FMO DATABASE

FMODB ID: 9RVJ2

Calculation Name: 4F0U-A-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: A

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	160
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1395883.134964
FMO2-HF: Nuclear repulsion	1335586.106309
FMO2-HF: Total energy	-60297.028656
FMO2-MP2: Total energy	-60474.313388

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:3:SER)

Summations of interaction energy for fragment #1(A:3:SER)

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.
-164.881	-157.136	25.097	-17.162	-15.677	-0.173

Interaction energy analysis for fragmet #1(A:3:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.806 / q_NPA : 0.885

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	5	VAL	0	0.038	0.018	2.652	7.360	9.621	0.244	-1.009	-1.495	-0.004
4	A	6	SER	0	0.034	0.017	2.047	-11.710	-10.682	3.941	-2.316	-2.653	-0.032
5	A	7	LYS	1	0.884	0.943	3.417	69.346	70.036	0.004	-0.209	-0.485	-0.001
28	A	30	PHE	0	-0.019	-0.012	3.182	-2.970	-1.602	0.246	-0.728	-0.886	-0.009
97	A	101	SER	0	-0.059	-0.049	2.762	-7.493	-5.789	0.739	-0.927	-1.515	0.006
98	A	102	GLY	0	0.028	0.007	2.290	-21.983	-18.901	4.117	-3.596	-3.603	-0.041
99	A	103	ASP	-1	-0.852	-0.898	1.736	-111.237	-113.848	15.808	-8.321	-4.876	-0.092
100	A	104	ILE	0	0.078	0.045	4.146	4.181	4.284	0.000	-0.047	-0.056	0.000
101	A	105	THR	0	-0.022	-0.030	4.335	3.284	3.330	-0.001	-0.005	-0.039	0.000
102	A	106	PRO	0	-0.045	-0.026	4.582	3.200	3.274	-0.001	-0.004	-0.069	0.000
6	A	8	SER	0	0.007	-0.006	5.685	6.917	6.917	0.000	0.000	0.000	0.000
7	A	9	ILE	0	0.001	-0.005	7.096	3.865	3.865	0.000	0.000	0.000	0.000
8	A	10	VAL	0	0.021	0.018	7.663	2.942	2.942	0.000	0.000	0.000	0.000
9	A	11	ASN	0	-0.049	-0.023	9.726	1.880	1.880	0.000	0.000	0.000	0.000
10	A	12	ALA	0	-0.018	-0.012	11.853	1.901	1.901	0.000	0.000	0.000	0.000
11	A	13	ASP	-1	-0.928	-0.956	12.705	-19.190	-19.190	0.000	0.000	0.000	0.000
12	A	14	ALA	0	-0.007	0.000	13.822	1.548	1.548	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.883	-0.920	15.712	-17.861	-17.861	0.000	0.000	0.000	0.000
14	A	16	ALA	0	-0.046	-0.012	17.510	0.937	0.937	0.000	0.000	0.000	0.000
15	A	17	ARG	1	0.686	0.820	14.125	21.439	21.439	0.000	0.000	0.000	0.000
16	A	18	TYR	0	0.020	0.002	16.140	-1.060	-1.060	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.005	-0.003	9.749	-0.021	-0.021	0.000	0.000	0.000	0.000
18	A	20	SER	0	-0.006	-0.019	14.095	1.440	1.440	0.000	0.000	0.000	0.000
