FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 7N1LK

Calculation Name: 6JPR-L-Xray547

Preferred Name:

Target Type:

Ligand Name: phycocyanobilin | n-methyl asparagine | glycerol

Ligand 3-letter code: CYC | MEN | GOL

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 6JPR

Chain ID: L

ChEMBL ID:

UniProt ID: A0A5H1

Base Structure: X-ray

Registration Date: 2025-10-04

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 172
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1508138.673617
FMO2-HF: Nuclear repulsion 1445091.589235
FMO2-HF: Total energy -63047.084381
FMO2-MP2: Total energy -63232.675633


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/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.
-163.485-151.1658.034-9.428-10.926-0.107
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 : 0.728 / q_NPA : 0.874
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   
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].
3A3ASP-1-0.814-0.9082.869-57.935-54.4160.282-2.002-1.799-0.014
101A101ASP-1-0.813-0.9024.312-56.244-56.091-0.001-0.050-0.1020.000
103A103SER00.0220.0102.011-26.834-23.5864.918-4.060-4.106-0.058
104A104VAL0-0.057-0.0342.339-5.330-3.5331.255-1.133-1.919-0.010
105A105LEU00.0120.0123.2009.0339.1130.0930.080-0.253-0.001
107A107ASP-1-0.874-0.9592.668-69.169-65.8821.488-2.250-2.525-0.024
108A108ARG10.8690.9214.36951.59851.834-0.001-0.013-0.2220.000
4A4ALA00.0270.0055.6412.4072.4070.0000.0000.0000.000
5A5PHE0-0.011-0.0029.1493.1443.1440.0000.0000.0000.000
6A6ALA0-0.006-0.0066.5581.5881.5880.0000.0000.0000.000
7A7LYS10.9000.9557.05231.07231.0720.0000.0000.0000.000
8A8VAL0-0.017-0.0097.9782.3052.3050.0000.0000.0000.000
9A9VAL00.0190.00710.2351.6291.6290.0000.0000.0000.000
10A10ALA00.0270.0226.7181.5691.5690.0000.0000.0000.000
11A11GLN0-0.009-0.0078.5990.0970.0970.0000.0000.0000.000
12A12ALA0-0.0120.00610.7661.3471.3470.0000.0000.0000.000
13A13ASP-1-0.895-0.94510.953-18.458-18.4580.0000.0000.0000.000
14A14THR0-0.062-0.0459.8641.2461.2460.0000.0000.0000.000
15A15ARG10.7680.87212.71217.32117.3210.0000.0000.0000.000
16A16GLY0-0.0110.00615.6540.8620.8620.0000.0000.0000.000
17A17GLU-1-0.917-0.93316.682-13.623-13.6230.0000.0000.0000.000
18A18TYR0-0.015-0.01516.698-0.683-0.6830.0000.0000.0000.000
19A19LEU0-0.023-0.01414.166-0.130-0.1300.0000.0000.0000.000
20A20THR0-0.005-0.01718.1350.7570.7570.0000.0000.0000.000
21A21ASP-1-0.852-0.92921.011-12.730-12.7300.0000.0000.0000.000
22A22ALA00.0520.02322.970-0.382-0.3820.0000.0000.0000.000
23A23GLN0-0.022-0.00516.915-0.203-0.2030.0000.0000.0000.000
24A24LEU0-0.0060.00118.303-1.072-1.0720.0000.0000.0000.000
25A25ASP-1-0.880-0.94119.774-13.332-13.3320.0000.0000.0000.000
26A26ALA0-0.044-0.02818.522-0.201-0.2010.0000.0000.0000.000
