FMO DATABASE

FMODB ID: MNYLZ

Calculation Name: 3OMD-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name: cysteinesulfonic acid

ligand 3-letter code: OCS

PDB ID: 3OMD

Chain ID: A

ChEMBL ID:
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UniProt ID:
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Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	145
LigandCharge	OCS=-1
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1436579.516084
FMO2-HF: Nuclear repulsion	1377281.384064
FMO2-HF: Total energy	-59298.132021
FMO2-MP2: Total energy	-59472.217389

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:-4:LEU)

Summations of interaction energy for fragment #1(A:-4:LEU)

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.
-1.456	2.342	0.323	-1.555	-2.565	0

Interaction energy analysis for fragmet #1(A:-4:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.040 / q_NPA : 0.028

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].
3	A	-2	PHE	0	-0.007	-0.014	3.207	-2.446	1.181	0.324	-1.539	-2.412
4	A	-1	GLN	0	-0.030	-0.008	4.398	0.275	0.419	0.000	-0.012	-0.131
5	A	0	GLY	0	0.048	0.023	6.097	0.116	0.116	0.000	0.000	0.000
6	A	1	MET	0	-0.026	-0.002	7.242	0.066	0.066	0.000	0.000	0.000
7	A	2	ASP	-1	-0.753	-0.834	9.757	0.322	0.322	0.000	0.000	0.000
8	A	3	LEU	0	-0.020	-0.006	11.221	-0.020	-0.020	0.000	0.000	0.000
9	A	4	THR	0	-0.049	-0.042	13.622	0.010	0.010	0.000	0.000	0.000
10	A	5	LYS	1	0.782	0.874	13.057	-0.258	-0.258	0.000	0.000	0.000
11	A	6	GLN	0	-0.050	-0.022	12.643	-0.035	-0.035	0.000	0.000	0.000
12	A	7	PHE	0	0.024	0.020	17.157	0.013	0.013	0.000	0.000	0.000
13	A	8	PRO	0	-0.042	0.004	17.400	-0.021	-0.021	0.000	0.000	0.000
14	A	9	ARG	1	0.777	0.819	17.478	0.222	0.222	0.000	0.000	0.000
15	A	10	SER	0	-0.008	-0.019	21.414	0.003	0.003	0.000	0.000	0.000
16	A	11	PRO	0	-0.014	-0.009	25.096	-0.012	-0.012	0.000	0.000	0.000
17	A	12	VAL	0	-0.013	-0.010	26.711	-0.005	-0.005	0.000	0.000	0.000
18	A	13	ASP	-1	-0.845	-0.913	23.672	-0.122	-0.122	0.000	0.000	0.000
19	A	14	ARG	1	0.802	0.878	25.358	0.062	0.062	0.000	0.000	0.000
20	A	15	LEU	0	-0.012	-0.008	21.713	-0.005	-0.005	0.000	0.000	0.000
21	A	16	GLY	0	0.051	0.019	25.872	0.001	0.001	0.000	0.000	0.000
22	A	17	GLY	0	-0.036	-0.008	28.265	0.006	0.006	0.000	0.000	0.000
23	A	18	MET	0	-0.023	-0.008	27.075	0.005	0.005	0.000	0.000	0.000
24	A	19	ASH	0	0.015	-0.035	27.480	-0.007	-0.007	0.000	0.000	0.000
25	A	20	HIS	0	0.019	0.021	22.255	-0.002	-0.002	0.000	0.000	0.000
26	A	21	LEU	0	-0.017	-0.003	21.500	-0.009	-0.009	0.000	0.000	0.000
27	A	22	LYS	1	0.850	0.920	20.241	0.122	0.122	0.000	0.000	0.000
28	A	23	ARG	1	0.815	0.887	19.085	0.039	0.039	0.000	0.000	0.000
