FMO DATABASE

FMODB ID: KKN23

Calculation Name: 2C7J-A-Xray547

Preferred Name:

Target Type:

Ligand Name: biliverdine ix alpha | phycocyanobilin

Ligand 3-letter code: BLA | CYC

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2C7J

Chain ID: A

ChEMBL ID:

UniProt ID: P00309

Base Structure: X-ray

Registration Date: 2025-10-03

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	162
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1433047.623086
FMO2-HF: Nuclear repulsion	1371316.623619
FMO2-HF: Total energy	-61730.999467
FMO2-MP2: Total energy	-61910.908646

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.
-121.311	-110.408	15.72	-10.189	-16.436	-0.102

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 : 0.829 / q_NPA : 0.932

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	THR	0	0.016	-0.003	2.632	7.592	9.855	0.333	-0.829	-1.767	-0.004
4	A	4	PRO	0	0.118	0.051	4.777	0.051	0.104	-0.001	-0.013	-0.040	0.000
6	A	6	THR	0	-0.039	-0.007	4.059	-0.176	-0.011	-0.001	-0.044	-0.119	0.000
97	A	97	TYR	0	0.048	0.013	4.693	-0.208	-0.089	-0.001	-0.007	-0.111	0.000
101	A	101	VAL	0	-0.037	-0.020	3.258	-1.015	-0.258	0.547	-0.273	-1.031	0.000
105	A	105	GLY	0	0.000	0.023	2.800	-0.423	0.020	0.427	-0.244	-0.626	0.000
106	A	106	PRO	0	0.015	-0.017	2.808	-6.732	-5.505	4.217	-1.209	-4.235	-0.008
107	A	107	LEU	0	0.015	0.000	3.838	1.498	1.281	0.053	0.364	-0.201	0.000
108	A	108	ASP	-1	-0.779	-0.856	4.758	-32.742	-32.723	-0.001	-0.004	-0.014	0.000
109	A	109	ASP	-1	-0.847	-0.944	2.136	-90.786	-86.134	8.554	-7.193	-6.014	-0.079
110	A	110	TYR	0	-0.084	-0.045	2.773	-1.120	0.302	1.593	-0.737	-2.278	-0.011
5	A	5	LEU	0	-0.006	-0.010	8.046	1.797	1.797	0.000	0.000	0.000	0.000
7	A	7	GLU	-1	-0.898	-0.949	7.426	-30.028	-30.028	0.000	0.000	0.000	0.000
8	A	8	ALA	0	0.000	0.001	9.534	2.221	2.221	0.000	0.000	0.000	0.000
9	A	9	ILE	0	-0.024	-0.015	9.475	1.665	1.665	0.000	0.000	0.000	0.000
10	A	10	ALA	0	0.025	0.013	8.485	1.482	1.482	0.000	0.000	0.000	0.000
11	A	11	ALA	0	-0.005	0.001	10.599	1.687	1.687	0.000	0.000	0.000	0.000
12	A	12	ALA	0	-0.033	-0.021	13.901	1.451	1.451	0.000	0.000	0.000	0.000
13	A	13	ASP	-1	-0.894	-0.951	12.512	-21.182	-21.182	0.000	0.000	0.000	0.000
14	A	14	LEU	0	-0.007	-0.005	12.971	1.151	1.151	0.000	0.000	0.000	0.000
15	A	15	ARG	1	0.712	0.836	15.636	18.095	18.095	0.000	0.000	0.000	0.000
16	A	16	GLY	0	-0.007	0.010	17.744	0.929	0.929	0.000	0.000	0.000	0.000
17	A	17	SER	0	-0.088	-0.037	18.240	1.035	1.035	0.000	0.000	0.000	0.000