27A27LEU0-0.030-0.01813.375-0.823-0.8230.0000.0000.0000.000
28A28SER0-0.0120.01116.763-0.429-0.4290.0000.0000.0000.000
29A29GLU-1-0.890-0.97119.556-13.579-13.5790.0000.0000.0000.000
30A30LEU0-0.038-0.00812.406-0.108-0.1080.0000.0000.0000.000
31A31VAL0-0.009-0.01015.353-0.548-0.5480.0000.0000.0000.000
32A32LYS10.8940.96517.04312.92412.9240.0000.0000.0000.000
33A33GLU-1-0.870-0.92918.719-13.907-13.9070.0000.0000.0000.000
34A34GLY00.0250.01015.967-0.403-0.4030.0000.0000.0000.000
35A35ASN0-0.022-0.02016.766-0.857-0.8570.0000.0000.0000.000
36A36LYS10.8560.91719.18713.88913.8890.0000.0000.0000.000
37A37ARG10.7810.85211.42424.16224.1620.0000.0000.0000.000
38A38ALA00.0120.00415.260-0.745-0.7450.0000.0000.0000.000
39A39ASP-1-0.882-0.94716.382-14.126-14.1260.0000.0000.0000.000
40A40ALA0-0.033-0.01516.5900.2980.2980.0000.0000.0000.000
41A41VAL00.0140.00712.3780.0430.0430.0000.0000.0000.000
42A42ASN00.0140.01915.4050.0870.0870.0000.0000.0000.000
43A43ARG10.8360.92418.42113.25613.2560.0000.0000.0000.000
44A44ILE00.0270.01616.2680.5870.5870.0000.0000.0000.000
45A45THR0-0.035-0.04015.9790.0400.0400.0000.0000.0000.000
46A46SER0-0.057-0.03518.1500.5990.5990.0000.0000.0000.000
47A47ASN0-0.061-0.03321.3541.2171.2170.0000.0000.0000.000
48A48ALA00.0310.03018.6370.3310.3310.0000.0000.0000.000
49A49SER00.031-0.00320.4620.1840.1840.0000.0000.0000.000
50A50ALA0-0.019-0.00523.2530.3970.3970.0000.0000.0000.000
51A51ILE0-0.0010.00620.2720.3890.3890.0000.0000.0000.000
52A52VAL00.0130.01020.0610.2260.2260.0000.0000.0000.000
53A53ALA0-0.010-0.01122.7380.4030.4030.0000.0000.0000.000
54A54ALA0-0.065-0.03626.2220.5070.5070.0000.0000.0000.000
55A55ALA00.0330.02123.3160.3060.3060.0000.0000.0000.000
56A56VAL0-0.006-0.01524.4210.1770.1770.0000.0000.0000.000
57A57ARG10.9250.98626.72510.68310.6830.0000.0000.0000.000
58A58ASP-1-0.863-0.95228.937-10.257-10.2570.0000.0000.0000.000
59A59LEU0-0.026-0.00725.2850.2220.2220.0000.0000.0000.000
60A60TRP0-0.040-0.05127.3800.3380.3380.0000.0000.0000.000
61A61ALA0-0.030-0.00731.5140.3160.3160.0000.0000.0000.000
62A62GLU-1-0.847-0.90430.458-10.336-10.3360.0000.0000.0000.000
63A63GLN00.0140.02628.8630.0870.0870.0000.0000.0000.000
64A64PRO00.0800.04933.082-0.139-0.1390.0000.0000.0000.000
65A65GLN0-0.003-0.02335.625-0.090-0.0900.0000.0000.0000.000
66A66LEU0-0.0340.00128.584-0.073-0.0730.0000.0000.0000.000
67A67ILE0-0.013-0.01631.747-0.091-0.0910.0000.0000.0000.000
68A68ALA00.0070.01534.0750.2230.2230.0000.0000.0000.000
69A69PRO0-0.004-0.02336.771-0.188-0.1880.0000.0000.0000.000
70A70GLY00.0030.00537.1270.1140.1140.0000.0000.0000.000
71A71GLY00.0430.03734.364-0.166-0.1660.0000.0000.0000.000
72A72ASN00.0040.01127.543-0.385-0.3850.0000.0000.0000.000
73A73ALA00.0400.01328.491-0.254-0.2540.0000.0000.0000.000
74A74TYR00.0360.03829.9150.1240.1240.0000.0000.0000.000