19	A	21	PRO	0	0.025	-0.006	14.576	-1.206	-1.206	0.000	0.000	0.000	0.000
20	A	22	GLY	0	0.069	0.028	15.188	-0.467	-0.467	0.000	0.000	0.000	0.000
21	A	23	GLU	-1	-0.778	-0.864	10.769	-26.231	-26.231	0.000	0.000	0.000	0.000
22	A	24	LEU	0	0.022	0.008	10.254	-2.284	-2.284	0.000	0.000	0.000	0.000
23	A	25	GLU	-1	-0.984	-0.978	11.924	-19.041	-19.041	0.000	0.000	0.000	0.000
24	A	26	ARG	1	0.982	0.994	8.731	24.623	24.623	0.000	0.000	0.000	0.000
25	A	27	ILE	0	-0.016	0.003	6.457	-2.113	-2.113	0.000	0.000	0.000	0.000
26	A	28	LYS	1	0.953	0.970	8.109	18.234	18.234	0.000	0.000	0.000	0.000
27	A	29	THR	0	-0.014	-0.015	10.515	0.971	0.971	0.000	0.000	0.000	0.000
29	A	31	VAL	0	-0.028	-0.017	7.027	0.051	0.051	0.000	0.000	0.000	0.000
30	A	32	VAL	0	-0.022	-0.013	8.379	1.265	1.265	0.000	0.000	0.000	0.000
31	A	33	GLY	0	0.019	0.019	9.950	1.506	1.506	0.000	0.000	0.000	0.000
32	A	34	GLY	0	0.008	0.005	8.265	-0.235	-0.235	0.000	0.000	0.000	0.000
33	A	35	ASP	-1	-0.888	-0.956	9.194	-19.653	-19.653	0.000	0.000	0.000	0.000
34	A	36	ARG	1	0.728	0.849	12.331	18.598	18.598	0.000	0.000	0.000	0.000
35	A	37	ARG	1	0.820	0.897	6.749	32.277	32.277	0.000	0.000	0.000	0.000
36	A	38	LEU	0	0.000	0.002	8.916	0.405	0.405	0.000	0.000	0.000	0.000
37	A	39	ARG	1	0.973	0.984	11.532	16.772	16.772	0.000	0.000	0.000	0.000
38	A	40	ILE	0	0.017	0.031	13.131	0.857	0.857	0.000	0.000	0.000	0.000
39	A	41	ALA	0	0.011	0.003	11.310	0.628	0.628	0.000	0.000	0.000	0.000
40	A	42	GLN	0	-0.074	-0.036	13.406	0.226	0.226	0.000	0.000	0.000	0.000
41	A	43	THR	0	0.006	-0.008	15.972	0.835	0.835	0.000	0.000	0.000	0.000
42	A	44	ILE	0	0.018	0.009	15.339	0.829	0.829	0.000	0.000	0.000	0.000
43	A	45	ALA	0	-0.012	-0.008	16.144	0.653	0.653	0.000	0.000	0.000	0.000
44	A	46	GLU	-1	-0.932	-0.959	18.168	-13.199	-13.199	0.000	0.000	0.000	0.000
45	A	47	SER	0	0.003	0.003	21.272	0.875	0.875	0.000	0.000	0.000	0.000
46	A	48	ARG	1	0.919	0.956	20.056	14.443	14.443	0.000	0.000	0.000	0.000
47	A	49	GLU	-1	-0.851	-0.924	22.358	-10.328	-10.328	0.000	0.000	0.000	0.000
48	A	50	ARG	1	0.907	0.951	25.840	10.913	10.913	0.000	0.000	0.000	0.000
49	A	51	ILE	0	-0.014	0.004	21.050	0.289	0.289	0.000	0.000	0.000	0.000
50	A	52	VAL	0	0.049	0.023	23.038	0.218	0.218	0.000	0.000	0.000	0.000
51	A	53	LYS	1	0.872	0.943	25.516	10.324	10.324	0.000	0.000	0.000	0.000
52	A	54	GLN	0	-0.026	-0.017	28.228	0.425	0.425	0.000	0.000	0.000	0.000
53	A	55	ALA	0	0.019	0.003	25.556	0.270	0.270	0.000	0.000	0.000	0.000
54	A	56	GLY	0	0.049	0.015	27.594	0.163	0.163	0.000	0.000	0.000	0.000