18	A	18	TYR	0	0.043	0.010	17.815	-0.794	-0.794	0.000	0.000	0.000	0.000
19	A	19	LEU	0	-0.009	-0.004	14.625	0.050	0.050	0.000	0.000	0.000	0.000
20	A	20	SER	0	-0.014	-0.029	18.427	1.059	1.059	0.000	0.000	0.000	0.000
21	A	21	ASN	0	0.036	-0.009	20.251	-0.669	-0.669	0.000	0.000	0.000	0.000
22	A	22	THR	0	0.012	0.004	19.868	0.075	0.075	0.000	0.000	0.000	0.000
23	A	23	GLU	-1	-0.701	-0.784	16.097	-18.253	-18.253	0.000	0.000	0.000	0.000
24	A	24	LEU	0	0.004	0.008	16.286	-0.821	-0.821	0.000	0.000	0.000	0.000
25	A	25	GLN	0	0.011	-0.005	18.153	-0.337	-0.337	0.000	0.000	0.000	0.000
26	A	26	ALA	0	-0.004	0.012	15.300	0.006	0.006	0.000	0.000	0.000	0.000
27	A	27	VAL	0	-0.001	-0.007	12.513	-0.621	-0.621	0.000	0.000	0.000	0.000
28	A	28	PHE	0	-0.013	-0.011	14.612	-0.096	-0.096	0.000	0.000	0.000	0.000
29	A	29	GLY	0	0.004	-0.001	17.545	0.341	0.341	0.000	0.000	0.000	0.000
30	A	30	ARG	1	0.932	0.974	8.935	23.956	23.956	0.000	0.000	0.000	0.000
31	A	31	PHE	0	0.010	-0.013	13.261	0.031	0.031	0.000	0.000	0.000	0.000
32	A	32	ASN	0	-0.054	-0.022	15.791	0.277	0.277	0.000	0.000	0.000	0.000
33	A	33	ARG	1	0.952	0.975	15.456	15.490	15.490	0.000	0.000	0.000	0.000
34	A	34	ALA	0	-0.034	-0.011	13.773	-0.001	-0.001	0.000	0.000	0.000	0.000
35	A	35	ARG	1	0.975	0.988	14.598	13.174	13.174	0.000	0.000	0.000	0.000
36	A	36	ALA	0	0.054	0.041	17.194	0.095	0.095	0.000	0.000	0.000	0.000
37	A	37	GLY	0	0.080	0.040	13.158	0.178	0.178	0.000	0.000	0.000	0.000
38	A	38	LEU	0	-0.025	-0.021	11.885	-0.300	-0.300	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.843	-0.916	14.394	-13.245	-13.245	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.004	0.011	14.759	0.396	0.396	0.000	0.000	0.000	0.000
41	A	41	ALA	0	0.002	-0.004	11.936	0.166	0.166	0.000	0.000	0.000	0.000
42	A	42	ARG	1	0.843	0.913	13.585	14.004	14.004	0.000	0.000	0.000	0.000
43	A	43	ALA	0	0.003	0.008	16.739	0.547	0.547	0.000	0.000	0.000	0.000
44	A	44	PHE	0	-0.003	-0.018	13.887	0.371	0.371	0.000	0.000	0.000	0.000
45	A	45	ALA	0	-0.057	-0.024	14.559	0.252	0.252	0.000	0.000	0.000	0.000
46	A	46	ASN	0	-0.074	-0.028	15.853	0.670	0.670	0.000	0.000	0.000	0.000
47	A	47	ASN	0	-0.008	-0.018	19.680	0.715	0.715	0.000	0.000	0.000	0.000
48	A	48	GLY	0	0.064	0.049	16.946	0.226	0.226	0.000	0.000	0.000	0.000
49	A	49	LYS	1	0.844	0.891	15.508	15.215	15.215	0.000	0.000	0.000	0.000
50	A	50	LYS	1	0.994	1.004	19.526	10.749	10.749	0.000	0.000	0.000	0.000
51	A	51	TRP	0	0.000	-0.007	17.642	0.176	0.176	0.000	0.000	0.000	0.000
52	A	52	ALA	0	0.025	0.023	18.370	0.105	0.105	0.000	0.000	0.000	0.000