75A75THR0-0.054-0.03732.621-0.179-0.1790.0000.0000.0000.000
76A76SER00.0710.01431.594-0.261-0.2610.0000.0000.0000.000
77A77ARG10.9740.98826.04311.31911.3190.0000.0000.0000.000
78A78ARG10.8400.93027.2899.4979.4970.0000.0000.0000.000
79A79ALA00.0640.04626.965-0.420-0.4200.0000.0000.0000.000
80A80ALA00.009-0.00526.217-0.382-0.3820.0000.0000.0000.000
81A81ALA0-0.039-0.01523.158-0.572-0.5720.0000.0000.0000.000
82A82CYS00.0340.01822.119-0.562-0.5620.0000.0000.0000.000
83A83ILE0-0.0050.00422.493-0.418-0.4180.0000.0000.0000.000
84A84ARG10.8960.93518.71914.76814.7680.0000.0000.0000.000
85A85ASP-1-0.792-0.86817.766-17.136-17.1360.0000.0000.0000.000
86A86LEU00.0010.00216.955-1.093-1.0930.0000.0000.0000.000
87A87ASP-1-0.920-0.95817.375-17.902-17.9020.0000.0000.0000.000
88A88ILE0-0.051-0.02912.844-1.357-1.3570.0000.0000.0000.000
89A89ILE00.0260.01012.683-2.112-2.1120.0000.0000.0000.000
90A90LEU00.0100.01512.910-1.440-1.4400.0000.0000.0000.000
91A91ARG10.9440.97811.13722.84822.8480.0000.0000.0000.000
92A92TYR00.005-0.0066.570-2.580-2.5800.0000.0000.0000.000
93A93VAL00.0200.0168.512-3.775-3.7750.0000.0000.0000.000
94A94THR0-0.061-0.04210.713-0.731-0.7310.0000.0000.0000.000
95A95TYR0-0.004-0.0046.3030.0560.0560.0000.0000.0000.000
96A96ALA00.0140.0166.551-3.811-3.8110.0000.0000.0000.000
97A97ILE00.0030.0047.5590.6160.6160.0000.0000.0000.000
98A98PHE0-0.033-0.0127.7081.5251.5250.0000.0000.0000.000
99A99ALA0-0.0110.0004.8720.9210.9210.0000.0000.0000.000
100A100GLY00.0180.0136.8101.2471.2470.0000.0000.0000.000
102A102SER0-0.013-0.0235.666-3.115-3.1150.0000.0000.0000.000
106A106ASP-1-0.740-0.8396.464-30.530-30.5300.0000.0000.0000.000
109A109ALA0-0.0310.0007.4272.9652.9650.0000.0000.0000.000
110A110LEU0-0.0190.0059.9562.6812.6810.0000.0000.0000.000
111A111ASN0-0.050-0.0198.9314.2504.2500.0000.0000.0000.000
112A112GLY00.0500.04211.3980.3320.3320.0000.0000.0000.000
113A113LEU0-0.0170.01514.6061.4681.4680.0000.0000.0000.000
114A114ARG10.8810.93216.28717.65417.6540.0000.0000.0000.000
115A115GLU-1-0.869-0.94817.339-16.403-16.4030.0000.0000.0000.000
116A116THR0-0.042-0.02817.5210.8620.8620.0000.0000.0000.000
117A117TYR0-0.056-0.07318.8860.6080.6080.0000.0000.0000.000
118A118LEU0-0.012-0.00522.4070.7890.7890.0000.0000.0000.000
119A119ALA0-0.033-0.01023.1360.6270.6270.0000.0000.0000.000
120A120LEU0-0.074-0.03522.4150.4360.4360.0000.0000.0000.000
121A121GLY0-0.0100.01025.9680.4320.4320.0000.0000.0000.000
122A122THR0-0.068-0.04423.8970.3580.3580.0000.0000.0000.000
123A123PRO0-0.010-0.00725.620-0.294-0.2940.0000.0000.0000.000
124A124GLY00.0820.03922.820-0.122-0.1220.0000.0000.0000.000
125A125ALA00.0490.02022.877-0.368-0.3680.0000.0000.0000.000
126A126SER0-0.034-0.04025.2640.0430.0430.0000.0000.0000.000
127A127VAL0-0.0020.00419.8040.0090.0090.0000.0000.0000.000