29	A	24	VAL	0	0.018	0.005	18.663	0.001	0.001	0.000	0.000	0.000
30	A	25	ILE	0	-0.009	-0.007	15.745	-0.028	-0.028	0.000	0.000	0.000
31	A	26	ASP	-1	-0.769	-0.861	14.671	-0.253	-0.253	0.000	0.000	0.000
32	A	27	LYS	1	0.834	0.911	13.646	0.058	0.058	0.000	0.000	0.000
33	A	28	ALA	0	0.004	0.013	13.494	0.011	0.011	0.000	0.000	0.000
34	A	29	ARG	1	0.825	0.908	10.323	0.470	0.470	0.000	0.000	0.000
35	A	30	ALA	0	0.015	0.007	8.896	-0.085	-0.085	0.000	0.000	0.000
36	A	31	HIS	0	-0.005	-0.006	9.510	0.117	0.117	0.000	0.000	0.000
37	A	32	VAL	0	-0.053	-0.027	6.165	0.050	0.050	0.000	0.000	0.000
38	A	33	ALA	0	-0.044	-0.020	4.768	-0.233	-0.206	-0.001	-0.004	-0.022
39	A	34	GLY	0	0.004	0.024	5.819	0.518	0.518	0.000	0.000	0.000
40	A	35	THR	0	-0.074	-0.050	7.370	0.064	0.064	0.000	0.000	0.000
41	A	36	LEU	0	0.009	-0.008	10.090	-0.066	-0.066	0.000	0.000	0.000
42	A	37	GLY	0	0.010	-0.003	13.417	-0.026	-0.026	0.000	0.000	0.000
43	A	38	GLU	-1	-0.923	-0.957	15.689	0.101	0.101	0.000	0.000	0.000
44	A	39	TYR	0	-0.057	-0.042	16.965	-0.020	-0.020	0.000	0.000	0.000
45	A	40	THR	0	0.001	-0.014	17.471	0.020	0.020	0.000	0.000	0.000
46	A	41	TYR	0	-0.062	-0.056	15.298	-0.026	-0.026	0.000	0.000	0.000
47	A	42	ASN	0	-0.013	-0.018	17.309	0.008	0.008	0.000	0.000	0.000
48	A	43	OCS	-1	-0.836	-0.883	20.236	-0.030	-0.030	0.000	0.000	0.000
49	A	44	PRO	0	0.059	0.006	22.662	-0.012	-0.012	0.000	0.000	0.000
50	A	45	LEU	0	0.000	0.005	24.611	-0.005	-0.005	0.000	0.000	0.000
51	A	46	ASP	-1	-0.741	-0.862	19.553	-0.107	-0.107	0.000	0.000	0.000
52	A	47	GLN	0	-0.055	-0.031	23.029	-0.008	-0.008	0.000	0.000	0.000
53	A	48	ALA	0	0.000	0.005	25.242	-0.004	-0.004	0.000	0.000	0.000
54	A	49	PHE	0	-0.003	-0.009	23.195	-0.003	-0.003	0.000	0.000	0.000
55	A	50	PHE	0	-0.010	-0.027	19.026	-0.005	-0.005	0.000	0.000	0.000
56	A	51	SER	0	0.007	0.010	25.258	-0.003	-0.003	0.000	0.000	0.000
57	A	52	PHE	0	0.001	0.011	28.626	0.001	0.001	0.000	0.000	0.000
58	A	53	PHE	0	0.006	-0.007	27.254	0.001	0.001	0.000	0.000	0.000
59	A	54	GLY	0	0.008	0.040	28.725	-0.006	-0.006	0.000	0.000	0.000
60	A	55	LEU	0	-0.062	-0.028	23.139	-0.011	-0.011	0.000	0.000	0.000
61	A	56	ASP	-1	-0.758	-0.871	20.446	-0.159	-0.159	0.000	0.000	0.000
62	A	57	HIS	0	0.020	0.008	18.244	-0.033	-0.033	0.000	0.000	0.000
63	A	58	GLU	-1	-0.866	-0.908	16.291	-0.162	-0.162	0.000	0.000	0.000
64	A	59	LYS	1	0.878	0.908	15.676	0.117	0.117	0.000	0.000	0.000
65	A	60	PHE	0	-0.011	-0.004	16.625	-0.042	-0.042	0.000	0.000	0.000
66	A	61	ALA	0	0.018	0.003	12.689	-0.042	-0.042	0.000	0.000	0.000
67	A	62	GLU	-1	-0.820	-0.903	11.303	-0.852	-0.852	0.000	0.000	0.000
68	A	63	ALA	0	-0.046	-0.014	13.108	-0.090	-0.090	0.000	0.000	0.000
