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: QM88Y

Calculation Name: 2PRZ-B-Xray547

Preferred Name:

Target Type:

Ligand Name: orotidine-5'-monophosphate

Ligand 3-letter code: OMP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2PRZ

Chain ID: B

ChEMBL ID:

UniProt ID: P13298

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 223
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2603087.84696
FMO2-HF: Nuclear repulsion 2518766.490726
FMO2-HF: Total energy -84321.356234
FMO2-MP2: Total energy -84570.990846


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:2:ILE)


Summations of interaction energy for fragment #1(A:2:ILE)
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.
-86.063-76.3165.938-5.191-10.492-0.05
Interaction energy analysis for fragmet #1(A:2:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.839 / q_NPA : 0.919
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].
3A4LEU0-0.007-0.0202.623-5.945-1.9731.259-2.078-3.152-0.020
4A5GLU-1-0.860-0.9314.573-23.964-23.860-0.001-0.017-0.0850.000
195A196ILE00.0310.0102.469-3.161-1.7791.189-0.495-2.076-0.005
196A197HIS00.0080.0072.918-8.166-5.6070.640-0.940-2.258-0.007
197A198ILE0-0.0030.0053.6520.8890.8870.0070.059-0.0640.000
199A200THR0-0.071-0.0472.106-9.912-8.2602.845-1.697-2.800-0.018
200A201TYR0-0.042-0.0554.4620.9761.056-0.001-0.023-0.0570.000
5A6ASP-1-0.891-0.9448.179-21.753-21.7530.0000.0000.0000.000
6A7TYR00.012-0.00610.5070.8530.8530.0000.0000.0000.000
7A8GLN0-0.002-0.0095.889-1.986-1.9860.0000.0000.0000.000
8A9LYS10.9140.9747.68632.33132.3310.0000.0000.0000.000
9A10ASN00.001-0.0039.7981.5241.5240.0000.0000.0000.000
10A11PHE0-0.0070.00211.4431.2471.2470.0000.0000.0000.000
11A12LEU00.011-0.0107.3200.9330.9330.0000.0000.0000.000
12A13GLU-1-0.759-0.81611.848-19.494-19.4940.0000.0000.0000.000
13A14LEU0-0.013-0.01714.4231.2661.2660.0000.0000.0000.000
14A15ALA00.013-0.00414.0910.8790.8790.0000.0000.0000.000
15A16ILE0-0.023-0.00113.3390.5640.5640.0000.0000.0000.000
16A17GLU-1-0.945-0.96517.117-13.342-13.3420.0000.0000.0000.000
17A18CYS0-0.069-0.01419.8140.5370.5370.0000.0000.0000.000
18A19GLN0-0.029-0.02620.3080.4150.4150.0000.0000.0000.000
19A20ALA0-0.0100.00517.7630.1890.1890.0000.0000.0000.000
20A21LEU0-0.029-0.00312.142-0.087-0.0870.0000.0000.0000.000
21A22ARG10.9200.95916.25213.39213.3920.0000.0000.0000.000
22A23PHE00.0720.03412.682-0.403-0.4030.0000.0000.0000.000
23A24GLY0-0.009-0.00618.2840.7450.7450.0000.0000.0000.000
24A25SER00.001-0.00120.901-0.413-0.4130.0000.0000.0000.000
25A26PHE0-0.050-0.02619.9610.4670.4670.0000.0000.0000.000
26A27LYS10.8870.95122.50110.32410.3240.0000.0000.0000.000
