FMO DATABASE

FMODB ID: LV389

Calculation Name: 4F0U-B-Xray547

Preferred Name:

Target Type:

Ligand Name: phycocyanobilin | n-methyl asparagine

Ligand 3-letter code: CYC | MEN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4F0U

Chain ID: B

ChEMBL ID:

UniProt ID: Q31RG0

Base Structure: X-ray

Registration Date: 2025-10-05

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	161
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1424482.283921
FMO2-HF: Nuclear repulsion	1363303.273578
FMO2-HF: Total energy	-61179.010344
FMO2-MP2: Total energy	-61356.928336

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:1:MET)

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

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.
-204.852	-200.967	28.977	-16.2	-16.663	-0.152

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.744 / q_NPA : 0.861

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	ASP	-1	-0.837	-0.911	3.314	-41.597	-39.035	0.071	-1.125	-1.508	-0.004
4	A	4	ALA	0	0.021	0.007	4.814	0.744	0.784	-0.001	-0.004	-0.036	0.000
94	A	97	TYR	0	-0.027	-0.008	4.382	0.197	0.346	-0.001	-0.017	-0.131	0.000
95	A	98	ALA	0	0.027	0.018	4.432	-2.686	-2.593	-0.001	-0.015	-0.077	0.000
98	A	101	ALA	0	0.012	0.020	2.634	0.349	0.703	0.439	-0.178	-0.614	-0.001
99	A	102	GLY	0	-0.003	0.002	4.625	0.533	0.569	-0.001	-0.008	-0.027	0.000
100	A	103	ASP	-1	-0.802	-0.868	4.708	-48.596	-48.440	-0.001	-0.011	-0.143	0.000
102	A	105	SER	0	-0.006	-0.001	2.287	-10.975	-9.414	3.492	-2.524	-2.530	-0.017
103	A	106	ILE	0	-0.023	-0.025	2.609	-5.051	-3.598	3.605	-1.216	-3.842	0.004
104	A	107	LEU	0	-0.014	-0.016	3.418	4.842	4.830	0.055	0.114	-0.157	0.000
106	A	109	GLU	-1	-0.827	-0.920	1.754	-139.310	-141.817	21.320	-11.216	-7.598	-0.134
5	A	5	ILE	0	-0.007	-0.019	8.114	2.056	2.056	0.000	0.000	0.000	0.000
6	A	6	THR	0	-0.017	-0.015	6.445	2.839	2.839	0.000	0.000	0.000	0.000
7	A	7	ALA	0	0.007	0.016	7.841	1.327	1.327	0.000	0.000	0.000	0.000
8	A	8	VAL	0	-0.046	-0.025	9.174	2.634	2.634	0.000	0.000	0.000	0.000
9	A	9	ILE	0	0.006	0.010	11.297	1.942	1.942	0.000	0.000	0.000	0.000
10	A	10	ASN	0	0.024	0.016	7.901	3.797	3.797	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.023	-0.011	12.096	1.495	1.495	0.000	0.000	0.000	0.000
12	A	12	SER	0	-0.070	-0.039	14.279	2.016	2.016	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.913	-0.956	14.575	-19.209	-19.209	0.000	0.000	0.000	0.000
14	A	14	VAL	0	0.004	0.003	13.690	1.037	1.037	0.000	0.000	0.000	0.000
