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: ZL9VN

Calculation Name: 4LMX-B-Xray547

Preferred Name:

Target Type:

Ligand Name: 15,16-dihydrobiliverdin | phycoerythrobilin | 5-hydroxylysine

Ligand 3-letter code: DBV | PEB | LYZ

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4LMX

Chain ID: B

ChEMBL ID:

UniProt ID: U5TBU5

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 177
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1584121.23385
FMO2-HF: Nuclear repulsion 1517966.716639
FMO2-HF: Total energy -66154.517211
FMO2-MP2: Total energy -66341.638382


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.
-86.917-80.80118.45-12.503-12.059-0.123
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 : 0.793 / q_NPA : 0.893
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-1-0.767-0.8622.559-50.677-46.1052.366-2.941-3.997-0.026
4A4ALA0-0.033-0.0043.2476.6677.4040.025-0.219-0.542-0.001
5A5PHE00.0530.0084.3794.6464.8100.000-0.022-0.1420.000
7A7LYS10.8680.9112.97140.63241.2281.066-0.546-1.1160.006
19A19VAL00.0110.0044.347-4.694-4.622-0.001-0.006-0.0650.000
23A23ASP-1-0.819-0.9121.999-135.132-135.31914.997-8.731-6.078-0.102
24A24LEU0-0.0140.0014.119-0.629-0.611-0.001-0.0190.0030.000
26A26ALA0-0.025-0.0164.6733.1563.194-0.001-0.002-0.0340.000
27A27LEU00.006-0.0054.6343.0383.144-0.001-0.017-0.0880.000
6A6SER00.0630.0277.7321.7601.7600.0000.0000.0000.000
8A8VAL00.0220.0138.2492.0472.0470.0000.0000.0000.000
9A9ILE0-0.0270.00510.6331.9501.9500.0000.0000.0000.000
10A10THR0-0.028-0.01711.1031.3481.3480.0000.0000.0000.000
11A11SER0-0.079-0.01811.3180.7980.7980.0000.0000.0000.000
12A12ALA00.023-0.00613.1510.9740.9740.0000.0000.0000.000
13A13ASP-1-0.878-0.94112.165-20.531-20.5310.0000.0000.0000.000
14A14GLY0-0.0020.00715.6830.5260.5260.0000.0000.0000.000
15A15LYS10.8680.93612.27719.80519.8050.0000.0000.0000.000
16A16ALA00.0270.02012.137-0.946-0.9460.0000.0000.0000.000
17A17ALA00.0030.0036.993-0.733-0.7330.0000.0000.0000.000
18A18TYR0-0.023-0.0118.4281.5201.5200.0000.0000.0000.000
20A20GLY00.0440.0106.5885.3825.3820.0000.0000.0000.000
21A21GLY00.0100.0017.103-4.509-4.5090.0000.0000.0000.000
22A22ALA00.0550.0167.049-0.183-0.1830.0000.0000.0000.000
25A25GLN0-0.032-0.0137.1352.6452.6450.0000.0000.0000.000
28A28LYS10.8770.9327.38626.97226.9720.0000.0000.0000.000
29A29LYS10.9260.9709.84727.21627.2160.0000.0000.0000.000
30A30PHE0-0.029-0.0079.0221.0201.0200.0000.0000.0000.000
31A31VAL00.0340.03611.1441.5931.5930.0000.0000.0000.000
32A32SER00.0400.02014.1360.1650.1650.0000.0000.0000.000
33A33GLU-1-0.814-0.92017.414-14.134-14.1340.0000.0000.0000.000
34A34GLY00.0570.03814.5490.2450.2450.0000.0000.0000.000
35A35ASN0-0.015-0.01815.337-1.637-1.6370.0000.0000.0000.000
36A36LYS10.9190.93617.29413.23213.2320.0000.0000.0000.000