53	A	53	GLU	-1	-0.889	-0.952	20.291	-11.202	-11.202	0.000	0.000	0.000	0.000
54	A	54	ALA	0	-0.038	-0.002	23.941	0.303	0.303	0.000	0.000	0.000	0.000
55	A	55	ALA	0	0.028	0.015	21.495	0.307	0.307	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.008	-0.013	22.775	0.134	0.134	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.074	-0.046	24.300	0.582	0.582	0.000	0.000	0.000	0.000
58	A	58	HIS	0	-0.009	0.001	25.604	0.524	0.524	0.000	0.000	0.000	0.000
59	A	59	VAL	0	0.005	0.001	24.453	0.246	0.246	0.000	0.000	0.000	0.000
60	A	60	TYR	0	0.035	0.009	26.750	0.087	0.087	0.000	0.000	0.000	0.000
61	A	61	GLN	0	0.009	-0.001	30.070	0.352	0.352	0.000	0.000	0.000	0.000
62	A	62	LYS	1	0.901	0.972	28.301	10.185	10.185	0.000	0.000	0.000	0.000
63	A	63	PHE	0	-0.006	-0.003	26.604	0.084	0.084	0.000	0.000	0.000	0.000
64	A	64	PRO	0	0.076	0.047	31.010	-0.096	-0.096	0.000	0.000	0.000	0.000
65	A	65	TYR	0	0.040	0.017	29.871	-0.050	-0.050	0.000	0.000	0.000	0.000
66	A	66	THR	0	-0.012	-0.014	27.828	0.016	0.016	0.000	0.000	0.000	0.000
67	A	67	THR	0	-0.035	-0.019	30.182	-0.129	-0.129	0.000	0.000	0.000	0.000
68	A	68	GLN	0	-0.044	-0.021	32.442	0.302	0.302	0.000	0.000	0.000	0.000
69	A	69	MET	0	-0.032	0.005	33.599	0.108	0.108	0.000	0.000	0.000	0.000
70	A	70	GLN	0	0.032	0.006	33.590	-0.428	-0.428	0.000	0.000	0.000	0.000
71	A	71	GLY	0	-0.011	-0.006	31.166	-0.038	-0.038	0.000	0.000	0.000	0.000
72	A	72	PRO	0	-0.047	0.002	30.367	-0.056	-0.056	0.000	0.000	0.000	0.000
73	A	73	GLN	0	0.000	-0.013	26.027	0.031	0.031	0.000	0.000	0.000	0.000
74	A	74	TYR	0	0.014	0.013	26.768	-0.274	-0.274	0.000	0.000	0.000	0.000
75	A	75	ALA	0	0.006	0.009	26.706	0.016	0.016	0.000	0.000	0.000	0.000
76	A	76	SER	0	0.008	0.016	28.570	0.099	0.099	0.000	0.000	0.000	0.000
77	A	77	THR	0	0.049	0.013	30.645	0.110	0.110	0.000	0.000	0.000	0.000
78	A	78	PRO	0	0.032	0.001	30.197	-0.248	-0.248	0.000	0.000	0.000	0.000
79	A	79	GLU	-1	-0.876	-0.944	27.122	-10.363	-10.363	0.000	0.000	0.000	0.000
80	A	80	GLY	0	0.032	0.016	26.169	-0.448	-0.448	0.000	0.000	0.000	0.000
81	A	81	LYS	1	0.841	0.907	25.311	8.816	8.816	0.000	0.000	0.000	0.000
82	A	82	ALA	0	0.003	0.006	24.563	-0.310	-0.310	0.000	0.000	0.000	0.000
83	A	83	LYS	1	0.882	0.939	21.525	10.805	10.805	0.000	0.000	0.000	0.000
84	A	84	CYS	0	0.011	0.018	20.527	-0.680	-0.680	0.000	0.000	0.000	0.000
85	A	85	VAL	0	0.038	0.011	20.425	-0.521	-0.521	0.000	0.000	0.000	0.000
86	A	86	ARG	1	0.834	0.898	16.976	13.925	13.925	0.000	0.000	0.000	0.000
87	A	87	ASP	-1	-0.769	-0.859	16.138	-15.563	-15.563	0.000	0.000	0.000	0.000