15	A	15	GLN	0	-0.073	-0.037	16.679	1.832	1.832	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.013	0.005	19.458	0.913	0.913	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.769	0.887	20.458	15.026	15.026	0.000	0.000	0.000	0.000
18	A	18	TYR	0	0.027	0.002	20.198	-0.753	-0.753	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.014	-0.012	15.906	-0.045	-0.045	0.000	0.000	0.000	0.000
20	A	20	ASP	-1	-0.782	-0.874	20.047	-13.326	-13.326	0.000	0.000	0.000	0.000
21	A	21	SER	0	0.017	0.000	21.225	-0.585	-0.585	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.048	0.022	21.261	-0.538	-0.538	0.000	0.000	0.000	0.000
23	A	23	ALA	0	0.001	0.010	17.375	-0.707	-0.707	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.025	-0.002	17.013	-0.736	-0.736	0.000	0.000	0.000	0.000
25	A	25	ASP	-1	-0.896	-0.955	18.310	-13.531	-13.531	0.000	0.000	0.000	0.000
26	A	26	ARG	1	0.873	0.938	14.552	17.656	17.656	0.000	0.000	0.000	0.000
27	A	27	LEU	0	0.006	0.020	12.737	-0.589	-0.589	0.000	0.000	0.000	0.000
28	A	28	LYS	1	0.955	0.985	14.769	12.483	12.483	0.000	0.000	0.000	0.000
29	A	29	SER	0	-0.025	-0.013	16.587	0.302	0.302	0.000	0.000	0.000	0.000
30	A	30	TYR	0	-0.007	-0.016	7.274	0.466	0.466	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.024	0.003	12.289	0.049	0.049	0.000	0.000	0.000	0.000
32	A	32	GLN	0	-0.035	-0.018	14.640	0.669	0.669	0.000	0.000	0.000	0.000
33	A	33	SER	0	-0.028	-0.001	13.562	0.203	0.203	0.000	0.000	0.000	0.000
34	A	34	GLY	0	0.041	0.015	12.199	-0.348	-0.348	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.924	-0.969	13.144	-13.276	-13.276	0.000	0.000	0.000	0.000
36	A	36	LEU	0	-0.028	-0.007	14.837	0.260	0.260	0.000	0.000	0.000	0.000
37	A	37	ARG	1	0.809	0.870	9.551	21.006	21.006	0.000	0.000	0.000	0.000
38	A	38	VAL	0	0.029	0.010	11.460	-0.214	-0.214	0.000	0.000	0.000	0.000
39	A	39	ARG	1	0.944	0.974	12.861	12.354	12.354	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.044	0.030	13.463	0.542	0.542	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.026	0.010	10.602	0.248	0.248	0.000	0.000	0.000	0.000
42	A	42	ALA	0	-0.026	-0.010	12.576	0.296	0.296	0.000	0.000	0.000	0.000
43	A	43	THR	0	-0.010	-0.021	15.572	0.425	0.425	0.000	0.000	0.000	0.000
44	A	44	ILE	0	0.039	0.015	13.521	0.541	0.541	0.000	0.000	0.000	0.000
45	A	45	SER	0	-0.046	-0.020	14.083	0.264	0.264	0.000	0.000	0.000	0.000
46	A	46	ALA	0	-0.001	0.003	15.803	0.353	0.353	0.000	0.000	0.000	0.000
47	A	47	ASN	0	-0.017	-0.013	19.159	0.866	0.866	0.000	0.000	0.000	0.000
48	A	48	SER	0	-0.018	0.000	16.776	0.334	0.334	0.000	0.000	0.000	0.000