37A37ARG10.7330.83615.04318.79318.7930.0000.0000.0000.000
38A38MET0-0.023-0.00812.891-0.681-0.6810.0000.0000.0000.000
39A39ASP-1-0.891-0.94616.706-14.846-14.8460.0000.0000.0000.000
40A40SER0-0.023-0.02620.3800.8520.8520.0000.0000.0000.000
41A41VAL00.0140.01016.0280.5070.5070.0000.0000.0000.000
42A42ASN0-0.0030.00219.1280.6000.6000.0000.0000.0000.000
43A43ALA0-0.015-0.00220.3470.5970.5970.0000.0000.0000.000
44A44ILE00.0190.02721.1150.6190.6190.0000.0000.0000.000
45A45VAL00.000-0.01618.8080.5080.5080.0000.0000.0000.000
46A46SER0-0.045-0.02822.0080.3490.3490.0000.0000.0000.000
47A47ASN0-0.057-0.03624.1220.9160.9160.0000.0000.0000.000
48A48ALA00.0410.03324.4500.4450.4450.0000.0000.0000.000
49A49SER00.0420.01026.5750.2260.2260.0000.0000.0000.000
50A50CYS0-0.066-0.02729.6510.2540.2540.0000.0000.0000.000
51A51ILE00.0540.03227.0070.2780.2780.0000.0000.0000.000
52A52VAL00.0060.02228.7280.2700.2700.0000.0000.0000.000
53A53SER0-0.020-0.00931.4530.3510.3510.0000.0000.0000.000
54A54ASP-1-0.899-0.93634.572-8.333-8.3330.0000.0000.0000.000
55A55SER0-0.001-0.02032.9350.2130.2130.0000.0000.0000.000
56A56VAL00.002-0.01234.4990.2030.2030.0000.0000.0000.000
57A57SER0-0.039-0.03137.1320.3140.3140.0000.0000.0000.000
58A58GLY00.0330.00538.9810.2400.2400.0000.0000.0000.000
59A59MET0-0.0380.00438.2840.1930.1930.0000.0000.0000.000
60A60VAL0-0.040-0.02940.6510.2090.2090.0000.0000.0000.000
61A61CYS0-0.061-0.02043.2270.1770.1770.0000.0000.0000.000
62A62GLU-1-0.776-0.84142.530-7.499-7.4990.0000.0000.0000.000
63A63ASN00.0050.02444.6490.2880.2880.0000.0000.0000.000
64A64PRO00.0760.03945.737-0.071-0.0710.0000.0000.0000.000
65A65SER0-0.063-0.05347.9080.0080.0080.0000.0000.0000.000
66A66LEU0-0.021-0.02041.675-0.017-0.0170.0000.0000.0000.000
67A67ILE0-0.015-0.00744.032-0.123-0.1230.0000.0000.0000.000
68A68ALA00.0300.03145.9220.1000.1000.0000.0000.0000.000
69A69PRO00.025-0.01248.228-0.126-0.1260.0000.0000.0000.000
70A70ASN0-0.048-0.02848.0230.0430.0430.0000.0000.0000.000
71A71GLY00.0470.05946.037-0.080-0.0800.0000.0000.0000.000
72A72GLY00.002-0.01041.871-0.085-0.0850.0000.0000.0000.000
73A73VAL0-0.008-0.02438.745-0.169-0.1690.0000.0000.0000.000
74A74TYR00.0180.03441.3830.0410.0410.0000.0000.0000.000
75A75THR0-0.018-0.02943.492-0.110-0.1100.0000.0000.0000.000
76A76ASN00.0650.01340.202-0.172-0.1720.0000.0000.0000.000
77A77ARG10.9620.99039.0297.4447.4440.0000.0000.0000.000
78A78LYS10.8910.94837.8147.2387.2380.0000.0000.0000.000
79A79MET00.0400.03437.590-0.260-0.2600.0000.0000.0000.000
80A80ALA00.0020.00135.136-0.235-0.2350.0000.0000.0000.000
81A81ALA0-0.021-0.00633.329-0.328-0.3280.0000.0000.0000.000
82A82CYS00.0380.01832.646-0.235-0.2350.0000.0000.0000.000
83A83LEU0-0.0060.00332.723-0.259-0.2590.0000.0000.0000.000
84A84ARG10.8670.90828.4649.8419.8410.0000.0000.0000.000