27A28LEU00.0140.00518.8020.1150.1150.0000.0000.0000.000
28A29LYS10.9150.95123.13511.78211.7820.0000.0000.0000.000
29A30SER0-0.0100.00121.7530.3900.3900.0000.0000.0000.000
30A31GLY00.0050.00524.8920.0670.0670.0000.0000.0000.000
31A32ARG10.8060.89818.48214.60714.6070.0000.0000.0000.000
32A33GLU-1-0.843-0.91823.204-11.267-11.2670.0000.0000.0000.000
33A34SER0-0.014-0.01917.879-0.735-0.7350.0000.0000.0000.000
34A35PRO0-0.0060.00916.3720.5060.5060.0000.0000.0000.000
35A36TYR00.0510.00812.578-0.476-0.4760.0000.0000.0000.000
36A37PHE0-0.0210.01316.9730.2510.2510.0000.0000.0000.000
37A38PHE00.0720.02313.013-0.435-0.4350.0000.0000.0000.000
38A39ASN0-0.011-0.00616.7970.4520.4520.0000.0000.0000.000
39A40LEU00.0680.03117.0440.1190.1190.0000.0000.0000.000
40A41GLY0-0.055-0.02819.7250.2770.2770.0000.0000.0000.000
41A42LEU0-0.023-0.00621.5540.6110.6110.0000.0000.0000.000
42A43PHE00.000-0.00116.1500.1310.1310.0000.0000.0000.000
43A44ASN0-0.019-0.01421.9450.1610.1610.0000.0000.0000.000
44A45THR00.0620.03425.2820.3810.3810.0000.0000.0000.000
45A46GLY00.0290.00925.404-0.331-0.3310.0000.0000.0000.000
46A47LYS10.9510.98121.64913.05813.0580.0000.0000.0000.000
47A48LEU0-0.0020.01320.241-0.482-0.4820.0000.0000.0000.000
48A49LEU00.0390.01620.863-0.551-0.5510.0000.0000.0000.000
49A50SER00.0080.00922.318-0.341-0.3410.0000.0000.0000.000
50A51ASN00.0040.00816.404-0.670-0.6700.0000.0000.0000.000
51A52LEU00.0450.02417.170-0.606-0.6060.0000.0000.0000.000
52A53ALA0-0.010-0.01018.112-0.489-0.4890.0000.0000.0000.000
53A54THR0-0.004-0.02117.9130.0990.0990.0000.0000.0000.000
54A55ALA00.0040.00313.806-0.455-0.4550.0000.0000.0000.000
55A56TYR00.018-0.01714.560-0.774-0.7740.0000.0000.0000.000
56A57ALA0-0.0010.00416.563-0.161-0.1610.0000.0000.0000.000
57A58ILE00.0050.00213.4660.1050.1050.0000.0000.0000.000
58A59ALA00.0290.02512.425-0.200-0.2000.0000.0000.0000.000
59A60ILE0-0.013-0.01013.6050.1070.1070.0000.0000.0000.000
60A61ILE0-0.039-0.00816.9330.4340.4340.0000.0000.0000.000
61A62GLN0-0.010-0.0089.772-0.033-0.0330.0000.0000.0000.000
62A63SER0-0.058-0.03814.203-0.027-0.0270.0000.0000.0000.000
63A64ASP-1-0.868-0.94415.073-13.831-13.8310.0000.0000.0000.000
64A65LEU0-0.0560.00618.2480.9270.9270.0000.0000.0000.000
65A66LYS10.9140.94520.02011.10111.1010.0000.0000.0000.000
66A67PHE00.021-0.00221.5730.0730.0730.0000.0000.0000.000
67A68ASP-1-0.782-0.85525.573-9.515-9.5150.0000.0000.0000.000
68A69VAL0-0.027-0.01927.9080.2000.2000.0000.0000.0000.000
69A70ILE00.0010.01622.863-0.307-0.3070.0000.0000.0000.000
70A71PHE00.0200.00125.3300.3990.3990.0000.0000.0000.000
71A72GLY00.0330.01924.694-0.531-0.5310.0000.0000.0000.000
72A73PRO0-0.0240.00324.2820.5280.5280.0000.0000.0000.000