128A128ALA00.0190.01620.839-0.457-0.4570.0000.0000.0000.000
129A129VAL00.0110.01021.897-0.156-0.1560.0000.0000.0000.000
130A130GLY00.0130.00423.0410.1640.1640.0000.0000.0000.000
131A131ILE00.003-0.00317.030-0.092-0.0920.0000.0000.0000.000
132A132GLN0-0.022-0.01120.039-0.421-0.4210.0000.0000.0000.000
133A133LYS10.8250.90422.47311.39111.3910.0000.0000.0000.000
134A134LEU0-0.015-0.00117.6090.1460.1460.0000.0000.0000.000
135A135LYS10.8140.92119.33514.99914.9990.0000.0000.0000.000
136A136ASP-1-0.854-0.90520.560-11.668-11.6680.0000.0000.0000.000
137A137ALA00.0240.00223.5830.2450.2450.0000.0000.0000.000
138A138SER00.015-0.01419.191-0.031-0.0310.0000.0000.0000.000
139A139LEU0-0.012-0.00619.7850.0450.0450.0000.0000.0000.000
140A140LYS10.8340.90822.53011.66711.6670.0000.0000.0000.000
141A141ILE0-0.019-0.00322.2270.3020.3020.0000.0000.0000.000
142A142VAL0-0.020-0.00719.059-0.022-0.0220.0000.0000.0000.000
143A143ASN0-0.055-0.04322.2370.0940.0940.0000.0000.0000.000
144A144ASP-1-0.801-0.87225.292-10.393-10.3930.0000.0000.0000.000
145A145PRO0-0.032-0.00727.471-0.229-0.2290.0000.0000.0000.000
146A146ASN0-0.077-0.05430.0010.4970.4970.0000.0000.0000.000
147A147GLY0-0.015-0.01229.008-0.325-0.3250.0000.0000.0000.000
148A148ILE00.0110.01923.446-0.259-0.2590.0000.0000.0000.000
149A149THR0-0.008-0.00526.9310.5530.5530.0000.0000.0000.000
150A150ARG10.9540.97627.3379.3209.3200.0000.0000.0000.000
151A151GLY00.0210.00027.3440.2740.2740.0000.0000.0000.000
152A152ASP-1-0.822-0.88025.945-12.521-12.5210.0000.0000.0000.000
153A153CYS00.0230.01221.679-0.488-0.4880.0000.0000.0000.000
154A154SER0-0.026-0.03021.571-0.855-0.8550.0000.0000.0000.000
155A155ALA00.0260.01119.820-0.371-0.3710.0000.0000.0000.000
156A156LEU00.0390.02815.188-0.833-0.8330.0000.0000.0000.000
157A157ALA0-0.006-0.00517.331-0.873-0.8730.0000.0000.0000.000
158A158ALA00.0080.00119.171-0.242-0.2420.0000.0000.0000.000
159A159GLU-1-0.741-0.81012.001-25.379-25.3790.0000.0000.0000.000
160A160ILE00.0110.00414.362-1.194-1.1940.0000.0000.0000.000
161A161ALA0-0.023-0.01415.507-0.434-0.4340.0000.0000.0000.000
162A162SER0-0.033-0.02714.114-0.570-0.5700.0000.0000.0000.000
163A163TYR0-0.021-0.0389.057-1.630-1.6300.0000.0000.0000.000
164A164PHE00.026-0.00112.824-0.427-0.4270.0000.0000.0000.000
165A165ASP-1-0.812-0.89415.808-15.525-15.5250.0000.0000.0000.000
166A166ARG10.8040.8749.28529.33429.3340.0000.0000.0000.000
167A167ALA00.009-0.00913.357-0.011-0.0110.0000.0000.0000.000
168A168ALA0-0.030-0.02014.7410.6680.6680.0000.0000.0000.000
169A169ALA00.002-0.00917.3060.6310.6310.0000.0000.0000.000
170A170ALA0-0.036-0.01314.6490.3640.3640.0000.0000.0000.000
171A171VAL0-0.056-0.03116.6560.0210.0210.0000.0000.0000.000
172A172ALA-1-0.865-0.90319.169-13.816-13.8160.0000.0000.0000.000