85A85ASP-1-0.761-0.84428.099-10.673-10.6730.0000.0000.0000.000
86A86ALA00.0270.01728.119-0.358-0.3580.0000.0000.0000.000
87A87GLU-1-0.818-0.90225.238-12.540-12.5400.0000.0000.0000.000
88A88ILE0-0.034-0.01623.422-0.660-0.6600.0000.0000.0000.000
89A89ILE00.0370.01623.205-0.671-0.6710.0000.0000.0000.000
90A90LEU0-0.0150.00023.911-0.502-0.5020.0000.0000.0000.000
91A91ARG10.8200.89220.24613.27313.2730.0000.0000.0000.000
92A92TYR00.0630.03918.167-1.261-1.2610.0000.0000.0000.000
93A93VAL00.0020.01719.554-0.713-0.7130.0000.0000.0000.000
94A94SER0-0.074-0.05319.202-0.615-0.6150.0000.0000.0000.000
95A95TYR00.0590.00611.645-1.597-1.5970.0000.0000.0000.000
96A96SER0-0.0150.00315.548-1.119-1.1190.0000.0000.0000.000
97A97LEU0-0.028-0.00817.267-0.517-0.5170.0000.0000.0000.000
98A98LEU0-0.050-0.01911.583-0.379-0.3790.0000.0000.0000.000
99A99SER0-0.068-0.05312.402-1.389-1.3890.0000.0000.0000.000
100A100GLY0-0.017-0.00513.421-0.874-0.8740.0000.0000.0000.000
101A101ASP-1-0.853-0.89214.540-19.052-19.0520.0000.0000.0000.000
102A102SER00.013-0.03117.569-0.200-0.2000.0000.0000.0000.000
103A103SER0-0.069-0.04815.9980.4670.4670.0000.0000.0000.000
104A104VAL00.013-0.00514.0800.5610.5610.0000.0000.0000.000
105A105LEU0-0.0170.00017.4950.5490.5490.0000.0000.0000.000
106A106GLU-1-0.794-0.88220.738-12.430-12.4300.0000.0000.0000.000
107A107ASP-1-0.894-0.95719.436-13.982-13.9820.0000.0000.0000.000
108A108ARG10.8620.92116.59716.32216.3220.0000.0000.0000.000
109A109CYS0-0.089-0.02920.9140.2970.2970.0000.0000.0000.000
110A110LEU0-0.0050.00023.5710.5530.5530.0000.0000.0000.000
111A111ASN0-0.0160.01223.9200.9980.9980.0000.0000.0000.000
112A112GLY00.0760.04926.654-0.026-0.0260.0000.0000.0000.000
113A113LEU0-0.042-0.00527.8070.3540.3540.0000.0000.0000.000
114A114LYS10.8290.89530.2558.8658.8650.0000.0000.0000.000
115A115GLU-1-0.945-0.96333.318-8.670-8.6700.0000.0000.0000.000
116A116THR0-0.002-0.00431.7520.2430.2430.0000.0000.0000.000
117A117TYR0-0.033-0.05431.1680.2090.2090.0000.0000.0000.000
118A118ALA0-0.0070.00635.8210.2560.2560.0000.0000.0000.000
119A119SER0-0.077-0.04436.8640.2240.2240.0000.0000.0000.000
120A120LEU0-0.033-0.02035.0310.1570.1570.0000.0000.0000.000
121A121GLY0-0.0130.00939.2520.1240.1240.0000.0000.0000.000
122A122VAL0-0.053-0.02836.0080.1120.1120.0000.0000.0000.000
123A123PRO0-0.014-0.00838.937-0.058-0.0580.0000.0000.0000.000
124A124ALA00.0810.02937.623-0.107-0.1070.0000.0000.0000.000
125A125ALA00.0140.01138.042-0.155-0.1550.0000.0000.0000.000
126A126GLY00.0280.00739.788-0.040-0.0400.0000.0000.0000.000
127A127ASN00.0290.01033.565-0.296-0.2960.0000.0000.0000.000
128A128ALA00.0370.01834.829-0.244-0.2440.0000.0000.0000.000
129A129ARG10.7850.85635.7347.9427.9420.0000.0000.0000.000
130A130THR00.0500.02133.112-0.095-0.0950.0000.0000.0000.000
131A131ILE00.003-0.00230.230-0.235-0.2350.0000.0000.0000.000