55	A	57	ASN	0	-0.029	-0.011	29.695	0.273	0.273	0.000	0.000	0.000	0.000
56	A	58	GLN	0	-0.048	-0.023	29.923	0.386	0.386	0.000	0.000	0.000	0.000
57	A	59	LEU	0	0.021	0.025	27.682	0.151	0.151	0.000	0.000	0.000	0.000
58	A	60	PHE	0	0.000	-0.018	30.824	0.208	0.208	0.000	0.000	0.000	0.000
59	A	61	GLN	0	-0.043	-0.024	34.343	0.178	0.178	0.000	0.000	0.000	0.000
60	A	62	LYS	1	0.835	0.924	29.759	10.624	10.624	0.000	0.000	0.000	0.000
61	A	63	ARG	1	0.806	0.868	31.980	9.639	9.639	0.000	0.000	0.000	0.000
62	A	64	PRO	0	0.072	0.043	34.876	-0.060	-0.060	0.000	0.000	0.000	0.000
63	A	65	ASP	-1	-0.821	-0.872	36.055	-8.862	-8.862	0.000	0.000	0.000	0.000
64	A	66	VAL	0	0.023	0.008	31.974	0.071	0.071	0.000	0.000	0.000	0.000
65	A	67	VAL	0	0.012	0.006	34.922	-0.045	-0.045	0.000	0.000	0.000	0.000
66	A	68	SER	0	-0.030	-0.012	37.390	0.316	0.316	0.000	0.000	0.000	0.000
67	A	69	PRO	0	-0.016	-0.017	40.237	-0.115	-0.115	0.000	0.000	0.000	0.000
68	A	70	GLY	0	-0.026	-0.020	41.274	0.047	0.047	0.000	0.000	0.000	0.000
69	A	71	GLY	0	0.013	0.026	37.627	-0.117	-0.117	0.000	0.000	0.000	0.000
70	A	72	ASN	0	-0.040	-0.025	31.372	-0.270	-0.270	0.000	0.000	0.000	0.000
71	A	75	ALA	0	0.028	0.009	32.471	-0.195	-0.195	0.000	0.000	0.000	0.000
72	A	76	TYR	0	-0.038	-0.011	34.387	0.174	0.174	0.000	0.000	0.000	0.000
73	A	77	GLY	0	0.038	0.013	38.147	0.034	0.034	0.000	0.000	0.000	0.000
74	A	78	GLU	-1	-0.923	-0.967	36.718	-8.224	-8.224	0.000	0.000	0.000	0.000
75	A	79	ASP	-1	-0.865	-0.921	34.984	-8.855	-8.855	0.000	0.000	0.000	0.000
76	A	80	MET	0	-0.013	0.004	33.092	-0.483	-0.483	0.000	0.000	0.000	0.000
77	A	81	THR	0	-0.049	-0.027	31.912	-0.358	-0.358	0.000	0.000	0.000	0.000
78	A	82	ALA	0	0.004	-0.002	30.922	-0.382	-0.382	0.000	0.000	0.000	0.000
79	A	83	THR	0	-0.039	-0.025	28.319	-0.493	-0.493	0.000	0.000	0.000	0.000
80	A	84	CYS	0	-0.010	-0.002	27.154	-0.585	-0.585	0.000	0.000	0.000	0.000
81	A	85	LEU	0	0.001	-0.007	26.407	-0.503	-0.503	0.000	0.000	0.000	0.000
82	A	86	ARG	1	0.865	0.920	23.679	11.855	11.855	0.000	0.000	0.000	0.000
83	A	87	ASP	-1	-0.768	-0.841	22.473	-13.567	-13.567	0.000	0.000	0.000	0.000
84	A	88	LEU	0	-0.015	-0.004	21.449	-0.758	-0.758	0.000	0.000	0.000	0.000
85	A	89	ASP	-1	-0.915	-0.969	21.064	-15.159	-15.159	0.000	0.000	0.000	0.000
86	A	90	TYR	0	-0.027	-0.027	18.482	-0.906	-0.906	0.000	0.000	0.000	0.000
87	A	91	TYR	0	0.027	-0.002	16.663	-0.973	-0.973	0.000	0.000	0.000	0.000
88	A	92	LEU	0	-0.027	0.001	16.410	-1.074	-1.074	0.000	0.000	0.000	0.000