49	A	49	ALA	0	0.016	-0.008	18.725	0.096	0.096	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.069	-0.026	21.910	0.363	0.363	0.000	0.000	0.000	0.000
51	A	51	ILE	0	0.058	0.017	18.170	0.157	0.157	0.000	0.000	0.000	0.000
52	A	52	VAL	0	0.015	0.014	19.599	0.143	0.143	0.000	0.000	0.000	0.000
53	A	53	LYS	1	0.922	0.967	22.153	10.723	10.723	0.000	0.000	0.000	0.000
54	A	54	GLU	-1	-0.873	-0.944	25.345	-10.065	-10.065	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.015	0.010	22.937	0.250	0.250	0.000	0.000	0.000	0.000
56	A	56	VAL	0	0.000	0.009	24.460	0.177	0.177	0.000	0.000	0.000	0.000
57	A	57	ALA	0	-0.030	-0.026	26.727	0.278	0.278	0.000	0.000	0.000	0.000
58	A	58	LYS	1	0.849	0.923	26.769	10.886	10.886	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.027	-0.033	26.613	-0.058	-0.058	0.000	0.000	0.000	0.000
60	A	60	LEU	0	0.020	0.005	25.049	0.299	0.299	0.000	0.000	0.000	0.000
61	A	61	LEU	0	-0.083	-0.036	29.480	0.270	0.270	0.000	0.000	0.000	0.000
62	A	62	TYR	0	0.017	0.021	32.471	0.300	0.300	0.000	0.000	0.000	0.000
63	A	64	SER	0	-0.047	-0.025	31.913	0.038	0.038	0.000	0.000	0.000	0.000
64	A	65	ASP	-1	-0.856	-0.941	34.140	-8.050	-8.050	0.000	0.000	0.000	0.000
65	A	66	ILE	0	-0.020	-0.003	28.327	0.043	0.043	0.000	0.000	0.000	0.000
66	A	67	THR	0	0.002	-0.012	32.091	-0.110	-0.110	0.000	0.000	0.000	0.000
67	A	68	ARG	1	0.954	0.984	34.097	7.809	7.809	0.000	0.000	0.000	0.000
68	A	69	PRO	0	-0.033	-0.033	36.694	-0.166	-0.166	0.000	0.000	0.000	0.000
69	A	70	GLY	0	0.001	0.008	36.831	0.163	0.163	0.000	0.000	0.000	0.000
70	A	71	GLY	0	0.037	0.030	34.037	-0.184	-0.184	0.000	0.000	0.000	0.000
71	A	72	ASN	0	-0.010	-0.019	28.486	0.164	0.164	0.000	0.000	0.000	0.000
72	A	75	MET	0	0.025	0.026	27.935	-0.469	-0.469	0.000	0.000	0.000	0.000
73	A	76	TYR	0	0.036	0.036	29.898	0.159	0.159	0.000	0.000	0.000	0.000
74	A	77	THR	0	-0.059	-0.043	31.813	-0.267	-0.267	0.000	0.000	0.000	0.000
75	A	78	THR	0	0.069	0.017	31.207	-0.285	-0.285	0.000	0.000	0.000	0.000
76	A	79	ARG	1	0.991	1.001	26.781	10.527	10.527	0.000	0.000	0.000	0.000
77	A	80	ARG	1	0.889	0.960	26.923	9.351	9.351	0.000	0.000	0.000	0.000
78	A	81	TYR	0	0.049	0.028	26.315	-0.452	-0.452	0.000	0.000	0.000	0.000
79	A	82	ALA	0	0.016	0.000	25.933	-0.323	-0.323	0.000	0.000	0.000	0.000
80	A	83	ALA	0	-0.035	-0.013	22.664	-0.467	-0.467	0.000	0.000	0.000	0.000
81	A	84	CYS	0	-0.014	-0.001	21.526	-0.665	-0.665	0.000	0.000	0.000	0.000
82	A	85	ILE	0	0.010	0.003	21.734	-0.407	-0.407	0.000	0.000	0.000	0.000
83	A	86	ARG	1	0.888	0.934	18.361	14.589	14.589	0.000	0.000	0.000	0.000
84	A	87	ASP	-1	-0.794	-0.854	17.335	-16.352	-16.352	0.000	0.000	0.000	0.000