69	A	64	VAL	0	0.073	0.008	11.538	-0.032	-0.032	0.000	0.000	0.000
70	A	65	LYS	1	0.792	0.898	7.955	0.835	0.835	0.000	0.000	0.000
71	A	66	SER	0	-0.031	-0.015	9.390	-0.103	-0.103	0.000	0.000	0.000
72	A	67	ARG	1	0.841	0.936	12.124	0.534	0.534	0.000	0.000	0.000
73	A	68	PRO	0	0.039	0.030	11.292	0.006	0.006	0.000	0.000	0.000
74	A	69	GLN	0	0.006	0.007	12.952	0.067	0.067	0.000	0.000	0.000
75	A	70	ASP	-1	-0.775	-0.877	16.588	-0.239	-0.239	0.000	0.000	0.000
76	A	71	GLN	0	0.010	-0.011	19.131	0.011	0.011	0.000	0.000	0.000
77	A	72	ASP	-1	-0.810	-0.901	16.630	-0.365	-0.365	0.000	0.000	0.000
78	A	73	MET	0	-0.011	0.006	16.698	-0.013	-0.013	0.000	0.000	0.000
79	A	74	LEU	0	-0.026	0.010	19.450	0.019	0.019	0.000	0.000	0.000
80	A	75	ALA	0	0.021	0.008	22.458	0.016	0.016	0.000	0.000	0.000
81	A	76	TRP	0	0.004	0.007	20.187	0.004	0.004	0.000	0.000	0.000
82	A	77	VAL	0	0.054	0.034	22.025	0.015	0.015	0.000	0.000	0.000
83	A	78	HIS	0	-0.019	-0.028	24.222	0.015	0.015	0.000	0.000	0.000
84	A	79	SER	0	-0.127	-0.086	23.922	0.009	0.009	0.000	0.000	0.000
85	A	80	GLN	0	-0.043	-0.022	22.878	0.010	0.010	0.000	0.000	0.000
86	A	81	SER	0	0.003	-0.009	26.258	0.016	0.016	0.000	0.000	0.000
87	A	82	PRO	0	0.005	-0.010	28.874	0.000	0.000	0.000	0.000	0.000
88	A	83	ARG	1	0.805	0.885	31.854	0.077	0.077	0.000	0.000	0.000
89	A	84	SER	0	0.001	-0.007	28.698	0.001	0.001	0.000	0.000	0.000
90	A	85	LYS	1	0.902	0.967	30.288	0.132	0.132	0.000	0.000	0.000
91	A	86	ASN	0	0.015	0.016	32.937	0.005	0.005	0.000	0.000	0.000
92	A	87	PRO	0	0.055	0.016	35.103	0.001	0.001	0.000	0.000	0.000
93	A	88	LYS	1	0.857	0.907	36.133	0.063	0.063	0.000	0.000	0.000
94	A	89	GLU	-1	-0.789	-0.883	35.278	-0.063	-0.063	0.000	0.000	0.000
95	A	90	VAL	0	-0.009	0.013	31.369	0.000	0.000	0.000	0.000	0.000
96	A	91	GLU	-1	-0.851	-0.910	33.599	-0.063	-0.063	0.000	0.000	0.000
97	A	92	SER	0	-0.063	-0.014	36.399	0.005	0.005	0.000	0.000	0.000
98	A	93	PHE	0	0.020	0.016	28.066	0.003	0.003	0.000	0.000	0.000
99	A	94	ASN	0	0.015	-0.012	31.560	0.001	0.001	0.000	0.000	0.000
100	A	95	ARG	1	0.941	0.975	33.553	0.045	0.045	0.000	0.000	0.000
101	A	96	GLU	-1	-0.806	-0.869	34.471	-0.044	-0.044	0.000	0.000	0.000
102	A	97	TYR	0	-0.036	-0.041	25.955	0.006	0.006	0.000	0.000	0.000
103	A	98	GLU	-1	-0.795	-0.859	32.590	-0.056	-0.056	0.000	0.000	0.000
104	A	99	SER	0	-0.089	-0.041	34.049	0.005	0.005	0.000	0.000	0.000
105	A	100	ARG	1	0.838	0.903	30.918	0.051	0.051	0.000	0.000	0.000
106	A	101	SER	0	0.055	0.013	34.467	0.002	0.002	0.000	0.000	0.000
107	A	102	PRO	0	-0.035	-0.024	36.023	-0.001	-0.001	0.000	0.000	0.000
108	A	103	ASP	-1	-0.814	-0.855	35.618	-0.005	-0.005	0.000	0.000	0.000