73A74ALA0-0.0260.00327.189-0.146-0.1460.0000.0000.0000.000
74A75TYR0-0.032-0.05429.418-0.026-0.0260.0000.0000.0000.000
75A76LYS10.9750.96724.05711.65911.6590.0000.0000.0000.000
76A77GLY00.1110.06124.165-0.296-0.2960.0000.0000.0000.000
77A78ILE0-0.030-0.00325.161-0.076-0.0760.0000.0000.0000.000
78A79PRO0-0.001-0.00225.7820.0570.0570.0000.0000.0000.000
79A80LEU00.0000.00620.730-0.057-0.0570.0000.0000.0000.000
80A81ALA00.0590.01923.866-0.193-0.1930.0000.0000.0000.000
81A82ALA00.0010.00725.4850.0420.0420.0000.0000.0000.000
82A83ILE0-0.032-0.02522.7540.0360.0360.0000.0000.0000.000
83A84VAL00.0200.01420.512-0.164-0.1640.0000.0000.0000.000
84A85CYS0-0.0530.00023.1730.0430.0430.0000.0000.0000.000
85A86VAL00.0180.00626.0550.0800.0800.0000.0000.0000.000
86A87LYS10.8590.92321.83212.00512.0050.0000.0000.0000.000
87A88LEU00.0090.00020.255-0.184-0.1840.0000.0000.0000.000
88A89ALA0-0.0080.01323.8900.0500.0500.0000.0000.0000.000
89A90GLU-1-0.895-0.93226.171-10.690-10.6900.0000.0000.0000.000
90A91ILE0-0.046-0.03319.9480.0150.0150.0000.0000.0000.000
91A92GLY00.0230.01622.805-0.357-0.3570.0000.0000.0000.000
92A93GLY00.0070.01423.6220.1190.1190.0000.0000.0000.000
93A94SER00.004-0.01527.244-0.043-0.0430.0000.0000.0000.000
94A95LYS10.8010.91021.30013.22713.2270.0000.0000.0000.000
95A96PHE00.013-0.00621.380-0.043-0.0430.0000.0000.0000.000
96A97GLN0-0.049-0.03627.2180.2940.2940.0000.0000.0000.000
97A98ASN0-0.031-0.01230.7120.3190.3190.0000.0000.0000.000
98A99ILE0-0.0300.01525.2350.1070.1070.0000.0000.0000.000
99A100GLN00.0190.01829.4680.1910.1910.0000.0000.0000.000
100A101TYR00.008-0.00128.210-0.357-0.3570.0000.0000.0000.000
101A102ALA00.0160.00629.0360.3680.3680.0000.0000.0000.000
102A103PHE0-0.0010.00429.070-0.374-0.3740.0000.0000.0000.000
103A104ASN00.0290.00330.652-0.055-0.0550.0000.0000.0000.000
104A105ARG10.8590.93533.0547.4627.4620.0000.0000.0000.000
105A106LYS10.8840.95429.5519.5489.5480.0000.0000.0000.000
106A107GLU-1-0.817-0.91235.895-7.198-7.1980.0000.0000.0000.000
107A108ALA00.0470.01839.727-0.065-0.0650.0000.0000.0000.000
108A109LYS10.8060.88141.4817.1137.1130.0000.0000.0000.000
109A110ASP-1-0.829-0.91941.632-6.994-6.9940.0000.0000.0000.000
110A111HIS00.0270.02838.523-0.255-0.2550.0000.0000.0000.000
111A112GLY00.0280.02840.2510.1480.1480.0000.0000.0000.000
112A113GLU-1-0.856-0.93037.571-7.655-7.6550.0000.0000.0000.000
113A114GLY0-0.002-0.00639.9550.0050.0050.0000.0000.0000.000
114A115GLY0-0.039-0.01740.5870.1680.1680.0000.0000.0000.000
115A116ILE0-0.058-0.03135.885-0.151-0.1510.0000.0000.0000.000
116A117ILE00.0180.01833.273-0.334-0.3340.0000.0000.0000.000
117A118VAL0-0.044-0.02234.5250.2440.2440.0000.0000.0000.000