88	A	88	ILE	0	0.014	0.014	15.427	-0.923	-0.923	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.825	-0.898	14.631	-16.835	-16.835	0.000	0.000	0.000	0.000
90	A	90	HIS	0	0.032	0.029	11.770	-1.583	-1.583	0.000	0.000	0.000	0.000
91	A	91	TYR	0	0.041	0.039	10.633	-1.600	-1.600	0.000	0.000	0.000	0.000
92	A	92	LEU	0	0.003	-0.002	11.414	-1.040	-1.040	0.000	0.000	0.000	0.000
93	A	93	ARG	1	0.891	0.938	8.122	21.552	21.552	0.000	0.000	0.000	0.000
94	A	94	THR	0	0.009	0.005	5.882	-1.864	-1.864	0.000	0.000	0.000	0.000
95	A	95	ILE	0	0.040	0.015	7.400	-1.703	-1.703	0.000	0.000	0.000	0.000
96	A	96	SER	0	-0.067	-0.038	9.706	-0.102	-0.102	0.000	0.000	0.000	0.000
98	A	98	CYS	0	-0.049	0.000	6.405	-1.717	-1.717	0.000	0.000	0.000	0.000
99	A	99	CYS	0	-0.046	-0.005	7.327	0.483	0.483	0.000	0.000	0.000	0.000
100	A	100	VAL	0	-0.019	-0.003	7.709	0.598	0.598	0.000	0.000	0.000	0.000
102	A	102	GLY	0	-0.015	0.002	6.592	-0.494	-0.494	0.000	0.000	0.000	0.000
103	A	103	GLY	0	-0.004	-0.022	6.926	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	104	THR	0	-0.017	-0.038	6.721	-0.154	-0.154	0.000	0.000	0.000	0.000
111	A	111	VAL	0	-0.023	-0.009	6.385	2.897	2.897	0.000	0.000	0.000	0.000
112	A	112	VAL	0	-0.001	0.015	9.043	2.174	2.174	0.000	0.000	0.000	0.000
113	A	113	ALA	0	0.008	0.002	8.931	2.117	2.117	0.000	0.000	0.000	0.000
114	A	114	GLY	0	0.042	0.022	10.841	0.321	0.321	0.000	0.000	0.000	0.000
115	A	115	LEU	0	-0.027	0.008	13.506	1.515	1.515	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.984	0.966	15.067	16.579	16.579	0.000	0.000	0.000	0.000
117	A	117	GLU	-1	-0.966	-0.949	17.803	-16.203	-16.203	0.000	0.000	0.000	0.000
118	A	118	PHE	0	0.043	0.023	16.957	0.752	0.752	0.000	0.000	0.000	0.000
119	A	119	ASN	0	0.028	-0.001	18.124	0.656	0.656	0.000	0.000	0.000	0.000
120	A	120	SER	0	-0.110	-0.073	20.485	0.792	0.792	0.000	0.000	0.000	0.000
121	A	121	ALA	0	0.023	0.016	22.287	0.341	0.341	0.000	0.000	0.000	0.000
122	A	122	LEU	0	-0.034	-0.015	21.445	0.488	0.488	0.000	0.000	0.000	0.000
123	A	123	GLY	0	0.000	0.006	23.967	0.373	0.373	0.000	0.000	0.000	0.000
124	A	124	LEU	0	-0.031	-0.003	20.044	0.373	0.373	0.000	0.000	0.000	0.000
125	A	125	SER	0	0.033	0.001	22.990	-0.323	-0.323	0.000	0.000	0.000	0.000
126	A	126	PRO	0	0.033	0.005	20.306	-0.105	-0.105	0.000	0.000	0.000	0.000
127	A	127	SER	0	0.011	0.017	21.533	-0.164	-0.164	0.000	0.000	0.000	0.000
128	A	128	TRP	0	-0.016	-0.023	23.376	0.112	0.112	0.000	0.000	0.000	0.000
129	A	129	TYR	0	-0.011	-0.021	18.374	0.160	0.160	0.000	0.000	0.000	0.000