109	A	104	SER	0	0.012	-0.017	38.225	0.001	0.001	0.000	0.000	0.000
110	A	105	PRO	0	0.002	-0.015	39.755	0.001	0.001	0.000	0.000	0.000
111	A	106	GLU	-1	-0.887	-0.930	37.369	0.018	0.018	0.000	0.000	0.000
112	A	107	LYS	1	0.884	0.917	34.056	0.003	0.003	0.000	0.000	0.000
113	A	108	TRP	0	0.000	-0.004	36.419	0.000	0.000	0.000	0.000	0.000
114	A	109	ASP	-1	-0.843	-0.904	39.061	0.012	0.012	0.000	0.000	0.000
115	A	110	TYR	0	0.000	0.006	29.233	0.000	0.000	0.000	0.000	0.000
116	A	111	PHE	0	-0.021	-0.013	34.034	0.001	0.001	0.000	0.000	0.000
117	A	112	ARG	1	0.824	0.899	35.411	-0.007	-0.007	0.000	0.000	0.000
118	A	113	SER	0	0.008	0.009	35.919	0.001	0.001	0.000	0.000	0.000
119	A	114	VAL	0	0.006	0.021	30.462	0.003	0.003	0.000	0.000	0.000
120	A	115	ARG	1	0.825	0.894	33.524	-0.001	-0.001	0.000	0.000	0.000
121	A	116	ASP	-1	-0.844	-0.918	35.230	0.007	0.007	0.000	0.000	0.000
122	A	117	SER	0	-0.069	-0.040	33.565	0.003	0.003	0.000	0.000	0.000
123	A	118	LEU	0	-0.033	-0.002	29.764	0.001	0.001	0.000	0.000	0.000
124	A	119	ALA	0	-0.025	-0.034	33.807	-0.001	-0.001	0.000	0.000	0.000
125	A	120	PRO	0	0.019	0.024	36.887	-0.003	-0.003	0.000	0.000	0.000
126	A	121	GLY	0	-0.022	-0.001	40.194	-0.001	-0.001	0.000	0.000	0.000
127	A	122	ARG	1	0.736	0.817	36.792	0.011	0.011	0.000	0.000	0.000
128	A	123	THR	0	0.017	-0.005	39.751	-0.001	-0.001	0.000	0.000	0.000
129	A	124	ASP	-1	-0.782	-0.853	39.948	-0.013	-0.013	0.000	0.000	0.000
130	A	125	ILE	0	-0.036	-0.004	34.789	-0.003	-0.003	0.000	0.000	0.000
131	A	126	THR	0	-0.005	-0.019	37.889	0.002	0.002	0.000	0.000	0.000
132	A	127	THR	0	-0.016	0.005	35.155	0.001	0.001	0.000	0.000	0.000
133	A	128	TRP	0	0.049	0.000	30.237	0.001	0.001	0.000	0.000	0.000
134	A	129	VAL	0	-0.031	-0.003	29.436	0.001	0.001	0.000	0.000	0.000
135	A	130	LYS	1	0.983	0.985	30.015	0.032	0.032	0.000	0.000	0.000
136	A	131	LEU	0	0.022	0.026	30.739	0.001	0.001	0.000	0.000	0.000
137	A	132	LEU	0	0.038	0.015	25.171	0.002	0.002	0.000	0.000	0.000
138	A	133	ASP	-1	-0.757	-0.860	26.927	-0.051	-0.051	0.000	0.000	0.000
139	A	134	LEU	0	-0.054	-0.016	28.472	0.001	0.001	0.000	0.000	0.000
140	A	135	GLU	-1	-0.916	-0.956	26.104	0.020	0.020	0.000	0.000	0.000
141	A	136	GLU	-1	-0.757	-0.814	22.587	-0.033	-0.033	0.000	0.000	0.000
142	A	137	LYS	1	0.898	0.948	25.425	-0.030	-0.030	0.000	0.000	0.000
143	A	138	ARG	1	0.814	0.891	22.252	0.048	0.048	0.000	0.000	0.000
144	A	139	PRO	0	-0.011	-0.017	28.967	0.004	0.004	0.000	0.000	0.000
145	A	140	VAL	0	-0.010	0.023	31.775	-0.003	-0.003	0.000	0.000	0.000

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Graph

Overview

Highlights

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:-4:LEU)