85	A	88	LEU	0	-0.007	-0.001	16.813	-0.879	-0.879	0.000	0.000	0.000	0.000
86	A	89	GLU	-1	-0.904	-0.960	17.177	-14.213	-14.213	0.000	0.000	0.000	0.000
87	A	90	TYR	0	-0.081	-0.047	13.325	-0.877	-0.877	0.000	0.000	0.000	0.000
88	A	91	TYR	0	0.027	-0.004	12.716	-1.663	-1.663	0.000	0.000	0.000	0.000
89	A	92	LEU	0	0.046	0.034	12.923	-0.897	-0.897	0.000	0.000	0.000	0.000
90	A	93	ARG	1	0.930	0.974	10.402	19.538	19.538	0.000	0.000	0.000	0.000
91	A	94	TYR	0	0.026	-0.007	6.923	-1.661	-1.661	0.000	0.000	0.000	0.000
92	A	95	ALA	0	0.042	0.030	7.877	-2.277	-2.277	0.000	0.000	0.000	0.000
93	A	96	THR	0	-0.022	-0.031	9.164	-0.178	-0.178	0.000	0.000	0.000	0.000
96	A	99	MET	0	-0.040	0.011	5.913	-0.082	-0.082	0.000	0.000	0.000	0.000
97	A	100	LEU	0	-0.010	-0.006	5.714	1.086	1.086	0.000	0.000	0.000	0.000
101	A	104	THR	0	0.022	0.007	5.352	-1.188	-1.188	0.000	0.000	0.000	0.000
105	A	108	ASP	-1	-0.779	-0.867	6.019	-31.957	-31.957	0.000	0.000	0.000	0.000
107	A	110	ARG	1	0.825	0.908	4.965	36.724	36.724	0.000	0.000	0.000	0.000
108	A	111	VAL	0	-0.056	-0.012	7.113	3.306	3.306	0.000	0.000	0.000	0.000
109	A	112	LEU	0	0.043	0.014	9.750	2.015	2.015	0.000	0.000	0.000	0.000
110	A	113	ASN	0	-0.028	0.001	9.823	1.621	1.621	0.000	0.000	0.000	0.000
111	A	114	GLY	0	0.028	0.025	11.794	0.277	0.277	0.000	0.000	0.000	0.000
112	A	115	LEU	0	-0.027	0.005	13.971	1.327	1.327	0.000	0.000	0.000	0.000
113	A	116	LYS	1	0.878	0.938	16.106	16.709	16.709	0.000	0.000	0.000	0.000
114	A	117	GLU	-1	-0.875	-0.942	17.698	-16.256	-16.256	0.000	0.000	0.000	0.000
115	A	118	THR	0	-0.032	-0.017	17.975	0.936	0.936	0.000	0.000	0.000	0.000
116	A	119	TYR	0	-0.020	-0.043	19.380	0.772	0.772	0.000	0.000	0.000	0.000
117	A	120	ASN	0	0.007	0.001	21.808	0.922	0.922	0.000	0.000	0.000	0.000
118	A	121	SER	0	-0.076	-0.051	23.204	0.586	0.586	0.000	0.000	0.000	0.000
119	A	122	LEU	0	-0.056	-0.022	22.191	0.478	0.478	0.000	0.000	0.000	0.000
120	A	123	GLY	0	-0.012	0.011	25.934	0.360	0.360	0.000	0.000	0.000	0.000
121	A	124	VAL	0	-0.038	-0.023	22.388	0.425	0.425	0.000	0.000	0.000	0.000
122	A	125	PRO	0	-0.025	-0.013	24.997	-0.146	-0.146	0.000	0.000	0.000	0.000
123	A	126	ILE	0	0.106	0.050	21.432	0.013	0.013	0.000	0.000	0.000	0.000
124	A	127	GLY	0	0.023	0.021	23.302	-0.203	-0.203	0.000	0.000	0.000	0.000
125	A	128	ALA	0	0.010	0.003	25.697	0.030	0.030	0.000	0.000	0.000	0.000
126	A	129	THR	0	-0.034	-0.026	20.710	-0.210	-0.210	0.000	0.000	0.000	0.000
127	A	130	VAL	0	0.040	0.022	20.587	-0.287	-0.287	0.000	0.000	0.000	0.000