118A119GLY00.0320.00833.967-0.329-0.3290.0000.0000.0000.000
119A120SER0-0.029-0.03535.5610.2910.2910.0000.0000.0000.000
120A121ALA00.0330.01635.466-0.206-0.2060.0000.0000.0000.000
121A122LEU0-0.016-0.02131.138-0.126-0.1260.0000.0000.0000.000
122A123GLU-1-0.877-0.92933.261-7.761-7.7610.0000.0000.0000.000
123A124ASN0-0.061-0.03433.8550.0050.0050.0000.0000.0000.000
124A125LYS10.8560.95231.0628.4888.4880.0000.0000.0000.000
125A126ARG10.8210.88226.4309.8009.8000.0000.0000.0000.000
126A127ILE0-0.004-0.01125.611-0.006-0.0060.0000.0000.0000.000
127A128LEU00.0070.02219.056-0.294-0.2940.0000.0000.0000.000
128A129ILE00.000-0.00721.3690.3240.3240.0000.0000.0000.000
129A130ILE0-0.034-0.01219.444-0.665-0.6650.0000.0000.0000.000
130A131ASP-1-0.836-0.94319.297-12.263-12.2630.0000.0000.0000.000
131A132ASP-1-0.909-0.95218.573-14.433-14.4330.0000.0000.0000.000
132A133VAL0-0.028-0.02314.886-1.158-1.1580.0000.0000.0000.000
133A134MET0-0.0260.01814.7780.7620.7620.0000.0000.0000.000
134A135THR0-0.001-0.01415.144-0.696-0.6960.0000.0000.0000.000
135A136ALA00.0240.01217.108-0.346-0.3460.0000.0000.0000.000
136A137GLY00.0350.00319.1300.3340.3340.0000.0000.0000.000
137A138THR0-0.055-0.02620.1140.1280.1280.0000.0000.0000.000
138A139ALA00.0430.02222.2730.3600.3600.0000.0000.0000.000
139A140ILE00.0650.03418.9050.3190.3190.0000.0000.0000.000
140A141ASN00.008-0.00322.4020.2480.2480.0000.0000.0000.000
141A142GLU-1-0.908-0.96625.085-10.220-10.2200.0000.0000.0000.000
142A143ALA0-0.022-0.01124.7560.3620.3620.0000.0000.0000.000
143A144PHE00.024-0.00221.7110.1650.1650.0000.0000.0000.000
144A145GLU-1-0.891-0.94827.052-9.240-9.2400.0000.0000.0000.000
145A146ILE0-0.069-0.02829.8860.3380.3380.0000.0000.0000.000
146A147ILE0-0.004-0.00326.6750.2420.2420.0000.0000.0000.000
147A148SER0-0.0300.00230.6700.2530.2530.0000.0000.0000.000
148A149ASN0-0.016-0.01232.1120.3190.3190.0000.0000.0000.000
149A150ALA0-0.034-0.01733.5620.2510.2510.0000.0000.0000.000
150A151LYS10.9300.97434.1017.6877.6870.0000.0000.0000.000
151A152GLY00.0190.02430.8290.0490.0490.0000.0000.0000.000
152A153GLN0-0.009-0.02027.272-0.332-0.3320.0000.0000.0000.000
153A154VAL0-0.008-0.00622.700-0.173-0.1730.0000.0000.0000.000
154A155VAL0-0.005-0.00522.672-0.029-0.0290.0000.0000.0000.000
155A156GLY00.0340.01219.175-0.474-0.4740.0000.0000.0000.000
156A157SER0-0.047-0.01417.8010.5530.5530.0000.0000.0000.000
157A158ILE0-0.0010.00714.460-0.859-0.8590.0000.0000.0000.000
158A159ILE0-0.033-0.00212.6810.8300.8300.0000.0000.0000.000
159A160ALA00.0270.00313.912-0.948-0.9480.0000.0000.0000.000
160A161LEU0-0.011-0.0159.811-1.425-1.4250.0000.0000.0000.000
161A162ASP-1-0.770-0.8759.171-21.034-21.0340.0000.0000.0000.000