132A132SER0-0.061-0.03731.935-0.151-0.1510.0000.0000.0000.000
133A133ILE00.0280.02634.347-0.031-0.0310.0000.0000.0000.000
134A134MET0-0.0060.02229.111-0.257-0.2570.0000.0000.0000.000
135A135LYS10.7590.87929.5529.8839.8830.0000.0000.0000.000
136A136ALA00.0130.00130.613-0.157-0.1570.0000.0000.0000.000
137A137THR0-0.014-0.01631.0050.0500.0500.0000.0000.0000.000
138A138VAL0-0.022-0.01025.306-0.141-0.1410.0000.0000.0000.000
139A139ILE00.0270.00928.034-0.215-0.2150.0000.0000.0000.000
140A140GLY00.0370.04029.7230.0650.0650.0000.0000.0000.000
141A141PHE0-0.031-0.03227.8480.1030.1030.0000.0000.0000.000
142A142ILE0-0.021-0.00924.2140.0130.0130.0000.0000.0000.000
143A143THR0-0.054-0.03927.5840.0950.0950.0000.0000.0000.000
144A144ASN0-0.025-0.01030.3630.3600.3600.0000.0000.0000.000
145A145ASN00.010-0.00232.5580.5580.5580.0000.0000.0000.000
146A146SER0-0.025-0.01232.5080.1850.1850.0000.0000.0000.000
147A147GLN0-0.023-0.01334.5310.0620.0620.0000.0000.0000.000
148A148GLN00.0340.01036.826-0.153-0.1530.0000.0000.0000.000
149A149LYS10.9120.95528.66810.83610.8360.0000.0000.0000.000
150A150LYS10.8750.95231.6369.0669.0660.0000.0000.0000.000
151A151LEU00.0290.01625.361-0.163-0.1630.0000.0000.0000.000
152A152SER0-0.021-0.00626.6170.3950.3950.0000.0000.0000.000
153A153THR0-0.0020.00423.906-0.377-0.3770.0000.0000.0000.000
154A154PRO0-0.003-0.00924.1000.4710.4710.0000.0000.0000.000
155A155ALA00.0060.01227.139-0.060-0.0600.0000.0000.0000.000
156A156GLY00.005-0.01028.250-0.104-0.1040.0000.0000.0000.000
157A157ASP-1-0.797-0.86328.835-10.826-10.8260.0000.0000.0000.000
158A158CYS0-0.008-0.00225.336-0.759-0.7590.0000.0000.0000.000
159A159SER0-0.002-0.02326.412-0.322-0.3220.0000.0000.0000.000
160A160ALA00.0160.02624.6610.0530.0530.0000.0000.0000.000
161A161LEU00.0310.01319.772-0.139-0.1390.0000.0000.0000.000
162A162ALA0-0.018-0.00623.697-0.101-0.1010.0000.0000.0000.000
163A163SER0-0.005-0.01826.8660.3560.3560.0000.0000.0000.000
164A164GLU-1-0.773-0.83019.733-16.394-16.3940.0000.0000.0000.000
165A165VAL00.003-0.00422.991-0.038-0.0380.0000.0000.0000.000
166A166GLY00.006-0.00224.4400.2550.2550.0000.0000.0000.000
167A167GLY00.0600.02826.6060.2950.2950.0000.0000.0000.000
168A168TYR0-0.030-0.03919.5350.1750.1750.0000.0000.0000.000
169A169PHE00.0510.00624.8900.1180.1180.0000.0000.0000.000
170A170ASP-1-0.789-0.85728.006-9.864-9.8640.0000.0000.0000.000
171A171LYS10.8170.90924.15912.78712.7870.0000.0000.0000.000
172A172VAL0-0.004-0.00626.0960.1910.1910.0000.0000.0000.000
173A173SER0-0.038-0.03728.3600.3820.3820.0000.0000.0000.000
174A174SER0-0.048-0.04530.6780.3800.3800.0000.0000.0000.000
175A175ALA0-0.0140.01028.9020.1880.1880.0000.0000.0000.000
176A176LEU0-0.048-0.03130.4040.1510.1510.0000.0000.0000.000
177A177ALA-1-0.839-0.88733.529-8.206-8.2060.0000.0000.0000.000