038	31.750	0.002	0.002	0.000	0.000	0.000
132	A	158	HOH	0	-0.036	-0.035	30.416	0.000	0.000	0.000	0.000	0.000
133	B	378	HOH	0	-0.041	-0.016	49.817	-0.001	-0.001	0.000	0.000	0.000
134	C	154	HOH	0	0.038	0.035	46.358	-0.001	-0.001	0.000	0.000	0.000
135	C	155	HOH	0	0.037	0.034	48.429	0.000	0.000	0.000	0.000	0.000
136	C	157	HOH	0	0.043	0.040	41.525	0.002	0.002	0.000	0.000	0.000
137	C	226	HOH	0	-0.055	-0.035	55.329	0.001	0.001	0.000	0.000	0.000
138	C	237	HOH	0	-0.049	-0.028	35.551	0.001	0.001	0.000	0.000	0.000
139	C	284	HOH	0	-0.040	-0.019	51.846	0.000	0.000	0.000	0.000	0.000
140	C	497	HOH	0	-0.068	-0.044	58.368	0.001	0.001	0.000	0.000	0.000
141	C	526	HOH	0	-0.052	-0.023	36.537	0.002	0.002	0.000	0.000	0.000
142	C	540	HOH	0	-0.073	-0.057	52.167	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(C:10:ACE)