162A163ARG10.7680.8569.90415.42315.4230.0000.0000.0000.000
163A164GLN0-0.014-0.0095.816-2.353-2.3530.0000.0000.0000.000
164A165GLU-1-0.722-0.81611.010-16.354-16.3540.0000.0000.0000.000
165A166VAL00.0320.04014.7000.1720.1720.0000.0000.0000.000
166A167VAL0-0.037-0.01717.4300.4040.4040.0000.0000.0000.000
167A168SER0-0.069-0.06220.4370.3010.3010.0000.0000.0000.000
168A169THR00.0380.00821.625-0.435-0.4350.0000.0000.0000.000
169A170ASP-1-0.890-0.92422.961-11.131-11.1310.0000.0000.0000.000
170A171ASP-1-0.899-0.94020.203-13.358-13.3580.0000.0000.0000.000
171A172LYS10.9560.96621.37910.56810.5680.0000.0000.0000.000
172A173GLU-1-0.870-0.92118.187-14.062-14.0620.0000.0000.0000.000
173A174GLY00.0480.04117.471-0.724-0.7240.0000.0000.0000.000
174A175LEU0-0.009-0.00115.206-1.102-1.1020.0000.0000.0000.000
175A176SER00.0500.00612.1830.7300.7300.0000.0000.0000.000
176A177ALA0-0.0030.00114.4630.8210.8210.0000.0000.0000.000
177A178THR0-0.007-0.03611.3731.0011.0010.0000.0000.0000.000
178A179GLN00.0600.03710.1491.6691.6690.0000.0000.0000.000
179A180THR0-0.029-0.02214.2431.0201.0200.0000.0000.0000.000
180A181VAL0-0.032-0.02417.7270.7390.7390.0000.0000.0000.000
181A182SER0-0.049-0.02415.0960.4160.4160.0000.0000.0000.000
182A183LYS10.8370.89817.10514.11414.1140.0000.0000.0000.000
183A184LYS10.8810.95718.97811.52611.5260.0000.0000.0000.000
184A185TYR0-0.021-0.02621.0790.7400.7400.0000.0000.0000.000
185A186GLY00.0190.02920.1780.3290.3290.0000.0000.0000.000
186A187ILE0-0.0380.00118.384-0.052-0.0520.0000.0000.0000.000
187A188PRO00.0130.00714.786-0.695-0.6950.0000.0000.0000.000
188A189VAL0-0.025-0.01613.9430.7520.7520.0000.0000.0000.000
189A190LEU0-0.0080.00011.783-1.253-1.2530.0000.0000.0000.000
190A191SER0-0.005-0.0168.8010.5400.5400.0000.0000.0000.000
191A192ILE0-0.0110.02210.188-1.029-1.0290.0000.0000.0000.000
192A193VAL0-0.024-0.0057.326-2.397-2.3970.0000.0000.0000.000
193A194SER00.0420.0195.3493.4053.4050.0000.0000.0000.000
194A195LEU00.0400.0246.124-2.471-2.4710.0000.0000.0000.000
198A199ILE00.019-0.0016.3330.7740.7740.0000.0000.0000.000
201A202LEU0-0.0170.0016.6333.2053.2050.0000.0000.0000.000
202A203GLU-1-0.877-0.9308.261-27.529-27.5290.0000.0000.0000.000
203A204GLY0-0.038-0.0199.9401.2501.2500.0000.0000.0000.000
204A205ARG10.7860.85212.37022.32822.3280.0000.0000.0000.000
205A206ILE0-0.0260.01710.7120.8380.8380.0000.0000.0000.000
206A207THR00.000-0.03814.386-0.129-0.1290.0000.0000.0000.000
207A208ALA00.025-0.00616.563-0.646-0.6460.0000.0000.0000.000
208A209GLU-1-0.898-0.93718.167-13.783-13.7830.0000.0000.0000.000
209A210GLU-1-0.811-0.89316.497-16.579-16.5790.0000.0000.0000.000
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