130	A	130	ILE	0	0.032	0.024	19.981	-0.184	-0.184	0.000	0.000	0.000	0.000
131	A	131	ALA	0	-0.008	0.003	21.358	0.058	0.058	0.000	0.000	0.000	0.000
132	A	132	ALA	0	-0.028	-0.018	20.993	0.282	0.282	0.000	0.000	0.000	0.000
133	A	133	LEU	0	0.007	-0.010	15.320	-0.099	-0.099	0.000	0.000	0.000	0.000
134	A	134	GLU	-1	-0.948	-0.975	19.619	-11.458	-11.458	0.000	0.000	0.000	0.000
135	A	135	PHE	0	-0.006	-0.001	22.713	0.201	0.201	0.000	0.000	0.000	0.000
136	A	136	VAL	0	0.001	-0.015	18.519	0.173	0.173	0.000	0.000	0.000	0.000
137	A	137	ARG	1	0.815	0.908	20.478	12.092	12.092	0.000	0.000	0.000	0.000
138	A	138	ASP	-1	-0.847	-0.910	21.297	-11.079	-11.079	0.000	0.000	0.000	0.000
139	A	139	ASN	0	-0.049	-0.030	24.539	0.296	0.296	0.000	0.000	0.000	0.000
140	A	140	HIS	0	-0.051	-0.014	19.556	0.467	0.467	0.000	0.000	0.000	0.000
141	A	141	GLY	0	0.016	0.014	22.737	0.087	0.087	0.000	0.000	0.000	0.000
142	A	142	LEU	0	-0.080	-0.045	18.445	0.093	0.093	0.000	0.000	0.000	0.000
143	A	143	THR	0	-0.043	-0.016	23.071	0.108	0.108	0.000	0.000	0.000	0.000
144	A	144	GLY	0	0.085	0.017	23.348	0.371	0.371	0.000	0.000	0.000	0.000
145	A	145	ASP	-1	-0.924	-0.947	21.002	-13.518	-13.518	0.000	0.000	0.000	0.000
146	A	146	VAL	0	-0.012	-0.017	18.512	-0.557	-0.557	0.000	0.000	0.000	0.000
147	A	147	ALA	0	0.018	0.005	18.361	-0.540	-0.540	0.000	0.000	0.000	0.000
148	A	148	GLY	0	0.014	0.018	19.359	-0.241	-0.241	0.000	0.000	0.000	0.000
149	A	149	GLU	-1	-0.917	-0.954	14.126	-18.446	-18.446	0.000	0.000	0.000	0.000
150	A	150	ALA	0	0.011	-0.005	14.611	-0.824	-0.824	0.000	0.000	0.000	0.000
151	A	151	ASN	0	0.045	0.013	15.379	-0.697	-0.697	0.000	0.000	0.000	0.000
152	A	152	THR	0	-0.039	-0.011	14.117	0.117	0.117	0.000	0.000	0.000	0.000
153	A	153	TYR	0	0.025	-0.008	10.405	-0.609	-0.609	0.000	0.000	0.000	0.000
154	A	154	ILE	0	-0.009	0.002	13.027	-0.499	-0.499	0.000	0.000	0.000	0.000
155	A	155	ASN	0	0.035	0.005	15.691	0.486	0.486	0.000	0.000	0.000	0.000
156	A	156	TYR	0	-0.060	-0.033	9.377	1.060	1.060	0.000	0.000	0.000	0.000
157	A	157	ALA	0	0.010	-0.005	12.878	-0.192	-0.192	0.000	0.000	0.000	0.000
158	A	158	ILE	0	-0.005	-0.003	14.221	0.264	0.264	0.000	0.000	0.000	0.000
159	A	159	ASN	0	-0.052	-0.036	16.369	0.751	0.751	0.000	0.000	0.000	0.000
160	A	160	ALA	0	-0.002	0.002	13.424	0.299	0.299	0.000	0.000	0.000	0.000
161	A	161	LEU	0	-0.099	-0.050	15.452	0.002	0.002	0.000	0.000	0.000	0.000
162	A	162	SER	-1	-0.965	-0.963	18.011	-13.100	-13.100	0.000	0.000	0.000	0.000

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