89	A	93	ARG	1	0.914	0.952	14.788	17.274	17.274	0.000	0.000	0.000	0.000
90	A	94	LEU	0	-0.010	0.008	12.157	-1.655	-1.655	0.000	0.000	0.000	0.000
91	A	95	VAL	0	0.032	0.018	11.362	-2.692	-2.692	0.000	0.000	0.000	0.000
92	A	96	THR	0	-0.075	-0.047	11.393	-1.768	-1.768	0.000	0.000	0.000	0.000
93	A	97	TYR	0	0.040	0.018	8.383	-1.084	-1.084	0.000	0.000	0.000	0.000
94	A	98	GLY	0	0.036	0.047	6.892	-5.454	-5.454	0.000	0.000	0.000	0.000
95	A	99	VAL	0	0.019	0.015	6.516	-4.315	-4.315	0.000	0.000	0.000	0.000
96	A	100	VAL	0	-0.015	-0.005	5.526	-1.921	-1.921	0.000	0.000	0.000	0.000
103	A	107	ILE	0	-0.003	-0.004	7.425	3.421	3.421	0.000	0.000	0.000	0.000
104	A	108	GLU	-1	-0.862	-0.932	9.609	-24.850	-24.850	0.000	0.000	0.000	0.000
105	A	109	GLU	-1	-0.907	-0.963	9.661	-23.135	-23.135	0.000	0.000	0.000	0.000
106	A	110	ILE	0	-0.102	-0.041	10.384	1.554	1.554	0.000	0.000	0.000	0.000
107	A	111	GLY	0	0.017	0.005	13.576	1.574	1.574	0.000	0.000	0.000	0.000
108	A	112	ILE	0	-0.014	-0.001	13.697	0.766	0.766	0.000	0.000	0.000	0.000
109	A	113	VAL	0	-0.002	-0.002	13.823	1.344	1.344	0.000	0.000	0.000	0.000
110	A	114	GLY	0	0.013	0.009	16.522	0.403	0.403	0.000	0.000	0.000	0.000
111	A	115	VAL	0	0.010	0.017	18.412	0.822	0.822	0.000	0.000	0.000	0.000
112	A	116	ARG	1	0.971	0.983	21.083	14.147	14.147	0.000	0.000	0.000	0.000
113	A	117	GLU	-1	-0.911	-0.962	23.121	-12.412	-12.412	0.000	0.000	0.000	0.000
114	A	118	MET	0	0.013	0.021	21.209	0.589	0.589	0.000	0.000	0.000	0.000
115	A	119	TYR	0	0.020	-0.021	22.511	0.397	0.397	0.000	0.000	0.000	0.000
116	A	120	LYS	1	0.922	0.971	26.821	10.764	10.764	0.000	0.000	0.000	0.000
117	A	121	SER	0	-0.108	-0.064	28.353	0.436	0.436	0.000	0.000	0.000	0.000
118	A	122	LEU	0	-0.001	0.001	26.941	0.301	0.301	0.000	0.000	0.000	0.000
119	A	123	GLY	0	-0.011	0.006	30.815	0.233	0.233	0.000	0.000	0.000	0.000
120	A	124	THR	0	-0.037	-0.030	27.698	0.156	0.156	0.000	0.000	0.000	0.000
121	A	125	PRO	0	-0.036	-0.017	29.196	-0.221	-0.221	0.000	0.000	0.000	0.000
122	A	126	ILE	0	0.046	0.008	23.861	-0.076	-0.076	0.000	0.000	0.000	0.000
123	A	127	GLU	-1	-0.890	-0.940	25.496	-10.971	-10.971	0.000	0.000	0.000	0.000
124	A	128	ALA	0	-0.046	-0.028	27.316	0.018	0.018	0.000	0.000	0.000	0.000
125	A	129	VAL	0	-0.013	0.001	22.918	-0.032	-0.032	0.000	0.000	0.000	0.000
126	A	130	ALA	0	0.026	0.016	22.669	-0.394	-0.394	0.000	0.000	0.000	0.000
127	A	131	GLU	-1	-0.946	-0.982	23.496	-10.936	-10.936	0.000	0.000	0.000	0.000