128	A	131	GLN	0	-0.032	-0.019	22.144	0.082	0.082	0.000	0.000	0.000	0.000
129	A	132	ALA	0	0.011	0.010	22.822	0.122	0.122	0.000	0.000	0.000	0.000
130	A	133	ILE	0	0.001	0.003	17.298	-0.011	-0.011	0.000	0.000	0.000	0.000
131	A	134	GLN	0	-0.014	-0.020	20.094	-0.558	-0.558	0.000	0.000	0.000	0.000
132	A	135	ALA	0	-0.019	-0.011	22.343	0.175	0.175	0.000	0.000	0.000	0.000
133	A	136	ILE	0	0.014	0.000	17.520	0.193	0.193	0.000	0.000	0.000	0.000
134	A	137	LYS	1	0.808	0.927	18.816	13.781	13.781	0.000	0.000	0.000	0.000
135	A	138	GLU	-1	-0.833	-0.896	19.929	-10.771	-10.771	0.000	0.000	0.000	0.000
136	A	139	VAL	0	0.016	0.019	22.508	0.176	0.176	0.000	0.000	0.000	0.000
137	A	140	THR	0	-0.022	-0.020	17.040	0.019	0.019	0.000	0.000	0.000	0.000
138	A	141	ALA	0	0.026	0.009	19.844	0.118	0.118	0.000	0.000	0.000	0.000
139	A	142	SER	0	-0.115	-0.064	21.310	0.388	0.388	0.000	0.000	0.000	0.000
140	A	143	LEU	0	0.001	-0.002	21.361	0.302	0.302	0.000	0.000	0.000	0.000
141	A	144	VAL	0	-0.057	-0.020	17.020	-0.024	-0.024	0.000	0.000	0.000	0.000
142	A	145	GLY	0	0.013	0.022	20.072	0.037	0.037	0.000	0.000	0.000	0.000
143	A	146	PRO	0	0.011	-0.011	21.038	-0.501	-0.501	0.000	0.000	0.000	0.000
144	A	147	ASP	-1	-0.841	-0.918	20.241	-12.391	-12.391	0.000	0.000	0.000	0.000
145	A	148	ALA	0	0.043	0.009	16.223	-0.579	-0.579	0.000	0.000	0.000	0.000
146	A	149	GLY	0	0.020	0.018	16.250	-0.726	-0.726	0.000	0.000	0.000	0.000
147	A	150	ARG	1	0.815	0.901	18.095	12.486	12.486	0.000	0.000	0.000	0.000
148	A	161	GLU	-1	-0.827	-0.889	12.474	-19.919	-19.919	0.000	0.000	0.000	0.000
149	A	162	MET	0	0.008	-0.013	12.485	-1.432	-1.432	0.000	0.000	0.000	0.000
150	A	163	GLY	0	0.004	-0.005	14.286	-0.529	-0.529	0.000	0.000	0.000	0.000
151	A	164	VAL	0	0.005	0.017	12.936	-0.072	-0.072	0.000	0.000	0.000	0.000
152	A	165	TYR	0	0.004	-0.012	8.669	-1.282	-1.282	0.000	0.000	0.000	0.000
153	A	166	LEU	0	-0.017	-0.004	11.973	-0.552	-0.552	0.000	0.000	0.000	0.000
154	A	167	ASP	-1	-0.805	-0.902	14.952	-14.722	-14.722	0.000	0.000	0.000	0.000
155	A	168	TYR	0	-0.067	-0.048	9.729	1.100	1.100	0.000	0.000	0.000	0.000
156	A	169	ILE	0	-0.012	-0.002	11.758	-0.257	-0.257	0.000	0.000	0.000	0.000
157	A	170	SER	0	0.005	-0.015	14.119	0.446	0.446	0.000	0.000	0.000	0.000
158	A	171	SER	0	-0.055	-0.044	16.897	0.296	0.296	0.000	0.000	0.000	0.000
159	A	172	GLY	0	0.035	0.031	14.785	0.056	0.056	0.000	0.000	0.000	0.000
160	A	173	LEU	0	-0.061	-0.039	15.737	0.210	0.210	0.000	0.000	0.000	0.000
161	A	174	SER	-1	-0.881	-0.917	18.439	-13.953	-13.953	0.000	0.000	0.000	0.000

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