128	A	132	GLY	0	0.046	0.009	25.655	0.032	0.032	0.000	0.000	0.000	0.000
129	A	133	VAL	0	0.001	-0.006	18.737	-0.174	-0.174	0.000	0.000	0.000	0.000
130	A	134	ARG	1	0.962	0.992	21.544	12.021	12.021	0.000	0.000	0.000	0.000
131	A	135	GLU	-1	-0.837	-0.892	23.696	-11.042	-11.042	0.000	0.000	0.000	0.000
132	A	136	LEU	0	-0.022	-0.008	20.603	0.054	0.054	0.000	0.000	0.000	0.000
133	A	137	LYS	1	0.827	0.908	19.104	15.014	15.014	0.000	0.000	0.000	0.000
134	A	138	SER	0	-0.031	-0.006	21.143	0.036	0.036	0.000	0.000	0.000	0.000
135	A	139	ALA	0	-0.040	-0.026	24.634	0.238	0.238	0.000	0.000	0.000	0.000
136	A	140	ALA	0	-0.015	-0.005	19.708	0.126	0.126	0.000	0.000	0.000	0.000
137	A	141	THR	0	-0.052	-0.056	19.230	0.091	0.091	0.000	0.000	0.000	0.000
138	A	142	ALA	0	-0.012	0.007	21.605	0.181	0.181	0.000	0.000	0.000	0.000
139	A	143	LEU	0	-0.065	-0.029	22.622	0.505	0.505	0.000	0.000	0.000	0.000
140	A	144	LEU	0	-0.047	0.000	17.623	-0.305	-0.305	0.000	0.000	0.000	0.000
141	A	145	THR	0	0.004	-0.009	21.129	0.676	0.676	0.000	0.000	0.000	0.000
142	A	146	GLY	0	0.005	0.003	20.963	-0.396	-0.396	0.000	0.000	0.000	0.000
143	A	147	GLU	-1	-0.771	-0.885	16.897	-16.582	-16.582	0.000	0.000	0.000	0.000
144	A	148	ASP	-1	-0.860	-0.913	16.238	-17.861	-17.861	0.000	0.000	0.000	0.000
145	A	149	ALA	0	-0.026	-0.025	16.746	-0.622	-0.622	0.000	0.000	0.000	0.000
146	A	150	ASP	-1	-0.904	-0.955	17.249	-15.669	-15.669	0.000	0.000	0.000	0.000
147	A	161	GLU	-1	-0.860	-0.925	10.274	-28.216	-28.216	0.000	0.000	0.000	0.000
148	A	162	ALA	0	0.015	-0.006	12.789	-1.241	-1.241	0.000	0.000	0.000	0.000
149	A	163	GLY	0	-0.005	-0.006	14.483	-0.103	-0.103	0.000	0.000	0.000	0.000
150	A	164	ALA	0	0.037	0.022	12.793	0.339	0.339	0.000	0.000	0.000	0.000
151	A	165	TYR	0	-0.014	-0.009	6.397	-0.209	-0.209	0.000	0.000	0.000	0.000
152	A	166	PHE	0	0.022	-0.001	12.633	0.259	0.259	0.000	0.000	0.000	0.000
153	A	167	ASP	-1	-0.826	-0.893	16.292	-15.439	-15.439	0.000	0.000	0.000	0.000
154	A	168	TYR	0	-0.076	-0.042	11.634	0.564	0.564	0.000	0.000	0.000	0.000
155	A	169	VAL	0	0.013	0.001	14.221	0.307	0.307	0.000	0.000	0.000	0.000
156	A	170	ILE	0	-0.061	-0.034	16.441	0.913	0.913	0.000	0.000	0.000	0.000
157	A	171	GLY	0	-0.015	-0.009	18.685	0.727	0.727	0.000	0.000	0.000	0.000
158	A	172	ALA	0	-0.022	-0.001	16.012	0.216	0.216	0.000	0.000	0.000	0.000
159	A	173	LEU	0	-0.088	-0.042	18.112	0.276	0.276	0.000	0.000	0.000	0.000
160	A	174	SER	-1	-0.952	-0.963	21.150	-12.460	-12.460	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:SER)